The gut mycobiome of the Human Microbiome Project healthy cohort.

TitleThe gut mycobiome of the Human Microbiome Project healthy cohort.
Publication TypeJournal Article
Year of Publication2017
AuthorsNash, AK, Auchtung, TA, Wong, MC, Smith, DP, Gesell, JR, Ross, MC, Stewart, CJ, Metcalf, GA, Muzny, DM, Gibbs, RA, Ajami, NJ, Petrosino, JF
Date Published2017 Nov 25
KeywordsCandida, Cohort Studies, DNA, Ribosomal Spacer, Feces, Fungi, Gastrointestinal Microbiome, Genetic Variation, Healthy Volunteers, High-Throughput Nucleotide Sequencing, Humans, Malassezia, Metagenomics, Microbiota, Mycobiome, RNA, Ribosomal, 18S, Saccharomyces, Sequence Analysis, DNA

BACKGROUND: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.RESULTS: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.CONCLUSIONS: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.

Alternate JournalMicrobiome
PubMed ID29178920
PubMed Central IDPMC5702186
Grant ListP30 DK056338 / DK / NIDDK NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
2 U54 HG003273 / / National Human Genome Research Institute /

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