A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing

•SIP determined microorganisms in MFCs operated under different conditions.•Substrate type and electricity generation affected anodic communities.•Geobacter, Rhodocyclaceae and Enterobacteriaceae were involved in carbon uptake.

Stable isotope probing and high throughput sequencing were used to characterize the microbial communities involved in carbon uptake in microbial fuel cells at two levels of electricity generation. With acetate, the dominant phylotypes involved in carbon uptake included Geobacter and Rhodocyclaceae. With glucose, both Enterobacteriaceae and Geobacter were dominant.