Integration analysis of muscle transcriptomic profile and microbiome intestinal tract of pigs fed diets enriched with oleic acid

• Grant number: 24/02056-8
• Support Opportunities: Regular Research Grants
• Start date: August 01, 2024
• End date: July 31, 2026
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Agreement: CNPq
• Principal Investigator: Aline Silva Mello Cesar
• Grantee: Aline Silva Mello Cesar
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 21/01664-6 - Characterization of Single Nucleotide Polymorphisms (SNPs) associated with intestinal microbiota in pigs fed diets rich in oleic acid, AP.R
• Associated scholarship(s): 24/14334-2 - Integration analysis of muscle transcriptomic profile and intestinal microbiome of pigs fed diets enriched with oleic acid, BP.JD

Abstract

The main goal of this proposal is to identify differences in the microbial community of pigs fed a basal diet with the addition of 3% degummed soybean oil (SOJ) vs. a basal diet with the addition of 3%canola oil (CAN) and to explore the correlations between the transcriptomic profile and the microbiome of these animals. The pig is an excellent animal model for studying metabolic disorders that can occur in humans. Therefore, 48 immunocastrated male Large White pigs from the experimental population of the Young Researcher FAPESP project (2017/25180-2) were subjected to experimental diets (SOJ and CAN), and were slaughtered at 169 days of age (final average live weight of 133.9 + 9.4 kg). The skeletal muscle (transcriptomic analysis) and cecum content (microbiome) were collected at slaughter. Feces were collected directly from the animals' rectums at 166 days of life (microbiome). The characterization of the microbiome will be carried out sequencing of the 16S rRNA gene, following the 16S Metagenomic Sequencing Library Preparation protocol (Illumina), and using the Illumina MiSeq platform. To integrate the transcriptomic profile and microbiome of the animals in each of the diets (SOJ and CAN), gene co expression networks will be constructed using the R package WGCNA (Weighted Correlation Network Analysis). This analysis will reveal gene modules correlated with the abundance of bacteria (genus level) identified in the animals' cecum. Finally, Spearman's coefficient correlation analysis will be used to calculate the correlation between the hub-genes of the significant modules and the bacteria's abundances in the cecum. To our knowledge, this will be the first study in pigs that aims to integrate transcriptomic and microbiome data using gene co-expression networks. The innovative potential of the study lies on the identification of changes in the microbiome of the gastrointestinal tract as a result of different diets, which may contribute to individualized diet programs and mitigation of metabolic diseases in humans. This proposal is linked to the research grant # 2021/01664-6, valid until July 31, 2025. (AU)