Fig. 3

Influenza A virus infection eliminates small intestinal microbiota. a Individual Shannon H-index of SI 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. b 2D-PCoA plots of SI 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 Mean UNIFRAC distances for the comparison of indicated experimental groups. Statistical significance ((*) towards all-within group (#) all between group) was determined by two-tailed student’s T test. d Relative abundance (%) of indicated bacteria is depicted for individual mock (black symbols) or IAV-infected (red symbols) mice. e Normalized abundance of total or indicated groups of bacteria based on qPCR (16S/18S) samples is shown; each symbol represents one animal; mock-treated (black) and IAV-infected (red). Pooled data from four independent cages are depicted (n = 18 per time point, per group from two independent experiments, representative data shown). f 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 and IAV infected (black for mock, red for H5N1, green for H1N1 (n = 6 per group per condition, two independent experiments))