bioRxiv2026
Non-typeable Haemophilus influenzae (NTHi) is a prominent opportunistic pathogen relevant to chronic respiratory diseases. NTHis metabolic diversity enables its survival in a wide range of environmental conditions within the host. As such, deeper research into the metabolic pathways of NTHi may open an avenue for novel therapies aimed at combating NTHi-associated respiratory diseases. Draft genome sequences from nine NTHi clinical strains from three isolation sites - ear (ear sample, ES), pharynx (pharynx sample, PS), and lower respiratory tract (Lungs) - were analyzed and annotated using RAST, PROKKA, KEGG KAAS, and antiSMASH. Pathway module coverage per-strain was computed and summarized by per-group for significant annotated metabolites. Metabolites were analyzed by LC/HRMS, identified by Metaboscape, and statistically compared using MetaboAnalyst and R software. Gene content across the tested NTHi strains was largely conserved, with limited core-genome SNP variation. Gene annotation for metabolite-related pathways revealed that all nine strains possessed largely similar sets of metabolic pathway genes, despite minor nucleotide-level differences, indicating broadly comparable metabolic capacities. In contrast, metabolomics data revealed differential metabolic profiles among the body-site groups. In a principal component analysis (PCA), the ES group was significantly separated from both the PS and Lung groups, which overlapped considerably. Detailed metabolite analyses showed that inosine, hypoxanthine, and uracil were highly significant in the ES group compared to the PS and Lung groups. For the first time, our study sheds light on the extent of metabolic differences associated with NTHi inhabiting diverse host niches. The observed metabolic differences suggest that NTHi may modulate its metabolism in a site-specific manner that is affected by environmental factors. These findings add to our understanding of how NTHi metabolism contributes to site-specific colonization. Author summaryHaemophilus influenzae is widely recognized as a causative agent of meningitis and pneumonia. In particular, H. influenzae strains with a polysaccharide capsule--known as H. influenzae type b (Hib)--were historically a major cause of invasive disease. However, Hib has been largely eradicated following implementation of the Hib vaccine. Nonetheless, there are H. influenzae strains that lack this capsule and are therefore not targeted by the vaccine. These are known as non-typeable H. influenzae (NTHi). Following the decline of Hib, NTHi has rapidly occupied the ecological niche in the lower respiratory tract, becoming the most prominent pathogen in patients with chronic respiratory infections--particularly in those with chronic obstructive pulmonary disease (COPD), where it frequently triggers exacerbations. Importantly, NTHi is also a common component of the normal microbiome in healthy individuals, typically residing in the upper respiratory tract without causing disease. In our study, we investigated the metabolic characteristics of NTHi isolates obtained from different body sites in patients to better understand what distinguishes strains capable of colonizing specific anatomical niches. We successfully identified several distinct metabolic features associated with NTHi strains from the ear, pharynx, and lung. These findings may serve as a foundation for future research into patient-tailored biomarkers and targeted therapies, ultimately aiming to eradicate NTHi in chronic lung infections.