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Nat Ecol Evol. 2017 Nov;1(11):1606-1615. doi: 10.1038/s41559-017-0340-2. Epub 2017 Oct 16.

The microbiome beyond the horizon of ecological and evolutionary theory.

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Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK.
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08450, USA.


The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges. Furthermore, a number of unique characteristics of microbial species, such as horizontal gene transfer, the production of public goods, toxin and antibiotic production, rapid evolution, and feedbacks between the microbiome and its host, are not easily accommodated by current ecological and evolutionary theory. Here we highlight potential pitfalls in the application of existing theoretical tools without careful consideration of the unique complexities of the microbiome, focusing particularly on the issue of human health, and anchoring our discussion in existing empirical evidence.

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