Oral and gut microbiome biomarkers of susceptibility to respiratory tract infection in adults: a longitudinal cohort feasibility study

Abstract Background and aim: Respiratory tract infections (RTIs) are common in the community. There is some evidence that microbial biomarkers can be used to identify individuals most susceptible to RTI acquisition. We investigated the feasibility of recruiting healthy adults to collect at-home self-reported socio-demographic data and biological samples, saliva (oral) and stool (gut) at three time points (TPs): baseline/start of the study (TP-A), during an RTI (TP-B) and end of study (TP-C). Methods: Healthy adults were recruited from two urban Bristol GP practices. To identify respiratory pathogens in all saliva samples and RTI-S stool samples reverse transcriptase PCR (RT-PCR) was applied. We compared oral and gut samples from participants who developed RTI symptoms (RTI-S) and those who remained healthy (no-RTI) using 16S rRNA profiling microbiome analysis to identify the core microbiome, alpha and beta diversity, and biomarkers for susceptibility to RTIs from baseline samples (TP-A) when all participants were healthy. Results: We recruited 56 participants but due to the UK COVID-19 pandemic disruption we did not receive samples from 16 participants leaving 19 RTI-S and 21 no-RTI participants with socio-demographic and microbiome data. RT-PCR revealed coagulase-negative Staphylococcus carriage was significantly higher in RTI-S participants compared to those who remained healthy and RTI symptoms may have been due to viral influenzae and bacterial co-infection with Haemophilus influenzae. Core microbiomes of no-RTI participants contained a greater number of taxa compared to RTI-S participants. Microbial biomarkers of RTI susceptibility in the oral cavity were an increased abundance of the pathobiont Streptococcus sobrinus and decreased probiotic bacterium Lactobacillus salivarius whereas in the gut there was an increased abundance of the genus Veillonella and decreased abundance of Coprobacillus. Conclusion: In our feasibility study we found oral and gut microbial biomarkers for susceptibility to RTI acquisition. Strategies to identify those most vulnerable to RTI in the community could lead to novel interventions to decrease respiratory infection and associated health services burden.