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Hu J, Chen J, Ma L, Hou Q, Zhang Y, Kong X, Huang X, Tang Z, Wei H, Wang X, Yan X. Characterizing core microbiota and regulatory functions of the pig gut microbiome. ISME J 2024; 18:wrad037. [PMID: 38366194 PMCID: PMC10873858 DOI: 10.1093/ismejo/wrad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/23/2023] [Indexed: 02/18/2024]
Abstract
Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.
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Affiliation(s)
- Jun Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Jianwei Chen
- BGI Research, Qingdao, Shandong 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Libao Ma
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Qiliang Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Yong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiangfeng Kong
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xingguo Huang
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hong Wei
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xianghua Yan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice. IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.
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Xie H, Yang C, Sun Y, Igarashi Y, Jin T, Luo F. PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning. Front Genet 2020; 11:516269. [PMID: 33101371 PMCID: PMC7506068 DOI: 10.3389/fgene.2020.516269] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
PacBio long reads sequencing presents several potential advantages for DNA assembly, including being able to provide more complete gene profiling of metagenomic samples. However, lower single-pass accuracy can make gene discovery and assembly for low-abundance organisms difficult. To evaluate the application and performance of PacBio long reads and Illumina HiSeq short reads in metagenomic analyses, we directly compared various assemblies involving PacBio and Illumina sequencing reads based on two anaerobic digestion microbiome samples from a biogas fermenter. Using a PacBio platform, 1.58 million long reads (19.6 Gb) were produced with an average length of 7,604 bp. Using an Illumina HiSeq platform, 151.2 million read pairs (45.4 Gb) were produced. Hybrid assemblies using PacBio long reads and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length, contig N50 size, and number of large contigs. Interestingly, depth-based hybrid assemblies generated a higher percentage of complete genes (98.86%) compared to those based on HiSeq contigs only (40.29%), because the PacBio reads were long enough to cover many repeating short elements and capture multiple genes in a single read. Additionally, the incorporation of PacBio long reads led to considerable advantages regarding reducing contig numbers and increasing the completeness of the genome reconstruction, which was poorly assembled and binned when using HiSeq data alone. From this comparison of PacBio long reads with Illumina HiSeq short reads related to complex microbiome samples, we conclude that PacBio long reads can produce longer contigs, more complete genes, and better genome binning, thereby offering more information about metagenomic samples.
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Affiliation(s)
- Haiying Xie
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Chongqing, China.,PUROTON Gene Medical Institute Co., Ltd., Chongqing, China
| | - Caiyun Yang
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Chongqing, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin Biochip Co., Ltd., Tianjin, China
| | - Yasuo Igarashi
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Chongqing, China
| | - Tao Jin
- The Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Chongqing, China.,PUROTON Gene Medical Institute Co., Ltd., Chongqing, China
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Lesker TR, Durairaj AC, Gálvez EJC, Lagkouvardos I, Baines JF, Clavel T, Sczyrba A, McHardy AC, Strowig T. An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Cell Rep 2020; 30:2909-2922.e6. [PMID: 32130896 PMCID: PMC7059117 DOI: 10.1016/j.celrep.2020.02.036] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/02/2019] [Accepted: 02/07/2020] [Indexed: 01/06/2023] Open
Abstract
The complexity of host-associated microbial ecosystems requires host-specific reference catalogs to survey the functions and diversity of these communities. We generate a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 metagenome-assembled genomes (MAGs), many (485 MAGs, 73%) of which are linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution of the mouse gut microbiota; i.e., more than 92% of MAGs lack species-level representatives in public repositories (<95% ANI match). The integration of MAGs and 16S rRNA gene data allows more accurate prediction of functional profiles of communities than predictions based on 16S rRNA amplicons alone. Accompanying iMGMC, we provide a set of MAGs representing 1,296 gut bacteria obtained through complementary assembly strategies. We envision that integrated resources such as iMGMC, together with MAG collections, will enhance the resolution of numerous existing and future sequencing-based studies.
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Affiliation(s)
- Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Abilash C Durairaj
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany; Institute for Experimental Medicine, Kiel University, 24118 Kiel, Germany
| | - Thomas Clavel
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany; Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany
| | - Alexander Sczyrba
- Faculty of Technology and Center for Biotechnology, Bielefeld University, 33501 Bielefeld, Germany; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Alice C McHardy
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology, 38106 Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Hanover Medical School, 30625 Hannover, Germany; RESIST, Cluster of Excellence 2155, Hanover Medical School, 30625 Hanover, Germany.
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Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019; 26:283-295.e8. [PMID: 31415755 PMCID: PMC6716383 DOI: 10.1016/j.chom.2019.07.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/01/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.
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Affiliation(s)
- Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Christina Baek
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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