Osteoporosis and its precursor osteopenia are a common metabolic bone diseases in postmenopausal women. Improvement of peak bone mass in younger age and reducing bone loss in aging are two strategies to reduce the risk for developing osteoporosis. Modulating intestinal calcium absorption by diet can contribute to improvement of bone mass, and reduction of inflammation during menopause can reduce the risk of bone loss. Prebiotics are fermented by the gut bacteria resulting in the production of organic acids which reduce the pH in the large intestine and may improve solubility of minerals thus increasing passive diffusion via the paracellular pathway. Probiotics have been reported to increase the immune system efficiency, enhance vitamin and mineral absorption as well as generate organic acids and amino acids. Bone turnover is regulated by hormones, immune cells, and the gastrointestinal system supporting mineral absorption. In addition, the intestine also produces endocrine factors such as incretins and serotonins that signal (crosstalk) to bone cells. A growing body of evidence suggests that the gut microbiota is involved in the regulation of bone metabolism but there are few studies examining how gut microbiomes in osteoporosis and osteopenia may differ from those in healthy individuals. In a pilot study the diversity, composition, and functional gene potential of the gut microbiota of healthy, osteopenic, and osteoporotic women were characterised. Both osteoporotic and osteopenic taxonomic compositions were found to be significantly different from healthy participants. Modulation of the microbiome may prove to be beneficial for the prevention of bone loss.