Effects of lysozyme-rich milk on intestinal gene expression of malnourished piglets challenged with E.coli
16 Sep 2022
Period
2014 - 2019
Colaborators
Responsible: Raquel Pinho
PI: Dr.Elizabeth Maga, University of Californa, Davis, CA - United States
Colaborator: Dr. Lydia Garas, University of Californa, Davis, CA - United States
Colaborator: Dr. Elizabeth Maga, University of Californa, Davis, CA - United States
Colaborator: Dr. Bart Weimer, University of Californa, Davis, CA - United States
Colaborator: Dr. Carol Huang, University of Californa, Davis, CA - United States
Location
- University of California, Davis, CA - United States
Raquel Pinho’s main responsabilities
- Experiment design and project writing.
- Library construction for RNA-sequencing.
- RNA-seq data processing in Linux.
- RNA-seq data analysis in R.
- RNA-seq data visualization in R.
- Weighted co-expression network analysis using WGCNA.
- Integration of intestinal transcriptome, hepatic metabolome and intestinal microbiota 16S data using MixOmics.
- Validation of NGS results using qPCR for relative gene expression analysis.
Description
Goat milk containing human lysozyme (hLZ) has shown beneficial effects on microbiome composition, gastro-intestinal (GI) morphology and the clinical condition of pigs including during infection if enterotoxigenic E.coli (ETEC) . To explore the effect of infection and hLZ milk supplementation before/during infection on intestinal gene expression in malnourished animals, RNA-seq was conducted with tissue from the duodenum, jejunum and ileum of malnourished piglets fed with hLZ milk, regular goat milk or with no milk supplementation and then challenged with ETEC . Gene co-expression analysis and pheno- typic correlations were made with WGCNA, while integration of transcriptome with microbiota information and the hepatic metabolite profile was done using mixOmics.
Data
BioProject: PRJNA823693
Publications
- PINHO, R. M.; GARAS L.C.; HUANG B.C; WEIMER B.C.; MAGA, E.A.. Lysozyme-rich milk affects gene expression along the length of porcine small intestine before and during enteropathogenic Escherichia coli infection. (submitted 2022).