Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces

A novel strictly anaerobic, cellobiose-degrading bacterium, strain Cello, was isolated from a human faecal sample by combining enrichments in liquid and soft-agar basal media. A noteworthy characteristic was its inability to grow on normal agar plates and in roll tubes. The cells were coccus shaped and non-motile, with an extracellular slime layer. Growth of strain Cello T occurred between 20 and 40 degreesC, with optimal growth at 37 degreesC. The pH range for growth was 5-7-5 with an optimum at 6-5. In pure culture, strain Cello T could only grow on a variety of sugars. Glucose was converted to acetate, ethanol and H-2. The doubling time on glucose was 0.5 h. In a syntrophic co-culture with Methanospirillum hungatei strain JF-1(T), strain Cello(T) converted glucose to acetate and H-2. The G+C content was 59.2 mol%. 16S rDNA analysis revealed that the closest relatives of strain Cello(T) were two uncultured bacteria from anaerobic digesters, both with 94% 16S rDNA sequence similarity. The closest cultured representatives belong to genera of the bacterial division 'Verrucomicrobia'. The name Victivallis vadensis gen. nov., sp. nov. is proposed for strain Cello(T) (=DSM 14823(T) =ATCC BAA-548(T))

The host genotype affects the bacterial community in the human gastrointestinal tract

The gastrointestinal (GI) tract is one of the most complex ecosystems consisting of microbial and host cells. It is suggested that the host genotype, the physiology of the host and environmental factors affect the composition and function of the bacterial community in the intestine. However, the relative impact of these factors is unknown. In this study, we used a culture-independent approach to analyze the bacterial composition in the GI tract. Denaturing gradient gel electrophoresis (DGGE) profiles of fecal bacterial 16S rDNA amplicons from adult humans with varying degrees of genetic relatedness were compared by determining the similarity indices of the profiles compared. The similarity between fecal DGGE profiles of monozygotic twins were significantly higher than those for unrelated individuals (ts = 2.73, p1-tail = 0.0063, df=21). In addition, a positive relationship (F1, 30 = 8.63, p = 0.0063) between the similarity indices and the genetic relatedness of the hosts was observed. In contrast, fecal DGGE profiles of marital partners, which are living in the same environment and which have comparable feeding habits, showed low similarity which was not significantly different from that of unrelated individuals (ts = 1.03, p1-tail = 0.1561, df=27). Our data indicate that factors related to the host genotype have an important effect on determining the bacterial composition in the GI tract

Gelria glutamica gen. nov., sp. a thermophilic oligately syntrophic glutamate-degrading anaerobe

A novel anaerobic, Gram-positive, thermophilic, spore-forming, obligately syntrophic, glutamate-degrading bacterium, strain TGO(T), was isolated from a propionate-oxidizing methanogenic enrichment culture. The axenic culture was obtained by growing the bacterium on pyruvate. Cells were rod-shaped and non-motile. The optimal temperature for growth was 50--55 degrees C and growth occurred between 37 and 60 degrees C. The pH range for growth was 5.5--8 with optimum growth at pH 7. In pure culture, strain TGO(T) could grow on pyruvate, lactate, glycerol and several sugars. In co-culture with the hydrogenotrophic methanogen Methanobacterium thermautotrophicum strain Z-245, strain TGO(T) could grow on glutamate, proline and Casamino acids. Glutamate was converted to H(2), CO(2), propionate and traces of succinate. Strain TGO(T) was not able to utilize sulphate, sulphite, thiosulphate, nitrate or fumarate as electron acceptors. The G C content was 33.8 mol%. Sequence analysis of the 16S rDNA revealed that strain TGO(T) belongs to the thermophilic, endospore-forming anaerobes, though no close relations were found. Its closest relations were Moorella glycerini (92%) and Moorella thermoacetica (90%). Strain TGO(T) had an unusually long 16S rDNA of more than 1700 bp. The additional base pairs were found as long loops in the V1, V7 and V9 regions of the 16S rDNA. However, the loops were not found in the 16S rRNA. The name Gelria glutamica gen. nov., sp. nov. is proposed for strain TGO(T)

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota

The human small intestine is a key site for interactions between the intestinal microbiota and the mucosal immune system. Here we investigated the immunomodulatory properties of representative species of commonly dominant small-intestinal microbial communities, including six streptococcal strains (four Streptococcus salivarius, one S. equinus, one S. parasanguinis) one Veillonella parvula strain, one Enterococcus gallinarum strain, and Lactobacillus plantarum WCFS1 as a bench mark strain on human monocyte-derived dendritic cells. The different streptococci induced varying levels of the cytokines IL-8, TNF-a, and IL-12p70, while the V. parvula strain showed a strong capacity to induce IL-6. E. gallinarum strain was a potent inducer of cytokines and TLR2/6 signalling. As Streptococcus and Veillonella can potentially interact metabolically and frequently co-occur in ecosystems, immunomodulation by pair-wise combinations of strains were also tested for their combined immunomodulatory properties. Strain combinations induced cytokine responses in dendritic cells that differed from what might be expected on the basis of the results obtained with the individual strains. A combination of (some) streptococci with Veillonella appeared to negate IL-12p70 production, while augmenting IL-8, IL-6, IL-10, and TNF-a responses. This suggests that immunomodulation data obtained in vitro with individual strains are unlikely to adequately represent immune responses to mixtures of gut microbiota communities in vivo. Nevertheless, analysing the immune responses of strains representing the dominant species in the intestine may help to identify immunomodulatory mechanisms that influence immune homeostasis

Human intestinal microbiota composition is associated with local and systemic inflammation in obesity.

OBJECTIVE: Intestinal microbiota have been suggested to contribute to development of obesity, but the mechanism remains elusive. We relationship between microbiota composition, intestinal permeability, inflammation in non-obese and obese subjects. DESIGN AND METHODS: Fecal microbiota composition of 28 subjects (BMI 18.6-60.3kg/m2 ) was analyzed phylogenetic profiling microarray. Fecal calprotectin and plasma C- protein levels were determined to evaluate intestinal and systemic Furthermore, HbA1c , and plasma levels of transaminases and lipids were Gastroduodenal, small intestinal, and colonic permeability were assessed multi-saccharide test. RESULTS: Based on microbiota composition, the population segregated into two clusters with predominantly obese (15/19) exclusively non-obese (9/9) subjects. Whereas intestinal permeability differ between clusters, the obese cluster showed reduced bacterial decreased Bacteroidetes/Firmicutes ratio, and an increased abundance of pro-inflammatory Proteobacteria. Interestingly, fecal calprotectin was detectable in subjects within the obese microbiota cluster (n=8/19, Plasma C-reactive protein was also increased in these subjects correlated with the Bacteroidetes/Firmicutes ratio (rs =-0.41, p=0.03). CONCLUSIONS: Intestinal microbiota alterations in obese subjects are with local and systemic inflammation, suggesting that the obesity- microbiota composition has a pro-inflammatory effect

Reduction of colonic inflammation in HLA-B27 transgenic rats by feeding Marie Ménard apples, rich in polyphenols

Inflammatory bowel diseases (IBD) are immunomediated ailments affecting millions of individuals. Although diet is regarded as an important factor influencing IBD, there are no accepted dietary recommendations presently available. We administered 7.6 % lyophilised apples obtained from two cultivars (Golden Delicious and Marie Ménard, low and high in polyphenols, respectively) to HLA-B27 transgenic rats which develop spontaneous IBD. After 3 months feeding, rats fed Marie Ménard apples had reduced myeloperoxidase activity (3.6 (sem 0.3) v. 2.2 (sem 0.2) U/g tissue; P <0.05) and reduced cyclo-oxygenase-2 (P <0.05) and inducible NO synthase gene expression (P <0.01) in the colon mucosa and significantly less diarrhoea (P <0.05), compared with control rats. Cell proliferation in the colon mucosa was reduced significantly by feeding Golden Delicious apples, with a borderline effect of Marie Ménard apples. Gene expression profiling of the colon mucosa, analysed using the Whole Rat Genome 4 x 44 K Agilent Arrays, revealed a down-regulation of the pathways of PG synthesis, mitogen-activated protein kinase (MAPK) signalling and TNFalpha-NF-kappaB in Marie Ménard-fed rats. In the stools of the animals of this group we also measured a significant reduction of bacteria of the Bacteriodes fragilis group. In conclusion, the administration of Marie Ménard apples, rich in polyphenols and used at present only in the manufacturing of cider, ameliorates colon inflammation in transgenic rats developing spontaneous intestinal inflammation, suggesting the possible use of these and other apple varieties to control inflammation in IBD patient

The intestinal microenvironment and functional gastrointestinal disorders

For decades, interactions between the enteric neuromuscular apparatus and the central nervous system have served as the primary focus of pathophysiological research in the functional gastrointestinal disorders. The accumulation of patient reports, as well as clinical observations, has belatedly led to an interest in the role of various luminal factors and their interactions with each other and the host in functional gastrointestinal disorders. Most prominent among these factors has been the role of food. As a consequence, while not always evidence-based, dietary interventions are enjoying a renaissance in irritable bowel syndrome management. Not surprisingly, given its exploration in many disease states, the gut microbiota has also been studied in functional gastrointestinal disorders; data remain inconclusive. Likewise, there is also a considerable body of experimental and some clinical data to link functional gastrointestinal disorders pathogenesis to disturbances in epithelial barrier integrity, abnormal entero-endocrine signaling and immune activation. These data provide growing evidence supporting the existence of micro-organic changes, particularly in subgroups of patients with functional dyspepsia and IBS. However, their exact role in the complex pathophysiology and symptom generation of functional gastrointestinal disorders needs to be further studied and elucidated particularly with longitudinal and interventional studies.Giovanni Barbara, Christine Feinle-Bisset, Uday C. Ghoshal, Javier Santos, Stepen J. Vanner, Nathalie Vergnolle, Erwin G. Zoetendal, and Eamonn M. Quigle

Microbiome Analysis of Stool Samples from African Americans with Colon Polyps

Background: Colonic polyps are common tumors occurring in similar to 50% of Western populations with similar to 10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation. Aim: To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions. Materials & Methods: We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing. Results: Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes. Conclusion: This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size

Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration

Research on gut microbiota has generally focused on fecal samples, representing luminal content of the large intestine. However, nutrient uptake is restricted to the small intestine. Abundant immune cell populations at this anatomical site combined with diminished mucus secretion and looser junctions (partly to allow for more efficient fluid and nutrient absorption) also results in intimate host-microbe interactions despite more rapid transit. It is thus crucial to dissect key differences in both ecology and physiology between small and large intestine to better leverage the immense potential of human gut microbiota imprinting, including probiotic engraftment at biological sensible niches. Here, we provide a detailed review unfolding how the physiological and anatomical differences between the small and large intestine affect gut microbiota composition, function, and plasticity. This information is key to understanding how gut microbiota manipulation, including probiotic administration, may strain-dependently transform host-microbe interactions at defined locations

Towards standards for human fecal sample processing in metagenomic studies

Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses