Identifying Colonization Resistance Activities of the Commensal Upper Respiratory Tract Microbiota

Abstract

Background: The upper respiratory tract (URT) microbiome contributes to colonization resistance against respiratory pathogens such as Streptococcus pneumoniae, a causative agent of pneumonia. Bacterial pneumonia often begins with pathogen colonization in the URT before spreading to the lower airways. The resident microbiota serves as a first line of defense by competing for nutrients and space, as well as by producing antimicrobial compounds. We hypothesize that these microbiota-derived antimicrobial molecules can suppress pneumococcal growth and colonization. This study aimed to identify and characterize URT commensal bacteria with anti-S. pneumoniae activity and define bioactive products.

Methods: A collection of nasal commensals from healthy adults was cultured and screened for antimicrobial activity against S. pneumoniae using agar-based inhibition assays. Active strains underwent activity-guided purification, liquid chromatography-mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR) spectroscopy for structural elucidation of the bioactive molecule. Whole-genome analysis and comparative genomics were performed to identify relevant biosynthetic gene clusters (BGCs).

Results: Over 2,000 bacterial isolates representing diverse URT taxa were assembled, and 48 strains from various genera exhibited anti-pneumococcal activity. Micrococcus luteus GC1842 showed potent inhibition of S. pneumoniae. The produced bioactive metabolites were identified as geninthiocin-family molecules, encoded by a unique thiopeptide BGC. These compounds inhibited S. pneumoniae with limited activity against other respiratory bacteria, suggesting a targeted mechanism which may contribute to minimizing microbiota disruption.

Conclusions: We identify a human-associated M. luteus strain that produces a geninthiocin-like thiopeptide active against S. pneumoniae. Overall, findings demonstrate that colonization resistance in the URT is mediated by diverse commensal bacteria and distinct mechanisms, including thiopeptide antibiotics. We identify novel mechanisms of competition in the URT and expand the ecological and chemical scope of nasal commensals, prioritizing isolates with the potential to be developed into probiotics or postbiotic strategies that reinforce colonization resistance to prevent pneumococcal disease.