However, the limited number of samples from healthy subjects and the impact of subject-specificity on the overall variation between samples hamper a more detailed comparison between ileostomy effluent and small intestinal lumen samples. Figure 1 (a) Relative contribution of different microbial groups that Paclitaxel clinical are present in samples derived from the small intestine and feces of four and two healthy individuals, respectively, and those from five healthy ileostomists. The taxonomic classification is … Microbiome of small intestine is less complex than that of the colon To obtain insight into the genetic potential and population dynamics within the small intestinal microbiota, a metagenomic library was constructed from the ileostoma effluent from a healthy individual who had the stoma for more than 20 years and did not require any stoma-related medication.

As the ileostomy effluent microbiota composition fluctuates over time (Booijink et al., 2010), the metagenome library was constructed on four different morning and afternoon effluent samples. The entire library encompassed 25344 fosmid clones with an average insert size of more than 25000bp, and thus, containing in total more than 700Mb (Supplementary Table S1). After initial quality control (see Supplementary Materials), three libraries representing the morning (1M) and afternoon (1A) of the same day and a morning sample taken 1 year earlier (A) were subjected to end sequencing (Sanger) and GS-FLX random sequencing (Supplementary Table S1), generating a total of 178Mb of sequence information.

146Mb of sequence information could be assembled into contigs that collectively encompass 63Mb, with the largest contig being 78kb, and leaving only 13% of the sequence-reads unassembled. This assembled proportion of sequences is considerably higher than previously observed with fecal metagenomes (Gill et al., 2006; Kurokawa et al., 2007), indicating a lower species diversity in the small intestine as compared with the colon, which is in line with the previous observations based on 16S rRNA genes (Hartman et al., 2009; Booijink et al., 2010). More than 170000 genes could be assigned in the assembled contigs, of which 16% was complete. Microbiome of the small intestine consists of various microbial phyla Phylogenetic positioning of sequences suggested that they originated from a wide variety of phylotypes, with Clostridium sp.

, Streptococcus sp. and coliforms as dominant phylogenetic groups (Supplementary Figure S1), which is consistent with the 16S rRNA-based analyses. In addition, an unexpectedly large fraction of high G+C Gram positives Batimastat was observed, which may be due to the commonly encountered underestimation of these microbial groups by regular 16S rRNA gene amplification (Hayashi et al., 2004).