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Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [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: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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Xiong X, Rao Y, Ma J, Wang Z, He Q, Gong J, Sheng W, Xu J, Zhu X, Tan Y, Yang Y. A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome. Poult Sci 2023; 102:102931. [PMID: 37499616 PMCID: PMC10393819 DOI: 10.1016/j.psj.2023.102931] [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: 05/25/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China.
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Jinge Ma
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Qin He
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Jishang Gong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Wentao Sheng
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Jiguo Xu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Xuenong Zhu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Yuwen Tan
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Yanbei Yang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
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3
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Kim JE, Tun HM, Bennett DC, Leung FC, Cheng KM. Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae). Sci Rep 2023; 13:4488. [PMID: 36934111 PMCID: PMC10024708 DOI: 10.1038/s41598-023-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 03/20/2023] Open
Abstract
Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.
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Affiliation(s)
- Ji Eun Kim
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Hein M Tun
- School of Public Health, Li Ka Shing, Faculty of Medicine, HKU-Pasteur Research Pole, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Darin C Bennett
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Animal Science Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kimberly M Cheng
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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Wang X, Wu B, Sun G, Gao J, Huang T, Liu J, Zhou Q, He X, Zhang S, Wang CY, Zhang Z, Zhu H. Dietary selenomethionine attenuates obesity by enhancing beiging process in white adipose tissue. J Nutr Biochem 2023; 113:109230. [PMID: 36435293 DOI: 10.1016/j.jnutbio.2022.109230] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 09/21/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022]
Abstract
Imbalanced nutrient intake causes abnormal energy metabolism, which results in obesity. There is feasible evidence that selenium-rich (Se-rich) foods may alleviate obesity and enhance general public health, but the underlying mechanisms remain elusive. Herein we examined the effect of Se supplementation on white adipose tissue beiging process. The mice were fed with a normal diet or a Se-deficient high-fat diet (DHFD) until significant differences in terms of body weight, glucose tolerance and insulin sensitivity. Next, mice in the DHFD group were changed to a high-fat diet (HFD) containing specified amounts of selenomethionine (SeMet) (0, 150, 300, and 600 μg/kg) and continued to feed for 14 weeks. Notably, 150 μg/kg SeMet supplement highly protected mice from DHFD-induced obesity, insulin resistance, and lipid deposits in the liver and kidney, and featured by the enhanced beiging process in white adipose tissue and increased energy expenditure. Moreover, upon cold challenge, 150 μg/kg SeMet supplement enhanced cold tolerance in mice by inducing adipose beiging to promote energy expenditure, as evidenced by the increased expression of uncoupling protein-1 (UCP1) in adipocytes. Similarly, SeMet (10 μM) promoted the differentiation of beige adipocytes from the stromal vascular fraction. Collectively, our data support that optimal supplementation of SeMet could enhance the beiging process to attenuate HFD-induced obesity, which provides new insights into the relationship between dietary SeMet and type 2 diabetes.
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Affiliation(s)
- Xiaohui Wang
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Bo Wu
- The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Guogen Sun
- Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Jia Gao
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Teng Huang
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Jing Liu
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Qing Zhou
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xiaoyu He
- Branch of National Clinical Research Center for Metabolic Diseases, Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shu Zhang
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Cong-Yi Wang
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Zixiong Zhang
- The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Hubei Selenium and Human Health Institute, Enshi, Hubei, China.
| | - He Zhu
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China.
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Liu J, Lin H, Cao M, Lin T, Lin A, Xu W, Wang H, He J, Li Y, Tang H, Zhang B. Shifts and importance of viable bacteria in treatment of DSS-induced ulcerative colitis mice with FMT. Front Cell Infect Microbiol 2023; 13:1124256. [PMID: 36814445 PMCID: PMC9939747 DOI: 10.3389/fcimb.2023.1124256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Background and Aims Ulcerative colitis (UC) has become a global public health concern, and is in urgent need of novel therapies. Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been applied to the treatment of UC. Despite its recent successes, it is still largely unknown how FMT functionally modulates the gut microbiota and improves the disease. Methods We prospectively collected fecal samples from the 40 mice (30 mice for dextran sulfate sodium (DSS)-induced, 10 for controls), followed by Propidium monoazide treatment for 16S rRNA gene sequencing. These 30 mice were divided equally into 3 groups, which were transplanted with original donor microbiota (DO), inactivated donor microbiota (DI) and saline, respectively. Subsequently, we used 16S rRNA gene sequencing to analyze the viable gut bacteria of ulcerative colitis (UC) mice and histological analysis to evaluate the effects of fecal microbiota transplantation (FMT) with viable microbiota. Results We demonstrated that the community structure of viable bacteria was significantly different from fecal bacteria based on total DNA. Furthermore, the intestinal viable microbiota and colonic mucosal structure of mice were significantly changed by DSS induction. The histological analysis showed that only the mice treated with original donor microbiota group (HF) achieved a significant improvement. Compared with inactivated donor microbiota group (IF) and saline (NF), Lactobacillus and Halomonas were significantly enriched in the HF group. Conclusion We inferred that only live bacteria from human donor reversed the histopathology and symptoms of UC in mice and altered the gut microbiota. The activity of gut microbiota in donor samples should be considered in FMT and that detailed analysis of viable microbiota is essential to understand the mechanisms by which FMT produces therapeutic effects in the future.
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Affiliation(s)
- Jinglong Liu
- Department of Gastroenterology, Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Hao Lin
- Center for Microecological Medical Technology, Xiamen Institute of Union Respiratory Health, Xiamen, China
| | - Man Cao
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Tan Lin
- Center for Microecological Medical Technology, Xiamen Institute of Union Respiratory Health, Xiamen, China
| | - Aiqiang Lin
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Wei Xu
- Center for Microecological Medical Technology, Xiamen Institute of Union Respiratory Health, Xiamen, China
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Han Wang
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Jianquan He
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Yuantao Li
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- *Correspondence: Yuantao Li, ; Hailing Tang, ; Bangzhou Zhang,
| | - Hailing Tang
- Division of Gastroenterology, Xi’an Central Hospital, Xi’an, China
- *Correspondence: Yuantao Li, ; Hailing Tang, ; Bangzhou Zhang,
| | - Bangzhou Zhang
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Yuantao Li, ; Hailing Tang, ; Bangzhou Zhang,
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6
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Xu SS, Zhang XL, Liu SS, Feng ST, Xiang GM, Xu CJ, Fan ZY, Xu K, Wang N, Wang Y, Che JJ, Liu ZG, Mu YL, Li K. Multi-Omic Analysis in a Metabolic Syndrome Porcine Model Implicates Arachidonic Acid Metabolism Disorder as a Risk Factor for Atherosclerosis. Front Nutr 2022; 9:807118. [PMID: 35284467 PMCID: PMC8906569 DOI: 10.3389/fnut.2022.807118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background The diet-induced gut microbiota dysbiosis has been suggested as a major risk factor for atherothrombosis, however, the detailed mechanism linking these conditions is yet to be fully understood. Methods We established a long-term excessive-energy diet-induced metabolic syndrome (MetS) inbred Wuzhishan minipig model, which is characterized by its genetic stability, small size, and human-like physiology. The metabolic parameters, atherosclerotic lesions, gut microbiome, and host transcriptome were analyzed. Metabolomics profiling revealed a linkage between gut microbiota and atherothrombosis. Results We showed that white atheromatous plaque was clearly visible on abdominal aorta in the MetS model. Furthermore, using metagenome and metatranscriptome sequencing, we discovered that the long-term excessive energy intake altered the local intestinal microbiota composition and transcriptional profile, which was most dramatically illustrated by the reduced abundance of SCFAs-producing bacteria including Bacteroides, Lachnospiraceae, and Ruminococcaceae in the MetS model. Liver and abdominal aorta transcriptomes in the MetS model indicate that the diet-induced gut microbiota dysbiosis activated host chronic inflammatory responses and significantly upregulated the expression of genes related to arachidonic acid-dependent signaling pathways. Notably, metabolomics profiling further revealed an intimate linkage between arachidonic acid metabolism and atherothrombosis in the host-gut microbial metabolism axis. Conclusions These findings provide new insights into the relationship between atherothrombosis and regulation of gut microbiota via host metabolomes and will be of potential value for the treatment of cardiovascular diseases in MetS.
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Affiliation(s)
- Song-Song Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiu-Ling Zhang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sha-Sha Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Animal Husbandry and Veterinary Department, Beijing Vocational College of Agriculture, Beijing, China
| | - Shu-Tang Feng
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang-Ming Xiang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chang-Jiang Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yao Fan
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing-Jing Che
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Guo Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Lian Mu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yu-Lian Mu
| | - Kui Li
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kui Li
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7
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Ma JE, Xiong XW, Xu JG, Gong JS, Li J, Xu Q, Li YF, Yang YB, Zhou M, Zhu XN, Tan YW, Sheng WT, Wang ZF, Tu XT, Zeng CY, Zhang XQ, Rao YS. Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail. Front Vet Sci 2021; 8:693755. [PMID: 34660751 PMCID: PMC8517240 DOI: 10.3389/fvets.2021.693755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear. Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail. Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.
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Affiliation(s)
- Jing-E Ma
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Xin-Wei Xiong
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Ji-Guo Xu
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Ji-Shang Gong
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Jin Li
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China
| | - Qiao Xu
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Yuan-Fei Li
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Yang-Bei Yang
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Min Zhou
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Xue-Nong Zhu
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Yu-Wen Tan
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Wen-Tao Sheng
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Zhang-Feng Wang
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Xu-Tang Tu
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Cheng-Yao Zeng
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
| | - Xi-Quan Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - You-Sheng Rao
- Institution of Biological Technology, Nanchang Normal University, Nanchang, China.,Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Nanchang, China
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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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Uebanso T, Shimohata T, Mawatari K, Takahashi A. Functional Roles of B‐Vitamins in the Gut and Gut Microbiome. Mol Nutr Food Res 2020; 64:e2000426. [DOI: 10.1002/mnfr.202000426] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Takaaki Shimohata
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Kazuaki Mawatari
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Akira Takahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
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Vollmar S, Wellmann R, Borda-Molina D, Rodehutscord M, Camarinha-Silva A, Bennewitz J. The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail ( Coturnix japonica) Assessed by Mixed Linear Models. G3 (BETHESDA, MD.) 2020; 10:2553-2562. [PMID: 32471941 PMCID: PMC7341145 DOI: 10.1534/g3.120.401424] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023]
Abstract
It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.
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Affiliation(s)
- Solveig Vollmar
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Robin Wellmann
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | | | | | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
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Borda-Molina D, Roth C, Hérnandez-Arriaga A, Rissi D, Vollmar S, Rodehutscord M, Bennewitz J, Camarinha-Silva A. Effects on the Ileal Microbiota of Phosphorus and Calcium Utilization, Bird Performance, and Gender in Japanese Quail. Animals (Basel) 2020; 10:ani10050885. [PMID: 32438715 PMCID: PMC7278395 DOI: 10.3390/ani10050885] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 12/18/2022] Open
Abstract
In this study, we aimed to investigate the ileum digesta of a large cohort of Japanese quail fed the same diet, with similar environmental conditions. We also address how P utilization (PU), Ca utilization (CaU), and bird performance (feed intake (FI), feed conversion (FC), and body weight gain (BWG)) modify intestinal microbiota of male and female quail. Despite the great number of samples analyzed (760), a core microbiome was composed of five bacteria. The Unc. Lactobacillus, Unc. Clostridaceae 1, Clostridium sensu stricto, Escherichia coli, and Streptococcus alactolyticus were detected in all samples and contributed to more than 70% of the total community. Depending on the bird predisposition for PU, CaU, FI, BWG, and FC, those species were present in higher or lower abundances. There was a significant gender effect on the ileal microbial community. While females had higher abundances of Lactobacillus, males were more colonized by Streptococcus alactolyticus. The entire cohort was highly colonized by Escherichia coli (8%-15%), an enteropathogenic bacteria. It remains unclear, if microbiota composition followed the mechanisms that caused different PU, CaU, FI, FC, and BWG or if the change in microbiota composition and function caused the differences in PU, CaU, and performance traits.
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