High Prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae Detected in the Human Gut Using an Improved DNA Detection Protocol

Background: The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool. Methodology/Principal Findings: Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens ( 15 for M. smithii and 15 for M. stadtmanae) yielded a sequence similarity of 99-100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences. Conclusions/Significance: In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome

Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

International audienceThe biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation

Intestinal microbiota in human health and disease: the impact of probiotics

The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with specific attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis

Antimicrobial viscose fabric prepared by treatment in DBD and subsequent deposition of silver and copper ions-Investigation of plasma aging effect

In this work, the effect of dielectric barrier discharge (DBD) in ambient air on preparation of antimicrobial viscose fabric was studied. DBD plasma treatment was applied under constant discharge power and different exposure times. Vertical wicking test was used to evaluate optimal conditions for plasma treatment of viscose in order to increase fabrics' wettability and consequently improve sorption properties. Investigation of aging effect of plasma treatment revealed that there was no significant change in wettability of viscose samples 21 days after plasma treatment, which suggests good durability of treatment. After DBD plasma treatment, fabrics were modified with silver and copper ions in order to impart antimicrobial properties on viscose fabric. Viscose samples, modified with Ag (I) and Cu (II) ions immediately and 1, 7, 14 and 21 days after DBD treatment were tested in vitro against microorganisms S. aureus, E. coli and C. albicans using agar diffusion test. Obtained results showed that modification with DBD, prior to sorption of Ag (I) and Cu (II) ions, leads to improvement of antimicrobial activity of viscose samples, with a possibility to provide specific activity against different microorganisms by altering the days after DBD treatment prior ions sorption

From Agricultural Waste to Biofuel: Enzymatic Potential of a Bacterial Isolate Streptomyces fulvissimus CKS7 for Bioethanol Production

Purpose To avoid a negative environmental and economic impact of agricultural wastes, and following the principles of circular economy, the reuse of agricultural wastes is necessary. For this purpose, isolation of novel microorganisms with potential biotechnological application is recommended. The current researches in bioethanol production are aimed to reduce the production costs using low-cost substrates and in-house produced enzymes by novel isolated microorganisms. In line with this, in this study valorization of these agricultural by-products by novel isolate S. fulvissimus CKS7 to biotechnological value added products was done. Methods Standard microbiological methods were used for the isolation and characterization of strain. Enzymes activities were determinated using DNS method while, the ethanol concentration was determined based on the density of the alcohol distillate at 20 degrees C. Results The maximal enzymatic activities for amylase, cellulases (carboxymethyl cellulase and Avicelase), pectinase and xylanase were achieved using rye bran as a waste substrate for CKS7 growth. Obtained crude bacterial enzymes were used for enzymatic hydrolysis of lignocellulosic materials including horsetail waste, yellow gentian waste, corn stover, cotton material and corona pre-treated cotton material. The maximum yield of reducing sugars was obtained on horsetail waste and corona pre-treated cotton material. Waste brewer's yeast Saccharomyces cerevisiae was successfully used for the production of bioethanol using horsetail waste hydrolysate and corona pre-treated cotton material hydrolysate. Conclusion The obtained results showed that bacterial strain CKS7 has a significant, still unexplored enzymatic potential that could be used to achieve a cleaner, environmental friendly and economically acceptable biofuel production. [GRAPHICS]

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H(2)-CO(2) utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H(+) rather than Na(+) transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na(+) and H(+) chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations