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RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt, Bas Teusink
2019 PLoS Computational Biology  
Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes.  ...  We employed the RedCom approach for modeling communities of up to nine organisms involved in typical degradation steps of anaerobic digestion in biogas plants.  ...  Reduced metabolic modeling of microbial communities and application for the biogas process in (B) ).  ... 
doi:10.1371/journal.pcbi.1006759 pmid:30707687 pmcid:PMC6373973 fatcat:ngorerlqtbc5xdhhmrk7mrgaoi

gapseq: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models [article]

Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
2020 bioRxiv   pre-print
Here, we present gapseq: a novel tool for automated pathway prediction and metabolic network reconstruction from microbial genome sequences. gapseq combines databases of reference protein sequences (UniProt  ...  Furthermore, we illustrate the application of gapseq-reconstructed models to simulate biochemical interactions between microorganisms in multi-species communities.  ...  for analyzing 862 experimental datasets from anaerobic digestion.  ... 
doi:10.1101/2020.03.20.000737 fatcat:ns7g4rei6nbzzkxonhhybynlt4