Beyond abundance: ecological and functional relevance of intestinal fungi in the fish gut microbiome.

Fish gut microbiome research primarily focuses on bacterial communities, while intestinal fungi are often treated as low-abundance background signals or environmental contaminants. Here, we argue that this asymmetry is no longer justified. 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.