Networks of energetic and metabolic interactions define dynamics in microbial communities
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Significance: Microbial communities are critical to global carbon cycling and particularly important in oxygen-limited environments, such as sediments and parts of the human microbiome. However, the uncultured members of these communities often hinder the study of community composition and interspecies interactions at a deeper level. Here, we integrate metagenomic binning, metatranscriptomic analysis, and metabolic modeling to obtain quantitative information about interspecies interactions between individual species present in methanogenic communities. We found that these communities are defined by not only metabolic interactions but also additional interdependencies, such as amino acid auxotrophies. Strategic usage of antimicrobials by specific community members further reinforces this intricate interspecies network, thereby enforcing strong collaboration among community members.
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Genome sequences and quantitative models are used to reconstruct metabolic pathways and investigate microbial consortia dynamics.
“Genome sequences and quantitative models are used to reconstruct metabolic pathways and investigate microbial consortia dynamics [109].”
From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [109]
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- Authors
- Embree, M., Liu, J. K., Al-Bassam, M. M., & Zengler, K.
- Affiliations
- University of Washington (US)
- Department of Bioengineering, University of California, San Diego, CA 92091
- Corresponding author
- Zengler, Karsten
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-11-30
- Volume
- 112
- Issue
- 50
- Pages
- 15450-15455
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4687543
- OpenAlex
- W2208966601
- Cited by
- 256
- References
- 2
- Citations by year
- 2026: 23 · 2025: 29 · 2024: 24 · 2023: 26 · 2022: 17 · 2021: 24 · 2020: 27 · 2019: 34 · 2018: 23 · 2017: 16 · 2016: 13
- FWCI
- 21.83
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DE-SC0004485, DE-SC0004917)
- Topics
- Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
- Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- methanogenic archaea, interspecies interactions, metabolic redundancy, amino acid auxotrophy, community robustness, community dynamics, species richness, carbon cycle, metagenome binning, metabolic modeling
- MeSH terms
- Amino Acids, Bacteria, Colicins, Energy Metabolism, Methane, Molecular Sequence Data, Species Specificity, Thermodynamics, Genome, Bacterial, Metabolic Networks and Pathways, Microbial Interactions
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