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Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models
- Source :
- mSystems, Vol 5, Iss 5 (2020), mSystems
- Publication Year :
- 2020
- Publisher :
- American Society for Microbiology, 2020.
-
Abstract
- 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.<br />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.
- Subjects :
- Physiology
medium-chain fatty acids
microbiome
010501 environmental sciences
01 natural sciences
Biochemistry
Microbiology
03 medical and health sciences
Human health
Metabolomics
Mixed culture
octanoic acid
Genetics
Microbiome
Food science
Molecular Biology
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
0105 earth and related environmental sciences
0303 health sciences
medium-chain carboxylic acids
community modeling
Applied and Environmental Science
Chemistry
QR1-502
Computer Science Applications
mixed-culture fermentation
Metabolic pathway
Microbial population biology
Modeling and Simulation
Guild
Fermentation
carboxylate platform
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 23795077
- Volume :
- 5
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- mSystems
- Accession number :
- edsair.doi.dedup.....7c506afb582b15074282cac62a67ac24