1
|
Zhong Q, Liao B, Liu J, Shen W, Wang J, Wei L, Ma Y, Dong PT, Bor B, McLean JS, Chang Y, Shi W, Cen L, Wu M, Liu J, Li Y, He X, Le S. Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence. Proc Natl Acad Sci U S A 2024; 121:e2319790121. [PMID: 38593079 PMCID: PMC11032452 DOI: 10.1073/pnas.2319790121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024] Open
Abstract
Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.
Collapse
Affiliation(s)
- Qiu Zhong
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| | - Binyou Liao
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan610041, China
| | - Jiazhen Liu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| | - Wei Shen
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, the Second Affiliated Hospital of Chongqing Medical University, Chongqing401336, China
| | - Jing Wang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| | - Leilei Wei
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing400038, China
| | - Yansong Ma
- Department of Orthodontics, Capital Medical University, Beijing100050, China
| | - Pu-Ting Dong
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Batbileg Bor
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA02115
| | - Jeffrey S. McLean
- Department of Periodontics, University of Washington, Seattle, WA98119
- Department of Microbiology, University of Washington, Seattle, WA98195
| | - Yunjie Chang
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang310058, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang310058, China
| | - Wenyuan Shi
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Lujia Cen
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Miaomiao Wu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan610041, China
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan610041, China
| | - Xuesong He
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA02115
| | - Shuai Le
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| |
Collapse
|
2
|
Luo S, Ru J, Mirzaei MK, Xue J, Peng X, Ralser A, Mejías-Luque R, Gerhard M, Deng L. Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection. Gut Microbes 2023; 15:2257291. [PMID: 37747149 PMCID: PMC10578192 DOI: 10.1080/19490976.2023.2257291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc+/1638N mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.
Collapse
Affiliation(s)
- Shiqi Luo
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Xue Peng
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Faculty of Biology, Biocenter, Ludwig Maximilian University of Munich, Munich, Germany
| | - Anna Ralser
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Raquel Mejías-Luque
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| |
Collapse
|
3
|
Li T, Zhang Y, Dong K, Kuo CJ, Li C, Zhu YQ, Qin J, Li QT, Chang YF, Guo X, Zhu Y. Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078. mSystems 2020; 5:e00017-20. [PMID: 32371470 DOI: 10.1128/mSystems.00017-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
C. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage, JD032, and analyzed the global transcriptomic changes in the hypervirulent RT078 C. difficile strain, TW11, during phage JD032 infection. We found that bacterial host mRNA was progressively replaced with phage transcripts, three temporal categories of JD032 gene expression, the extensive interplay between phage-bacterium, antiphage-like responses of the host and phage evasion, and decreased expression of sporulation- and virulence-related genes of the host after phage infection. These findings confirmed the complexity of interactions between C. difficile and phages and suggest that phages undergoing a lytic cycle may also cause different phenotypes in hosts, similar to prophages, which may inspire phage therapy for the control of C. difficile. Insights into the interaction between phages and their bacterial hosts are crucial for the development of phage therapy. However, only one study has investigated global gene expression of Clostridioides (formerly Clostridium) difficile carrying prophage, and transcriptional reprogramming during lytic infection has not been studied. Here, we presented the isolation, propagation, and characterization of a newly discovered 35,109-bp phage, JD032, and investigated the global transcriptomes of both JD032 and C. difficile ribotype 078 (RT078) strain TW11 during JD032 infection. Transcriptome sequencing (RNA-seq) revealed the progressive replacement of bacterial host mRNA with phage transcripts. The expressed genes of JD032 were clustered into early, middle, and late temporal categories that were functionally similar. Specifically, a gene (JD032_orf016) involved in the lysis-lysogeny decision was identified as an early expression gene. Only 17.7% (668/3,781) of the host genes were differentially expressed, and more genes were downregulated than upregulated. The expression of genes involved in host macromolecular synthesis (DNA/RNA/proteins) was altered by JD032 at the level of transcription. In particular, the expression of the ropA operon was downregulated. Most noteworthy is that the gene expression of some antiphage systems, including CRISPR-Cas, restriction-modification, and toxin-antitoxin systems, was suppressed by JD032 during infection. In addition, bacterial sporulation, adhesion, and virulence factor genes were significantly downregulated. This study provides the first description of the interaction between anaerobic spore-forming bacteria and phages during lytic infection and highlights new aspects of C. difficile phage-host interactions. IMPORTANCEC. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage, JD032, and analyzed the global transcriptomic changes in the hypervirulent RT078 C. difficile strain, TW11, during phage JD032 infection. We found that bacterial host mRNA was progressively replaced with phage transcripts, three temporal categories of JD032 gene expression, the extensive interplay between phage-bacterium, antiphage-like responses of the host and phage evasion, and decreased expression of sporulation- and virulence-related genes of the host after phage infection. These findings confirmed the complexity of interactions between C. difficile and phages and suggest that phages undergoing a lytic cycle may also cause different phenotypes in hosts, similar to prophages, which may inspire phage therapy for the control of C. difficile.
Collapse
|