The human gut mycobiome: Pitfalls and potentials-a mycologist's perspective

Mallory J. Suhr, Heather E. Hallen-Adams

Research output: Contribution to journalArticlepeer-review

82 Scopus citations


We have entered the Age of the Microbiome, with new studies appearing constantly and whole journals devoted to the human microbiome. While bacteria outnumber other gut microbes by orders of magnitude, eukaryotes are consistently found in the human gut and are represented primarily by the fungi. Compiling 36 studies 1917-2015 we found at least 267 distinct fungal taxa have been reported from the human gut, and seemingly every new study includes one or more fungi not previously described from this niche. This diversity, while impressive, is illusory. If we examine gut fungi, we will quickly observe a division between a small number of commonly detected species (Candida yeasts, Saccharomyces and yeasts in the Dipodascaceae, and Malassezia species) and a long tail of taxa that have been reported only once. Furthermore, an investigation into the ecology of these rare species reveals that many of them are incapable of colonization or long-term persistence in the gut. This paper examines what we know and have yet to learn about the fungal component of the gut microbiome, or "mycobiome", and an overview of methods. We address the potential of the field while introducing some caveats and argue for the necessity of including mycologists in mycobiome studies.

Original languageEnglish (US)
Pages (from-to)1057-1073
Number of pages17
Issue number6
StatePublished - Nov 1 2015


  • Candida
  • Human health
  • Microbiome
  • Nextgeneration sequencing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • Molecular Biology
  • Genetics
  • Cell Biology


Dive into the research topics of 'The human gut mycobiome: Pitfalls and potentials-a mycologist's perspective'. Together they form a unique fingerprint.

Cite this