Assessing gut microbial provisioning of essential amino acids to host in a mouse model with reconstituted gut microbiomes

Gut microbial provisioning of essential amino acids (EAAs) represents a critical but poorly understood aspect of mammalian nutrition, with direct implications for host metabolism, growth, and disease resistance. While advances in microbiome research have highlighted the potential significance of these microbial-host nutritional interactions, direct empirical evidence quantifying actual microbial contributions to host EAA supply remains surprisingly limited, particularly under controlled experimental conditions. Here, we show using stable carbon isotope analysis of six EAAs across brain, kidney, liver, and muscle tissues that germ-free mice maintained on a high-protein diet and conventionalized mice with reconstituted gut microbiomes fed a low-protein diet for twenty days exhibit no significant differences in δ ¹³ C-EAA values. Our results reveal no detectable microbial contribution to host EAA pools, as δ ¹³ C-EAA patterns remain nearly identical between treatment groups across all organs examined. Microbial profiling confirms that conventionalized mice successfully established diverse gut microbiota communities dominated by typical Firmicutes and Bacteroidetes phyla. These findings contrast with recent δ ¹³ C-EAA based studies that reported substantial microbial EAA contributions in wild-type mice, raising important questions about functional restoration of reconstituted gut microbiomes and underscoring the need to critically revisit experimental designs and analytical frameworks to better understand microbial nutrient provisioning dynamics.