Selective colonization of insoluble substrates by human faecal bacteria

Abstract

Insoluble plant polysaccharides and endogenous mucin are important energy sources for human colonic microorganisms. The object of this study was to determine whether or not specific communities colonize these substrates. Using faecal samples from four individuals as inocula for an anaerobic in vitro continuous flow system, the colonization of wheat bran, high amylose starch and porcine gastric mucin was examined. Recovered substrates were extensively washed and the remaining tightly attached bacterial communities were identified using polymerase chain reaction-amplified 16S rRNA gene sequences and fluorescent in situ hybridization. The substrate had a major influence on the species of attached bacteria detected. Sequences retrieved from bran were dominated by clostridial cluster XIVa bacteria, including uncultured relatives of Clostridium hathewayi, Eubacterium rectale and Roseburia species. Bacteroides species were also detected. The most abundant sequences recovered from starch were related to the cultured species Ruminococcus bromii, Bifidobacterium adolescentis, Bifidobacterium breve and E. rectale. The most commonly recovered sequences from mucin were from Bifidobacterium bifidum and uncultured bacteria related to Ruminococcus lactaris. This study suggests that a specific subset of bacteria is likely to be the primary colonizers of particular insoluble colonic substrates. For a given substrate, however, the primary colonizing species may vary between host individuals.

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

“…Despite the fact that, in living animals, the continuous desquamation of mucus into the luminal content obscures the distinction between luminal and mucosal microbes, recent in vivo studies also show an enrichment of Firmicutes (especially Clostridium cluster XIVa4 Lachnospiraceae family), over Bacteroidetes in biopsies compared with luminal or faecal samples, both in rodents (Hill et al, 2009;Nava et al, 2011) and humans (Eckburg et al, 2005;Frank et al, 2007;Shen et al, 2010;Wang et al, 2010;Willing et al, 2010;Hong et al, 2011). This in vivo enrichment of Firmicutes in mucus, although sometimes less strong as during our in vitro study, suggests that similar forces may drive the mucosal microbiota composition in vivo and in vitro, likely to include selection of specific groups that adhere to mucins (Leitch et al, 2007) or insoluble substrates in general (Walker et al, 2008). Furthermore, as opposed to the luminal content where the pH was maintained constant, local accumulation of acids in mucus may cause a lower pH, selecting for Firmicutes over Bacteroidetes and Proteobacteria (Duncan et al, 2009).…”

Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

“…The intestinal mucus layer provides an ecological niche, and mucus can be seen as a rich carbon and energy source for intestinal microbiota (Derrien et al, 2004). Remarkably, it has been shown that not only are mucin beads added to a two-stage intestinal model system readily colonized by bacterial biofilms, but also that mucin is largely degraded by luminal microbiota, reinforcing the notion that mucin can serve as substrate for a variety of intestinal micro-organisms (Leitch et al, 2007;Macfarlane et al, 2005).…”

“…Furthermore, procedure IN2 had a pronounced impact on members of the phylum Bacteroidetes, which made its composition more deviant from that present in healthy adults. The specific enrichment of primarily Bacteroides vulgatus-like organisms was most likely induced by the addition of mucus, since B. vulgatus was found to be the predominant mucus colonizer of two out of four analysed subjects in a recent study (Leitch et al, 2007). The ability to extract these data directly from the microbiota profiles emphasizes the advantage of phylogenetic microarray-based fingerprints in comparison with those obtained using other, wellestablished fingerprinting techniques such as DGGE, and reinforces earlier evidence for the superiority of phylogenetic microarrays (Neufeld et al, 2006).…”

Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota

“…R. flavefaciens and Ruminococcus albus, isolated from the rumen, are the only Ruminococcus species able to degrade cellulose (Flint et al, 2008). Ruminococcus bromii and Ruminococcus callidus, isolated from the human gut, are able to degrade other complex polysaccharides such as starch or xylan (Leitch et al, 2007). However, the presence of cellulolytic Ruminococcus-like strains in the human Strain 18P13 T was isolated from a fresh faecal sample of a 38-year-old methane-excreting healthy human female who had not received antibiotics in the last 3 months, had no diagnosed gastrointestinal disease, consumed a diverse Western diet that included at least 15 g dietary fibre per day and had a normal body mass index (18-25 kg m 22 ).…”