Gut-resident bacteria produce a diverse array of metabolites, either directly synthesized or derived from dietary and host substrates. These metabolites, among them lipid mediators, can signal to influence gut health, maintain immune and metabolic homeostasis, and enable communication between the gut and distant organs. Critically, these biochemical interactions may shift with microbial dynamics across life stages, forming unique species and strain level metabolic fingerprints. The common ground in strain and species shifts lies in their functions—the metabolites they produce or transform. Among early colonisers, Bacteroideales (notably Bacteroides) mega-lipid producers and Proteobacteria (including E. coli) oxygen depleters, are abundant but remain under characterised in terms of their metabolite contributions to the host–microbe interactions. We aimed to understand the metabolite contributions of these bacteria, once isolated from the infant gut.  Why is this important? These first gut colonizers are understudied, they represent an untapped potential probiotic resource, they are not yet extensively and experimentally characterized, as individuals, for any unique features that may impact colonization, gut development, and immune system training among other functions, diet may alter their metabolite landscape. Studying isolated individual strains and their genetics may reveal functional contributions that influence early life development, for longer term health.