The respiratory microbiota: associations with influenza symptomatology and viral shedding

Kyu Han Lee, Betsy Foxman, Guillermina Kuan, Roger López, Kerby Shedden, Sophia Ng, Angel Balmaseda, Aubree Gordon

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Purpose: Manifestations of infection and the degree of influenza virus vary. We hypothesized that the nose/throat microbiota modifies the duration of influenza symptoms and viral shedding. Exploring these relationships may help identify additional methods for reducing influenza severity and transmission. Methods: Using a household transmission study in Nicaragua, we identified secondary cases of influenza virus infection, defined as contacts with detectable virus or a greater than 4-fold change in hemagglutinin inhibition antibody titer. We characterized the nose/throat microbiota of secondary cases before infection and explored whether the duration of symptoms and shedding differed by bacterial community characteristics. Results: Among 124 secondary cases of influenza, higher bacterial community diversity before infection was associated with longer shedding duration (Shannon acceleration factor [AF]: 1.61, 95% confidence interval [CI]: 1.24, 2.10) and earlier time to infection (Shannon AF: 0.72, 95% CI: 0.53, 0.97; Chao1 AF: 0.992, 95% CI: 0.986, 0.998). Neisseria and multiple other oligotypes were significantly associated with symptom and shedding durations and time to infection. Conclusions: The nose/throat microbiota before influenza virus infection was associated with influenza symptoms and shedding durations. Further studies are needed to determine if the nose/throat microbiota is a viable target for reducing influenza symptoms and transmission.

Original languageEnglish (US)
Pages (from-to)51-56.e6
JournalAnnals of epidemiology
StatePublished - Sep 2019
Externally publishedYes


  • Influenza
  • Microbiota
  • Signs and symptoms
  • Virus shedding

ASJC Scopus subject areas

  • Epidemiology


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