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The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis , indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development. [Display omitted] • Gut microbiomes of infants from Bangladesh harbored three Bifidobacterium longum clades • Transitional B. longum clade carried enzymes to utilize breast milk and food substrates in weaning • B. longum clades and associated metabolites were implicated in diarrhea and growth Transitional B. longum , a clade prevalent in Bangladeshi children during weaning, harbors enzymes for utilizing both breast milk and solid food substrates. [ABSTRACT FROM AUTHOR]