Differences in gut, oral and skin microbiota have been observed in patients with heart valve disease and infective endocarditis compared with those without the infection, although researchers have cautioned that antibiotic exposure may have influenced the findings.

Infective endocarditis is a serious infection of the endocardium associated with substantial morbidity and mortality. Although infective endocarditis can be caused by bacteria normally found in the mouth, gut and skin, relatively little is known about the broader relationship between the host microbiota and infective endocarditis.

Previous research has largely focused on the oral microbiota, with few studies examining other microbial communities.

Researchers in Italy therefore investigated whether oral, skin and gut microbiota differed between patients with heart valve disease with and without infective endocarditis.

Published in the journal Microbiology Spectrum, the prospective observational pilot study included 36 patients awaiting heart valve replacement at Monaldi Hospital in Naples between November 2021 and December 2022.

Of these, 25 had definite infective endocarditis with positive blood cultures and 11 had non-infective valve disease requiring surgery. Faecal, oral and skin samples were collected before surgery and microbiota composition assessed using 16S ribosomal RNA amplicon sequencing.

Six patients with infective endocarditis were enrolled before receiving antibiotics, while 19 had already received antibiotics for a median of five days.

Microbiota differences in infective endocarditis

Patients with infective endocarditis had lower microbial diversity in oral and skin samples compared with controls, while no difference in diversity was identified in the gut. Skin microbial composition also differed significantly between the two groups when assessed using unweighted UniFrac analysis.

Differences in the relative abundance of bacterial groups were identified across all three body sites. Oral samples from patients with infective endocarditis showed lower proportions of several bacterial groups, including Streptococcus, Neisseria, Haemophilus and Fusobacterium, while Oxalobacteraceae were more abundant.

In the gut, patients with infective endocarditis had greater relative abundance of Bacteroides alongside lower abundance of several bacterial groups, including members of the Lachnospiraceae and Ruminococcaceae families. Differences in skin microbiota were smaller but included higher proportions of Streptococcaceae.

Blood cultures predominantly identified Staphylococcus, Streptococcus and Enterococcus species as the causative organisms. However, concordance between bacteria identified in blood cultures and changes in the microbiota at the three sampled sites was generally low.

Antibiotic exposure complicates microbiota findings

When researchers compared patients who had received no antibiotics with those treated for more than three days, they observed some microbiota differences in both treated and untreated patients, while others were identified only among those who had received antibiotics.

For example, differences involving oral Neisseria and several gut bacterial groups, including Bacteroides, were observed irrespective of antibiotic exposure. Other oral and gut changes were found only in antibiotic-treated patients.

The authors stressed that antibiotic exposure was an important confounding factor, making it difficult to distinguish microbiota changes associated with infective endocarditis from those related to treatment.

Other limitations included the small sample size, lack of a true reference group, absence of detailed information on potentially important confounders such as lifestyle and dietary habits, and the inability of 16S rRNA sequencing to provide strain-level resolution.

The researchers concluded that patients with heart valve disease and infective endocarditis showed dysbiotic features across the oral, gut and skin microbiota compared with patients with non-infective valve disease.

However, they cautioned that the exploratory findings cannot establish a pathogenetic role for dysbiosis and should be considered hypothesis-generating.

Larger longitudinal studies, including antibiotic-naive patients where possible, are needed to validate the findings, clarify the effects of antibiotic exposure and investigate potential pathogenetic mechanisms, they added.

Reference
Mengoli M et al. Oral, gut, and skin microbiota characterization in patients with heart valve disease with or without infective endocarditis: a pilot study. Microbiol Spectr 2026:doi:10.1128/spectrum.01908-25.