The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
The large-scale organization of the bacterial network of ecological co-occurrence interactions
Open accessAbstract
In their natural environments, microorganisms form complex systems of interactions. Understating the structure and organization of bacterial communities is likely to have broad medical and ecological consequences, yet a comprehensive description of the network of environmental interactions is currently lacking. Here, we mine co-occurrences in the scientific literature to construct such a network and demonstrate an expected pattern of association between the species' lifestyle and the recorded number of co-occurring partners. We further focus on the well-annotated gut community and show that most co-occurrence interactions of typical gut bacteria occur within this community. The network is then clustered into species-groups that significantly correspond with natural occurring communities. The relationships between resource competition, metabolic yield and growth rate within the clusters correspond with the r/K selection theory. Overall, these results support the constructed clusters as a first approximation of a bacterial ecosystem model. This comprehensive collection of predicted communities forms a new data resource for further systematic characterization of the ecological design principals shaping communities. Here, we demonstrate its utility for predicting cooperation and inhibition within communities.
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Cites
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
The diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277
The microbial ocean from genomes to biomes
DeLong, E. F. (2009) · Nature · doi:10.1038/nature08059 · Cited by 217
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The convergence of carbohydrate active gene repertoires in human gut microbes
Lozupone, C. A., Hamady, M., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Gordon, J. I., & Knight, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807339105 · Cited by 139
Cited by
Using network analysis to explore co-occurrence patterns in soil microbial communities
Barberán, A., Bates, S. T., Casamayor, E. O., & Fierer, N. (2012) · The ISME Journal · doi:10.1038/ismej.2011.119 · Cited by 3,044
Microbial co-occurrence relationships in the human microbiome
Faust, K., Sathirapongsasuti, J. F., Izard, J., Segata, N., Gevers, D., Raes, J., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002606 · Cited by 1,527
Greenblum, S., Turnbaugh, P. J., & Borenstein, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116053109 · Cited by 821
Bergström, A., Skov, T. H., Bahl, M. I., Roager, H. M., Christensen, L. B., Ejlerskov, K. T., Mølgaard, C., Michaelsen, K. F., & Licht, T. R. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00342-14 · Cited by 532
Aguiar-Pulido, V., Huang, W., Suarez-Ulloa, V., Cickovski, T., Mathee, K., & Narasimhan, G. (2016) · Evolutionary Bioinformatics · doi:10.4137/ebo.s36436 · Cited by 499
Metadata
- Authors
- Freilich, S., Kreimer, A., Meilijson, I., Gophna, U., Sharan, R., & Ruppin, E.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-02-27
- Volume
- 38
- Issue
- 12
- Pages
- 3857-3868
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1979328481
- Cited by
- 312
- References
- 6
- FWCI
- 4.25
- Type
- journal article
- Language
- en
- Open access
- gold
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- Freilich, S., Kreimer, A., Meilijson, I., Gophna, U., Sharan, R., & Ruppin, E. (2010). The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Research. https://doi.org/10.1093/nar/gkq118
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
