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Appl Environ Microbiol. 2019 Nov 8. pii: AEM.02242-19. doi: 10.1128/AEM.02242-19. [Epub ahead of print]

Medium-chain fatty acid synthesis by Candidatus Weimeria bifida, gen. nov., sp. nov., and Candidatus Pseudoramibacter fermentans, sp. nov.

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The Great Lakes Bioenergy Research Center, UW-Madison, Madison, WI.
The Department of Civil and Environmental Engineering, UW-Madison, Madison, WI.
The Department of Bacteriology, UW-Madison, Madison, WI.
The Great Lakes Bioenergy Research Center, UW-Madison, Madison, WI


Chain elongation is emerging as a bioprocess to produce valuable medium-chain fatty acids (MCFA; 6 to 8 carbons in length) from organic waste streams by harnessing the metabolism of anaerobic microbiomes. Although our understanding of chain elongation physiology is still evolving, the reverse β-oxidation pathway has been identified as a key metabolic function to elongate the intermediate products of fermentation to MCFA. Here, we describe two uncultured chain-elongating microorganisms that were enriched in an anaerobic microbiome transforming the residues from a lignocellulosic biorefining process. Based on a multi-omic analysis, we describe Candidatus Weimeria bifida, gen. nov., sp. nov. and Candidatus Pseudoramibacter fermentans, sp. nov., both predicted to produce MCFA but using different substrates. The analysis of a time-series meta-transcriptomic dataset suggests that Ca. W. bifida is an effective xylose utilizer since both the pentose phosphate pathway and the Bifid shunt are active. Furthermore, the metatranscriptomic data suggests that energy conservation during MCFA production in this organism is essential and occurs via the creation of an ion motive force using both the RNF complex and an energy-conserving hydrogenase. For Ca. P. fermentans, predicted to produce MCFA from lactate, the meta-transcriptomic analysis reveals the activity of an electron-confurcating lactate dehydrogenase, energy conservation via the RNF complex, H2 production for redox balance, and glycerol utilization. A thermodynamic analysis also suggests the possibility of glycerol being a substrate for MCFA production by Ca. P. fermentans. In total, this work reveals unknown characteristics of MCFA production in two novel organisms.IMPORTANCE Chain elongation by medium chain fatty acid (MCFA)-producing microbiomes offer an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain elongation is only beginning to be studied, and many of these organisms remain uncultured. We analyzed MCFA production by two uncultured organisms that were identified as the main MCFA producers in a microbial community enriched from an anaerobic digester; this characterization, which is based on meta-multi-omic analysis, complements the knowledge that has been acquired from pure culture studies. The analysis revealed previously unreported features of the metabolism of MCFA-producing organisms.

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