Diversity of anaerobic fungi population (phylum Neocallimastigomycota) in the horse hindgut

This thesis aims to study the diversity of symbiotic gut anaerobic fungi (phylum Neocallimastigomycota) in the different segments of the equine hindgut (cecum, right ventral colon, left ventral colon, left dorsal colon, right dorsal colon, and rectum). A clone library of fungal ITS1 fragments of rDNA was prepared for each hindgut segment. These fragments were sequenced and phylogenetically analysed.The major finding of this study is the prevalence of uncultured Neocallimastigales in the horse lower digestive tract, representing 81% of the hindgut fungi and the completely different diversity of gut fungi of feces compared to cecum and colon content. The fecal sample did not reflect the microbial population composition of hindgut. The fungal population similarity between LVC and feces was evidenced in this study. RVC, LDC and RDC are inhabited by unknown gut fungi. A significant proportion of uncultured sequences is highly similar to the sequences of a new group of anaerobic fungi, which is specific for the Equidae family. Moreover a new cluster of anaerobic fungi was found in the digestive tract of horse (Anglo-Arabian reared in Sardinia). The horse digestive tract is populated by unknown, not yet cultivated species of anaerobic fungi and only a limited percentage of identified sequences can be classified into known species of gut fungi. The conventional microbiological cultivation techniques underestimate the diversity of the anaerobic fungal population in the horse hindgut.