Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models.

Matthew J Scarborough,Joshua J Hamilton,Daniel R Noguera,Elizabeth A Erb,Timothy J Donohue,Michael Rust

doi:10.1128/msystems.00755-20

Abstract

Multispecies microbial communities determine the fate of materials in the environment and can be harnessed to produce beneficial products from renewable resources. In a recent example, fermentations by microbial communities have produced medium-chain fatty acids (MCFAs). Tools to predict, assess, and improve the performance of these communities, however, are limited. To provide such tools, we constructed two metabolic models of MCFA-producing microbial communities based on available genomic, transcriptomic, and metabolomic data. The first model is a unicellular model (iFermCell215), while the second model (iFermGuilds789) separates fermentation activities into functional guilds. Ethanol and lactate are fermentation products known to serve as substrates for MCFA production, while acetate is another common cometabolite during MCFA production. Simulations with iFermCell215 predict that low molar ratios of acetate to ethanol favor MCFA production, whereas the products of lactate and acetate coutilization are less dependent on the acetate-to-lactate ratio. In simulations of an MCFA-producing community fed a complex organic mixture derived from lignocellulose, iFermGuilds789 predicted that lactate was an extracellular cometabolite that served as a substrate for butyrate (C4) production. Extracellular hexanoic (C6) and octanoic (C8) acids were predicted by iFermGuilds789 to be from community members that directly metabolize sugars. Modeling results provide several hypotheses that can improve our understanding of microbial roles in an MCFA-producing microbiome and inform strategies to increase MCFA production. Further, these models represent novel tools for exploring the role of mixed microbial communities in carbon recycling in the environment, as well as in beneficial reuse of organic residues.IMPORTANCE Microbiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three medium-chain fatty acid-producing guilds and identified potential strategies to increase production of medium-chain fatty acids. This work demonstrates the role of metabolic models in augmenting multi-omic studies to gain greater insights into microbiome behavior.

Highlights

Mixed microbial fermentations have benefited humanity throughout history.[1]
These results suggest that sugars, glycerol, and lactate can produce significant amounts of multiple fermentation products, including C2, C4, C6, and C8, while supporting optimal biomass production, and that production of ethanol or lactate, the two common fermentation products described as intermediates in medium-chain fatty acids (MCFAs) production,[28] are not as energetically favorable as producing other fermentation products
Like ethanol and C2 co-utilization, lactate and C2 co-utilization is not predicted by iFermCell[215] to be impacted by bioreactor H2 partial pressure (Fig S7). These results suggest that when lactate is a key intermediate in an MCFA-producing community, controlling the relative amounts of C2 and lactate may not be an effective strategy for increasing C6 and C8 production

Summary

Introduction

Mixed microbial fermentations have benefited humanity throughout history.[1]. Since the mid-18th century, mixed culture fermentations have produced valuable chemicals and recovered energy from wastes.[2]. Fermentation products like acetic acid (C2) and H2 are used to support microbial production of methane, enabling the recovery of a large fraction of the chemical energy originally present in the complex organic substrates. While anaerobic digestion technologies are well established, other strategies to expand the range of potential products of mixed culture fermentations are only beginning to emerge. One example of such a mixed culture fermentation is the carboxylate platform, which produces medium-chain fatty acids (MCFAs) as a potentially valuable set of bio-based products.[3]

Methods

Results

Conclusion