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Journal Cover Microorganisms
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  This is an Open Access Journal Open Access journal
   ISSN (Online) 2076-2607
   Published by MDPI Homepage  [198 journals]
  • Microorganisms, Vol. 6, Pages 28: Symbiotic Plant-Bacterial Endospheric
           Interactions

    • Authors: Sharon Doty
      First page: 28
      Abstract: While plant-microbe symbioses involving root nodules (Rhizobia and Frankia) or the root-soil interface (rhizosphere) have been well studied, the intimate interaction of microbial endophytes with the plant host is a relatively new field of research.[...]
      Citation: Microorganisms
      PubDate: 2018-03-22
      DOI: 10.3390/microorganisms6020028
      Issue No: Vol. 6, No. 2 (2018)
       
  • Microorganisms, Vol. 6, Pages 29: Special Issue: Response of Microbial
           Communities to Environmental Changes

    • Authors: Ulrich Stingl
      First page: 29
      Abstract: Environmental issues such as eutrophication, ocean acidification, sea level rise, saltwater intrusion, increase in carbon dioxide levels, or rise of average global temperatures, among many others, are impacting and changing whole ecosystems [...]
      Citation: Microorganisms
      PubDate: 2018-03-30
      DOI: 10.3390/microorganisms6020029
      Issue No: Vol. 6, No. 2 (2018)
       
  • Microorganisms, Vol. 6, Pages 30: Translation and Translational Control in
           Dinoflagellates

    • Authors: Sougata Roy, Rosemary Jagus, David Morse
      First page: 30
      Abstract: Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.
      Citation: Microorganisms
      PubDate: 2018-04-07
      DOI: 10.3390/microorganisms6020030
      Issue No: Vol. 6, No. 2 (2018)
       
  • Microorganisms, Vol. 6, Pages 31: Production and Characterization of an
           Extracellular Acid Protease from Thermophilic Brevibacillus sp. OA30
           Isolated from an Algerian Hot Spring

    • Authors: Mohamed Gomri, Agustín Rico-Díaz, Juan-José Escuder-Rodríguez, Tedj El Moulouk Khaldi, María-Isabel González-Siso, Karima Kharroub
      First page: 31
      Abstract: Proteases have numerous biotechnological applications and the bioprospection for newly-thermostable proteases from the great biodiversity of thermophilic microorganisms inhabiting hot environments, such as geothermal sources, aims to discover more effective enzymes for processes at higher temperatures. We report in this paper the production and the characterization of a purified acid protease from strain OA30, a moderate thermophilic bacterium isolated from an Algerian hot spring. Phenotypic and genotypic study of strain OA30 was followed by the production of the extracellular protease in a physiologically-optimized medium. Strain OA30 showed multiple extracellular proteolytic enzymes and protease 32-F38 was purified by chromatographic methods and its biochemical characteristics were studied. Strain OA30 was affiliated with Brevibacillus thermoruber species. Protease 32-F38 had an estimated molecular weight of 64.6 kDa and was optimally active at 50 °C. It showed a great thermostability after 240 min and its optimum pH was 6.0. Protease 32-F38 was highly stable in the presence of different detergents and solvents and was inhibited by metalloprotease inhibitors. The results of this work suggest that protease 32-F38 might have interesting biotechnological applications.
      Citation: Microorganisms
      PubDate: 2018-04-12
      DOI: 10.3390/microorganisms6020031
      Issue No: Vol. 6, No. 2 (2018)
       
  • Microorganisms, Vol. 6, Pages 2: Unusually High Incidences of
           Staphylococcus aureus Infection within Studies of Ventilator Associated
           Pneumonia Prevention Using Topical Antibiotics: Benchmarking the Evidence
           Base

    • Authors: James Hurley
      First page: 2
      Abstract: Selective digestive decontamination (SDD, topical antibiotic regimens applied to the respiratory tract) appears effective for preventing ventilator associated pneumonia (VAP) in intensive care unit (ICU) patients. However, potential contextual effects of SDD on Staphylococcus aureus infections in the ICU remain unclear. The S. aureus ventilator associated pneumonia (S. aureus VAP), VAP overall and S. aureus bacteremia incidences within component (control and intervention) groups within 27 SDD studies were benchmarked against 115 observational groups. Component groups from 66 studies of various interventions other than SDD provided additional points of reference. In 27 SDD study control groups, the mean S. aureus VAP incidence is 9.6% (95% CI; 6.9–13.2) versus a benchmark derived from 115 observational groups being 4.8% (95% CI; 4.2–5.6). In nine SDD study control groups the mean S. aureus bacteremia incidence is 3.8% (95% CI; 2.1–5.7) versus a benchmark derived from 10 observational groups being 2.1% (95% CI; 1.1–4.1). The incidences of S. aureus VAP and S. aureus bacteremia within the control groups of SDD studies are each higher than literature derived benchmarks. Paradoxically, within the SDD intervention groups, the incidences of both S. aureus VAP and VAP overall are more similar to the benchmarks.
      Citation: Microorganisms
      PubDate: 2018-01-04
      DOI: 10.3390/microorganisms6010002
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 3: Pichia pastoris is a Suitable Host for
           the Heterologous Expression of Predicted Class I and Class II Hydrophobins
           for Discovery, Study, and Application in Biotechnology

    • Authors: Julie-Anne Gandier, Emma Master
      First page: 3
      Abstract: The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing systems for their heterologous expression challenging. In this article, we describe the development of Pichia pastoris KM71H strains capable of solubly producing the full set of predicted Cordyceps militaris hydrophobins CMil1 (Class IA), CMil2 (Class II), and CMil3 (IM) at mg/L yields with the use of 6His-tags not only for purification but for their detection. This result further demonstrates the feasibility of using P. pastoris as a host organism for the production of hydrophobins from all Ascomycota Class I subdivisions (a classification our previous work defined) as well as Class II. We highlight the specific challenges related to the production of hydrophobins, notably the challenge in detecting the protein that will be described, in particular during the screening of transformants. Together with the literature, our results continue to show that P. pastoris is a suitable host for the soluble heterologous expression of hydrophobins with a wide range of properties.
      Citation: Microorganisms
      PubDate: 2018-01-05
      DOI: 10.3390/microorganisms6010003
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 4: Increase of Salt Tolerance in
           Carbon-Starved Cells of Rhodopseudomonas palustris Depending on
           Photosynthesis or Respiration

    • Authors: Sawa Wasai, Nanako Kanno, Katsumi Matsuura, Shin Haruta
      First page: 4
      Abstract: Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after carbon starvation under photosynthetic conditions in comparison with anaerobic and aerobic dark conditions. Tolerance to a treatment with high concentration of salt (2.5 M NaCl for 1 h) was largely increased after starvation under anaerobically light and aerobically dark conditions. The starved cells under the conditions of photosynthesis or aerobic respiration contained high levels of cellular ATP, but starvation under the anaerobic dark conditions resulted in a decrease of cellular ATP contents. To observe the large increase of the salt tolerance, incubation of starved cells for more than 18 h under illumination was needed. These results suggest that the ATP-dependent rearrangement of cells induced salt tolerance.
      Citation: Microorganisms
      PubDate: 2018-01-06
      DOI: 10.3390/microorganisms6010004
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 5: Enzymatic Preparation of
           2,5-Furandicarboxylic Acid (FDCA)—A Substitute of Terephthalic Acid—By
           the Joined Action of Three Fungal Enzymes

    • Authors: Alexander Karich, Sebastian Kleeberg, René Ullrich, Martin Hofrichter
      First page: 5
      Abstract: Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different reaction steps was evaluated and apparent kinetic data (Michaelis-Menten constants, turnover numbers, specific constants) were calculated for different enzyme-substrate ratios and enzyme combinations. Finally, the target product, 2,5-furandicarboxylic acid (FDCA), was prepared in a multi-enzyme cascade reaction combining three fungal oxidoreductases at micro-scale. Furthermore, an oxidase-like reaction is proposed for heme-containing peroxidases, such as UPO, horseradish peroxidase, or catalase, causing the conversion of 5-formyl-2-furancarboxylic acid into FDCA in the absence of exogenous hydrogen peroxide.
      Citation: Microorganisms
      PubDate: 2018-01-09
      DOI: 10.3390/microorganisms6010005
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 6: Evaluation of an Accelerated Workflow for
           Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using
           Amplicon-Based Next-Generation Sequencing and Automated Analysis

    • Authors: Nilay Peker, John Rossen, Ruud Deurenberg, Paula Langereis, Erwin Raangs, Jan Kluytmans, Alexander Friedrich, Jacobien Veenemans, Bhanu Sinha
      First page: 6
      Abstract: Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.
      Citation: Microorganisms
      PubDate: 2018-01-11
      DOI: 10.3390/microorganisms6010006
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 7: Acknowledgement to Reviewers of
           Microorganisms in 2017

    • Authors: Microorganisms Editorial Office
      First page: 7
      Abstract: Peer review is an essential part in the publication process, ensuring that Microorganisms maintains high quality standards for its published papers [...]
      Citation: Microorganisms
      PubDate: 2018-01-12
      DOI: 10.3390/microorganisms6010007
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 8: Biogenic Weathering: Solubilization of
           Iron from Minerals by Epilithic Freshwater Algae and Cyanobacteria

    • Authors: George Mustoe
      First page: 8
      Abstract: A sandstone outcrop exposed to freshwater seepage supports a diverse assemblage of photosynthetic microbes. Dominant taxa are two cyanophytes (Oscillatoria sp., Rivularia sp.) and a unicellular green alga (Palmellococcus sp.). Less abundant taxa include a filamentous green alga, Microspora, and the desmid Cosmarium. Biologic activity is evidenced by measured levels of chlorophyll and lipids. Bioassay methods confirm the ability of these microbes to dissolve and metabolize Fe from ferruginous minerals. Chromatographic analysis reveals citric acid as the likely chelating agent; this low molecular weight organic acid is detectable in interstitial fluid in the sandstone, measured as 0.0756 mg/mL. Bioassays using a model organism, Synechoccus elongates strain UTEX 650, show that Fe availability varies among different ferruginous minerals. In decreasing order of Fe availability: magnetite > limonite > biotite > siderite > hematite. Biotite was selected for detailed study because it is the most abundant iron-bearing mineral in the sandstone. SEM images support the microbiologic evidence, showing weathering of biotite compared to relatively undamaged grains of other silicate minerals.
      Citation: Microorganisms
      PubDate: 2018-01-15
      DOI: 10.3390/microorganisms6010008
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 9: Therapeutic Management of Pseudomonas
           aeruginosa Bloodstream Infection Non-Susceptible to Carbapenems but
           Susceptible to “Old” Cephalosporins and/or to Penicillins

    • Authors: Ronit Zaidenstein, Asaf Miller, Ruthy Tal-Jasper, Hadas Ofer-Friedman, Menachem Sklarz, David Katz, Tsillia Lazarovitch, Paul Lephart, Bethlehem Mengesha, Oran Tzuman, Mor Dadon, Chen Daniel, Jacob Moran-Gilad, Dror Marchaim
      First page: 9
      Abstract: It is unknown as to whether other beta-lactams can be used for bloodstream infections (BSI) resulting from Pseudomonas aeruginosa (PA) which are non-susceptible to one or more carbapenem. We conducted a retrospective cohort study at the Assaf Harofeh Medical Center (AHMC) from January 2010 to August 2014. Adult patients with PA-BSI non-susceptible to a group 2 carbapenem but susceptible to ceftazidime or piperacillin (with or without tazobactam), were enrolled. We compared the outcomes of patients who received an appropriate beta-lactam antibiotic (“cases”) to those who received an appropriate non-beta-lactam antibiotic (“controls”). Whole genome sequencing was performed for one of the isolates. Twenty-six patients with PA-BSI met inclusion criteria: 18 received a beta-lactam and 8 a non-beta-lactam (three a fluoroquinolone, two colistin, one a fluoroquinolone and an aminoglycoside, one a fluoroquinolone and colistin, and one colistin and an aminoglycoside). All clinical outcomes were similar between the groups. There were large variations in the phenotypic susceptibilities of the strains. A detailed molecular investigation of one isolate revealed a strain that belonged to MLST-137, with the presence of multiple efflux pumps, OXA-50, and a chromosomally mediated Pseudomonas-derived cephalosporinase (PDC). The oprD gene was intact. Non-carbapenem-β-lactams may still be effective alternatives for short duration therapy (up to 14 days) for BSI caused by a carbapenem non-susceptible (but susceptible to ceftazidime, piperacillin, and/or piperacillin-tazobactam) PA strain. This observation requires further confirmatory analyses. Future molecular investigations should be performed, in order to further analyze additional potential mechanisms for this prevalent phenotype.
      Citation: Microorganisms
      PubDate: 2018-01-16
      DOI: 10.3390/microorganisms6010009
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 10: Investigating Potential Chromosomal
           Rearrangements during Laboratory Culture of Neisseria gonorrhoeae

    • Authors: Russell Spencer-Smith, Simon Gould, Madhuri Pulijala, Lori Snyder
      First page: 10
      Abstract: Comparisons of genome sequence data between different strains and isolates of Neisseria spp., such as Neisseria gonorrhoeae, reveal that over the evolutionary history of these organisms, large scale chromosomal rearrangements have occurred. Factors within the genomes, such as repetitive sequences and prophage, are believed to have contributed to these observations. However, the timescale in which rearrangements occur is not clear, nor whether it might be expected for them to happen in the laboratory. In this study, N. gonorrhoeae was repeatedly passaged in the laboratory and assessed for large scale chromosomal rearrangements. Using gonococcal strain NCCP11945, for which there is a complete genome sequence, cultures were passaged for eight weeks in the laboratory. The resulting genomic DNA was assessed using Pulsed Field Gel Electrophoresis, comparing the results to the predicted results from the genome sequence data. Three cultures generated Pulsed Field Gel Electrophoresis patterns that varied from the genomic data and were further investigated for potential chromosomal rearrangements.
      Citation: Microorganisms
      PubDate: 2018-01-20
      DOI: 10.3390/microorganisms6010010
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 11: Defining Multidrug Resistance of
           Gram-Negative Bacteria in the Dutch–German Border Region—Impact of
           National Guidelines

    • Authors: Robin Köck, Philipp Siemer, Jutta Esser, Stefanie Kampmeier, Matthijs Berends, Corinna Glasner, Jan Arends, Karsten Becker, Alexander Friedrich
      First page: 11
      Abstract: Preventing the spread of multidrug-resistant Gram-negative bacteria (MDRGNB) is a public health priority. However, the definition of MDRGNB applied for planning infection prevention measures such as barrier precautions differs depending on national guidelines. This is particularly relevant in the Dutch–German border region, where patients are transferred between healthcare facilities located in the two different countries, because clinicians and infection control personnel must understand antibiograms indicating MDRGNB from both sides of the border and using both national guidelines. This retrospective study aimed to compare antibiograms of Gram-negative bacteria and classify them using the Dutch and German national standards for MDRGNB definition. A total of 31,787 antibiograms from six Dutch and four German hospitals were classified. Overall, 73.7% were no MDRGNB according to both guidelines. According to the Dutch and German guideline, 7772/31,787 (24.5%) and 4586/31,787 (12.9%) were MDRGNB, respectively (p < 0.0001). Major divergent classifications were observed for extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae, non-carbapenemase-producing carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. The observed differences show that medical staff must carefully check previous diagnostic findings when patients are transferred across the Dutch–German border, as it cannot be assumed that MDRGNB requiring special hygiene precautions are marked in the transferred antibiograms in accordance with both national guidelines.
      Citation: Microorganisms
      PubDate: 2018-01-26
      DOI: 10.3390/microorganisms6010011
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 12: Responses of an Agricultural Soil
           Microbiome to Flooding with Seawater after Managed Coastal Realignment

    • Authors: Kamilla Sjøgaard, Thomas Valdemarsen, Alexander Treusch
      First page: 12
      Abstract: Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with seawater. How flooding with seawater impacts soil microbiomes and the biogeochemical cycling of elements is poorly understood. To address this, we conducted a microcosm experiment using soil cores collected at the nature restoration project site Gyldensteen Strand (Denmark), which were flooded with seawater and monitored over six months. Throughout the experiment, biogeochemical analyses, microbial community fingerprinting and the quantification of marker genes documented clear shifts in microbiome composition and activity. The flooding with seawater initially resulted in accelerated heterotrophic activity that entailed high ammonium production and net removal of nitrogen from the system, also demonstrated by a concurrent increase in the abundances of marker genes for ammonium oxidation and denitrification. Due to the depletion of labile soil organic matter, microbial activity decreased after approximately four months. The event of flooding caused the largest shifts in microbiome composition with the availability of labile organic matter subsequently being the most important driver for the succession in microbiome composition in soils flooded with seawater.
      Citation: Microorganisms
      PubDate: 2018-01-26
      DOI: 10.3390/microorganisms6010012
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 13: Biomarkers’ Responses to Reductive
           Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM

    • Authors: Gretchen Heavner, Cresten Mansfeldt, Garrett Debs, Sage Hellerstedt, Annette Rowe, Ruth Richardson
      First page: 13
      Abstract: Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10−12 to 5.9 × 10−10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R2 = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain.
      Citation: Microorganisms
      PubDate: 2018-02-08
      DOI: 10.3390/microorganisms6010013
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 14: Bacterial Microbiota of Rice Roots:
           16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity,
           Endophytes Isolation and Simplified Endophytic Community

    • Authors: Felix Moronta-Barrios, Fabrizia Gionechetti, Alberto Pallavicini, Edgloris Marys, Vittorio Venturi
      First page: 14
      Abstract: Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosphere of two high-yield rice cultivars—Pionero 2010 FL and DANAC SD20A—extensively grown in Venezuela in 2014. Fifteen putative bacterial endophytes were then isolated from surface-sterilized roots and further studied in vitro and in planta. We have then performed inoculation of rice seedlings with a simplified community composed by 10 of the isolates and we have tracked them in the course of 30 days in greenhouse cultivation. The results obtained suggest that a set was able to significantly colonize together the rice endorhizospheres, indicating possible cooperation and the ability to form a stable multispecies community. This approach can be useful in the development of microbial solutions for a more sustainable rice production.
      Citation: Microorganisms
      PubDate: 2018-02-11
      DOI: 10.3390/microorganisms6010014
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 15: Comparison of Rumen and Manure
           Microbiomes and Implications for the Inoculation of Anaerobic Digesters

    • Authors: Emine Ozbayram, Orhan Ince, Bahar Ince, Hauke Harms, Sabine Kleinsteuber
      First page: 15
      Abstract: Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.
      Citation: Microorganisms
      PubDate: 2018-02-14
      DOI: 10.3390/microorganisms6010015
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 16: Core Sulphate-Reducing Microorganisms in
           Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of
           Methanogens

    • Authors: Maryam Rezadehbashi, Susan Baldwin
      First page: 16
      Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.
      Citation: Microorganisms
      PubDate: 2018-02-23
      DOI: 10.3390/microorganisms6010016
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 17: Identification of Uncultured Bacterial
           Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as
           Candidate Cellulose Utilizers from the Rumen of Beef Cows

    • Authors: Lee Opdahl, Michael Gonda, Benoit St-Pierre
      First page: 17
      Abstract: The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6–50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcus flavefaciens and Fibrobacter succinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides.
      Citation: Microorganisms
      PubDate: 2018-02-24
      DOI: 10.3390/microorganisms6010017
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 18: World-Wide Variation in Incidence of
           Staphylococcus aureus Associated Ventilator-Associated Pneumonia: A
           Meta-Regression

    • Authors: James Hurley
      First page: 18
      Abstract: Staphylococcus aureus (S. aureus) is a common Ventilator-Associated Pneumonia (VAP) isolate. The objective here is to define the extent and possible reasons for geographic variation in the incidences of S. aureus-associated VAP, MRSA-VAP and overall VAP. A meta-regression model of S. aureus-associated VAP incidence per 1000 Mechanical Ventilation Days (MVD) was undertaken using random effects methods among publications obtained from a search of the English language literature. This model incorporated group level factors such as admission to a trauma ICU, year of publication and use of bronchoscopic sampling towards VAP diagnosis. The search identified 133 publications from seven worldwide regions published over three decades. The summary S. aureus-associated VAP incidence was 4.5 (3.9–5.3) per 1000 MVD. The highest S. aureus-associated VAP incidence is amongst reports from the Mediterranean (mean; 95% confidence interval; 6.1; 4.1–8.5) versus that from Asian ICUs (2.1; 1.5–3.0). The incidence of S. aureus-associated VAP varies by up to three-fold (for the lowest versus highest incidence) among seven geographic regions worldwide, whereas the incidence of VAP varies by less than two-fold. Admission to a trauma unit is the most important group level correlate for S. aureus-associated VAP.
      Citation: Microorganisms
      PubDate: 2018-02-27
      DOI: 10.3390/microorganisms6010018
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 19: Inteins: Localized Distribution, Gene
           Regulation, and Protein Engineering for Biological Applications

    • Authors: Theetha Pavankumar
      First page: 19
      Abstract: Inteins are self-splicing polypeptides with an ability to excise themselves from flanking host protein regions with remarkable precision; in the process, they ligate flanked host protein fragments. Inteins are distributed sporadically across all three domains of life (bacteria, archaea, and unicellular eukaryotes). However, their apparent localized distribution in DNA replication, repair, and recombination proteins (the 3Rs), particularly in bacteria and archaea, is enigmatic. Our understanding of the localized distribution of inteins in the 3Rs, and their possible regulatory role in such distribution, is still only partial. Nevertheless, understanding the chemistry of post-translational self-splicing of inteins has opened up opportunities for protein chemists to modify, manipulate, and bioengineer proteins. Protein-splicing technology is adapted to a wide range of applications, starting with untagged protein purification, site-specific protein labeling, protein biotinylation, isotope incorporation, peptide cyclization, as an antimicrobial target, and so on. This review is focused on the chemistry of splicing; the localized distribution of inteins, particularly in the 3Rs and their possible role in regulating host protein function; and finally, the use of protein-splicing technology in various protein engineering applications.
      Citation: Microorganisms
      PubDate: 2018-02-28
      DOI: 10.3390/microorganisms6010019
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 20: Differential Transcriptional Activation
           of Genes Encoding Soluble Methane Monooxygenase in a Facultative Versus an
           Obligate Methanotroph

    • Authors: Angela Smirnova, Peter Dunfield
      First page: 20
      Abstract: Methanotrophs are a specialized group of bacteria that can utilize methane (CH4) as a sole energy source. A key enzyme responsible for methane oxidation is methane monooxygenase (MMO), of either a soluble, cytoplasmic type (sMMO), or a particulate, membrane-bound type (pMMO). Methylocella silvestris BL2 and Methyloferula stellata AR4 are closely related methanotroph species that oxidize methane via sMMO only. However, Methyloferula stellata is an obligate methanotroph, while Methylocella silvestris is a facultative methanotroph able to grow on several multicarbon substrates in addition to methane. We constructed transcriptional fusions of the mmo promoters of Methyloferula stellata and Methylocella silvestris to a promoterless gfp in order to compare their transcriptional regulation in response to different growth substrates, in the genetic background of both organisms. The following patterns were observed: (1) The mmo promoter of the facultative methanotroph Methylocella silvestris was either transcriptionally downregulated or repressed by any growth substrate other than methane in the genetic background of Methylocella silvetris; (2) Growth on methane alone upregulated the mmo promoter of Methylocella silvetris in its native background but not in the obligate methanotroph Methyloferula stellata; (3) The mmo promoter of Methyloferula stellata was constitutive in both organisms regardless of the growth substrate, but with much lower promoter activity than the mmo promoter of Methylocella silvetris. These results support a conclusion that a different mode of transcriptional regulation of sMMO contributes to the facultative lifestyle of Methylocella silvetris compared to the obligate methanotroph Methyloferula stellata.
      Citation: Microorganisms
      PubDate: 2018-03-06
      DOI: 10.3390/microorganisms6010020
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 21: Fungal Disease Prevention in Seedlings
           of Rice (Oryza sativa) and Other Grasses by Growth-Promoting
           Seed-Associated Endophytic Bacteria from Invasive Phragmites australis

    • Authors: Satish Verma, Kathryn Kingsley, Marshall Bergen, Kurt Kowalski, James White
      First page: 21
      Abstract: Non-cultivated plants carry microbial endophytes that may be used to enhance development and disease resistance of crop species where growth-promoting and protective microbes may have been lost. During seedling establishment, seedlings may be infected by several fungal pathogens that are seed or soil borne. Several species of Fusarium, Pythium and other water moulds cause seed rots during germination. Fusarium blights of seedlings are also very common and significantly affect seedling development. In the present study we screened nine endophytic bacteria isolated from the seeds of invasive Phragmites australis by inoculating onto rice, Bermuda grass (Cynodon dactylon), or annual bluegrass (Poa annua) seeds to evaluate plant growth promotion and protection from disease caused by Fusarium oxysporum. We found that three bacteria belonging to genus Pseudomonas spp. (SLB4-P. fluorescens, SLB6-Pseudomonas sp. and SY1-Pseudomonas sp.) promoted seedling development, including enhancement of root and shoot growth, and stimulation of root hair formation. These bacteria were also found to increase phosphate solubilization in in vitro experiments. Pseudomonas sp. (SY1) significantly protected grass seedlings from Fusarium infection. In co-culture experiments, strain SY1 strongly inhibited fungal pathogens with 85.71% growth inhibition of F. oxysporum, 86.33% growth inhibition of Curvularia sp. and 82.14% growth inhibition of Alternaria sp. Seedlings previously treated with bacteria were found much less infected by F. oxysporum in comparison to non-treated controls. On microscopic observation we found that bacteria appeared to degrade fungal mycelia actively. Metabolite products of strain SY1 in agar were also found to inhibit fungal growth on nutrient media. Pseudomonas sp. (SY1) was found to produce antifungal volatiles. Polymerase chain reaction (PCR) amplification using specific primers for pyrrolnitirin synthesis and HCN (hydrogen cyanide) production suggested presence of genes for both compounds in the genome of SY1. HCN was detected in cultures of SY1. We conclude that microbes from non-cultivated plants may provide disease protection and promote growth of crop plants.
      Citation: Microorganisms
      PubDate: 2018-03-08
      DOI: 10.3390/microorganisms6010021
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 22: The Mycobiome: A Neglected Component in
           the Microbiota-Gut-Brain Axis

    • Authors: Raphaël Enaud, Louise-Eva Vandenborght, Noémie Coron, Thomas Bazin, Renaud Prevel, Thierry Schaeverbeke, Patrick Berger, Michael Fayon, Thierry Lamireau, Laurence Delhaes
      First page: 22
      Abstract: In recent years, the gut microbiota has been considered as a full-fledged actor of the gut–brain axis, making it possible to take a new step in understanding the pathophysiology of both neurological and psychiatric diseases. However, most of the studies have been devoted to gut bacterial microbiota, forgetting the non-negligible fungal flora. In this review, we expose how the role of the fungal component in the microbiota-gut-brain axis is legitimate, through its interactions with both the host, especially with the immune system, and the gut bacteria. We also discuss published data that already attest to a role of the mycobiome in the microbiota-gut-brain axis, and the impact of fungi on clinical and therapeutic research.
      Citation: Microorganisms
      PubDate: 2018-03-09
      DOI: 10.3390/microorganisms6010022
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 23: Effects of Elevated Hydrostatic Pressure
           against Mesophilic Background Microflora and Habituated Salmonella
           Serovars in Orange Juice

    • Authors: Abimbola Allison, Edward Daniels, Shahid Chowdhury, Aliyar Fouladkhah
      First page: 23
      Abstract: With recent improvements in the commercial feasibility of high pressure pasteurization units, the technology is gaining rapid acceptability across various sectors of food manufacturing, thus requiring extensive validation studies for effective adoption. Various times (1 min to 10 min) and intensity levels (0 MPa to 380 MPa) of elevated hydrostatic pressure were investigated for decontamination of mesophilic background microflora and inoculated Salmonella in orange juice. Results were analyzed by GLM procedure of SAS using Tukey- and Dunnett-adjusted ANOVA, additionally the Kmax and D-values were calculated using best-fitted (maximum R2) model obtained by GInaFit software. At 380 MPa, for treatments of 1 min to 10 min, D-value of 1.35, and inactivation Kmax of 3.34 were observed for Salmonella serovars. D-values were 5.90 and 14.68 for treatments of 241 MPa and 103 MPa, respectively. Up to 1.01 and >7.22 log CFU/mL reductions (p < 0.05) of habituated Salmonella serovars at planktonic stages were achieved using application of pressure at 380 MPa for 1 min and 10 min, respectively. Mesophilic background microflora counts were reduced (p < 0.05) by 1.68 to 5.29 log CFU/mL after treatment at 380 MPa for 1 min and 10 min, respectively. Treatments below two minutes were less efficacious (p ≥ 0.05) against the pathogen and background microflora, in vast majority of time and pressure combinations.
      Citation: Microorganisms
      PubDate: 2018-03-09
      DOI: 10.3390/microorganisms6010023
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 24: Description of New and Amended Clades of
           the Genus Photobacterium

    • Authors: Alejandro Labella, M. Castro, Manuel Manchado, Juan Borrego
      First page: 24
      Abstract: Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of gyrB, gapA, topA, ftsZ and mreB housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the Photobacterium clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus Photobacterium into the following 5 clades: Phosphoreum (comprises P. aquimaris, “P. carnosum,” P. iliopiscarium, P. kishitanii, P. phosphoreum, “P. piscicola” and “P. toruni”); clade Profundum (composed of P. aestuarii, P. alginatilyticum, P. frigidiphilum, P. indicum, P. jeanii, P. lipolyticum, “P. marinum,” and P. profundum); clade Damselae (two subspecies of P. damselae, damselae and piscicida); and two new clades: clade Ganghwense (includes P. aphoticum, P. aquae, P. galatheae, P. ganghwense, P. halotolerans, P. panuliri and P. proteolyticum); and clade Leiognathi (composed by P. angustum, P. leiognathi subsp. leiognathi and “P. leiognathi subsp. mandapamensis”). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only P. aplysiae could not be included in none of the established clade, constituting an orphan clade.
      Citation: Microorganisms
      PubDate: 2018-03-12
      DOI: 10.3390/microorganisms6010024
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 25: Antibody-Based Agents in the Management
           of Antibiotic-Resistant Staphylococcus aureus Diseases

    • Authors: Pietro Speziale, Simonetta Rindi, Giampiero Pietrocola
      First page: 25
      Abstract: Staphylococcus aureus is a human pathogen that can cause a wide spectrum of diseases, including sepsis, pneumonia, arthritis, and endocarditis. Ineffective treatment of a number of staphylococcal infections with antibiotics is due to the development and spread of antibiotic-resistant strains following decades of antibiotic usage. This has generated renewed interest within the scientific community in alternative therapeutic agents, such as anti-S. aureus antibodies. Although the role of antibodies in the management of S. aureus diseases is controversial, the success of this pathogen in neutralizing humoral immunity clearly indicates that antibodies offer the host extensive protection. In this review, we report an update on efforts to develop antibody-based agents, particularly monoclonal antibodies, and their therapeutic potential in the passive immunization approach to the treatment and prevention of S. aureus infections.
      Citation: Microorganisms
      PubDate: 2018-03-13
      DOI: 10.3390/microorganisms6010025
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 26: Identification of sucA, Encoding
           β-Fructofuranosidase, in Rhizopus microsporus

    • Authors: Yoshitake Orikasa, Yuji Oda, Takuji Ohwada
      First page: 26
      Abstract: Rhizopus microsporus NBRC 32995 was found to hydrolyze fructooligosaccharides (FOS), as well as sucrose, almost completely into monosaccharides through the production of sufficient amounts of organic acids, indicating that the complete hydrolysis of FOS was caused by the secretion of β-fructofuranosidase from fungal cells. Thus, the sucA gene, encoding a β-fructofuranosidase, was amplified by degenerate PCR, and its complete nucleotide sequence was determined. The total length of the sucA gene was 1590 bp, and the SucA protein of R. microsporus NBRC 32995 belonged to clade VIa, which also contains Rhizopus delemar and is closely related to Saccharomycotina, a subdivision of the Ascomycota.
      Citation: Microorganisms
      PubDate: 2018-03-13
      DOI: 10.3390/microorganisms6010026
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 27: Responses of Salt Marsh Plant
           Rhizosphere Diazotroph Assemblages to Drought

    • Authors: Debra Davis, Sparkle Malone, Charles Lovell
      First page: 27
      Abstract: Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are also nitrogen limited and depend on plant associated diazotrophs as their source of ‘new’ nitrogen. A 4-year study was conducted to investigate the structure and composition of the rhizosphere diazotroph assemblages associated with 5 distinct plant zones in one such salt marsh. A period of greatly restricted tidal inundation and precipitation, as well as two periods of drought (June–July 2004, and May 2007) occurred during the study. DGGE of nifH PCR amplicons from rhizosphere samples, Principal Components Analysis of the resulting banding patterns, and unconstrained ordination analysis of taxonomic data and environmental parameters were conducted. Diazotroph assemblages were organized into 5 distinct groups (R2 = 0.41, p value < 0.001) whose presence varied with the environmental conditions of the marsh. Diazotroph assemblage group detection differed during and after the drought event, indicating that persistent diazotrophs maintained populations that provided reduced supplies of new nitrogen for vegetation during the periods of drought.
      Citation: Microorganisms
      PubDate: 2018-03-15
      DOI: 10.3390/microorganisms6010027
      Issue No: Vol. 6, No. 1 (2018)
       
  • Microorganisms, Vol. 6, Pages 1: Over a Decade of recA and tly Gene
           Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have
           We Learnt'

    • Authors: Andrew McDowell
      First page: 1
      Abstract: The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail.
      Citation: Microorganisms
      PubDate: 2017-12-21
      DOI: 10.3390/microorganisms6010001
      Issue No: Vol. 6, No. 1 (2017)
       
  • Microorganisms, Vol. 5, Pages 64: Markers of Microbial Translocation and
           Immune Activation Predict Cognitive Processing Speed in Heavy-Drinking Men
           Living with HIV

    • Authors: Mollie Monnig, Christopher Kahler, Patricia Cioe, Peter Monti, Kenneth Mayer, David Pantalone, Ronald Cohen, Bharat Ramratnam
      First page: 64
      Abstract: HIV infection and alcohol use disorder are associated with deficits in neurocognitive function. Emerging evidence points to pro-inflammatory perturbations of the gut-brain axis as potentially contributing to neurocognitive impairment in the context of HIV and chronic heavy alcohol use. This study examined whether plasma markers of microbial translocation (LPS) from the gastrointestinal tract and related immune activation (sCD14, EndoCAb) were associated with neurocognition in 21 men living with HIV who were virally suppressed on antiretroviral therapy. All participants met federal criteria for heavy drinking and were enrolled in a randomized controlled trial (RCT) of a brief alcohol intervention. This secondary analysis utilized blood samples and cognitive scores (learning, memory, executive function, verbal fluency, and processing speed) obtained at baseline and three-month follow-up of the RCT. In generalized estimating equation models, LPS, sCD14, and EndoCAb individually were significant predictors of processing speed. In a model with all biomarkers, higher LPS and sCD14 both remained significant predictors of lower processing speed. These preliminary findings suggest that inflammation stemming from HIV and/or alcohol could have negative effects on the gut-brain axis, manifested as diminished processing speed. Associations of microbial translocation and immune activation with processing speed in heavy-drinking PLWH warrant further investigation in larger-scale studies.
      Citation: Microorganisms
      PubDate: 2017-09-21
      DOI: 10.3390/microorganisms5040064
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 65: Nutritional Requirements and Their
           Importance for Virulence of Pathogenic Cryptococcus Species

    • Authors: Rhys Watkins, Jason King, Simon Johnston
      First page: 65
      Abstract: Cryptococcus sp. are basidiomycete yeasts which can be found widely, free-living in the environment. Interactions with natural predators, such as amoebae in the soil, are thought to have promoted the development of adaptations enabling the organism to survive inside human macrophages. Infection with Cryptococcus in humans occurs following inhalation of desiccated yeast cells or spore particles and may result in fatal meningoencephalitis. Human disease is caused almost exclusively by the Cryptococcus neoformans species complex, which predominantly infects immunocompromised patients, and the Cryptococcus gattii species complex, which is capable of infecting immunocompetent individuals. The nutritional requirements of Cryptococcus are critical for its virulence in animals. Cryptococcus has evolved a broad range of nutrient acquisition strategies, many if not most of which also appear to contribute to its virulence, enabling infection of animal hosts. In this review, we summarise the current understanding of nutritional requirements and acquisition in Cryptococcus and offer perspectives to its evolution as a significant pathogen of humans.
      Citation: Microorganisms
      PubDate: 2017-09-30
      DOI: 10.3390/microorganisms5040065
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 66: The Gut Microbiome Feelings of the
           Brain: A Perspective for Non-Microbiologists

    • Authors: Aaron Lerner, Sandra Neidhöfer, Torsten Matthias
      First page: 66
      Abstract: Objectives: To comprehensively review the scientific knowledge on the gut–brain axis. Methods: Various publications on the gut–brain axis, until 31 July 2017, were screened using the Medline, Google, and Cochrane Library databases. The search was performed using the following keywords: “gut-brain axis”, “gut-microbiota-brain axis”, “nutrition microbiome/microbiota”, “enteric nervous system”, “enteric glial cells/network”, “gut-brain pathways”, “microbiome immune system”, “microbiome neuroendocrine system” and “intestinal/gut/enteric neuropeptides”. Relevant articles were selected and reviewed. Results: Tremendous progress has been made in exploring the interactions between nutrients, the microbiome, and the intestinal, epithelium–enteric nervous, endocrine and immune systems and the brain. The basis of the gut–brain axis comprises of an array of multichannel sensing and trafficking pathways that are suggested to convey the enteric signals to the brain. These are mediated by neuroanatomy (represented by the vagal and spinal afferent neurons), the neuroendocrine–hypothalamic–pituitary–adrenal (HPA) axis (represented by the gut hormones), immune routes (represented by multiple cytokines), microbially-derived neurotransmitters, and finally the gate keepers of the intestinal and brain barriers. Their mutual and harmonious but intricate interaction is essential for human life and brain performance. However, a failure in the interaction leads to a number of inflammatory-, autoimmune-, neurodegenerative-, metabolic-, mood-, behavioral-, cognitive-, autism-spectrum-, stress- and pain-related disorders. The limited availability of information on the mechanisms, pathways and cause-and-effect relationships hinders us from translating and implementing the knowledge from the bench to the clinic. Implications: Further understanding of this intricate field might potentially shed light on novel preventive and therapeutic strategies to combat these disorders. Nutritional approaches, microbiome manipulations, enteric and brain barrier reinforcement and sensing and trafficking modulation might improve physical and mental health outcomes.
      Citation: Microorganisms
      PubDate: 2017-10-12
      DOI: 10.3390/microorganisms5040066
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 67: A Two-Step Bioconversion Process for
           Canolol Production from Rapeseed Meal Combining an Aspergillus niger
           Feruloyl Esterase and the Fungus Neolentinus lepideus

    • Authors: Elise Odinot, Frédéric Fine, Jean-Claude Sigoillot, David Navarro, Oscar Laguna, Alexandra Bisotto, Corinne Peyronnet, Christian Ginies, Jérôme Lecomte, Craig Faulds, Anne Lomascolo
      First page: 67
      Abstract: Rapeseed meal is a cheap and abundant raw material, particularly rich in phenolic compounds of biotechnological interest. In this study, we developed a two-step bioconversion process of naturally occurring sinapic acid (4-hydroxy-3,5-dimethoxycinnamic acid) from rapeseed meal into canolol by combining the complementary potentialities of two filamentous fungi, the micromycete Aspergillus niger and the basidiomycete Neolentinus lepideus. Canolol could display numerous industrial applications because of its high antioxidant, antimutagenic and anticarcinogenic properties. In the first step of the process, the use of the enzyme feruloyl esterase type-A (named AnFaeA) produced with the recombinant strain A. niger BRFM451 made it possible to release free sinapic acid from the raw meal by hydrolysing the conjugated forms of sinapic acid in the meal (mainly sinapine and glucopyranosyl sinapate). An amount of 39 nkat AnFaeA per gram of raw meal, at 55 °C and pH 5, led to the recovery of 6.6 to 7.4 mg of free sinapic acid per gram raw meal, which corresponded to a global hydrolysis yield of 68 to 76% and a 100% hydrolysis of sinapine. Then, the XAD2 adsorbent (a styrene and divinylbenzene copolymer resin), used at pH 4, enabled the efficient recovery of the released sinapic acid, and its concentration after elution with ethanol. In the second step, 3-day-old submerged cultures of the strain N. lepideus BRFM15 were supplied with the recovered sinapic acid as the substrate of bioconversion into canolol by a non-oxidative decarboxylation pathway. Canolol production reached 1.3 g/L with a molar yield of bioconversion of 80% and a productivity of 100 mg/L day. The same XAD2 resin, when used at pH 7, allowed the recovery and purification of canolol from the culture broth of N. lepideus. The two-step process used mild conditions compatible with green chemistry.
      Citation: Microorganisms
      PubDate: 2017-10-14
      DOI: 10.3390/microorganisms5040067
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 68: Linking Compositional and Functional
           Predictions to Decipher the Biogeochemical Significance in DFAA Turnover
           of Abundant Bacterioplankton Lineages in the North Sea

    • Authors: Bernd Wemheuer, Franziska Wemheuer, Dimitri Meier, Sara Billerbeck, Helge-Ansgar Giebel, Meinhard Simon, Christoph Scherber, Rolf Daniel
      First page: 68
      Abstract: Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.
      Citation: Microorganisms
      PubDate: 2017-11-05
      DOI: 10.3390/microorganisms5040068
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 69: Unexpected High Diversity of Terrestrial
           Cyanobacteria from the Campus of the University of the Ryukyus, Okinawa,
           Japan

    • Authors: Xuan Nguyen, Shinpei Sumimoto, Shoichiro Suda
      First page: 69
      Abstract: Terrestrial cyanobacterial strains were isolated from the Nishihara campus of the University of the Ryukyus, Okinawa, Japan. The 13 sampling sites were distributed in a 200 m radius and appeared as dry, blackened stains. From these small areas, 143 cyanobacterial strains were established. The strains were divided into five morphotypes, including unicells, unicells with baeocytes, non-branching filaments, false-branching filaments, and heterocystous strains. From the strains, 105 partial 16S rRNA gene sequences were obtained and could be classified into 30 generic types. Among them, 22 unique strains and over 1100 bps of data were selected for further phylogenetic analyses. These sequences were positioned into six main clades corresponding to cyanobacterial orders: Nostocales, Chroococidiopsidales, Chroococcales, Oscillatoriales, Pleurocapsales, and Synechococcales. Almost all sequences had no identical matching data in GenBank and many of them had no closely related data. These data suggest that the terrestrial cyanobacteria are very divese even within close sampling areas, such as within the campus of the University of the Ryukyus. The established strains are not only important for classification of terrestrial cyanobacteria but also for possible application studies in the future.
      Citation: Microorganisms
      PubDate: 2017-11-07
      DOI: 10.3390/microorganisms5040069
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 70: Transmission of Bacterial Endophytes

    • Authors: Anna Frank, Jessica Saldierna Guzmán, Jackie Shay
      First page: 70
      Abstract: Plants are hosts to complex communities of endophytic bacteria that colonize the interior of both below- and aboveground tissues. Bacteria living inside plant tissues as endophytes can be horizontally acquired from the environment with each new generation, or vertically transmitted from generation to generation via seed. A better understanding of bacterial endophyte transmission routes and modes will benefit studies of plant–endophyte interactions in both agricultural and natural ecosystems. In this review, we provide an overview of the transmission routes that bacteria can take to colonize plants, including vertically via seeds and pollen, and horizontally via soil, atmosphere, and insects. We discuss both well-documented and understudied transmission routes, and identify gaps in our knowledge on how bacteria reach the inside of plants. Where little knowledge is available on endophytes, we draw from studies on bacterial plant pathogens to discuss potential transmission routes. Colonization of roots from soil is the best studied transmission route, and probably the most important, although more studies of transmission to aerial parts and stomatal colonization are needed, as are studies that conclusively confirm vertical transfer. While vertical transfer of bacterial endophytes likely occurs, obligate and strictly vertically transferred symbioses with bacteria are probably unusual in plants. Instead, plants appear to benefit from the ability to respond to a changing environment by acquiring its endophytic microbiome anew with each generation, and over the lifetime of individuals.
      Citation: Microorganisms
      PubDate: 2017-11-10
      DOI: 10.3390/microorganisms5040070
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 71: Special Issue: Beneficial Microorganisms
           for Food Manufacturing—Fermented and Biopreserved Foods and Beverages

    • Authors: Régine Talon, Monique Zagorec
      First page: 71
      Abstract: Food fermentation is an ancient technology, disseminated worldwide, which harness microorganisms and their enzymes to improve and diversify the human diet [...]
      Citation: Microorganisms
      PubDate: 2017-11-13
      DOI: 10.3390/microorganisms5040071
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 72: Paralytic Shellfish Toxins and
           Cyanotoxins in the Mediterranean: New Data from Sardinia and Sicily
           (Italy)

    • Authors: Antonella Lugliè, Maria Grazia Giacobbe, Elena Riccardi, Milena Bruno, Silvia Pigozzi, Maria Antonietta Mariani, Cecilia Teodora Satta, Daniela Stacca, Anna Maria Bazzoni, Tiziana Caddeo, Pasqualina Farina, Bachisio Mario Padedda, Silvia Pulina, Nicola Sechi, Anna Milandri
      First page: 72
      Abstract: Harmful algal blooms represent a severe issue worldwide. They affect ecosystem functions and related services and goods, with consequences on human health and socio-economic activities. This study reports new data on paralytic shellfish toxins (PSTs) from Sardinia and Sicily (Italy), the largest Mediterranean islands where toxic events, mainly caused by Alexandrium species (Dinophyceae), have been ascertained in mussel farms since the 2000s. The toxicity of the A. minutum, A. tamarense and A. pacificum strains, established from the isolation of vegetative cells and resting cysts, was determined by high performance liquid chromatography (HPLC). The analyses indicated the highest toxicity for A. pacificum strains (total PSTs up to 17.811 fmol cell−1). The PSTs were also assessed in a strain of A. tamarense. The results encourage further investigation to increase the knowledge of toxic species still debated in the Mediterranean. This study also reports new data on microcystins (MCs) and β-N-methylamino-L-alanine (BMAA) from a Sardinian artificial lake (Lake Bidighinzu). The presence of MCs and BMAA was assessed in natural samples and in cell cultures by enzyme-linked immunosorbent assay (ELISA). BMAA positives were found in all the analysed samples with a maximum of 17.84 µg L−1. The obtained results added further information on cyanotoxins in Mediterranean reservoirs, particularly BMAA, which have not yet been thoroughly investigated.
      Citation: Microorganisms
      PubDate: 2017-11-16
      DOI: 10.3390/microorganisms5040072
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 73: Physiological Peculiarities of
           Lignin-Modifying Enzyme Production by the White-Rot Basidiomycete
           Coriolopsis gallica Strain BCC 142

    • Authors: Vladimir Elisashvili, Eva Kachlishvili, Mikheil Asatiani, Ramona Darlington, Katarzyna Kucharzyk
      First page: 73
      Abstract: Sixteen white-rot Basidiomycota isolates were screened for production of lignin-modifying enzymes (LME) in glycerol- and mandarin peel-containing media. In the synthetic medium, Cerrena unicolor strains were the only high laccase (Lac) (3.2–9.4 U/mL) and manganese peroxidase (MnP) (0.56–1.64 U/mL) producers while one isolate Coriolopsis gallica was the only lignin peroxidase (LiP) (0.07 U/mL) producer. Addition of mandarin peels to the synthetic medium promoted Lac production either due to an increase in fungal biomass (Funalia trogii, Trametes hirsuta, and T. versicolor) or enhancement of enzyme production (C. unicolor, Merulius tremellosus, Phlebia radiata, Trametes ochracea). Mandarin peels favored enhanced MnP and LiP secretion by the majority of the tested fungi. The ability of LiP activity production by C. gallica, C. unicolor, F. trogii, T. ochracea, and T. zonatus in the medium containing mandarin-peels was reported for the first time. Several factors, such as supplementation of the nutrient medium with a variety of lignocellulosic materials, nitrogen source or surfactant (Tween 80, Triton X-100) significantly influenced production of LME by a novel strain of C. gallica. Moreover, C. gallica was found to be a promising LME producer with a potential for an easy scale up cultivation in a bioreactor and high enzyme yields (Lac-9.4 U/mL, MnP-0.31 U/mL, LiP-0.45 U/mL).
      Citation: Microorganisms
      PubDate: 2017-11-17
      DOI: 10.3390/microorganisms5040073
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 74: Pan-Cellulosomics of Mesophilic
           Clostridia: Variations on a Theme

    • Authors: Bareket Dassa, Ilya Borovok, Vincent Lombard, Bernard Henrissat, Raphael Lamed, Edward Bayer, Sarah Moraïs
      First page: 74
      Abstract: The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature. We explored the genomic organization of key cellulosome components by comparing the cellulosomal gene clusters in each bacterial species, and the conserved sequence features of the specific cellulosomal modules (cohesins and dockerins), on the background of their phylogenetic relationship. Additionally, we performed comparative analyses of the species-specific repertoire of carbohydrate-degrading enzymes for each of the clostridial species, and classified each cellulosomal enzyme into a specific CAZy family, thus indicating their putative enzymatic activity (e.g., cellulases, hemicellulases, and pectinases). Our work provides, for this large group of bacteria, a broad overview of the blueprints of their multi-component cellulosomal complexes. The high similarity of their scaffoldin clusters and dockerin-based recognition residues suggests a common ancestor, and/or extensive horizontal gene transfer, and potential cross-species recognition. In addition, the sporadic spatial organization of the numerous dockerin-containing genes in several of the genomes, suggests the importance of the cellulosome paradigm in the given bacterial species. The information gained in this work may be utilized directly or developed further by genetically engineering and optimizing designer cellulosome systems for enhanced biotechnological biomass deconstruction and biofuel production.
      Citation: Microorganisms
      PubDate: 2017-11-18
      DOI: 10.3390/microorganisms5040074
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 75: Combating Fusarium Infection Using
           Bacillus-Based Antimicrobials

    • Authors: Noor Khan, Maskit Maymon, Ann Hirsch
      First page: 75
      Abstract: Despite efforts to control toxigenic Fusarium species, wilt and head-blight infections are destructive and economically damaging diseases that have global effects. The utilization of biological control agents in disease management programs has provided an effective, safe, and sustainable means to control Fusarium-induced plant diseases. Among the most widely used microbes for biocontrol agents are members of the genus Bacillus. These species influence plant and fungal pathogen interactions by a number of mechanisms such as competing for essential nutrients, antagonizing pathogens by producing fungitoxic metabolites, or inducing systemic resistance in plants. The multivariate interactions among plant-biocontrol agent-pathogen are the subject of this study, in which we survey the advances made regarding the research on the Bacillus-Fusarium interaction and focus on the principles and mechanisms of action among plant-growth promoting Bacillus species. In particular, we highlight their use in limiting and controlling Fusarium spread and infestations of economically important crops. This knowledge will be useful to define strategies for exploiting this group of beneficial bacteria for use as inoculants by themselves or in combination with other microbes for enhanced crop protection.
      Citation: Microorganisms
      PubDate: 2017-11-22
      DOI: 10.3390/microorganisms5040075
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 76: Biotechnological Applications of
           Microbial (Per)chlorate Reduction

    • Authors: Ouwei Wang, John Coates
      First page: 76
      Abstract: While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration. This ability, along with other novel aspects of the metabolism, have resulted in a wide and disparate range of potential biotechnological applications being proposed, including enzymatic perchlorate detection; gas gangrene therapy; enhanced xenobiotic bioremediation; oil reservoir bio-souring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and, biogenic oxygen production for planetary exploration. While previous reviews focus on the fundamental science of microbial (per)chlorate reduction (for example see Youngblut et al., 2016), here, we provide an overview of the emerging biotechnological applications of (per)chlorate respiration and the underlying organisms and enzymes to environmental and biotechnological industries.
      Citation: Microorganisms
      PubDate: 2017-11-24
      DOI: 10.3390/microorganisms5040076
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 77: Bacterial Endophyte Colonization and
           Distribution within Plants

    • Authors: Shyam Kandel, Pierre Joubert, Sharon Doty
      First page: 77
      Abstract: The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.
      Citation: Microorganisms
      PubDate: 2017-11-25
      DOI: 10.3390/microorganisms5040077
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 78: The Small Regulatory RNA Spot42 Inhibits
           Indole Biosynthesis to Negatively Regulate the Locus of Enterocyte
           Effacement of Enteropathogenic Escherichia coli

    • Authors: Shantanu Bhatt, Valerie Jenkins, Elisabeth Mason, Sarah Muche
      First page: 78
      Abstract: The locus of enterocyte effacement is necessary for enteropathogenic Escherichia coli (EPEC) to form attaching and effacing (A/E) lesions. A/E lesions are characterized by intimate bacterial adherence to intestinal cells and destruction of microvilli, which leads to diarrhea. Therefore, studies interrogating the regulation of the locus of enterocyte effacement (LEE) are critical for understanding the molecular epidemiology of EPEC infections and developing interventional strategies. Hitherto, most studies have centered on protein-based regulators, whereas the role of small regulatory RNAs remains underappreciated. Previously, we identified the first sRNAs—MgrR, RyhB, and McaS—that regulate the LEE of EPEC. This study was undertaken to identify additional sRNAs that impact the LEE. Our results suggest that the catabolite-responsive sRNA, Spot42, indirectly controls the LEE by inhibiting synthesis of its inducer, indole. Spot42 base-pairs with the tnaCAB mRNA and presumably destabilizes the transcript, thereby preventing expression of the regulatory and structural proteins that are involved in the import and hydrolysis of tryptophan into indole. The absence of intracellular indole leads to reduced transcription of the LEE1-encoded master transcriptional activator Ler, thereby maintaining the LEE in its silenced state and delaying A/E lesion morphogenesis. Our results highlight the importance of riboregulators that synchronize metabolic and virulence pathways in bacterial infection.
      Citation: Microorganisms
      PubDate: 2017-12-01
      DOI: 10.3390/microorganisms5040078
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 79: Relationship among Phosphorus
           Circulation Activity, Bacterial Biomass, pH, and Mineral Concentration in
           Agricultural Soil

    • Authors: Dinesh Adhikari, Tianyi Jiang, Taiki Kawagoe, Takamitsu Kai, Kenzo Kubota, Kiwako Araki, Motoki Kubo
      First page: 79
      Abstract: Improvement of phosphorus circulation in the soil is necessary to enhance phosphorus availability to plants. Phosphorus circulation activity is an index of soil’s ability to supply soluble phosphorus from organic phosphorus in the soil solution. To understand the relationship among phosphorus circulation activity; bacterial biomass; pH; and Fe, Al, and Ca concentrations (described as mineral concentration in this paper) in agricultural soil, 232 soil samples from various agricultural fields were collected and analyzed. A weak relationship between phosphorus circulation activity and bacterial biomass was observed in all soil samples (R2 = 0.25), and this relationship became significantly stronger at near-neutral pH (6.0–7.3; R2 = 0.67). No relationship between phosphorus circulation activity and bacterial biomass was observed at acidic (pH < 6.0) or alkaline (pH > 7.3) pH. A negative correlation between Fe and Al concentrations and phosphorus circulation activity was observed at acidic pH (R2 = 0.72 and 0.73, respectively), as well as for Ca at alkaline pH (R2 = 0.64). Therefore, bacterial biomass, pH, and mineral concentration should be considered together for activation of phosphorus circulation activity in the soil. A relationship model was proposed based on the effects of bacterial biomass and mineral concentration on phosphorus circulation activity. The suitable conditions of bacterial biomass, pH, and mineral concentration for phosphorus circulation activity could be estimated from the relationship model.
      Citation: Microorganisms
      PubDate: 2017-12-04
      DOI: 10.3390/microorganisms5040079
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 80: Bioactive Compounds Produced by
           Hypoxylon fragiforme against Staphylococcus aureus Biofilms

    • Authors: Kamila Tomoko Yuyama, Clara Chepkirui, Lucile Wendt, Diana Fortkamp, Marc Stadler, Wolf-Rainer Abraham
      First page: 80
      Abstract: Treating infections organized in biofilms is a challenge due to the resistance of the pathogens against antibiotics and host immune cells. Many fungi grow in a wet environment, favorable for the growth of bacterial biofilms, and we speculated that fungi possess some strategies to control these bacterial biofilms. A fungus identified as Hypoxylon fragiforme, was collected in the Harz Mountains, Germany, and its mycelial culture was fermented in different culture media for 67 days to test its biological potential against bacterial biofilms. Sclerin, sclerin diacid and its 3-methyl monoester (methyl 1-(5-hydroxy-6-carboxylic-2,3,4-trimethylphenyl) propionate) are here described for the first time from this fungus. Sclerin and its diacid interfered with the biofilm formation of the pathogen Staphylococcus aureus, inhibiting 86% and 80% of the biofilm at 256 μg mL−1, respectively, but not killing the bacterium. Interestingly, the monomethylester of sclerin diacid was inactive. Although these compounds did not possess any activity against a pre-formed biofilm, they prevented its formation at subtoxic concentrations. Furthermore, sclerin and its diacid displayed a high specificity against Staphylococcus aureus, indicating a good strategy against pathogenic biofilms when combined with antibiotics.
      Citation: Microorganisms
      PubDate: 2017-12-12
      DOI: 10.3390/microorganisms5040080
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 81: The Seagrass Holobiont and Its
           Microbiome

    • Authors: Kelly Ugarelli, Seemanti Chakrabarti, Peeter Laas, Ulrich Stingl
      First page: 81
      Abstract: Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses. One of the main reasons for seagrass die-offs all over the world is increased sulfide concentrations in the sediment that result from the activity of sulfate-reducing prokaryotes, which perform the last step of the anaerobic food chain in marine sediments and reduce sulfate to H2S. Recent seagrass die-offs, e.g., in the Florida and Biscayne Bays, were caused by an increase in pore-water sulfide concentrations in the sediment, which were the combined result of unfavorable environmental conditions and the activities of various groups of heterotrophic bacteria in the sulfate-rich water-column and sediment that are stimulated through increased nutrient concentrations. Under normal circumstances, seagrasses are able to withstand low levels of sulfide, probably partly due to microbial symbionts, which detoxify sulfide by oxidizing it to sulfur or sulfate. Novel studies are beginning to give greater insights into the interactions of microbes and seagrasses, not only in the sulfur cycle. Here, we review the literature on the basic ecology and biology of seagrasses and focus on studies describing their microbiome.
      Citation: Microorganisms
      PubDate: 2017-12-15
      DOI: 10.3390/microorganisms5040081
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 82: What Kills the Hindgut Flagellates of
           Lower Termites during the Host Molting Cycle'

    • Authors: Christine Nalepa
      First page: 82
      Abstract: Subsocial wood feeding cockroaches in the genus Cryptocercus, the sister group of termites, retain their symbiotic gut flagellates during the host molting cycle, but in lower termites, closely related flagellates die prior to host ecdysis. Although the prevalent view is that termite flagellates die because of conditions of starvation and desiccation in the gut during the host molting cycle, the work of L.R. Cleveland in the 1930s through the 1960s provides a strong alternate hypothesis: it was the changed hormonal environment associated with the origin of eusociality and its concomitant shift in termite developmental ontogeny that instigates the death of the flagellates in termites. Although the research on termite gut microbial communities has exploded since the advent of modern molecular techniques, the role of the host hormonal environment on the life cycle of its gut flagellates has been neglected. Here Cleveland’s studies are revisited to provide a basis for re-examination of the problem, and the results framed in the context of two alternate hypotheses: the flagellate symbionts are victims of the change in host social status, or the flagellates have become incorporated into the life cycle of the eusocial termite colony. Recent work on parasitic protists suggests clear paths for exploring these hypotheses and for resolving long standing issues regarding sexual-encystment cycles in flagellates of the Cryptocercus-termite lineage using molecular methodologies, bringing the problem into the modern era.
      Citation: Microorganisms
      PubDate: 2017-12-18
      DOI: 10.3390/microorganisms5040082
      Issue No: Vol. 5, No. 4 (2017)
       
  • Microorganisms, Vol. 5, Pages 35: Free and Nanoencapsulated Tobramycin:
           Effects on Planktonic and Biofilm Forms of Pseudomonas

    • Authors: Eulalia Sans-Serramitjana, Marta Jorba, Ester Fusté, José Pedraz, Teresa Vinuesa, Miguel Viñas
      First page: 35
      Abstract: Cystic fibrosis (CF) is a genetic disorder in which frequent pulmonary infections develop secondarily. One of the major pulmonary pathogens colonizing the respiratory tract of CF patients and causing chronic airway infections is Pseudomonas aeruginosa. Although tobramycin was initially effective against P. aeruginosa, tobramycin-resistant strains have emerged. Among the strategies for overcoming resistance to tobramycin and other antibiotics is encapsulation of the drugs in nanoparticles. In this study, we explored the antimicrobial activity of nanoencapsulated tobramycin, both in solid lipid nanoparticles (SLN) and in nanostructured lipid carriers (NLC), against clinical isolates of P. aeruginosa obtained from CF patients. We also investigated the efficacy of these formulations in biofilm eradication. In both experiments, the activities of SLN and NLC were compared with that of free tobramycin. The susceptibility of planktonic bacteria was determined using the broth microdilution method and by plotting bacterial growth. The minimal biofilm eradication concentration (MBEC) was determined to assess the efficacy of the different tobramycin formulations against biofilms. The activity of tobramycin-loaded SLN was less than that of either tobramycin-loaded NLC or free tobramycin. The minimum inhibitory concentration (MIC) and MBEC of nanoencapsulated tobramycin were slightly lower (1–2 logs) than the corresponding values of the free drug when determined in tobramycin-susceptible isolates. However, in tobramycin-resistant strains, the MIC and MBEC did not differ between either encapsulated form and free tobramycin. Our results demonstrate the efficacy of nanoencapsulated formulations in killing susceptible P. aeruginosa from CF and from other patients.
      PubDate: 2017-06-26
      DOI: 10.3390/microorganisms5030035
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 36: Reply to the Comment on “Melanisation
           of Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of
           Both DOPA and DHN Types of Pigments in Submerged Culture'
           Microorganisms 2017, 5, 22”

    • Authors: Elina Palonen, Sheetal Raina, Annika Brandt, Jussi Meriluoto, Tajalli Keshavarz, Juhani Soini
      First page: 36
      Abstract: n/a
      PubDate: 2017-07-04
      DOI: 10.3390/microorganisms5030036
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 37: Antifungal Microbial Agents for Food
           Biopreservation—A Review

    • Authors: Marcia Leyva Salas, Jérôme Mounier, Florence Valence, Monika Coton, Anne Thierry, Emmanuel Coton
      First page: 37
      Abstract: Food spoilage is a major issue for the food industry, leading to food waste, substantial economic losses for manufacturers and consumers, and a negative impact on brand names. Among causes, fungal contamination can be encountered at various stages of the food chain (e.g., post-harvest, during processing or storage). Fungal development leads to food sensory defects varying from visual deterioration to noticeable odor, flavor, or texture changes but can also have negative health impacts via mycotoxin production by some molds. In order to avoid microbial spoilage and thus extend product shelf life, different treatments—including fungicides and chemical preservatives—are used. In parallel, public authorities encourage the food industry to limit the use of these chemical compounds and develop natural methods for food preservation. This is accompanied by a strong societal demand for ‘clean label’ food products, as consumers are looking for more natural, less severely processed and safer products. In this context, microbial agents corresponding to bioprotective cultures, fermentates, culture-free supernatant or purified molecules, exhibiting antifungal activities represent a growing interest as an alternative to chemical preservation. This review presents the main fungal spoilers encountered in food products, the antifungal microorganisms tested for food bioprotection, and their mechanisms of action. A focus is made in particular on the recent in situ studies and the constraints associated with the use of antifungal microbial agents for food biopreservation.
      PubDate: 2017-07-08
      DOI: 10.3390/microorganisms5030037
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 38: Strategies for Pathogen Biocontrol Using
           Lactic Acid Bacteria and Their Metabolites: A Focus on Meat Ecosystems and
           Industrial Environments

    • Authors: Patricia Castellano, Mariana Pérez Ibarreche, Mariana Blanco Massani, Cecilia Fontana, Graciela Vignolo
      First page: 38
      Abstract: The globalization of trade and lifestyle ensure that the factors responsible for the emergence of diseases are more present than ever. Despite biotechnology advancements, meat-based foods are still under scrutiny because of the presence of pathogens, which causes a loss of consumer confidence and consequently a fall in demand. In this context, Lactic Acid Bacteria (LAB) as GRAS organisms offer an alternative for developing pathogen-free foods, particularly avoiding Listeria monocytogenes, with minimal processing and fewer additives while maintaining the foods’ sensorial characteristics. The use of LAB strains, enabling us to produce antimicrobial peptides (bacteriocins) in addition to lactic acid, with an impact on quality and safety during fermentation, processing, and/or storage of meat and ready-to-eat (RTE) meat products, constitutes a promising tool. A number of bacteriocin-based strategies including the use of bioprotective cultures, purified and/or semi-purified bacteriocins as well as their inclusion in varied packaging materials under different storage conditions, have been investigated. The application of bacteriocins as part of hurdle technology using non-thermal technologies was explored for the preservation of RTE meat products. Likewise, considering that food contamination with L. monocytogenes is a consequence of the post-processing manipulation of RTE foods, the role of bacteriocinogenic LAB in the control of biofilms formed on industrial surfaces is also discussed.
      Citation: Microorganisms
      PubDate: 2017-07-11
      DOI: 10.3390/microorganisms5030038
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 39: Microorganisms in Fermented Apple
           Beverages: Current Knowledge and Future Directions

    • Authors: Fabien Cousin, Rozenn Le Guellec, Margot Schlusselhuber, Marion Dalmasso, Jean-Marie Laplace, Marina Cretenet
      First page: 39
      Abstract: Production of fermented apple beverages is spread all around the world with specificities in each country. ‘French ciders’ refer to fermented apple juice mainly produced in the northwest of France and often associated with short periods of consumption. Research articles on this kind of product are scarce compared to wine, especially on phenomena associated with microbial activities. The wine fermentation microbiome and its dynamics, organoleptic improvement for healthy and pleasant products and development of starters are now widely studied. Even if both beverages seem close in terms of microbiome and process (with both alcoholic and malolactic fermentations), the inherent properties of the raw materials and different production and environmental parameters make research on the specificities of apple fermentation beverages worthwhile. This review summarizes current knowledge on the cider microbial ecosystem, associated activities and the influence of process parameters. In addition, available data on cider quality and safety is reviewed. Finally, we focus on the future role of lactic acid bacteria and yeasts in the development of even better or new beverages made from apples.
      Citation: Microorganisms
      PubDate: 2017-07-25
      DOI: 10.3390/microorganisms5030039
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 40: Should Research on the Nutritional
           Potential and Health Benefits of Fermented Cereals Focus More on the
           General Health Status of Populations in Developing Countries'

    • Authors: Caroline Laurent-Babot, Jean-Pierre Guyot
      First page: 40
      Abstract: Cereal foods fermented by lactic acid bacteria are staples in many countries around the world particularly in developing countries, but some aspects of the nutritional and health benefits of traditional fermented foods in developing countries have not been sufficiently investigated compared to fermented foods in high-income countries. Today, malnutrition worldwide is characterized by a double burden, excess leading to non-communicable diseases like obesity or diabetes alongside micronutrient deficiencies. In addition, populations in developing countries suffer from infectious and parasitic diseases that can jeopardize the health benefits provided by their traditional fermented foods. Using examples, we argue that research on traditional fermented cereals in developing countries should focus more on their effect on inflammation and oxidative stress under conditions including infectious or non-infectious gut inflammation.
      Citation: Microorganisms
      PubDate: 2017-07-25
      DOI: 10.3390/microorganisms5030040
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 41: Inoculation with Azospirillum sp. and
           Herbaspirillum sp. Bacteria Increases the Tolerance of Maize to Drought
           Stress

    • Authors: José Curá, Diego Franz, Julián Filosofía, Karina Balestrasse, Lautaro Burgueño
      First page: 41
      Abstract: Stress drought is an important abiotic factor that leads to immense losses in crop yields around the world. Strategies are urgently needed to help plants adapt to drought in order to mitigate crop losses. Here we investigated the bioprotective effects of inoculating corn grown under drought conditions with two types of plant growth-promoting rhizobacteria (PGPR), A. brasilense, strain SP-7, and H. seropedicae, strain Z-152. Plants inoculated with the bacteria were grown in a greenhouse with perlite as a substrate. Two hydric conditions were tested: normal well-watered conditions and drought conditions. Compared to control non-inoculated plants, those that were inoculated with PGPR bacteria showed a higher tolerance to the negative effects of water stress in drought conditions, with higher biomass production; higher carbon, nitrogen, and chlorophyll levels; and lower levels of abscisic acid and ethylene, which are plant hormones that affect the stress response. The oxidative stress levels of these plants were similar to those of non-inoculated plants grown in well-watered conditions, showing fewer injuries to the cell membrane. We also noted higher relative water content in the vegetal tissue and better osmoregulation in drought conditions in inoculated plants, as reflected by significantly lower proline content. Finally, we observed lower gene expression of ZmVP14 in the inoculated plants; notably, ZmVP14 is involved in the biosynthesis of abscisic acid. Taken together, these results demonstrate that these bacteria could be used to help plants cope with the negative effects of drought stress conditions.
      Citation: Microorganisms
      PubDate: 2017-07-26
      DOI: 10.3390/microorganisms5030041
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 42: Diversity and Control of Spoilage Fungi
           in Dairy Products: An Update

    • Authors: Lucille Garnier, Florence Valence, Jérôme Mounier
      First page: 42
      Abstract: Fungi are common contaminants of dairy products, which provide a favorable niche for their growth. They are responsible for visible or non-visible defects, such as off-odor and -flavor, and lead to significant food waste and losses as well as important economic losses. Control of fungal spoilage is a major concern for industrials and scientists that are looking for efficient solutions to prevent and/or limit fungal spoilage in dairy products. Several traditional methods also called traditional hurdle technologies are implemented and combined to prevent and control such contaminations. Prevention methods include good manufacturing and hygiene practices, air filtration, and decontamination systems, while control methods include inactivation treatments, temperature control, and modified atmosphere packaging. However, despite technology advances in existing preservation methods, fungal spoilage is still an issue for dairy manufacturers and in recent years, new (bio) preservation technologies are being developed such as the use of bioprotective cultures. This review summarizes our current knowledge on the diversity of spoilage fungi in dairy products and the traditional and (potentially) new hurdle technologies to control their occurrence in dairy foods.
      Citation: Microorganisms
      PubDate: 2017-07-28
      DOI: 10.3390/microorganisms5030042
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 43: Effect of Non-Dairy Food Matrices on the
           Survival of Probiotic Bacteria during Storage

    • Authors: Min Min, Craig Bunt, Susan Mason, Grant Bennett, Malik Hussain
      First page: 43
      Abstract: The viability of probiotics in non-dairy food products during storage is required to meet content criteria for probiotic products. This study investigated whether non-dairy foods could be matrices for probiotics. Selected probiotic bacteria were coated on non-dairy foods under two storage conditions, and viabilities were assessed. The non-dairy foods were coated with 5–7 log cfu g−1 of Lactobacillus acidophilus ATCC4356T, Lactobacillus plantarum RC30, and Bifidobacterium longum ATCC15707T. The coated non-dairy foods were stored at 20 °C and 20% relative humidity (RH) or 30 °C and 50% RH. Viability of probiotic bacteria was determined after 0, 2, and 4 weeks of storage. B. longum showed the highest survival at week 4 of 6.5–6.7 log cfu g−1 on wheat bran and oat, compared with 3.7–3.9 log cfu g−1 of L. acidophilus and 4.2–4.8 log cfu g−1 of L. plantarum at 20 °C 20% RH. Under the storage conditions of 30 °C 50% RH, survival of 4.5 log cfu g−1 of B. longum was also found on oat and peanut. This was two and four times higher than the population of L. acidophilus and L. plantarum, respectively. The results suggest that probiotics can survive on non-dairy foods under ambient storage conditions. However, the storage conditions, food matrices, and probiotic strains should be carefully chosen to maximize probiotic bacteria survival.
      Citation: Microorganisms
      PubDate: 2017-08-01
      DOI: 10.3390/microorganisms5030043
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 44: Filamentous Fungal Human Pathogens from
           Food Emphasising Aspergillus, Fusarium and Mucor

    • Authors: R. Paterson, Nelson Lima
      First page: 44
      Abstract: Disease caused by filamentous fungal human pathogens (FFHP) is increasing. These organisms cause severe mycoses in immunosuppressed individuals, such as those: (a) with AIDS; (b) having undergone transplantation; and/or (c) undergoing chemotherapy. Immunocompetent people can become infected. Some FFHP are isolated from foods which may be fomites. However, the information concerning particular species on specific food is large, dispersed and difficult to obtain. Reports of filamentous fungi from food/crops and causing human disease are frequently only available in the literature of food mycology/plant pathology and medical mycology, respectively: it is seldom cross-referenced. Aspergillus contains some species with strains that are the most dangerous FFHP, with Aspergillus fumigatus causing the most serious diseases. Fusarium and Mucor also contain species of high importance and approximately 15 other genera are involved. A checklist and database of FFHP species isolated from food is presented herein with emphasis on Aspergillus, Fusarium and Mucor in summary tables to increase awareness of the connection between food and FFHP. Metadata on all FFHP is provided in a large supplementary table for updating and revision when necessary. Previous names of fungi have been revised to reflect current valid usage whenever appropriate. The information will form a foundation for future research and taxonomic revisions in the field. The paper will be highly useful for medical practitioners, food mycologists, fungal taxonomists, patients, regulators and food producers interested in reducing infectious diseases and producing high quality food.
      Citation: Microorganisms
      PubDate: 2017-08-02
      DOI: 10.3390/microorganisms5030044
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 45: Growth and Photosynthetic
           Characteristics of Toxic and Non-Toxic Strains of the Cyanobacteria
           Microcystis aeruginosa and Anabaena circinalis in Relation to Light

    • Authors: M. Islam, John Beardall
      First page: 45
      Abstract: Cyanobacteria are major bloom-forming organisms in freshwater ecosystems and many strains are known to produce toxins. Toxin production requires an investment in energy and resources. As light is one of the most important factors for cyanobacterial growth, any changes in light climate might affect cyanobacterial toxin production as well as their growth and physiology. To evaluate the effects of light on the growth and physiological parameters of both toxic and non-toxic strains of Microcystis aeruginosa and Anabaena circinalis, cultures were grown at a range of light intensities (10, 25, 50, 100, 150 and 200 µmol m−2 s−1). The study revealed that the toxic strains of both species (CS558 for M. aeruginosa and CS537 and CS541 for A. circinalis) showed growth (µ) saturation at a higher light intensity compared to the non-toxic strains (CS338 for M. aeruginosa and CS534 for A. circinalis). Both species showed differences in chlorophyll a, carotenoid, allophycocyanin (APC) and phycoerythrin (PE) content between strains. There were also differences in dark respiration (Rd), light saturated oxygen evolution rates (Pmax) and efficiency of light harvesting (α) between strains. All other physiological parameters showed no statistically significant differences between strains. This study suggest that the different strains respond differently to different light habitats. Thus, changes in light availability may affect bloom intensity of toxic and nontoxic strains of cyanobacteria by changing the dominance and succession patterns.
      Citation: Microorganisms
      PubDate: 2017-08-04
      DOI: 10.3390/microorganisms5030045
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 46: Culturing Toxic Benthic Blooms: The Fate
           of Natural Biofilms in a Microcosm System

    • Authors: Francesca Di Pippo, Roberta Congestri
      First page: 46
      Abstract: A microcosm designed for culturing aquatic phototrophic biofilms on artificial substrata was used to perform experiments with microphytobenthos sampled during summer toxic outbreaks of Ostreopsis cf. ovata along the Middle Tyrrhenian coast. This dynamic approach aimed at exploring the unique and complex nature of O. cf. ovata bloom development in the benthic system. Epibenthic assemblages were used as inocula for co-cultures of bloom organisms on polycarbonate slides at controlled environmental conditions. Biofilm surface adhesion, growth, and spatial structure were evaluated along with shifts in composition and matrix production in a low disturbance regime, simulating source habitat. Initial adhesion and substratum colonisation appeared as stochastic processes, then community structure and physiognomy markedly changed with time. Dominance of filamentous cyanobacteria and diatoms, and dense clusters of Amphidinium cf. carterae at the mature biofilm phases, were recorded by light and confocal microscopy, whilst O. cf. ovata growth was visibly limited in the late culture phases. Life-form strategies, competitiveness for resources, and possibly allelopathic interactions shaped biofilm structure during culture growth. HPLC (High Performance Liquid Chromatography) analysis of exopolysaccharidic matrix revealed variations in sugar total amounts and composition. No toxic compounds were detected in the final communities tested by LC-MS (Liquid Chromatography- Mass Spectrometry) and MALDI-TOF MS (Matrix Assisted Laser Desorption Ionization Time OF Flight Mass Spectroscopy) techniques.
      Citation: Microorganisms
      PubDate: 2017-08-06
      DOI: 10.3390/microorganisms5030046
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 47: MALDI-TOF MS for the Identification of
           Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near
           Unconventional Natural Gas Extraction Sites

    • Authors: Inês Santos, Misty Martin, Doug Carlton, Catarina Amorim, Paula Castro, Zacariah Hildenbrand, Kevin Schug
      First page: 47
      Abstract: Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.
      Citation: Microorganisms
      PubDate: 2017-08-10
      DOI: 10.3390/microorganisms5030047
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 48: Phosphate Acquisition and Virulence in
           Human Fungal Pathogens

    • Authors: Mélanie Ikeh, Yasmin Ahmed, Janet Quinn
      First page: 48
      Abstract: The ability of pathogenic fungi to acquire essential macro and micronutrients during infection is a well-established virulence trait. Recent studies in the major human fungal pathogens Candida albicans and Cryptococcus neoformans have revealed that acquisition of the essential macronutrient, phosphate, is essential for virulence. The phosphate sensing and acquisition pathway in fungi, known as the PHO pathway, has been extensively characterized in the model yeast Saccharomyces cerevisiae. In this review, we highlight recent advances in phosphate sensing and signaling mechanisms, and use the S. cerevisiae PHO pathway as a platform from which to compare the phosphate acquisition and storage strategies employed by several human pathogenic fungi. We also explore the multi-layered roles of phosphate acquisition in promoting fungal stress resistance to pH, cationic, and oxidative stresses, and describe emerging roles for the phosphate storage molecule polyphosphate (polyP). Finally, we summarize the recent studies supporting the necessity of phosphate acquisition in mediating the virulence of human fungal pathogens, highlighting the concept that this requirement is intimately linked to promoting resistance to host-imposed stresses.
      Citation: Microorganisms
      PubDate: 2017-08-22
      DOI: 10.3390/microorganisms5030048
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 49: Transcriptional Analysis Allows Genome
           Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient
           Restriction during Infection

    • Authors: Patrícia Aline Gröhs Ferrareze, Rodrigo Silva Araujo Streit, Patricia Ribeiro dos Santos, Francine Melise dos Santos, Rita Maria Cunha de Almeida, Augusto Schrank, Livia Kmetzsch, Marilene Henning Vainstein, Charley Christian Staats
      First page: 49
      Abstract: Cryptococcus gattii is a human and animal pathogen that infects healthy hosts and caused the Pacific Northwest outbreak of cryptococcosis. The inhalation of infectious propagules can lead to internalization of cryptococcal cells by alveolar macrophages, a niche in which C. gattii cells can survive and proliferate. Although the nutrient composition of macrophages is relatively unknown, the high induction of amino acid transporter genes inside the phagosome indicates a preference for amino acid uptake instead of synthesis. However, the presence of countable errors in the R265 genome annotation indicates significant inhibition of transcriptomic analysis in this hypervirulent strain. Thus, we analyzed RNA-Seq data from in vivo and in vitro cultures of C. gattii R265 to perform the reannotation of the genome. In addition, based on in vivo transcriptomic data, we identified highly expressed genes and pathways of amino acid metabolism that would enable C. gattii to survive and proliferate in vivo. Importantly, we identified high expression in three APC amino acid transporters as well as the GABA permease. The use of amino acids as carbon and nitrogen sources, releasing ammonium and generating carbohydrate metabolism intermediaries, also explains the high expression of components of several degradative pathways, since glucose starvation is an important host defense mechanism.
      Citation: Microorganisms
      PubDate: 2017-08-23
      DOI: 10.3390/microorganisms5030049
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 50: Bacterial Contaminants of Poultry Meat:
           Sources, Species, and Dynamics

    • Authors: Amélie Rouger, Odile Tresse, Monique Zagorec
      First page: 50
      Abstract: With the constant increase in poultry meat consumption worldwide and the large variety of poultry meat products and consumer demand, ensuring the microbial safety of poultry carcasses and cuts is essential. In the present review, we address the bacterial contamination of poultry meat from the slaughtering steps to the use-by-date of the products. The different contamination sources are identified. The contaminants occurring in poultry meat cuts and their behavior toward sanitizing treatments or various storage conditions are discussed. A list of the main pathogenic bacteria of concern for the consumer and those responsible for spoilage and waste of poultry meat is established.
      Citation: Microorganisms
      PubDate: 2017-08-25
      DOI: 10.3390/microorganisms5030050
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 51: The Sea as a Rich Source of Structurally
           Unique Glycosaminoglycans and Mimetics

    • Authors: Ariana Vasconcelos, Vitor Pomin
      First page: 51
      Abstract: Glycosaminoglycans (GAGs) are sulfated glycans capable of regulating various biological and medical functions. Heparin, heparan sulfate, chondroitin sulfate, dermatan sulfate, keratan sulfate and hyaluronan are the principal classes of GAGs found in animals. Although GAGs are all composed of disaccharide repeating building blocks, the sulfation patterns and the composing alternating monosaccharides vary among classes. Interestingly, GAGs from marine organisms can present structures clearly distinct from terrestrial animals even considering the same class of GAG. The holothurian fucosylated chondroitin sulfate, the dermatan sulfates with distinct sulfation patterns extracted from ascidian species, the sulfated glucuronic acid-containing heparan sulfate isolated from the gastropode Nodipecten nodosum, and the hybrid heparin/heparan sulfate molecule obtained from the shrimp Litopenaeus vannamei are some typical examples. Besides being a rich source of structurally unique GAGs, the sea is also a wealthy environment of GAG-resembling sulfated glycans. Examples of these mimetics are the sulfated fucans and sulfated galactans found in brown, red and green algae, sea urchins and sea cucumbers. For adequate visualization, representations of all discussed molecules are given in both Haworth projections and 3D models.
      Citation: Microorganisms
      PubDate: 2017-08-28
      DOI: 10.3390/microorganisms5030051
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 52: Insight into the Genome of
           Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products
           

    • Authors: Sabine Leroy, Aurore Vermassen, Geoffrey Ras, Régine Talon
      First page: 52
      Abstract: Staphylococcus xylosus belongs to the vast group of coagulase-negative staphylococci. It is frequently isolated from meat products, either fermented or salted and dried, and is commonly used as starter cultures in sausage manufacturing. Analysis of the S. xylosus genome together with expression in situ in a meat model revealed that this bacterium is well adapted to meat substrates, being able to use diverse substrates as sources of carbon and energy and different sources of nitrogen. It is well-equipped with genes involved in osmotic, oxidative/nitrosative, and acidic stress responses. It is responsible for the development of the typical colour of cured meat products via its nitrate reductase activity. It contributes to sensorial properties, mainly by the the catabolism of pyruvate and amino acids resulting in odorous compounds and by the limiting of the oxidation of fatty acids, thereby avoiding rancidity.
      Citation: Microorganisms
      PubDate: 2017-08-29
      DOI: 10.3390/microorganisms5030052
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 53: Multiple Antibiotic-Resistant, Extended
           Spectrum-β-Lactamase (ESBL)-Producing Enterobacteria in Fresh Seafood

    • Authors: Asem Sanjit Singh, Manjusha Lekshmi, Sreepriya Prakasan, Binaya Nayak, Sanath Kumar
      First page: 53
      Abstract: Members of the family Enterobacteriaceae include several human pathogens that can be acquired through contaminated food and water. In this study, the incidence of extended spectrum β-lactamase (ESBL)-producing enterobacteria was investigated in fresh seafood sold in retail markets. The ESBL-positive phenotype was detected in 169 (78.60%) isolates, with Escherichia coli being the predominant species (53), followed by Klebsiella oxytoca (27), and K. pneumoniae (23). More than 90% of the isolates were resistant to third generation cephalosporins, cefotaxime, ceftazidime, and cefpodoxime. Sixty-five percent of the isolates were resistant to the monobactam drug aztreonam, 40.82% to ertapenem, and 31.36% to meropenem. Resistance to at least five antibiotics was observed in 38.46% of the isolates. Polymerase Chain Reaction (PCR) analysis of ESBL-encoding genes detected blaCTX, blaSHV, and blaTEM genes in 76.92%, 63.3%, and 44.37% of the isolates, respectively. Multiple ESBL genes were detected in majority of the isolates. The recently discovered New Delhi metallo-β-lactamase gene (blaNDM-1) was detected in two ESBL+ isolates. Our study shows that secondary contamination of fresh seafood with enteric bacteria resistant to multiple antibiotics may implicate seafood as a potential carrier of antibiotic resistant bacteria and emphasizes an urgent need to prevent environmental contamination and dissemination of such bacteria.
      Citation: Microorganisms
      PubDate: 2017-08-30
      DOI: 10.3390/microorganisms5030053
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 54: Comments to Article by Willetts A. et
           al., Microorganisms 2016, 4, 38

    • Authors: Jennifer Littlechild, Mikail Isupov
      First page: 54
      Abstract: We would like to comment on recent work published in your journal in October 2016 by Willetts A. et al. [1].[...]
      Citation: Microorganisms
      PubDate: 2017-09-06
      DOI: 10.3390/microorganisms5030054
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 55: Reply to the Comment by Littlechild and
           Isupov

    • Authors: Andrew Willetts, David Kelly
      First page: 55
      Abstract: I thank Drs. Littlechild and Isupov for their recent comments, which are considered below. Before addressing these specifically, their correspondence raises two more general issues which require initial clarification.[...]
      Citation: Microorganisms
      PubDate: 2017-09-06
      DOI: 10.3390/microorganisms5030055
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 56: Lactobacillus sakei: A Starter for
           Sausage Fermentation, a Protective Culture for Meat Products

    • Authors: Monique Zagorec, Marie-Christine Champomier-Vergès
      First page: 56
      Abstract: Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture. The emerging exploration of the microbial ecology of meat products also revealed the multiplicity of bacterial interactions L. sakei has to face and their various consequences on microbial quality and safety at the end of storage.
      Citation: Microorganisms
      PubDate: 2017-09-06
      DOI: 10.3390/microorganisms5030056
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 57: The Skin Bacterium Propionibacterium
           acnes Employs Two Variants of Hyaluronate Lyase with Distinct Properties

    • Authors: Seven Nazipi, Kristian Stødkilde, Carsten Scavenius, Holger Brüggemann
      First page: 57
      Abstract: Hyaluronic acid (HA) and other glycosaminoglycans are extracellular matrix components in the human epidermis and dermis. One of the most prevalent skin microorganisms, Propionibacterium acnes, possesses HA-degrading activity, possibly conferred by the enzyme hyaluronate lyase (HYL). In this study, we identified the HYL of P. acnes and investigated the genotypic and phenotypic characteristics. Investigations include the generation of a P. acnes hyl knockout mutant and HYL activity assays to determine the substrate range and formed products. We found that P. acnes employs two distinct variants of HYL. One variant, HYL-IB/II, is highly active, resulting in complete HA degradation; it is present in strains of the phylotypes IB and II. The other variant, HYL-IA, has low activity, resulting in incomplete HA degradation; it is present in type IA strains. Our findings could explain some of the observed differences between P. acnes phylotype IA and IB/II strains. Whereas type IA strains are primarily found on the skin surface and associated with acne vulgaris, type IB/II strains are more often associated with soft and deep tissue infections, which would require elaborate tissue invasion strategies, possibly accomplished by a highly active HYL-IB/II.
      Citation: Microorganisms
      PubDate: 2017-09-12
      DOI: 10.3390/microorganisms5030057
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 58: Rapid and Highly Sensitive
           Non-Competitive Immunoassay for Specific Detection of Nodularin

    • Authors: Sultana Akter, Markus Vehniäinen, Harri Kankaanpää, Urpo Lamminmäki
      First page: 58
      Abstract: Nodularin (NOD) is a cyclic penta-peptide hepatotoxin mainly produced by Nodularia spumigena, reported from the brackish water bodies of various parts of the world. It can accumulate in the food chain and, for safety reasons, levels of NOD not only in water bodies but also in food matrices are of interest. Here, we report on a non-competitive immunoassay for the specific detection of NOD. A phage display technique was utilized to interrogate a synthetic antibody phage library for binders recognizing NOD bound to an anti-ADDA (3-Amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4(E),6(E)-dienoic acid) monoclonal antibody (Mab). One of the obtained immunocomplex binders, designated SA32C11, showed very high specificity towards nodularin-R (NOD-R) over to the tested 10 different microcystins (microcystin-LR, -dmLR, -RR, -dmRR, -YR, -LY, -LF, -LW, -LA, -WR). It was expressed in Escherichia coli as a single chain antibody fragment (scFv) fusion protein and used to establish a time-resolved fluorometry-based assay in combination with the anti-ADDA Mab. The detection limit (blank + 3SD) of the immunoassay, with a total assay time of 1 h 10 min, is 0.03 µg/L of NOD-R. This represents the most sensitive immunoassay method for the specific detection of NOD reported so far. The assay was tested for its performance to detect NOD using spiked (0.1 to 3 µg/L of NOD-R) water samples including brackish sea and coastal water and the recovery ranged from 79 to 127%. Furthermore, a panel of environmental samples, including water from different sources, fish and other marine tissue specimens, were analyzed for NOD using the assay. The assay has potential as a rapid screening tool for the analysis of a large number of water samples for the presence of NOD. It can also find applications in the analysis of the bioaccumulation of NOD in marine organisms and in the food chain.
      Citation: Microorganisms
      PubDate: 2017-09-12
      DOI: 10.3390/microorganisms5030058
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 59: Effect of Environmental Factors on
           Intra-Specific Inhibitory Activity of Carnobacterium maltaromaticum

    • Authors: Peipei Zhang, Mandeep Kaur, John Bowman, David Ratkowsky, Mark Tamplin
      First page: 59
      Abstract: Carnobacterium maltaromaticum is frequently associated with foods having extended shelf-life due to its inhibitory activity to other bacteria. The quantification of such inhibition interactions affected by various environmental factors is limited. This study investigated the effect of environmental factors relevant to vacuum-packaged beef on inhibition between two model isolates of C. maltaromaticum, D0h and D8c, specifically D8c sensitivity to D0h inhibition and D0h inhibitor production. The effects of temperature (−1, 7, 15, 25 °C), atmosphere (aerobic and anaerobic), pH (5.5, 6, 6.5), lactic acid (0, 25, 50 mM) and glucose (0, 0.56, 5.55 mM) on D8c sensitivity (diameter of an inhibition zone) were measured. The effects of pH, glucose, lactic acid and atmosphere on D0h inhibitor production were measured at 25 °C. Sensitivity of D8c was the highest at 15 °C, under aerobic atmosphere, at higher concentrations of undissociated lactic acid and glucose, and at pH 5.5 (p < 0.001). pH significantly affected D0h inhibitor production (p < 0.001), which was the highest at pH 6.5. The effect of lactic acid depended upon pH level; at relatively low pH (5.5), lactic acid decreased the production rate (arbitrary inhibition unit (AU)/mL/h). This study provides a quantitative description of intra-species interactions, studied in in vitro environments that are relevant to vacuum-packaged beef.
      Citation: Microorganisms
      PubDate: 2017-09-14
      DOI: 10.3390/microorganisms5030059
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 60: Proteomic Characterization of Armillaria
           mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary
           Metabolism Profiles

    • Authors: Cassandra Collins, Rachel Hurley, Nada Almutlaqah, Grainne O’Keeffe, Thomas Keane, David Fitzpatrick, Rebecca Owens
      First page: 60
      Abstract: Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein), indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM) enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.
      Citation: Microorganisms
      PubDate: 2017-09-17
      DOI: 10.3390/microorganisms5030060
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 61: Microbial Community Structure and
           Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine
           Water

    • Authors: Malin Bomberg, Jarno Mäkinen, Marja Salo, Mona Arnold
      First page: 61
      Abstract: Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L−1 sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance.
      Citation: Microorganisms
      PubDate: 2017-09-20
      DOI: 10.3390/microorganisms5030061
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 62: Diagnostic Value of Endotracheal
           Aspirates Sonication on Ventilator-Associated Pneumonia Microbiologic
           Diagnosis

    • Authors: Laia Fernández-Barat, Ana Motos, Otavio Ranzani, Gianluigi Bassi, Elisabet Aguilera Xiol, Tarek Senussi, Chiara Travierso, Chiara Chiurazzi, Francesco Idone, Laura Muñoz, Jordi Vila, Miquel Ferrer, Paolo Pelosi, Francesco Blasi, Massimo Antonelli, Antoni Torres
      First page: 62
      Abstract: Microorganisms are able to form biofilms within respiratory secretions. Methods to disaggregate such biofilms before utilizing standard, rapid, or high throughput diagnostic technologies may aid in pathogen detection during ventilator associated pneumonia (VAP) diagnosis. Our aim was to determine if sonication of endotracheal aspirates (ETA) would increase the sensitivity of qualitative, semi-quantitative, and quantitative bacterial cultures in an animal model of pneumonia caused by Pseudomonas aeruginosa or by methicillin resistant Staphylococcus aureus (MRSA). Material and methods: P. aeruginosa or MRSA was instilled into the lungs or the oropharynx of pigs in order to induce severe VAP. Time point assessments for qualitative and quantitative bacterial cultures of ETA and bronchoalveolar lavage (BAL) samples were performed at 24, 48, and 72 h after bacterial instillation. In addition, at 72 h (autopsy), lung tissue was harvested to perform quantitative bacterial cultures. Each ETA sample was microbiologically processed with and without applying sonication for 5 min at 40 KHz before bacterial cultures. Sensitivity and specificity were determined using BAL as a gold-standard. Correlation with BAL and lung bacterial burden was also determined before and after sonication. Assessment of biofilm clusters and planktonic bacteria was performed through both optical microscopy utilizing Gram staining and Confocal Laser Scanning Microscopy utilizing the LIVE/DEAD®BacLight kit. Results: 33 pigs were included, 27 and 6 from P. aeruginosa and MRSA pneumonia models, respectively. Overall, we obtained 85 ETA, 69 (81.2%) from P. aeruginosa and 16 (18.8%) from MRSA challenged pigs. Qualitative cultures did not significantly change after sonication, whereas quantitative ETA cultures did significantly increase bacterial counting. Indeed, sonication consistently increased bacterial burden in ETAs at 24, 48, and 72 h after bacterial challenge. Sonication also improved sensitivity of ETA quantitative cultures and maintained specificity at levels previously reported and accepted for VAP diagnosis. Conclusion: The use of sonication in ETA respiratory samples needs to be clinically validated since sonication could potentially improve pathogen detection before standard, rapid, or high throughput diagnostic methods used in routine microbial diagnostics.
      Citation: Microorganisms
      PubDate: 2017-09-20
      DOI: 10.3390/microorganisms5030062
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 63: Bioprospecting for Exopolysaccharides
           from Deep-Sea Hydrothermal Vent Bacteria: Relationship between Bacterial
           Diversity and Chemical Diversity

    • Authors: Christine Delbarre-Ladrat, Marcia Leyva Salas, Corinne Sinquin, Agata Zykwinska, Sylvia Colliec-Jouault
      First page: 63
      Abstract: Many bacteria biosynthesize structurally diverse exopolysaccharides (EPS) and excrete them into their surrounding environment. The EPS functional features have found many applications in industries such as cosmetics and pharmaceutics. In particular, some EPS produced by marine bacteria are composed of uronic acids, neutral sugars, and N-acetylhexosamines, and may also bear some functional sulfate groups. This suggests that they can share common structural features with glycosaminoglycans (GAG) like the two EPS (HE800 and GY785) originating from the deep sea. In an attempt to discover new EPS that may be promising candidates as GAG-mimetics, fifty-one marine bacterial strains originating from deep-sea hydrothermal vents were screened. The analysis of the EPS chemical structure in relation to bacterial species showed that Vibrio, Alteromonas, and Pseudoalteromonas strains were the main producers. Moreover, they produced EPS with distinct structural features, which might be useful for targeting marine bacteria that could possibly produce structurally GAG-mimetic EPS.
      Citation: Microorganisms
      PubDate: 2017-09-20
      DOI: 10.3390/microorganisms5030063
      Issue No: Vol. 5, No. 3 (2017)
       
  • Microorganisms, Vol. 5, Pages 14: Identification and Characterization of
           Spontaneous Auxotrophic Mutants in Fusarium langsethiae

    • Authors: Olga Gavrilova, Anna Skritnika, Tatiana Gagkaeva
      First page: 14
      Abstract: Analysis of 49 strains of Fusarium langsethiae originating from northern Europe (Russia, Finland, Sweden, UK, Norway, and Latvia) revealed the presence of spontaneous auxotrophic mutants that reflect natural intraspecific diversity. Our investigations detected that 49.0% of F. langsethiae strains were auxotrophic mutants for biotin, and 8.2% of the strains required thiamine as a growth factor. They failed to grow on vitamin-free media. For both prototrophic and auxotrophic strains, no growth defect was observed in rich organic media. Without essential vitamins, a significant reduction in the growth of the auxotrophic strains results in a decrease of the formation of T-2 toxin and diacetoxyscirpenol. In addition, all analysed F. langsethiae strains were distinguished into two subgroups based on PCR product sizes. According to our results, 26 and 23 strains of F. langsethiae belong to subgroups I and II respectively. We determined that the deletion in the intergenic spacer (IGS) region of the rDNA of F. langsethiae belonging to subgroup II is linked with temperature sensitivity and causes a decrease in strain growth at 30 °C. Four thiamine auxotrophic strains were found in subgroup I, while 21 biotin auxotrophic strains were detected in subgroups II. To the best of our knowledge, the spontaneous mutations in F. langsethiae observed in the present work have not been previously reported.
      PubDate: 2017-03-31
      DOI: 10.3390/microorganisms5020014
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 15: Approaches to Dispersing Medical
           Biofilms

    • Authors: Derek Fleming, Kendra Rumbaugh
      First page: 15
      Abstract: Biofilm-associated infections pose a complex problem to the medical community, in that residence within the protection of a biofilm affords pathogens greatly increased tolerances to antibiotics and antimicrobials, as well as protection from the host immune response. This results in highly recalcitrant, chronic infections and high rates of morbidity and mortality. Since as much as 80% of human bacterial infections are biofilm-associated, many researchers have begun investigating therapies that specifically target the biofilm architecture, thereby dispersing the microbial cells into their more vulnerable, planktonic mode of life. This review addresses the current state of research into medical biofilm dispersal. We focus on three major classes of dispersal agents: enzymes (including proteases, deoxyribonucleases, and glycoside hydrolases), antibiofilm peptides, and dispersal molecules (including dispersal signals, anti-matrix molecules, and sequestration molecules). Throughout our discussion, we provide detailed lists and summaries of some of the most prominent and extensively researched dispersal agents that have shown promise against the biofilms of clinically relevant pathogens, and we catalog which specific microorganisms they have been shown to be effective against. Lastly, we discuss some of the main hurdles to development of biofilm dispersal agents, and contemplate what needs to be done to overcome them.
      PubDate: 2017-04-01
      DOI: 10.3390/microorganisms5020015
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 16: Insights on Klebsiella pneumoniae
           Biofilms Assembled on Different Surfaces Using Phenotypic and Genotypic
           Approaches

    • Authors: Maria Bandeira, Vítor Borges, João Gomes, Aida Duarte, Luisa Jordao
      First page: 16
      Abstract: Klebsiella pneumoniae is a prominent etiological agent of healthcare associated infections (HAIs). In this context, multidrug-resistant and biofilm-producing bacteria are of special public health concern due to the difficulties associated with treatment of human infections and eradication from hospital environments. Here, in order to study the impact of medical devices-associated materials on the biofilm dynamics, we performed biofilm phenotypic analyses through a classic and a new scanning electron microscopy (SEM) technique for three multidrug-resistant K. pneumoniae isolates growing on polystyrene and silicone. We also applied whole-genome sequencing (WGS) to search for genetic clues underlying biofilm phenotypic differences. We found major differences in the extracellular polymeric substances (EPS) content among the three strains, which were further corroborated by in-depth EPS composition analysis. WGS analysis revealed a high nucleotide similarity within the core-genome, but relevant differences in the accessory genome that may account for the detected biofilm phenotypic dissimilarities, such as genes already associated with biofilm formation in other pathogenic bacteria (e.g., genes coding haemogglutinins and haemolysins). These data reinforce that the research efforts to defeat bacterial biofilms should take into account that their dynamics may be contingent on the medical devices-associated materials.
      PubDate: 2017-04-03
      DOI: 10.3390/microorganisms5020016
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 17: Probiotic Microorganisms: A Closer Look

    • Authors: Julio Villena, Haruki Kitazawa
      First page: 17
      Abstract: n/a
      PubDate: 2017-04-08
      DOI: 10.3390/microorganisms5020017
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 18: High Prevalence of blaNDM-1, blaVIM,
           qacE, and qacEΔ1 Genes and Their Association with Decreased
           Susceptibility to Antibiotics and Common Hospital Biocides in Clinical
           Isolates of Acinetobacter baumannii

    • Authors: Fatma Gomaa, Zeinab Helal, Mazhar Khan
      First page: 18
      Abstract: The objective of this study was to evaluate the susceptibility of metallo-β-lactamase (MBL)-producing Acinetobacter baumannii (A. baumannii) clinical isolates to biocides. We also determined the prevalence and correlation of efflux pump genes, class 1 integron and MBL encoding genes. In addition, blaVIM, blaNDM-1, qacE and qacEΔ1 nucleotide sequence analysis was performed and compared to sequences retrieved from GenBank at the National Center for Biotechnology Information database. A. baumannii had a resistance rate to carbapenem of 71.4% and 39.3% and was found to be a MBL producer. The minimum inhibitory concentrations (MICs) of chlorhexidine and cetrimide were higher than the recommended concentrations for disinfection in 54.5% and 77.3% of MBL-positive isolates respectively and their MICs were significantly higher among qac gene-positive isolates. Coexistence of qac genes was detected in 68.1% and 50% of the isolates with blaVIM and blaNDM-1 respectively. There was a significant correlation between the presence of qac genes and MBL-encoding blaVIM and blaNDM-1 genes. Each of the blaNDM-1, blaVIM, qacE and qacEΔ1 DNA sequences showed homology with each other and with similar sequences reported from other countries. The high incidence of Verona integron-encoded metallo-β-lactamases (VIM) and New-Delhi-metallo-β-lactamase (NDM) and qac genes in A. baumannii highlights emerging therapeutic challenges for being readily transferable between clinically relevant bacteria. In addition reduced susceptibility to chlorhexidine and cetrimide and the potential for cross resistance to some antibiotics necessitates the urgent need for healthcare facilities to periodically evaluate biocides efficacy, to address the issue of antiseptic resistance and to initiate a “biocidal stewardship”.
      PubDate: 2017-04-12
      DOI: 10.3390/microorganisms5020018
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 19: The Status of Biofilms in Penile
           Implants

    • Authors: Matthew Faller, Tobias Kohler
      First page: 19
      Abstract: Erectile dysfunction is prevalent among men and will continue to become more so with the aging population. Of the available treatment options, implantable prosthetic devices are typically thought of as a third line treatment even though they have the highest satisfaction rate and continually improving success rates. Infection and mechanical failure are the most common reasons for implant revision in the past. Since the development of more reliable devices, bacterial biofilms are coming to the forefront of discussion as causes of required revision. Biofilms are problematic as they are ubiquitous and exceedingly difficult to prevent or treat.
      PubDate: 2017-04-18
      DOI: 10.3390/microorganisms5020019
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 20: Tellurite and Tellurate Reduction by the
           Aerobic Anoxygenic Phototroph Erythromonas ursincola, Strain KR99 Is
           Carried out by a Novel Membrane Associated Enzyme

    • Authors: Chris Maltman, Lynda Donald, Vladimir Yurkov
      First page: 20
      Abstract: Erythromonas ursincola, strain KR99 isolated from a freshwater thermal spring of Kamchatka Island in Russia, resists and reduces very high levels of toxic tellurite under aerobic conditions. Reduction is carried out by a constitutively expressed membrane associated enzyme, which was purified and characterized. The tellurite reductase has a molecular weight of 117 kDa, and is comprised of two subunits (62 and 55 kDa) in a 1:1 ratio. Optimal activity occurs at pH 7.0 and 28 °C. Tellurite reduction has a Vmax of 5.15 µmol/min/mg protein and a Km of 3.36 mM. The enzyme can also reduce tellurate with a Vmax and Km of 1.08 µmol/min/mg protein and 1.44 mM, respectively. This is the first purified membrane associated Te oxyanion reductase.
      PubDate: 2017-04-19
      DOI: 10.3390/microorganisms5020020
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 21: Hyperbaric Oxygen Therapy is Ineffective
           as an Adjuvant to Daptomycin with Rifampicin Treatment in a Murine Model
           of Staphylococcus aureus in Implant-Associated Osteomyelitis

    • Authors: Nis Jørgensen, Kasper Hansen, Caroline Andreasen, Michael Pedersen, Kurt Fuursted, Rikke Meyer, Eskild Petersen
      First page: 21
      Abstract: Implant-associated infections caused by bacterial biofilms are difficult to treat. Surgical intervention is often necessary to cure the patient, as the antibiotic recalcitrance of biofilms renders them untreatable with conventional antibiotics. Intermittent hyperbaric oxygen treatment (HBOT) has been proposed as an adjuvant to conventional antibiotic treatment and it has been speculated that combining HBOT with antibiotics could improve treatment outcomes for biofilm infections. In this study we addressed whether HBOT could improve treatment outcomes of daptomycin and rifampicin combination therapy. The effect of HBOT on the treatment outcomes of daptomycin and rifampicin against implant-associated osteomyelitis was quantified in a murine model. In total, 80 mice were randomized into two groups receiving antibiotics, either alone or in combination with daily intermittent HBOT (304 kPa for 60 min) following injection of antibiotics. Treatment was initiated 11 days after animals were infected with Staphylococcus aureus and treatment duration was 14 days. We found that HBOT did not improve the cure rate and did not reduce the bacterial load on the implant surface or in the surrounding tissue. Cure rates of daptomycin + rifampicin were 40% in infected tibias and 75% for implants while cure rates for HBOT-daptomycin + rifampicin were 50% and 85%, respectively, which were not significantly higher (Fisher’s exact test). While it is encouraging that the combination of daptomycin and rifampicin is very effective, our study demonstrates that this efficacy cannot be improved by adjuvant HBOT.
      PubDate: 2017-04-25
      DOI: 10.3390/microorganisms5020021
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 22: Melanisation of Aspergillus terreus—Is
           Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of
           Pigments in Submerged Culture'

    • Authors: Elina Palonen, Sheetal Raina, Annika Brandt, Jussi Meriluoto, Tajalli Keshavarz, Juhani Soini
      First page: 22
      Abstract: Pigments and melanins of fungal spores have been investigated for decades, revealing important roles in the survival of the fungus in hostile environments. The key genes and the encoded enzymes for pigment and melanin biosynthesis have recently been found in Ascomycota, including Aspergillus spp. In Aspergillus terreus, the pigmentation has remained mysterious with only one class of melanin biogenesis being found. In this study, we examined an intriguing, partially annotated gene cluster of A. terreus strain NIH2624, utilizing previously sequenced transcriptome and improved gene expression data of strain MUCL 38669, under the influence of a suggested quorum sensing inducing metabolite, butyrolactone I. The core polyketide synthase (PKS) gene of the cluster was predicted to be significantly longer on the basis of the obtained transcriptional data, and the surrounding cluster was positively regulated by butyrolactone I at the late growth phase of submerged culture, presumably during sporulation. Phylogenetic analysis of the extended PKS revealed remarkable similarity with a group of known pigments of Fusarium spp., indicating a similar function for this PKS. We present a hypothesis of this PKS cluster to biosynthesise a 1,8-dihydroxynaphthalene (DHN)-type of pigment during sporulation with the influence of butyrolactone I under submerged culture.
      PubDate: 2017-05-04
      DOI: 10.3390/microorganisms5020022
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 23: Lactic Fermentation as an Efficient Tool
           to Enhance the Antioxidant Activity of Tropical Fruit Juices and Teas

    • Authors: Amandine Fessard, Ashish Kapoor, Jessica Patche, Sophie Assemat, Mathilde Hoarau, Emmanuel Bourdon, Theeshan Bahorun, Fabienne Remize
      First page: 23
      Abstract: Tropical fruits like pineapple, papaya, mango, and beverages such as green or black teas, represent an underestimated source of antioxidants that could exert health-promoting properties. Most food processing technologies applied to fruit beverages or teas result in an impairment of inherent nutritional properties. Conversely, we hypothesise that lactic acid fermentation may constitute a promising route to maintain and even improve the nutritional qualities of processed fruits. Using specific growth media, lactic acid bacteria were selected from the fruit phyllosphere diversity and fruit juice, with the latter undergoing acidification kinetics analyses and characterised for exopolysaccharide production. Strains able to ferment tropical fruit juices or teas into pleasant beverages, within a short time, were of particular interest. Strains Weissella cibaria 64 and Leuconostoc mesenteroides 12b, able to increase antioxidant activity, were specifically studied as potential starters for lactic fermented pineapple juice.
      PubDate: 2017-05-10
      DOI: 10.3390/microorganisms5020023
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 24: Dairy Propionibacteria: Versatile
           Probiotics

    • Authors: Houem Rabah, Fillipe Rosa do Carmo, Gwénaël Jan
      First page: 24
      Abstract: Dairy propionibacteria are used as cheese ripening starters, as biopreservative and as beneficial additives, in the food industry. The main species, Propionibacterium freudenreichii, is known as GRAS (Generally Recognized As Safe, USA, FDA). In addition to another dairy species, Propionibacterium acidipropionici, they are included in QPS (Qualified Presumption of Safety) list. Additional to their well-known technological application, dairy propionibacteria increasingly attract attention for their promising probiotic properties. The purpose of this review is to summarize the probiotic characteristics of dairy propionibacteria reported by the updated literature. Indeed, they meet the selection criteria for probiotic bacteria, such as the ability to endure digestive stressing conditions and to adhere to intestinal epithelial cells. This is a prerequisite to bacterial persistence within the gut. The reported beneficial effects are ranked according to property’s type: microbiota modulation, immunomodulation, and cancer modulation. The proposed molecular mechanisms are discussed. Dairy propionibacteria are described as producers of nutraceuticals and beneficial metabolites that are responsible for their versatile probiotic attributes include short chain fatty acids (SCFAs), conjugated fatty acids, surface proteins, and 1,4-dihydroxy-2-naphtoic acid (DHNA). These metabolites possess beneficial properties and their production depends on the strain and on the growth medium. The choice of the fermented food matrix may thus determine the probiotic properties of the ingested product. This review approaches dairy propionibacteria, with an interest in both technological abilities and probiotic attributes.
      PubDate: 2017-05-13
      DOI: 10.3390/microorganisms5020024
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 25: Microbial Diversity in Extreme Marine
           Habitats and Their Biomolecules

    • Authors: Annarita Poli, Ilaria Finore, Ida Romano, Alessia Gioiello, Licia Lama, Barbara Nicolaus
      First page: 25
      Abstract: Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.
      PubDate: 2017-05-16
      DOI: 10.3390/microorganisms5020025
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 26: Adding Value to Goat Meat: Biochemical
           and Technological Characterization of Autochthonous Lactic Acid Bacteria
           to Achieve High-Quality Fermented Sausages

    • Authors: Miriam Nediani, Luis García, Lucila Saavedra, Sandra Martínez, Soledad López Alzogaray, Silvina Fadda
      First page: 26
      Abstract: Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product.
      PubDate: 2017-05-17
      DOI: 10.3390/microorganisms5020026
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 27: From Genome to Phenotype: An Integrative
           Approach to Evaluate the Biodiversity of Lactococcus lactis

    • Authors: Valérie Laroute, Hélène Tormo, Christel Couderc, Muriel Mercier-Bonin, Pascal Le Bourgeois, Muriel Cocaign-Bousquet, Marie-Line Daveran-Mingot
      First page: 27
      Abstract: Lactococcus lactis is one of the most extensively used lactic acid bacteria for the manufacture of dairy products. Exploring the biodiversity of L. lactis is extremely promising both to acquire new knowledge and for food and health-driven applications. L. lactis is divided into four subspecies: lactis, cremoris, hordniae and tructae, but only subsp. lactis and subsp. cremoris are of industrial interest. Due to its various biotopes, Lactococcus subsp. lactis is considered the most diverse. The diversity of L. lactis subsp. lactis has been assessed at genetic, genomic and phenotypic levels. Multi-Locus Sequence Type (MLST) analysis of strains from different origins revealed that the subsp. lactis can be classified in two groups: “domesticated” strains with low genetic diversity, and “environmental” strains that are the main contributors of the genetic diversity of the subsp. lactis. As expected, the phenotype investigation of L. lactis strains reported here revealed highly diverse carbohydrate metabolism, especially in plant- and gut-derived carbohydrates, diacetyl production and stress survival. The integration of genotypic and phenotypic studies could improve the relevance of screening culture collections for the selection of strains dedicated to specific functions and applications.
      PubDate: 2017-05-19
      DOI: 10.3390/microorganisms5020027
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 28: Regulatory and Safety Requirements for
           Food Cultures

    • Authors: Svend Laulund, Anette Wind, Patrick Derkx, Véronique Zuliani
      First page: 28
      Abstract: The increased use of food cultures to ferment perishable raw materials has potentiated the need for regulations to assess and assure the safety of food cultures and their uses. These regulations differ from country to country, all aimed at assuring the safe use of food cultures which has to be guaranteed by the food culture supplier. Here we highlight national differences in regulations and review a list of methods and methodologies to assess the safety of food cultures at strain level, at production, and in the final product.
      PubDate: 2017-05-23
      DOI: 10.3390/microorganisms5020028
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 29: Toxin Variability Estimations of 68
           Alexandrium ostenfeldii (Dinophyceae) Strains from The Netherlands Reveal
           a Novel Abundant Gymnodimine

    • Authors: Helge Martens, Urban Tillmann, Kirsi Harju, Carmela Dell’Aversano, Luciana Tartaglione, Bernd Krock
      First page: 29
      Abstract: Alexandrium ostenfeldii is a toxic dinoflagellate that has recently bloomed in Ouwerkerkse Kreek, The Netherlands, and which is able to cause a serious threat to shellfish consumers and aquacultures. We used a large set of 68 strains to the aim of fully characterizing the toxin profiles of the Dutch A. ostenfeldii in consideration of recent reports of novel toxins. Alexandrium ostenfeldii is known as a causative species of paralytic shellfish poisoning, and consistently in the Dutch population we determined the presence of several paralytic shellfish toxins (PST) including saxitoxin (STX), GTX2/3 (gonyautoxins), B1 and C1/C2. We also examined the production of spiroimine toxins by the Dutch A. ostenfeldii strains. An extensive liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed a high intraspecific variability of spirolides (SPX) and gymnodimines (GYM). Spirolides included 13-desMethyl-spirolide C generally as the major compound and several other mostly unknown SPX-like compounds that were detected and characterized. Besides spirolides, the presence of gymnodimine A and 12-Methyl-gymnodimine A was confirmed, together with two new gymnodimines. One of these was tentatively identified as an analogue of gymnodimine D and was the most abundant gymnodimine (calculated cell quota up to 274 pg cell−1, expressed as GYM A equivalents). Our multi-clonal approach adds new analogues to the increasing number of compounds in these toxin classes and revealed a high strain variability in cell quota and in toxin profile of toxic compounds within a single population.
      PubDate: 2017-05-26
      DOI: 10.3390/microorganisms5020029
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 30: Table Olive Fermentation Using Starter
           Cultures with Multifunctional Potential

    • Authors: Stamatoula Bonatsou, Chrysoula Tassou, Efstathios Panagou, George-John Nychas
      First page: 30
      Abstract: Table olives are one of the most popular plant-derived fermented products. Their enhanced nutritional value due to the presence of phenolic compounds and monounsaturated fatty acids makes olives an important food commodity of the Mediterranean diet. However, despite its economic significance, table olive fermentation is mainly craft-based and empirically driven by the autochthonous microbiota of the olives depending on various intrinsic and extrinsic factors, leading to a spontaneous process and a final product of variable quality. The use of microorganisms previously isolated from olive fermentations and studied for their probiotic potential and technological characteristics as starter cultures may contribute to the reduction of spoilage risk resulting in a controlled fermentation process. This review focuses on the importance of the development and implementation of multifunctional starter cultures related to olives with desirable probiotic and technological characteristics for possible application on table olive fermentation with the main purpose being the production of a health promoting and sensory improved functional food.
      PubDate: 2017-05-28
      DOI: 10.3390/microorganisms5020030
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 31: Changes in Microbial (Bacteria and
           Archaea) Plankton Community Structure after Artificial Dispersal in
           Grazer-Free Microcosms

    • Authors: Hera Karayanni, Alexandra Meziti, Sofie Spatharis, Savvas Genitsaris, Claude Courties, Konstantinos Kormas
      First page: 31
      Abstract: Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.
      PubDate: 2017-06-03
      DOI: 10.3390/microorganisms5020031
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 32: Interaction of Candida Species with the
           Skin

    • Authors: Andreas Kühbacher, Anke Burger-Kentischer, Steffen Rupp
      First page: 32
      Abstract: The human skin is commonly colonized by diverse fungal species. Some Candida species, especially C. albicans, do not only reside on the skin surface as commensals, but also cause infections by growing into the colonized tissue. However, defense mechanisms at the skin barrier level are very efficient, involving residential non-immune and immune cells as well as immune cells specifically recruited to the site of infection. Therefore, the skin is an effective barrier against fungal infection. While most studies about commensal and pathogenic interaction of Candida species with host epithelia focus on the interaction with mucosal surfaces such as the vaginal and gastrointestinal epithelia, less is known about the mechanisms underlying Candida interaction with the skin. In this review, we focus on the ecology and molecular pathogenesis of Candida species on the skin and give an overview of defense mechanisms against C. albicans in this context. We also discuss new research avenues in dermal infection, including the involvement of neurons, fibroblasts, and commensal bacteria in both mouse and human model systems.
      PubDate: 2017-06-07
      DOI: 10.3390/microorganisms5020032
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 33: Purine Acquisition and Synthesis by
           Human Fungal Pathogens

    • Authors: Jessica Chitty, James Fraser
      First page: 33
      Abstract: While members of the Kingdom Fungi are found across many of the world’s most hostile environments, only a limited number of species can thrive within the human host. The causative agents of the most common invasive fungal infections are Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans. During the infection process, these fungi must not only combat the host immune system while adapting to dramatic changes in temperature and pH, but also acquire sufficient nutrients to enable growth and dissemination in the host. One class of nutrients required by fungi, which is found in varying concentrations in their environmental niches and the human host, is the purines. These nitrogen-containing heterocycles are one of the most abundant organic molecules in nature and are required for roles as diverse as signal transduction, energy metabolism and DNA synthesis. The most common life-threatening fungal pathogens can degrade, salvage and synthesize de novo purines through a number of enzymatic steps that are conserved. While these enable them to adapt to the changing purine availability in the environment, only de novo purine biosynthesis is essential during infection and therefore an attractive antimycotic target.
      PubDate: 2017-06-08
      DOI: 10.3390/microorganisms5020033
      Issue No: Vol. 5, No. 2 (2017)
       
  • Microorganisms, Vol. 5, Pages 34: Comment on: “Melanisation of
           Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of
           Both DOPA and DHN Types of Pigments in Submerged Culture'
           Microorganisms 2017, 5, 22”

    • Authors: Elena Geib, Matthias Brock
      First page: 34
      Abstract: A recent article by Palonen et al. describes the effect of butyrolactone I on the expression of a secondary metabolite biosynthesis gene cluster from Aspergillus terreus that shows similarities to fusarubin biosynthesis gene clusters from Fusarium species. The authors claim that two different types of pigments are formed in Aspergillus terreus conidia, whereby one pigment is termed a DOPA-type melanin and the second a DHN-type melanin. Unfortunately, the terminology of the classification of melanin-types requires revision as Asp-melanin present in A. terreus conidia is clearly distinct from DOPA-melanins. In addition, some hypotheses in this manuscript are based on questionable data published previously, resulting in incorrect conclusions. Finally, as biochemical data are lacking and metabolite production is only deduced from bioinformatics and transcriptomic data, the production of a second pigment type in A. terreus conidia appears highly speculative.
      PubDate: 2017-06-21
      DOI: 10.3390/microorganisms5020034
      Issue No: Vol. 5, No. 2 (2017)
       
 
 
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