Diversity and community structure of anaerobic gut fungi in camel feces

Anaerobic gut fungi (AGF) are key members of the herbivorous gut microbiome. While AGF communities have been well-studied in foregut and hindgut fermenters, they remain poorly characterized in pseudoruminants such as camels. Here, we present a comprehensive culture-independent diversity survey of 142 fecal samples from all three extant camel species (Camelus dromedarius, Camelus bactrianus, and Camelus ferus). The AGF community in Camelus was highly diverse, with representatives of 42 AGF genus-level lineages identified. However, this diversity was unevenly distributed, with three AGF genera (Neocallimastix, Caecomyces, and Orpinomyces) accounting for 70.7% of sequences encountered, and only 12 AGF genus-level lineages exceeding 1% relative abundance in the entire dataset. While several of the AGF genus-level lineages identified as major components of the AGF community in camels are highly ubiquitous in all herbivores, others, including the genera Oontomyces, Aestipascuomyces, Liebetanzomyces, as well as the yet-uncultured genera NY09, NY03, and JV-2025d identified through culture-independent surveys are extremely rare in ruminants and hindgut fermenters, hinting at their preference and potential co-evolution with the Camelidae. Ordination approaches identified host species and biogeography as key determinants driving AGF community structure differences between various camel species. Comparative community structure analysis between AGF community in camels versus reference foregut and hindgut fermenters identified the relative enrichment of the genera Oontomyces and Aestipascuomyces in pseudoruminants datasets. Our results demonstrate a distinct AGF community composition in Camelidae, elucidate factors impacting AGF diversity and community structure variations in Camelus, and identify key distinct taxa differentially enriched in pseudoruminants compared to ruminants and hindgut fermenters. The ecological and evolutionary drivers of such patterns are discussed.