Comparison of Faecal Anaerobic Fungi of Cows and Goats Offered Similar Diet

BACKGROUND: Anaerobic fungi (AF) are key contributors to fibre degradation in ruminants, yet their host-associated patterns remain poorly understood. The aim of this study was to compare the diversity and composition of AF in faeces of goats and cows offered similar diet and to evaluate the influence of animal species on the gut mycobiome. METHODS: A total of 15 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. The fungal structure in faeces was examined by high-throughput sequencing using the D2 LSU region. RESULTS: Alpha diversity measurements revealed significantly lower species richness and evenness in goats compared to cows. Beta diversity analysis showed statistical dissimilarities and distinct community structures between the two ruminant species confirming host-specific clustering. Taxonomic composition differed significantly, cow samples were dominated by Caecomycetaceae and Neocallimastigaceae, particularly the genera Orpinomyces, Caecomyces and Cyllamyces. Goat samples were dominated by Anaeromyces, Caecomyces and according to relative abundance they formed two distinct clusters with highly similar fungal profile. Differential abundance analysis further highlighted the enrichment of Anaeromyces, unclassified genus within Caecomycetaceae, Feramyces and Pecoramyces in goats, whereas Caecomyces and Piromyces were more abundant in cows. CONCLUSION: These findings underscore the strong influence of host phylogeny on the faecal anaerobic fungal community.