The large-scale organization of the bacterial network of ecological co-occurrence interactions
Open Access
- 27 February 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (12), 3857-3868
- https://doi.org/10.1093/nar/gkq118
Abstract
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.Keywords
This publication has 55 references indexed in Scilit:
- The convergence of carbohydrate active gene repertoires in human gut microbesProceedings of the National Academy of Sciences of the United States of America, 2008
- Large-scale reconstruction and phylogenetic analysis of metabolic environmentsProceedings of the National Academy of Sciences of the United States of America, 2008
- The Human Microbiome ProjectNature, 2007
- Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsNature Methods, 2007
- An obesity-associated gut microbiome with increased capacity for energy harvestNature, 2006
- Conserved patterns of protein interaction in multiple speciesProceedings of the National Academy of Sciences of the United States of America, 2005
- Evidence for dynamically organized modularity in the yeast protein–protein interaction networkNature, 2004
- Detection of functional modules from protein interaction networksProteins, 2003
- KEGG: Kyoto Encyclopedia of Genes and GenomesNucleic Acids Research, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997