Fig. 2

Influenza A virus infection has minor impact on global LRT microbiome. a Individual Shannon H-index of LRT microbiota of baseline (gray circles), mock-treated (black squares) and IAV-infected mice (red triangles) pooled from four independent cages are depicted for indicated days of sampling. Median Shannon index per experimental group is indicated. b 2D-PCoA plots of LRT microbiota of mock-treated (blue triangle) or IAV-infected mice (red circle) mice at indicated time points post infection. Each symbol represents one individual mouse. Percentages explain variation in PC1 (x-axis) and PC2 (y-axis). c Normalized individual 16S/18S qPCR results (n-fold relative to mean of mock samples) and median are depicted for individual days for mock-treated (black circle) and IAV-infected (red square) (n = 18 per time point, per group from two independent experiments, representative data shown). d Relative abundance of bacteria of the LRT determined by 16S rRNA gene-specific NGS is indicated for individual classes. Pooled data from two independent experiments with median are shown. e Individual bacterial titers (cfu/organ) and median determined under aerobic (left) and anaerobic conditions (right) on Columbia or Chocolate agar are depicted for mock treated (black symbols) and IAV infected (red symbols). Pooled data from two independent experiments are shown (n = 6 per group per condition). f Left panel: Enterobacteriaceae (OTU-ID 1111294)-like colonies in serial dilutions of LRT homogenate on Columbia (left) and Chocolate agar (right) from mock treated (left half) and infected animals (right half). Representative plates are shown. Right panel: quantification of titers of Escherichia (OTU ID 1111294)-like colonies from mock-treated (black symbols) or IAV-infected LRT homogenates (red symbols). Individual titers (cfu/organ) and median of homogenates grown on indicated agars from two independent experiments are shown (n = 6 per group per condition). g S. pneumoniae bacterial lung titers (cfu/organ) 24 h post infection from mock treated of IAV preinfected animals from two independent experimental sets are shown (mock (n = 10), IAV (n = 9))