Characterizing the microbiome composition of the nares, oropharynx, and hand of monozygotic twins and its interplay with Staphylococcus aureus carriage

Abstract

Abstract Background Staphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic resistant strains causing 11,000 deaths yearly and ~ 2% of the population nasally colonized with MRSA, a search for predictive markers and causal relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with spatial microbiome analyses to characterize impacts of S. aureus on composition. Results: We recruited 147 monozygotic twin pairs and characterized three sites: nares, oropharynx, and hand microbiomes using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. Prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. All microbiome sites were significantly modified by the presence of S. aureus as illustrated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins’ nares that were S. aureus culture positive concordant, whereas twins that were culture negative concordant had the most similarity in the Oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively. Based on Maaslin2 analyses, we identify that S. aureus prevalence significantly affected pathways associated with Biosynthesis of Secondary Metabolites, Infectious Diseases, Amino Acid Metabolism, Cellular Processes and Signaling, and Immune System Diseases only in the nares microbiome. Conclusions: This improved understanding of S. aureus colonization on nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome are influenced by host genetics and S. aureus carriage.