Sequence-based methods for detecting and evaluating the human gut mycobiome.

We surveyed the fungal microbiota in 16 faecal samples from healthy humans with a vegetarian diet. Fungi were identified using molecular cloning, 454 pyrosequencing and a Luminex analyte-specific reagent (ASR) assay, all targeting the ITS region of the rRNA genes. Fungi were detected in each faecal sample and at least 46 distinct fungal operational taxonomic units (OTUs) were detected, from two phyla - Ascomycota and Basidiomycota. Fusarium was the most abundant genus, followed by Malassezia, Penicillium, Aspergillus 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. No single method identified the full diversity of fungi in all samples; pyrosequencing detected more distinct OTUs than the other methods, but failed to detect OTUs in some samples that were detected by cloning and/or ASR assays. ASRs were limited by the commercially available assays, but the potential to design new, optimized assays, coupled with speed and cost, makes the ASR method worthy of further study. Fungi play a role in human gut ecology and health. The field lags immensely behind bacterial gut microbiota research, and studies continue to identify new fungi in faecal samples from healthy humans. However, many of these 'new' species are incapable of growth in the human GI tract, let alone making a meaningful contribution to the gut microbial community. Fungi actually inhabiting and impacting the gut likely constitute a small set of species, and an optimized, targeted, probe-based assay may prove to be the most sensible way of quantifying their abundances.

Suhr MJ ，Banjara N ，Hallen-Adams HE 《-》

The gut mycobiome of the Human Microbiome Project healthy cohort.

Nash AK ，Auchtung TA ，Wong MC ，Smith DP ，Gesell JR ，Ross MC ，Stewart CJ ，Metcalf GA ，Muzny DM ，Gibbs RA ，Ajami NJ ，Petrosino JF ... -  《Microbiome》

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi.

Auchtung TA ，Fofanova TY ，Stewart CJ ，Nash AK ，Wong MC ，Gesell JR ，Auchtung JM ，Ajami NJ ，Petrosino JF ... -  《mSphere》

Fungi in the healthy human gastrointestinal tract.

Hallen-Adams HE ，Suhr MJ 《-》

Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota.

Hamad I ，Ranque S ，Azhar EI ，Yasir M ，Jiman-Fatani AA ，Tissot-Dupont H ，Raoult D ，Bittar F ... -  《Scientific Reports》