Food Science and Technology Department


Date of this Version



Suhr MJ, Hallen-Adams HE (2015) The human gut mycobiome: pitfalls and potentials - a mycologist's perspective. Mycologia 107:1057-1073.


Copyright © 2015 by The Mycological Society of America, Lawrence, KS 66044-8897. Used by permission.


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 spanning from 1917 to 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 which have only been reported 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.