The DOI matches its Crossref record; 86 of the 86 references it cites were found in a registry or an index.
Deciphering microbial interactions in synthetic human gut microbiome communities
Open accessAbstract
ABSTRACT The human gut microbiota comprises a dynamic ecological system that contributes significantly to human health and disease. The ecological forces that govern community assembly and stability in the gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-order consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse 12-member human gut microbiome synthetic community. We show that microbial growth parameters and pairwise interactions are the major drivers of multi-species community dynamics, as opposed to context-dependent (conditional) interactions. The inferred microbial interaction network as well as a top-down approach to community assembly pinpointed both ecological driver and responsive species that were significantly modulated by microbial inter-relationships. Our model demonstrated that negative pairwise interactions could generate history-dependent responses of initial species proportions on physiological timescales that frequently does not originate from bistability. The model elucidated a topology for robust coexistence in pairwise assemblages consisting of a negative feedback loop that balances disparities in monospecies fitness levels. Bayesian statistical methods were used to evaluate the constraint of model parameters by the experimental data. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis for competitive and cooperative interactions in the community. However, these data failed to predict influential organisms shaping community assembly. In sum, these methods defined the ecological roles of key species shaping community assembly and illuminated network design principles of microbial communities.
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Cited by
Sorbara, M. T., & Pamer, E. G. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00667-9 · Cited by 468
Understanding Competition and Cooperation within the Mammalian Gut Microbiome
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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
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High-throughput microbial culturomics using automation and machine learning
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Revisit gut microbiota and its impact on human health and disease
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Metadata
- Authors
- Venturelli, O. S., Carr, A. V., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Hromada, S., Northen, T., & Arkin, A. P.
- Venue
- Molecular Systems Biology
- Published
- 2018-06
- Volume
- 14
- Issue
- 6
- Pages
- e8157-e8157
- ISSN
- 1744-4292 (ISSN-L)
- OpenAlex
- W2773368689
- Cited by
- 544
- References
- 86
- FWCI
- 14.99
- Type
- journal article
- Language
- en
- Open access
- gold
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- Venturelli, O. S., Carr, A. V., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Hromada, S., Northen, T., & Arkin, A. P. (2018). Deciphering microbial interactions in synthetic human gut microbiome communities. Molecular Systems Biology. https://doi.org/10.15252/msb.20178157
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