  Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP)
and the Human Microbiome Project (HMP) have revealed robust ecological patterns
across different environments. A major goal in ecology is to leverage these
patterns to identify the ecological processes shaping microbial ecosystems. One
promising approach is to use minimal models that can relate mechanistic
assumptions at the microbe scale to community-level patterns. Here, we
demonstrate the utility of this approach by showing that the Microbial Consumer
Resource Model (MiCRM) -- a minimal model for microbial communities with
resource competition, metabolic crossfeeding and stochastic colonization -- can
qualitatively reproduce patterns found in survey data including compositional
gradients, dissimilarity/overlap correlations, richness/harshness correlations,
and nestedness of community composition. By using the MiCRM to generate
synthetic data with different environmental and taxonomical structure, we show
that large scale patterns in the EMP can be reproduced by considering the
energetic cost of surviving in harsh environments and HMP patterns may reflect
the importance of environmental filtering in shaping competition. We also show
that recently discovered dissimilarity-overlap correlations in the HMP likely
arise from communities that share similar environments rather than reflecting
universal dynamics. We identify ecologically meaningful changes in parameters
that alter or destroy each one of these patterns, suggesting new mechanistic
hypotheses for further investigation. These findings highlight the promise of
minimal models for microbial ecology.
