Emily Skalla

Colonizing bacteria within the infant gut (the "microbiome") are important for the development of long-term health. Diet and birth mode are key early-life exposures that affect microbiome composition. Fungi also colonize the gut (the "mycobiome"), with some being implicated in health outcomes such as asthma and obesity. Despite the potential importance of fungi in health, there has been a lack of study regarding how infant mycobiomes develop and are affected by biological and environmental factors. The goal of this study was to test the hypothesis that common neonatal factors affect gut mycobiome composition in a cohort of infants who are exclusively breastfeeding. We characterized mycobiomes from healthy mothers (milk) and their exclusively breastfeeding infants (feces) enrolled in the Mothers and Infants Linked for Healthy Growth (MILk) study (n=70 dyads) by sequencing the internal transcribed spacer region 2 (ITS2) of the fungal rDNA locus. Statistical comparisons of mycobiome features were performed using the R software package. Mycobiomes of breastmilk and feces were significantly different from each other (p<0.01) as were fecal mycobiomes of male versus female infants (p<0.05). Vaginally delivered one-month old infants had significantly different fecal mycobiomes than infants delivered by cesarean section (p<0.05), with a significantly higher relative abundance of Malassezia restricta, a skin-associated fungus, in the feces of infants born by cesarean section (p<0.01). Continued study of how early-life exposures affect mycobiomes/microbiomes is needed to develop strategies that promote the development of healthy human-associated microbial communities.