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Li W, Lin X, Liang H, Wu Z, Wang M, Sun J, Li X, He W, Gao X, Hu T, Xiao L, Zou Y. Genomic and functional diversity of the human-derived isolates of Faecalibacterium. Front Microbiol 2024; 15:1379500. [PMID: 38873165 PMCID: PMC11169845 DOI: 10.3389/fmicb.2024.1379500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Faecalibacterium is one of the most abundant bacteria in the gut microbiota of healthy adults, highly regarded as a next-generation probiotic. However, the functions of Faecalibacterium genomes from cultured strains and the distribution of different species in populations may differ among different sources. Methods We here performed an extensive analysis of pan-genomes, functions, and safety evaluation of 136 Faecalibacterium genomes collected from 10 countries. Results The genomes are clustered into 11 clusters, with only five of them were characterized and validly nomenclated. Over 80% of the accessory genes and unique genes of Faecalibacterium are found with unknown function, which reflects the importance of expanding the collection of Faecalibacterium strains. All the genomes have the potential to produce acetic acid and butyric acid. Nine clusters of Faecalibacterium are found significantly enriched in the healthy individuals compared with patients with type II diabetes.. Discussion This study provides a comprehensive view of genomic characteristic and functions and of culturable Faecalibacterium bacterium from human gut, and enables clinical advances in the future.
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Affiliation(s)
- Wenxi Li
- BGI-Shenzhen, Shenzhen, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hewei Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Wang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingxi Sun
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofang Li
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | | | - Tongyuan Hu
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark
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Rui W, Li X, Wang L, Tang X, Yang J. Potential Applications of Blautia wexlerae in the Regulation of Host Metabolism. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10274-8. [PMID: 38703323 DOI: 10.1007/s12602-024-10274-8] [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] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Blautia wexlerae (B. wexlerae) is a strong candidate with the potential to become a next-generation probiotics (NGPs) and has recently been shown for the first time to exhibit potential in modulating host metabolic levels and alleviating metabolic diseases. However, the factors affecting the change in abundance of B. wexlerae and the pattern of its abundance change in the associated indications remain to be further investigated. Here, we summarize information from published studies related to B. wexlerae; analyze the effects of food source factors such as prebiotics, probiotics, low protein foods, polyphenols, vitamins, and other factors on the abundance of B. wexlerae; and explore the patterns of changes in the abundance of B. wexlerae in metabolic diseases, neurological diseases, and other diseases. At the same time, the development potential of B. wexlerae was evaluated in the direction of functional foods and special medical foods.
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Affiliation(s)
- Wen Rui
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, 2 Xuelin Road, Nanjing, China
| | - Xiaoqian Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, 2 Xuelin Road, Nanjing, China
| | - Lijun Wang
- Department of Endodontology, Affiliated Hospital of Medical School, Nanjing Stomatological Hospital, Nanjing University, Nanjing, China.
| | - Xuna Tang
- Department of Specialist Clinic, Affiliated Hospital of Medical School, Nanjing Stomatological Hospital, Research Institute of Stomatology, Nanjing University, Nanjing, China.
| | - Jingpeng Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, 2 Xuelin Road, Nanjing, China.
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Li W, Liang H, He W, Gao X, Wu Z, Hu T, Lin X, Wang M, Zhong Y, Zhang H, Ge L, Jin X, Xiao L, Zou Y. Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota. Heliyon 2024; 10:e27270. [PMID: 38463766 PMCID: PMC10923715 DOI: 10.1016/j.heliyon.2024.e27270] [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: 08/27/2023] [Revised: 02/14/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.
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Affiliation(s)
- Wenxi Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- BGI Research, Shenzhen, 518083, China
| | | | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | | | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- BGI Research, Shenzhen, 518083, China
| | - Mengmeng Wang
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiyi Zhong
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Haifeng Zhang
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Lan Ge
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
- BGI Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China
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Darmadi D, Pakpahan C, Singh R, Saharan A, Pasaribu WS, Hermansyah H, Rezano A. Inflammatory bowel disease (ulcerative colitis type) severity shows inverse correlation with semen parameters and testosterone levels. Asian J Androl 2024; 26:155-159. [PMID: 37934180 PMCID: PMC10919423 DOI: 10.4103/aja202353] [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: 07/25/2023] [Accepted: 09/05/2023] [Indexed: 11/08/2023] Open
Abstract
Individuals with inflammatory bowel disease (IBD) have been reported to be at an increased risk of infertility and sexual dysfunction. Although the relationship between them remains unclear, IBD severity is suspected to affect hormone levels and fertility. To analyze the impact of IBD severity on semen parameters and sex hormone levels in ulcerative colitis-type IBD (UC-IBD), we conducted a cross-sectional study involving 120 patients with UC-IBD in Adam Malik General Hospital, Medan, Indonesia. The patients were classified into three groups based on the Mayo score for UC, followed by a comparison of various semen and hormone parameters among these groups. In addition to the cross-sectional analysis, a simple correlation test was conducted irrespective of the patient grouping. Sperm concentration, motility, and morphology were found to decline significantly with an increase in IBD severity. Without classifying patients with IBD into subgroups, the Mayo score showed negative correlations with sperm concentration ( r = -0.375, P < 0.0001), rapid progressive motility ( r = -0.660, P < 0.0001), free testosterone ( r = -0.732, P < 0.0001), and total testosterone ( r = -0.721, P < 0.0001), and positive correlations with immotile sperm ( r = 0.660, P < 0.0001), abnormal morphology ( r = 0.657, P < 0.0001), and sex hormone-binding globulin (SHBG; r = 0.278, P = 0.002). Sperm concentration, motility, and morphology declined significantly with the severity of IBD. This study suggests a significant negative impact of IBD severity on semen quality and sex hormones.
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Affiliation(s)
- Darmadi Darmadi
- Department of Internal Medicine, Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Cennikon Pakpahan
- Andrology Study Program, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Rajender Singh
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh 226031, India
| | - Ankur Saharan
- Amity University, Lucknow, Uttar Pradesh 226010, India
| | | | - Hermansyah Hermansyah
- Andrology Study Program, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Andri Rezano
- Andrology Study Program, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang 45363, Indonesia
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Liu X, Tong X, Zou L, Ju Y, Liu M, Han M, Lu H, Yang H, Wang J, Zong Y, Liu W, Xu X, Jin X, Xiao L, Jia H, Guo R, Zhang T. A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Commun Biol 2024; 7:139. [PMID: 38291185 PMCID: PMC10828421 DOI: 10.1038/s42003-024-05822-5] [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: 06/27/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1401 healthy individuals, we demonstrated that the top three host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10-10): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational correlation and Mendelian randomization analyses consistently suggested the causal effects of Serratia grimesii and Yokenella regensburgei on cardiometabolic biomarkers (cystine, glutamic acid, and creatine). This study suggested that the host genome plays an important role in shaping the nasal microbiome.
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Affiliation(s)
- Xiaomin Liu
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Tong
- BGI Research, Shenzhen, 518083, China
| | | | - Yanmei Ju
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Mo Han
- BGI Research, Shenzhen, 518083, China
| | - Haorong Lu
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jian Wang
- BGI Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Yang Zong
- BGI Research, Shenzhen, 518083, China
| | | | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huijue Jia
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China.
- School of Life Sciences, Fudan University, Shanghai, China.
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6
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Hu T, Chen J, Lin X, He W, Liang H, Wang M, Li W, Wu Z, Han M, Jin X, Kristiansen K, Xiao L, Zou Y. Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly. Sci Rep 2024; 14:1292. [PMID: 38221534 PMCID: PMC10788345 DOI: 10.1038/s41598-024-51725-0] [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: 08/11/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
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Affiliation(s)
- Tongyuan Hu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | - Hewei Liang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Wenxi Li
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
| | - Mo Han
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China.
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7
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Liu X, Zou L, Nie C, Qin Y, Tong X, Wang J, Yang H, Xu X, Jin X, Xiao L, Zhang T, Min J, Zeng Y, Jia H, Hou Y. Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity. Sci Rep 2023; 13:5127. [PMID: 36991009 PMCID: PMC10052271 DOI: 10.1038/s41598-023-31115-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
Although recent studies have revealed the association between the human microbiome especially gut microbiota and longevity, their causality remains unclear. Here, we assess the causal relationships between the human microbiome (gut and oral microbiota) and longevity, by leveraging bidirectional two-sample Mendelian randomization (MR) analyses based on genome-wide association studies (GWAS) summary statistics of the gut and oral microbiome from the 4D-SZ cohort and longevity from the CLHLS cohort. We found that some disease-protected gut microbiota such as Coriobacteriaceae and Oxalobacter as well as the probiotic Lactobacillus amylovorus were related to increased odds of longevity, whereas the other gut microbiota such as colorectal cancer pathogen Fusobacterium nucleatum, Coprococcus, Streptococcus, Lactobacillus, and Neisseria were negatively associated with longevity. The reverse MR analysis further revealed genetically longevous individuals tended to have higher abundances of Prevotella and Paraprevotella but lower abundances of Bacteroides and Fusobacterium species. Few overlaps of gut microbiota-longevity interactions were identified across different populations. We also identified abundant links between the oral microbiome and longevity. The additional analysis suggested that centenarians genetically had a lower gut microbial diversity, but no difference in oral microbiota. Our findings strongly implicate these bacteria to play a role in human longevity and underscore the relocation of commensal microbes among different body sites that would need to be monitored for long and healthy life.
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Affiliation(s)
- Xiaomin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Chao Nie
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xin Tong
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Tao Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Junxia Min
- School of Medicine, The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University, Hangzhou, China.
| | - Yi Zeng
- Center for Healthy Aging and Development Studies, National School of Development, Raissun Institute for Advanced Studies, Peking University, Beijing, China.
| | - Huijue Jia
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Shanghai, China.
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, 518083, China.
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Lin X, Hu T, Chen J, Liang H, Zhou J, Wu Z, Ye C, Jin X, Xu X, Zhang W, Jing X, Yang T, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. The genomic landscape of reference genomes of cultivated human gut bacteria. Nat Commun 2023; 14:1663. [PMID: 36966151 PMCID: PMC10039858 DOI: 10.1038/s41467-023-37396-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.
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Affiliation(s)
- Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | | | - Jianwei Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | | | - Jianwei Zhou
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiaohuan Jing
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450, Copenhagen, Denmark.
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
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Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus. NPJ Biofilms Microbiomes 2022; 8:102. [PMID: 36564415 PMCID: PMC9789086 DOI: 10.1038/s41522-022-00366-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
The gut microbiota plays an important role in human health and longevity, and the gut microbiota of centenarians shows unique characteristics. Nowadays, most microbial research on longevity is usually limited to the bioinformatics level, lacking validating information on culturing functional microorganisms. Here, we combined metagenomic sequencing and large-scale in vitro culture to reveal the unique gut microbial structure of the world's longevity town-Jiaoling, China, centenarians and people of different ages. Functional strains were isolated and screened in vitro, and the possible relationship between gut microbes and longevity was explored and validated in vivo. 247 healthy Cantonese natives of different ages participated in the study, including 18 centenarians. Compared with young adults, the gut microbiota of centenarians exhibits higher microbial diversity, xenobiotics biodegradation and metabolism, oxidoreductases, and multiple species (the potential probiotics Lactobacillus, Akkermansia, the methanogenic Methanobrevibacter, gut butyrate-producing members Roseburia, and SCFA-producing species uncl Clostridiales, uncl Ruminococcaceae) known to be beneficial to host metabolism. These species are constantly changing with age. We also isolated 2055 strains from these samples by large-scale in vitro culture, most of which were detected by metagenomics, with clear complementarity between the two approaches. We also screened an age-related gut-resident Lactobacillus with independent intellectual property rights, and its metabolite (L-ascorbic acid) and itself have good antioxidant effects. Our findings underscore the existence of age-related trajectories in the human gut microbiota, and that distinct gut microbiota and gut-resident as antioxidant systems may contribute to health and longevity.
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10
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Zhu J, Tian L, Chen P, Han M, Song L, Tong X, Sun X, Yang F, Lin Z, Liu X, Liu C, Wang X, Lin Y, Cai K, Hou Y, Xu X, Yang H, Wang J, Kristiansen K, Xiao L, Zhang T, Jia H, Jie Z. Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:246-259. [PMID: 34492339 PMCID: PMC9684161 DOI: 10.1016/j.gpb.2021.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/13/2021] [Accepted: 08/23/2021] [Indexed: 01/05/2023]
Abstract
The oral cavity of each person is home to hundreds of bacterial species. While taxa for oral diseases have been studied using culture-based characterization as well as amplicon sequencing, metagenomic and genomic information remains scarce compared to the fecal microbiome. Here, using metagenomic shotgun data for 3346 oral metagenomic samples together with 808 published samples, we obtain 56,213 metagenome-assembled genomes (MAGs), and more than 64% of the 3589 species-level genome bins (SGBs) contain no publicly available genomes. The resulting genome collection is representative of samples around the world and contains many genomes from candidate phyla radiation (CPR) that lack monoculture. Also, it enables the discovery of new taxa such as a genus Candidatus Bgiplasma within the family Acholeplasmataceae. Large-scale metagenomic data from massive samples also allow the assembly of strains from important oral taxa such as Porphyromonas and Neisseria. The oral microbes encode genes that could potentially metabolize drugs. Apart from these findings, a strongly male-enriched Campylobacter species was identified. Oral samples would be more user-friendly collected than fecal samples and have the potential for disease diagnosis. Thus, these data lay down a genomic framework for future inquiries of the human oral microbiome.
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Affiliation(s)
- Jie Zhu
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Liu Tian
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Peishan Chen
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China
| | - Mo Han
- BGI-Shenzhen, Shenzhen 518083, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Liju Song
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Tong
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | | | - Xing Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chuan Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Kaiye Cai
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China,BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Tao Zhang
- BGI-Shenzhen, Shenzhen 518083, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China,Corresponding authors.
| | - Zhuye Jie
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark,Corresponding authors.
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11
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Jie Z, Chen C, Hao L, Li F, Song L, Zhang X, Zhu J, Tian L, Tong X, Cai K, Zhang Z, Ju Y, Yu X, Li Y, Zhou H, Lu H, Qiu X, Li Q, Liao Y, Zhou D, Lian H, Zuo Y, Chen X, Rao W, Ren Y, Wang Y, Zi J, Wang R, Liu N, Wu J, Zhang W, Liu X, Zong Y, Liu W, Xiao L, Hou Y, Xu X, Yang H, Wang J, Kristiansen K, Jia H. Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:304-321. [PMID: 34118463 PMCID: PMC9684086 DOI: 10.1016/j.gpb.2021.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/31/2021] [Indexed: 01/05/2023]
Abstract
The vagina contains at least a billion microbial cells, dominated by lactobacilli. Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age, as well as cervical, fecal, and salivary samples from a second cohort of 632 women. Factors such as pregnancyhistory, delivery history, cesarean section, and breastfeeding were all more important than menstrual cycle in shaping the microbiome, and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data. Greater proportion of Bifidobacterium breve was seen with older age at sexual debut. The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history. Potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, and contraceptives were also identified. Lactobacilli were rare during breastfeeding or post-menopause. Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome. Gut and salivary microbiomes, plasma vitamins, metals, amino acids, and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.
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Affiliation(s)
- Zhuye Jie
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China,Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Chen Chen
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China,Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark,Corresponding authors.
| | - Lilan Hao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fei Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liju Song
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jie Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liu Tian
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Tong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kaiye Cai
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhe Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yanmei Ju
- BGI-Shenzhen, Shenzhen 518083, China,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xinlei Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongcheng Zhou
- China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Haorong Lu
- China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | | | - Qiang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Heng Lian
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Zuo
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Yan Ren
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yuan Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen 518083, China
| | - Rong Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Na Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Zong
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Liang Xiao
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China,BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China,Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark,BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen 518083, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China,Corresponding authors.
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12
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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome. Nat Genet 2022; 54:52-61. [PMID: 34980918 DOI: 10.1038/s41588-021-00968-y] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 10/14/2021] [Indexed: 01/27/2023]
Abstract
The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacter and Alistipes were causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter, and members of Proteobacteria were influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate and selenium. Two-sample Mendelian randomization with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies.
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13
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Liu X, Tong X, Zhu J, Tian L, Jie Z, Zou Y, Lin X, Liang H, Li W, Ju Y, Qin Y, Zou L, Lu H, Zhu S, Jin X, Xu X, Yang H, Wang J, Zong Y, Liu W, Hou Y, Jia H, Zhang T. Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome. Cell Discov 2021; 7:117. [PMID: 34873157 PMCID: PMC8648780 DOI: 10.1038/s41421-021-00356-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for both the tongue dorsum (n = 2017) and saliva (n = 1915). We identified five genetic loci associated with oral microbiota at study-wide significance (p < 3.16 × 10-11). Four of the five associations were well replicated in an independent cohort of 1439 individuals: rs1196764 at APPL2 with Prevotella jejuni, Oribacterium uSGB 3339 and Solobacterium uSGB 315; rs3775944 at the serum uric acid transporter SLC2A9 with Oribacterium uSGB 1215, Oribacterium uSGB 489 and Lachnoanaerobaculum umeaense; rs4911713 near OR11H1 with species F0422 uSGB 392; and rs36186689 at LOC105371703 with Eggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of host genome-microbiome associations including six genome-wide significant associations mutually validated between the two niches. As many of the oral microbiome-associated genetic variants lie near miRNA genes, we tentatively validated the potential of host miRNAs to modulate the growth of specific oral bacteria. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk scores dominated over oral microbiome in predicting risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.
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Affiliation(s)
- Xiaomin Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Xin Tong
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jie Zhu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Liu Tian
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhuye Jie
- BGI-Shenzhen, Shenzhen, Guangdong, China
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, Denmark
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, Guangdong, China
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, Shandong, China
| | - Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, Guangdong, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, Guangdong, China
| | | | - Wenxi Li
- BGI-Shenzhen, Shenzhen, Guangdong, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, Guangdong, China
| | - Yanmei Ju
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Youwen Qin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Leying Zou
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Haorong Lu
- China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Yang Zong
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Weibin Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, Guangdong, China.
| | - Tao Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, China.
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, Denmark.
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14
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Jie Z, Liang S, Ding Q, Li F, Sun X, Lin Y, Chen P, Cai K, Zhou H, Lu H, Wang X, Zhang T, Xiao L, Yang H, Wang J, Hou Y, Kristiansen K, Jia H, Xu X. Disease trends in a young Chinese cohort according to fecal metagenome and plasma metabolites. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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15
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Dairy consumption and physical fitness tests associated with fecal microbiome in a Chinese cohort. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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