Fig. 5

Composition of MBRA core communities and comparison with fecal inocula. We analyzed the phylogenetic distribution of OTUs in the individual core communities and compared this with the phylogenetic distribution of the original fecal inocula. To provide better representation of the fecal inocula, those OTUs absent from the individual core communities that contributed at least 0.5 % of sequences to a fecal sample were also included in our analyses. As in Fig. 4, data present is the mean abundance for each OTU across days 8–21. Following determination of consensus classifications for each OTU (as described in Methods), we plotted the percent abundance of sequences in each phylum (a), genus within Bacteroidetes (b), family within Firmicutes (c), and genus within Proteobacteria (d). If a consensus classification for the phylogenetic level plotted could not be determined with confidence, the next highest classification assigned with ≥80 % is given preceded by the designation “unclassified.” To simplify presentation of abundances in c, several families with low abundance across all samples were condensed in to the designation “other Firmicutes”, which includes Clostridiales Incertae Sedis XIII, Eubacteriaceae, Incertae Sedis XI, unclassified Firmicutes, unclassified Clostridia, unclassified Clostridiales, and Veillonellaceae