Oral, gut, and skin microbiota characterization in patients with heart valve disease with or without infective endocarditis: a pilot study

ABSTRACT The relationship between host microbiota and infective endocarditis (IE) has been investigated by few studies. We compared the oral, gut, and skin microbiota profiles of patients awaiting heart valve replacement, both with and without IE, and correlated the profiles with the patients’ clinical data, including the etiological agents and antibiotics received. Thirty-six patients were enrolled in a prospective, observational pilot study: 25 with IE (cases) and 11 with non-infective valve disease requiring surgery (controls). Clinical data and oral, fecal, and skin samples were collected before surgical treatment. Microbiota was profiled using 16S rRNA amplicon sequencing. Cases and controls were comparable, except for inflammatory parameters and prevalence of prosthetic valves, which were higher in cases. Causative IE pathogens were Staphylococcus spp., Streptococcus spp., and Enterococcus spp. Compared to controls, cases showed dysbiotic features in their oral, gut, and skin microbiota, including lower diversity in oral and skin communities and overall community depletion. Only a few bacteria were enriched, such as Oxalobacteraceae in the oral cavity and Bacteroides in the gut. There was low concordance between bacterial changes and blood isolates for most IE-causing pathogens, suggesting that dysbiosis may have effects beyond merely acting as a reservoir for specific pathogens. Dysbiosis may be a relevant yet underexplored factor associated with IE. Further studies are needed to clarify the underlying pathogenetic mechanisms. IMPORTANCE The relationship between microbiota alterations and infective endocarditis has been explored in the literature, but the majority of available studies focus only on the oral microbiota. In this prospective observational pilot study, we analyzed three microbial ecosystems (oral, skin, and gut) in patients awaiting heart valve replacement with and without infective endocarditis. We observed dysbiotic features that are potentially associated with infective endocarditis. While these findings are preliminary, they suggest that future studies should investigate whether microbiota-targeted interventions, such as a probiotic regimen, could play a preventive role in patients with established IE risk factors, including valve defects, presence of prosthesis, or a history of prior IE.