Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis

Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.

We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.

We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.