Increasing evidence suggests that gut microbiota plays an important role in host health and disease. The gut microbiota co-evolves with host from birth, diversifies with age and gradually shifts toward an adulthood configuration. Indigestible ε-polylysine, a food-grade antimicrobial agent, is found to exert a transit effect on adult murine gut microbiota structure and predicted function. Such transit alternation suggests microbial adaption to ε-polylysine at the community level, highlighting the stability and resilience of adult gut microbiota. In contrast, early life gut microbiota is regarded as the most dynamic stage that is susceptible to host nutrition and life-style, subsequently affect gut microbiota maturation and diversity in later life. Human milk guides the structure and function of microbial communities that colonize the nursing infant gut. Indigestible molecules dissolved in human milk establish a microbiome often dominated by bifidobacteria capable of utilizing these substrates. Accordingly, human milk contains a high concentration of urea and human milk oligosaccharides (HMOs) as indigestible non-protein nitrogen (NPN), representing a potential nitrogen reservoir for microbiome. Microbiome-mediated NPN recycling may be a critical metabolic operation during lactation and neonatal development. To test this hypothesis, Bifidobacterium longum subsp. infantis (B. infantis) strains were evaluated for their capacity to subsist on urea and HMOs as a primary nitrogen source. B. infantis strains tested are competent for urea and HMOs nitrogen utilization, constituting a phenotype previously unknown in commensal bacteria. Urease and HMOs catabolism gene expression and downstream nitrogen metabolism pathways are induced during NPN utilization. Moreover, the nexus between nitrogen and carbon metabolism is significantly influenced by NPN catabolism as evidenced by differential metabolite secretion. Specifically, acetate production (relative to lactate) is increased in response to NPN, suggesting a link to anti-inflammatory properties previously ascribed to B. infantis. In addition, for specific strains, adhesion rates to Caco-2 cells are significantly increased when B. infantis subsisting on NPN. In aggregate, the often-dominant B. infantis possesses the requisite phenotypic foundation to participate in human milk NPN recycling and thus may be a key contributor to nitrogen homeostasis early in life.