LAUSR

&NA; A mechanistic understanding of microbial community establishment and product formation in open fermentative systems can aid the development of bioprocesses utilising organic waste. Kinetically, a single rate‐limiting substrate is expected to result in one dominant species. Four enrichment cultures were operated to ferment either xylose or glucose in a sequencing batch reactor (SBR) or a continuous‐flow stirred tank reactor (CSTR) mode. The combination of 16S rRNA gene‐based analysis and fluorescence in situ hybridisation revealed no complete dominance of one species in the community. The glucose‐fed and xylose‐fed SBR enrichments were dominated >80% by one species. Enterobacteriaceae dominated the SBRs enrichments, with Citrobacter freundii dominant for xylose and Enterobacter cloacae for glucose. Clostridium, Enterobacteriaceae and Lachnospiraceae affiliates dominated the CSTRs enrichments. Independent of substrate, SBR communities displayed 2‐3 times higher biomass‐specific rate of substrate uptake (qsmax) and 50% lower biomass yield on ATP, to CSTR communities. Butyrate production was linked to dominance of Clostridium and low qsmax (1.06 Cmols Cmolx‐1 h‐1), while acetate and ethanol production was linked to dominance of Enterobacteriaceae and Lachnospiraceae and high qsmax (1.72 Cmols Cmolx‐1 h‐1 and higher). Overall, more diversity than expected through competition was observed, indicating mutualistic mechanisms might shape microbial diversity. &NA; Graphical Abstract Figure. We demonstrate that sequencing batch culturing promotes r‐organisms identified as Enterobacteriaceae, while continuous culturing promotes K‐organisms identified as Enterobactericiaceae, Clostridium and Lachnospiraceae.