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Evidence from fish systems demonstrates recurrent gut-associated fungi, context-dependent assembly shaped by the host and environment, and multiple routes by which fungi influence host outcomes despite low read fractions. These include extracellular enzymatic activity, immune modulation, and cross-kingdom ecological interactions. Importantly, low fungal read fractions do not indicate low abundance or activity, as cross-kingdom sequencing comparisons are complicated by technical factors, including differential DNA extraction and host DNA contamination. Integrating fungi into conceptual models of the fish gut microbiome requires moving beyond abundance-based interpretations toward a framework grounded in ecological filtering, functional specialization, and redundancy.<\/jats:p>","DOI":"10.1093\/femsle\/fnag114","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:36:32Z","timestamp":1790681792000},"source":"Crossref","is-referenced-by-count":0,"title":["Beyond abundance: ecological and functional relevance of intestinal fungi in the fish gut microbiome"],"prefix":"10.1093","volume":"373","author":[{"given":"Francisco","family":"Vargas-Albores","sequence":"first","affiliation":[{"name":"Centro de Investigaci\u00f3n en Alimentaci\u00f3n y Desarrollo , A.C. 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