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Zhu Y, Lu S, Cidan Y, Wang H, Li K, Basang W. Comparative analysis of intestinal microbiota composition between free-ranged captive yak populations in Nimu County. Front Cell Infect Microbiol 2024; 14:1420389. [PMID: 38983117 PMCID: PMC11231391 DOI: 10.3389/fcimb.2024.1420389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 05/29/2024] [Indexed: 07/11/2024] Open
Abstract
The intestinal microbiota assumes a pivotal role in modulating host metabolism, immune responses, overall health, and additional physiological dimensions. The structural and functional characteristics of the intestinal microbiota may cause alterations within the host's body to a certain extent. The composition of the gut microbiota is associated with environmental factors, dietary habits, and other pertinent conditions. The investigation into the gut microbiota of yaks remained relatively underexplored. An examination of yak gut microbiota holds promise in elucidating the complex relationship between microbial communities and the adaptive responses of the host to its environment. In this study, yak were selected from two distinct environmental conditions: those raised in sheds (NS, n=6) and grazed in Nimu County (NF, n=6). Fecal samples were collected from the yaks and subsequently processed for analysis through 16S rDNA and ITS sequencing methodologies. The results revealed that different feeding styles result in significant differences in the Alpha diversity of fungi in the gut of yaks, while the gut microbiota of captive yaks was relatively conserved. In addition, significant differences appeared in the abundance of microorganisms in different taxa, phylum Verrucomicrobiota was significantly enriched in group NF while Firmicutes was higher in group NS. At the genus level, Akkermansia, Paenibacillus, Roseburia, Dorea, UCG_012, Anaerovorax and Marvinbryantia were enriched in group NF while Desemzia, Olsenella, Kocuria, Ornithinimicrobium and Parvibacter were higher in group NS (P<0.05 or P<0.01). There was a significant difference in the function of gut microbiota between the two groups. The observed variations are likely influenced by differences in feeding methods and environmental conditions both inside and outside the pen. The findings of this investigation offer prospective insights into enhancing the yak breeding and expansion of the yak industry.
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Affiliation(s)
- Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Sijia Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yangji Cidan
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Hongzhuang Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Kun Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wangdui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
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Ribeiro DM, Costa MM, Trevisi P, Carvalho DFP, Correa F, Martins CF, Pinho M, Mourato M, de Almeida AM, Freire JPB, Mestre Prates JA. Piglets performance, nutrient digestibility and gut health in response to feeding Ulva lactuca seaweed supplemented with a recombinant ulvan lyase or a commercial carbohydrase mixture. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 38890812 DOI: 10.1111/jpn.14005] [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: 08/22/2023] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
Ulva lactuca, a green seaweed, may be an alternative source of nutrients and bioactive compounds for weaned piglets. However, it has a recalcitrant cell wall rich in a sulphated polysaccharide - ulvan - that is indigestible to monogastrics. The objective of this study was to evaluate the effect of dietary incorporation of 7% U. lactuca, combined with carbohydrases supplementation (commercial carbohydrase mixture or recombinant ulvan lyase), on growth performance, nutrient digestibility and gut health parameters (morphology and microbiota) of weaned piglets. The experiment was conducted over 14 days using 40 weaned piglets randomly allocated to one of four experimental diets: a control diet based on wheat-maize-soybean meal, a diet with 7% U. lactuca replacing the control diet (UL), a diet with UL supplemented with 0.005% Rovabio® Excel AP, and a diet with UL supplemented with 0.01% of a recombinant ulvan lyase. The dietary treatments had no major effects on growth performance, nitrogen balance and gut content variables, as well as histological measurements. Contrarily, dry matter and organic matter digestibility decreased with dietary seaweed inclusion, while hemicellulose digestibility increased, suggesting a high fermentability of this cell wall fraction independently of carbohydrases supplementation. Some beneficial microbial populations increased as a consequence of enzymatic supplementation (e.g., Prevotella), while seaweed diets as a whole led to an increased abundance of Shuttleworthia, Anaeroplasma and Lachnospiraceae_NK3A20_group, all related with a healthier gut. It also decreased Lactobacillus when compared to controls, which is possibly related to increased bioavailability of seaweed zinc. This study indicates that, under these experimental conditions, up to 7% dietary U. lactuca has no detrimental effect on piglet growth, despite decreasing acid detergent fibre digestibility. Carbohydrases supplementation of Ulva diets is not required at this incorporation level.
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Affiliation(s)
- David Miguel Ribeiro
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica M Costa
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisboa, Portugal
| | - Paolo Trevisi
- DISTAL - Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Daniela Filipa Pires Carvalho
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Federico Correa
- DISTAL - Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Cátia F Martins
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisboa, Portugal
| | - Mário Pinho
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisboa, Portugal
| | - Miguel Mourato
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - André M de Almeida
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - João Pedro Bengala Freire
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisboa, Portugal
| | - José António Mestre Prates
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisboa, Portugal
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Kern-Lunbery RJ, Rathert-Williams AR, Foote AP, Cunningham-Hollinger HC, Kuehn LA, Meyer AM, Lindholm-Perry AK. Genes involved in the cholecystokinin receptor signaling map were differentially expressed in the jejunum of steers with variation in residual feed intake. Vet Anim Sci 2024; 24:100357. [PMID: 38812584 PMCID: PMC11133974 DOI: 10.1016/j.vas.2024.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
The jejunum is a critical site for nutrient digestion and absorption, and variation in its ability to take up nutrients within the jejunum is likely to affect feed efficiency. The purpose of this study was to determine differences in gene expression in the jejunum of beef steers divergent for residual feed intake (RFI) in one cohort of steers (Year 1), and to validate those genes in animals from a second study (Year 2). Steers from Year 1 (n = 16) were selected for high and low RFI. Jejunum mucosal tissue was obtained for RNA-seq. Thirty-two genes were differentially expressed (PFDR≤0.15), and five were over-represented in pathways including inflammatory mediator, cholecystokinin receptor (CCKR) signaling, and p38 MAPK pathways. Several differentially expressed genes (ALOX12, ALPI, FABP6, FABP7, FLT1, GSTA2, MEF2B, PDK4, SPP1, and TTF2) have been previously associated with RFI in other studies. Real-time qPCR was used to validate nine differentially expressed genes in the Year 1 steers used for RNA-seq, and in the Year 2 validation cohort. Six genes were validated as differentially expressed (P < 0.1) using RT-qPCR in the Year 1 population. In the Year 2 population, five genes displayed the same direction of expression as the Year 1 population and 3 were differentially expressed (P < 0.1). The CCKR pathway is involved in digestion, appetite control, and regulation of body weight making it a compelling candidate for feed efficiency in cattle, and the validation of these genes in a second population of cattle is suggestive of a role in feed efficiency.
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Affiliation(s)
- Rebecca J. Kern-Lunbery
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- Ward Laboratories, Inc., Kearney, NE 68848, USA
| | - Abigail R. Rathert-Williams
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- University of Missouri, Division of Animal Sciences, Columbia, MO 65211, USA
| | - Andrew P. Foote
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- Oklahoma State University, Department of Animal & Food Sciences, Stillwater, OK 74078, USA
| | | | - Larry A. Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Allison M. Meyer
- University of Missouri, Division of Animal Sciences, Columbia, MO 65211, USA
- University of Wyoming, Department of Animal Science, Laramie, WY 82071, USA
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Mo Q, Yao H, Wu H, Zhao D. Impact of Environmental Food Intake on the Gut Microbiota of Endangered Père David's Deer: Primary Evidence for Population Reintroduction. Animals (Basel) 2024; 14:728. [PMID: 38473113 DOI: 10.3390/ani14050728] [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: 11/15/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 03/14/2024] Open
Abstract
Reintroduction has been successful in re-establishing several endangered wild animals in their historical habitats, including Père David's deer (Elaphurus davidianus). Continuous monitoring of reintroduced individuals is essential for improving the sustainability of ex situ conservation efforts. Despite an increased recognition of the significance of the gut microbiome for animal health, the correlation between diet and the gut microbiome in E. davidianus is unclear. In this study, 15 fresh fecal samples of E. davidianus were collected from Tianjin Qilihai Wetland and the association between dietary and gut microbiota composition was evaluated. Microscopic observations showed that Nymphoides peltata [relative density (RD = 0.3514), Phragmites australis (RD = 0.2662), Setaria viridis (RD = 0.1211), and Typha orientalis (RD = 0.1085) were the main dietary plants in the fecal samples. High-throughput 16S rRNA sequencing showed a predominance of the phyla Firmicutes and Proteobacteria and the genus Psychrobacillus (26.53%) in the gut microbiota. The RD of N. peltata was significantly positively correlated with the abundance of Firmicutes (p = 0.005) and the genus UCG-005 (p = 0.024). This study indicates a close association between food digestion and nutrient intake, providing basic monitoring data for the full reintroduction and recovery of wild E. davidianus.
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Affiliation(s)
- Qiying Mo
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Hongyu Yao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
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Mizoguchi Y, Guan LL. - Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality. Anim Biosci 2024; 37:346-359. [PMID: 38186252 PMCID: PMC10838664 DOI: 10.5713/ab.23.0387] [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: 09/26/2023] [Revised: 11/06/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.
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Affiliation(s)
- Yasushi Mizoguchi
- School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa 214-8571,
Japan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5,
Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5,
Canada
- Faculty of Land and Food Systems, the University of British Columbia, Vancouver, British Columbia, V6T 1Z4,
Canada
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Xu D, Wang X, Wang W, Zhang D, Li X, Zhang Y, Zhao Y, Cheng J, Zhao L, Wang J, Lin C, Yang X, Weng X, Zhang X, Zheng W. Detection of single nucleotide polymorphism in HTR4 and its relationship with growth traits in sheep. Anim Biotechnol 2023; 34:4600-4607. [PMID: 36780324 DOI: 10.1080/10495398.2023.2174877] [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] [Indexed: 02/14/2023]
Abstract
In this study, a single nucleotide polymorphism of HTR4 (hydroxytryptamine receptor 4) was detected using DNA sequencing and KASPar (Kompetitive Allele-Specific PCR) technique with the aim of analyzing its effect on growth traits in 1102 sheep. A synonymous mutation g.101220 C > T located on the fifth intron of the ovis HTR4 gene was detected, and association analysis showed that this mutation was significantly associated with growth traits in sheep (p <.05), with TT genotypes having significantly lower body weight, height, length and chest circumference than TC and CC genotypes. It showed that the polymorphism of this locus was significantly associated with growth traits in sheep. In addition, qRT-PCR results showed that HTR4 was expressed in different tissues of sheep. It is highly expressed in the liver, spleen and duodenum. As important metabolic, immune and digestive absorption organs in animals, the above tissues can regulate the excitability of intestinal smooth muscle by participating in the body metabolism and nutrient metabolism of sheep, so that sheep can show better growth characteristics. In conclusion, the polymorphic locus identified in HTR4 gene can be used as candidate molecular marker in sheep breeding.
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Affiliation(s)
- Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
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Du Y, Tu Y, Zhou Z, Hong R, Yan J, Zhang GW. Effects of organic and inorganic copper on cecal microbiota and short-chain fatty acids in growing rabbits. Front Vet Sci 2023; 10:1179374. [PMID: 37275607 PMCID: PMC10235478 DOI: 10.3389/fvets.2023.1179374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/17/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Copper (Cu) is an essential trace element for the growth of rabbits. This study aimed to investigate the effects of different Cu sources on intestinal microorganisms and short-chain fatty acids (SCFAs) in growing rabbits. Methods The experimental animals were randomly divided into four experimental groups, each group comprised eight replicates, with six rabbits (half male and half female) per replicate. And they were fed diets was composed by mixing the basal diet with 20 mg/kg Cu from one of the two inorganic Cu (cupric sulfate and dicopper chloride trihydroxide) or two organic Cu (cupric citrate and copper glycinate). Cecal contents of four rabbits were collected from four experimental groups for 16S rDNA gene amplification sequencing and gas chromatography analysis. Results Our results indicate that the organic Cu groups were less variable than the inorganic Cu groups. Compared with the inorganic Cu groups, the CuCit group had a significantly higher relative abundance of Rikenella Tissierella, Lachnospiraceae_NK3A20_group, Enterococcus, and Paeniclostridium, while the relative abundance of Novosphingobium and Ruminococcus were significantly lower (p < 0.05). The SCFAs level decreased in the organic Cu groups than in the inorganic Cu groups. Among the SCFAs, the butyric acid level significantly decreased in the CuCit group than in the CuSO4 and CuCl2 groups. The relative abundance of Rikenella and Turicibacter genera was significantly negatively correlated with the butyric acid level in the CuCit group compared with both inorganic Cu groups. These results revealed that the organic Cu (CuCit) group had an increased abundance of Rikenella, Enterococcus, Lachnospiraceae_NK3A20_group, and Turicibacter genera in the rabbit cecum. Discussion In summary, this study found that organic Cu and inorganic Cu sources had different effects on cecal microbiota composition and SCFAs in rabbits. The CuCit group had the unique higher relative abundance of genera Rikenella and Lachnospiraceae_NK3A20_group, which might be beneficial to the lower incidence of diarrhea in rabbits.
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Affiliation(s)
- Yanan Du
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yun Tu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Zeyang Zhou
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Rui Hong
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Jiayou Yan
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Gong-Wei Zhang
- College of Animal Science and Technology, Southwest University, Chongqing, China
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Casto-Rebollo C, Argente MJ, García ML, Blasco A, Ibáñez-Escriche N. Effect of environmental variance-based resilience selection on the gut metabolome of rabbits. Genet Sel Evol 2023; 55:15. [PMID: 36894894 PMCID: PMC9996918 DOI: 10.1186/s12711-023-00791-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Gut metabolites are key actors in host-microbiota crosstalk with effect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its effect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal mechanisms that underlie animal resilience because of its influence on host immunity. Environmental variance (VE), specifically the residual variance, is one measure of resilience. The aim of this study was to identify gut metabolites that underlie differences in the resilience potential of animals originating from a divergent selection for VE of litter size (LS). We performed an untargeted gut metabolome analysis in two divergent rabbit populations for low (n = 13) and high (n = 13) VE of LS. Partial least square-discriminant analysis was undertaken, and Bayesian statistics were computed to determine dissimilarities in the gut metabolites between these two rabbit populations. RESULTS We identified 15 metabolites that discriminate rabbits from the divergent populations with a prediction performance of 99.2% and 90.4% for the resilient and non-resilient populations, respectively. These metabolites were suggested to be biomarkers of animal resilience as they were the most reliable. Among these, five that derived from the microbiota metabolism (3-(4-hydroxyphenyl)lactate, 5-aminovalerate, and equol, N6-acetyllysine, and serine), were suggested to be indicators of dissimilarities in the microbiome composition between the rabbit populations. The abundances of acylcarnitines and metabolites derived from the phenylalanine, tyrosine, and tryptophan metabolism were low in the resilient population and these pathways can, therefore impact the inflammatory response and health status of animals. CONCLUSIONS This is the first study to identify gut metabolites that could act as potential resilience biomarkers. The results support differences in resilience between the two studied rabbit populations that were generated by selection for VE of LS. Furthermore, selection for VE of LS modified the gut metabolome, which could be another factor that modulates animal resilience. Further studies are needed to determine the causal role of these metabolites in health and disease.
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Affiliation(s)
- Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - María José Argente
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO_UMH), Miguel Hernández University, 03312, Orihuela, Spain
| | - María Luz García
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO_UMH), Miguel Hernández University, 03312, Orihuela, Spain
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain.
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Kim M. - Invited Review - Assessment of the gastrointestinal microbiota using 16S ribosomal RNA gene amplicon sequencing in ruminant nutrition. Anim Biosci 2023; 36:364-373. [PMID: 36701925 PMCID: PMC9899581 DOI: 10.5713/ab.22.0382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
The gastrointestinal (GI) tract of ruminants contains diverse microbes that ferment various feeds ingested by animals to produce various fermentation products, such as volatile fatty acids. Fermentation products can affect animal performance, health, and well-being. Within the GI microbes, the ruminal microbes are highly diverse, greatly contribute to fermentation, and are the most important in ruminant nutrition. Although traditional cultivation methods provided knowledge of the metabolism of GI microbes, most of the GI microbes could not be cultured on standard culture media. By contrast, amplicon sequencing of 16S rRNA genes can be used to detect unculturable microbes. Using this approach, ruminant nutritionists and microbiologists have conducted a plethora of nutritional studies, many including dietary interventions, to improve fermentation efficiency and nutrient utilization, which has greatly expanded knowledge of the GI microbiota. This review addresses the GI content sampling method, 16S rRNA gene amplicon sequencing, and bioinformatics analysis and then discusses recent studies on the various factors, such as diet, breed, gender, animal performance, and heat stress, that influence the GI microbiota and thereby ruminant nutrition.
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Affiliation(s)
- Minseok Kim
- Division of Animal Science, Chonnam National University, Gwangju 61186,
Korea,Corresponding Author: Minseok Kim, Tel: +82-62-530-2128, Fax: +82-62-530-2129, E-mail:
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