Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models

Abstract

19Multi-species microbial communities determine the fate of materials in the environment 20 and can be harnessed to produce beneficial products from renewable resources. In a recent 21 example, fermentations by mixed microbial communities have produced medium-chain fatty acids 22 (MCFA). Tools to predict, assess, and improve the performance of these communities, however, 23 are limited. To provide such tools, we constructed two metabolic models of a MCFA-producing 24 community fed a byproduct from a biofuel fermentation. The first model is a unicellular model 25 (iFerment156) that contains a diverse set of fermentation pathways, including reverse b-oxidation 26 for MCFA production while the second model (iFermGuilds564) separates fermentation activities 27 into functional guilds. Both models predicted an energetic advantage for this community to 28 produce octanoic acid as a major fermentation product. Simulations with iFermGuilds564 29 predicted that 6-and 8-carbon MCFA were largely produced by a sugar-consuming guild, while 30 short-chain fatty acids were mainly produced by a guild consuming lactate. These models represent 31 novel tools for exploring the role of mixed microbial communities on carbon recycling in the 32 environment, as well as on beneficial reuse of organic residues. 33 well established, other strategies to expand the range of potential products of mixed culture 42 fermentations are only beginning to emerge, such as the carboxylate platform, which produces 43 medium-chain fatty acids (MCFA) as a potentially valuable set of bio-based products. 3, 4 44 MCFA are an attractive carboxylate platform product because of their many industrial 45 uses. 5 Octanoic acid (C8), an 8-carbon linear monocarboxylic acid, is a particularly valuable 46 MCFA because of its numerous uses, high market value, and relative ease of recovery. Further, 47 when C8 is reduced to its corresponding alkane, it can substitute for octane in liquid transportation 48 fuels. Recent research has demonstrated the feasibility of using mixed culture fermentations to 49 transform renewable resources into MCFA. 6-8 While C8 is produced in some self-assembled 50 microbial communities that develop in MCFA-producing bioreactors, hexanoic acid (C6) is often 51 the primary MCFA, along with acetic and butyric (C4) acids. 6-13 52Mathematical models have been established for the design and optimization of methane 53 production via anaerobic digestion. 14 These models describe the kinetics and stoichiometry of 54 reactions attributed to the individual members of the community that are responsible for hydrolysis 55 of complex organics, the fermentation of hydrolysis products, the transformation of fermentation 56 products to acetic acid and H2, and finally, the transformation of these intermediates to methane. 14 57The metabolic networks in these models are well defined, with interspecies H2 transfer known to 58 regulate critical metabolic steps, and therefore, anaerobic digestion models are predictive of the 59 behavior of self-assembled meth...

Mixed Acid Fermentation of Carbohydrate-Rich Dairy Manure Hydrolysate

“…The association of Clostridium sensu stricto 12 and Caproiciproducens with Acetobacter in this study might suggest a role of C2 in the microbial networks that formed during DCDA hydrolysate fermentation. Scarborough et al used a metabolic model to explore the potential effect of C2 co-utilization during chain elongation ( Scarborough et al, 2020 ). The metabolic model predicted C4 to be the sole product during utilization of acetic acid and lactic acid at high acetic acid:lactic acid ratios (greater than 0.96, as is the case in this study).…”