coli and Clostridium in sample A (Supplementary Figures S1 and S2), confirming high population and functional dynamics in this ecosystem. Table 1 pH and metabolites (mM) in ileostomy effluent PTS and carbohydrate metabolism are highly expressed in small intestine As the metagenome provides only insight into the genetic potential of the ecosystem, total RNA was isolated selleckchem JQ1 from an ileostomy effluent sample and enriched for mRNA by selective capture methodology, followed by metatranscriptome analysis. Phylogenetic profiling of the mRNA-derived sequences indicated that the majority of these transcripts originated from Streptococcus sp. and coliforms (Supplementary Figure S4). Relative to the metagenome, the fast-growing facultative anaerobic organisms were prominently represented at the transcription level, whereas transcripts from the strict anaerobes were virtually absent from this library.

As intestinal facultative anaerobes are, in general, opportunists with an r-strategy, that is they increase their proportion in the total community under favorable conditions, we speculate that they adapt fast to the fluctuating conditions in the small intestine and hence may contain higher mRNA levels when compared with strict anaerobes. The metatranscriptome was strongly enriched for PTS and other carbohydrate transport systems, as well as energy- and central metabolic, and amino acid conversion pathways as compared with the metagenome, which is indicative for fast adaptation to nutrient availability (Figure 3b; Supplementary Table S5 and S6).

Phylogenetic profiling of the PTS transcripts indicated that a majority was expressed by streptococci, suggesting that these bacteria are the main utilizers of the available carbohydrates in the small intestinal lumen (Figure 3b). Although genes related to formate and acetate production were found to be overrepresented in the metatranscriptome compared with the metagenome, transcripts of other Short Chain Fatty Acids (SCFAs) and lactate fermentation pathways were also frequently detected. Notably, carbohydrate utilization and central metabolism functions were also overrepresented in fecal communities, but appeared to be more dedicated to the degradation of complex carbohydrates rather than simple sugars (Klaassens et al., 2009; Turnbaugh et al., 2010).

Moreover, shotgun metaproteomics revealed the enrichment of translation, energy production and carbohydrate metabolism in feces (Verberkmoes et al., 2009). Neither of these studies revealed a high enrichment of sugar PTS transport modules, which contrast to our observations of the small intestine microbiota. These findings indicate Dacomitinib that rapid internalization and conversion of the available (simple) carbohydrates to support growth is a prominent strategy for microbial proliferation and maintenance in the small intestine.