Understanding the axis of the human microbiome and physiological homeostasis is an essential task in managing deep-space travel associated health risks. The NASA led Rodent Research 5 mission enabled an ancillary investigation of the gut microbiome varying exposure to microgravity (flight) relative to ground controls in the context of previously shown bone mineral density (BMD) loss that was observed in these flight groups. We demonstrate elevated abundance of Lactobacillus murinus and Dorea sp. during microgravity exposure relative to ground control through whole genome sequencing and 16S rRNA analyses. Specific functionally assigned gene clusters of Lactobacillus murinus and Dorea sp. capable of producing metabolites, lactic acid, leucine/isoleucine, and glutathione are enriched. These metabolites are elevated in the microgravity-exposed host serum through LC-MS/MS metabolomic analysis. Along with BMD loss, ELISA analysis reveals increases of osteocalcin and reductions in tartrate-resistant acid phosphatase 5b signifying additional loss of bone homeostasis in flight.