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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  [140 journals]
  • 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

    • 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. 3, Pages 588-611: Bioprotective Role of Yeasts

    • Authors: Serena Muccilli, Cristina Restuccia
      Pages: 588 - 611
      Abstract: The yeasts constitute a large group of microorganisms characterized by the ability to grow and survive in different and stressful conditions and then to colonize a wide range of environmental and human ecosystems. The competitive traits against other microorganisms have attracted increasing attention from scientists, who proposed their successful application as bioprotective agents in the agricultural, food and medical sectors. These antagonistic activities rely on the competition for nutrients, production and tolerance of high concentrations of ethanol, as well as the synthesis of a large class of antimicrobial compounds, known as killer toxins, which showed clearly a large spectrum of activity against food spoilage microorganisms, but also against plant, animal and human pathogens. This review describes the antimicrobial mechanisms involved in the antagonistic activity, their applications in the processed and unprocessed food sectors, as well as the future perspectives in the development of new bio-drugs, which may overcome the limitations connected to conventional antimicrobial and drug resistance.
      PubDate: 2015-10-10
      DOI: 10.3390/microorganisms3040588
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 612-624: Fungal Biodiversity in the Alpine
           Tarfala Valley

    • Pages: 612 - 624
      Abstract: Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.
      PubDate: 2015-10-10
      DOI: 10.3390/microorganisms3040612
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 625-640: Alicyclobacillus spp.: New Insights
           on Ecology and Preserving Food Quality through New Approaches

    • Authors: Emanuela Ciuffreda, Antonio Bevilacqua, Milena Sinigaglia, Maria Corbo
      Pages: 625 - 640
      Abstract: Alicyclobacillus spp. includes spore-forming and thermo-acidophilic microorganisms, usually recovered from soil, acidic drinks, orchards and equipment from juice producers. The description of the genus is generally based on the presence of ω-fatty acids in the membrane, although some newly described species do not possess them. The genus includes different species and sub-species, but A. acidoterrestris is generally regarded as the most important spoiler for acidic drinks and juices. The main goal of this review is a focus on the ecology of the genus, mainly on the species A. acidoterrestris, with a special emphasis on the different phenotypic properties and genetic traits, along with the correlation among them and with the primary source of isolation. Finally, the last section of the review reports on some alternative approaches to heat treatments (natural compounds and other chemical treatments) to control and/or reduce the contamination of food by Alicyclobacillus.
      PubDate: 2015-10-10
      DOI: 10.3390/microorganisms3040625
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 641-666: The Gut Microbiota as a Therapeutic
           Target in IBD and Metabolic Disease: A Role for the Bile Acid Receptors
           FXR and TGR5

    • Authors: Annemarie Baars, Annemarie Oosting, Jan Knol, Johan Garssen, Jeroen van Bergenhenegouwen
      Pages: 641 - 666
      Abstract: The gut microbiota plays a crucial role in regulating many physiological systems of the host, including the metabolic and immune system. Disturbances in microbiota composition are increasingly correlated with disease; however, the underlying mechanisms are not well understood. Recent evidence suggests that changes in microbiota composition directly affect the metabolism of bile salts. Next to their role in digestion of dietary fats, bile salts function as signaling molecules for bile salt receptors such as Farnesoid X receptor (FXR) and G protein-coupled bile acid receptor (TGR5). Complementary to their role in metabolism, FXR and TGR5 are shown to play a role in intestinal homeostasis and immune regulation. This review presents an overview of evidence showing that changes in bile salt pool and composition due to changes in gut microbial composition contribute to the pathogenesis of inflammatory bowel disease and metabolic disease, possibly through altered activation of TGR5 and FXR. We further discuss how dietary interventions, such as pro- and synbiotics, may be used to treat metabolic disease and inflammatory bowel disease (IBD) through normalization of bile acid dysregulation directly or indirectly through normalization of the intestinal microbiota.
      PubDate: 2015-10-10
      DOI: 10.3390/microorganisms3040641
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 667-694: Novel and Unexpected Microbial
           Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by
           Culture-Independent Approaches

    • Pages: 667 - 694
      Abstract: Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential novelty in terms of both phylogenetic/taxonomic and functional diversity.
      PubDate: 2015-10-13
      DOI: 10.3390/microorganisms3040667
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 695-706: How to Show the Real Microbial
           Biodiversity' A Comparison of Seven DNA Extraction Methods for
           Bacterial Population Analyses in Matrices Containing Highly Charged
           Natural Nanoparticles

    • Authors: Rene Kaden, Peter Krolla-Sidenstein
      Pages: 695 - 706
      Abstract: A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay.
      PubDate: 2015-10-20
      DOI: 10.3390/microorganisms3040695
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 707-724: Sulfur Oxygenase Reductase (Sor) in
           the Moderately Thermoacidophilic Leaching Bacteria: Studies in
           Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus

    • Authors: Claudia Janosch, Francisco Remonsellez, Wolfgang Sand, Mario Vera
      Pages: 707 - 724
      Abstract: The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293T. The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the “thermophilic” nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293T was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant.
      PubDate: 2015-10-21
      DOI: 10.3390/microorganisms3040707
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 725-745: Dynamic In Vitro Models of the
           Human Gastrointestinal Tract as Relevant Tools to Assess the Survival of
           Probiotic Strains and Their Interactions with Gut Microbiota

    • Pages: 725 - 745
      Abstract: The beneficial effects of probiotics are conditioned by their survival during passage through the human gastrointestinal tract and their ability to favorably influence gut microbiota. The main objective of this study was to use dynamic in vitro models of the human digestive tract to investigate the effect of fasted or fed state on the survival kinetics of the new probiotic Saccharomyces cerevisiae strain CNCM I-3856 and to assess its influence on intestinal microbiota composition and activity. The probiotic yeast showed a high survival rate in the upper gastrointestinal tract whatever the route of admistration, i.e., within a glass of water or a Western-type meal. S. cerevisiae CNCM I-3856 was more sensitive to colonic conditions, as the strain was not able to colonize within the bioreactor despite a twice daily administration. The main bacterial populations of the gut microbiota, as well as the production of short chain fatty acids were not influenced by the probiotic treatment. However, the effect of the probiotic on the gut microbiota was found to be individual dependent. This study shows that dynamic in vitro models can be advantageously used to provide useful insight into the behavior of probiotic strains in the human digestive environment.
      PubDate: 2015-10-23
      DOI: 10.3390/microorganisms3040725
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 746-758: Carbon-Starvation Induces
           Cross-Resistance to Thermal, Acid, and Oxidative Stress in Serratia

    • Pages: 746 - 758
      Abstract: The broad host-range pathogen Serratia marcescens survives in diverse host and non-host environments, often enduring conditions in which the concentration of essential nutrients is growth-limiting. In such environments, carbon and energy source starvation (carbon-starvation) is one of the most common forms of stress encountered by S. marcescens. Related members of the family Enterobacteriaceae are known to undergo substantial changes in gene expression and physiology in response to the specific stress of carbon-starvation, enabling non-spore-forming cells to survive periods of prolonged starvation and exposure to other forms of stress (i.e., starvation-induced cross-resistance). To determine if carbon-starvation also results in elevated levels of cross-resistance in S. marcescens, both log-phase and carbon-starved cultures, depleted of glucose before the onset of high cell-density stationary-phase, were grown in minimal media at either 30 °C or 37 °C and were then challenged for resistance to high temperature (50 °C), low pH (pH 2.8), and oxidative stress (15 mM H2O2). In general, carbon-starved cells exhibited a higher level of resistance to thermal stress, acid stress, and oxidative stress compared to log-phase cells. The extent of carbon-starvation-induced cross-resistance was dependent on incubation temperature and on the particular strain of S. marcescens. In addition, strain- and temperature-dependent variations in long-term starvation survival were also observed. The enhanced stress-resistance of starved S. marcescens cells could be an important factor in their survival and persistence in many non-host environments and within certain host microenvironments where the availability of carbon sources is suboptimal for growth.
      PubDate: 2015-10-26
      DOI: 10.3390/microorganisms3040746
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 759-791: Gut Microbiota and Host Reaction in
           Liver Diseases

    • Authors: Hiroshi Fukui
      Pages: 759 - 791
      Abstract: Although alcohol feeding produces evident intestinal microbial changes in animals, only some alcoholics show evident intestinal dysbiosis, a decrease in Bacteroidetes and an increase in Proteobacteria. Gut dysbiosis is related to intestinal hyperpermeability and endotoxemia in alcoholic patients. Alcoholics further exhibit reduced numbers of the beneficial Lactobacillus and Bifidobacterium. Large amounts of endotoxins translocated from the gut strongly activate Toll-like receptor 4 in the liver and play an important role in the progression of alcoholic liver disease (ALD), especially in severe alcoholic liver injury. Gut microbiota and bacterial endotoxins are further involved in some of the mechanisms of nonalcoholic fatty liver disease (NAFLD) and its progression to nonalcoholic steatohepatitis (NASH). There is experimental evidence that a high-fat diet causes characteristic dysbiosis of NAFLD, with a decrease in Bacteroidetes and increases in Firmicutes and Proteobacteria, and gut dysbiosis itself can induce hepatic steatosis and metabolic syndrome. Clinical data support the above dysbiosis, but the details are variable. Intestinal dysbiosis and endotoxemia greatly affect the cirrhotics in relation to major complications and prognosis. Metagenomic approaches to dysbiosis may be promising for the analysis of deranged host metabolism in NASH and cirrhosis. Management of dysbiosis may become a cornerstone for the future treatment of liver diseases.
      PubDate: 2015-10-28
      DOI: 10.3390/microorganisms3040759
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 792-808: Thermus thermophilus as a Source of
           Thermostable Lipolytic Enzymes

    • Pages: 792 - 808
      Abstract: Lipolytic enzymes, esterases (EC and lipases (EC, catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. At present, they represent about 20% of commercialized enzymes for industrial use. Lipolytic enzymes from thermophilic microorganisms are preferred for industrial use to their mesophilic counterparts, mainly due to higher thermostability and resistance to several denaturing agents. However, the production at an industrial scale from the native organisms is technically complicated and expensive. The thermophilic bacterium Thermus thermophilus (T. thermophilus) has high levels of lipolytic activity, and its whole genome has been sequenced. One esterase from the T. thermophilus strain HB27 has been widely characterized, both in its native form and in recombinant forms, being expressed in mesophilic microorganisms. Other putative lipases/esterases annotated in the T. thermophilus genome have been explored and will also be reviewed in this paper.
      PubDate: 2015-11-04
      DOI: 10.3390/microorganisms3040792
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 809-825: Movement of Salmonella serovar
           Typhimurium and E. coli O157:H7 to Ripe Tomato Fruit Following Various
           Routes of Contamination

    • Authors: Amanda Deering, Dan Jack, Robert Pruitt, Lisa Mauer
      Pages: 809 - 825
      Abstract: Salmonella serovars have been associated with the majority of foodborne illness outbreaks involving tomatoes, and E. coli O157:H7 has caused outbreaks involving other fresh produce. Contamination by both pathogens has been thought to originate from all points of the growing and distribution process. To determine if Salmonella serovar Typhimurium and E. coli O157:H7 could move to the mature tomato fruit of different tomato cultivars following contamination, three different contamination scenarios (seed, leaf, and soil) were examined. Following contamination, each cultivar appeared to respond differently to the presence of the pathogens, with most producing few fruit and having overall poor health. The Micro-Tom cultivar, however, produced relatively more fruit and E. coli O157:H7 was detected in the ripe tomatoes for both the seed- and leaf- contaminated plants, but not following soil contamination. The Roma cultivar produced fewer fruit, but was the only cultivar in which E. coli O157:H7 was detected via all three routes of contamination. Only two of the five cultivars produced tomatoes following seed-, leaf-, and soil- contamination with Salmonella Typhimurium, and no Salmonella was found in any of the tomatoes. Together these results show that different tomato cultivars respond differently to the presence of a human pathogen, and for E. coli O157:H7, in particular, tomato plants that are either contaminated as seeds or have a natural opening or a wound, that allows bacteria to enter the leaves can result in plants that have the potential to produce tomatoes that harbor internalized pathogenic bacteria.
      PubDate: 2015-11-05
      DOI: 10.3390/microorganisms3040809
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 826-838: The Effect of Tellurite on Highly
           Resistant Freshwater Aerobic Anoxygenic Phototrophs and Their Strategies
           for Reduction

    • Authors: Chris Maltman, Vladimir Yurkov
      Pages: 826 - 838
      Abstract: Six fresh water aerobic anoxygenic phototrophs (Erythromicrobium ezovicum, strain E1; Erythromicrobium hydrolyticum, E4(1); Erythromicrobium ramosum, E5; Erythromonas ursincola, KR99; Sandaracinobacter sibiricus, RB 16-17; and Roseococcus thiosulfatophilus, RB3) possessing high level resistance to TeO32− and the ability to reduce it to elemental Te were studied to understand their interaction with this highly toxic oxyanion. Tested organic carbon sources, pH, and level of aeration all had an impact on reduction. Physiological and metabolic responses of cells to tellurite varied among strains. In its presence, versus absence, cellular biomass either increased (KR99, 66.6% and E5, 21.2%) or decreased (RB3, 66.1%, E1, 57.8%, RB 16-17, 41.5%, and E4(1), 21.3%). The increase suggests a possible benefit from tellurite. Cellular ATP production was similarly affected, resulting in an increase (KR99, 15.2% and E5, 38.9%) or decrease (E4(1), 31.9%; RB 16-17, 48.8%; RB3, 55.9%; E1, 35.9%). Two distinct strategies to tellurite reduction were identified. The first, found in E4(1), requires de novo protein preparations as well as an undisturbed whole cell. The second strategy, in which reduction depended on a membrane associated constitutive reductase, was used by the remaining strains.
      PubDate: 2015-11-06
      DOI: 10.3390/microorganisms3040826
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 839-850: The Potential of the Yeast
           Debaryomyces hansenii H525 to Degrade Biogenic Amines in Food

    • Pages: 839 - 850
      Abstract: Twenty-six yeasts from different genera were investigated for their ability to metabolize biogenic amines. About half of the yeast strains produced one or more different biogenic amines, but some strains of Debaryomyces hansenii and Yarrowia lipolytica were also able to degrade such compounds. The most effective strain D. hanseniii H525 metabolized a broad spectrum of biogenic amines by growing and resting cells. Degradation of biogenic amines by this yeast isolate could be attributed to a peroxisomal amine oxidase activity. Strain H525 may be useful as a starter culture to reduce biogenic amines in fermented food.
      PubDate: 2015-11-06
      DOI: 10.3390/microorganisms3040839
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 851-865: Bioactivities of Ketones Terpenes:
           Antifungal Effect on F. verticillioides and Repellents to Control Insect
           Fungal Vector, S. zeamais

    • Authors: Romina Pizzolitto, Jimena Herrera, Yesica Zaio, Jose Dambolena, Maria Zunino, Mauro Gallucci, Julio Zygadlo
      Pages: 851 - 865
      Abstract: Maize is one the most important staple foods in the world. However, numerous pests, such as fungal pathogens, e.g., Fusarium verticillioides, and insects, such as Sitophlilus zeamais, attack maize grains during storage. Many F. verticillioides strains produce fumonisins, one of the most important mycotoxin that causes toxic effects on human and animal health. This situation is aggravated by the insect fungal vector, Sitophlilus zeamais, which contributes to the dispersal of fungal spores, and through feeding damage, provide entry points for fungal infections. The aim of this study was to evaluate in vitro bioassays, the antifungal activity on F. verticillioides M3125 and repellent effects against S. zeamais of ketone terpenes. In addition, we performed Quantitative structure–activity relationship (Q-SAR) studies between physico-chemical properties of ketone terpenes and the antifungal effect. Thymoquinone was the most active compound against F. verticillioides (Minimum Inhibitory Concentration, MIC: 0.87) affecting the lag phase and the growth rate showing a total inhibition of growth at concentration higher than 2 mM (p < 0.05). The Q-SAR model revealed that the antifungal activity of ketone compounds is related to the electronic descriptor, Pi energy. Thymoquinone showed a strong repellent effect (−77.8 ± 8.5, p < 0.001) against S. zeamais. These findings make an important contribution to the search for new compounds to control two stored pests of maize.
      PubDate: 2015-11-12
      DOI: 10.3390/microorganisms3040851
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 866-889: Hydrogen Sulfide in Physiology and
           Diseases of the Digestive Tract

    • Authors: Sudha Singh, Henry Lin
      Pages: 866 - 889
      Abstract: Hydrogen sulfide (H2S) is a Janus-faced molecule. On one hand, several toxic functions have been attributed to H2S and exposure to high levels of this gas is extremely hazardous to health. On the other hand, H2S delivery based clinical therapies are being developed to combat inflammation, visceral pain, oxidative stress related tissue injury, thrombosis and cancer. Since its discovery, H2S has been found to have pleiotropic effects on physiology and health. H2S is a gasotransmitter that exerts its effect on different systems, such as gastrointestinal, neuronal, cardiovascular, respiratory, renal, and hepatic systems. In the gastrointestinal tract, in addition to H2S production by mammalian cystathionine-β-synthase (CBS), cystathionine-γ-lyase (CSE), H2S is also generated by the metabolic activity of resident gut microbes, mainly by colonic Sulfate-Reducing Bacteria (SRB) via a dissimilatory sulfate reduction (DSR) pathway. In the gut, H2S regulates functions such as inflammation, ischemia/ reperfusion injury and motility. H2S derived from gut microbes has been found to be associated with gastrointestinal disorders such as ulcerative colitis, Crohn’s disease and irritable bowel syndrome. This underscores the importance of gut microbes and their production of H2S on host physiology and pathophysiology.
      PubDate: 2015-11-12
      DOI: 10.3390/microorganisms3040866
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 890-902: The Microbial Resource Research
           Infrastructure MIRRI: Strength through Coordination

    • Pages: 890 - 902
      Abstract: Microbial resources have been recognized as essential raw materials for the advancement of health and later for biotechnology, agriculture, food technology and for research in the life sciences, as their enormous abundance and diversity offer an unparalleled source of unexplored solutions. Microbial domain biological resource centres (mBRC) provide live cultures and associated data to foster and support the development of basic and applied science in countries worldwide and especially in Europe, where the density of highly advanced mBRCs is high. The not-for-profit and distributed project MIRRI (Microbial Resource Research Infrastructure) aims to coordinate access to hitherto individually managed resources by developing a pan-European platform which takes the interoperability and accessibility of resources and data to a higher level. Providing a wealth of additional information and linking to datasets such as literature, environmental data, sequences and chemistry will enable researchers to select organisms suitable for their research and enable innovative solutions to be developed. The current independent policies and managed processes will be adapted by partner mBRCs to harmonize holdings, services, training, and accession policy and to share expertise. The infrastructure will improve access to enhanced quality microorganisms in an appropriate legal framework and to resource-associated data in a more interoperable way.
      PubDate: 2015-11-18
      DOI: 10.3390/microorganisms3040890
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 903-912: Susceptibility of Select Agents to
           Predation by Predatory Bacteria

    • Authors: Riccardo Russo, Richard Chae, Somdatta Mukherjee, Eric Singleton, James Occi, Daniel Kadouri, Nancy Connell
      Pages: 903 - 912
      Abstract: Select Agents are microorganisms and toxins considered to be exploitable as biological weapons. Although infections by many Select Agents can be treated by conventional antibiotics, the risk of an emerging or engineered drug resistant strain is of great concern. One group of microorganisms that is showing potential to control drug resistant Gram-negative bacteria are the predatory bacteria from the genera Bdellovibrio spp. and Micavibrio spp. In this study, we have examined the ability of Bdellovibrio bacteriovorus (B. bacteriovorus) strain 109J, HD100 and Micavibrio aeruginosavorus (M. aeruginosavorus) ARL-13 to prey on a variety of Select Agents. Our findings demonstrate that B. bacteriovorus and M. aeruginosavorus are able to prey efficiently on Yersinia pestis and Burkholderia mallei. Modest predation was also measured in co-cultures of B. bacteriovorus and Francisella tularensis. However, neither of the predators showed predation when Burkholderia pseudomallei and Brucella melitensis were used as prey.
      PubDate: 2015-12-02
      DOI: 10.3390/microorganisms3040903
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 913-932: Metabolic Interactions in the
           Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and
           Bacteriophage Influences

    • Authors: Luis Vitetta, Sean Hall, Samantha Coulson
      Pages: 913 - 932
      Abstract: Life on this planet has been intricately associated with bacterial activity at all levels of evolution and bacteria represent the earliest form of autonomous existence. Plants such as those from the Leguminosae family that form root nodules while harboring nitrogen-fixing soil bacteria are a primordial example of symbiotic existence. Similarly, cooperative activities between bacteria and animals can also be observed in multiple domains, including the most inhospitable geographical regions of the planet such as Antarctica and the Lower Geyser Basin of Yellowstone National Park. In humans bacteria are often classified as either beneficial or pathogenic and in this regard we posit that this artificial nomenclature is overly simplistic and as such almost misinterprets the complex activities and inter-relationships that bacteria have with the environment as well as the human host and the plethora of biochemical activities that continue to be identified. We further suggest that in humans there are neither pathogenic nor beneficial bacteria, just bacteria embraced by those that tolerate the host and those that do not. The densest and most complex association exists in the human gastrointestinal tract, followed by the oral cavity, respiratory tract, and skin, where bacteria—pre- and post-birth—instruct the human cell in the fundamental language of molecular biology that normally leads to immunological tolerance over a lifetime. The overall effect of this complex output is the elaboration of a beneficial milieu, an environment that is of equal or greater importance than the bacterium in maintaining homeostasis.
      PubDate: 2015-12-17
      DOI: 10.3390/microorganisms3040913
      Issue No: Vol. 3, No. 4 (2015)
  • Microorganisms, Vol. 3, Pages 310-326: Temporal Study of the Microbial
           Diversity of the North Arm of Great Salt Lake, Utah, U.S.

    • Authors: Swati Almeida-Dalmet, Masoumeh Sikaroodi, Patrick Gillevet, Carol Litchfield, Bonnie Baxter
      Pages: 310 - 326
      Abstract: We employed a temporal sampling approach to understand how the microbial diversity may shift in the north arm of Great Salt Lake, Utah, U.S. To determine how variations in seasonal environmental factors affect microbial communities, length heterogeneity PCR fingerprinting was performed using consensus primers for the domain Bacteria, and the haloarchaea. The archaeal fingerprints showed similarities during 2003 and 2004, but this diversity changed during the remaining two years of the study, 2005 and 2006. We also performed molecular phylogenetic analysis of the 16S rRNA genes of the whole microbial community to characterize the taxa in the samples. Our results indicated that in the domain, Bacteria, the Salinibacter group dominated the populations in all samplings. However, in the case of Archaea, as noted by LIBSHUFF for phylogenetic relatedness analysis, many of the temporal communities were distinct from each other, and changes in community composition did not track with environmental parameters. Around 20–23 different phylotypes, as revealed by rarefaction, predominated at different periods of the year. Some phylotypes, such as Haloquadradum, were present year-round although they changed in their abundance in different samplings, which may indicate that these species are affected by biotic factors, such as nutrients or viruses, that are independent of seasonal temperature dynamics.
      PubDate: 2015-07-02
      DOI: 10.3390/microorganisms3030310
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 327-343: Tetrachloromethane-Degrading
           Bacterial Enrichment Cultures and Isolates from a Contaminated Aquifer

    • Pages: 327 - 343
      Abstract: The prokaryotic community of a groundwater aquifer exposed to high concentrations of tetrachloromethane (CCl4) for more than three decades was followed by terminal restriction fragment length polymorphism (T-RFLP) during pump-and-treat remediation at the contamination source. Bacterial enrichments and isolates were obtained under selective anoxic conditions, and degraded 10 mg·L−1 CCl4, with less than 10% transient formation of chloroform. Dichloromethane and chloromethane were not detected. Several tetrachloromethane-degrading strains were isolated from these enrichments, including bacteria from the Klebsiella and Clostridium genera closely related to previously described CCl4 degrading bacteria, and strain TM1, assigned to the genus Pelosinus, for which this property was not yet described. Pelosinus sp. TM1, an oxygen-tolerant, Gram-positive bacterium with strictly anaerobic metabolism, excreted a thermostable metabolite into the culture medium that allowed extracellular CCl4 transformation. As estimated by T-RFLP, phylotypes of CCl4-degrading enrichment cultures represented less than 7%, and archaeal and Pelosinus strains less than 0.5% of the total prokaryotic groundwater community.
      PubDate: 2015-07-02
      DOI: 10.3390/microorganisms3030327
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 344-363: Copahue Geothermal System: A
           Volcanic Environment with Rich Extreme Prokaryotic Biodiversity

    • Pages: 344 - 363
      Abstract: The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea.
      PubDate: 2015-07-08
      DOI: 10.3390/microorganisms3030344
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 364-390: Extremophiles in Mineral Sulphide
           Heaps: Some Bacterial Responses to Variable Temperature, Acidity and
           Solution Composition

    • Authors: Helen Watling, Denis Shiers, David Collinson
      Pages: 364 - 390
      Abstract: In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or reagents used during mineral processing. The impacts of variable solution acidity and composition, as well as temperature on the three microbiological functions have been examined for up to four bacterial species found in mineral sulphide heaps. The results indicate that bacteria adapt to sufficiently high metal concentrations (Cu, Ni, Co, Zn, As) to allow them to function in mineral sulphide heaps and, by engaging alternative metabolic pathways, to extend the solution pH range over which growth is sustained. Fluctuating temperatures during start up in sulphide heaps pose the greatest threat to efficient bacterial colonisation. The large masses of ores in bioleaching heaps mean that high temperatures arising from sulphide oxidation are hard to control initially, when the sulphide content of the ore is greatest. During that period, mesophilic and moderately thermophilic bacteria are markedly reduced in both numbers and activity.
      PubDate: 2015-07-09
      DOI: 10.3390/microorganisms3030364
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 391-406: Cold-Active, Heterotrophic Bacteria
           from the Highly Oligotrophic Waters of Lake Vanda, Antarctica

    • Authors: Nicole Vander Schaaf, Anna Cunningham, Brandon Cluff, CodyJo Kraemer, Chelsea Reeves, Carli Riester, Lauren Slater, Michael Madigan, W. Sattley
      Pages: 391 - 406
      Abstract: The permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica are distinctive ecosystems that consist strictly of microbial communities. In this study, water samples were collected from Lake Vanda, a stratified Dry Valley lake whose upper waters (from just below the ice cover to nearly 60 m) are highly oligotrophic, and used to establish enrichment cultures. Six strains of psychrotolerant, heterotrophic bacteria were isolated from lake water samples from a depth of 50 or 55 m. Phylogenetic analyses showed the Lake Vanda strains to be species of Nocardiaceae, Caulobacteraceae, Sphingomonadaceae, and Bradyrhizobiaceae. All Lake Vanda strains grew at temperatures near or below 0 °C, but optimal growth occurred from 18 to 24 °C. Some strains showed significant halotolerance, but no strains required NaCl for growth. The isolates described herein include cold-active species not previously reported from Dry Valley lakes, and their physiological and phylogenetic characterization broadens our understanding of these limnologically unique lakes.
      PubDate: 2015-07-24
      DOI: 10.3390/microorganisms3030391
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 407-416: Pyruvate: A key Nutrient in
           Hypersaline Environments'

    • Authors: Aharon Oren
      Pages: 407 - 416
      Abstract: Some of the most commonly occurring but difficult to isolate halophilic prokaryotes, Archaea as well as Bacteria, require or prefer pyruvate as carbon and energy source. The most efficient media for the enumeration and isolation of heterotrophic prokaryotes from natural environments, from freshwater to hypersaline, including the widely used R2A agar medium, contain pyruvate as a key ingredient. Examples of pyruvate-loving halophiles are the square, extremely halophilic archaeon Haloquadratum walsbyi and the halophilic gammaproteobacterium Spiribacter salinus. However, surprisingly little is known about the availability of pyruvate in natural environments and about the way it enters the cell. Some halophilic Archaea (Halorubrum saccharovorum, Haloarcula spp.) partially convert sugars and glycerol to pyruvate and other acids (acetate, lactate) which are excreted to the medium. Pyruvate formation from glycerol was also shown during a bloom of halophilic Archaea in the Dead Sea. However, no pyruvate transporters were yet identified in the genomes of halophilic Archaea, and altogether, our understanding of pyruvate transport in the prokaryote world is very limited. Therefore, the preference for pyruvate by fastidious and often elusive halophiles and the empirically proven enhanced colony recovery on agar media containing pyruvate are still poorly understood.
      PubDate: 2015-08-07
      DOI: 10.3390/microorganisms3030407
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 417-427: Live Yeast and Yeast Cell Wall
           Supplements Enhance Immune Function and Performance in Food-Producing
           Livestock: A Review †,‡

    • Authors: Paul Broadway, Jeffery Carroll, Nicole Sanchez
      Pages: 417 - 427
      Abstract: More livestock producers are seeking natural alternatives to antibiotics and antimicrobials, and searching for supplements to enhance growth performance, and general animal health and well-being. Some of the compounds currently being utilized and studied are live yeast and yeast-based products derived from the strain Saccharomyces cerevisiae. These products have been reported to have positive effects both directly and indirectly on the immune system and its subsequent biomarkers, thereby mitigating negative effects associated with stress and disease. These yeast-based products have also been reported to simultaneously enhance growth and performance by enhancing dry matter intake (DMI) and average daily gain (ADG) perhaps through the establishment of a healthy gastrointestinal tract. These products may be especially useful in times of potential stress such as during birth, weaning, early lactation, and during the receiving period at the feedlot. Overall, yeast supplements appear to possess the ability to improve animal health and metabolism while decreasing morbidity, thereby enhancing profitability of these animals.
      PubDate: 2015-08-07
      DOI: 10.3390/microorganisms3030417
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 428-440: Assessment of the Factors
           Contributing to the Growth or Spoilage of Meyerozyma guilliermondii in
           Organic Yogurt: Comparison of Methods for Strain Differentiation

    • Pages: 428 - 440
      Abstract: In this work we analyze the spoiling potential of Meyerozyma guilliermondii in yogurt. The analysis was based on contaminated samples sent to us by an industrial laboratory over two years. All the plain and fruit yogurt packages were heavily contaminated by yeasts, but only the last ones, containing fermentable sugars besides lactose, were spoiled by gas swelling. These strains were unable to grow and ferment lactose (as the type strain); they did grow on lactate plus galactose, fermented glucose and sucrose, and galactose (weakly), but did not compete with lactic acid bacteria for lactose. This enables them to grow in any yogurt, although only those with added jam were spoiled due to the fermentation of the fruit sugars. Fermentation, but not growth, was strongly inhibited at 8 °C. In consequence, in plain yogurt as well as in any yogurt maintained at low temperature, yeast contamination would not be detected by the consumer. The risk could be enhanced because the species has been proposed for biological control of fungal infections in organic agriculture. The combination of the IGS PCR-RFLP (amplification of the intergenic spacer region of rDNA followed by restriction fragment length polymorphism analysis) method and mitochondrial DNA-RFLP makes a good tool to trace and control the contamination by M. guilliermondii.
      PubDate: 2015-08-19
      DOI: 10.3390/microorganisms3030428
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 441-463: Quantitative Characterization of
           the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size,
           Growth Medium and Culture Conditions

    • Authors: Julie Bornot, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gorret
      Pages: 441 - 463
      Abstract: Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled conditions in flask and bioreactor cultures. The growth of D. geothermalis type strains was compared. Among the strains tested, the strain from the German Collection of Microorganisms (Deutsche Sammlung von Mikroorganismen DSM) DSM-11302 was found to give the highest biomass concentration and growth rate: in a complex medium with glucose, the growth rate reached 0.75 h−1 at 45 °C. Yeast extract concentration in the medium had significant constitutive and catalytic effects. Furthermore, the results showed that the physiological descriptors were not affected by the inoculum preparation steps. A batch culture of D. geothermalis DSM-11302 on defined medium was carried out: cells grew exponentially with a maximal growth rate of 0.28 h−1 and D. geothermalis DSM-11302 biomass reached 1.4 g·L−1 in 20 h. Then, 1.4 gDryCellWeight of biomass (X) was obtained from 5.6 g glucose (Glc) consumed as carbon source, corresponding to a yield of 0.3 CmolX·CmolGlc−1; cell specific oxygen uptake and carbon dioxide production rates reached 216 and 226 mmol.CmolX−1·h−1, respectively, and the respiratory quotient (QR) value varied from 1.1 to 1.7. This is the first time that kinetic parameters and yields are reported for D. geothermalis DSM-11302 grown on a mineral medium in well-controlled batch culture.
      PubDate: 2015-08-20
      DOI: 10.3390/microorganisms3030441
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 464-483: Role of Bacterial
           Exopolysaccharides as Agents in Counteracting Immune Disorders Induced by
           Herpes Virus

    • Pages: 464 - 483
      Abstract: Extreme marine environments, such as the submarine shallow vents of the Eolian Islands (Italy), offer an almost unexplored source of microorganisms producing unexploited and promising biomolecules for pharmaceutical applications. Thermophilic and thermotolerant bacilli isolated from Eolian vents are able to produce exopolysaccharides (EPSs) with antiviral and immunomodulatory effects against Herpes simplex virus type 2 (HSV-2). HSV-2 is responsible for the most common and continuously increasing viral infections in humans. Due to the appearance of resistance to the available treatments, new biomolecules exhibiting different mechanisms of action could provide novel agents for treating viral infections. The EPSs hinder the HSV-2 replication in human peripheral blood mononuclear cells (PBMC) but not in WISH (Wistar Institute Susan Hayflic) cells line, indicating that cell-mediated immunity was involved in the antiviral activity. High levels of Th1-type cytokines were detected in PBMC treated with all EPSs, while Th2-type cytokines were not induced. These EPSs are water soluble exopolymers able to stimulate the immune response and thus contribute to the antiviral immune defense, acting as immunomodulators. As stimulants of Th1 cell-mediated immunity, they could lead to the development of novel drugs as alternative in the treatment of herpes virus infections, as well as in immunocompromised host.
      PubDate: 2015-08-21
      DOI: 10.3390/microorganisms3030464
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 484-499: Novel Methanotrophs of the Family
           Methylococcaceae from Different Geographical Regions and Habitats

    • Pages: 484 - 499
      Abstract: Terrestrial methane seeps and rice paddy fields are important ecosystems in the methane cycle. Methanotrophic bacteria in these ecosystems play a key role in reducing methane emission into the atmosphere. Here, we describe three novel methanotrophs, designated BRS-K6, GFS-K6 and AK-K6, which were recovered from three different habitats in contrasting geographic regions and ecosystems: waterlogged rice-field soil and methane seep pond sediments from Bangladesh; and warm spring sediments from Armenia. All isolates had a temperature range for growth of 8–35 °C (optimal 25–28 °C) and a pH range of 5.0–7.5 (optimal 6.4–7.0). 16S rRNA gene sequences showed that they were new gammaproteobacterial methanotrophs, which form a separate clade in the family Methylococcaceae. They fell into a cluster with thermotolerant and mesophilic growth tendency, comprising the genera Methylocaldum-Methylococcus-Methyloparacoccus-Methylogaea. So far, growth below 15 °C of methanotrophs from this cluster has not been reported. The strains possessed type I intracytoplasmic membranes. The genes pmoA, mxaF, cbbL, nifH were detected, but no mmoX gene was found. Each strain probably represents a novel species either belonging to the same novel genus or each may even represent separate genera. These isolates extend our knowledge of methanotrophic Gammaproteobacteria and their physiology and adaptation to different ecosystems.
      PubDate: 2015-08-21
      DOI: 10.3390/microorganisms3030484
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 500-517: A Three-Component Microbial
           Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic
           Glycine Betaine Degradation with Methanogenesis

    • Pages: 500 - 517
      Abstract: Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. Here, we investigated a stable three-component microbial consortium obtained from the brine of the recently discovered deep-sea salt-saturated Lake Thetis. The trophic network of this consortium, established at salinities up to 240, relies on fermentative decomposition of common osmoprotectant glycine betaine (GB). Similarly to known extreme halophilic anaerobic GB-degrading enrichments, the initial step of GB degradation starts with its reductive cleavage to trimethylamine and acetate, carried out by the fermenting member of the Thetis enrichment, Halobacteroides lacunaris TB21. In contrast to acetate, which cannot be easily oxidized in salt-saturated anoxic environments, trimethylamine represents an advantageous C1-substrate for methylotrophic methanogenic member of the Thetis enrichment, Methanohalophilus sp. TA21. This second member of the consortium likely produces hydrogen via methylotrophic modification of reductive acetyl-CoA pathway because the initial anaerobic GB cleavage reaction requires the consumption of reducing equivalents. Ecophysiological role of the third member of the Thetis consortium, Halanaerobium sp. TB24, which lacks the capability of either GB or trimethylamine degradation, remains yet to be elucidated. As it is true for cultivated members of family Halanaerobiaceae, the isolate TB24 can obtain energy primarily by fermenting simple sugars and producing hydrogen as one of the end products. Hence, by consuming of TB21 and TA21 metabolites, Halanaerobium sp. TB24 can be an additional provider of reducing equivalents required for reductive degradation of GB. Description of the Thetis GB-degrading consortium indicated that anaerobic degradation of osmoregulatory molecules may play important role in the overall turnover of organic carbon in anoxic hypersaline biotopes.
      PubDate: 2015-09-09
      DOI: 10.3390/microorganisms3030500
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 518-534: The Effects of Perchlorates on the
           Permafrost Methanogens: Implication for Autotrophic Life on Mars

    • Authors: Viktoria Shcherbakova, Viktoria Oshurkova, Yoshitaka Yoshimura
      Pages: 518 - 534
      Abstract: The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist in frozen subsurface environments on Mars, which has no free oxygen, inaccessible organic matter, and extremely low amounts of unfrozen water. Our research on the genesis of methane, its content and distribution in permafrost horizons of different ages and origin demonstrated the presence of methane in permanently frozen fine-grained sediments. Earlier, we isolated and described four strains of methanogenic archaea of Methanobacterium and Methanosarcina genera from samples of Pliocene and Holocene permafrost from Eastern Siberia. In this paper we study the effect of sodium and magnesium perchlorates on growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. In this paper we study the effect of sodium and magnesium perchlorates on the growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. Furthermore, as shown in the studies strain M2T M. arcticum, probably can use perchlorate anion as an electron acceptor in anaerobic methane oxidation. Earth’s subzero subsurface environments are the best approximation of environments on Mars, which is most likely to harbor methanogens; thus, a biochemical understanding of these pathways is expected to provide a basis for designing experiments to detect autotrophic methane-producing life forms on Mars.
      PubDate: 2015-09-09
      DOI: 10.3390/microorganisms3030518
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 535-550: Effect of Lemongrass Essential Oil
           Vapors on Microbial Dynamics and Listeria monocytogenes Survival on Rocket
           and Melon Stored under Different Packaging Conditions and Temperatures

    • Authors: Agni Hadjilouka, Melissanthi Polychronopoulou, Spiros Paramithiotis, Periklis Tzamalis, Eleftherios Drosinos
      Pages: 535 - 550
      Abstract: The aim of the present study was to examine the effect of lemongrass essential oil vapors on the dynamics of surface microbiota and L. monocytogenes growth on rocket and melon under different packaging conditions and storage temperature. For that purpose, rocket and melon were placed on Expanded Polystyrene (EPS) trays, sprayed with L. monocytogenes to a population of 4.5–5.0 log CFU·g−1, packaged using microperforated Oriented Polypropylene (OPP) film in either air or Microperforated Active Modified Atmosphere (MAMA) (initial atmosphere 5% O2, 10% CO2) including a Whatman paper containing the essential oil, without contact with the product, and stored at 0, 5, 10, and 15 °C. Application of lemongrass exhibited a bactericidal effect on enterococci and a fungistatic effect on yeast-mould populations but only during air storage of rocket. The former took place at all temperatures and the latter only at 10 and 15 °C. No effect on shelf life of both products was recorded. However, an important effect on the sensorial properties was observed; during the first 4–5 days of storage both products were organoleptically unacceptable. Regarding MAMA packaging, it affected only Pseudomonas spp. population resulting in a reduction of 1–2 log CFU·g−1 in both products.
      PubDate: 2015-09-09
      DOI: 10.3390/microorganisms3030535
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 551-566: Evaluation of Potential Effects of
           NaCl and Sorbic Acid on Staphylococcal Enterotoxin A Formation

    • Pages: 551 - 566
      Abstract: The prophage-encoded staphylococcal enterotoxin A (SEA) is recognized as the main cause of staphylococcal food poisoning (SFP), a common foodborne intoxication disease, caused by Staphylococcus aureus. Studies on the production of SEA suggest that activation of the SOS response and subsequent prophage induction affect the regulation of the sea gene and the SEA produced, increasing the risk for SFP. The present study aims to evaluate the effect of NaCl and sorbic acid, in concentrations relevant to food production, on SOS response activation, prophage induction and SEA production. The impact of stress was initially evaluated on steady state cells for a homogenous cell response. NaCl 2% was found to activate the SOS response, i.e., recA expression, and trigger prophage induction, in a similar way as the phage-inducer mitomycin C. In contrast, sorbic acid decreased the pH of the culture to a level where prophage induction was probably suppressed, even when combined with NaCl stress. The impact of previous physiological state of the bacteria was also addressed on cells pre-exposed to NaCl, and was found to potentially affect cell response upon exposure to further stress. The results obtained highlight the possible SFP-related risks arising from the use of preservatives during food processing.
      PubDate: 2015-09-17
      DOI: 10.3390/microorganisms3030551
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 567-587: Membrane Association and Catabolite
           Repression of the Sulfolobus solfataricus α-Amylase

    • Authors: Edith Soo, Deepak Rudrappa, Paul Blum
      Pages: 567 - 587
      Abstract: Sulfolobus solfataricus is a thermoacidophilic member of the archaea whose envelope consists of an ether-linked lipid monolayer surrounded by a protein S-layer. Protein translocation across this envelope must accommodate a steep proton gradient that is subject to temperature extremes. To better understand this process in vivo, studies were conducted on the S. solfataricus glycosyl hydrolyase family 57 α-Amylase (AmyA). Cell lines harboring site specific modifications of the amyA promoter and AmyA structural domains were created by gene replacement using markerless exchange and characterized by Western blot, enzyme assay and culture-based analysis. Fusion of amyA to the malAp promoter overcame amyAp-mediated regulatory responses to media composition including glucose and amino acid repression implicating action act at the level of transcription. Deletion of the AmyA Class II N-terminal signal peptide blocked protein secretion and intracellular protein accumulation. Deletion analysis of a conserved bipartite C-terminal motif consisting of a hydrophobic region followed by several charged residues indicated the charged residues played an essential role in membrane-association but not protein secretion. Mutants lacking the C-terminal bipartite motif exhibited reduced growth rates on starch as the sole carbon and energy source; therefore, association of AmyA with the membrane improves carbohydrate utilization. Widespread occurrence of this motif in other secreted proteins of S. solfataricus and of related Crenarchaeota suggests protein association with membranes is a general trait used by these organisms to influence external processes.
      PubDate: 2015-09-18
      DOI: 10.3390/microorganisms3030567
      Issue No: Vol. 3, No. 3 (2015)
  • Microorganisms, Vol. 3, Pages 113-136: High Throughput Sequencing to
           Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae
           in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp
           Preserve, West Virginia, USA

    • Authors: Evan Lau, Edward IV, Zachary Dillard, Ryan Dague, Amanda Semple, Wendi Wentzell
      Pages: 113 - 136
      Abstract: Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. Methylacidiphilum-like methanotrophs were not detected. Proteobacterial methanotrophic bacteria constitute <2% of microbiota in these environments, with the Methylocystaceae one to two orders of magnitude more abundant than the Methylococcaceae in all environments sampled. The Methylococcaceae are also less diverse in forest soil compared to the other two habitats. Nonmetric multidimensional scaling analyses indicated that the majority of methanotrophs from the Methylococcaceae and Methylocystaceae tend to occur in one habitat only (peat or Sphagnum moss) or co-occurred in both Sphagnum moss and peat. This study provides insights into the structure of methanotrophic communities in relationship to habitat type, and suggests that peat and Sphagnum moss can influence methanotroph community structure and biogeography.
      PubDate: 2015-04-02
      DOI: 10.3390/microorganisms3020113
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 137-151: Interactions of Methylotrophs with
           Plants and Other Heterotrophic Bacteria

    • Authors: Hiroyuki Iguchi, Hiroya Yurimoto, Yasuyoshi Sakai
      Pages: 137 - 151
      Abstract: Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO2, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs.
      PubDate: 2015-04-02
      DOI: 10.3390/microorganisms3020137
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 152-174: Parallel and Divergent Evolutionary
           Solutions for the Optimization of an Engineered Central Metabolism in
           Methylobacterium extorquens AM1

    • Authors: Sean Carroll, Lon Chubiz, Deepa Agashe, Christopher Marx
      Pages: 152 - 174
      Abstract: Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety in the numbers and types of mutations that occurred, including instances of parallel mutations at targets that may have been “rationalized” by the bioengineer, plus other “illogical” mutations that demonstrate the ability of evolution to expose unforeseen optimization solutions. Notably, we investigated mutations to RNA polymerase, which provided a massive growth benefit but are linked to highly aberrant transcriptional profiles. Overall, we highlight the power of experimental evolution to present genetic and physiological solutions for strain optimization, particularly in systems where the challenges of engineering are too many or too difficult to overcome via traditional engineering methods.
      PubDate: 2015-04-09
      DOI: 10.3390/microorganisms3020152
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 175-197: C1-Pathways in Methyloversatilis
           universalis FAM5: Genome Wide Gene Expression and Mutagenesis Studies

    • Authors: Nathan Good, Andrew Lamb, David Beck, N. Martinez-Gomez, Marina Kalyuzhnaya
      Pages: 175 - 197
      Abstract: Methyloversatilis universalis FAM5 utilizes single carbon compounds such as methanol or methylamine as a sole source of carbon and energy. Expression profiling reveals distinct sets of genes altered during growth on methylamine vs methanol. As expected, all genes for the N-methylglutamate pathway were induced during growth on methylamine. Among other functions responding to the aminated source of C1-carbon, are a heme-containing amine dehydrogenase (Qhp), a distant homologue of formaldehyde activating enzyme (Fae3), molybdenum-containing formate dehydrogenase, ferredoxin reductase, a set of homologues to urea/ammonium transporters and amino-acid permeases. Mutants lacking one of the functional subunits of the amine dehydrogenase (ΔqhpA) or Δfae3 showed no growth defect on C1-compounds. M. universalis FAM5 strains with a lesion in the H4-folate pathway were not able to use any C1-compound, methanol or methylamine. Genes essential for C1-assimilation (the serine cycle and glyoxylate shunt) and H4MTP-pathway for formaldehyde oxidation showed similar levels of expression on both C1-carbon sources. M. universalis FAM5 possesses three homologs of the formaldehyde activating enzyme, a key enzyme of the H4MTP-pathway. Strains lacking the canonical Fae (fae1) lost the ability to grow on both C1-compounds. However, upon incubation on methylamine the fae1-mutant produced revertants (Δfae1R), which regained the ability to grow on methylamine. Double and triple mutants (Δfae1RΔfae3, or Δfae1RΔfae2 or Δfae1RΔfae2Δfae3) constructed in the revertant strain background showed growth similar to the Δfae1R phenotype. The metabolic pathways for utilization of methanol and methylamine in Methyloversatilis universalis FAM5 are reconstructed based on these gene expression and phenotypic data.
      PubDate: 2015-04-09
      DOI: 10.3390/microorganisms3020175
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 198-212: Comparison of Microbiological and
           Probiotic Characteristics of Lactobacilli Isolates from Dairy Food
           Products and Animal Rumen Contents

    • Authors: Neethu Jose, Craig Bunt, Malik Hussain
      Pages: 198 - 212
      Abstract: Lactobacilli are employed in probiotic food preparations and as feed additives in poultry and livestock, due to health benefits associated with their consumption. The objective of this study was to evaluate and compare the probiotic potential of ten lactobacilli strains isolated from commercial dairy food products and animal rumen contents in New Zealand. Genetic identification of the isolates revealed that all belonged to the genus Lactobacillus, specifically the species L. reuteri, L. rhamnosus and L. plantarum. All isolates did not show any haemolytic behaviour. Isolates of dairy origin showed better tolerance to low pH stress. On the other hand, rumen isolates exhibited a higher tolerance to presence of bile salts. All isolates exhibited resistance to aminoglycoside antibiotics, however most were sensitive to ampicillin. Isolates of rumen origin demonstrated a higher inhibitory effect on Listeria monocytogenes, Enterobacter aerogenes and Salmonella menston. Bacterial adherence of all isolates increased with a decrease in pH. This screening study on lactobacilli isolates has assessed and identified potential probiotic candidates for further evaluation.
      PubDate: 2015-04-15
      DOI: 10.3390/microorganisms3020198
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 213-235: Does the Gut Microbiota Contribute
           to Obesity' Going beyond the Gut Feeling

    • Authors: Marisol Aguirre, Koen Venema
      Pages: 213 - 235
      Abstract: Increasing evidence suggests that gut microbiota is an environmental factor that plays a crucial role in obesity. However, the aetiology of obesity is rather complex and depends on different factors. Furthermore, there is a lack of consensus about the exact role that this microbial community plays in the host. The aim of this review is to present evidence about what has been characterized, compositionally and functionally, as obese gut microbiota. In addition, the different reasons explaining the so-far unclear role are discussed considering evidence from in vitro, animal and human studies.
      PubDate: 2015-04-27
      DOI: 10.3390/microorganisms3020213
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 236-267: Tackling Drug Resistant Infection
           Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and
           Epidemiological Genomics

    • Authors: Tim Downing
      Pages: 236 - 267
      Abstract: High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)—a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.
      PubDate: 2015-05-20
      DOI: 10.3390/microorganisms3020236
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 268-289: Generation of PHB from Spent
           Sulfite Liquor Using Halophilic Microorganisms

    • Pages: 268 - 289
      Abstract: Halophilic microorganisms thrive at elevated concentrations of sodium chloride up to saturation and are capable of growing on a wide variety of carbon sources like various organic acids, hexose and also pentose sugars. Hence, the biotechnological application of these microorganisms can cover many aspects, such as the treatment of hypersaline waste streams of different origin. Due to the fact that the high osmotic pressure of hypersaline environments reduces the risk of contamination, the capacity for cost-effective non-sterile cultivation can make extreme halophilic microorganisms potentially valuable organisms for biotechnological applications. In this contribution, the stepwise use of screening approaches, employing design of experiment (DoE) on model media and subsequently using industrial waste as substrate have been implemented to investigate the applicability of halophiles to generate PHB from the industrial waste stream spent sulfite liquor (SSL). The production of PHB on model media as well as dilutions of industrial substrate in a complex medium has been screened for by fluorescence microscopy using Nile Blue staining. Screening was used to investigate the ability of halophilic microorganisms to withstand the inhibiting substances of the waste stream without negatively affecting PHB production. It could be shown that neither single inhibiting substances nor a mixture thereof inhibited growth in the investigated range, hence, leaving the question on the inhibiting mechanisms open. However, it could be demonstrated that some haloarchaea and halophilic bacteria are able to produce PHB when cultivated on 3.3% w/w dry matter spent sulfite liquor, whereas H. halophila was even able to thrive on 6.6% w/w dry matter spent sulfite liquor and still produce PHB.
      PubDate: 2015-06-08
      DOI: 10.3390/microorganisms3020268
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 290-309: Methane Oxidation and Molecular
           Characterization of Methanotrophs from a Former Mercury Mine Impoundment

    • Authors: Shaun Baesman, Laurence Miller, Jeremy Wei, Yirang Cho, Emily Matys, Roger Summons, Paula Welander, Ronald Oremland
      Pages: 290 - 309
      Abstract: The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO2 with some CH4 present. The δ13CH4 value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively 12C-enriched CO2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.
      PubDate: 2015-06-23
      DOI: 10.3390/microorganisms3020290
      Issue No: Vol. 3, No. 2 (2015)
  • Microorganisms, Vol. 3, Pages 1-16: Identification of Multiple
           Bacteriocins in Enterococcus spp. Using an Enterococcus-Specific
           Bacteriocin PCR Array

    • Authors: Chris Henning, Dhiraj Gautam, Peter Muriana
      Pages: 1 - 16
      Abstract: Twenty-two bacteriocin-producing Enterococcus isolates obtained from food and animal sources, and demonstrating activity against Listeria monocytogenes, were screened for bacteriocin-related genes using a bacteriocin PCR array based on known enterococcal bacteriocin gene sequences in the NCBI GenBank database. The 22 bacteriocin-positive (Bac+) enterococci included En. durans (1), En. faecalis (4), En. faecium (12), En. hirae (3), and En. thailandicus (2). Enterocin A (entA), enterocins mr10A and mr10B (mr10AB), and bacteriocin T8 (bacA) were the most commonly found structural genes in order of decreasing prevalence. Forty-five bacteriocin genes were identified within the 22 Bac+ isolates, each containing at least one of the screened structural genes. Of the 22 Bac+ isolates, 15 possessed two bacteriocin genes, seven isolates contained three different bacteriocins, and three isolates contained as many as four different bacteriocin genes. These results may explain the high degree of bactericidal activity observed with various Bac+ Enterococcus spp. Antimicrobial activity against wild-type L. monocytogenes and a bacteriocin-resistant variant demonstrated bacteriocins having different modes-of-action. Mixtures of bacteriocins, especially those with different modes-of-action and having activity against foodborne pathogens, such as L. monocytogenes, may play a promising role in the preservation of food.
      PubDate: 2015-02-04
      DOI: 10.3390/microorganisms3010001
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 17-33: Rapid Reactivation of Deep Subsurface
           Microbes in the Presence of C-1 Compounds

    • Pages: 17 - 33
      Abstract: Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.
      PubDate: 2015-02-05
      DOI: 10.3390/microorganisms3010017
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 34-46: Fumaric Acid and Slightly Acidic
           Electrolyzed Water Inactivate Gram Positive and Gram Negative Foodborne

    • Authors: Charles Tango, Ahmad Mansur, Deog-Hwan Oh
      Pages: 34 - 46
      Abstract: Sanitizing effectiveness of slightly acidic electrolyzed water (SAEW) and fumaric acid (FA) at different dipping temperatures (25–60 °C), times (1–5 min), and concentrations (5–30 ppm for SAEW and 0.125%–0.5% for FA) on pure cultures of two Gram positive pathogens Staphylococcus aureus (SA) and Listeria monocytogenes (LM) and two Gram negative pathogens Escherichia coli O157:H7 (EC) and Salmonella Typhimurium (ST) was evaluated. FA (0.25%) showed the strongest sanitizing effect, demonstrating complete inactivation of EC, ST, and LM, while SA was reduced by 3.95–5.76 log CFU/mL at 25–60 °C, respectively, after 1 min of treatment. For SAEW, the complete inactivation was obtained when available chlorine concentration was increased to 20 ppm at 40 °C for 3 and 5 min. Moreover, Gram positive pathogens have been shown to resist to all treatment trends more than Gram negative pathogens throughout this experiment. Regardless of the different dipping temperatures, concentrations, and times, FA treatment was more effective than treatment with SAEW for reduction of foodborne pathogens. This study demonstrated that application of FA in food systems may be useful as a method for inactivation of foodborne pathogens.
      PubDate: 2015-02-12
      DOI: 10.3390/microorganisms3010034
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 47-59: Role of NAD+-Dependent Malate
           Dehydrogenase in the Metabolism of Methylomicrobium alcaliphilum 20Z and
           Methylosinus trichosporium OB3b

    • Authors: Olga Rozova, Valentina Khmelenina, Ksenia Bocharova, Ildar Mustakhimov, Yuri Trotsenko
      Pages: 47 - 59
      Abstract: We have expressed the l-malate dehydrogenase (MDH) genes from aerobic methanotrophs Methylomicrobium alcaliphilum 20Z and Methylosinus trichosporium OB3b as his-tagged proteins in Escherichia coli. The substrate specificities, enzymatic kinetics and oligomeric states of the MDHs have been characterized. Both MDHs were NAD+-specific and thermostable enzymes not affected by metal ions or various organic metabolites. The MDH from M. alcaliphilum 20Z was a homodimeric (2 × 35 kDa) enzyme displaying nearly equal reductive (malate formation) and oxidative (oxaloacetate formation) activities and higher affinity to malate (Km = 0.11 mM) than to oxaloacetate (Km = 0.34 mM). The MDH from M. trichosporium OB3b was homotetrameric (4 × 35 kDa), two-fold more active in the reaction of oxaloacetate reduction compared to malate oxidation and exhibiting higher affinity to oxaloacetate (Km = 0.059 mM) than to malate (Km = 1.28 mM). The kcat/Km ratios indicated that the enzyme from M. alcaliphilum 20Z had a remarkably high catalytic efficiency for malate oxidation, while the MDH of M. trichosporium OB3b was preferable for oxaloacetate reduction. The metabolic roles of the enzymes in the specific metabolism of the two methanotrophs are discussed.
      PubDate: 2015-02-27
      DOI: 10.3390/microorganisms3010047
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 60-79: Experimental Horizontal Gene Transfer
           of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and
           Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal
           N-Methylglutamate Pathway

    • Authors: Dipti Nayak, Christopher Marx
      Pages: 60 - 79
      Abstract: Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. Two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic Proteobacteria: Methylamine dehydrogenase and the N-methylglutamate pathway. Recent work suggests the N-methylglutamate (NMG) pathway may be more common in nature than the well-studied methylamine dehydrogenase (MaDH, encoded by the mau gene cluster). However, the distribution of these pathways across methylotrophs has never been analyzed. Furthermore, even though horizontal gene transfer (HGT) is commonly invoked as a means to transfer these pathways between strains, the physiological barriers to doing so have not been investigated. We found that the NMG pathway is both more abundant and more universally distributed across methylotrophic Proteobacteria compared to MaDH, which displays a patchy distribution and has clearly been transmitted by HGT even amongst very closely related strains. This trend was especially prominent in well-characterized strains of the Methylobacterium extroquens species, which also display significant phenotypic variability during methylamine growth. Strains like Methylobacterium extorquens PA1 that only encode the NMG pathway grew on methylamine at least five-fold slower than strains like Methylobacterium extorquens AM1 that also possess the mau gene cluster. By mimicking a HGT event through the introduction of the M. extorquens AM1 mau gene cluster into the PA1 genome, the resulting strain instantaneously achieved a 4.5-fold increase in growth rate on methylamine and a 11-fold increase in fitness on methylamine, which even surpassed the fitness of M. extorquens AM1. In contrast, when three replicate populations of wild type M. extorquens PA1 were evolved on methylamine as the sole carbon and energy source for 150 generations neither fitness nor growth rate improved. These results suggest that the NMG pathway permits slow growth on methylamine and is widely distributed in methylotrophs; however, rapid growth on methylamine can be achieved quite readily through acquisition of the mau cluster by HGT.
      PubDate: 2015-03-10
      DOI: 10.3390/microorganisms3010060
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 80-93: Isolation and Taxonomic Identity of
           Bacteriocin-Producing Lactic Acid Bacteria from Retail Foods and Animal

    • Authors: Chris Henning, Paul Vijayakumar, Raj Adhikari, Badrinath Jagannathan, Dhiraj Gautam, Peter Muriana
      Pages: 80 - 93
      Abstract: Bacteriocin-producing (Bac+) lactic acid bacteria (LAB) were isolated from a variety of food products and animal sources. Samples were enriched in de Man, Rogosa, and Sharpe (MRS) Lactocilli broth and plated onto MRS agar plates using a “sandwich overlay” technique. Inhibitory activity was detected by the “deferred antagonism” indicator overlay method using Listeria monocytogenes as the primary indicator organism. Antimicrobial activity against L. monocytogenes was detected by 41 isolates obtained from 23 of 170 food samples (14%) and 11 of 110 samples from animal sources (10%) tested. Isolated Bac+ LAB included Lactococcus lactis, Lactobacillus curvatus, Carnobacterium maltaromaticum, Leuconostoc mesenteroides, and Pediococcus acidilactici, as well as Enterococcus faecium, Enterococcus faecalis, Enterococcus hirae, and Enterococcus thailandicus. In addition to these, two Gram-negative bacteria were isolated (Serratia plymuthica, and Serratia ficaria) that demonstrated inhibitory activity against L. monocytogenes, Staphylococcus aureus, and Enterococcus faecalis (S. ficaria additionally showed activity against Salmonella Typhimurium). These data continue to demonstrate that despite more than a decade of antimicrobial interventions on meats and produce, a wide variety of food products still contain Bac+ microbiota that are likely eaten by consumers and may have application as natural food preservatives.
      PubDate: 2015-03-19
      DOI: 10.3390/microorganisms3010080
      Issue No: Vol. 3, No. 1 (2015)
  • Microorganisms, Vol. 3, Pages 94-112: Genomics of Methylotrophy in
           Gram-Positive Methylamine-Utilizing Bacteria

    • Authors: Tami McTaggart, David Beck, Usanisa Setboonsarng, Nicole Shapiro, Tanja Woyke, Mary Lidstrom, Marina Kalyuzhnaya, Ludmila Chistoserdova
      Pages: 94 - 112
      Abstract: Gram-positive methylotrophic bacteria have been known for a long period of time, some serving as model organisms for characterizing the specific details of methylotrophy pathways/enzymes within this group. However, genome-based knowledge of methylotrophy within this group has been so far limited to a single species, Bacillus methanolicus (Firmicutes). The paucity of whole-genome data for Gram-positive methylotrophs limits our global understanding of methylotrophy within this group, including their roles in specific biogeochemical cycles, as well as their biotechnological potential. Here, we describe the isolation of seven novel strains of Gram-positive methylotrophs that include two strains of Bacillus and five representatives of Actinobacteria classified within two genera, Arthrobacter and Mycobacterium. We report whole-genome sequences for these isolates and present comparative analysis of the methylotrophy functional modules within these genomes. The genomic sequences of these seven novel organisms, all capable of growth on methylated amines, present an important reference dataset for understanding the genomic basis of methylotrophy in Gram-positive methylotrophic bacteria. This study is a major contribution to the field of methylotrophy, aimed at closing the gap in the genomic knowledge of methylotrophy within this diverse group of bacteria.
      PubDate: 2015-03-20
      DOI: 10.3390/microorganisms3010094
      Issue No: Vol. 3, No. 1 (2015)
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