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Microorganisms, Volume 3, Issue 4 (December 2015) – 19 articles , Pages 588-932

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955 KiB  
Review
Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences
by Luis Vitetta, Sean Hall and Samantha Coulson
Microorganisms 2015, 3(4), 913-932; https://doi.org/10.3390/microorganisms3040913 - 17 Dec 2015
Cited by 8 | Viewed by 9443
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Metabolic Interactions)
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Communication
Susceptibility of Select Agents to Predation by Predatory Bacteria
by Riccardo Russo, Richard Chae, Somdatta Mukherjee, Eric J. Singleton, James L. Occi, Daniel E. Kadouri and Nancy D. Connell
Microorganisms 2015, 3(4), 903-912; https://doi.org/10.3390/microorganisms3040903 - 2 Dec 2015
Cited by 12 | Viewed by 5806
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 [...] Read more.
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. Full article
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Essay
The Microbial Resource Research Infrastructure MIRRI: Strength through Coordination
by Erko Stackebrandt, Manuela Schüngel, Dunja Martin and David Smith
Microorganisms 2015, 3(4), 890-902; https://doi.org/10.3390/microorganisms3040890 - 18 Nov 2015
Cited by 10 | Viewed by 7802
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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346 KiB  
Review
Hydrogen Sulfide in Physiology and Diseases of the Digestive Tract
by Sudha B. Singh and Henry C. Lin
Microorganisms 2015, 3(4), 866-889; https://doi.org/10.3390/microorganisms3040866 - 12 Nov 2015
Cited by 161 | Viewed by 16245
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Metabolic Interactions)
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Article
Bioactivities of Ketones Terpenes: Antifungal Effect on F. verticillioides and Repellents to Control Insect Fungal Vector, S. zeamais
by Romina P. Pizzolitto, Jimena M. Herrera, Yesica P. Zaio, Jose S. Dambolena, Maria P. Zunino, Mauro N. Gallucci and Julio A. Zygadlo
Microorganisms 2015, 3(4), 851-865; https://doi.org/10.3390/microorganisms3040851 - 12 Nov 2015
Cited by 19 | Viewed by 8342
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Activity in Food)
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Article
The Potential of the Yeast Debaryomyces hansenii H525 to Degrade Biogenic Amines in Food
by Mathias Bäumlisberger, Urs Moellecken, Helmut König and Harald Claus
Microorganisms 2015, 3(4), 839-850; https://doi.org/10.3390/microorganisms3040839 - 6 Nov 2015
Cited by 44 | Viewed by 9458
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. [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Activity in Food)
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Article
The Effect of Tellurite on Highly Resistant Freshwater Aerobic Anoxygenic Phototrophs and Their Strategies for Reduction
by Chris Maltman and Vladimir Yurkov
Microorganisms 2015, 3(4), 826-838; https://doi.org/10.3390/microorganisms3040826 - 6 Nov 2015
Cited by 17 | Viewed by 4915
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Extremophiles)
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Article
Movement of Salmonella serovar Typhimurium and E. coli O157:H7 to Ripe Tomato Fruit Following Various Routes of Contamination
by Amanda J. Deering, Dan R. Jack, Robert E. Pruitt and Lisa J. Mauer
Microorganisms 2015, 3(4), 809-825; https://doi.org/10.3390/microorganisms3040809 - 5 Nov 2015
Cited by 15 | Viewed by 8688
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. [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Activity in Food)
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Review
Thermus thermophilus as a Source of Thermostable Lipolytic Enzymes
by Olalla López-López, María-Esperanza Cerdán and María-Isabel González-Siso
Microorganisms 2015, 3(4), 792-808; https://doi.org/10.3390/microorganisms3040792 - 4 Nov 2015
Cited by 14 | Viewed by 8193
Abstract
Lipolytic enzymes, esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3), 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 [...] Read more.
Lipolytic enzymes, esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3), 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. Full article
(This article belongs to the Special Issue Extremophiles)
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321 KiB  
Review
Gut Microbiota and Host Reaction in Liver Diseases
by Hiroshi Fukui
Microorganisms 2015, 3(4), 759-791; https://doi.org/10.3390/microorganisms3040759 - 28 Oct 2015
Cited by 45 | Viewed by 8328
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Metabolic Interactions)
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Article
Carbon-Starvation Induces Cross-Resistance to Thermal, Acid, and Oxidative Stress in Serratia marcescens
by Joseph R. Pittman, La’Kesha C. Kline and William J. Kenyon
Microorganisms 2015, 3(4), 746-758; https://doi.org/10.3390/microorganisms3040746 - 26 Oct 2015
Cited by 3 | Viewed by 6503
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 [...] Read more.
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. Full article
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Article
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
by Charlotte Cordonnier, Jonathan Thévenot, Lucie Etienne-Mesmin, Sylvain Denis, Monique Alric, Valérie Livrelli and Stéphanie Blanquet-Diot
Microorganisms 2015, 3(4), 725-745; https://doi.org/10.3390/microorganisms3040725 - 23 Oct 2015
Cited by 68 | Viewed by 8362
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Metabolic Interactions)
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Article
Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus
by Claudia Janosch, Francisco Remonsellez, Wolfgang Sand and Mario Vera
Microorganisms 2015, 3(4), 707-724; https://doi.org/10.3390/microorganisms3040707 - 21 Oct 2015
Cited by 19 | Viewed by 7227
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Extremophiles)
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Article
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
by Rene Kaden and Peter Krolla-Sidenstein
Microorganisms 2015, 3(4), 695-706; https://doi.org/10.3390/microorganisms3040695 - 20 Oct 2015
Cited by 3 | Viewed by 5385
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 [...] Read more.
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. Full article
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Article
Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches
by Antonio García-Moyano, Andreas Erling Austnes, Anders Lanzén, Elena González-Toril, Ángeles Aguilera and Lise Øvreås
Microorganisms 2015, 3(4), 667-694; https://doi.org/10.3390/microorganisms3040667 - 13 Oct 2015
Cited by 42 | Viewed by 9629
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Extremophiles)
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733 KiB  
Review
The Gut Microbiota as a Therapeutic Target in IBD and Metabolic Disease: A Role for the Bile Acid Receptors FXR and TGR5
by Annemarie Baars, Annemarie Oosting, Jan Knol, Johan Garssen and Jeroen Van Bergenhenegouwen
Microorganisms 2015, 3(4), 641-666; https://doi.org/10.3390/microorganisms3040641 - 10 Oct 2015
Cited by 61 | Viewed by 10197
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Metabolic Interactions)
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251 KiB  
Review
Alicyclobacillus spp.: New Insights on Ecology and Preserving Food Quality through New Approaches
by Emanuela Ciuffreda, Antonio Bevilacqua, Milena Sinigaglia and Maria Rosaria Corbo
Microorganisms 2015, 3(4), 625-640; https://doi.org/10.3390/microorganisms3040625 - 10 Oct 2015
Cited by 30 | Viewed by 10463
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Activity in Food)
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Article
Fungal Biodiversity in the Alpine Tarfala Valley
by Claudia Coleine, Laura Selbmann, Stefano Ventura, Luigi Paolo D’Acqui, Silvano Onofri and Laura Zucconi
Microorganisms 2015, 3(4), 612-624; https://doi.org/10.3390/microorganisms3040612 - 10 Oct 2015
Cited by 9 | Viewed by 6681
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Extremophiles)
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688 KiB  
Review
Bioprotective Role of Yeasts
by Serena Muccilli and Cristina Restuccia
Microorganisms 2015, 3(4), 588-611; https://doi.org/10.3390/microorganisms3040588 - 10 Oct 2015
Cited by 106 | Viewed by 10221
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Activity in Food)
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