Emergent simplicity in microbial community assembly

By J. Goldford, Nanxi Lu, Djordje Bajić, Sylvie Estrela, Mikhail Tikhonov, A. Sanchez-Gorostiaga, Daniel Segrè, Pankaj Mehta, Álvaro Sánchez. Science, 2017

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Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range of contexts, from biotechnological applications to what happens in our guts. Goldford et al. sampled the microbial communities from soil and plants containing hundreds to thousands of sequence variants. The organisms were passaged after culture in low concentrations of single carbon sources and were cross-fed with each other's metabolites; then, the resulting communities were sequenced using 16S ribosomal RNA, and the outcomes were modeled mathematically. The mix of species that survived under steady conditions converged reproducibly to reflect the experimentally imposed conditions rather than the mix of species initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science, this issue p. 469 Microbial communities assemble into similar family-level compositions containing divergent genera and species. A major unresolved question in microbiome research is whether the complex taxonomic architectures observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media. Both the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability. By generalizing classical ecological models to include widespread nonspecific cross-feeding, we show that these features are all emergent properties of the assembly of large microbial communities, explaining their ubiquity in natural microbiomes.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9c39a618f9397073c36dc21ed7a6585607984d7