FUNGAL-BACTERIAL MICROBIOME INTERACTIONS IN THE DEVELOPING INFANT GUT

AbstractEmerging research supports a role for gut microbiota in early-life programming of metabolism and immunity.Although fungi are part of the commensal gut microbiota, particularly during infancy, they have received muchless study for their role in health as compared to bacteria. Until recently, fungi were considered to have onlypathogenic interactions with humans. However, new studies support that idea that commensal fungi provideprotection from disease. Despite this probable importance to public health, we lack fundamental knowledgeabout the structure and dynamics of gut fungal microbiota (mycobiomes) and how they co-develop withbacterial microbiomes during early life. This has prevented the potential discovery of important mechanisms forinteractions between the microbiota and human physiology. For this R21 research, we propose to begin toclose this knowledge gap by studying fungal-bacterial microbiome co-development during the first year of life,taking advantage of a large, diverse infant cohort from the Children's Hospital of Philadelphia Care Network(NIH-funded Microbiome, Antibiotics and Growth Infant Cohort [MAGIC] study). In Aim 1, we will gainfoundational knowledge about co-maturation of gut mycobiome features with bacterial microbiome structuresand functions. This will provide a 'healthy microbiome' benchmark for future studies seeking to understandhow microbiomes and interkingdom relationships during early life contribute to later-life health and diseaseoutcomes. To further test the hypothesis that fungal and bacteria microbiomes interact with each other, in Aim2 we will study the extent to which antibacterial antibiotics disrupt mycobiomes and interkingdom structural andfunctional relationships, and the durability of these effects. Through these Aims, we expect to gain newknowledge about early-life gut mycobiomes and how they are related to bacterial microbiomes, therebyexpanding current microbiome paradigms beyond bacteria to incude fungi and fungal-bacterial inter-kingdomrelationships within the human gut . Altogether, these new insights will support further research towarddiscovering mechanistic links between gut microbiota and human health along the life-span and will providestrong rationale for the development of clincial strategies for the modulation of fungi, along with bacteria, toimprove infant and adult health.