Characterization of the human gut mycobiome: vegetarian diet as a case study. human gut metagenome

Here we present a survey of the fungal microbiota in 16 fecal samples from healthy humans with a vegetarian diet. Fungal taxa were identified using molecular cloning and 454/Roche amplicon pyrosequencing of ITS gene tags (molecular cloning data is available as GenBank nucleotide accessions KP196567-KP196602). Two fungal phyla were detected, with Ascomycota present in all samples and Basidiomycota present in 81% of samples. Both methodologies detected fungi in all the fecal samples and in combination identified at least 57 fungal taxa. The number of taxa in each sample ranged between 2 and 25. A total of 31 fungal genera were found overall; 14 genera were present in only one sample and 4 genera were present in only two samples. Malassezia was the most abundant genus, followed by Aspergillus and Fusarium. Other abundant genera included Penicillium, Alternaria, and Candida. Commonly detected fungi such as Aspergillus and Penicillium, as well as known dietary fungi Agaricus bisporus and Ophiocordyceps sinensis, are presumed to be transient, allochthonous members due to their abundance in the environment or dietary associations. We also detected 17 fungal species not previously reported from the gut. It is apparent that a wide variety of fungi can be identified from the human gastrointestinal tract.