The respiratory microbiome and susceptibility to influenza virus infection
Authors: Lee Kyu Han , Gordon Aubree , Shedden Kerby , Kuan Guillermina , Ng Sophia , Balmaseda Angel , Foxman Betsy 
Published: July 2018

Influenza is a major cause of morbidity and mortality worldwide. However, vaccine effectiveness has been low to moderate in recent years and vaccine coverage remains low, especially in low- and middle-income countries. Supplementary methods of prevention should be explored to reduce the high burden of influenza.

A potential target is the respiratory tract microbiome, complex microbial communities which envelop the respiratory epithelium and play an important role in shaping host immunity. Using a household transmission study, we examined whether the nose/throat microbiota was associated with influenza susceptibility among participants exposed to influenza virus in the household. Further, we characterized changes in the nose/throat microbiota to explore whether community stability was influenced by influenza virus infection.

Using a generalized linear mixed effects model, we found a bacterial community type associated with decreased susceptibility to influenza. The community type was rare and transitory among young children but a prevalent and stable community type among adults. Using boosting and linear mixed effects models, we found associations between the nose/throat microbiota and influenza also existed at the taxa level, specifically with the relative abundance of Alloprevotella, Prevotella, and Bacteroides oligotypes.

We found high rates of change in the bacterial community among both secondary cases and household contacts who were not infected during follow up. Preliminary results suggest short-term changes in the bacterial community structure may differ between the two groups, but further work is needed to validate our observations.

Lastly, age was strongly associated with susceptibility to influenza and the nose/throat bacterial community structure. Although additional studies are needed to determine causality, our results suggest the nose/throat microbiome may be a potential target for reducing the burden of influenza.

Author summary

Microbiome research has transformed our understanding of microbes and human health. Resident bacteria can protect the host from pathogens by shaping immunological responses. These new insights suggest the microbiome could be a target for preventing influenza virus infection, a major cause of illness and death worldwide. In this study, we explored the relationship between the nose/throat microbiota and influenza virus in Nicaraguan households.

Household members were enrolled immediately after one member was diagnosed with influenza virus infection. This study design allowed us to identify associations between the microbiota and influenza susceptibility. We also explored whether influenza virus infection altered the bacterial community structure and found short-term changes were common among both secondary cases and household members who remained influenza negative during follow up. Lastly, we found age played major roles in both influenza susceptibility and in short-terms changes in the microbiota. Although much work is needed to determine causal relationships, our findings suggest strategies that appropriately modify the microbiome might be useful in preventing influenza virus infections.