Gene expression profiles of germ-free and conventional piglets from the same litter

Scientific Reports
Jing SunLiangpeng Ge

Abstract

Germ-free (GF) pigs have clear microbiological backgrounds, and are extensively used as large animal models in the biomedical sciences. However, investigations of the transcriptomic differences between GF and cesarean-derived conventional (CV) piglets are limited. To improve our understanding of GF pigs, and to increase the utility of pigs as an alternative non-rodent model, we used RNA sequencing to profile gene expression in five tissues (the oral mucosae, jejunum, colon, liver, and spleen) of four male GF piglets and four male CV piglets from the same litter. We identified 14 genes that were differentially expressed in all five tissues. Seven of these common differentially expressed genes (DEGs) were interferon-inducible genes, and all 14 were consistently downregulated in the GF piglets as compared to the CV piglets. Compared to the other tissues tested, the expression of transcription factors (TFs) in the colon was most affected by the absence of a microbiota. The expression patterns of immune-related genes were downregulated in the GF piglets as compared to the CV piglets, indicating that the intestinal microbiota influenced gene expression in other tissues besides the gut. Gene Ontology (GO) analysis indicated that, in p...Continue Reading

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Citations

Apr 7, 2020·Journal of Applied Microbiology·H M ZmudaH Beyenal
Jan 10, 2020·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Alexis Pierre ArnaudGaëlle Boudry
Aug 28, 2020·Frontiers in Oncology·Faraz BishehsariYue Zhang
Apr 25, 2021·Letters in Applied Microbiology·Jing SunLiangpeng Ge
Nov 5, 2021·Proceedings of the National Academy of Sciences of the United States of America·Carolyn BomidiSarah E Blutt

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Methods Mentioned

BETA
RNA-Seq
PCR
GTPases
hysterectomy
RNA Assay
Assay

Software Mentioned

TopHat2 aligner
GOseq R package
HTSeq
DEGSeq package
Cufflinks
TopHat

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