Small Intestinal Bacterial Overgrowth (SIBO) is linked to various diseases and has been associated with altered serum amino acid levels. However, the direct role of the gut microbiome in these changes remains unconfirmed. This study employs genome-scale metabolic modeling to predict amino acid auxotrophy and peptidase gene profiles in the small intestinal microbiomes of SIBO and non-SIBO subjects. Auxotrophy and peptidase gene profiles were further examined in the large intestinal microbiome under non-dysbiotic conditions to assess their similarity to the microbial SIBO profile. Our analysis revealed that the abundance of auxotrophic bacteria is higher in the microbiota of the small intestine than in the large intestine in non-dysbiotic controls. In patients with SIBO, the abundance of auxotrophies in the small intestine decreased compared to non-SIBO subjects. Peptidase gene profiles in non-dysbiotic individuals were distinct between small and large intestinal microbiomes, with fewer extracellular peptidase genes in small intestine microbiomes. In SIBO, extracellular peptidase genes increased compared to non-SIBO subjects. Further, there were more significant associations between the abundance of auxotrophies and peptidase genes in microbiomes of the small intestine compared to the large intestine. In conclusion, the auxotrophy and peptidase gene profiles of the small and large intestinal microbiomes were distinct. In SIBO, the small intestinal microbiome shifts towards a metabolic state resembling that of the large intestine, particularly in its increased abundance of extracellular peptidase genes. This highlights the potential of genome-scale metabolic modeling in identifying metabolic disruptions associated with SIBO, which could inform the development of targeted interventions.