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Advances in Pig Genetics and Breeding

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Dear Colleagues,

Owing to various novel technological applications, the genetic improvement of pigs has rapidly progressed in recent decades. Nowadays, more and more economically relevant traits are being expanded as breeding objectives, such as litter size, birth weight, feed efficiency, lean percentage, meat quality, lifetime reproduction, and robustness. In addition, there have been rapid developments in high-throughput genome and cell molecular biology methods, and the processes involved in the identification of genes related to important phenotypic traits and genetic markers for pig selection have been significantly enhanced, leading to the development of fast, cost-effective, and more accurate methods for use in the implementation of breeding programs. In addition, artificial intelligence is now being employed to identify relevant new phenotypes and to implement tools to effectively measure traits. For this Special Issue, articles addressing all aspects of pig genetics and phenotypes are welcome, especially with a focus on the quantitative genetics of new phenotypes, the use of artificial intelligence to link phenotypes, genomic selection, breeding programs, gene polymorphisms, quantitative trait locus mapping, the identification of the genetic regulatory mechanisms and causative mutations affecting economically relevant traits, and the exploitation of native pig genetic resources.

Dr. Linyuan Shen
Dr. Mailin Gan
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Research

15 pages, 5773 KiB

Open AccessArticle

Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets

by Xianrui Zheng, Liming Xu, Qingqing Tang, Kunpeng Shi, Ziyang Wang, Lisha Shi, Yueyun Ding, Zongjun Yin and Xiaodong Zhang

Genes 2024, 15(8), 970; https://doi.org/10.3390/genes15080970 - 23 Jul 2024

Viewed by 435

Abstract

(1) Background: Weaning is a challenging and stressful event in the pig’s life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student’s t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses—350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages. Full article

(This article belongs to the Special Issue Advances in Pig Genetics and Breeding)

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