Learning the functional landscape of microbial communities
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Abstract
Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines emergent function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes – analogs to fitness landscapes – that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically-inferred landscapes quantitatively predict community functions from knowledge of strain presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species, and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes are typically not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show this observation is generic across many ecological models, suggesting community-function landscapes can be applied broadly across many contexts. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.
Article activity feed
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emergent functional properties
I believe 'emergent functional properties' can have multiple definitions. One definition is 'any functional property that is only observed in the community context and never in single organisms' and another, maybe broader definition, is 'any functional property observed in the community that cannot be predicted as the sum of individual behavior/function alone'. I assume this is the latest definition that is implied in this study, but it would be helpful to state it clearly.
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ecological contexts
Have the authors any ideas/thoughts about contexts that involved less metabolism related function like the community response to a perturbation (invader, predator, antimicrobial compound, temperature change, radiation...). If the function outcome that is measured is community biomass or individual species abundance, can we expect low-order approximations of landscape to work well as for the biomass prediction demonstrated in this work?
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The approach we have demonstrated could enable the design of communities in a wide range of contexts, from biotechnology to therapeutics.
This is really exciting and really promising. Very interesting and clear work!
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The approach we have demonstrated could enable the design of communities in a wide range of contexts, from biotechnology to therapeutics.
This is really exciting and really promising. Very interesting and clear work!
-
ecological contexts
Have the authors any ideas/thoughts about contexts that involved less metabolism related function like the community response to a perturbation (invader, predator, antimicrobial compound, temperature change, radiation...). If the function outcome that is measured is community biomass or individual species abundance, can we expect low-order approximations of landscape to work well as for the biomass prediction demonstrated in this work?
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emergent functional properties
I believe 'emergent functional properties' can have multiple definitions. One definition is 'any functional property that is only observed in the community context and never in single organisms' and another, maybe broader definition, is 'any functional property observed in the community that cannot be predicted as the sum of individual behavior/function alone'. I assume this is the latest definition that is implied in this study, but it would be helpful to state it clearly.
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