The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

http://www.klinikaikozpont.u-szeged.hu/pedia/images/pdf/CME_TEL/Full-Text/25.pdf

The Hallmarks of Aging

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the lower bacterial richness group also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese participants. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.

/pdf/richness-of-human-gut-microbiome-correlates-with-metabolic-1i65keoatj.pdf

Richness of human gut microbiome correlates with metabolic markers

The link between the microbes in the human gut and the development of obesity, cardiovascular disease and metabolic syndromes, such as type 2 diabetes, is becoming clearer. However, because of the complexity of the microbial community, the functional connections are less well understood. Studies in both mice and humans are helping to show what effect the gut microbiota has on host metabolism by improving energy yield from food and modulating dietary or the host-derived compounds that alter host metabolic pathways. Through increased knowledge of the mechanisms involved in the interactions between the microbiota and its host, we will be in a better position to develop treatments for metabolic disease.

Functional interactions between the gut microbiota and host metabolism

La presente invention concerne des bacteries isolees qui sont caracterisees comme pouvant etre mises en culture, derivees d'un tractus gastro-intestinal neonatal humain, et pouvant produire de l'acide gamma-aminobutyrique. Cette invention concerne en outre l'utilisation de ces bacteries productrices de GABA pour traiter ou reguler la fonction cardiovasculaire, les troubles de l'humeur, l'anxiete, le stress, la douleur et les troubles caracterises par une proliferation.

Bactéries pouvant être mises en culture, produisant de l'acide gaba et dérivées du tractus gastro-intestinal

Aim: Dietary fibre is important for shaping gut microbiota. The aim of this pilot study was to investigate the impact of dietary fibres on pathogen performance in the presence of gut microbiota. Methods: In an ex vivo gut model, pooled faecal samples were spiked with a cocktail of representative gastrointestinal pathogens and fermented with yeast β-glucan for 24 hours, after which 16S rRNA amplicon sequencing and short-chain and branched-chain fatty acid (SCFA and BCFA) analyses were performed. In addition, oat β-glucan, arabinoxylan, yeast β-glucan, and galactooligosaccharides were each tested against individual representative pathogens and pathogen growth was assessed via qPCR. Glucose served as a control carbon source. Results: Based on 16S rRNA amplicon sequencing, yeast β-glucan was selected for higher proportions of Bacteroides (P = 0.0005, ~6 fold) and Clostridia (P = 0.005, ~3.6 fold) while species of Escherichia/Shigella (P = 0.021, ~2.8 fold) and Lactobacillus (P = 0.007, ~ 15.7-fold) were higher in glucose. Pathogen relative abundance did not differ between glucose and yeast β-glucan. In the absence of pathogens, higher production of BCFAs (P = 0.002) and SCFAs (P = 0.002) fatty acids was observed for fibre group(s). For individual pathogens, yeast β-glucan increased growth of Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes (P < 0.05), arabinoxylan increased S. typhimurium (P < 0.05). Tested fibres decreased vancomycin-resistant Enterococcus faecium (P < 0.05), with yeast β-glucan causing a 1-log reduction (P < 0.01), while galactooligosaccharides decreased L. monocytogenes (P < 0.05). Conclusion: Tested fibres differentially influenced the growth of pathogens, but yeast β-glucan could represent a dietary strategy to help limit vancomycin-resistant enterococci (VRE) expansion in the gut.

A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion

A linoleate isomerase complex including myosin-cross-reactive antigen, short-chain dehydrogenase/oxidoreductase, and acetoacetate decarboxylase has been confirmed as the pivotal factor for conjugated linoleic acid (CLA) production in Lactobacillus plantarum. However, its role in the metabolism and health-associated benefits of Lactobacillus remain unclear. In the current study, the mild type, knockout, and complemented mutants of the linoleate isomerase complex of L. plantarum ZS2058 were used to investigate those putative effects. The metabonomic results showed that a linoleate isomerase complex could significantly influence the glycol-metabolism, lipid metabolism, and antioxidant compounds. Especially, with the stress of linoleic acid, linoleate isomerase complex knockout mutants induced the increase of several antioxidant compounds, such as glutamic acid, glycine, l-cysteine, glycerol, and l-sorbosone. Moreover, the linoleate isomerase complex played a pivotal role in ameliorating DSS-induced colitis. The knockout mutants showed effects similar to those in the DSS group, whereas complementation of the corresponding gene in the knockout mutants could restore the anti-inflammatory activity, wherein the integrity of a mucus layer was repaired, the level of pro-inflammatory cytokines decreased, and the amount of anti-inflammatory cytokines increased significantly. All the results indicated that the linoleate isomerase complex plays a key role in CLA production and metabolism as well as the health-associated benefits of L. plantarum ZS2058. These results are conducive to promote clinical trials and product development of probiotics for colitis.

Linoleate Isomerase Complex Contributes to Metabolism and Remission of DSS-Induced Colitis in Mice of Lactobacillus plantarum ZS2058.

The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system is an important adaptive immune system for bacteria to resist foreign DNA infection, which has been widely used in genotyping and gene editing. To provide a theoretical basis for the application of the CRISPR-Cas system in Bifidobacterium breve , the occurrence and diversity of CRISPR-Cas systems were analysed in 150 B. breve strains. Specifically, 47 % (71/150) of B. breve genomes possessed the CRISPR-Cas system, and type I-C CRISPR-Cas system was the most widely distributed among those strains. The spacer sequences present in B. breve can be used as a genotyping marker. Additionally, the phage assembly-related proteins were important targets of the type I-C CRISPR-Cas system in B. breve , and the protospacer adjacent motif sequences were further characterized in B. breve type I-C system as 5′-TTC-3′. All these results might provide a molecular basis for the development of endogenous genome editing tools in B. breve .

Characterization of CRISPR-Cas systems in Bifidobacterium breve

In this study, wheat and oat bran fibres were used to investigate the potential beneficial prebiotic-enhancing effects of superheated steam (SHS) treatment. Following SHS treatment of fibres, in-vitro simulated gastric and intestinal digestion followed by batch culture fermentation was performed. 16S rRNA gene sequencing and short chain fatty acid analysis were conducted, which demonstrated that SHS treatment was associated with significant differences in beta diversity and the relative abundances of several microbial taxa. Principal Coordinate Analysis (PCoA) revealed significant separation between SHS-treated oat and non-treated oat (p = 0.013), and between SHS-treated wheat and non-treated wheat following in vitro batch fermentation (p = 0.042). Abundances of Ruminococcus were found to be significantly higher by 1.09-log in SHS-treated oat when compared with non-treated oat while abundances of Escherichia_Shigella, and Alistipes were significantly lower by 1.47-log and 0.39-log, respectively in the SHS-treated oat samples than the non-treated oat samples (p = 6.85E-06, p = 0.002037, p = 0.002458; respectively). These data demonstrate that SHS treatment of dietary fibre enhanced its effectiveness to modulate the gut microbiome. Industrial Relevance: Superheated steam (SHS) treatment has emerged as an effective method to improve the shelf-life of grains by reducing lipid hydrolysis and oxidation. Our results revealed that SHS treatment of wheat and oat brans led to increased physiological and chemical properties including higher water-binding capacity, water-extractable arabinoxylan, and total phenolics as well as improvement in human gut microbiota. Our results suggest that this method could be implemented in the food industry in order to improve beneficial properties of oat and wheat brans. 

Catherine Stanton

Papers

Bactéries pouvant être mises en culture, produisant de l'acide gaba et dérivées du tractus gastro-intestinal

A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion

Linoleate Isomerase Complex Contributes to Metabolism and Remission of DSS-Induced Colitis in Mice of Lactobacillus plantarum ZS2058.

Characterization of CRISPR-Cas systems in Bifidobacterium breve

The microbiome modulating potential of superheated steam (SHS) treatment of dietary fibres