{"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/evidence-for-a-multi-level-trophic","title":"Evidence for a multi-level trophic organization of the human gut microbiome","arxiv_id":"1908.10963","date":"2019-08-28","proceeding":null,"authors":[],"abstract":"The human gut microbiome is a complex ecosystem, in which hundreds of\nmicrobial species and metabolites coexist, in part due to an extensive network\nof cross-feeding interactions. However, both the large-scale trophic\norganization of this ecosystem, and its effects on the underlying metabolic\nflow, remain unexplored. Here, using a simplified model, we provide\nquantitative support for a multi-level trophic organization of the human gut\nmicrobiome, where microbes consume and secrete metabolites in multiple\niterative steps. Using a manually-curated set of metabolic interactions between\nmicrobes, our model suggests about four trophic levels, each characterized by a\nhigh level-to-level metabolic transfer of byproducts. It also quantitatively\npredicts the typical metabolic environment of the gut (fecal metabolome) in\napproximate agreement with the real data. To understand the consequences of\nthis trophic organization, we quantify the metabolic flow and biomass\ndistribution, and explore patterns of microbial and metabolic diversity in\ndifferent levels. The hierarchical trophic organization suggested by our model\ncan help mechanistically establish causal links between the abundances of\nmicrobes and metabolites in the human gut.","url_abs":"http://arxiv.org/abs/1908.10963v1","url_pdf":"http://arxiv.org/pdf/1908.10963v1.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":"evidence-for-a-multi-level-trophic","repo_url":"https://github.com/eltanin4/trophic_gut","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"diversity","task_name":"Diversity"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}