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Liu Y, Huang Q, Zhuang Z, Yang H, Gou X, Xu T, Liu K, Wang J, Liu B, Gao P, Cao F, Yang B, Zhang C, Chen M, Fan G. Gut virome alterations in patients with chronic obstructive pulmonary disease. Microbiol Spectr 2024; 12:e0428723. [PMID: 38785444 DOI: 10.1128/spectrum.04287-23] [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: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the primary causes of mortality and morbidity worldwide. The gut microbiome, particularly the bacteriome, has been demonstrated to contribute to the progression of COPD. However, the influence of gut virome on the pathogenesis of COPD is rarely studied. Recent advances in viral metagenomics have enabled the rapid discovery of its remarkable role in COPD. In this study, deep metagenomics sequencing of fecal virus-like particles and bacterial 16S rRNA sequencing was performed on 92 subjects from China to characterize alterations of the gut virome in COPD. Lower richness and diversity of the gut virome were observed in the COPD subjects compared with the healthy individuals. Sixty-four viral species, including Clostridium phage, Myoviridae sp., and Synechococcus phage, showed positive relationships with pulmonary ventilation functions and had markedly declined population in COPD subjects. Multiple viral functions, mainly involved in bacterial susceptibility and the interaction between bacteriophages and bacterial hosts, were significantly declined in COPD. In addition, COPD was characterized by weakened viral-bacterial interactions compared with those in the healthy cohort. The gut virome showed diagnostic performance with an area under the curve (AUC) of 88.7%, which indicates the potential diagnostic value of the gut virome for COPD. These results suggest that gut virome may play an important role in the development of COPD. The information can provide a reference for the future investigation of diagnosis, treatment, and in-depth mechanism research of COPD. IMPORTANCE Previous studies showed that the bacteriome plays an important role in the progression of chronic obstructive pulmonary disease (COPD). However, little is known about the involvement of the gut virome in COPD. Our study explored the disease-specific virome signatures of patients with COPD. We found the diversity and compositions altered of the gut virome in COPD subjects compared with healthy individuals, especially those viral species positively correlated with pulmonary ventilation functions. Additionally, the declined bacterial susceptibility, the interaction between bacteriophages and bacterial hosts, and the weakened viral-bacterial interactions in COPD were observed. The findings also suggested the potential diagnostic value of the gut virome for COPD. The results highlight the significance of gut virome in COPD. The novel strategies for gut virome rectifications may help to restore the balance of gut microecology and represent promising therapeutics for COPD.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qingsong Huang
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenhua Zhuang
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Hongjing Yang
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoling Gou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tong Xu
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Ke Liu
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jun Wang
- Department of Respiratory Medicine, Chengdu Fifth People's Hospital, Chengdu, China
| | - Bo Liu
- Department of Respiratory Medicine, Chengdu Fifth People's Hospital, Chengdu, China
| | - Peiyang Gao
- Department of Critical Care Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Feng Cao
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Bin Yang
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Chuantao Zhang
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mei Chen
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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2
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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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3
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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024:S1673-8527(24)00098-5. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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4
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Ma J, Qian C, Hu Q, Zhang J, Gu G, Liang X, Zhang L. The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation. Food Res Int 2024; 184:114244. [PMID: 38609223 DOI: 10.1016/j.foodres.2024.114244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.
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Affiliation(s)
- Jiawen Ma
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Chenggong Qian
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Qijie Hu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Jianping Zhang
- Haining Yufeng Brewing Co., Ltd, Haining, Zhejiang Province 314408, China
| | - Guizhang Gu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
| | - Lei Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
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5
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Wu LY, Wijesekara Y, Piedade GJ, Pappas N, Brussaard CPD, Dutilh BE. Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biol 2024; 25:97. [PMID: 38622738 PMCID: PMC11020464 DOI: 10.1186/s13059-024-03236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. RESULTS We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. CONCLUSIONS Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.
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Affiliation(s)
- Ling-Yi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix Hausdorff Str. 8, 17475, Greifswald, Germany
| | - Gonçalo J Piedade
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Corina P D Brussaard
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
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6
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Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
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Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
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7
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Zeng S, Almeida A, Li S, Ying J, Wang H, Qu Y, Paul Ross R, Stanton C, Zhou Z, Niu X, Mu D, Wang S. A metagenomic catalog of the early-life human gut virome. Nat Commun 2024; 15:1864. [PMID: 38424077 PMCID: PMC10904392 DOI: 10.1038/s41467-024-45793-z] [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: 06/29/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Early-life human gut microbiome is a pivotal driver of gut homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish the Early-Life Gut Virome (ELGV), a catalog of 160,478 non-redundant DNA and RNA viral sequences from 8130 gut virus-like particles (VLPs) enriched or bulk metagenomes in the first three years of life. By clustering, 82,141 viral species are identified, 68.3% of which are absent in existing databases built mainly from adults, and 64 and 8 viral species based on VLPs-enriched and bulk metagenomes, respectively, exhibit potentials as biomarkers to distinguish infants from adults. With the largest longitudinal population of infants profiled by either VLPs-enriched or bulk metagenomic sequencing, we track the inherent instability and temporal development of the early-life human gut virome, and identify differential viruses associated with multiple clinical factors. The mother-infant shared virome and interactions between gut virome and bacteriome early in life are further expanded. Together, the ELGV catalog provides the most comprehensive and complete metagenomic blueprint of the early-life human gut virome, facilitating the discovery of pediatric disease-virome associations in future.
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Affiliation(s)
- Shuqin Zeng
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Shiping Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Junjie Ying
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hua Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yi Qu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Zhemin Zhou
- Pasteurien College, Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xiaoyu Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Dezhi Mu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Shaopu Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
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8
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Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB. Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nat Commun 2024; 15:1791. [PMID: 38424056 PMCID: PMC10904388 DOI: 10.1038/s41467-024-46033-0] [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: 08/25/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
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Affiliation(s)
- Paula Istvan
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Einar Birkeland
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ekaterina Avershina
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Vahid Bemanian
- Pathology Department, Akershus University Hospital, Lørenskog, Norway
| | - Barbara Pardini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Sonia Tarallo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Paula Berstad
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Trine B Rounge
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway.
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
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9
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Kirk D, Costeira R, Visconti A, Khan Mirzaei M, Deng L, Valdes AM, Menni C. Bacteriophages, gut bacteria, and microbial pathways interplay in cardiometabolic health. Cell Rep 2024; 43:113728. [PMID: 38300802 DOI: 10.1016/j.celrep.2024.113728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Cardiometabolic diseases are leading causes of mortality in Western countries. Well-established risk factors include host genetics, lifestyle, diet, and the gut microbiome. Moreover, gut bacterial communities and their activities can be altered by bacteriophages (also known simply as phages), bacteria-infecting viruses, making these biological entities key regulators of human cardiometabolic health. The manipulation of bacterial populations by phages enables the possibility of using phages in the treatment of cardiometabolic diseases through phage therapy and fecal viral transplants. First, however, a deeper understanding of the role of the phageome in cardiometabolic diseases is required. In this review, we first introduce the phageome as a component of the gut microbiome and discuss fecal viral transplants and phage therapy in relation to cardiometabolic diseases. We then summarize the current state of phageome research in cardiometabolic diseases and propose how the phageome might indirectly influence cardiometabolic health through gut bacteria and their metabolites.
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Affiliation(s)
- Daniel Kirk
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK
| | - Ricardo Costeira
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK; Center for Biostatistics, Epidemiology, and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, 85764 Neuherberg, Germany; School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, 85764 Neuherberg, Germany; School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Ana M Valdes
- Academic Rheumatology, Clinical Sciences Building, Nottingham City Hospital, University of Nottingham, Nottingham, UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK.
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10
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-w] [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: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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11
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Gao SM, Fei HL, Li Q, Lan LY, Huang LN, Fan PF. Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations. Nat Commun 2024; 15:1254. [PMID: 38341424 PMCID: PMC10858875 DOI: 10.1038/s41467-024-45663-8] [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: 06/25/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Han-Lan Fei
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
- College of Life Science, China West Normal University, Nanchong, 637002, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
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12
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Peña Rodríguez M, Fagan A, Sikaroodi M, Gillevet PM, Bajaj JS. Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis. Clin Transl Gastroenterol 2024; 15:e00659. [PMID: 37937851 PMCID: PMC10887442 DOI: 10.14309/ctg.0000000000000659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
INTRODUCTION Proton pump inhibitors (PPIs) modulate the progression of cirrhosis to hepatic encephalopathy (HE) and can affect the bacterial microbiome. However, the impact of PPI on the virome in cirrhosis using viral-like particle (VLP) analysis is unclear. METHODS We determined the VLP in the stool microbiome in patients with cirrhosis cross-sectionally (ascites, HE, and PPI use analyzed) who were followed up for 6-month hospitalizations and through 2 clinical trials of PPI withdrawal and initiation. RESULTS In a cross-sectional study, PPI users had greater ascites prevalence and 6-month hospitalizations, but VLP α diversity was similar. Among phages, PPI users had lower Autographviridae and higher Streptococcus phages and Herelleviridae than nonusers, whereas opposite trends were seen in ascites and HE. Trends of eukaryotic viruses (higher Adenoviridae and lower Virgaviridae/Smacoviridae) were similar for PPI, HE, and ascites. Twenty-one percent were hospitalized, mostly due to HE. α Diversity was similar in the hospitalized/nonhospitalized/not groups. Higher Gokushovirinae and lower crAssphages were related to hospitalizations such as HE-related cross-sectional VLP changes. As part of the clinical trial, PPIs were added and withdrawn in 2 different decompensated groups over 14 days. No changes in α diversity were observed. Withdrawal reduced crAssphages, and initiation reduced Gokushovirinae and Bacteroides phages. DISCUSSION In cirrhosis, PPI use has a gut microbial VLP phage signature that is different from that in HE and ascites, and VLP changes are linked with hospitalizations over 6 months, independent of clinical biomarkers. Eukaryotic viral patterns were consistent across PPI use, HE, and ascites, indicating a relationship with the progression of cirrhosis. PPIs alone showed modest VLP changes with withdrawal or initiation. Distinct phage and eukaryotic viral patterns are associated with the use of PPIs in cirrhosis.
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Affiliation(s)
| | - Andrew Fagan
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | | | - Jasmohan S. Bajaj
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
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13
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Ding Y, Zhao L, Wang G, Shi Y, Guo G, Liu C, Chen Z, Coker OO, She J, Yu J. PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages. Nucleic Acids Res 2023; 51:12140-12149. [PMID: 37904586 PMCID: PMC10711547 DOI: 10.1093/nar/gkad977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Gut phages have an important impact on human health. Methylation plays key roles in DNA recognition, gene expression regulation and replication for phages. However, the DNA methylation landscape of gut phages is largely unknown. Here, with PacBio sequencing (2120×, 4785 Gb), we detected gut phage methylation landscape based on 22 673 gut phage genomes, and presented diverse methylation motifs and methylation differences in genomic elements. Moreover, the methylation rate of phages was associated with taxonomy and host, and N6-methyladenine methylation rate was higher in temperate phages than in virulent phages, suggesting an important role for methylation in phage-host interaction. In particular, 3543 (15.63%) phage genomes contained restriction-modification system, which could aid in evading clearance by the host. This study revealed the DNA methylation landscape of gut phage and its potential roles, which will advance the understanding of gut phage survival and human health.
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Affiliation(s)
- Yanqiang Ding
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Guoping Wang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yu Shi
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gang Guo
- Center for Gut Microbiome Research, Department of Surgery, Med-X Institute, Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changan Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Olabisi Oluwabukola Coker
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junjun She
- Center for Gut Microbiome Research, Department of Surgery, Med-X Institute, Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
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14
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Pavia G, Marascio N, Matera G, Quirino A. Does the Human Gut Virome Contribute to Host Health or Disease? Viruses 2023; 15:2271. [PMID: 38005947 PMCID: PMC10674713 DOI: 10.3390/v15112271] [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: 09/20/2023] [Revised: 11/04/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The human gastrointestinal (GI) tract harbors eukaryotic and prokaryotic viruses and their genomes, metabolites, and proteins, collectively known as the "gut virome". This complex community of viruses colonizing the enteric mucosa is pivotal in regulating host immunity. The mechanisms involved in cross communication between mucosal immunity and the gut virome, as well as their relationship in health and disease, remain largely unknown. Herein, we review the literature on the human gut virome's composition and evolution and the interplay between the gut virome and enteric mucosal immunity and their molecular mechanisms. Our review suggests that future research efforts should focus on unraveling the mechanisms of gut viruses in human homeostasis and pathophysiology and on developing virus-prompted precision therapies.
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Affiliation(s)
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Græcia” University Hospital of Catanzaro, 88100 Catanzaro, Italy
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15
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. MICROBIOME 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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16
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Parizadeh M, Arrieta MC. The global human gut microbiome: genes, lifestyles, and diet. Trends Mol Med 2023; 29:789-801. [PMID: 37516570 DOI: 10.1016/j.molmed.2023.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.
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Affiliation(s)
- Mona Parizadeh
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada.
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17
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Kirchberger PC, Ochman H. Microviruses: A World Beyond phiX174. Annu Rev Virol 2023; 10:99-118. [PMID: 37774127 DOI: 10.1146/annurev-virology-100120-011239] [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] [Indexed: 10/01/2023]
Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
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Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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18
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Abstract
The gut microbiome is a dense and metabolically active consortium of microorganisms and viruses located in the lower gastrointestinal tract of the human body. Bacteria and their viruses (phages) are the most abundant members of the gut microbiome. Investigating their biology and the interplay between the two is important if we are to understand their roles in human health and disease. In this review, we summarize recent advances in resolving the taxonomic structure and ecological functions of the complex community of phages in the human gut-the gut phageome. We discuss how age, diet, and geography can all have a significant impact on phageome composition. We note that alterations to the gut phageome have been observed in several diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, and we evaluate whether these phageome changes can directly or indirectly contribute to disease etiology and pathogenesis. We also highlight how lack of standardization in studying the gut phageome has contributed to variation in reported results.
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Affiliation(s)
- Ciara A Tobin
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
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19
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Dikareva E, Matharu D, Lahtinen E, Kolho KL, De Vos WM, Salonen A, Ponsero AJ. An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny. Front Microbiol 2023; 14:1254535. [PMID: 37731926 PMCID: PMC10508911 DOI: 10.3389/fmicb.2023.1254535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Background and aims The acquisition and gradual maturation of gut microbial communities during early childhood is central to an individual's healthy development. Bacteriophages have the potential to shape the gut bacterial communities. However, the complex ecological interactions between phages and their bacterial host are still poorly characterized. In this study, we investigated the abundance and diversity of integrated prophages in infant and adult gut bacteria by detecting integrated prophages in metagenome assembled genomes (MAGs) of commensal bacteria. Methods Our study included 88 infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 323 total samples), and their parents around delivery time (n = 138 total samples). Fecal DNA was extracted and characterized by using shotgun metagenomic sequencing, and a collection of prokaryotic MAGs was generated. The MAG collection was screened for the presence of integrated bacteriophage sequences, allowing their taxonomic and functional characterization. Results A large collection of 6,186 MAGs from infant and adult gut microbiota was obtained and screened for integrated prophages, allowing the identification of 7,165 prophage sequences longer than 10 kb. Strikingly, more than 70% of the near-complete MAGs were identified as lysogens. The prevalence of prophages in MAGs varied across bacterial families, with a lower prevalence observed among Coriobacteriaceae, Eggerthellaceae, Veillonellaceae and Burkholderiaceae, while a very high prevalence of lysogen MAGs were observed in Oscillospiraceae, Enterococcaceae, and Enterobacteriaceae. Interestingly for several bacterial families such as Bifidobacteriaceae and Bacteroidaceae, the prevalence of prophages in MAGs was higher in early infant time point (3 weeks and 3 months) than in later sampling points (6 and 12 months) and in adults. The prophage sequences were clustered into 5,616 species-like vOTUs, 77% of which were novel. Finally, we explored the functional repertoire of the potential auxiliary metabolic genes carried by these prophages, encoding functions involved in carbohydrate metabolism and degradation, amino acid metabolism and carbon metabolism. Conclusion Our study provides an enhanced understanding of the diversity and prevalence of lysogens in infant and adult gut microbiota and suggests a complex interplay between prophages and their bacterial hosts.
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Affiliation(s)
- Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emilia Lahtinen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, Paediatric Research Centre, University of Helsinki and HUS, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Willem M. De Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J. Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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20
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Chao H, Balcazar JL, Wu Y, Cai A, Ye M, Sun M, Hu F. Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil. ENVIRONMENT INTERNATIONAL 2023; 179:108175. [PMID: 37683504 DOI: 10.1016/j.envint.2023.108175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/13/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Organic fertilizer microbiomes play substantial roles in soil ecological functions, including improving soil structure, crop yield, and pollutant dissipation. However, limited information is available about the ecological functions of phages and phage-encoded auxiliary metabolic genes (AMGs) in orga9nic fertilizers. Here we used a combination of metagenomics and phage transplantation trials to investigate the phage profiles and their potential roles in pesticide degradation in four organic fertilizers from different sources. Phage annotation results indicate that the two vermicomposts made from swine (PV) and cattle (CV) dung had more similar phage community structures than the swine (P) and cattle (C) manures. After vermicomposting, the organic fertilizers (PV and CV) exhibited enriched phage-host pairings and phage AMG diversity in relative to the two organic fertilizers (P and C) without composting. In addition, the number of broad-host-range phages in the vermicomposts (182) was higher than that in swine (153) and cattle (103) manures. Notably, phage AMGs associated with metabolism and pesticide biodegradation were detected across the four organic fertilizers. The phage transplantation demonstrated that vermicompost phages were most effective at facilitating the degradation of pesticide precursor p-nitrochlorobenzene (p-NCB) in soil, as compared to swine and cattle manures (P < 0.05). Taken together, our findings highlight the significance of phages in vermicompost for biogeochemical cycling and biodegradation of pesticide-associated chemicals in contaminated soils.
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Affiliation(s)
- Huizhen Chao
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China
| | - Jose Luis Balcazar
- Catalan Institute for Water Research (ICRA), Girona 17003, Spain; University of Girona, Girona 17004, Spain
| | - Yunling Wu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China
| | - Anjuan Cai
- Jiangsu Environmental Engineering Technology Co., Ltd., 210019, China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mingming Sun
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China.
| | - Feng Hu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China
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21
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Nicholas-Haizelden K, Murphy B, Hoptroff M, Horsburgh MJ. Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products. Microorganisms 2023; 11:1899. [PMID: 37630459 PMCID: PMC10456854 DOI: 10.3390/microorganisms11081899] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial or therapeutic applications. The human skin is an ecological niche which harbours a rich and compositional diversity microbiome stemming from the multifactorial interactions between the host and microbiota facilitated by exploitable effector compounds. Advances in the understanding of microbial colonisation mechanisms alongside species and strain interactions have revealed a novel chemical and biological understanding which displays applicative potential. Studies elucidating the organismal interfaces and concomitant understanding of the central processes of skin biology have begun to unravel a potential wealth of molecules which can exploited for their proposed functions. A variety of skin-microbiome-derived compounds display prospective therapeutic applications, ranging from antioncogenic agents relevant in skin cancer therapy to treatment strategies for antimicrobial-resistant bacterial and fungal infections. Considerable opportunities have emerged for the translation to personal care products, such as topical agents to mitigate various skin conditions such as acne and eczema. Adjacent compound developments have focused on cosmetic applications such as reducing skin ageing and its associated changes to skin properties and the microbiome. The skin microbiome contains a wealth of prospective compounds with therapeutic and commercial applications; however, considerable work is required for the translation of in vitro findings to relevant in vivo models to ensure translatability.
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Affiliation(s)
- Keir Nicholas-Haizelden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
| | - Barry Murphy
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Malcolm J. Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
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22
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Abbasi A, Bazzaz S, Da Cruz AG, Khorshidian N, Saadat YR, Sabahi S, Ozma MA, Lahouty M, Aslani R, Mortazavian AM. A Critical Review on Akkermansia muciniphila: Functional Mechanisms, Technological Challenges, and Safety Issues. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10118-x. [PMID: 37432597 DOI: 10.1007/s12602-023-10118-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Due to its physiological benefits from in vitro and in vivo points of view, Akkermansia muciniphila, a common colonizer in the human gut mucous layer, has consistently been identified as an option for the next-generation probiotic. A. muciniphila is a significant bacterium that promotes host physiology. However, it also has a great deal of potential to become a probiotic due to its physiological advantages in a variety of therapeutic circumstances. Therefore, it can be established that the abundance of A. muciniphila in the gut environment, which is controlled by many genetic and dietary variables, is related to the biological behaviors of the intestinal microbiota and gut dysbiosis/eubiosis circumstances. Before A. muciniphila is widely utilized as a next-generation probiotic, regulatory obstacles, the necessity for significant clinical trials, and the sustainability of manufacturing must be eliminated. In this review, the outcomes of recent experimental and clinical reports are comprehensively reviewed, and common colonization patterns, main factors involved in the colonization of A. muciniphila in the gut milieu, their functional mechanisms in establishing homeostasis in the metabolic and energy pathways, the promising delivery role of microencapsulation, potential genetic engineering strategies, and eventually safety issues of A. muciniphila have been discussed.
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Affiliation(s)
- Amin Abbasi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Bazzaz
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adriano G Da Cruz
- Department of Food Processing, Federal Institute of Science and Technology Education of Rio de Janeiro (IFRJ) - Campus Maracanã, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nasim Khorshidian
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Sahar Sabahi
- Department of Nutrition, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahdi Asghari Ozma
- Department of Medical Bacteriology and Virology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Lahouty
- Department of Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ramin Aslani
- Food Safety and Hygiene Division, Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir M Mortazavian
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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23
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Zhang Y, Wang R. The human gut phageome: composition, development, and alterations in disease. Front Microbiol 2023; 14:1213625. [PMID: 37476672 PMCID: PMC10354272 DOI: 10.3389/fmicb.2023.1213625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The human gastrointestinal tract is colonized by a large number of microorganisms, including bacteria, archaea, viruses, and eukaryotes. The bacterial community has been widely confirmed to have a significant impact on human health, while viruses, particularly phages, have received less attention. Phages are viruses that specifically infect bacteria. They are abundant in the biosphere and exist in a symbiotic relationship with their host bacteria. Although the application of high-throughput sequencing and bioinformatics technology has greatly improved our understanding of the genomic diversity, taxonomic composition, and spatio-temporal dynamics of the human gut phageome, there is still a large portion of sequencing data that is uncharacterized. Preliminary studies have predicted that the phages play a crucial role in driving microbial ecology and evolution. Prior to exploring the function of phages, it is necessary to address the obstacles that hinder establishing a comprehensive sequencing database with sufficient biological properties and understanding the impact of phage-bacteria interactions on human health. In this study, we provide an overview of the human gut phageome, including its composition, structure, and development. We also explore the various factors that may influence the phageome based on current research, including age, diet, ethnicity, and geographical location. Additionally, we summarize the relationship between the phageome and human diseases, such as IBD, IBS, obesity, diabetes, and metabolic syndrome.
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24
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Kazakova P, Abasolo N, de Cripan SM, Marquès E, Cereto-Massagué A, Garcia L, Canela N, Tormo R, Torrell H. Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples. Int J Mol Sci 2023; 24:ijms24098069. [PMID: 37175775 PMCID: PMC10179101 DOI: 10.3390/ijms24098069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.
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Affiliation(s)
- Polina Kazakova
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Nerea Abasolo
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Sara Martinez de Cripan
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | | | - Adrià Cereto-Massagué
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Lorena Garcia
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Ramón Tormo
- ESPGHAN, European Society for Paediatric Gastroenterology, Hepatology and Nutrition, 1201 Geneva, Switzerland
- Gastroenterology and Nutrition Pediatric Center, 08006 Barcelona, Spain
| | - Helena Torrell
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
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25
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Ladeira R, Tap J, Derrien M. Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy. MICROBIOME RESEARCH REPORTS 2023; 2:9. [PMID: 38047280 PMCID: PMC10688807 DOI: 10.20517/mrr.2023.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 12/05/2023]
Abstract
Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.
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Affiliation(s)
- Ruben Ladeira
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
| | - Julien Tap
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas 78350, France
| | - Muriel Derrien
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
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26
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Nagata N, Takeuchi T, Masuoka H, Aoki R, Ishikane M, Iwamoto N, Sugiyama M, Suda W, Nakanishi Y, Terada-Hirashima J, Kimura M, Nishijima T, Inooka H, Miyoshi-Akiyama T, Kojima Y, Shimokawa C, Hisaeda H, Zhang F, Yeoh YK, Ng SC, Uemura N, Itoi T, Mizokami M, Kawai T, Sugiyama H, Ohmagari N, Ohno H. Human Gut Microbiota and Its Metabolites Impact Immune Responses in COVID-19 and Its Complications. Gastroenterology 2023; 164:272-288. [PMID: 36155191 PMCID: PMC9499989 DOI: 10.1053/j.gastro.2022.09.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS We investigate interrelationships between gut microbes, metabolites, and cytokines that characterize COVID-19 and its complications, and we validate the results with follow-up, the Japanese 4D (Disease, Drug, Diet, Daily Life) microbiome cohort, and non-Japanese data sets. METHODS We performed shotgun metagenomic sequencing and metabolomics on stools and cytokine measurements on plasma from 112 hospitalized patients with SARS-CoV-2 infection and 112 non-COVID-19 control individuals matched by important confounders. RESULTS Multiple correlations were found between COVID-19-related microbes (eg, oral microbes and short-chain fatty acid producers) and gut metabolites (eg, branched-chain and aromatic amino acids, short-chain fatty acids, carbohydrates, neurotransmitters, and vitamin B6). Both were also linked to inflammatory cytokine dynamics (eg, interferon γ, interferon λ3, interleukin 6, CXCL-9, and CXCL-10). Such interrelationships were detected highly in severe disease and pneumonia; moderately in the high D-dimer level, kidney dysfunction, and liver dysfunction groups; but rarely in the diarrhea group. We confirmed concordances of altered metabolites (eg, branched-chain amino acids, spermidine, putrescine, and vitamin B6) in COVID-19 with their corresponding microbial functional genes. Results in microbial and metabolomic alterations with severe disease from the cross-sectional data set were partly concordant with those from the follow-up data set. Microbial signatures for COVID-19 were distinct from diabetes, inflammatory bowel disease, and proton-pump inhibitors but overlapping for rheumatoid arthritis. Random forest classifier models using microbiomes can highly predict COVID-19 and severe disease. The microbial signatures for COVID-19 showed moderate concordance between Hong Kong and Japan. CONCLUSIONS Multiomics analysis revealed multiple gut microbe-metabolite-cytokine interrelationships in COVID-19 and COVID-19related complications but few in gastrointestinal complications, suggesting microbiota-mediated immune responses distinct between the organ sites. Our results underscore the existence of a gut-lung axis in COVID-19.
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Affiliation(s)
- Naoyoshi Nagata
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan; Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Tadashi Takeuchi
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroaki Masuoka
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ryo Aoki
- Mechanism-based Research Laboratory, Ezaki Glico Co, Ltd, Osaka, Japan
| | - Masahiro Ishikane
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Noriko Iwamoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Japan,Department of Viral Pathogenesis and Controls, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yumiko Nakanishi
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Junko Terada-Hirashima
- Division of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Moto Kimura
- Department of Clinical Research Strategic Planning Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Hiroshi Inooka
- Mechanism-based Research Laboratory, Ezaki Glico Co, Ltd, Osaka, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yasushi Kojima
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Chikako Shimokawa
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hajime Hisaeda
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fen Zhang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center, Hong Kong, China,Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center, Hong Kong, China,Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Siew C. Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center, Hong Kong, China,Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Naomi Uemura
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan,Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Kohnodai Hospital, Tokyo, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Takashi Kawai
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan
| | - Haruhito Sugiyama
- Division of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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27
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Jansen D, Matthijnssens J. The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance. Viruses 2023; 15:173. [PMID: 36680214 PMCID: PMC9861652 DOI: 10.3390/v15010173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.
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Affiliation(s)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Rega Institute, Department of Microbiology, Immunology and Transplantation, University of Leuven, B-3000 Leuven, Belgium
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28
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Henrot C, Petit M. Signals triggering prophage induction in the gut microbiota. Mol Microbiol 2022; 118:494-502. [PMID: 36164818 PMCID: PMC9827884 DOI: 10.1111/mmi.14983] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/15/2022] [Accepted: 09/18/2022] [Indexed: 01/12/2023]
Abstract
Compared to bacteria of the gut microbiota, bacteriophages are still poorly characterised, and their physiological importance is far less known. Temperate phages are probably a major actor in the gut, as it is estimated that 80% of intestinal bacteria are lysogens, meaning that they are carrying prophages. In addition, prophage induction rates are higher in the gut than in vitro. However, studies on the signals leading to prophage induction have essentially focused on genotoxic agents with poor relevance for this environment. In this review, we sum up recent findings about signals able to trigger prophage induction in the gut. Three categories of signals are at play: those originating from interactions between intestinal microbes, those from the human or animal host physiology and those from external intakes. These recent results highlight the diversity of factors influencing prophage induction in the gut, and start to unveil ways by which microbiota composition may be modulated.
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Affiliation(s)
- Caroline Henrot
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis InstituteJouy‐en‐JosasFrance,Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1Université de LyonLyonFrance
| | - Marie‐Agnès Petit
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
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