{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/a-minimal-model-for-microbial-biodiversity","title":"A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns","arxiv_id":"1904.12914","date":"2020-01-23","proceeding":null,"authors":[],"abstract":"Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP)\nand the Human Microbiome Project (HMP) have revealed robust ecological patterns\nacross different environments. A major goal in ecology is to leverage these\npatterns to identify the ecological processes shaping microbial ecosystems. One\npromising approach is to use minimal models that can relate mechanistic\nassumptions at the microbe scale to community-level patterns. Here, we\ndemonstrate the utility of this approach by showing that the Microbial Consumer\nResource Model (MiCRM) -- a minimal model for microbial communities with\nresource competition, metabolic crossfeeding and stochastic colonization -- can\nqualitatively reproduce patterns found in survey data including compositional\ngradients, dissimilarity/overlap correlations, richness/harshness correlations,\nand nestedness of community composition. By using the MiCRM to generate\nsynthetic data with different environmental and taxonomical structure, we show\nthat large scale patterns in the EMP can be reproduced by considering the\nenergetic cost of surviving in harsh environments and HMP patterns may reflect\nthe importance of environmental filtering in shaping competition. We also show\nthat recently discovered dissimilarity-overlap correlations in the HMP likely\narise from communities that share similar environments rather than reflecting\nuniversal dynamics. We identify ecologically meaningful changes in parameters\nthat alter or destroy each one of these patterns, suggesting new mechanistic\nhypotheses for further investigation. These findings highlight the promise of\nminimal models for microbial ecology.","url_abs":"http://arxiv.org/abs/1904.12914v3","url_pdf":"http://arxiv.org/pdf/1904.12914v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"a-minimal-model-for-microbial-biodiversity","repo_url":"https://github.com/Emergent-Behaviors-in-Biology/microbiome-patterns","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}