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

Causal effects of specific gut microbiota on bone mineral density: a two-sample Mendelian randomization study

Background

Recent studies have reported that the gut microbiota is essential for preventing and delaying the progression of osteoporosis. Nonetheless, the causal relationship between the gut microbiota and the risk of osteoporosis has not been fully revealed.

Methods

A two-sample Mendelian randomization (MR) analysis based on a large-scale genome-wide association study (GWAS) was conducted to investigate the causal relationship between the gut microbiota and bone mineral density (BMD). Instrumental variables for 211 gut microbiota taxa were obtained from the available GWAS meta-analysis (n = 18,340) conducted by the MiBioGen consortium. The summary-level data for BMD were from the Genetic Factors for Osteoporosis (GEFOS) Consortium, which involved a total of 32,735 individuals of European ancestry. The inverse variance-weighted (IVW) method was performed as a primary analysis to estimate the causal effect, and the robustness of the results was tested via sensitivity analyses by using multiple methods. Finally, a reverse MR analysis was applied to evaluate reverse causality.

Results

According to the IVW method, we found that nine, six, and eight genetically predicted gut microbiota were associated with lumbar spine (LS) BMD, forearm (FA) BMD, and femoral neck (FN) BMD, respectively. Among them, the higher genetically predicted Genus Prevotella9 level was correlated with increased LS-BMD [β = 0.125, 95% confidence interval (CI): 0.050-0.200, P = 0.001] and FA-BMD (β = 0.129, 95% CI: 0.007-0.251, P = 0.039). The higher level of genetically predicted Family Prevotellaceae was associated with increased FA-BMD (β = 0.154, 95% CI: 0.020-0.288, P = 0.025) and FN-BMD (β = 0.080, 95% CI: 0.015-0.145, P = 0.016). Consistent directional effects for all analyses were observed in both the MR-Egger and weighted median methods. Subsequently, sensitivity analyses revealed no heterogeneity, directional pleiotropy, or outliers for the causal effect of specific gut microbiota on BMD (P > 0.05). In reverse MR analysis, there was no evidence of reverse causality between LS-BMD, FA-BMD, and FN-BMD and gut microbiota (P > 0.05).

Conclusion

Genetic evidence suggested a causal relationship between the gut microbiota and BMD and identified specific bacterial taxa that regulate bone mass variation. Further exploration of the potential microbiota-related mechanisms of bone metabolism might provide new approaches for the prevention and treatment of osteoporosis.

Trimethylamine-N-Oxide Promotes Osteoclast Differentiation and Bone Loss via Activating ROS-Dependent NF-κB Signaling Pathway

Trimethylamine-N-oxide (TMAO), an important gut microbiota (GM)-derived metabolite, has been shown to be abnormally increased in osteoporosis. However, the role and underlying mechanism of TMAO in regulating bone loss during osteoporosis have not been fully investigated. In the current study, we found that 100–400 μM TMAO dose-dependently enhanced TRAP-positive osteoclasts, F-actin ring formation, and resorption area on bovine bone slices and up-regulated osteoclast-related gene expression (Calcr, Traf6, Dcstamp, Acp5, C-Fos, and NFATc1). Western blotting validated that TMAO not only activated NF-κB signaling pathway but also stimulated c-Fos and NFATc1 protein expression in a dose-dependent manner. Furthermore, BAY 11-7082, an NF-κB inhibitor, pretreatment markedly suppressed TRAP-positive osteoclast formation and osteoclast-related genes under TMAO treatment. BAY 11-7082 also inhibited p-p65/p65, c-Fos, and NFATc1 protein expression promoted by TMAO. Moreover, TMAO significantly increased ROS production, which was inhibited by N-acetylcysteine (NAC), an ROS antagonist. In addition, we proved that NAC pretreatment could inhibit TMAO-promoted NF-κB activation. NAC also suppressed TRAP-positive osteoclast formation, osteoclast-related gene expression, and protein expression of c-Fos and NFATc1 under TMAO treatment. In vivo studies showed significantly decreased bone mass and increased TRAP-positive osteoclasts in TMAO-treated C57BL/6 mice. Moreover, western-blotting and immunohistochemical staining showed that TMAO administration markedly stimulated NF-κB p65 expression. Additionally, TMAO administration significantly promoted the gene and protein expression of C-Fos and NFATc1. In conclusion, TMAO could promote osteoclast differentiation and induce bone loss in mice by activating the ROS-dependent NF-κB signaling pathway.

Gut Microbiota Feature of Senile Osteoporosis by Shallow Shotgun Sequencing Using Aged Rats Model

Senile osteoporosis is defined as an age-related bone metabolic disorder, which is characterized by bone loss and decreased bone fragility. Gut microbiota (GM) could regulate the bone metabolic process and be closely related to senile osteoporosis. Several genus-level GM were found to increase in osteoporotic animals and patients. However, to reveal the pathogenic bacteria in senile osteoporosis, further studies are still needed to investigate the complete characteristics of bacteria species. In the present study, the rats were equally divided into two groups: the control group (Con, 6-month-old) and the osteoporosis group (OP, 22-month-old). Fecal samples were freshly collected to conduct the shallow shotgun sequencing. Then, we compared the species numbers, microbial diversity, GM composition at genus and species-level, and functional metabolic pathways in the two groups. The results showed that the species number was lower in the OP group (1272) than in the control group (1413), and 1002 GM species were shared between the two groups. The OP group had the decreased α diversity compared with the control group. As for β diversity, The PCA revealed that samples in the two groups had distinguishable ecological distance in each coordinate. At the species level, Bacteroide coprocola (B. coprocola), Acinetobacter baumannii (A. baumannii), Parabacteroides distasonis (P. distasonis), and Prevotella copri (P. copri) were higher in the OP group, while Corynebacterium stationis (C. stationis), Akkermansia muciniphila (A. muciniphila), and Alistipes indistinctus (A. indistinctus) were decreased. Moreover, functional metabolic analysis revealed that metabolic pathways of fatty acid biosynthesis, valine/isoleucine biosynthesis, GABA biosynthesis, and ubiquinone biosynthesis were enriched in the senile osteoporotic rats. In conclusion, GM at the species level in senile osteoporotic rats was significantly altered in structure, composition, and function. The altered GM structure, increased GM species such as P. copri, and decreased GM species such as A. muciniphila might be linked with the development of senile osteoporosis.