Identification of Cartilage Microbial DNA Signatures and Associations With Knee and Hip Osteoarthritis

Arthritis Rheumatol. 2020 Jul;72(7):1111-1122. doi: 10.1002/art.41210. Epub 2020 May 12.


Objective: Alterations of the gut microbiota have been implicated in many forms of arthritis, but an examination of cartilage microbial patterns has not been performed. This study was undertaken to characterize the microbial DNA profile of articular cartilage and determine changes associated with osteoarthritis (OA).

Methods: We performed 16S ribosomal RNA gene deep sequencing on eroded and intact cartilage samples from knee OA patients (n = 21 eroded and 21 intact samples) and hip OA patients (n = 34 eroded and 33 intact samples) and cadaver controls (n = 10 knee samples and 10 hip samples). Microbial DNA diversity was assessed, groups were compared, and metagenomic profiles were reconstructed. Confirmation was performed in an independent cohort by clade-specific quantitative polymerase chain reaction. Findings in human cartilage were compared to those in cartilage from OA-susceptible C57BL/6 (B6) mice and OA-resistant MRL/MpJ (MRL) mice. Germ-free B6 mouse cartilage was analyzed as a methodologic control.

Results: Alpha diversity was reduced in human OA versus control samples (P < 0.0001), and in hip versus knee samples (P < 0.0001). Numerous clades were different in human OA versus control samples, and similar findings were noted in comparisons of murine B6 versus MRL mice. Hip samples were microbiologically distinct from knee samples. OA microbial DNA demonstrated increased gram-negative constituents (P = 0.02). Functional analysis demonstrated increases in lipopolysaccharide production (P = 9.9 × 10-3 ), phosphatidylinositol signaling (P = 4.2 × 10-4 ), and nitrogen metabolism (P = 8 × 10-3 ) and decreases in sphingolipid metabolism (P = 7.7 × 10-4 ) associated with OA.

Conclusion: Our study reveals a microbial DNA signature in human and mouse cartilage. Alterations in this signature, including increases in gram-negative constituents, occur during the development and progression of human OA. Furthermore, our findings indicate that strain-specific signatures exist within mouse cartilage that mirror human patterns. Further study of the establishment and potential pathogenic role of these DNA signatures is needed.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Animals
  • Arthroplasty, Replacement, Hip
  • Arthroplasty, Replacement, Knee
  • Cartilage, Articular / metabolism
  • Cartilage, Articular / microbiology*
  • Cartilage, Articular / pathology
  • Classification
  • DNA, Bacterial / analysis*
  • Disease Susceptibility
  • Female
  • Genetic Variation
  • Humans
  • Male
  • Metagenome / genetics*
  • Mice
  • Microbiota / genetics*
  • Middle Aged
  • Osteoarthritis, Hip / microbiology*
  • Osteoarthritis, Hip / surgery
  • Osteoarthritis, Knee / microbiology*
  • Osteoarthritis, Knee / surgery
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S / genetics*


  • DNA, Bacterial
  • RNA, Ribosomal, 16S