Rumen mycobiome dynamics and dairy productivity: functional contributions of fungi to milk yield in bovine ruminants

Abstract

The rumen microbiome is a key factor influencing feed efficiency and milk production in ruminants. However, most studies have focused on the bacterial and archaeal components, with the fungal fraction of the rumen being relatively understudied. The unique ability of anaerobic rumen fungi of the phylum Neocallimastigomycota to colonize and degrade lignocellulosic biomass in the rumen through mechanical disruption of plant cell walls has now made them well known as important functional members of the rumen ecosystem. These fungi are armed with a plethora of carbohydrate-active enzymes degrading fiber and increase the availability of substrates for microbial fermentation. This leads to increased production of volatile fatty acids, especially acetate, which is a major precursor for milk fat production. Recent research evidence has indicated that rumen fungal communities are associated with feed efficiency, fermentation dynamics, and milk composition traits such as fat and protein content in bovine ruminants such as cattle and buffalo. However, most of the studies available are correlative, and the direct causal relationships between fungal activity and milk productivity are poorly delineated. High-throughput sequencing and multi-omics approaches have broadened our knowledge of fungal diversity and function; however, there are still limitations in reference databases and methodological biases. This review summarizes the current knowledge of the diversity, ecological roles, and functional contributions of anaerobic rumen fungi, with special reference to their association with milk production. It also highlights significant methodological and conceptual gaps and proposes future avenues for the integration of fungal ecology into microbiome-based approaches to improve dairy productivity. We need a holistic multi-kingdom view of the rumen microbiome to design efficient and sustainable dairy production systems.