Microbial colonization during early life plays a relevant role in healthy immune and metabolic development of an infant. Until now, research has been focused on studying the role of gut bacterial communities in the health outcomes of infants, and little is known regarding the role of colonizing fungi (the mycobiome) in the first months of life.

A recent study, led by Prof. Cheryl Gale from the Department of Paediatrics at the University of Minnesota (Minneapolis, Minnesota, USA), has found that mycobiome differences exist at each infant body site over the first month of life and mode of birth influences key fungal groups.

In this pilot study, the researchers characterized the skin, oral cavity, and anus (a mix of skin and faeces) mycobiomes of infants (n = 17) over the first month of life and the anal and vaginal mycobiomes of mothers (n = 16) through amplicon sequencing of the internal transcribed spacer region 2 of the ribosomal ribonucleic acid locus (ITS2), which is considered a universal deoxyribonucleic acid barcode marker for fungi.

Infant mycobiomes varied by body site over the first month of life. Specifically, the infant mycobiomes at the anal sites were different from those at the skin and oral sites. Anal samples exhibited increased relative abundances of Candida albicans versus skin and oral mycobiomes, and increased abundances of C. parapsilosis in anal samples versus skin samples.

Both infant and maternal mycobiomes tended to be dominated by few taxa. The taxa of highest prevalence and relative abundance across all infant body sites were Candida species, with C. parapsilosis and C. tropicalis having the highest relative abundance in the skin, oral, and anal regions. C. albicans and Saccharomyces cerevisiae were also prominent, depending on the body site. Malassezia accounted for only 2% of the relative abundance in the infant skin mycobiome, whereas in adults Malassezia is a predominant colonizer of the skin, together with Candida and Saccharomyces. Similarly, the maternal vaginal and anal mycobiomes were also dominated by a single taxon, with C. albicans as the most abundant in the vaginal mycobiome and C. albicans, S. cerevisiae, and C. parapsilosis as the most abundant in the maternal anal mycobiome.

Infant mycobiomes were individualized and variable across studied infants. Skin mycobiomes showed within-infant similarity over time, whereas the oral and anal mycobiomes of infants exhibited high intraindividual variability. Besides this, alpha diversities of infant mycobiomes did not significantly change over the first 30 days of life, regardless of body site, which suggests a lack of new species acquisition and limited increases in richness within the first month of life. Regarding alpha diversity (the average species diversity at the same body site) and beta diversity (the differentiation among different body sites) measures, infant mycobiomes as a group over the first 30 days of life looked similar to the maternal mycobiomes as a group.

Mode of delivery influenced the relative abundances of specific fungal groups in infant skin and oral mycobiomes. Candida albicans fungi were present in a higher proportion on the skin of vaginally born infants on day 30 and C. orthopsilosis were the most abundant fungi in the oral cavity of caesarean section-born infants during the first month of life. However, vaginal birth did not result in infant mycobiomes that were more similar to the mother’s vaginal mycobiome. These data suggest that other sources of transmission of fungi from mother to the infant are involved beyond vertical transmission.

In conclusion, this is the first study that has explored the structure of the infant mycobiome by body site and depending on mode of delivery. Further research is needed in order to study the contribution of early-life mycobiome establishment to infant health and to explore whether there was a clear progression toward a different or mature infant mycobiome composition as occurs with the infant bacterial microbiome.




Ward TL, Dominguez-Bello MG, Heisel T, et al. Development of the human mycobiome over the first month of life and across body sites. mSystems. 2018; 3(3). doi: 10.1128/mSystems.00140-17.