The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

Abstract

The human gastrointestinal tract (GI tract) harbors a complex community of microbes. The microbiota composition varies between different locations in the GI tract, but most studies focus on the fecal microbiota, and that inhabiting the colonic mucosa. Consequently, little is known about the microbiota at other parts of the GI tract, which is especially true for the small intestine because of its limited accessibility. Here we deduce an ecological model of the microbiota composition and function in the small intestine, using complementing culture-independent approaches. Phylogenetic microarray analyses demonstrated that microbiota compositions that are typically found in effluent samples from ileostomists (subjects without a colon) can also be encountered in the small intestine of healthy individuals. Phylogenetic mapping of small intestinal metagenome of three different ileostomy effluent samples from a single individual indicated that Streptococcus sp., Escherichia coli, Clostridium sp. and high G þ C organisms are most abundant in the small intestine. The compositions of these populations fluctuated in time and correlated to the short-chain fatty acids profiles that were determined in parallel. Comparative functional analysis with fecal metagenomes identified functions that are overrepresented in the small intestine, including simple carbohydrate transport phosphotransferase systems (PTS), central metabolism and biotin production. Moreover, metatranscriptome analysis supported high level in-situ expression of PTS and carbohydrate metabolic genes, especially those belonging to Streptococcus sp. Overall, our findings suggest that rapid uptake and fermentation of available carbohydrates contribute to maintaining the microbiota in the human small intestine.

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

“…Pigs are hindgut fermenters and rely on these beneficial microbes in their large intestine to ferment complex carbohydrates that remain in the food to extract more energy. The lack of PCW degradation was complemented by enrichment for carbohydrate transport phosphotransferase systems in the ileum, as has been shown in human ileostomy samples (Zoetendal et al, 2012). Comparative genome analyses of human intestinal Firmicutes versus Bacteroidetes also showed carbohydrate transport phosphotransferase systems system and ABC transporter enrichment in Firmicutes, and PCWdegradation enzyme enrichment in Bacteroidetes (Mahowald et al, 2009).…”

“…Phages have an important role in the gut ecosystem as evidenced by the diversity of phages in swine fecal viromes (Allen et al, 2011), phage ubiquity across more than 100 human fecal metagenomes (Qin et al, 2010), and their enrichment in human ileostomy samples compared with fecal metagenomes (Zoetendal et al, 2012). The assembly of two partial phage genomes from the bacterial metagenomes of the ileum suggests that they are present in greater copy number than that expected for lysogens.…”

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

“…An enrichment of bacteria generally associated with the small intestine, such as Veillonella, Streptococcus or Lactobacillus species, was previously observed in patients with recurrent CDI before FMT (Khoruts et al, 2010;Zoetendal et al, 2012). Many of these trends can be explained by the history of antibiotic use of these patients (Vrieze, 2013), as most Lactobacillus spp.…”

Adaptation of faecal microbiota in sows after diet changes and consequences for in vitro fermentation capacity

“…These approaches, compared to 16S rRNA gene-targeted approaches such as DGGE-and PITChip analysis, can more directly provide information regarding the metabolic activity of intestinal microorganisms based on the identification of active pathways (Kolmeder et al, 2012;Zoetendal et al, 2012).…”