Microbiome-based conversion of glucose to butyrate and hexanoate: roles and limitations revealed through genome-centered metatranscriptomics

Abstract

Background Chain elongation is emerging as a biotechnological tool to convert waste organics to beneficial fermentation products with wide utility across industrial and agricultural sectors. Glucose, the most abundant sugar on earth, is present in organic feedstocks as both a monomer and as a constituent of complex polymers. In this work, glucose was used as the sole carbon and electron source to enrich a chain elongating microbial community using duplicate bioreactor systems and batch experiments were performed to assess the role of hydrogen supplementation on fermentation. Results Hexanoic acid was the most abundant MCCA produced in both bioreactors with steady-state concentrations of about 4 g COD L^− 1 while butyric acid was the most abundant carboxylic acid with concentrations of about 5 g COD L^− 1. Metagenomic and metatranscriptomic analyses showed that the microbial communities in the duplicate reactors were very similar, with Caproicibacter sp. 002316805 and Caproicibacterium sp. 002399445 emerging as the most abundant chain elongating bacteria in both bioreactors. The microbiomes also contained a high abundance of lactic acid bacteria, primarily the Coriobacteriaceae Tractidigestivibacter and Olegusella. H₂ supplementation with batch experiments resulted in marginal changes in the products compared to controls with N₂ supplementation, with butyric acid production being higher than but not hexanoate production. One low-abundance Clostridium_B increased expression of genes for the Wood Ljungdahl pathway during H₂ supplementation. Conclusions The duplicate bioreactors behaved similarly, with the same abundant species. Combined, Caproicibacter sp. 002316805, Caproicibacterium sp. 002399445, and Tractidigestivibacter sp902834555 accounted for > 65% of the transcriptome and analysis of transcribed genes suggests butyrate and hexanoate originate from both direct sugar conversion by Caproicibacter sp. 002316805 and Caproicibacterium sp. 002399445 as well as initial conversion to lactate by Tractidigestivibacter sp902834555. Further, it was found that Caproicibacter and Caproicibacterium differ in synteny of chain elongation genes. H₂ supplementation during batch experiments did not reliably increase hexanoate production.