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Doing so is particularly challenging in the context of microbe\u2013host and microbe\u2013microbe interactions that contribute to health or environmental outcomes. There are thousands of relevant microbial species, and millions of interactions among those microbes and with their environment or host. Integrated information (e.g., about host and microbial physiology, genetics, and metabolism) facilitates deeper understanding of complex mechanisms and helps interpret correlative results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The KG-Microbe construction framework is a novel approach to harmonizing bacterial and archaeal data in the form of a findable, accessible, interoperable, reusable and AI-ready knowledge graph (KG). Starting from a core KG with organismal traits, environments, and growth preferences and the integration of established ontologies, the framework generates a hierarchy of related KGs targeting specific use cases, including the human microbiome in the context of disease, or environmental microbiomes. The framework supports customizable taxa subsets representing communities or clades of interest. Evaluations of the KG-Microbe KGs through a series of competency questions demonstrate the accuracy and effectiveness of the data harmonization, and the utility of the resulting KGs in studies of inflammatory bowel disease and Parkinson\u2019s disease. Finally, the predictive and environmental capabilities of the KGs are demonstrated by predicting growth preferences using graph features.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The KG-Microbe framework unifies microbial contexts in a single resource to support integrative analyses across biomedical, host, and environmental domains. KG-Microbe is a flexible, modular enabling technology for humans and machine learning methods to uncover candidate mechanistic explanations of microbial associations.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giag077","type":"journal-article","created":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T11:53:08Z","timestamp":1783597988000},"source":"Crossref","is-referenced-by-count":1,"title":["KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9266-5813","authenticated-orcid":false,"given":"Brook E","family":"Santangelo","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus , Aurora, CO 80045 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2411-565X","authenticated-orcid":false,"given":"Harshad","family":"Hegde","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5705-7831","authenticated-orcid":false,"given":"J Harry","family":"Caufield","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2170-2250","authenticated-orcid":false,"given":"Justin","family":"Reese","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7261-0380","authenticated-orcid":false,"given":"Tomas","family":"Kliegr","sequence":"additional","affiliation":[{"name":"Faculty of Informatics and Statistics, Prague University of Economics and Business , n\u00e1m. 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Churchilla 1938\/4, 130 67 Prague 3 ,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1455-3370","authenticated-orcid":false,"given":"Lawrence E","family":"Hunter","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Chicago , Chicago, IL 60637 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4786-7202","authenticated-orcid":false,"given":"Catherine A","family":"Lozupone","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus , Aurora, CO 80045 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6601-2165","authenticated-orcid":false,"given":"Christopher J","family":"Mungall","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8175-045X","authenticated-orcid":false,"given":"Marcin P","family":"Joachimiak","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"2026090208513682800_bib1","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1038\/s12276-024-01262-7","article-title":"Genome-resolved metagenomics: a game changer for microbiome medicine","volume":"56","author":"Kim","year":"2024","journal-title":"Exp Mol Med"},{"key":"2026090208513682800_bib2","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"2026090208513682800_bib3","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2026090208513682800_bib4","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1038\/s41577-024-01014-8","article-title":"Short-chain fatty acids: linking diet, the microbiome and immunity","volume":"24","author":"Mann","year":"2024","journal-title":"Nat Rev Immunol"},{"key":"2026090208513682800_bib5","doi-asserted-by":"publisher","first-page":"1351678","DOI":"10.3389\/fmicb.2024.1351678","article-title":"Integrating biological knowledge for mechanistic inference in the host-associated microbiome","volume":"15","author":"Santangelo","year":"2024","journal-title":"Front Microbiol"},{"key":"2026090208513682800_bib6","doi-asserted-by":"publisher","first-page":"2360","DOI":"10.1038\/s41467-022-29993-z","article-title":"Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes","volume":"13","author":"Youn","year":"2022","journal-title":"Nat Commun"},{"key":"2026090208513682800_bib7","doi-asserted-by":"publisher","first-page":"D938","DOI":"10.1093\/nar\/gkad1082","article-title":"The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species","volume":"52","author":"Putman","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026090208513682800_bib8","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/s41597-024-03171-w","article-title":"An open source knowledge graph ecosystem for the life sciences","volume":"11","author":"Callahan","year":"2024","journal-title":"Sci Data"},{"key":"2026090208513682800_bib9","doi-asserted-by":"publisher","first-page":"btag421","DOI":"10.1093\/bioinformatics\/btag421","article-title":"MetagenomicKG: a knowledge graph for metagenomic applications","volume":"42","author":"Ma","year":"2026","journal-title":"Bioinformatics"},{"key":"2026090208513682800_bib10","doi-asserted-by":"publisher","first-page":"1544432","DOI":"10.3389\/fsysb.2025.1544432","article-title":"MicrobiomeKG: bridging microbiome research and host health through knowledge graphs","volume":"5","author":"Goetz","year":"2025","journal-title":"Front. 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