The composition of the gut microbiota represents an early indicator of chronic post-radiation outcomes in elderly bone and gastrointestinal homeostasis. Fecal microbiota analyses revealed that the relative abundances of Bacteroides massiliensis, Muribaculum sp., or Prevotella denticola were different between conventional microbiota (CM) and anti-inflammatory restricted microbiota (RM). The murine RM was found conditional on mucosa-associated dysbiosis under both, disturbances of interleukin (IL)-17 signaling and exposure to radiation alone. This review discusses the hypothesis that intestinal microbiota induced alterations in DNA repair and expressed transforming growth factor (TGF)-β in the small intestine, thereby impacting bone microstructure and osteoblast dysfunction in silicon ion (1.5 Gy 28Si ions of 850 MeV/u) irradiated mice. Bacterial microbiota compositions influenced therapeutic approaches, correlated with clinical outcomes in radiotherapy and were associated with alterations of the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infections during the last global pandemics. In the absence of TGF-β, functional metagenomics, cytokine profiles, bacterial community analyses in human and murine mucosa cells, and inflammatory markers in rat intestines were analyzed. This research finally showed radiation-induced osteolytic damage to correlated with specific features of intestinal bacterial composition, and these relationships were expatiated together with radiation effects on normal tissue cell proliferation.