The large-scale organization of the bacterial network of ecological co-occurrence interactions

Shiri Freilich*, Anat Kreimer, Isacc Meilijson, Uri Gophna, Roded Sharan, Eytan Ruppin

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article numbergkq118
Pages (from-to)3857-3868
Number of pages12
JournalNucleic Acids Research
Issue number12
StatePublished - 27 Feb 2010


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