Neonatal microbes shape islet-immune interactions that determine life-long host metabolic capacity [scRNA-seq and bulk RNA-seq].

The composition of the resident microbiota changes and diversifies as its host develops. Enrichment of specific taxa early in life is important for immune system development and maturation, but the impact of early life commensals on other host developmental processes is little studied. Here, we describe a critical window of postnatal life when specific microbes are necessary to establish an adequate supply of insulin-producing tissue for lifelong metabolic homeostasis of the host. The main goal is to determine the effect of microbiota presence on developing neonatal pancreatic islets. Samples are pancreatic islets purified away from acinar tissue by several rounds of hand picking. scRNA-seq: Each sample is representative of pooled islets from 20 animals at 15 days old (P15), either Germ-free (GF) or specific pathogen free (SPF). bulk RNA-seq: Islets from Germ-free (GF) and specific pathogen free (SPF) mice 10 days old (P10) or 20 days old (P20) are included. Additionally, a subset of samples from P20 SPF mice were treated with Clodronate to diminish macrophages in order to investigate the effect of macrophages on neonatal islets. Pacncreatic islets from male and female mice for each group are included.