Longitudinal metataxonomic analysis of the small intestinal microbiota
Longitudinal microbial composition in ileostomy effluent was analysed by metataxonomic analysis, which was successful in 390 (> 90%) of the 432 collected effluent samples (27 per individual). The samples obtained from two subjects had the lowest success rate, which for at least one of the subjects appeared to be due to the low DNA recovery in the samples (Additional file The majority of the sequences were assigned to Firmicutes (78.6%) and Proteobacteria (11.9%), followed by Actinobacteria (6.3%) and Bacteroidetes (3.1%). The average microbiota composition per subject revealed a high degree of variation among the subjects (Supplementary Figure S