Early-Life Nutrition Interventions Improved Growth Performance and Intestinal Health via the Gut Microbiota in Piglets

Comprehensive Multi-Omic Evaluation of the Microbiota and Metabolites in the Colons of Diverse Swine Breeds

Pigs stand as a vital cornerstone in the realm of human sustenance, and the intricate composition of their intestinal microbiota wields a commanding influence over their nutritional and metabolic pathways. We employed multi-omic evaluations to identify microbial evidence associated with differential growth performance and metabolites, thereby offering theoretical support for the implementation of efficient farming practices for Tibetan pigs and establishing a robust foundation for enhancing pig growth and health. In this work, six Duroc × landrace × yorkshi (DLY) pigs and six Tibetan pigs were used for the experiment. Following humane euthanasia, a comprehensive analysis was undertaken to detect the presence of short-chain fatty acids (SCFAs), microbial populations, and metabolites within the colonic environment. Additionally, metabolites present within the plasma were also assessed. The outcomes of our analysis unveiled the key variables affecting the microbe changes causing the observed differences in production performance between these two distinct pig breeds. Specifically, noteworthy discrepancies were observed in the microbial compositions of DLY pigs, characterized by markedly higher levels of Alloprevotella and Prevotellaceae_UCG-003 (p < 0.05). These disparities, in turn, resulted in significant variations in the concentrations of acetic acid, propionic acid, and the cumulative SCFAs (p < 0.05). Consequently, the DLY pigs exhibited enhanced growth performance and overall well-being, which could be ascribed to the distinct metabolite profiles they harbored. Conversely, Tibetan pigs exhibited a significantly elevated relative abundance of the NK4A214_group, which consequently led to a pronounced increase in the concentration of L-cysteine. This elevation in L-cysteine content had cascading effects, further manifesting higher levels of taurine within the colon and plasma. It is noteworthy that taurine has the potential to exert multifaceted impacts encompassing microbiota dynamics, protein and lipid metabolism, as well as bile acid metabolism, all of which collectively benefit the pigs. In light of this, Tibetan pigs showcased enhanced capabilities in bile acid metabolism. In summation, our findings suggest that DLY pigs excel in their proficiency in short-chain fatty acid metabolism, whereas Tibetan pigs exhibit a more pronounced competence in the realm of bile acid metabolism. These insights underscore the potential for future studies to leverage these breed-specific differences, thereby contributing to the amelioration of production performance within these two distinct pig breeds.

Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds

In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.

Alternatives to antibiotics in pig production: looking through the lens of immunophysiology

In the livestock production system, the evolution of porcine gut microecology is consistent with the idea of "The Hygiene Hypothesis" in humans. I.e., improved hygiene conditions, reduced exposure to environmental microorganisms in early life, and frequent use of antimicrobial drugs drive immune dysregulation. Meanwhile, the overuse of antibiotics as feed additives for infectious disease prevention and animal growth induces antimicrobial resistance genes in pathogens and spreads related environmental pollutants. It justifies our attempt to review alternatives to antibiotics that can support optimal growth and improve the immunophysiological state of pigs. In the current review, we first described porcine mucosal immunity, followed by discussions of gut microbiota dynamics during the critical weaning period and the impacts brought by antibiotics usage. Evidence of in-feed additives with immuno-modulatory properties highlighting probiotics, prebiotics, and phytobiotics and their cellular and molecular networking are summarized and reviewed. It may provide insights into the immune regulatory mechanisms of antibiotic alternatives and open new avenues for health management in pig production.

Effects of high-altitude hypoxic environment on colonic inflammation, intestinal barrier and gut microbiota in three-way crossbred commercial pigs

In recent years, the three-way crossbred commercial pigs are extensively cultured in Tibet. However, there have been few studies about the effect of high-altitude hypoxic environment on intestinal health of them. Therefore, we selected Tibetan pigs (TP) and the three-way crossbred commercial pigs (CP-H) living in the Tibet (3,500–3,700 m in altitude) as a positive control group and treatment group, respectively. The three-way crossbred commercial pigs (CP-L) living at altitudes 800–1,000 m sea level were selected as a negative control group. The colonic chyme, colonic mucosa, colonic tissue and serum samples were collected for the detection of gut microbiota and intestinal inflammation. The results showed that high-altitude hypoxic environment promoted the occurrence of colonic inflammation, disrupted the colonic barrier to some extent. And Hematoxylin–Eosin (HE) staining revealed that mild inflammatory cell infiltration was observed in colon of CP-H. 16S rRNA gene sequencing revealed that the microbial community composition of CP-H was changed compared with CP-L. Gut bacterial communities formed distinctly different clusters in principal coordinates analysis (PCoA) space, and Chao 1 index of CP-H was also decreased. At the genus level, Terrisporobacter showed greater enrichment in the CP-H than lower-altitude pigs. Colstridium-sensu-stricto-1 showed lower enrichment in the CP-H than lower-altitude pigs. However, the concentration of valeric acid in colonic chyme of CP-H was higher than CP-L and TP. Correlation analysis indicated that Terrisporobacter was positively associated with the relative mRNA expression level of IL-1β and the content of lipopolysaccharide (LPS), and was negatively correlated with the relative mRNA expression level of IL-10. The Streptococcus was positively associated with the concentrations of valerate. In summary, high-altitude hypoxic environment changed compositions of gut microbiota, promoted the occurrence of colonic inflammation, and disrupted intestinal barrier of the three-way crossbred commercial pigs.

House feeding system improves the estrus rate in yaks (Bos grunniens) by increasing specific fecal microbiota and myo-inositol content in serum

Grazing (G) yaks (Bos grunniens) are generally of low fertility, which severely limits the income of local pastoralists. However, we recently found that yaks had a 52% higher estrus rate in house feeding (HF) than in G. Gas chromatography-mass spectrometry (GC-MS) and 16S rRNA gene sequencing were used to analyze serum metabolites and fecal microbiota of 20 rutting yaks in the G and HF systems, respectively, to explain this phenomenon. The results showed that 73 total metabolites differed significantly (p &lt; 0.05 and VIP &gt; 1) between the G and HF systems. In the HF system, 53 were upregulated and 20 were downregulated compared with the G system. Organic oxygen compounds, organic acids and their derivatives, and lipids and lipid-like molecules were the most common differential metabolites. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapper revealed that 25 metabolic signaling pathways differed significantly between the two systems. The top three enriched pathways included central carbon metabolism in cancer, aminoacyl–tRNA biosynthesis, and ABC transporters. The 16S rRNA gene sequencing data showed no significant differences in Chao 1 index between the two systems. According to principal component analysis (PCA), the HF and G systems were distinctly and separately clustered in terms of fecal microbiota distribution. The G system showed significantly higher abundances of Firmicutes. The HF system showed significantly higher abundances of Alistipes, Treponema, and Rikenellaceae_ RC9_ gut_ group. Pearson's correlation analysis and core network analysis revealed that Rikenellaceae_RC9_ gut_ group, Alistipes, and Treponema were positively correlated with myo-inositol and formed the core bacteria. In summary, the HF system promoted the estrus rate and changed the composition of yak fecal microbiota and serum metabolites. Increased estrus rate might be obtained due to enhanced myo-inositol content in yak serum via the HF system. Correlation analysis suggested that myo-inositol content might also be partly increased via yak-specific fecal microbiota, contributing to the estrus rate. These findings could lead to a novel therapeutic strategy for G yaks due to their low estrus rate.

House feeding pattern increased male yak fertility by improving gut microbiota and serum metabolites

Yaks usually live in an extremely harsh natural environment resulting in low reproductive performance, so the production of yak cannot meet local demand in China. In order to solve this problem, the experiment aims to explore the effect of different feeding modes on the semen quality of male yaks, so as to provide a theoretical basis for improving the yield of yaks in Tibet. We used the combined analysis of metabolomics and microbial sequencing to explore the underlying mechanisms that affect the differences in semen quality between the house feeding (HF) system and the free range (FR). The results showed that the sperm motility (P < 0.001) and sperm concentration (P < 0.05) in the HF group were significantly higher than the FR group, and the abnormal sperm rate (P < 0.01) in HF was significantly lower compared to FR. House feeding modes increased some beneficial materials in blood and testis especially some antioxidants, unsaturated fatty acids, and amino acids. House feeding group increased some gut microbiota at genus level namely Rikenellaceae, Bacteroides, Prevotellaceae_UCG-004, Bacteroidales_RF16, and Alloprevotella, DgA-11. It was interesting that blood metabolites, testicular metabolites, and fecal microbiota were well-correlated with sperm parameters. Meanwhile, the blood metabolites and testicular metabolites were well-correlated with microbes. The result indicated that the HF model was beneficial for yak semen quality by improving the gut microbiota and blood metabolism to increase yak fertility.