Fig. 5

Microbial competition within individual fermentor runs. Changes in Bacteroides species and in the Firmicutes bacteria F. prausnitzii and Eubacterium eligens are shown for 12 fermentors (as described in Fig. 2a–d) that involved inocula from donors D1, D2 and D3. The sequence of imposed pH changes is shown for each run. These plots show the proportional abundance of OTUs determined from analysis of 16S rRNA gene amplicon sequences (Additional file 2: Table S1). Three F. prausnitzii OTUs and one E. eligens OTU were detected in inocula from all three donors, while a fourth F. prausnitzii OTU0013 was also detected in D1 and D3 inocula. Similarly, four Bacteroides OTUs (B. uniformis, B. vulgatus/dorei, B. caccae and B. ovatus) were present in inocula from all three donors. Of the remaining four Bacteroides OTUs shown, B. cellulosilyticus/intestinalis was not detected in D1 inocula, B. thetaiotaomicron and B. stercoris were not detected in D1 and D2 inocula, and B. eggerthii was not found in D3 inocula