Early life enteric virome dynamics in Ghana and Zambia: Implications for host immunity and microbiome colonization

Infants are born with a nearly sterile gut, which is colonized rapidly after birth by bacteria, viruses, phages and microbial eukaryotes, derived from the mother or the environment. The infant enteric microbiota is essential to immune development, early-life metabolism, growth, and resistance to exogenous pathogens. This exact temporal process is still poorly understood, especially in low- and middle-income settings with high infant mortality. Although enteric viruses are often associated with disease, they are frequently asymptomatic and likely have underappreciated physiologic roles. Viral-bacterial, viral-viral, and viral-host interactions have the potential to alter microbiome colonization and training of host immunity. In the Afri-VIR project we will use longitudinal sample from infants in Ghana and Zambia to assess virome dynamics (1) in the first 100 days of life, when vaccines are administered and where children have the highest risk of infectious diseases and mortality, and (2) across the first 500 days of life, in order to assess longitudinal associations with environmental and sociodemographic variables, illness episodes, and antibiotic usage. Next, we will screen phage genomes for the presence of antibiotics resistance genes to assess their role in the emergence of multi-drug resistant bacteria and contrasted our data with age-matched infants in distinct geographical and socio-economic settings, to identify common or distinct gut microbiome developmental patterns.