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Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP)and the Human Microbiome Project (HMP) have revealed robust ecological patternsacross different environments. A major goal in ecology is to leverage thesepatterns to identify the ecological processes shaping microbial ecosystems. Onepromising approach is to use minimal models that can relate mechanisticassumptions at the microbe scale to community-level patterns. Here, wedemonstrate the utility of this approach by showing that the Microbial ConsumerResource Model (MiCRM) -- a minimal model for microbial communities withresource competition, metabolic crossfeeding and stochastic colonization -- canqualitatively reproduce patterns found in survey data including compositionalgradients, dissimilarity/overlap correlations, richness/harshness correlations,and nestedness of community composition. By using the MiCRM to generatesynthetic data with different environmental and taxonomical structure, we showthat large scale patterns in the EMP can be reproduced by considering theenergetic cost of surviving in harsh environments and HMP patterns may reflectthe importance of environmental filtering in shaping competition. We also showthat recently discovered dissimilarity-overlap correlations in the HMP likelyarise from communities that share similar environments rather than reflectinguniversal dynamics. We identify ecologically meaningful changes in parametersthat alter or destroy each one of these patterns, suggesting new mechanistichypotheses for further investigation. These findings highlight the promise ofminimal models for microbial ecology.

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns