Altered gut microbiome profile in patients with knee osteoarthritis

Abstract

Introduction: Osteoarthritis (OA) is a kind of chronic, degenerative disorder with unknown causes. In this study, we aimed to improve our understanding of the gut microbiota profile in patients with knee OA.

Methods: 16S rDNA gene sequencing was performed to detect the gut microbiota in fecal samples collected from the patients with OA (n = 32) and normal control (NC, n = 57). Then the metagenomic sequencing was used to identify the genes or functions linked with gut microbial changes at the species level in the fecal samples from patients with OA and NC groups.

Results: The Proteobacteria was identified as dominant bacteria in OA group. We identified 81 genera resulted significantly different in abundance between OA and NC. The abundance of Agathobacter, Ruminococcus, Roseburia, Subdoligranulum, and Lactobacillus showed significant decrease in the OA compared to the NC. The abundance of genera Prevotella_7, Clostridium, Flavonifractor and Klebsiella were increasing in the OA group, and the families Lactobacillaceae, Christensenellaceae, Clostridiaceae_1 and Acidaminococcaceae were increasing in the NC. The metagenomic sequencing showed that the abundance of Bacteroides stercoris, Bacteroides vulgatus and Bacteroides uniformis at the species level were significantly decreasing in the OA, and the abundance of Escherichia coli, Klebsiella pneumoniae, Shigella flexneri and Streptococcus salivarius were significantly increased in OA.

Discussion: The results of our study interpret a comprehensive profile of the gut microbiota in patients with knee OA and offer the evidence that the cartilage-gut-microbiome axis could play a crucial role in underlying the mechanisms and pathogenesis of OA.

Keywords: 16s rDNA sequencing; cartilage-gut-microbiome axis; gut microbiota biomarkers; metagenomic sequencing; osteoarthritis.

Figure 1

Gut microbiome diversity and structure analysis based on 16S rDNA sequencing data. (A) Species diversity differences in the OA and NC groups were estimated by the observed species, Shannon, Simpson, and Chao1 indices. NS, not significant. OA, patient in osteoarthritis group; and NC, normal control. (B) Venn diagram of the observed features in KBD and NC. (C,D) Principal coordinate analysis (PCoA) of the microbiota based on the unweighted (p= 0.001) and weighted (p= 0.049) UniFrac distance matrices for the OA and NC groups.

Figure 2

Gut microbiome differential analysis. (A) Component proportions of bacterial genus in each group; n= 32 for the OA group and n= 57 for the NC group. (B) Circos plot. The left side of the circle represents species and the right side represents sample groups, different colors represent different taxonomic categories and sample groups. From left to right, the thickness of the same color line in the inner ring represents the relative abundance of the species in different sample groups, from right to left, the thickness of the same color line in the inner ring represents the proportion of different species in the sample group. (C) The differences in abundance of Proteobacteria between the OA and NC group.

Figure 3

Gut microbiome differential and functional analysis. (A) Linear discriminant analysis (LDA) integrated with effect size (LEfSe). The differences in abundance between the OA and NC group. (B) Classification performance of a random forest model using 16 s rRNA genus abundance assessed by R random Forest package. (C) ROC curve displaying the top 3 biomarkers for classification between OA and NC. AUC, area under curve.

Figure 4

The gut microbiota differences in OA and NC group based on the metagenomic sequencing data. (A) Alpha diversity differences between the OA and NC groups were estimated by the observed species, Shannon, Simpson, and Chao1 indices. ^*p < 0.05. OA, patients with OA group; NC, normal control group. (B) The PCoA analysis based on the Bray-curtis distance matrix between the OA and NC group at the species level (p = 0.001). (C) The relative abundance of top 20 species enriched in OA versus KBD. The box represents the interquartile ranges, inner line denotes the median; n = 32 for the OA group and n = 35 for the NC group based on the metagenomic sequencing data.

Figure 5

(A) GO enrichment analysis of differentially expressed unigenes between OA and NC group. (B) Pathway classification based on KEGG enrichment analysis of differentially expressed unigenes between OA and NC group.