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Hou G, Wei L, Li R, Chen F, Yin J, Huang X, Yin Y. Lactobacillus delbrueckii Ameliorated Blood Lipids via Intestinal Microbiota Modulation and Fecal Bile Acid Excretion in a Ningxiang Pig Model. Animals (Basel) 2024; 14:1801. [PMID: 38929420 PMCID: PMC11201289 DOI: 10.3390/ani14121801] [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: 04/26/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Lactobacillus delbrueckii intervention can regulate body lipid metabolism, but the underlying mechanism remains unclear. Our study investigated the effects of L. delbrueckii on serum lipid levels, tissular fat metabolism and deposition, bile acid metabolism, and gut microbiota in Ningxiang pigs. Ninety-six pigs were divided into two groups and fed basal diets containing either 0 (CON) or 0.1% L. delbrueckii (LD) for 60 days. Dietary L. delbrueckii promoted fecal total bile acid (TBA) excretion and increased hepatic enzyme activities related to cholesterol and bile synthesis but decreased hepatic and serum lipid concentrations. L. delbrueckii downregulated gene expression associated with fatty acid synthesis but upregulated gene expression related to lipolysis and β-fatty acid oxidation in liver and subcutaneous fat. L. delbrueckii elevated gut Lactobacillus abundance and colonic short-chain fatty acid (SCFA)-producing bacteria but declined the abundance of some pathogenic bacteria. These findings demonstrated that L. delbrueckii modulated intestinal microbiota composition and facilitated fecal TBA excretion to regulate hepatic fat metabolism, which resulted in less lipid deposition in the liver and reduced levels of serum lipids.
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Affiliation(s)
- Gaifeng Hou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (Y.Y.)
| | - Liangkai Wei
- Hunan Co-Innovation Center of Safety Animal Production, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (J.Y.); (X.H.)
| | - Rui Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (Y.Y.)
| | - Fengming Chen
- Academician Workstation, Changsha Medical University, Changsha 410219, China;
| | - Jie Yin
- Hunan Co-Innovation Center of Safety Animal Production, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (J.Y.); (X.H.)
| | - Xingguo Huang
- Hunan Co-Innovation Center of Safety Animal Production, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (J.Y.); (X.H.)
| | - Yulong Yin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (Y.Y.)
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2
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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3
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Wang L, Valencak TG, Shan T. Fat infiltration in skeletal muscle: Influential triggers and regulatory mechanism. iScience 2024; 27:109221. [PMID: 38433917 PMCID: PMC10907799 DOI: 10.1016/j.isci.2024.109221] [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: 03/05/2024] Open
Abstract
Fat infiltration in skeletal muscle (also known as myosteatosis) is now recognized as a distinct disease from sarcopenia and is directly related to declining muscle capacity. Hence, understanding the origins and regulatory mechanisms of fat infiltration is vital for maintaining skeletal muscle development and improving human health. In this article, we summarized the triggering factors such as aging, metabolic diseases and metabolic syndromes, nonmetabolic diseases, and muscle injury that all induce fat infiltration in skeletal muscle. We discussed recent advances on the cellular origins of fat infiltration and found several cell types including myogenic cells and non-myogenic cells that contribute to myosteatosis. Furthermore, we reviewed the molecular regulatory mechanism, detection methods, and intervention strategies of fat infiltration in skeletal muscle. Based on the current findings, our review will provide new insight into regulating function and lipid metabolism of skeletal muscle and treating muscle-related diseases.
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Affiliation(s)
- Liyi Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | | | - Tizhong Shan
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
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4
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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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5
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Yang S, Liu G, Xia X, Gan D, Xiang S, Xiang M. α-Mangostin suppresses ethanol-induced gastric ulceration by regulating the Nrf2/HO-1 and NF-κB/NLRP3/caspase-1 signaling pathways and gut microbiota. Heliyon 2024; 10:e24339. [PMID: 38304797 PMCID: PMC10831614 DOI: 10.1016/j.heliyon.2024.e24339] [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] [Received: 08/04/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
α-Mangostin is a natural xanthone derivative isolated from Camellia atrophy (CA), commonly known as Lichuan black tea (LBT). The present study investigated the ameliorating effect and mechanism of α-mangostin on alcoholic gastric ulcers (GU) in rats. In vivo, α-mangostin relieved pathological symptoms. Moreover, α-mangostin regulated the activation of the nuclear factor (erythroid-derived 2)-like 2 (Nrf2)/heme oxygenase 1 (HO-1) and nuclear factor κB (NF-κB)/NLR family pyrin domain containing 3 (NLRP3)/caspase-1 pathways. Reactive oxygen species (ROS), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β) were significantly decreased and IL-10 were increased, the microtubule-associated protein light chain 3 (LC3)-II/LC3-I ratio was increased, p62 protein expression was decreased, and inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX-2) protein expression was down-regulated. The relevant mechanisms were validated using GSE-1 and RAW264.7 cells in an in vitro model. Furthermore, α-mangostin increased Ligilactobacillus and Muribaculum abundance as well as propionic acid and butyric acid contents. Therefore, α-mangostin possesses antioxidant and anti-inflammatory properties, and remodels intestinal flora dysbiosis through mechanisms that may involve regulation of the Nrf2/HO-1 pathway and NF-κB/NLRP3/caspase-1 pathway. It also increases propionic acid and butyric acid contents. This study provides novel evidence regarding the use of α-mangostin for treating GU.
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Affiliation(s)
- Suqin Yang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Gang Liu
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, China, 430060, Hubei, China
| | - Xiankun Xia
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Dali Gan
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Shijian Xiang
- Department of Laboratory Medicine, Renmin Hosipital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Meixian Xiang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
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6
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Wen C, Wang Q, Gu S, Jin J, Yang N. Emerging perspectives in the gut-muscle axis: The gut microbiota and its metabolites as important modulators of meat quality. Microb Biotechnol 2024; 17:e14361. [PMID: 37902307 PMCID: PMC10832551 DOI: 10.1111/1751-7915.14361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023] Open
Abstract
Animal breeding has made great genetic progress in increasing carcass weight and meat yield in recent decades. However, these improvements have come at the expense of meat quality. As the demand for meat quantity continues to rise, the meat industry faces the great challenge of maintaining and even increasing product quality. Recent research, including traditional statistical analyses and gut microbiota regulation research, has demonstrated that the gut microbiome exerts a considerable effect on meat quality, which has become increasingly intriguing in farm animals. Microbial metabolites play crucial roles as substrates or signalling factors to distant organs, influencing meat quality either beneficially or detrimentally. Interventions targeting the gut microbiota exhibit excellent potential as natural ways to foster the conversion of myofibres and promote intramuscular fat deposition. Here, we highlight the emerging roles of the gut microbiota in various dimensions of meat quality. We focus particularly on the effects of the gut microbiota and gut-derived molecules on muscle fibre metabolism and intramuscular fat deposition and attempt to summarize the potential underlying mechanisms.
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Affiliation(s)
- Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural AffairsChina Agricultural UniversityBeijingChina
- Department of Animal Genetics and Breeding, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversityHainanChina
| | - Qunpu Wang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural AffairsChina Agricultural UniversityBeijingChina
- Department of Animal Genetics and Breeding, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural AffairsChina Agricultural UniversityBeijingChina
- Department of Animal Genetics and Breeding, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Jiaming Jin
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural AffairsChina Agricultural UniversityBeijingChina
- Department of Animal Genetics and Breeding, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural AffairsChina Agricultural UniversityBeijingChina
- Department of Animal Genetics and Breeding, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversityHainanChina
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7
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Zhang J, Shu Z, Lv S, Zhou Q, Huang Y, Peng Y, Zheng J, Zhou Y, Hu C, Lan S. Fermented Chinese Herbs Improve the Growth and Immunity of Growing Pigs through Regulating Colon Microbiota and Metabolites. Animals (Basel) 2023; 13:3867. [PMID: 38136904 PMCID: PMC10740985 DOI: 10.3390/ani13243867] [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: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: the development of new antibiotic substitutes to promote pig growth and health has become an important way to solve the current dilemma and promote the pig industry. (2) Methods: to assess the effects of a fermented Chinese herbal (FCH) formula on the growth and immunity of growing pigs, 100 Duroc × Landrace × Yorshire three-way crossed growing pigs were randomly divided into control and treatment groups that were fed a basal diet, and a basal diet with 1% (group A), 2% (group B), and 3% (group C) FCH formulas, respectively. A sixty-day formal experiment was conducted, and their growth and serum indices, colonic microbiota, and metabolites were analyzed. (3) Results: the daily gain of growing pigs in groups A, B, and C increased by 7.93%, 17.68%, and 19.61%, respectively, and the feed-to-gain ratios decreased by 8.33%, 15.00%, and 14.58%, respectively. Serum immunity and antioxidant activities were significantly increased in all treatment groups. Particularly, adding a 2% FCH formula significantly changed the colon's microbial structure; the Proteobacteria significantly increased and Firmicutes significantly decreased, and the metabolite composition in the colon's contents significantly changed. (4) Conclusions: these results indicate that the FCH formula is a good feed additive for growing pigs, and the recommended addition ratio was 3%.
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Affiliation(s)
- Junhao Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Zhiheng Shu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Sixiao Lv
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Qingwen Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yuanhao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yingjie Peng
- Guangdong Chuangzhan Bona Agricultural Technology Co., Ltd., Guangning 526339, China;
| | - Jun Zheng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yi Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Chao Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Shile Lan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
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8
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Deng X, Zhang Y, Song G, Fu Y, Chen Y, Gao H, Wang Q, Jin Z, Yin Y, Xu K. Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring. Animals (Basel) 2023; 13:3321. [PMID: 37958077 PMCID: PMC10647668 DOI: 10.3390/ani13213321] [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: 08/18/2023] [Revised: 09/28/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F1 offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F1 offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F1 pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies.
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Affiliation(s)
- Xiaoxiao Deng
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yuebo Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Gang Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yawei Fu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yue Chen
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Hu Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Qian Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Zhao Jin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yulong Yin
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
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9
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Chen Y, Akhtar M, Ma Z, Hu T, Liu Q, Pan H, Zhang X, Nafady AA, Ansari AR, Abdel-Kafy ESM, Shi D, Liu H. Chicken cecal microbiota reduces abdominal fat deposition by regulating fat metabolism. NPJ Biofilms Microbiomes 2023; 9:28. [PMID: 37253749 DOI: 10.1038/s41522-023-00390-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/23/2023] [Indexed: 06/01/2023] Open
Abstract
Cecal microbiota plays an essential role in chicken health. However, its contribution to fat metabolism, particularly in abdominal fat deposition, which is a severe problem in the poultry industry, is still unclear. Here, chickens at 1, 4, and 12 months of age with significantly (p < 0.05) higher and lower abdominal fat deposition were selected to elucidate fat metabolism. A significantly (p < 0.05) higher mRNA expression of fat anabolism genes (ACSL1, FADS1, CYP2C45, ACC, and FAS), a significantly (p < 0.05) lower mRNA expression of fat catabolism genes (CPT-1 and PPARα) and fat transport gene APOAI in liver/abdominal fat of high abdominal fat deposition chickens indicated that an unbalanced fat metabolism leads to excessive abdominal fat deposition. Parabacteroides, Parasutterella, Oscillibacter, and Anaerofustis were found significantly (p < 0.05) higher in high abdominal fat deposition chickens, while Sphaerochaeta was higher in low abdominal fat deposition chickens. Further, Spearman correlation analysis indicated that the relative abundance of cecal Parabacteroides, Parasutterella, Oscillibacter, and Anaerofustis was positively correlated with abdominal fat deposition, yet cecal Sphaerochaeta was negatively correlated with fat deposition. Interestingly, transferring fecal microbiota from adult chickens with low abdominal fat deposition into one-day-old chicks significantly (p < 0.05) decreased Parabacteroides and fat anabolism genes, while markedly increased Sphaerochaeta (p < 0.05) and fat catabolism genes (p < 0.05). Our findings might help to assess the potential mechanism of cecal microbiota regulating fat deposition in chicken production.
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Affiliation(s)
- Yan Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Muhammad Akhtar
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Ziyu Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Tingwei Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qiyao Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Hong Pan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaolong Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Abdallah A Nafady
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Abdur Rahman Ansari
- Section of Anatomy and Histology, Department of Basic Sciences, College of Veterinary and Animal Sciences (CVAS) Jhang, University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
| | - El-Sayed M Abdel-Kafy
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Ministry of Agriculture, Giza, Egypt
| | - Deshi Shi
- Department of Preventive Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
| | - Huazhen Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
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10
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Liu S, Tu Y, Sun J, Cai P, Zhou Y, Huang Y, Zhang S, Chen W, Wang L, Du M, You W, Wang T, Wang Y, Lu Z, Shan T. Fermented mixed feed regulates intestinal microbial community and metabolism and alters pork flavor and umami. Meat Sci 2023; 201:109177. [PMID: 37023593 DOI: 10.1016/j.meatsci.2023.109177] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/10/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
This study aimed to determine the effects of fermented mixed feed (FMF) supplementation (0%, 5% and 10%) on the intestinal microbial community and metabolism, and the compositions of volatile flavor compounds and inosine monophosphate (IMP) contents in the longissimus thoracis. In this study, 144 finishing pigs (Duroc × Berkshire × Jiaxing Black) were randomly allocated to 3 groups with 4 replicate pens per group and 12 pigs per pen. The experiment lasted 38 days after 4 days of acclimation. The 16S rRNA gene sequences and an untargeted metabolomics analysis showed FMF altered the profiles of microbes and metabolites in the colon. Heracles flash GC e-nose analysis showed that 10% FMF (treatment 3) had a greater influence on the compositions of volatile flavor compounds than 5% FMF (treatment 2). Compared to 0% FMF (treatment 1), the contents of total aldehydes, (E,E)-2,4-nonadienal, dodecanal, nonanal and 2-decenal were significantly increased by treatment 3, and treatment 3 increased IMP concentrations and gene expressions related to its synthesis. Correlations analysis showed significantly different microbes and metabolites had strong correlations with the contents of IMP and volatile flavor compounds. In conclusion, treatment 3 regulated intestinal microbial community and metabolism, that in turn altered the compositions of volatile compounds, which contributed to improving pork flavor and umami.
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Affiliation(s)
- Shiqi Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Yuang Tu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Peiran Cai
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Yanbing Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Yuqin Huang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Shu Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Wentao Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Liyi Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Man Du
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Wenjing You
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Tenghao Wang
- Zhejiang Qinglian Food Co Ltd, Jiaxing, Zhejiang 314317, PR China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China
| | - Zeqing Lu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China.
| | - Tizhong Shan
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang 310058, PR China; Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang 310058, PR China.
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11
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Xu XJ, Lang JD, Yang J, Long B, Liu XD, Zeng XF, Tian G, You X. Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study. Front Immunol 2023; 14:1100816. [PMID: 36875075 PMCID: PMC9975759 DOI: 10.3389/fimmu.2023.1100816] [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: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Background Autism Spectrum Disorders (ASD) are defined as a group of pervasive neurodevelopmental disorders, and the heterogeneity in the symptomology and etiology of ASD has long been recognized. Altered immune function and gut microbiota have been found in ASD populations. Immune dysfunction has been hypothesized to involve in the pathophysiology of a subtype of ASD. Methods A cohort of 105 ASD children were recruited and grouped based on IFN-γ levels derived from ex vivo stimulated γδT cells. Fecal samples were collected and analyzed with a metagenomic approach. Comparison of autistic symptoms and gut microbiota composition was made between subgroups. Enriched KEGG orthologues markers and pathogen-host interactions based on metagenome were also analyzed to reveal the differences in functional features. Results The autistic behavioral symptoms were more severe for children in the IFN-γ-high group, especially in the body and object use, social and self-help, and expressive language performance domains. LEfSe analysis of gut microbiota revealed an overrepresentation of Selenomonadales, Negatiyicutes, Veillonellaceae and Verrucomicrobiaceae and underrepresentation of Bacteroides xylanisolvens and Bifidobacterium longum in children with higher IFN-γ level. Decreased metabolism function of carbohydrate, amino acid and lipid in gut microbiota were found in the IFN-γ-high group. Additional functional profiles analyses revealed significant differences in the abundances of genes encoding carbohydrate-active enzymes between the two groups. And enriched phenotypes related to infection and gastroenteritis and underrepresentation of one gut-brain module associated with histamine degradation were also found in the IFN-γ-High group. Results of multivariate analyses revealed relatively good separation between the two groups. Conclusions Levels of IFN-γ derived from γδT cell could serve as one of the potential candidate biomarkers to subtype ASD individuals to reduce the heterogeneity associated with ASD and produce subgroups which are more likely to share a more similar phenotype and etiology. A better understanding of the associations among immune function, gut microbiota composition and metabolism abnormalities in ASD would facilitate the development of individualized biomedical treatment for this complex neurodevelopmental disorder.
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Affiliation(s)
- Xin-Jie Xu
- Medical Science Research Center, Research Center for Translational Medicine, Department of Scientific Research, Peking Union Medical College Hospital, Beijing, China.,Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji-Dong Lang
- Precision Medicine Center, Geneis Beijing Co., Ltd., Beijing, China
| | - Jun Yang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Long
- Medical Science Research Center, Research Center for Translational Medicine, Department of Scientific Research, Peking Union Medical College Hospital, Beijing, China
| | - Xu-Dong Liu
- Medical Science Research Center, Research Center for Translational Medicine, Department of Scientific Research, Peking Union Medical College Hospital, Beijing, China
| | - Xiao-Feng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Geng Tian
- Precision Medicine Center, Geneis Beijing Co., Ltd., Beijing, China
| | - Xin You
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China.,Autism Special Fund, Peking Union Medical Foundation, Beijing, China
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12
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Begmatov S, Beletsky AV, Gruzdev EV, Mardanov AV, Glukhova LB, Karnachuk OV, Ravin NV. Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility. Microorganisms 2022; 10:2301. [PMID: 36422370 PMCID: PMC9692488 DOI: 10.3390/microorganisms10112301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 08/26/2023] Open
Abstract
The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Eugeny V. Gruzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Lubov B. Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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