Dietary Modulation of the Gut Mycobiome in Poultry and Monogastric Animals: A Systematic Review of Composition, Measurement, Trans-kingdom Interactions and the Absence of Fungal-targeted Nutrition Trials

Abstract

Fungi form a minor but functionally disproportionate fraction of the monogastric gut microbiota. Bacterial communities in poultry and pigs are well characterized, but the mycobiome remains poorly defined and its dietary responsiveness is largely assumed. This review establishes mycobiome composition and measurement in healthy poultry and pigs, synthesizes dietary and feed-processing drivers of fungal load and diversity, evaluates trans-kingdom interactions linked to performance, Candida overgrowth and mycotoxin dynamics and quantifies the gap in fungal-targeted dietary-intervention trials. A systematic search of Semantic Scholar, PubMed and Scopus used twenty structured queries across five sub-areas derived from a hybrid PICO-decomposition framework. Records were screened against a priori eligibility criteria centered on poultry and porcine hosts; methodological literature from other hosts was retained where it informed measurement validity. Of 387 records retrieved, 231 were unique and 80 met eligibility. The porcine mycobiome converges on Kazachstania slooffiae as a dominant post-weaning resident, whereas the chicken mycobiome is transient, diet-derived and lacks succession, an asymmetry with direct implications for intervention design. No marker-database combination performed universally and common ITS primers failed to amplify piglet-native fungi. Feed processing reduced viable mold counts by 27-65%, yet aflatoxin was higher in pelleted than mash feed. Critically, live-yeast and mycotoxin-mitigation trials, where the agent or hazard is itself fungal, almost universally reported bacterial endpoints alone; fewer than five controlled dietary trials in either species reported fungal community outcomes.