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In soil\u2010 and plant\u2010associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study\u2010specific thresholds or criteria. Synthesizing recent literature and cross\u2010site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset\u2010specific analytical criteria. Taxa designated as \u2018core\u2019 were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic \u2018core\u2019 members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, \u2018core microbiome\u2019 should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as \u2018explanatory subsets of taxa\u2019. Greater terminological precision will improve cross\u2010study comparability and strengthen ecological inference in plant\u2013soil microbiome research.<\/jats:p>","DOI":"10.1111\/nph.71509","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:45:33Z","timestamp":1787013933000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Rethinking the soil core microbiome"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9793-9473","authenticated-orcid":false,"given":"Jaejin","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Agricultural and Biosystems Engineering Iowa\u00a0State University  Ames IA 50011 USA"},{"name":"DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois Urbana\u2010Champaign  Urbana IL 61801 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2544-4551","authenticated-orcid":false,"given":"Bol\u00edvar","family":"Aponte Rol\u00f3n","sequence":"additional","affiliation":[{"name":"Department of Agricultural and Biosystems Engineering Iowa\u00a0State University  Ames IA 50011 USA"},{"name":"DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois Urbana\u2010Champaign  Urbana IL 61801 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3543-9644","authenticated-orcid":false,"given":"Phillip","family":"de Lorimier","sequence":"additional","affiliation":[{"name":"Department of Agricultural and Biosystems Engineering Iowa\u00a0State University  Ames IA 50011 USA"},{"name":"DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois Urbana\u2010Champaign  Urbana IL 61801 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3128-9439","authenticated-orcid":false,"given":"Jean\u2010Michel","family":"An\u00e9","sequence":"additional","affiliation":[{"name":"The Great Lakes Bioenergy Research Center University of Wisconsin\u2010Madison  Madison WI 53726 USA"},{"name":"Department of Bacteriology University of Wisconsin\u2010Madison  Madison WI 53706 USA"},{"name":"Department of Plant and Agroecosystem Sciences University of Wisconsin\u2010Madison  Madison WI 53706 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1589-947X","authenticated-orcid":false,"given":"Gian Maria Niccol\u00f2","family":"Benucci","sequence":"additional","affiliation":[{"name":"The Great Lakes Bioenergy Research Center University of Wisconsin\u2010Madison  Madison WI 53726 USA"},{"name":"Department of Plant, Soil and Microbial Sciences Michigan State University  East Lansing MI 48824 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1142-4709","authenticated-orcid":false,"given":"Alyssa A.","family":"Carrell","sequence":"additional","affiliation":[{"name":"Biosciences Division Oak Ridge National Laboratory  Oak Ridge TN 37831 USA"},{"name":"The Center for Bioenergy Innovation  Oak Ridge TN 37831 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2437-9524","authenticated-orcid":false,"given":"Yen Ning","family":"Chai","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory  Berkeley CA 94720 USA"},{"name":"Joint BioEnergy Institute  Berkeley CA 94608 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6357-500X","authenticated-orcid":false,"given":"Janith","family":"Chandrasoma","sequence":"additional","affiliation":[{"name":"DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois Urbana\u2010Champaign  Urbana IL 61801 USA"},{"name":"Carl R. 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