Additional file 3: Figure S2. of Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

(A) rarefection plot: number of sequences is plotted against Chao1 estimator. Error bars indicate SE. (B) Most abundant OTU found in baseline, mock or IAV-infected LRT samples 7 dpi on genus level. Median relative abundance (%) is depicted. (C) N-fold changes of 16S/18S DNA levels normalized to mean of mock samples of each day examined. Individual mice and median are depicted (n = 18 per group per time point, two independent experiments, representative data shown). (D) Individual lung titers of mock treated (black circles) and IAV (pH1N1, Neth/602) infected mice (red squares), median titers (pfu/organ) are indicated. Limit of detection (LoD) 50 pfu (n = 5 per group). (E) Relative abundance of total bacteria and Firmicutes based on qPCR (16S/18S) normalized to mean of mock samples is shown for individual mice and indicated time points treated with mock (black symbols) or indicated viruses (red symbols for pH1N1 6 dpi) (n = 5 per group). (F) Bacterial titers of cultivatable URT microbiota 7 dpi grown on indicated agar plates (n = 6 per group). (G) Sequence alignment of Sanger sequencing results of 16S rRNA gene V4 region of Enterobacteriaceae (OTU ID 1111294) colonies. (H) Sequence alignment of Sanger sequencing results of 16S rRNA gene V4 region of Lactobacillaceae (OTU ID 1107027) colonies. (PDF 1691 kb