Mapping the microbial landscape and variations based on biological sex, age, and biopsy location in the shoulder skin microbiome.

Abstract

The organisms responsible for periprosthetic joint infections (PJIs) of the shoulder are often skin pathogens originating from the patient's own skin flora at the time of surgery. Understanding the normal skin flora around the shoulder is an important step to identify the range of organisms that could be responsible for PJI and to ensure optimization of culture mediums to identify them. This study aimed to provide the first description of the shoulder skin microbiome using high-throughput next-generation sequencing methodology and explore variations by age, biological sex, and biopsy location. Patients undergoing arthroscopic surgery were approached for informed consent to have punch biopsies taken from anterior, lateral, and posterior arthroscopy portal sites. DNA extraction was undertaken followed by illumina sequencing, focusing on the V3-V4 regions of the 16S rRNA gene. Amplicon sequence variants (ASVs) were generated using Deblur workflow and used for taxonomic assignment. Variation in the microbiota community based on age, biological sex, and biopsy location was assessed through alpha and beta diversity metric calculations using phyloseq R package. Sixty-two patients (24 female, 38 male) aged 18-80 years were recruited, resulting in 186 punch biopsy samples for analysis. Following removal of low-prevalence taxa, 606 ASVs were aggregated at the genus level, resulting in 214 genera across 13 phyla. The top 20 most abundant genera accounted for 73.5% of the overall sequence count. Cutibacterium was the most abundant genus within the study population, followed by Ralstonia, Staphylococcus, Bacteroides, and Streptococcus. Significant differences were observed in beta diversity metrics when comparing by biological sex, which accounted for 3.9%-5.3% of the variation in the microbial community, but not age or biopsy location. Males displayed a greater proportion of gram-positive and aerobic bacteria, whereas females exhibited a greater proportion of gram-negative and stress-tolerant bacteria. This is the first study to look specifically at the microbiome of the cutaneous shoulder and describe the most abundant genera and compositional differences based on age, biological sex, and biopsy location. Biological sex was the only host covariant studied that reached significance in explaining microbiota variation. The top 20 most abundant genera, accounting for 74% of the overall sequence count, would be isolated with standard microbiological culture. As such, this study does not highlight a need to change current culture investigation practice for shoulder PJI, but it serves as an important catalog of skin commensals around the operative site in shoulder surgery.