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

Multifunctional jute fabrics obtained by different chemical modifications

Abstract: The aim of the present research is first to reduce the jute fabric non-cellulosic components by using different chemical modifications (i.e. alkali and oxidative) and then to analyze their influence on the jute fabric properties. For that purpose, the jute fabrics were characterized in terms of their chemical composition, structural parameters, mechanical properties, volume electrical resistivity, antibacterial activity and biosorption of Zn2+. Moreover, the jute fabrics were functionalized by incorporation of silver ions and the fabrics were evaluated as sorption material with a further perspective of reuse. After the alkali modifications, the hemicelluloses were selectively removed and the fabric structural parameters increased. Alkali modifications under mild conditions (1% NaOH for 30 min and 5% NaOH for 5 min) lead to a decrease, while the most intensive alkali modification (17.5% NaOH for 30 min) contributed to an increase in the volume electrical resistivity and fabric maximum force compared to unmodified fabric. A relationship between the jute fabric chemical composition, crystallinity index, conversion of cellulose I to cellulose II, fabric structural parameters and volume electrical resistivity was found. The oxidations lead to selective lignin removal, which consequently causes a decrease in the volume electrical resistivity and fabric maximum force. Ag+ incorporated in the selected samples decreased their electrical resistivity even further. Following the increased focus on the concept of circular economy and sustainable development goals, the biosorption potential of damaged and waste jute fabrics for Zn2+ was investigated. Jute fabrics with incorporated Ag+ and those obtained after the biosorption of Zn2+ provided maximum bacterial reduction (99.99%) for Escherichia coli and Staphylococcus aureus. The chemically modified jute fabrics can be utilized as carpet backing and protective clothing in environments sensitive to electrical discharges, but also as filters for water disinfection and biosorbents for Zn2+.Graphic abstract: [Figure not available: see fulltext.]

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

Genome Sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens

International audienc

Specific Hypersensitive Response–Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato

Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged. To combat these strains, new Cf genes are required. An effectoromics approach was employed to identify wild tomato accessions carrying new Cf genes. Proteomics and transcriptome sequencing were first used to identify 70 apoplastic in planta–induced C. fulvum SSPs. Based on sequence homology, 61 of these SSPs were novel or lacked known functional domains. Seven, however, had predicted structural homology to antimicrobial proteins, suggesting a possible role in mediating antagonistic microbe-microbe interactions in planta. Wild tomato accessions were then screened for HR-associated recognition of 41 SSPs, using the Potato virus X–based transient expression system. Nine SSPs were recognized by one or more accessions, suggesting that these plants carry new Cf genes available for incorporation into cultivated tomato

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]