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Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

ABSTRACT: 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. In this study, we show dynamic changes in respiratory and intestinal microbiota over the course of a sublethal IAV infection in a mouse model. 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 to influenza infection. In the lower respiratory tract, we observed only minor qualitative changes in microbiota composition. In the small intestine, IAV induced robust depletion of bacterial content, disruption of mucus layer integrity and higher levels of antimicrobial peptides in Paneth cells. By RNAseq approach, we tried to analyze changes in transcriptomics of lung, and small intestine on the day of maximum changes to dissect possible causal players leading to the phentype observed.

ORGANISM(S): Mus musculus

PROVIDER: GSE107488 | GEO | 2018/02/23

REPOSITORIES: GEO

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Project description:There is increasing appreciation for sexually dimorphic effects, but the molecular mechanisms underlying these effects are only partially understood. In the present study, we explored transcriptomics and epigenetic differences in the small intestine and colon of prepubescent male and female mice. In addition, the microbiota composition of the colonic luminal content has been examined. At postnatal day 14, male and female C57BL/6 mice were sacrificed and the small intestine, colon and content of luminal colon were isolated. Gene expression of both segments of the intestine was analysed by microarray analysis. DNA methylation of the promoter regions of selected sexually dimorphic genes was examined by pyrosequencing. Composition of the microbiota was explored by deep sequencing. Sexually dimorphic genes were observed in both segments of the intestine of 2-week-old mouse pups, with a stronger effect in the small intestine. Amongst the total of 349 genes displaying a sexually dimorphic effect in the small intestine and/or colon, several candidates exhibited a previously established function in the intestine (i.e. Nts, Nucb2, Alox5ap and Retnlγ). In addition, differential expression of genes linked to intestinal bowel disease (i.e. Ccr3, Ccl11 and Tnfr) and colorectal cancer development (i.e. Wt1 and Mmp25) was observed between males and females. Amongst the genes displaying significant sexually dimorphic expression, nine genes were histone-modifying enzymes, suggesting that epigenetic mechanisms might be a potential underlying regulatory mechanism. However, our results reveal no significant changes in DNA methylation of analysed CpGs within the selected differentially expressed genes. With respect to the bacterial community composition in the colon, a dominant effect of litter origin was found but no significant sex effect was detected. However, a sex effect on the dominance of specific taxa was observed. This study reveals molecular dissimilarities between males and females in the small intestine and colon of prepubescent mice, which might underlie differences in physiological functioning and in disease predisposition in the two sexes. Small intestine and colon were isolated from two-week old pups of dams fed a low-fat diet and subjected to gene expression profiling

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Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

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