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Zhang Y, Li H, Li B, He J, Peng C, Xie Y, Huang G, Zhao P, Wang Z. The Adaptive Alternation of Intestinal Microbiota and Regulation of Host Genes Jointly Promote Pigs to Digest Appropriate High-Fiber Diets. Animals (Basel) 2024; 14:2076. [PMID: 39061538 PMCID: PMC11274041 DOI: 10.3390/ani14142076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Although studies have revealed the significant impact of dietary fiber on growth performance and nutrient digestibility, the specific characteristics of the intestinal microbiota and gene regulation in pigs capable of digesting high-fiber diets remained unclear. To investigate the traits associated with roughage tolerance in the Chinese indigenous pig breed, we conducted comparative analysis of growth performance, apparent fiber digestibility, intestinal microbiota, SCFA concentrations and intestinal transcriptome in Tunchang pigs, feeding them diets with different wheat bran levels. The results indicated that the growth performance of Tunchang pigs was not significantly impacted, and the apparent total tract digestibility of crude fiber was significantly improved with increasing dietary fiber content. High-fiber diets altered the diversity of intestinal microbiota, and increased the relative abundance of Prevotella, CF231, as well as the concentrations of isobutyrate, valerate and isovalerate. The LDA analysis identified potential microbial biomarkers that could be associated with roughage tolerance, such as Prevotella stercorea, and Eubacterium biforme. In addition, appropriate high-fiber diets containing 4.34% crude fiber upregulated the mRNA expressions of PYY, AQP8, and SLC5A8, while downregulating the mRNA expressions of CKM and CNN1.This indicated that appropriate high-fiber diets may inhibit intestine motility and increase the absorption of water and SCFAs.
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Affiliation(s)
- Yunchao Zhang
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Hui Li
- Long Jian Animal Husbandry Company, Haikou 570100, China; (H.L.); (B.L.)
| | - Bengao Li
- Long Jian Animal Husbandry Company, Haikou 570100, China; (H.L.); (B.L.)
| | - Jiayi He
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Chen Peng
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Yanshe Xie
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Guiqing Huang
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Pengju Zhao
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Sanya 572000, China; (Y.Z.); (J.H.); (C.P.); (Y.X.); (G.H.); (P.Z.)
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
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Xue P, Xue M, Luo Y, Tang Q, Wang F, Sun R, Song Y, Chao Z, Fang M. Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of Short-Chain Fatty Acids in Local Pigs of Hainan. Microorganisms 2024; 12:1033. [PMID: 38930415 PMCID: PMC11205767 DOI: 10.3390/microorganisms12061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/05/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding'an and DLY pigs high and low levels of dietary fiber, respectively, to investigate factors contributing to high dietary fiber adaption in Ding'an pigs. Twelve Ding'an pigs and DLY pigs were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 3). Compared with commercial pigs, Ding'an pigs have a stronger ability to digest dietary fiber. Prevotella was more prevalent in Ding'an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding'an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding'an pigs. Among them, Prevotella. sp. CAG:520 may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria (r > 0.7). We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding'an pigs after increasing the fiber content, which resulted in the downregulated expression of inflammatory factors in colonic mucosa. Spearman's correlation coefficient revealed a strong correlation between microbiota and the apparent digestibility of dietary fiber (r > 0.7). The mRNA expressions of SLC16A1, PYY, and GCG were significantly increased in the colonic mucosa of Ding'an pigs fed on high-fiber diets, which indicates that Ding'an pigs have an enhanced absorption of SCFAs. Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding'an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.
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Affiliation(s)
- Pengxiang Xue
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Mingming Xue
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Yabiao Luo
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Qiguo Tang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Feng Wang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571101, China; (F.W.); (R.S.); (Z.C.)
| | - Ruiping Sun
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571101, China; (F.W.); (R.S.); (Z.C.)
| | - Yanxia Song
- Sanya Institute, China Agricultural University, Sanya 572024, China;
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571101, China; (F.W.); (R.S.); (Z.C.)
| | - Meiying Fang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
- Sanya Institute, China Agricultural University, Sanya 572024, China;
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Chen X, Li X, Chen D, Zhao W, Zhang X, Yuan W, Si H, Deng X, Du R, Xu C. Effects of Dietary Alfalfa Meal Supplementation on the Growth Performance, Nutrient Apparent Digestibility, Serum Parameters, and Intestinal Microbiota of Raccoon Dogs ( Nyctereutes procyonoides). Animals (Basel) 2024; 14:623. [PMID: 38396591 PMCID: PMC10886288 DOI: 10.3390/ani14040623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The raccoon dog (Nyctereutes procyonoides) is a typical omnivore possessing wide dietary adaptability and tolerance to rough feeding, which may be attributed to its intestinal microbiota. The study aimed to investigate the effect of dietary alfalfa meal levels on the growth performance, nutrient apparent digestibility, serum parameters, and intestinal microbiota of raccoon dogs. Sixty raccoon dogs were randomly divided into four dietary treatments containing 0% (AM0), 5% (AM5), 10% (AM10), and 15% (AM15) alfalfa meal for a 60-day experiment. The results showed that compared to raccoon dogs fed the AM0 diet, those fed the AM5 and AM10 diets had no significant difference in growth performance, while those fed the AM15 diet experienced a significant decrease. Raccoon dogs fed the AM5 diet had no significant effect on the nutrient apparent digestibility. Dietary supplementation with alfalfa meal significantly decreased serum urea levels and increased the antioxidant capacity of raccoon dogs. The intestinal microbiome analysis showed that the richness and diversity of colonic microbiota significantly increased in the AM15 group. With the increase in dietary alfalfa meal levels, the relative abundance of fiber-degrading bacteria in the colon of raccoon dogs, such as Treponema, Phascolarctobacterium, and Christensenellaceae R-7 group, increased. However, the relative abundance of pathogenic bacteria, including Anaerobiospirillum, decreased. In conclusion, the inclusion of 5% alfalfa meal in the raccoon dogs' diet had no effect on growth performance, but it exhibited the potential to improve serum antioxidant capacity and intestinal microbiota. This indicates that raccoon dogs have a certain tolerance to the addition of alfalfa meal in their diet.
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Affiliation(s)
- Xiaoli Chen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Xiao Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Danyang Chen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Weigang Zhao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Xiuli Zhang
- College of Veterinary Medicine, Jilin University, Changchun 130062, China; (X.Z.); (X.D.)
| | - Weitao Yuan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (H.S.); (R.D.)
| | - Xuming Deng
- College of Veterinary Medicine, Jilin University, Changchun 130062, China; (X.Z.); (X.D.)
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (H.S.); (R.D.)
| | - Chao Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (H.S.); (R.D.)
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Hu J, Chen J, Ma L, Hou Q, Zhang Y, Kong X, Huang X, Tang Z, Wei H, Wang X, Yan X. Characterizing core microbiota and regulatory functions of the pig gut microbiome. THE ISME JOURNAL 2024; 18:wrad037. [PMID: 38366194 PMCID: PMC10873858 DOI: 10.1093/ismejo/wrad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/23/2023] [Indexed: 02/18/2024]
Abstract
Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.
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Affiliation(s)
- Jun Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Jianwei Chen
- BGI Research, Qingdao, Shandong 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Libao Ma
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Qiliang Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Yong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiangfeng Kong
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xingguo Huang
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hong Wei
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xianghua Yan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
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Kuthyar S, Diaz J, Avalos-Villatoro F, Maltecca C, Tiezzi F, Dunn RR, Reese AT. Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population. J Evol Biol 2023; 36:1695-1711. [PMID: 37885134 DOI: 10.1111/jeb.14227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023]
Abstract
Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.
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Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Jessica Diaz
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | | | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Aspen T Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Li L, Li S, Luo J, Chen T, Xi Q, Zhang Y, Sun J. The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets. BMC Vet Res 2023; 19:174. [PMID: 37759242 PMCID: PMC10523759 DOI: 10.1186/s12917-023-03642-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/12/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The early development of intestinal microbiota plays a fundamental role in host health and development. To investigate the difference in the intestinal microbial composition between Lantang and Landrace newborn piglets, we amplified and sequenced the V3-V4 region of 16 S rRNA gene in jejunal microbiota of Lantang and landrace newborn. RESULTS The findings revealed that the dominant phyla in the jejunum of Lantang piglets were Firmicutes, Actinobacteria and Bacteroidetes, while the dominant phyla of Landrace is Proteobacteria and Fusobacteria. Specifically, Corynebacterium_1, Lactobacillus, Rothia, Granulicatella, Corynebacteriales_unclassified, Corynebacterium, Globicatella and Actinomycetales_unclassified were found to be the dominant genera of Lantang group, while Clostridium_sensu_stricto_1, Escherichia-Shigella, Actinobacillus and Bifidobacterium were the dominant genera of Landrace. Based on the functional prediction of bacteria, we found that bacterial communities from Lantang samples had a significantly greater abundance pathways of fatty acid synthesis, protein synthesis, DNA replication, recombination, repair and material transport across membranes, while the carrier protein of pathogenic bacteria was more abundant in Landrace samples. CONCLUSIONS Overall, there was a tremendous difference in the early intestinal flora composition between Landang and Landrace piglets, which was related to the breed characteristics and may be one of the reasons affecting the growth characteristics. However, more further extensive studies should be included to reveal the underlying relationship between early intestinal flora composition in different breeds and pig growth characteristics.
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Affiliation(s)
- Ling Li
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Shuai Li
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Junyi Luo
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ting Chen
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qianyun Xi
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yongliang Zhang
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
| | - Jiajie Sun
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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Du J, Gan M, Xie Z, Du G, Luo Y, Liu B, Zhu K, Chen L, Zhao Y, Niu L, Wang Y, Wang J, Zhu L, Shen L. A Comparative Study on the Growth Performance and Gut Microbial Composition of Duroc and Yorkshire Boars. Genes (Basel) 2023; 14:1726. [PMID: 37761866 PMCID: PMC10531244 DOI: 10.3390/genes14091726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The intestinal microbiota is required for maintaining the development and health of the host. However, the gut microbiota contributing to the regulation of the growth performance and health of Duroc and Yorkshire boars remains largely unknown. In this study, we first evaluated the difference in the growth performance between Duroc and Yorkshire boars when their body weight reached 100 kg. Relative to Duroc boars, Yorkshire boars weighed 100 kg at a younger age and exhibited a significantly lower backfat thickness and eye muscle area. Microbial analysis of the fecal samples revealed a marked difference in gut microbiota composition between the two pig models and remarkably increased α-diversity in Yorkshire boars compared to Duroc boars. Further analysis indicated that Bacteroidota, Prevotellaceae, and Ruminococcaceae might be associated with the growth performance and lean meat rate of Yorkshire boars. Taken together, these results highlight that Yorkshire boars exhibit a faster growth rate and higher lean meat rate compared to Duroc boars, and these differences may be attributed to the influence of the gut microbiota, thereby providing valuable insight into optimizing pig breeding systems and selecting terminal paternal sires to enhance overall productivity and quality.
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Affiliation(s)
- Junhua Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Xie
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gao Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Luo
- Sichuan Dekon Livestock Foodstuff Group, Chengdu 610200, China; (Y.L.); (B.L.); (K.Z.)
| | - Bin Liu
- Sichuan Dekon Livestock Foodstuff Group, Chengdu 610200, China; (Y.L.); (B.L.); (K.Z.)
| | - Kangping Zhu
- Sichuan Dekon Livestock Foodstuff Group, Chengdu 610200, China; (Y.L.); (B.L.); (K.Z.)
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyong Wang
- Chongqing Academy of Animal Science, Chongqing 402460, China;
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
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8
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Li Z, Zhang W, Su L, Huang Z, Zhang W, Ma L, Sun J, Guo J, Wen F, Mei K, El-Ashram S, Huang S, Zhao Y. Difference analysis of intestinal microbiota and metabolites in piglets of different breeds exposed to porcine epidemic diarrhea virus infection. Front Microbiol 2022; 13:990642. [PMID: 36386617 PMCID: PMC9665409 DOI: 10.3389/fmicb.2022.990642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
The gut microbial composition of the Luchuan (LC) piglet, one of China’s native breeds, has rarely been studied, especially when compared to other breeds. This study developed a porcine epidemic diarrhea virus (PEDV) infection model in LC and Largewhite (LW) piglets, and analyzed the patterns and differences of intestinal microbial communities and metabolites in piglets of these two breeds after infection. The diarrhea score, survival time, and distribution of viral antigens in the intestine of piglets infected with PEDV differed among breeds, with the jejunal immunohistochemistry score of LW piglets being significantly higher than that of LC piglets (P < 0.001). The results of 16S rRNA sequencing showed differences in microbial diversity and community composition in the intestine of piglets with different breeds between PEDV infection piglets and the healthy controls. There were differences in the species and number of dominant phyla and dominant genera in the same intestinal segment. The relative abundance of Shigella in the jejunum of LC piglets after PEDV infection was significantly lower than that of LW piglets (P < 0.05). The key microorganisms differed in the microbiota were Streptococcus alactolyticus, Roseburia faecis, Lactobacillus iners, Streptococcus equi, and Lactobacillus mucosae (P < 0.05). The non-targeted metabolite analysis revealed that intestinal metabolites showed great differences among the different breeds related to infection. Spearman correlation analysis was conducted to examine any links between the microbiota and metabolites. The metabolites in the intestine of different breeds related to infection were mainly involved in arginine biosynthesis, synaptic vesicle cycle, nicotinic acid and nicotinamide metabolism and mTOR signaling pathway, with significantly positive or negative correlations (P < 0.05) between the various microorganisms. This study provides a theoretical foundation for investigating the application of core microorganisms in the gut of piglets of different breeds in the digestive tracts of those infected with PEDV, and helps to tackle the antimicrobial resistance problem further.
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Affiliation(s)
- Zhili Li
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Wandi Zhang
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Langju Su
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Zongyang Huang
- College of Life Science and Engineering, Foshan University, Foshan, China
| | | | - Liangliang Ma
- Liaoning Agricultural Development Service Center, Shenyang, China
| | - Jingshuai Sun
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Jinyue Guo
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Feng Wen
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Kun Mei
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Saeed El-Ashram
- Faculty of Science, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Shujian Huang
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Yunxiang Zhao
- College of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Yunxiang Zhao,
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9
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Gao Q, Sun G, Duan J, Luo C, Yangji C, Zhong R, Chen L, Zhu Y, Wangdui B, Zhang H. Alterations in gut microbiota improve SCFA production and fiber utilization in Tibetan pigs fed alfalfa diet. Front Microbiol 2022; 13:969524. [PMID: 36338094 PMCID: PMC9634421 DOI: 10.3389/fmicb.2022.969524] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/29/2022] [Indexed: 07/30/2023] Open
Abstract
Tibetan pigs were thought to have good performances of rough feeding tolerance, which may be related to the gut microbiota. This study was conducted to investigate the changes of colonic microbiota contribute to fiber utilization in Tibetan pigs fed alfalfa supplementation diet compared with basal diet, and verified whether the microbial community in Tibetan pigs fed alfalfa diet was beneficial to utilize fiber using in vitro fermentation. A total of 40 Tibetan pigs were allocated into two groups and fed with a corn-soybean meal basal diet (CD) or a 50% alfalfa supplementation diet (AD) for 42d. Our results showed pigs fed CD diet improved carcass weight compared to pigs fed AD diet (p < 0.05), yet reduced the bacterial diversity (p < 0.05). Tibetan pigs fed CD diet increased certain pathogenic bacteria (Streptococcus) abundance (FDR < 0.05). Alfalfa consumption increased fiber-degrading bacteria abundance (UCG-005, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Alloprevotella, Marvinbryantia, and Anaerovibrio) in the colonic digesta (FDR < 0.05) and improved concentrations of acetate, propionate, butyrate, and total SCFA in colonic content (p < 0.05). Higher fermentation capacity of fecal microbiota from pig fed AD diet was verified by in vitro fermentation. Collectively, our results indicated that alfalfa supplementation in diets improved the abundance of fiber-degrading bacteria and SCFA production in the hindgut of Tibetan pig, as well as enhanced the fermentation capacity of fecal microbiota.
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Affiliation(s)
- Qingtao Gao
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangming Sun
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Jiujun Duan
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengzeng Luo
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Cidan Yangji
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Ruqing Zhong
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Chen
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Basang Wangdui
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Hongfu Zhang
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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10
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Velasco-Galilea M, Piles M, Ramayo-Caldas Y, Sánchez JP. The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes. Sci Rep 2021; 11:19495. [PMID: 34593949 PMCID: PMC8484599 DOI: 10.1038/s41598-021-99028-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
Gut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-average daily feed intake from 425 meat rabbits, in which cecal microbiota was assessed, and their cage mates. Despite microbiota was not measured in all animals, consideration of pedigree relationships with mixed models allowed the study of cage-average traits. The inclusion of microbial information into certain mixed models increased their predictive ability up to 20% and 46% for cage-average feed efficiency and individual growth traits, respectively. These gains were associated with large microbiability estimates and with reductions in the heritability estimates. However, large microbiabililty estimates were also obtained with certain models but without any improvement in their predictive ability. A large proportion of OTUs seems to be responsible for the prediction improvement in growth and feed efficiency traits, although specific OTUs taxonomically assigned to 5 different phyla have a higher weight. Rabbit growth and feed efficiency are influenced by host cecal microbiota, thus considering microbial information in models improves the prediction of these complex phenotypes.
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Affiliation(s)
- María Velasco-Galilea
- grid.8581.40000 0001 1943 6646Animal Breeding and Genetics, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Miriam Piles
- grid.8581.40000 0001 1943 6646Animal Breeding and Genetics, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- grid.8581.40000 0001 1943 6646Animal Breeding and Genetics, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Juan P. Sánchez
- grid.8581.40000 0001 1943 6646Animal Breeding and Genetics, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
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11
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Helm ET, Patience JF, Romoser MR, Johnson CD, Ross JW, Gabler NK. Evaluation of increased fiber, decreased amino acids, or decreased electrolyte balance as dietary approaches to slow finishing pig growth rates. J Anim Sci 2021; 99:skab164. [PMID: 34014285 PMCID: PMC8259844 DOI: 10.1093/jas/skab164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
In swine production, pig movement restrictions or packing plant closures may create the need to slow growth rates of finishing pigs to ensure they remain at a marketable body weight when packing plant access is restored. Although dietary formulations can be successful at slowing pig growth, precision is needed regarding how to best formulate diets to achieve growth rate reductions. Thus, the objective was to evaluate three dietary experimental approaches aimed at slowing growth rates in finishing pigs. These approaches consisted of either increasing neutral detergent fiber (NDF), reducing essential amino acids, or reducing the dietary electrolyte balance through the addition of acidogenic salts. A total of 94 mixed-sex pigs (72.4 ± 11.2 kg BW) across two replicates were individually penned and assigned to 1 of 8 dietary treatments (n = 11-12 pigs/treatment): 1) Control diet representative of a typical corn-soybean meal-based finisher diet (CON); 2) diet containing 15% NDF from soybean hulls (15% NDF); 3) diet containing 20% NDF from soybean hulls (20% NDF); 4) diet containing 25% NDF from soybean hulls (25% NDF); 5) diet formulated as per CON but with 50% of the soybean meal replaced with corn (89% Corn); 6) diet containing 97% corn and no soybean meal or synthetic amino acids (97% Corn); 7) diet containing 2% anhydrous calcium chloride (2% CaCl2); and 8) diet containing 4% anhydrous calcium chloride (4% CaCl2). Over 28 d, pig body weights and performance were recorded weekly. At d 28, all pigs were ultrasound scanned and switched to the CON diet to evaluate compensatory gain from d 28 to 35. Overall, increased NDF did not impact any growth performance parameter (P > 0.05). Amino acid restriction reduced average daily gain (ADG), average daily feed intake (ADFI), and gain:feed (G:F) linearly (linear P < 0.001). Similarly, ADG, ADFI, and G:F were linearly reduced with increased CaCl2 inclusion (linear P < 0.001). ADG differed during the compensatory gain period (P < 0.001), with 4% CaCl2-fed pigs having a 47% increase in ADG compared with CON-fed pigs. Conversely, 15% and 25% NDF-fed pigs had reduced ADG compared with CON-fed pigs during the compensatory gain period. Gain efficiency differed from day 28 to 35 (P < 0.001), with 4% CaCl2-fed pigs having a 36% increase in G:F compared with CON-fed pigs. Altogether, these data demonstrate that both amino acid restriction and CaCl2 inclusion are effective at slowing pig growth, albeit at greater inclusion rates.
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Affiliation(s)
- Emma T Helm
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - John F Patience
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Matthew R Romoser
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Iowa Pork Industry Center, Iowa State University, Ames, IA 50011, USA
| | - Colin D Johnson
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Iowa Pork Industry Center, Iowa State University, Ames, IA 50011, USA
| | - Jason W Ross
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Iowa Pork Industry Center, Iowa State University, Ames, IA 50011, USA
| | - Nicholas K Gabler
- Iowa Pork Industry Center, Iowa State University, Ames, IA 50011, USA
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12
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Effect of host breeds on gut microbiome and serum metabolome in meat rabbits. BMC Vet Res 2021; 17:24. [PMID: 33413361 PMCID: PMC7791989 DOI: 10.1186/s12917-020-02732-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS). RESULTS Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome. CONCLUSIONS Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.
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13
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Bergamaschi M, Maltecca C, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Fix J, Tiezzi F. Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters. Sci Rep 2020; 10:10134. [PMID: 32576852 PMCID: PMC7311463 DOI: 10.1038/s41598-020-66791-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
Despite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host's genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.
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Affiliation(s)
- Matteo Bergamaschi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Nathan P McNulty
- Matatu, Inc., 4340 Duncan Ave., Suite 211, St. Louis, MO, 63110, USA
| | | | | | - Justin Fix
- The Maschhoffs LLC, Carlyle, IL, 62231, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
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14
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Maltecca C, Bergamaschi M, Tiezzi F. The interaction between microbiome and pig efficiency: A review. J Anim Breed Genet 2019; 137:4-13. [PMID: 31576623 DOI: 10.1111/jbg.12443] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
Abstract
The existence of genetic control over the abundance of particular taxa and the link of these to energy balance and growth has been documented in model organisms and humans as well as several livestock species. Preliminary evidence of the same mechanisms is currently under investigation in pigs. Future research should expand these results and elicit the extent of genetic control of the gut microbiome population in swine and its relationship with growth efficiency. The quest for a more efficient pig at the interface between the host and its metagenome rests on the central hypothesis that the gut microbiome is an essential component of the variability of growth in all living organisms. Swine do not escape this general rule, and the identification of the significance of the interaction between host and its gut microbiota in the growth process could be a game-changer in the achievement of sustainable and efficient lean meat production. Standard sampling protocols, sequencing techniques, bioinformatic pipelines and methods of analysis will be paramount for the portability of results across experiments and populations. Likewise, characterizing and accounting for temporal and spatial variability will be a necessary step if microbiome is to be utilized routinely as an aid to selection.
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Affiliation(s)
- Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Matteo Bergamaschi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
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