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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  [148 journals]
  • Microorganisms, Vol. 5, Pages 2: Acknowledgement to Reviewers of
           Microorganisms in 2016

    • Authors: Microorganisms Editorial Office
      First page: 2
      Abstract: n/a
      PubDate: 2017-01-11
      DOI: 10.3390/microorganisms5010002
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 3: Using Network Extracted Ontologies to
           Identify Novel Genes with Roles in Appressorium Development in the Rice
           Blast Fungus Magnaporthe oryzae

    • Authors: Ryan Ames
      First page: 3
      Abstract: Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.
      PubDate: 2017-01-17
      DOI: 10.3390/microorganisms5010003
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 4: Phylogenetic Heatmaps Highlight
           Composition Biases in Sequenced Reads

    • Authors: Sulbha Choudhari, Andrey Grigoriev
      First page: 4
      Abstract: Due to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs), a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups. This method is well suited for finding noise and biases when comparing metagenomics samples. We apply PGHMs to detect noise and bias in the data produced with different DNA extraction protocols, different sequencing platforms and different experimental frameworks. In parallel, we use principal component analysis displaying different clustering of sequences from each sample to support our findings and illustrate the utility of PGHMs. We considered contributions of the read length and GC-content variation and observed that in most cases biases were generally due to the GC-content of the reads.
      PubDate: 2017-01-24
      DOI: 10.3390/microorganisms5010004
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 5: Fluorescence Lectin Bar-Coding of
           Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate
           Forming Microorganisms

    • Authors: Thomas Neu, Ute Kuhlicke
      First page: 5
      Abstract: Microbial biofilm systems are defined as interface-associated microorganisms embedded into a self-produced matrix. The extracellular matrix represents a continuous challenge in terms of characterization and analysis. The tools applied in more detailed studies comprise extraction/chemical analysis, molecular characterization, and visualisation using various techniques. Imaging by laser microscopy became a standard tool for biofilm analysis, and, in combination with fluorescently labelled lectins, the glycoconjugates of the matrix can be assessed. By employing this approach a wide range of pure culture biofilms from different habitats were examined using the commercially available lectins. From the results, a binary barcode pattern of lectin binding can be generated. Furthermore, the results can be fine-tuned and transferred into a heat map according to signal intensity. The lectin barcode approach is suggested as a useful tool for investigating the biofilm matrix characteristics and dynamics at various levels, e.g. bacterial cell surfaces, adhesive footprints, individual microcolonies, and the gross biofilm or bio-aggregate. Hence fluorescence lectin bar-coding (FLBC) serves as a basis for a subsequent tailor-made fluorescence lectin-binding analysis (FLBA) of a particular biofilm. So far, the lectin approach represents the only tool for in situ characterization of the glycoconjugate makeup in biofilm systems.  Furthermore, lectin staining lends itself to other fluorescence techniques in order to correlate it with cellular biofilm constituents in general and glycoconjugate producers in particular.
      PubDate: 2017-02-10
      DOI: 10.3390/microorganisms5010005
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 6: Effects of Dietary Yogurt on the Healthy
           Human Gastrointestinal (GI) Microbiome

    • Authors: Daniel Lisko, G. Johnston, Carl Johnston
      First page: 6
      Abstract: The gastrointestinal (GI) tract performs key functions that regulate the relationship between the host and the microbiota. Research has shown numerous benefits of probiotic intake in the modulation of immune responses and human metabolic processes. However, unfavorable attention has been paid to temporal changes of the microbial composition and diversity of the GI tract. This study aimed to investigate the effects of yogurt consumption on the GI microbiome bacteria community composition, structure and diversity during and after a short-term period (42 days). We used a multi-approach combining classical fingerprinting techniques (T-RFLPs), Sanger analyses and Illumina MiSeq 16S rRNA gene amplicon sequencing to elucidate bacterial communities and Lactobacilli and Bifidobacteria populations within healthy adults that consume high doses of yogurt daily. Results indicated that overall GI microbial community and diversity was method-dependent, yet we found individual specific changes in bacterial composition and structure in healthy subjects that consumed high doses of yogurt throughout the study.
      PubDate: 2017-02-15
      DOI: 10.3390/microorganisms5010006
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 7: Presence of Calcium Lowers the Expansion
           of Bacillus subtilis Colony Biofilms

    • Authors: Eisha Mhatre, Anandaroopan Sundaram, Theresa Hölscher, Mike Mühlstädt, Jörg Bossert, Ákos Kovács
      First page: 7
      Abstract: Robust colony formation by Bacillus subtilis is recognized as one of the sessile, multicellular lifestyles of this bacterium. Numerous pathways and genes are responsible for the architecturally complex colony structure development. Cells in the biofilm colony secrete extracellular polysaccharides (EPS) and protein components (TasA and the hydrophobin BslA) that hold them together and provide a protective hydrophobic shield. Cells also secrete surfactin with antimicrobial as well as surface tension reducing properties that aid cells to colonize the solid surface. Depending on the environmental conditions, these secreted components of the colony biofilm can also promote the flagellum-independent surface spreading of B. subtilis, called sliding. In this study, we emphasize the influence of Ca2+ in the medium on colony expansion of B. subtilis. Interestingly, the availability of Ca2+ has no major impact on the induction of complex colony morphology. However, in the absence of this divalent ion, peripheral cells of the colony expand radially at later stages of development, causing colony size to increase. We demonstrate that the secreted extracellular compounds, EPS, BslA, and surfactin facilitate colony expansion after biofilm maturation. We propose that Ca2+ hinders biofilm colony expansion by modifying the amphiphilic properties of surfactin.
      PubDate: 2017-02-16
      DOI: 10.3390/microorganisms5010007
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 8: Genome Sequence of Rhodoferax antarcticus
           ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic
           Microbial Mat

    • Authors: Jennifer Baker, Carli Riester, Blair Skinner, Austin Newell, Wesley Swingley, Michael Madigan, Deborah Jung, Marie Asao, Min Chen, Patrick Loughlin, Hao Pan, Yuankui Lin, Yaqiong Li, Jacob Shaw, Mindy Prado, Chris Sherman, Joseph Tang, Robert Blankenship, Tingting Zhao, Jeffrey Touchman, W. Sattley
      First page: 8
      Abstract: Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3), but not light-harvesting complex 2 (LH2), were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.
      PubDate: 2017-02-21
      DOI: 10.3390/microorganisms5010008
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 9: Microbial Biofilms and Chronic Wounds

    • Authors: Amin Omar, J. Wright, Gregory Schultz, Robert Burrell, Patricia Nadworny
      First page: 9
      Abstract: Background is provided on biofilms, including their formation, tolerance mechanisms, structure, and morphology within the context of chronic wounds. The features of biofilms in chronic wounds are discussed in detail, as is the impact of biofilm on wound chronicity. Difficulties associated with the use of standard susceptibility tests (minimum inhibitory concentrations or MICs) to determine appropriate treatment regimens for, or develop new treatments for use in, chronic wounds are discussed, with alternate test methods specific to biofilms being recommended. Animal models appropriate for evaluating biofilm treatments are also described. Current and potential future therapies for treatment of biofilm-containing chronic wounds, including probiotic therapy, virulence attenuation, biofilm phenotype expression attenuation, immune response suppression, and aggressive debridement combined with antimicrobial dressings, are described.
      PubDate: 2017-03-07
      DOI: 10.3390/microorganisms5010009
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 10: Lactobacillus gasseri PA-3 Uses the
           Purines IMP, Inosine and Hypoxanthine and Reduces their Absorption in Rats

    • Authors: Naruomi Yamada, Chizuru Saito-Iwamoto, Marie Nakamura, Misato Soeda, Yoshika Chiba, Hiroshi Kano, Yukio Asami
      First page: 10
      Abstract: Excessive intake of purine-rich foods elevates serum levels of uric acid. Animal and fish meats contain high amounts of inosine and its related purines, and the reduction of taking those purines is crucial for the improvement of serum uric acid levels. We previously showed that Lactobacillus gasseri PA-3 (PA-3) incorporates adenosine and its related purines and that oral treatment with PA-3 reduced adenosine absorption in rats. This study investigated whether PA-3 also incorporates IMP (inosine 5′-monophosphate), inosine, and hypoxanthine, and whether it reduces their absorption in rats. PA-3 was incubated in vitro with radioisotope (RI)-labeled IMP, inosine, and hypoxanthine, and the incorporation of these compounds by PA-3 was evaluated. In addition, rats were orally administered PA-3 along with RI-labeled inosine 5′-monophosphate, inosine, or hypoxanthine, and the ability of PA-3 to attenuate the absorption of these purines was determined. PA-3 incorporated all three purines and displayed greater proliferation in the presence than in the absence of these purines. Oral administration of PA-3 to rats reduced the absorption of IMP, inosine, and hypoxanthine. These results indicate that PA-3 reduces the absorption of purines contained in foods and it is expected that PA-3 contributes attenuation of the excessive intake of dietary purines.
      PubDate: 2017-03-08
      DOI: 10.3390/microorganisms5010010
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 11: The Food Production Environment and the
           Development of Antimicrobial Resistance in Human Pathogens of Animal

    • Authors: Manjusha Lekshmi, Parvathi Ammini, Sanath Kumar, Manuel F. Varela
      First page: 11
      Abstract: Food-borne pathogens are a serious human health concern worldwide, and the emergence of antibiotic-resistant food pathogens has further confounded this problem. Once-highly-efficacious antibiotics are gradually becoming ineffective against many important pathogens, resulting in severe treatment crises. Among several reasons for the development and spread of antimicrobial resistance, their overuse in animal food production systems for purposes other than treatment of infections is prominent. Many pathogens of animals are zoonotic, and therefore any development of resistance in pathogens associated with food animals can spread to humans through the food chain. Human infections by antibiotic-resistant pathogens such as Campylobacter spp., Salmonella spp., Escherichia coli and Staphylococcus aureus are increasing. Considering the human health risk due to emerging antibiotic resistance in food animal–associated bacteria, many countries have banned the use of antibiotic growth promoters and the application in animals of antibiotics critically important in human medicine. Concerted global efforts are necessary to minimize the use of antimicrobials in food animals in order to control the development of antibiotic resistance in these systems and their spread to humans via food and water.
      PubDate: 2017-03-14
      DOI: 10.3390/microorganisms5010011
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 12: Transcriptomic Complexity of Aspergillus
           terreus Velvet Gene Family under the Influence of Butyrolactone I

    • Authors: Elina Palonen, Sheetal Raina, Annika Brandt, Jussi Meriluoto, Tajalli Keshavarz, Juhani Soini
      First page: 12
      Abstract: Filamentous fungi of the Ascomycota phylum are known to contain a family of conserved conidiation regulating proteins with distinctive velvet domains. In Aspergilli, this velvet family includes four proteins, VeA, VelB, VelC and VosA, and is involved in conidiation and secondary metabolism along with a global regulator LaeA. In A. terreus, the overexpression of LaeA has been observed to increase the biogenesis of the pharmaceutically-important secondary metabolite, lovastatin, while the role of the velvet family has not been studied. The secondary metabolism and conidiation of A. terreus have also been observed to be increased by butyrolactone I in a quorum-sensing manner. An enlightenment of the interplay of these regulators will give potential advancement to the industrial use of this fungus, as well as in resolving the pathogenic features. In this study, the Aspergillus terreus MUCL 38669 transcriptome was strand-specifically sequenced to enable an in-depth gene expression analysis to further investigate the transcriptional role of butyrolactone I in these processes. The sequenced transcriptome revealed intriguing properties of the velvet family transcripts, including the regulator laeA, and uncovered the velC gene in A. terreus. The reliability refining microarray gene expression analysis disclosed a positive regulatory role for butyrolactone I in laeA expression, as well as an influence on the expression of the canonical conidiation-regulating genes under submerged culture. All of this supports the suggested regulative role of butyrolactone I in A. terreus secondary metabolism, as well as conidiation.
      PubDate: 2017-03-14
      DOI: 10.3390/microorganisms5010012
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 13: Immune Response to Coccidioidomycosis
           and the Development of a Vaccine

    • Authors: Natalia Castro-Lopez, Chiung-Yu Hung
      First page: 13
      Abstract: Coccidioidomycosis is a fungal infection caused by Coccidioides posadasii and Coccidioides immitis. It is estimated that 150,000 new infections occur in the United States each year. The incidence of this infection continues to rise in endemic regions. There is an urgent need for the development of better therapeutic drugs and a vaccine against coccidioidomycosis. This review discusses the features of host innate and adaptive immune responses to Coccidioides infection. The focus is on the recent advances in the immune response and host-pathogen interactions, including the recognition of spherules by the host and defining the signal pathways that guide the development of the adaptive T-cell response to Coccidioides infection. Also discussed is an update on progress in developing a vaccine against these fungal pathogens.
      PubDate: 2017-03-16
      DOI: 10.3390/microorganisms5010013
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 1: Improvement of Intestinal Immune Cell
           Function by Lactic Acid Bacteria for Dairy Products

    • Authors: Tomonori Kamiya, Yohei Watanabe, Seiya Makino, Hiroshi Kano, Noriko Tsuji
      First page: 1
      Abstract: Lactic acid bacteria (LAB) form a major component of gut microbiota and are often used as probiotics for fermented foods, such as yoghurt. In this study, we aimed to evaluate immunomodulatory activity of LAB, especially that of Lactobacillus bulgaricus ME-552 (ME552) and Streptococcus thermophilus ME-553 (ME553). In vivo/in vitro assay was performed in order to investigate their effects on T cell function. After oral administration of ME553 to C57BL/6 mice, the amount of both interferon γ (IFN-γ) and interleukin 17 (IL-17) produced by cluster of differentiation (CD) 4+ T cells from Peyer’s patches (PPs) were significantly enhanced. On the other hand, ME552 only up-regulated the production of IL-17 from PP cells. The extent of induction for IFN-γ production differed between ME552 and ME553. These results suggest that LAB modulate T cell effector functions and mucosal immunity.
      PubDate: 2016-12-23
      DOI: 10.3390/microorganisms5010001
      Issue No: Vol. 5, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 38: Flavin-Dependent Redox Transfers by the
           Two-Component Diketocamphane Monooxygenases of Camphor-Grown Pseudomonas
           putida NCIMB 10007

    • Authors: Andrew Willetts, David Kelly
      First page: 38
      Abstract: The progressive titres of key monooxygenases and their requisite native donors of reducing power were used to assess the relative contribution of various camphor plasmid (CAM plasmid)- and chromosome-coded activities to biodegradation of (rac)-camphor at successive stages throughout growth of Pseudomonas putida NCIMB 10007 on the bicylic monoterpenoid. A number of different flavin reductases (FRs) have the potential to supply reduced flavin mononucleotide to both 2,5- and 3,6-diketocamphane monooxygenase, the key isoenzymic two-component monooxygenases that delineate respectively the (+)- and (−)-camphor branches of the convergent degradation pathway. Two different constitutive chromosome-coded ferric reductases able to act as FRs can serve such as role throughout all stages of camphor-dependent growth, whereas Fred, a chromosome-coded inducible FR can only play a potentially significant role in the relatively late stages. Putidaredoxin reductase, an inducible CAM plasmid-coded flavoprotein that serves an established role as a redox intermediate for plasmid-coded cytochrome P450 monooxygenase also has the potential to serve as an important FR for both diketocamphane monooxygenases (DKCMOs) throughout most stages of camphor-dependent growth.
      PubDate: 2016-10-13
      DOI: 10.3390/microorganisms4040038
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 39: Natural Products for the Treatment of
           Chlamydiaceae Infections

    • Authors: Mika Brown, Michael Potroz, Seoh-Wei Teh, Nam-Joon Cho
      First page: 39
      Abstract: Due to the global prevalence of Chlamydiae, exploring studies of diverse antichlamydial compounds is important in the development of effective treatment strategies and global infectious disease management. Chlamydiaceae is the most widely known bacterial family of the Chlamydiae order. Among the species in the family Chlamydiaceae, Chlamydia trachomatis and Chlamydia pneumoniae cause common human diseases, while Chlamydia abortus, Chlamydia psittaci, and Chlamydia suis represent zoonotic threats or are endemic in human food sources. Although chlamydial infections are currently manageable in human populations, chlamydial infections in livestock are endemic and there is significant difficulty achieving effective treatment. To combat the spread of Chlamydiaceae in humans and other hosts, improved methods for treatment and prevention of infection are needed. There exist various studies exploring the potential of natural products for developing new antichlamydial treatment modalities. Polyphenolic compounds can inhibit chlamydial growth by membrane disruption, reestablishment of host cell apoptosis, or improving host immune system detection. Fatty acids, monoglycerides, and lipids can disrupt the cell membranes of infective chlamydial elementary bodies (EBs). Peptides can disrupt the cell membranes of chlamydial EBs, and transferrins can inhibit chlamydial EBs from attachment to and permeation through the membranes of host cells. Cellular metabolites and probiotic bacteria can inhibit chlamydial infection by modulating host immune responses and directly inhibiting chlamydial growth. Finally, early stage clinical trials indicate that polyherbal formulations can be effective in treating chlamydial infections. Herein, we review an important body of literature in the field of antichlamydial research.
      PubDate: 2016-10-16
      DOI: 10.3390/microorganisms4040039
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 40: Human Lactobacillus Strains from the
           Intestine can Suppress IgE-Mediated Degranulation of Rat Basophilic
           Leukaemia (RBL-2H3) Cells

    • Authors: Gaku Harata, Fang He, Kyoko Takahashi, Akira Hosono, Kenji Miyazawa, Kazutoyo Yoda, Masaru Hiramatsu, Shuichi Kaminogawa
      First page: 40
      Abstract: Mast cells play a critical role in immunoglobulin E (IgE)-mediated allergic diseases, and the degranulation of mast cells is important in the pathogenesis of these diseases. A disturbance of the intestinal microflora, especially of endogenous lactic acid bacteria, might be a contributing factor for IgE-mediated allergic diseases. Additional knowledge regarding the interaction of human intestinal Lactobacilli with mast cells is still necessary. Twenty-three strains of Lactobacilli, including commercial and reference strains and strains from the human intestine, were tested for their ability to regulate degranulation of cells from rat basophilic leukemia RBL-2H3 cells (RBL-2H3) in vitro based on a β-hexosaminidase release assay. Each of the tested Lactobacilli characteristically suppressed IgE-mediated degranulation of RBL-2H3 cells, and Lactobacillus GG showed the strongest inhibitory effect on the cells. Furthermore, the bacteria isolated from the human intestine significantly suppressed degranulation of RBL-2H3 cellsin comparison with the reference strains. These results suggest that Lactobacilli, particularly those from the human intestine, can affect the activation of mast cells in a strain-dependent manner. Further study should be conducted to analyse the understanding mechanism.
      PubDate: 2016-10-27
      DOI: 10.3390/microorganisms4040040
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 41: EPS—Then and Now

    • Authors: Hans-Curt Flemming
      First page: 41
      Abstract: “Slime” played a brief and spectacular role in the 19th century founded by the theory of primordial slime by Ernst Haeckel. However, that substance was never found and eventually abandoned. Further scientific attention slowly began in the 1930s referring to slime as a microbial product and then was inspired by “How bacteria stick” by Costerton et al. in 1978, and the matrix material was considered to be polysaccharides. Later, it turned out that proteins, nucleic acids and lipids were major other constituents of the extracellular polymeric substances (EPS), an acronym which was highly discussed. The role of the EPS matrix turns out to be fundamental for biofilms, in terms of keeping cells in proximity and allowing for extended interaction, resource capture, mechanical strength and other properties, which emerge from the life of biofilm organisms, including enhanced tolerance to antimicrobials and other stress. The EPS components are extremely complex and dynamic and fulfil many functional roles, turning biofilms into the most ubiquitous and successful form of life on Earth.
      PubDate: 2016-11-18
      DOI: 10.3390/microorganisms4040041
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 42: Dirty Money: A Matter of Bacterial
           Survival, Adherence, and Toxicity

    • Authors: Frank Vriesekoop, Jing Chen, Jenna Oldaker, Flavien Besnard, Reece Smith, William Leversha, Cheralee Smith-Arnold, Julie Worrall, Emily Rufray, Qipeng Yuan, Hao Liang, Amalia Scannell, Cryn Russell
      First page: 42
      Abstract: In this study we report the underlying reasons to why bacteria are present on banknotes and coins. Despite the use of credit cards, mobile phone apps, near-field-communication systems, and cryptocurrencies such as bitcoins which are replacing the use of hard currencies, cash exchanges still make up a significant means of exchange for a wide range of purchases. The literature is awash with data that highlights that both coins and banknotes are frequently identified as fomites for a wide range of microorganisms. However, most of these publications fail to provide any insight into the extent to which bacteria adhere and persist on money. We treated the various currencies used in this study as microcosms, and the bacterial loading from human hands as the corresponding microbiome. We show that the substrate from which banknotes are produced have a significant influence on both the survival and adherence of bacteria to banknotes. Smooth, polymer surfaces provide a poor means of adherence and survival, while coarser and more fibrous surfaces provide strong bacterial adherence and an environment to survive on. Coins were found to be strongly inhibitory to bacteria with a relatively rapid decline in survival on almost all coin surfaces tested. The inhibitory influence of coins was demonstrated through the use of antimicrobial disks made from coins. Despite the toxic effects of coins on many bacteria, bacteria do have the ability to adapt to the presence of coins in their environment which goes some way to explain the persistent presence of low levels of bacteria on coins in circulation.
      PubDate: 2016-11-23
      DOI: 10.3390/microorganisms4040042
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 43: Lead Discovery Strategies for
           Identification of Chlamydia pneumoniae Inhibitors

    • Authors: Leena Hanski, Pia Vuorela
      First page: 43
      Abstract: Throughout its known history, the gram-negative bacterium Chlamydia pneumoniae has remained a challenging target for antibacterial chemotherapy and drug discovery. Owing to its well-known propensity for persistence and recent reports on antimicrobial resistence within closely related species, new approaches for targeting this ubiquitous human pathogen are urgently needed. In this review, we describe the strategies that have been successfully applied for the identification of nonconventional antichlamydial agents, including target-based and ligand-based virtual screening, ethnopharmacological approach and pharmacophore-based design of antimicrobial peptide-mimicking compounds. Among the antichlamydial agents identified via these strategies, most translational work has been carried out with plant phenolics. Thus, currently available data on their properties as antichlamydial agents are described, highlighting their potential mechanisms of action. In this context, the role of mitogen-activated protein kinase activation in the intracellular growth and survival of C. pneumoniae is discussed. Owing to the complex and often complementary pathways applied by C. pneumoniae in the different stages of its life cycle, multitargeted therapy approaches are expected to provide better tools for antichlamydial therapy than agents with a single molecular target.
      PubDate: 2016-11-28
      DOI: 10.3390/microorganisms4040043
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 44: Modeling Lactic Fermentation of Gowé
           Using Lactobacillus Starter Culture

    • Authors: Bettencourt de J. C. Munanga, Gérard Loiseau, Joël Grabulos, Christian Mestres
      First page: 44
      Abstract: A global model of the lactic fermentation step of gowé was developed by assembling blocks hosting models for bacterial growth, lactic acid production, and the drop of pH during fermentation. Commercial strains of Lactobacillus brevis and of Lactobacillus plantarum were used; their growth was modeled using Rosso’s primary model and the gamma concept as a secondary model. The optimum values of pH and temperature were 8.3 ± 0.3, 44.6 ± 1.2 °C and 8.3 ± 0.3, 3.2 ± 37.1 °C with μmax values of 1.8 ± 0.2 and 1.4 ± 0.1 for L. brevis and L. plantarum respectively. The minimum inhibitory concentration of undissociated lactic acid was 23.7 mM and 35.6 mM for L. brevis and L. plantarum, respectively. The yield of lactic acid was five times higher for L. plantarum than for L. brevis, with a yield of glucose conversion to lactic acid close to 2.0 for the former and 0.8 for the latter. A model was developed to predict the pH drop during gowé fermentation. The global model was partially validated during manufacturing of gowé. The global model could be a tool to aid in the choice of suitable starters and to determine the conditions for the use of the starter.
      PubDate: 2016-12-01
      DOI: 10.3390/microorganisms4040044
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 45: Pb2+ Effects on Growth, Lipids, and
           Protein and DNA Profiles of the Thermophilic Bacterium Thermus

    • Authors: Barbara Nicolaus, Annarita Poli, Paola Di Donato, Ida Romano, Giusi Laezza, Alessia Gioiello, Sergio Ulgiati, Florinda Fratianni, Filomena Nazzaro, Pierangelo Orlando, Stefano Dumontet
      First page: 45
      Abstract: Extremophiles are organisms able to thrive in extreme environmental conditions and some of them show the ability to survive high doses of heavy metals thanks to defensive mechanisms provided by primary and secondary metabolic products, i.e., extremolytes, lipids, and extremozymes. This is why there is a growing scientific and industrial interest in the use of thermophilic bacteria in a host of tasks, from the environmental detoxification of heavy metal to industrial activities, such as bio-machining and bio-metallurgy. In this work Thermus thermophilus was challenged against increasing Pb2+ concentrations spanning from 0 to 300 ppm in order to ascertain the sensitiveness of this bacteria to the Pb environmental pollution and to give an insight on its heavy metal resistance mechanisms. Analysis of growth parameters, enzyme activities, protein profiles, and lipid membrane modifications were carried out. In addition, genotyping analysis of bacteria grown in the presence of Pb2+, using random amplified polymorphic DNA-PCR and DNA melting evaluation, were also performed. A better knowledge of the response of thermophilic bacteria to the different pollutants, as heavy metals, is necessary for optimizing their use in remediation or decontamination processes.
      PubDate: 2016-12-06
      DOI: 10.3390/microorganisms4040045
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 46: Microbiological Quality of Fresh Nopal

    • Authors: Ana Hernández-Anguiano, Patricia Landa-Salgado, Carlos Eslava-Campos, Mateo Vargas-Hernández, Jitendra Patel
      First page: 46
      Abstract: The consumption of fresh nopal cactus juice is widely popular among health-conscious consumers in Mexico. The juice is prepared from fresh cladodes that have only been rinsed with tap water and are not subjected to a pasteurization or terminal bacterial reduction process. The aim of this study was to evaluate the microbial quality of commercially available fresh juices (n = 162) made with nopal in Texcoco, State of Mexico, during the summer and spring season. Standard microbiological methods, the PCR technique and the serological method were used for isolation and identification of bacteria. All samples contained total coliforms and 91% were positive for Escherichia coli. Although total coliforms and E. coli were detected throughout the study, their populations were significantly lower (p < 0.05) in winter and spring, respectively. Citrobacter youngae was found in 20% of the samples, an unidentified species of Citrobacter in 10%, C. freundii and Proteus mirabilis in 3%, and Salmonella Javiana in 1%. The presence of these microorganisms, especially Salmonella, in the nopal juices is unacceptable due to its health significance. The information generated in this study is relevant for human health risk assessment associated with the consumption of unpasteurized nopal juices and potential interventions to minimize pathogen contamination.
      PubDate: 2016-12-10
      DOI: 10.3390/microorganisms4040046
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 47: Immunoregulation in Fungal Diseases

    • Authors: Jonathan Roussey, Michal Olszewski, John Osterholzer
      First page: 47
      Abstract: This review addresses specific regulatory mechanisms involved in the host immune response to fungal organisms. We focus on key cells and regulatory pathways involved in these responses, including a brief overview of their broader function preceding a discussion of their specific relevance to fungal disease. Important cell types discussed include dendritic cells and regulatory T cells, with a focus on specific studies relating to their effects on immune responses to fungi. We highlight the interleukin-10, programmed cell death 1, and cytotoxic T lymphocyte-associated protein 4 signaling pathways and emphasize interrelationships between these pathways and the regulatory functions of dendritic cells and regulatory T cells. Throughout our discussion, we identify selected studies best illustrating the role of these cells and pathways in response to specific fungal pathogens to provide a contextual understanding of the tightly-controlled network of regulatory mechanisms critical to determining the outcome of exposure to fungal pathogens. Lastly, we discuss two unique phenomena relating to immunoregulation, protective tolerance and immune reactivation inflammatory syndrome. These two clinically-relevant conditions provide perspective as to the range of immunoregulatory mechanisms active in response to fungi.
      PubDate: 2016-12-10
      DOI: 10.3390/microorganisms4040047
      Issue No: Vol. 4, No. 4 (2016)
  • Microorganisms, Vol. 4, Pages 22: A Look inside the Listeria monocytogenes
           Biofilms Extracellular Matrix

    • Authors: Angelo Colagiorgi, Pierluigi Di Ciccio, Emanuela Zanardi, Sergio Ghidini, Adriana Ianieri
      First page: 22
      Abstract: Listeria monocytogenes is a foodborne pathogen able to persist in food industry and is responsible for a severe illness called listeriosis. The ability of L. monocytogenes to persist in environments is due to its capacity to form biofilms that are a sessile community of microorganisms embedded in a self-produced matrix of extracellular polymeric substances (EPS’s). In this review, we summarized recent efforts performed in order to better characterize the polymeric substances that compose the extracellular matrix (ECM) of L. monocytogenes biofilms. EPS extraction and analysis led to the identification of polysaccharides, proteins, extracellular DNA, and other molecules within the listerial ECM. All this knowledge will be useful for increasing food protection, suggesting effective strategies for the minimization of persistence of L. monocytogenes in food industry environments.
      PubDate: 2016-07-05
      DOI: 10.3390/microorganisms4030022
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 23: Highly Variable Bacterial Communities
           Associated with the Octocoral Antillogorgia elisabethae

    • Authors: Veronica Robertson, Brad Haltli, Erin McCauley, David Overy, Russell Kerr
      First page: 23
      Abstract: Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome.
      PubDate: 2016-07-05
      DOI: 10.3390/microorganisms4030023
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 24: Enrichment of Fusobacteria in Sea
           Surface Oil Slicks from the Deepwater Horizon Oil Spill

    • Authors: Tony Gutierrez, David Berry, Andreas Teske, Michael Aitken
      First page: 24
      Abstract: The Deepwater Horizon (DWH) oil spill led to rapid microbial community shifts in the Gulf of Mexico, including the formation of unprecedented quantities of marine oil snow (MOS) and of a massive subsurface oil plume. The major taxa that bloomed in sea surface oil slicks during the spill included Cycloclasticus, and to a lesser extent Halomonas, Alteromonas, and Pseudoalteromonas—organisms that grow and degrade oil hydrocarbons aerobically. Here, we show that sea surface oil slicks at DWH contained obligate and facultative anaerobic taxa, including members of the obligate anaerobic phylum Fusobacteria that are commonly found in marine sediment environments. Pyrosequencing analysis revealed that Fusobacteria were strongly selected for when sea surface oil slicks were allowed to develop anaerobically. These organisms have been found in oil-contaminated sediments in the Gulf of Mexico, in deep marine oil reservoirs, and other oil-contaminated sites, suggesting they have putative hydrocarbon-degrading qualities. The occurrence and strong selection for Fusobacteria in a lab-based incubation of a sea surface oil slick sample collected during the spill suggests that these organisms may have become enriched in anaerobic zones of suspended particulates, such as MOS. Whilst the formation and rapid sinking of MOS is recognised as an important mechanism by which a proportion of the Macondo oil had been transported to the sea floor, its role in potentially transporting microorganisms, including oil-degraders, from the upper reaches of the water column to the seafloor should be considered. The presence of Fusobacteria on the sea surface—a highly oxygenated environment—is intriguing, and may be explained by the vertical upsurge of oil that provided a carrier to transport these organisms from anaerobic/micro-aerophilic zones in the oil plume or seabed to the upper reaches of the water column. We also propose that the formation of rapidly-sinking MOS may have re-transported these, and other microbial taxa, to the sediment in the Gulf of Mexico.
      PubDate: 2016-07-27
      DOI: 10.3390/microorganisms4030024
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 25: Diagnostic Procedures to Detect
           Chlamydia trachomatis Infections

    • Authors: Thomas Meyer
      First page: 25
      Abstract: The intracellular life style of chlamydia and the ability to cause persistent infections with low-grade replication requires tests with high analytical sensitivity to directly detect C. trachomatis (CT) in medical samples. Nucleic acid amplification tests (NAATs) are the most sensitive assays with a specificity similar to cell culture and are considered the method of choice for CT detection. In addition, NAATs can be performed on various clinical specimens that do not depend on specific transport and storage conditions, since NAATs do not require infectious bacteria. In the case of lower genital tract infections, first void urine and vaginal swabs are the recommended specimens for testing males and females, respectively. Infections of anorectal, oropharyngeal and ocular epithelia should also be tested by NAAT analysis of corresponding mucosal swabs. In particular, anorectal infections of men who have sex with men (MSM) should include evaluation of lymphogranuloma venereum (LGV) by identification of genotypes L1, L2 or L3. Detection of CT antigens by enzyme immunoassay (EIAs) or rapid diagnostic tests (RDTs) are unsuitable due to insufficient sensitivity and specificity. Recent PCR-based RDTs, however, are non-inferior to standard NAATs, and might be used at the point-of-care. Serology finds application in the diagnostic work-up of suspected chronic CT infection but is inappropriate to diagnose acute infections.
      PubDate: 2016-08-05
      DOI: 10.3390/microorganisms4030025
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 26: Biofilms from Klebsiella pneumoniae:
           Matrix Polysaccharide Structure and Interactions with Antimicrobial

    • Authors: Monica Benincasa, Cristina Lagatolla, Lucilla Dolzani, Annalisa Milan, Sabrina Pacor, Gianfranco Liut, Alessandro Tossi, Paola Cescutti, Roberto Rizzo
      First page: 26
      Abstract: Biofilm matrices of two Klebsiella pneumoniae clinical isolates, KpTs101 and KpTs113, were investigated for their polysaccharide composition and protective effects against antimicrobial peptides. Both strains were good biofilm producers, with KpTs113 forming flocs with very low adhesive properties to supports. Matrix exopolysaccharides were isolated and their monosaccharide composition and glycosidic linkage types were defined. KpTs101 polysaccharide is neutral and composed only of galactose, in both pyranose and furanose ring configurations. Conversely, KpTs113 polysaccharide is anionic due to glucuronic acid units, and also contains glucose and mannose residues. The susceptibility of the two strains to two bovine cathelicidin antimicrobial peptides, BMAP-27 and Bac7(1–35), was assessed using both planktonic cultures and biofilms. Biofilm matrices exerted a relevant protection against both antimicrobials, which act with quite different mechanisms. Similar protection was also detected when antimicrobial peptides were tested against planktonic bacteria in the presence of the polysaccharides extracted from KpTs101 and KpTs113 biofilms, suggesting sequestering adduct formation with antimicrobials. Circular dichroism experiments on BMAP-27 in the presence of increasing amounts of either polysaccharide confirmed their ability to interact with the peptide and induce an α-helical conformation.
      PubDate: 2016-08-10
      DOI: 10.3390/microorganisms4030026
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 27: Immunoregulatory Effects Triggered by
           Lactic Acid Bacteria Exopolysaccharides: New Insights into Molecular
           Interactions with Host Cells

    • Authors: Jonathan Laiño, Julio Villena, Paulraj Kanmani, Haruki Kitazawa
      First page: 27
      Abstract: Researchers have demonstrated that lactic acid bacteria (LAB) with immunomodulatory capabilities (immunobiotics) exert their beneficial effects through several molecules, including cell wall, peptidoglycan, and exopolysaccharides (EPS), that are able to interact with specific host cell receptors. EPS from LAB show a wide heterogeneity in its composition, meaning that biological properties depend on the strain and. therefore, only a part of the mechanism of action has been elucidated for these molecules. In this review, we summarize the current knowledge of the health-promoting actions of EPS from LAB with special focus on their immunoregulatory actions. In addition, we describe our studies using porcine intestinal epithelial cells (PIE cells) as a model to evaluate the molecular interactions of EPS from two immunobiotic LAB strains and the host cells. Our studies showed that EPS from immunobiotic LAB have anti-inflammatory capacities in PIE cells since they are able to reduce the production of inflammatory cytokines in cells challenged with the Toll-like receptor (TLR)-4-agonist lipopolysaccharide. The effects of EPS were dependent on TLR2, TLR4, and negative regulators of TLR signaling. We also reported that the radioprotective 105 (RP105)/MD1 complex, a member of the TLR family, is partially involved in the immunoregulatory effects of the EPS from LAB. Our work described, for the first time, that LAB and their EPS reduce inflammation in intestinal epithelial cells in a RP105/MD1-dependent manner. A continuing challenge for the future is to reveal more effector-receptor relationships in immunobiotic-host interactions that contribute to the beneficial effects of these bacteria on mucosal immune homeostasis. A detailed molecular understanding should lead to a more rational use of immunobiotics in general, and their EPS in particular, as efficient prevention and therapies for specific immune-related disorders in humans and animals.
      PubDate: 2016-08-15
      DOI: 10.3390/microorganisms4030027
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 28: Chlamydia-Like Organisms (CLOs) in
           Finnish Ixodes ricinus Ticks and Human Skin

    • Authors: Kati Hokynar, Jani Sormunen, Eero Vesterinen, Esa Partio, Thomas Lilley, Veera Timonen, Jaana Panelius, Annamari Ranki, Mirja Puolakkainen
      First page: 28
      Abstract: Ticks carry several human pathogenic microbes including Borreliae and Flavivirus causing tick-born encephalitis. Ticks can also carry DNA of Chlamydia-like organisms (CLOs). The purpose of this study was to investigate the occurrence of CLOs in ticks and skin biopsies taken from individuals with suspected tick bite. DNA from CLOs was detected by pan-Chlamydiales-PCR in 40% of adult ticks from southwestern Finland. The estimated minimal infection rate for nymphs and larvae (studied in pools) was 6% and 2%, respectively. For the first time, we show CLO DNA also in human skin as 68% of all skin biopsies studied contained CLO DNA as determined through pan-Chlamydiales-PCR. Sequence analyses based on the 16S rRNA gene fragment indicated that the sequences detected in ticks were heterogeneous, representing various CLO families; whereas the majority of the sequences from human skin remained “unclassified Chlamydiales” and might represent a new family-level lineage. CLO sequences detected in four skin biopsies were most closely related to “uncultured Chlamydial bacterium clones from Ixodes ricinus ticks” and two of them were very similar to CLO sequences from Finnish ticks. These results suggest that CLO DNA is present in human skin; ticks carry CLOs and could potentially transmit CLOs to humans.
      PubDate: 2016-08-18
      DOI: 10.3390/microorganisms4030028
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 29: Insights on the Horizontal Gene Transfer
           of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter

    • Authors: Gabriela Da Silva, Sara Domingues
      First page: 29
      Abstract: Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.
      PubDate: 2016-08-23
      DOI: 10.3390/microorganisms4030029
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 30: Coinfection of Chlamydiae and other
           Bacteria in Reactive Arthritis and Spondyloarthritis: Need for Future

    • Authors: Henning Zeidler, Alan Hudson
      First page: 30
      Abstract: Reactive (inflammatory) arthritis has been known for many years to follow genital infection with the intracellular bacterial pathogen Chlamydia trachomatis in some individuals. Recent studies from several groups have demonstrated that a related bacterium, the respiratory pathogen Chlamydia pneumoniae, can elicit a similar arthritis. Studies of these organisms, and of a set of gastrointestinal pathogens also associated with engendering inflammatory arthritis, have been relatively extensive. However, reports focusing on coinfections with these and/or other organisms, and the effects of such coinfections on the host immune and other systems, have been rare. In this article, we review the extant data regarding infections by multiple pathogens in the joint as they relate to engendering arthritis, and we suggest a number of research areas that must be given a high priority if we are to understand, and therefore to treat in an effective manner, such arthritides.
      PubDate: 2016-08-24
      DOI: 10.3390/microorganisms4030030
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 31: Correia Repeat Enclosed Elements and
           Non-Coding RNAs in the Neisseria Species

    • Authors: Sabrina Roberts, Russell Spencer-Smith, Mahwish Shah, Jean-Christophe Nebel, Richard Cook, Lori Snyder
      First page: 31
      Abstract: Neisseria gonorrhoeae is capable of causing gonorrhoea and more complex diseases in the human host. Neisseria meningitidis is a closely related pathogen that shares many of the same genomic features and virulence factors, but causes the life threatening diseases meningococcal meningitis and septicaemia. The importance of non-coding RNAs in gene regulation has become increasingly evident having been demonstrated to be involved in regulons responsible for iron acquisition, antigenic variation, and virulence. Neisseria spp. contain an IS-like element, the Correia Repeat Enclosed Element, which has been predicted to be mobile within the genomes or to have been in the past. This repeat, present in over 100 copies in the genome, has the ability to alter gene expression and regulation in several ways. We reveal here that Correia Repeat Enclosed Elements tend to be near non-coding RNAs in the Neisseria spp., especially N. gonorrhoeae. These results suggest that Correia Repeat Enclosed Elements may have disrupted ancestral regulatory networks not just through their influence on regulatory proteins but also for non-coding RNAs.
      PubDate: 2016-08-25
      DOI: 10.3390/microorganisms4030031
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 32: Phylogenetic Characterization of Marine
           Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial
           Pacific Ocean (ODP Site 1225)

    • Authors: Antje Lauer, Ketil Sørensen, Andreas Teske
      First page: 32
      Abstract: Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m water depth; 1.1 and 7.8 m sediment depth) was analyzed by PCR, cloning and sequencing, and by denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes. Three uncultured archaeal lineages with different depth distributions were found: Marine Group I (MG-I) within the Thaumarchaeota, its sister lineage Marine Benthic Group A (MBG-A), the phylum-level archaeal lineage Marine Benthic Group B (also known as Deep-Sea Archaeal Group or Lokiarchaeota), and the Deep-Sea Euryarchaeotal Group 3. The MG-I phylotypes included representatives of sediment clusters that are distinct from the pelagic members of this phylum. On the scale from fully oxidized, extremely organic carbon-depleted sediments (for example, those the South Pacific Gyre) to fully reduced, organic carbon-rich marine subsurface sediments (such as those of the Peru Margin), Ocean Drilling Program (ODP) Site 1225 falls into the non-extreme organic carbon-lean category, and harbors archaeal communities from both ends of the spectrum.
      PubDate: 2016-09-06
      DOI: 10.3390/microorganisms4030032
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 33: Achromobacter Species Isolated from
           Cystic Fibrosis Patients Reveal Distinctly Different Biofilm Morphotypes

    • Authors: Signe Nielsen, Niels Nørskov-Lauritsen, Thomas Bjarnsholt, Rikke Meyer
      First page: 33
      Abstract: Achromobacter species have attracted attention as emerging pathogens in cystic fibrosis. The clinical significance of Achromobacter infection is not yet fully elucidated; however, their intrinsic resistance to antimicrobials and ability to form biofilms renders them capable of establishing long-term chronic infections. Still, many aspects of Achromobacter biofilm formation remain uncharacterized. In this study, we characterized biofilm formation in clinical isolates of Achromobacter and investigated the effect of challenging the biofilm with antimicrobials and/or enzymes targeting the extracellular matrix. In vitro biofilm growth and subsequent visualization by confocal microscopy revealed distinctly different biofilm morphotypes: a surface-attached biofilm morphotype of small aggregates and an unattached biofilm morphotype of large suspended aggregates. Aggregates consistent with our in vitro findings were visualized in sputum samples from cystic fibrosis patients using an Achromobacter specific peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) probe, confirming the presence of Achromobacter biofilms in the CF lung. High antibiotic tolerance was associated with the biofilm phenotype, and biocidal antibiotic concentrations were up to 1000 fold higher than for planktonic cultures. Treatment with DNase or subtilisin partially dispersed the biofilm and reduced the tolerance to specific antimicrobials, paving the way for further research into using dispersal mechanisms to improve treatment strategies.
      PubDate: 2016-09-14
      DOI: 10.3390/microorganisms4030033
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 34: Adhesion Properties of Lactic Acid
           Bacteria on Intestinal Mucin

    • Authors: Keita Nishiyama, Makoto Sugiyama, Takao Mukai
      First page: 34
      Abstract: Lactic acid bacteria (LAB) are Gram-positive bacteria that are natural inhabitants of the gastrointestinal (GI) tracts of mammals, including humans. Since Mechnikov first proposed that yogurt could prevent intestinal putrefaction and aging, the beneficial effects of LAB have been widely demonstrated. The region between the duodenum and the terminal of the ileum is the primary region colonized by LAB, particularly the Lactobacillus species, and this region is covered by a mucus layer composed mainly of mucin-type glycoproteins. The mucus layer plays a role in protecting the intestinal epithelial cells against damage, but is also considered to be critical for the adhesion of Lactobacillus in the GI tract. Consequently, the adhesion exhibited by lactobacilli on mucin has attracted attention as one of the critical factors contributing to the persistent beneficial effects of Lactobacillus in a constantly changing intestinal environment. Thus, understanding the interactions between Lactobacillus and mucin is crucial for elucidating the survival strategies of LAB in the GI tract. This review highlights the properties of the interactions between Lactobacillus and mucin, while concomitantly considering the structure of the GI tract from a histochemical perspective.
      PubDate: 2016-09-20
      DOI: 10.3390/microorganisms4030034
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 35: Biofilm Forming Lactobacillus: New
           Challenges for the Development of Probiotics

    • Authors: María Salas-Jara, Alejandra Ilabaca, Marco Vega, Apolinaria García
      First page: 35
      Abstract: Probiotics are live bacteria, generally administered in food, conferring beneficial effects to the host because they help to prevent or treat diseases, the majority of which are gastrointestinal. Numerous investigations have verified the beneficial effect of probiotic strains in biofilm form, including increased resistance to temperature, gastric pH and mechanical forces to that of their planktonic counterparts. In addition, the development of new encapsulation technologies, which have exploited the properties of biofilms in the creation of double coated capsules, has given origin to fourth generation probiotics. Up to now, reviews have focused on the detrimental effects of biofilms associated with pathogenic bacteria. Therefore, this work aims to amalgamate information describing the biofilms of Lactobacillus strains which are used as probiotics, particularly L. rhamnosus, L. plantarum, L. reuteri, and L. fermentum. Additionally, we have reviewed the development of probiotics using technology inspired by biofilms.
      PubDate: 2016-09-20
      DOI: 10.3390/microorganisms4030035
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 36: Streptokinase Treatment Reverses
           Biofilm-Associated Antibiotic Resistance in Staphylococcus aureus

    • Authors: Nis Jørgensen, Natalia Zobek, Cindy Dreier, Jakob Haaber, Hanne Ingmer, Ole Larsen, Rikke Meyer
      First page: 36
      Abstract: Biofilms formed by Staphylococcus aureus is a serious complication to the use of medical implants. A central part of the pathogenesis relies on S. aureus’ ability to adhere to host extracellular matrix proteins, which adsorb to medical implants and stimulate biofilm formation. Being coagulase positive, S. aureus furthermore induces formation of fibrin fibers from fibrinogen in the blood. Consequently, we hypothesized that fibrin is a key component of the extracellular matrix of S. aureus biofilms under in vivo conditions, and that the recalcitrance of biofilm infections can be overcome by combining antibiotic treatment with a fibrinolytic drug. We quantified S. aureus USA300 biofilms grown on peg-lids in brain heart infusion (BHI) broth with 0%–50% human plasma. Young (2 h) and mature (24 h) biofilms were then treated with streptokinase to determine if this lead to dispersal. Then, the minimal biofilm eradication concentration (MBEC) of 24 h old biofilms was measured for vancomycin and daptomycin alone or in combination with 10 µg/mL rifampicin in the presence or absence of streptokinase in the antibiotic treatment step. Finally, biofilms were visualized by confocal laser scanning microscopy. Addition of human plasma stimulated biofilm formation in BHI in a dose-dependent manner, and biofilms could be partially dispersed by streptokinase. The biofilms could be eradicated with physiologically relevant concentrations of streptokinase in combination with rifampicin and vancomycin or daptomycin, which are commonly used antibiotics for treatment of S. aureus infections. Fibronolytic drugs have been used to treat thromboembolic events for decades, and our findings suggest that their use against biofilm infections has the potential to improve the efficacy of antibiotics in treatment of S. aureus biofilm infections.
      PubDate: 2016-09-20
      DOI: 10.3390/microorganisms4030036
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 37: Biotin Auxotrophy and Biotin Enhanced
           Germ Tube Formation in Candida albicans

    • Authors: Nur Ahmad Hussin, Ruvini Pathirana, Sahar Hasim, Swetha Tati, Jessica Scheib-Owens, Kenneth Nickerson
      First page: 37
      Abstract: Due to the increased number of immunocompromised patients, infections with the pathogen Candida albicans have significantly increased in recent years. C. albicans transition from yeast to germ tubes is one of the essential factors for virulence. In this study we noted that Lee’s medium, commonly used to induce filamentation, contained 500-fold more biotin than needed for growth and 40-fold more biotin than is typically added to growth media. Thus, we investigated the effects of excess biotin on growth rate and filamentation by C. albicans in different media. At 37 °C, excess biotin (4 µM) enhanced germ tube formation (GTF) ca. 10-fold in both Lee’s medium and a defined glucose-proline medium, and ca. 4-fold in 1% serum. Two biotin precursors, desthiobiotin and 7-keto-8-aminopelargonic acid (KAPA), also stimulated GTF. During these studies we also noted an inverse correlation between the number of times the inoculum had been washed and the concentration of serum needed to stimulate GTF. C. albicans cells that had been washed eight times achieved 80% GTF with only 0.1% sheep serum. The mechanism by which 1–4 µM biotin enhances GTF is still unknown except to note that equivalent levels of biotin are needed to create an internal supply of stored biotin and biotinylated histones. Biotin did not restore filamentation for any of the four known filamentation defective mutants tested. C. albicans is auxotrophic for biotin and this biotin auxotrophy was fulfilled by biotin, desthiobiotin, or KAPA. However, biotin auxotrophy is not temperature dependent or influenced by the presence of 5% CO2. Biotin starvation upregulated the biotin biosynthetic genes BIO2, BIO3, and BIO4 by 11-, 1500-, and 150-fold, respectively, and BIO2p is predicted to be mitochondrion-localized. Based on our findings, we suggest that biotin has two roles in the physiology of C. albicans, one as an enzymatic cofactor and another as a morphological regulator. Finally, we found no evidence supporting prior claims that C. albicans only forms hyphae at very low biotin (0.1 nM) growth conditions.
      PubDate: 2016-09-21
      DOI: 10.3390/microorganisms4030037
      Issue No: Vol. 4, No. 3 (2016)
  • Microorganisms, Vol. 4, Pages 18: Fed-Batch Production of Bacterial Ghosts
           Using Dielectric Spectroscopy for Dynamic Process Control

    • Authors: Andrea Meitz, Patrick Sagmeister, Werner Lubitz, Christoph Herwig, Timo Langemann
      First page: 18
      Abstract: The Bacterial Ghost (BG) platform technology evolved from a microbiological expression system incorporating the ϕX174 lysis gene E. E-lysis generates empty but structurally intact cell envelopes (BGs) from Gram-negative bacteria which have been suggested as candidate vaccines, immunotherapeutic agents or drug delivery vehicles. E-lysis is a highly dynamic and complex biological process that puts exceptional demands towards process understanding and control. The development of a both economic and robust fed-batch production process for BGs required a toolset capable of dealing with rapidly changing concentrations of viable biomass during the E-lysis phase. This challenge was addressed using a transfer function combining dielectric spectroscopy and soft-sensor based biomass estimation for monitoring the rapid decline of viable biomass during the E-lysis phase. The transfer function was implemented to a feed-controller, which followed the permittivity signal closely and was capable of maintaining a constant specific substrate uptake rate during lysis phase. With the described toolset, we were able to increase the yield of BG production processes by a factor of 8–10 when compared to currently used batch procedures reaching lysis efficiencies >98%. This provides elevated potentials for commercial application of the Bacterial Ghost platform technology.
      PubDate: 2016-03-24
      DOI: 10.3390/microorganisms4020018
      Issue No: Vol. 4, No. 2 (2016)
  • Microorganisms, Vol. 4, Pages 19: New Dimensions in Microbial
           Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role
           of Functional Microbial Groups in the Environment

    • Authors: Johannes Imhoff
      First page: 19
      Abstract: During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.
      PubDate: 2016-05-24
      DOI: 10.3390/microorganisms4020019
      Issue No: Vol. 4, No. 2 (2016)
  • Microorganisms, Vol. 4, Pages 20: Microbiome, Metabolome and Inflammatory
           Bowel Disease

    • Authors: Ishfaq Ahmed, Badal Roy, Salman Khan, Seth Septer, Shahid Umar
      First page: 20
      Abstract: Inflammatory Bowel Disease (IBD) is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD) or Ulcerative Colitis (UC), two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome) and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis.
      PubDate: 2016-06-15
      DOI: 10.3390/microorganisms4020020
      Issue No: Vol. 4, No. 2 (2016)
  • Microorganisms, Vol. 4, Pages 21: Establishment of a Quality Management
           System Based on ISO 9001 Standard in a Public Service Fungal Culture

    • Authors: Marta Simões, Nicolina Dias, Cledir Santos, Nelson Lima
      First page: 21
      Abstract: Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders.
      PubDate: 2016-06-22
      DOI: 10.3390/microorganisms4020021
      Issue No: Vol. 4, No. 2 (2016)
  • Microorganisms, Vol. 4, Pages 1: Microbial Biofilm Community Variation in
           Flowing Habitats: Potential Utility as Bioindicators of Postmortem
           Submersion Intervals

    • Authors: Jennifer Lang, Racheal Erb, Jennifer Pechal, John Wallace, Ryan McEwan, Mark Benbow
      First page: 1
      Abstract: Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context.
      PubDate: 2016-01-04
      DOI: 10.3390/microorganisms4010001
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 2: Influence of pH Regulation Mode in
           Glucose Fermentation on Product Selection and Process Stability

    • Authors: Zuhaida Mohd-Zaki, Juan Bastidas-Oyanedel, Yang Lu, Robert Hoelzle, Steven Pratt, Fran Slater, Damien Batstone
      First page: 2
      Abstract: Mixed culture anaerobic fermentation generates a wide range of products from simple sugars, and is potentially an effective process for producing renewable commodity chemicals. However it is difficult to predict product spectrum, and to control the process. One of the key control handles is pH, but the response is commonly dependent on culture history. In this work, we assess the impact of pH regulation mode on the product spectrum. Two regulation modes were applied: in the first, pH was adjusted from 4.5 to 8.5 in progressive steps of 0.5 and in the second, covered the same pH range, but the pH was reset to 5.5 before each change. Acetate, butyrate, and ethanol were produced throughout all pH ranges, but there was a shift from butyrate at pH < 6.5 to ethanol at pH > 6.5, as well as a strong and consistent shift from hydrogen to formate as pH increased. Microbial analysis indicated that progressive pH resulted in dominance by Klebsiella, while reset pH resulted in a bias towards Clostridium spp., particularly at low pH, with higher variance in community between different pH levels. Reset pH was more responsive to changes in pH, and analysis of Gibbs free energy indicated that the reset pH experiments operated closer to thermodynamic equilibrium, particularly with respect to the formate/hydrogen balance. This may indicate that periodically resetting pH conforms better to thermodynamic expectations.
      PubDate: 2016-01-04
      DOI: 10.3390/microorganisms4010002
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 3: In Silico Analysis of a Novel Plasmid
           from the Coral Pathogen Vibrio coralliilyticus Reveals Two Potential
           “Ecological Islands”

    • Authors: Jenny Wachter, Stuart Hill
      First page: 3
      Abstract: As virulence often correlates with the presence of plasmid replicons in several Vibrio spp., this study investigated whether non-chromosomal DNA could be found in the coral pathogen, Vibrio coralliilyticus BAA-450. A circular plasmid, 26,631 bp in size, was identified. DNA sequence analysis indicated that the plasmid contained 30 open reading frames, six tRNA genes, 12 inverted repeats, three direct repeats and presented no continuous sequence identity to other replicons within the database. Consequently, these findings indicate that this is a novel, previously unidentified, plasmid. Two putative “ecological islands” were also identified and are predicted to encode for various factors that would facilitate growth and survival under different ecological conditions. In addition, two open reading frames may encode proteins that contribute to the pathogenicity of the organism. Functional cooperativity is also indicated between several plasmid- and chromosomally-encoded proteins, which, in a single instance, would allow a fully functioning nutrient uptake system to be established.
      PubDate: 2016-01-04
      DOI: 10.3390/microorganisms4010003
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 4: Phage Inactivation of Listeria
           monocytogenes on San Daniele Dry-Cured Ham and Elimination of Biofilms
           from Equipment and Working Environments

    • Authors: Lucilla Iacumin, Marisa Manzano, Giuseppe Comi
      First page: 4
      Abstract: The anti-listerial activity of generally recognized as safe (GRAS) bacteriophage Listex P100 (phage P100) was demonstrated in broths and on the surface of slices of dry-cured ham against 5 strains or serotypes (i.e., Scott A, 1/2a, 1/2b, and 4b) of Listeria monocytogenes. In a broth model system, phage P100 at a concentration equal to or greater than 7 log PFU/mL completely inhibited 2 log CFU/cm2 or 3 log CFU/cm2 of L. monocytogenes growth at 30 °C. The temperature (4, 10, 20 °C) seemed to influence P100 activity; the best results were obtained at 4 °C. On dry-cured ham slices, a P100 concentration ranging from 5 to 8 log PFU/cm2 was required to obtain a significant reduction in L. monocytogenes. At 4, 10, and 20 °C, an inoculum of 8 log PFU/cm2 was required to completely eliminate 2 log L. monocytogenes/cm2 and to reach the absence in 25 g product according to USA food law. Conversely, it was impossible to completely eradicate L. monocytogenes with an inoculum of approximately of 3.0 and 4.0 log CFU/cm2 and with a P100 inoculum ranging from 1 to 7 log PFU/cm2. P100 remained stable on dry-cured ham slices over a 14-day storage period, with only a marginal loss of 0.2 log PFU/cm2 from an initial phage treatment of approximately 8 log PFU/cm2. Moreover, phage P100 eliminated free L. monocytogenes cells and biofilms on the machinery surfaces used for dry-cured ham production. These findings demonstrate that the GRAS bacteriophage Listex P100 at level of 8 log PFU/cm2 is listericidal and useful for reducing the L. monocytogenes concentration or eradicating the bacteria from dry-cured ham.
      PubDate: 2016-01-05
      DOI: 10.3390/microorganisms4010004
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 5: Metagenomic Analyses Reveal That Energy
           Transfer Gene Abundances Can Predict the Syntrophic Potential of
           Environmental Microbial Communities

    • Authors: Lisa Oberding, Lisa Gieg
      First page: 5
      Abstract: Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.
      PubDate: 2016-01-05
      DOI: 10.3390/microorganisms4010005
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 6: Molecular Ecology of Hypersaline
           Microbial Mats: Current Insights and New Directions

    • Authors: Hon Wong, Aria Ahmed-Cox, Brendan Burns
      First page: 6
      Abstract: Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.
      PubDate: 2016-01-05
      DOI: 10.3390/microorganisms4010006
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 7: Low Substrate Loading Limits
           Methanogenesis and Leads to High Coulombic Efficiency in
           Bioelectrochemical Systems

    • Authors: Tom Sleutels, Sam Molenaar, Annemiek Heijne, Cees Buisman
      First page: 7
      Abstract: A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future.
      PubDate: 2016-01-05
      DOI: 10.3390/microorganisms4010007
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 8: Extremophiles in an Antarctic Marine

    • Authors: Iain Dickinson, William Goodall-Copestake, Michael Thorne, Thomas Schlitt, Maria Ávila-Jiménez, David Pearce
      First page: 8
      Abstract: Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. In addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. Here, we focus on the extremophile community in the boundary region located between the Polar Front and the Southern Antarctic Circumpolar Current in the Southern Ocean, to explore the potential of metagenomic approaches as a tool for bioprospecting in the search for novel functional activity based on targeted sampling efforts. We assessed the microbial composition and diversity from a region north of the current limit for winter sea ice, north of the Southern Antarctic Circumpolar Front (SACCF) but south of the Polar Front. Although, most of the more frequently encountered sequences  were derived from common marine microorganisms, within these dominant groups, we found a proportion of genes related to secondary metabolism of potential interest in bioprospecting. Extremophiles were rare by comparison but belonged to a range of genera. Hence, they represented interesting targets from which to identify rare or novel functions. Ultimately, future shifts in environmental conditions favoring more cosmopolitan groups could have an unpredictable effect on microbial diversity and function in the Southern Ocean, perhaps excluding the rarer extremophiles.
      PubDate: 2016-01-11
      DOI: 10.3390/microorganisms4010008
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 9: Acknowledgement to Reviewers of
           Microorganisms in 2015

    • Authors: Microorganisms Editorial Office
      First page: 9
      Abstract: The editors of Microorganisms would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...]
      PubDate: 2016-01-25
      DOI: 10.3390/microorganisms4010009
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 10: Aspergillus oryzae–Saccharomyces
           cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex

    • Authors: Justin Jahnke, Thomas Hoyt, Hannah LeFors, James Sumner, David Mackie
      First page: 10
      Abstract: Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This “bio-hybrid FC” continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol—water mixtures, using the same FC. The A. oryzae–S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing.
      PubDate: 2016-02-04
      DOI: 10.3390/microorganisms4010010
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 11: The Opportunity for High-Performance
           Biomaterials from Methane

    • Authors: Peter Strong, Bronwyn Laycock, Syarifah Mahamud, Paul Jensen, Paul Lant, Gene Tyson, Steven Pratt
      First page: 11
      Abstract: Polyhydroxyalkanoate (PHA) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. Their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. Further, they are the only commodity polymer that can be synthesised intracellularly, ensuring stereoregularity and high molecular weight. However, despite offering enormous potential for many years, they are still not making a significant impact. This is broadly because commercial uptake has been limited by variable performance (inconsistent polymer properties) and high production costs of the raw polymer. Additionally, the main type of PHA produced naturally is poly-3-hydroxybutyrate (PHB), which has limited scope due to its brittle nature and low thermal stability, as well as its tendency to embrittle over time. Production cost is strongly impacted by the type of the feedstock used. In this article we consider: the production of PHAs from methanotrophs using methane as a cost-effective substrate; the use of mixed cultures, as opposed to pure strains; and strategies to generate a poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer (PHBV), which has more desirable qualities such as toughness and elasticity.
      PubDate: 2016-02-03
      DOI: 10.3390/microorganisms4010011
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 12: Staphylococcus aureus in Animals and
           Food: Methicillin Resistance, Prevalence and Population Structure. A
           Review in the African Continent

    • Authors: Carmen Lozano, Haythem Gharsa, Karim Ben Slama, Myriam Zarazaga, Carmen Torres
      First page: 12
      Abstract: The interest about Staphylococcus aureus (S. aureus) and methicillin resistant S. aureus (MRSA) in livestock, and domestic and wild animals has significantly increased. The spread of different clonal complexes related to livestock animals, mainly CC398, and the recent description of the new mecC gene, make it necessary to know more about the epidemiology and population structure of this microorganism all over the world. Nowadays, there are several descriptions about the presence of S. aureus and/or MRSA in different animal species (dogs, sheep, donkeys, bats, pigs, and monkeys), and in food of animal origin in African countries. In this continent, there is a high diversity of ethnicities, cultures or religions, as well as a high number of wild animal species and close contact between humans and animals, which can have a relevant impact in the epidemiology of this microorganism. This review shows that some clonal lineages associated with humans (CC1, CC15, CC72, CC80, CC101, and CC152) and animals (CC398, CC130 and CC133) are present in this continent in animal isolates, although the mecC gene has not been detected yet. However, available studies are limited to a few countries, very often with incomplete information, and many more studies are necessary to cover a larger number of African countries.
      PubDate: 2016-02-04
      DOI: 10.3390/microorganisms4010012
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 13: Carbapenem Resistance in Gram-Negative
           Bacteria: The Not-So-Little Problem in the Little Red Dot

    • Authors: Jocelyn Teo, Yiying Cai, Tze-Peng Lim, Thuan Tan, Andrea Kwa
      First page: 13
      Abstract: Singapore is an international travel and medical hub and faces a genuine threat for import and dissemination of bacteria with broad-spectrum resistance. In this review, we described the current landscape and management of carbapenem resistance in Gram-negative bacteria (GNB) in Singapore. Notably, the number of carbapenem-resistant Enterobacteriaceae has exponentially increased in the past two years. Resistance is largely mediated by a variety of mechanisms. Polymyxin resistance has also emerged. Interestingly, two Escherichia coli isolates with plasmid-mediated mcr-1 genes have been detected. Evidently, surveillance and infection control becomes critical in the local setting where resistance is commonly related to plasmid-mediated mechanisms, such as carbapenemases. Combination antibiotic therapy has been proposed as a last-resort strategy in the treatment of extensively drug-resistant (XDR) GNB infections, and is widely adopted in Singapore. The diversity of carbapenemases encountered, however, presents complexities in both carbapenemase detection and the selection of optimal antibiotic combinations. One unique strategy introduced in Singapore is a prospective in vitro combination testing service, which aids physicians in the selection of individualized combinations. The outcome of this treatment strategy has been promising. Unlike countries with a predominant carbapenemase type, Singapore has to adopt management strategies which accounts for diversity in resistance mechanisms.
      PubDate: 2016-02-16
      DOI: 10.3390/microorganisms4010013
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 14: Bacterial Multidrug Efflux Pumps: Much
           More Than Antibiotic Resistance Determinants

    • Authors: Paula Blanco, Sara Hernando-Amado, Jose Reales-Calderon, Fernando Corona, Felipe Lira, Manuel Alcalde-Rico, Alejandra Bernardini, Maria Sanchez, Jose Martinez
      First page: 14
      Abstract: Bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. With few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. In addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. Altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibiotics for human and animal therapy. In this regard, it is worth mentioning that efflux pumps can extrude a wide range of substrates that include, besides antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals or bacterial metabolites, among others. In the current review, we present information on the different functions that multidrug efflux pumps may have for the bacterial behaviour in different habitats as well as on their regulation by specific signals. Since, in addition to their function in non-clinical ecosystems, multidrug efflux pumps contribute to intrinsic, acquired, and phenotypic resistance of bacterial pathogens, the review also presents information on the search for inhibitors of multidrug efflux pumps, which are currently under development, in the aim of increasing the susceptibility of bacterial pathogens to antibiotics.
      PubDate: 2016-02-16
      DOI: 10.3390/microorganisms4010014
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 15: Metabolic Interaction of Helicobacter
           pylori Infection and Gut Microbiota

    • Authors: Yao-Jong Yang, Bor-Shyang Sheu
      First page: 15
      Abstract: As a barrier, gut commensal microbiota can protect against potential pathogenic microbes in the gastrointestinal tract. Crosstalk between gut microbes and immune cells promotes human intestinal homeostasis. Dysbiosis of gut microbiota has been implicated in the development of many human metabolic disorders like obesity, hepatic steatohepatitis, and insulin resistance in type 2 diabetes (T2D). Certain microbes, such as butyrate-producing bacteria, are lower in T2D patients. The transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome, but the exact pathogenesis remains unclear. H. pylori in the human stomach cause chronic gastritis, peptic ulcers, and gastric cancers. H. pylori infection also induces insulin resistance and has been defined as a predisposing factor to T2D development. Gastric and fecal microbiota may have been changed in H. pylori-infected persons and mice to promote gastric inflammation and specific diseases. However, the interaction of H. pylori and gut microbiota in regulating host metabolism also remains unknown. Further studies aim to identify the H. pylori-microbiota-host metabolism axis and to test if H. pylori eradication or modification of gut microbiota can improve the control of human metabolic disorders.
      PubDate: 2016-02-16
      DOI: 10.3390/microorganisms4010015
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 16: Extensive Intestinal Resection Triggers
           Behavioral Adaptation, Intestinal Remodeling and Microbiota Transition in
           Short Bowel Syndrome

    • Authors: Camille Mayeur, Laura Gillard, Johanne Le Beyec, André Bado, Francisca Joly, Muriel Thomas
      First page: 16
      Abstract: Extensive resection of small bowel often leads to short bowel syndrome (SBS). SBS patients develop clinical mal-absorption and dehydration relative to the reduction of absorptive area, acceleration of gastrointestinal transit time and modifications of the gastrointestinal intra-luminal environment. As a consequence of severe mal-absorption, patients require parenteral nutrition (PN). In adults, the overall adaptation following intestinal resection includes spontaneous and complex compensatory processes such as hyperphagia, mucosal remodeling of the remaining part of the intestine and major modifications of the microbiota. SBS patients, with colon in continuity, harbor a specific fecal microbiota that we called “lactobiota” because it is enriched in the Lactobacillus/Leuconostoc group and depleted in anaerobic micro-organisms (especially Clostridium and Bacteroides). In some patients, the lactobiota-driven fermentative activities lead to an accumulation of fecal d/l-lactates and an increased risk of d-encephalopathy. Better knowledge of clinical parameters and lactobiota characteristics has made it possible to stratify patients and define group at risk for d-encephalopathy crises.
      PubDate: 2016-03-08
      DOI: 10.3390/microorganisms4010016
      Issue No: Vol. 4, No. 1 (2016)
  • Microorganisms, Vol. 4, Pages 17: Process Recovery after CaO Addition Due
           to Granule Formation in a CSTR Co-Digester—A Tool to Influence the
           Composition of the Microbial Community and Stabilize the Process?

    • Authors: Marietta Liebrich, Anne Kleyböcker, Monika Kasina, Rona Miethling-Graff, Andrea Kassahun, Hilke Würdemann
      First page: 17
      Abstract: The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil.
      PubDate: 2016-03-17
      DOI: 10.3390/microorganisms4010017
      Issue No: Vol. 4, No. 1 (2016)
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