phylum-specific qPCR for streptomycin vs. mock-treated mice. Individual relative levels of Bacteroidetes or Firmicutes normalized to 18S and median are depicted. Pooled data from two independent mouse experiments are shown (n = 5 per group). (PDF 717 kb

Balaji Manicassamy (89161)

Béryl Mazel-Sanchez (4751274)

Matheswaran Kandasamy (105167)

Mirco Schmolke (145040)

Soner Yildiz (4751232)

Microbiome

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Additional file 12: Figure S7. of Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

Abstract Background Microbiota integrity is essential for a growing number of physiological processes. Consequently, disruption of microbiota homeostasis correlates with a variety of pathological states. Importantly, commensal microbiota provide a shield against invading bacterial pathogens, probably by direct competition. The impact of viral infections on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections. Here, we show dynamic changes in respiratory and intestinal microbiota over the course of a sublethal IAV infection in a mouse model. Results Using a combination of 16S rRNA gene-specific next generation sequencing and qPCR as well as culturing of bacterial organ content, we found body site-specific and transient microbiota responses. In the lower respiratory tract, we observed only minor qualitative changes in microbiota composition. No quantitative impact on bacterial colonization after IAV infection was detectable, despite a robust antimicrobial host response and increased sensitivity to bacterial super infection. In contrast, in the intestine, IAV induced robust depletion of bacterial content, disruption of mucus layer integrity, and higher levels of antimicrobial peptides in Paneth cells. As a functional consequence of IAV-mediated microbiota depletion, we demonstrated that the small intestine is rendered more susceptible to bacterial pathogen invasion, in a Salmonella typhimurium super infection model. Conclusion We show for the first time the consequences of IAV infection for lower respiratory tract and intestinal microbiobiota in a qualitative and quantitative fashion. The discrepancy of relative 16S rRNA gene next-generation sequencing (NGS) and normalized 16S rRNA gene-specific qPCR stresses the importance of combining qualitative and quantitative approaches to correctly analyze composition of organ associated microbial communities. The transiently induced dysbiosis underlines the overall stability of microbial communities to effects of acute infection. However, during a short-time window, specific ecological niches might lose their microbiota shield and remain vulnerable to bacterial invasion

Soner Yildiz

Béryl Mazel-Sanchez

Matheswaran Kandasamy

Balaji Manicassamy

Mirco Schmolke

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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) Alpha diversity depicted as shannon index for fecal microbiota of baseline (gray), mock-treated (black) or IAV-infected (red) mice. Individual values per mouse and median are depicted. (C) 2D PCoA plots of fecal microbiota mock-treated (blue) or IAV-infected mice (red) at indicated time points post infection. Each symbol represents one mouse. (D) Most abundant OTU on genus level. Median relative abundance (%) is depicted. (E) Relative abundance (%) of significantly changing OTUs of individual mice and median are depicted (mock red, IAV black). (F) Cultivatable bacterial cfu/fecal pellet of mock-treated (black) or IAV-infected (H5N1 red, H1N1 green) 7 dpi grown under aerobic or anaerobic conditions are depicted (n = 6 per group per time point, two independent experiments). (PDF 1343 kb

Additional file 9: Figure S4. of Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

https://figshare.com/articles/Additional_file_12_Figure_S7_of_Influenza_A_virus_infection_impacts_systemic_microbiota_dynamics_and_causes_quantitative_enteric_dysbiosis/5773479

Additional file 12: Figure S7. of Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

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