Species-level gut microbiota analysis in ovariectomized osteoporotic rats by Shallow shotgun sequencing

Gut microbiota was verified to regulate bone metabolism and was closely associated with osteoporosis. Using 16S rRNA sequencing, gut microbiota at genus level such as Helicobacter, Bacteroides, and Prevotella were found to increase in the osteoporotic animals and people. However, the changes of species-level gut microbiota and related functional alterations were still unknown. Female SD rats were divided into the ovariectomized (OVX) group and the control group, and the fecal samples were collected at 4, 8, and 12 weeks to analyze the information of gut microbiota. Using Shallow shotgun sequencing, we compared the species-level gut microbiota structure, composition, and functional pathways of the OVX group with the control group. Alpha diversity of the OVX rats were significantly decreased than those in the control group. Beta diversity showed that samples in the two groups could be distinguished in each coordinate at different time points. Furthermore, the relative abundance of gut microbiota at species-level and differential analysis found that bacteria species such as Helicobacter rodentium, Lachnospiraceae bacterium 10 1, and Lachnospiraceae bacterium A4 were markedly increased in the OVX rats. Furthermore, differential analysis of KEGG functional pathway revealed that lysine metabolism was enriched in the OVX group.In conclusion, gut microbiota were significantly altered in structure and composition estrogen-deficiency osteoporotic rats at the species level. Functional metabolism of gut microbiota was also changed in osteoporotic group. These changes in gut microbiota at the species level might be closely associated with osteoporosis caused by estrogen deficiency.