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Hu J, Chen J, Nie Y, Zhou C, Hou Q, Yan X. Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs. MICROBIOME 2024; 12:102. [PMID: 38840247 DOI: 10.1186/s40168-024-01818-9] [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: 12/30/2023] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Mammalian intestine harbors a mass of phages that play important roles in maintaining gut microbial ecosystem and host health. Pig has become a common model for biomedical research and provides a large amount of meat for human consumption. However, the knowledge of gut phages in pigs is still limited. RESULTS Here, we investigated the gut phageome in 112 pigs from seven pig breeds using PhaBOX strategy based on the metagenomic data. A total of 174,897 non-redundant gut phage genomes were assembled from 112 metagenomes. A total of 33,487 gut phage genomes were classified and these phages mainly belonged to phage families such as Ackermannviridae, Straboviridae, Peduoviridae, Zierdtviridae, Drexlerviridae, and Herelleviridae. The gut phages in seven pig breeds exhibited distinct communities and the gut phage communities changed with the age of pig. These gut phages were predicted to infect a broad range of 212 genera of prokaryotes, such as Candidatus Hamiltonella, Mycoplasma, Colwellia, and Lactobacillus. The data indicated that broad KEGG and CAZy functions were also enriched in gut phages of pigs. The gut phages also carried the antimicrobial resistance genes (ARGs) and the most abundant antimicrobial resistance genotype was diaminopyrimidine resistance. CONCLUSIONS Our research delineates a landscape for gut phages in seven pig breeds and reveals that gut phages serve as a key reservoir of ARGs in pigs. Video Abstract.
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Affiliation(s)
- Jun Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei, 430070, China
| | - Jianwei Chen
- BGI Research, Qingdao, Shandong, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Yangfan Nie
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | | | - Qiliang Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei, 430070, China
| | - Xianghua Yan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China.
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei, 430070, China.
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Chang THW, Pourtois JD, Haddock N, Furkuawa D, Hong T, Amanatullah D, Burgener E, Bollyky P. Using Genomic Tools to Predict Antimicrobial Resistance and Markers in Clinical Bacterial Samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.595912. [PMID: 38895396 PMCID: PMC11185549 DOI: 10.1101/2024.06.02.595912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Antimicrobial resistance (AMR) poses a critical threat to hospital infections particularly in the context of hospital-acquired infections (HAIs). This study leverages genomic tools to predict AMR and identify resistance markers in clinical bacterial samples associated with HAIs. Using comprehensive genomic and phenotypic analyses, we evaluated the genetic profiles of Pseudomonas aeruginosa and Staphylococcus aureus to uncover resistance mechanisms. Our results demonstrate that genomic tools, such as CARD-RGI and the Solu platform, can accurately identify resistance genes and predict AMR phenotypes in nosocomial pathogens. These findings underscore the potential of integrating genomic approaches into clinical practice to enhance the management of resistant infections in hospital settings and inform the development of novel antimicrobial strategies. Importance This study investigates the impact of prophages on antibiotic resistance in two clinically significant bacteria, Pseudomonas aeruginosa and Staphylococcus aureus. Understanding how prophages influence resistance mechanisms in these pathogens is crucial, as Pseudomonas aeruginosa is known for its role in chronic infections in cystic fibrosis patients, while Staphylococcus aureus, including MRSA strains, is a leading cause of hospital-acquired infections. By exploring the relationship between prophage presence and resistance, this research provides insights that could inform the development of more effective treatment strategies and enhance our ability to combat antibiotic-resistant infections, ultimately improving patient outcomes and public health.
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Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024; 15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [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: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.
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Affiliation(s)
- Carlos Willian Dias Dantas
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - David Tavares Martins
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Oscar Victor Cardenas Alegria
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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4
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Schmid N, Brandt D, Walasek C, Rolland C, Wittmann J, Fischer D, Müsken M, Kalinowski J, Thormann K. An autonomous plasmid as an inovirus phage satellite. Appl Environ Microbiol 2024; 90:e0024624. [PMID: 38597658 PMCID: PMC11107163 DOI: 10.1128/aem.00246-24] [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: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/11/2024] Open
Abstract
Bacterial viruses (phages) are potent agents of lateral gene transfer and thus are important drivers of evolution. A group of mobile genetic elements, referred to as phage satellites, exploits phages to disseminate their own genetic material. Here, we isolated a novel member of the family Inoviridae, Shewanella phage Dolos, along with an autonomously replicating plasmid, pDolos. Dolos causes a chronic infection in its host Shewanella oneidensis by phage production with only minor effects on the host cell proliferation. When present, plasmid pDolos hijacks Dolos functions to be predominantly packaged into phage virions and released into the environment and, thus, acts as a phage satellite. pDolos can disseminate further genetic material encoding, e.g., resistances or fluorophores to host cells sensitive to Dolos infection. Given the rather simple requirements of a plasmid for takeover of an inovirus and the wide distribution of phages of this group, we speculate that similar phage-satellite systems are common among bacteria.IMPORTANCEPhage satellites are mobile genetic elements, which hijack phages to be transferred to other host cells. The vast majority of these phage satellites integrate within the host's chromosome, and they all carry remaining phage genes. Here, we identified a novel phage satellite, pDolos, which uses an inovirus for dissemination. pDolos (i) remains as an autonomously replicating plasmid within its host, (ii) does not carry recognizable phage genes, and (iii) is smaller than any other phage satellites identified so far. Thus, pDolos is the first member of a new class of phage satellites, which resemble natural versions of phagemids.
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Affiliation(s)
- Nicole Schmid
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Claudia Walasek
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Clara Rolland
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Dorian Fischer
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research GmbH, Braunschweig, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
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5
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Li X, Chen T, Ren Q, Lu J, Cao S, Liu C, Li Y. Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172111. [PMID: 38565354 DOI: 10.1016/j.scitotenv.2024.172111] [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: 12/28/2023] [Revised: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.
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Affiliation(s)
- Xiaoting Li
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Tao Chen
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qinghai Ren
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Jianbiao Lu
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Shengliang Cao
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Cheng Liu
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Yubao Li
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China.
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6
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Faith DR, Kinnersley M, Brooks DM, Drecktrah D, Hall LS, Luo E, Santiago-Frangos A, Wachter J, Samuels DS, Secor PR. Characterization and genomic analysis of the Lyme disease spirochete bacteriophage ϕBB-1. PLoS Pathog 2024; 20:e1012122. [PMID: 38558079 PMCID: PMC11008901 DOI: 10.1371/journal.ppat.1012122] [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: 01/17/2024] [Revised: 04/11/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Lyme disease is a tick-borne infection caused by the spirochete Borrelia (Borreliella) burgdorferi. Borrelia species have highly fragmented genomes composed of a linear chromosome and a constellation of linear and circular plasmids some of which are required throughout the enzootic cycle. Included in this plasmid repertoire by almost all Lyme disease spirochetes are the 32-kb circular plasmid cp32 prophages that are capable of lytic replication to produce infectious virions called ϕBB-1. While the B. burgdorferi genome contains evidence of horizontal transfer, the mechanisms of gene transfer between strains remain unclear. While we know that ϕBB-1 transduces cp32 and shuttle vector DNA during in vitro cultivation, the extent of ϕBB-1 DNA transfer is not clear. Herein, we use proteomics and long-read sequencing to further characterize ϕBB-1 virions. Our studies identified the cp32 pac region and revealed that ϕBB-1 packages linear cp32s via a headful mechanism with preferential packaging of plasmids containing the cp32 pac region. Additionally, we find ϕBB-1 packages fragments of the linear chromosome and full-length plasmids including lp54, cp26, and others. Furthermore, sequencing of ϕBB-1 packaged DNA allowed us to resolve the covalently closed hairpin telomeres for the linear B. burgdorferi chromosome and most linear plasmids in strain CA-11.2A. Collectively, our results shed light on the biology of the ubiquitous ϕBB-1 phage and further implicates ϕBB-1 in the generalized transduction of diverse genes and the maintenance of genetic diversity in Lyme disease spirochetes.
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Affiliation(s)
- Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Margie Kinnersley
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Diane M. Brooks
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Eric Luo
- Vaccine and Infectious Disease Organization, Saskatoon, Canada
| | - Andrew Santiago-Frangos
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jenny Wachter
- Vaccine and Infectious Disease Organization, Saskatoon, Canada
| | - D. Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
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7
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Li Z, Guo X, Liu B, Huang T, Liu R, Liu X. Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants. WATER RESEARCH 2024; 253:121289. [PMID: 38341975 DOI: 10.1016/j.watres.2024.121289] [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: 10/24/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.
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Affiliation(s)
- Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Xiaoxiao Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Huang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
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8
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Workman RE, Stoltzfus MJ, Keith NC, Euler CW, Bondy-Denomy J, Modell JW. Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense. Cell Rep 2024; 43:113849. [PMID: 38427560 PMCID: PMC11078563 DOI: 10.1016/j.celrep.2024.113849] [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: 10/11/2023] [Revised: 01/04/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
CRISPR-Cas immune systems provide bacteria with adaptive immunity against bacteriophages, but they are often transcriptionally repressed to mitigate auto-immunity. In some cases, CRISPR-Cas expression increases in response to a phage infection, but the mechanisms of induction are largely unknown, and it is unclear whether induction occurs strongly and quickly enough to benefit the bacterial host. In S. pyogenes, Cas9 is both an immune effector and auto-repressor of CRISPR-Cas expression. Here, we show that phage-encoded anti-CRISPR proteins relieve Cas9 auto-repression and trigger a rapid increase in CRISPR-Cas levels during a single phage infective cycle. As a result, fewer cells succumb to lysis, leading to a striking survival benefit after multiple rounds of infection. CRISPR-Cas induction also reduces lysogeny, thereby limiting a route for horizontal gene transfer. Altogether, we show that Cas9 is not only a CRISPR-Cas effector and repressor but also a phage sensor that can mount an anti-anti-CRISPR transcriptional response.
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Affiliation(s)
- Rachael E Workman
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marie J Stoltzfus
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas C Keith
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chad W Euler
- Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA, USA
| | - Joshua W Modell
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Haudiquet M, Le Bris J, Nucci A, Bonnin RA, Domingo-Calap P, Rocha EPC, Rendueles O. Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency. Nat Commun 2024; 15:2032. [PMID: 38448399 PMCID: PMC10918111 DOI: 10.1038/s41467-024-46147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
- Ecole Doctoral FIRE-Programme Bettencourt, CRI, Paris, France.
| | - Julie Le Bris
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005, Paris, France
| | - Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Université Paris Saclay, CEA, Inserm, Le Kremlin-Bicêtre, Paris, France
- Service de bactériologie, Hôpital Bicêtre, Université Paris Saclay, AP-HP, Le Kremlin-Bicêtre, Paris, France
- Centre National de Référence Associé de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, Paris, France
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, 46980, Paterna, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
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10
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024:S0966-842X(24)00042-8. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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11
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Wan Y, Zhang L, Xu Z, Su Q, Leung TF, Chan D, Wong OWH, Chan S, Chan FKL, Tun HM, Ng SC. Alterations in fecal virome and bacteriome virome interplay in children with autism spectrum disorder. Cell Rep Med 2024; 5:101409. [PMID: 38307030 PMCID: PMC10897546 DOI: 10.1016/j.xcrm.2024.101409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Emerging evidence suggests autism spectrum disorder (ASD) is associated with altered gut bacteria. However, less is known about the gut viral community and its role in shaping microbiota in neurodevelopmental disorders. Herein, we perform a metagenomic analysis of gut-DNA viruses in 60 children with ASD and 64 age- and gender-matched typically developing children to investigate the effect of the gut virome on host bacteria in children with ASD. ASD is associated with altered gut virome composition accompanied by the enrichment of Clostridium phage, Bacillus phage, and Enterobacteria phage. These ASD-enriched phages are largely associated with disrupted viral ecology in ASD. Importantly, changes in the interplay between the gut bacteriome and virome seen in ASD may influence the encoding capacity of microbial pathways for neuroactive metabolite biosynthesis. These findings suggest an impaired bacteriome-virome ecology in ASD, which sheds light on the importance of bacteriophages in pathogenesis and the development of microbial therapeutics in ASD.
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Affiliation(s)
- Yating Wan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Dorothy Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China.
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12
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Zhao P, Zhao W, Zhai X, He Y, Shu W, Qiao G. Biological characterization and genomic analysis of a novel methicillin-resistant Staphylococcus aureus phage, SauPS-28. Microbiol Spectr 2024; 12:e0029523. [PMID: 38193720 PMCID: PMC10846126 DOI: 10.1128/spectrum.00295-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024] Open
Abstract
Staphylococcus aureus, a representative gram-positive bacterium, is a common infectious pathogen widely present in the natural environment. The increasing application of antibiotics is witnessing an increment in the number of clinically resistant strains (such as methicillin-resistant S. aureus [MRSA]), which has posed a great challenge to antimicrobial therapy. In this study, a novel MRSA phage, SauPS-28, was isolated from the lake water of the Guangxi Zhuang Autonomous Region. This phage has an incubation period of approximately 30 min, a lysis period of approximately 40 min, and a burst size of approximately 25 PFU/cell. The isolated phage exhibited good biological stability at a pH range of 6.0-9.0 and temperature range of 4°C-37°C. In addition, the identification of an elongated tail using transmission electron microscopy confirmed that SauPS-28 belongs to the long-tailed phage family. Whole-genome sequencing analysis revealed that SauPS-28 has a 43,286-bp-long genome with 31.03% G + C content. Moreover, SauPS-28 exhibited 95.69% sequence identity with ECel-2020k, while the query coverage was only 66%, which is a newly discovered phage. Whole-genome functional annotation results revealed that SauPS-28 had 68 open reading frames (ORFs). Of these, 30 ORFs are unknown proteins. The results suggest that SauPS-28 could be a lysogenic phage strain. This study thus provides preliminary data to conduct further in-depth analysis of the mechanism of phage-host interaction and provides a reference value for phage therapy.IMPORTANCEIn recent years, drug-resistant bacterial infections have become increasingly serious. As a kind of virus with the ability to infect and lyse drug-resistant bacteria, phage is expected to be a new therapeutic method. In this study, we isolated and purified a new methicillin-resistant Staphylococcus aureus bacteriophage SauPS-28, studied a series of biological characteristics of the bacteriophage, analyzed the genome and structural proteome data of the bacteriophage, and provided reference data for further study of the interaction mechanism between bacteriophage and host bacteria and promoted new antibacterial strategies.
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Affiliation(s)
- Peisong Zhao
- Department of Microbiology, School of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, China
- Department of Medical Laboratory, Handan Central Hospital, Handan, Hebei, China
| | - Wenli Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xin Zhai
- Office of Health Insurance, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yulin He
- Department of Microbiology, School of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, China
| | - Wei Shu
- College of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China
| | - Guanhua Qiao
- Department of Microbiology, School of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, China
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13
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Qiu J, Nie W, Ding H, Dai J, Wei Y, Li D, Zhang Y, Xie J, Tian X, Wu N, Qiu T. PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy. Brief Bioinform 2024; 25:bbae010. [PMID: 38344864 PMCID: PMC10859729 DOI: 10.1093/bib/bbae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/16/2023] [Accepted: 01/05/2024] [Indexed: 02/15/2024] Open
Abstract
Bacteriophages can help the treatment of bacterial infections yet require in-silico models to deal with the great genetic diversity between phages and bacteria. Despite the tolerable prediction performance, the application scope of current approaches is limited to the prediction at the species level, which cannot accurately predict the relationship of phages across strain mutants. This has hindered the development of phage therapeutics based on the prediction of phage-bacteria relationships. In this paper, we present, PB-LKS, to predict the phage-bacteria interaction based on local K-mer strategy with higher performance and wider applicability. The utility of PB-LKS is rigorously validated through (i) large-scale historical screening, (ii) case study at the class level and (iii) in vitro simulation of bacterial antiphage resistance at the strain mutant level. The PB-LKS approach could outperform the current state-of-the-art methods and illustrate potential clinical utility in pre-optimized phage therapy design.
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Affiliation(s)
- Jingxuan Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Wanchun Nie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hao Ding
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Jia Dai
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yiwen Wei
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Dezhi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yuxi Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Junting Xie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xinxin Tian
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
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14
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Faith DR, Kinnersley M, Brooks DM, Drecktrah D, Hall LS, Luo E, Santiago-Frangos A, Wachter J, Samuels DS, Secor PR. Characterization and genomic analysis of the Lyme disease spirochete bacteriophage ϕBB-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574763. [PMID: 38260690 PMCID: PMC10802411 DOI: 10.1101/2024.01.08.574763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Lyme disease is a tick-borne infection caused by the spirochete Borrelia (Borreliella) burgdorferi. Borrelia species have highly fragmented genomes composed of a linear chromosome and a constellation of linear and circular plasmids some of which are required throughout the enzootic cycle. Included in this plasmid repertoire by almost all Lyme disease spirochetes are the 32-kb circular plasmid cp32 prophages that are capable of lytic replication to produce infectious virions called ϕBB-1. While the B. burgdorferi genome contains evidence of horizontal transfer, the mechanisms of gene transfer between strains remain unclear. While we know that ϕBB-1 transduces cp32 and shuttle vector DNA during in vitro cultivation, the extent of ϕBB-1 DNA transfer is not clear. Herein, we use proteomics and long-read sequencing to further characterize ϕBB-1 virions. Our studies identified the cp32 pac region and revealed that ϕBB-1 packages linear cp32s via a headful mechanism with preferentially packaging of plasmids containing the cp32 pac region. Additionally, we find ϕBB-1 packages fragments of the linear chromosome and full-length plasmids including lp54, cp26, and others. Furthermore, sequencing of ϕBB-1 packaged DNA allowed us to resolve the covalently closed hairpin telomeres for the linear B. burgdorferi chromosome and most linear plasmids in strain CA-11.2A. Collectively, our results shed light on the biology of the ubiquitous ϕBB-1 phage and further implicates ϕBB-1 in the generalized transduction of diverse genes and the maintenance of genetic diversity in Lyme disease spirochetes.
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Affiliation(s)
- Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Margie Kinnersley
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Diane M. Brooks
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Eric Luo
- Vaccine and Infectious Disease Organization, Saskatoon, SK, Canada
| | | | - Jenny Wachter
- Vaccine and Infectious Disease Organization, Saskatoon, SK, Canada
| | - D. Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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15
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Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [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] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
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Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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16
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Cissell EC, McCoy SJ. Top-heavy trophic structure within benthic viral dark matter. Environ Microbiol 2023; 25:2303-2320. [PMID: 37381050 DOI: 10.1111/1462-2920.16457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
A better understanding of system-specific viral ecology in diverse environments is needed to predict patterns of virus-host trophic structure in the Anthropocene. This study characterised viral-host trophic structure within coral reef benthic cyanobacterial mats-a globally proliferating cause and consequence of coral reef degradation. We employed deep longitudinal multi-omic sequencing to characterise the viral assemblage (ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host-virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands. We recovered 11,012 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales. Gene-sharing network analyses provided evidence for extensive genomic novelty of mat viruses from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus-host abundance (from DNA) and activity (from RNA) ratios consistently exceeding 1:1, suggesting a top-heavy intra-mat trophic structure with respect to virus-host interactions. Overall, our article contributes a curated database of viral sequences found in Caribbean coral reef benthic cyanobacterial mats (vMAT database) and provides multiple lines of field-based evidence demonstrating that viruses are active members of mat communities, with broader implications for mat functional ecology and demography.
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Affiliation(s)
- Ethan C Cissell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sophie J McCoy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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17
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Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [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: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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18
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Yi Y, Liu S, Hao Y, Sun Q, Lei X, Wang Y, Wang J, Zhang M, Tang S, Tang Q, Zhang Y, Liu X, Wang Y, Xiao X, Jian H. A systematic analysis of marine lysogens and proviruses. Nat Commun 2023; 14:6013. [PMID: 37758717 PMCID: PMC10533544 DOI: 10.1038/s41467-023-41699-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
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Affiliation(s)
- Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinjuan Lei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yecheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingxue Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xipeng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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19
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Weisberg AJ, Chang JH. Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. Annu Rev Microbiol 2023; 77:603-624. [PMID: 37437216 DOI: 10.1146/annurev-micro-032521-022006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
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20
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Yao L, Bao Y, Hu J, Zhang B, Wang Z, Wang X, Guo W, Wang D, Qi J, Tian M, Bao Y, Li H, Wang S. A lytic phage to control multidrug-resistant avian pathogenic Escherichia coli (APEC) infection. Front Cell Infect Microbiol 2023; 13:1253815. [PMID: 37743864 PMCID: PMC10513416 DOI: 10.3389/fcimb.2023.1253815] [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: 07/06/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
The inappropriate use of antibiotics has led to the emergence of multidrug-resistant strains. Bacteriophages (phages) have gained renewed attention as promising alternatives or supplements to antibiotics. In this study, a lytic avian pathogenic Escherichia coli (APEC) phage designated as PEC9 was isolated and purified from chicken farm feces samples. The morphology, genomic information, optimal multiplicity of infection (MOI), one-step growth curve, thermal stability, pH stability, in vitro antibacterial ability and biofilm formation inhibition ability of the phage were determined. Subsequently, the therapeutic effects of the phages were investigated in the mice model. The results showed that PEC9 was a member of the siphovirus-like by electron microscopy observation. Biological characterization revealed that it could lyse two serotypes of E. coli, including O1 (9/20) and O2 (6/20). The optimal multiplicity of infection (MOI) of phage PEC9 was 0.1. Phage PEC9 had a latent period of 20 min and a burst period of 40 min, with an average burst size of 68 plaque-forming units (PFUs)/cell. It maintained good lytic activity at pH 3-11 and 4-50°C and could efficiently inhibit the bacterial planktonic cell growth and biofilm formation, and reduce bacterial counts within the biofilm, when the MOI was 0.01, 0.1, and 1, respectively. Whole-genome sequencing showed that PEC9 was a dsDNA virus with a genome of 44379 bp and GC content of 54.39%. The genome contains 56 putative ORFs and no toxin, virulence, or resistance-related genes were detected. Phylogenetic tree analysis showed that PEC9 is closely related to E. coli phages vB_EcoS_Zar3M, vB_EcoS_PTXU06, SECphi18, ZCEC10, and ZCEC11, but most of these phages exhibit different gene arrangement. The phage PEC9 could successfully protect mice against APEC infection, including improved survival rate, reduced bacterial loads, and organ lesions. To conclude, our results suggest that phage PEC9 may be a promising candidate that can be used as an alternative to antibiotics in the control of APEC infection.
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Affiliation(s)
- Lan Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Yinli Bao
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Fujian, China
| | - Jiangang Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Beibei Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyang Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinyu Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Weiqi Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Di Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jingjing Qi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Mingxing Tian
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yanqing Bao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Haihua Li
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
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21
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Yan M, Pratama AA, Somasundaram S, Li Z, Jiang Y, Sullivan MB, Yu Z. Interrogating the viral dark matter of the rumen ecosystem with a global virome database. Nat Commun 2023; 14:5254. [PMID: 37644066 PMCID: PMC10465536 DOI: 10.1038/s41467-023-41075-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.
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Affiliation(s)
- Ming Yan
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Akbar Adjie Pratama
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Sripoorna Somasundaram
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Matthew B Sullivan
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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22
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Kozlova AP, Saksaganskaia AS, Afonin AM, Muntyan VS, Vladimirova ME, Dzyubenko EA, Roumiantseva ML. A Temperate Sinorhizobium Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis. Viruses 2023; 15:1701. [PMID: 37632043 PMCID: PMC10460002 DOI: 10.3390/v15081701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s-1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place.
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Affiliation(s)
- Alexandra P. Kozlova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia; (A.P.K.); (A.S.S.); (V.S.M.); (M.E.V.)
| | - Alla S. Saksaganskaia
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia; (A.P.K.); (A.S.S.); (V.S.M.); (M.E.V.)
| | - Alexey M. Afonin
- Laboratory of Genetics of Plant-Microbe Interactions, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia;
| | - Victoria S. Muntyan
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia; (A.P.K.); (A.S.S.); (V.S.M.); (M.E.V.)
| | - Maria E. Vladimirova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia; (A.P.K.); (A.S.S.); (V.S.M.); (M.E.V.)
| | - Elena A. Dzyubenko
- N. I. Vavilov Institute of Plant Genetic Resources (VIR), 190031 Saint Petersburg, Russia;
| | - Marina L. Roumiantseva
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia; (A.P.K.); (A.S.S.); (V.S.M.); (M.E.V.)
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23
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Kaiser KG, Delattre V, Frost VJ, Buck GW, Phu JV, Fernandez TG, Pavel IE. Nanosilver: An Old Antibacterial Agent with Great Promise in the Fight against Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1264. [PMID: 37627684 PMCID: PMC10451389 DOI: 10.3390/antibiotics12081264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance in bacteria is a major problem worldwide that costs 55 billion USD annually for extended hospitalization, resource utilization, and additional treatment expenditures in the United States. This review examines the roles and forms of silver (e.g., bulk Ag, silver salts (AgNO3), and colloidal Ag) from antiquity to the present, and its eventual incorporation as silver nanoparticles (AgNPs) in numerous antibacterial consumer products and biomedical applications. The AgNP fabrication methods, physicochemical properties, and antibacterial mechanisms in Gram-positive and Gram-negative bacterial models are covered. The emphasis is on the problematic ESKAPE pathogens and the antibiotic-resistant pathogens of the greatest human health concern according to the World Health Organization. This review delineates the differences between each bacterial model, the role of the physicochemical properties of AgNPs in the interaction with pathogens, and the subsequent damage of AgNPs and Ag+ released by AgNPs on structural cellular components. In closing, the processes of antibiotic resistance attainment and how novel AgNP-antibiotic conjugates may synergistically reduce the growth of antibiotic-resistant pathogens are presented in light of promising examples, where antibiotic efficacy alone is decreased.
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Affiliation(s)
- Kyra G. Kaiser
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Victoire Delattre
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Victoria J. Frost
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Gregory W. Buck
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Julianne V. Phu
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Timea G. Fernandez
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Ioana E. Pavel
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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24
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Chen X, Chi J, Liu Y, Du R, Guo M, Xu W. Synthetic symbiotic bacteria reduces the toxicity of mercury ingested via contaminated food. Food Chem Toxicol 2023:113937. [PMID: 37433354 DOI: 10.1016/j.fct.2023.113937] [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: 05/04/2023] [Revised: 06/22/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Mercury contamination in food poses a significant threat to human health. In this article, we propose a novel approach to solve this problem by enhancing the function of gut microbiota against mercury using a synthetically engineered bacterial strain. An engineered Escherichia coli biosensor MerR with mercury binding function was introduced into the intestines of mice for colonization, whereafter the mice were challenged with oral mercury. Compared with the control mice and mice colonized with unengineered Escherichia coli, the mice with biosensor MerR cells in their gut showed significantly stronger mercury resistance. Furthermore, mercury distribution analysis revealed that biosensor MerR cells promoted the excretion of oral mercury with feces, thereby blocking the entry of mercury into the mice, decreasing the concentration of mercury in the circulatory system and organs, and, thus, attenuating the toxicity of mercury to the liver, kidneys and intestines. Colonization with the biosensor MerR did not result in significant health problems in the mice, nor were genetic circuit mutations or lateral transfers identified during the experiments, thus demonstrating the safety of this approach. This study elucidates the remarkable promise of synthetic biology for modulating gut microbiota function.
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Affiliation(s)
- Xiaolin Chen
- School of Food and Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Jiani Chi
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yanger Liu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Ruoxi Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Mingzhang Guo
- School of Food and Health, Beijing Technology and Business University, Beijing, 100048, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
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25
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Zhang Q, Zhou L, Zhao Y, Gao S, Yang Y, Chen Q, Li W, Qi Q, Dong Q, Lei J, Guo X, Gao Q, Yang Y. Uncovering the virome and its interaction with antibiotic resistome during compost fertilization. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131763. [PMID: 37311294 DOI: 10.1016/j.jhazmat.2023.131763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.
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Affiliation(s)
- Qingxia Zhang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Lei Zhou
- Center for professional training and service, China Association for Science and Technology, China
| | - Yilong Zhao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuhong Gao
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yanjun Yang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qingyun Chen
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Wenhui Li
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qi Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Dong
- Institute of Chemical Defense, Beijing 102205, China
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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26
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Gao R, Ma B, Hu M, Fang L, Chen G, Zhang W, Wang Y, Song X, Li F. Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162289. [PMID: 36804971 DOI: 10.1016/j.scitotenv.2023.162289] [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: 11/02/2022] [Revised: 01/21/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
This work revealed the profile of viral communities in paddy soils with different levels of arsenic (As) contamination during the flooded period. The structure of viral communities differed significantly in highly and moderately As-contaminated soils. The diversity of soil viral communities under high As contamination decreased. Siphoviridae, Podoviridae, Myoviridae, and Microviridae were the dominant viral families in all samples, and the relative abundances of five of the top 20 viral genera were significantly different between highly and moderately As-contaminated groups. Seventeen dissimilatory As(V)-reducing bacteria were predicted to host 161 viral operational taxonomic units (vOTUs), mainly affiliated with the genera of Sulfurospirillum, Deferribacter, Bacillus and Fusibacter. Among them, 28 vOTUs were also associated with Fe(III)-reducing bacteria, which belonged to different species of the genus Shewanella. Procrustes analysis showed that the community structure of soil viruses was strongly correlated with both prokaryotic community structure and geochemical properties. Random forest analyses revealed that the Total-Fe, DCB-Fe and oxalate-Fe were the most significant variables on viral community richness, while the total-As concentration was an important factor on the Shannon index. Furthermore, As resistance genes (ArsC, ArsR and ArsD), As methylation genes (arsM) and As transporter genes (Pst and Pit) were identified among the auxiliary metabolic genes (AMGs) of the virome. This work revealed that the viruses might influence microbial adaptation in response to As-induced stress, and provided a perspective on the potential virus-mediated biogeochemical cycling of As.
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Affiliation(s)
- Ruichuan Gao
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Min Hu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Liping Fang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guanhong Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Wenqiang Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinwei Song
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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27
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Raeisi H, Noori M, Azimirad M, Mohebbi SR, Asadzadeh Aghdaei H, Yadegar A, Zali MR. Emerging applications of phage therapy and fecal virome transplantation for treatment of Clostridioides difficile infection: challenges and perspectives. Gut Pathog 2023; 15:21. [PMID: 37161478 PMCID: PMC10169144 DOI: 10.1186/s13099-023-00550-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023] Open
Abstract
Clostridioides difficile, which causes life-threatening diarrheal disease, is considered an urgent threat to healthcare setting worldwide. The current standards of care solely rely on conventional antibiotic treatment, however, there is a risk of promoting recurrent C. difficile infection (rCDI) because of the emergence of antibiotic-resistant strains. Globally, the alarming spread of antibiotic-resistant strains of C. difficile has resulted in a quest for alternative therapeutics. The use of fecal microbiota transplantation (FMT), which involves direct infusion of fecal suspension from a healthy donor into a diseased recipient, has been approved as a highly efficient therapeutic option for patients with rCDI. Bacteriophages or phages are a group of viruses that can infect and destroy bacterial hosts, and are recognized as the dominant viral component of the human gut microbiome. Accumulating data has demonstrated that phages play a vital role in microbial balance of the human gut microbiome. Recently, phage therapy and fecal virome transplantation (FVT) have been introduced as promising alternatives for the treatment of C. difficile -related infections, in particular drug-resistant CDI. Herein, we review the latest updates on C. difficile- specific phages, and phage-mediated treatments, and highlight the current and future prospects of phage therapy in the management of CDI.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Noori
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Shaalan H, Cattan-Tsaushu E, Li K, Avrani S. Sequencing the genomes of LPP-1, the first isolated cyanophage, and its relative LPP-2 reveal different integration mechanisms in closely related phages. HARMFUL ALGAE 2023; 124:102409. [PMID: 37164560 DOI: 10.1016/j.hal.2023.102409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 05/12/2023]
Abstract
In the early 1960s, the first cyanophage was isolated. The description of this phage, named LPP-1, led to the extensive investigation of various cyanophages and to the study of their interactions with their cyanobacterial hosts towards controlling blooms. Here, the genomes of LPP-1 and its putative relative, LPP-2 were sequenced. Sequencing these genomes revealed that LPP-1 and LPP-2 are members of a group of short-tailed cyanophages, which are distantly related to the T7-like cyanophages. Most of the phages in this group have the ability to lysogenize their hosts. Their ability to switch between lytic and lysogenic infection may explain the formation of cyanobacterial blooms despite the persistence of their phages. This lysogenic capacity of the LPP-1-like phages occurs despite the lack of an obvious integrase gene within their genomes. Interestingly, we show that LPP-2 integrates into the host genome through an integration site in high proximity to a recombination endonuclease that may have integrase activity. Further understanding of cyanobacterial-phage relationships may provide insight into their population dynamics and suggest novel approaches for control of destructive cyanobacterial blooms.
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Affiliation(s)
- Hanaa Shaalan
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eti Cattan-Tsaushu
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | - Ke Li
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | - Sarit Avrani
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel.
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McKerral JC, Papudeshi B, Inglis LK, Roach MJ, Decewicz P, McNair K, Luque A, Dinsdale EA, Edwards RA. The Promise and Pitfalls of Prophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537752. [PMID: 37131798 PMCID: PMC10153245 DOI: 10.1101/2023.04.20.537752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell's energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations.
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Affiliation(s)
- Jody C. McKerral
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Antoni Luque
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
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30
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Verster KI, Cinege G, Lipinszki Z, Magyar LB, Kurucz É, Tarnopol RL, Ábrahám E, Darula Z, Karageorgi M, Tamsil JA, Akalu SM, Andó I, Whiteman NK. Evolution of insect innate immunity through domestication of bacterial toxins. Proc Natl Acad Sci U S A 2023; 120:e2218334120. [PMID: 37036995 PMCID: PMC10120054 DOI: 10.1073/pnas.2218334120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/01/2023] [Indexed: 04/12/2023] Open
Abstract
Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B (cdtB) and apoptosis-inducing protein of 56 kDa (aip56), were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular (cdtB) or fused copies (cdtB::aip56) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo's serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.
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Affiliation(s)
- Kirsten I. Verster
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Gyöngyi Cinege
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Lilla B. Magyar
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
- Doctoral School of Biology, University of Szeged, Szeged6720, Hungary
| | - Éva Kurucz
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Rebecca L. Tarnopol
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
| | - Edit Ábrahám
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Szeged6728, Hungary
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | | | - Josephine A. Tamsil
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Saron M. Akalu
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - István Andó
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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31
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Zhang M, Hao Y, Yi Y, Liu S, Sun Q, Tan X, Tang S, Xiao X, Jian H. Unexplored diversity and ecological functions of transposable phages. THE ISME JOURNAL 2023:10.1038/s41396-023-01414-z. [PMID: 37069234 DOI: 10.1038/s41396-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.
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Affiliation(s)
- Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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32
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Derdouri N, Ginet N, Denis Y, Ansaldi M, Battesti A. The prophage-encoded transcriptional regulator AppY has pleiotropic effects on E. coli physiology. PLoS Genet 2023; 19:e1010672. [PMID: 36930675 PMCID: PMC10057817 DOI: 10.1371/journal.pgen.1010672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/29/2023] [Accepted: 02/18/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial genome diversity is influenced by prophages, which are viral genomes integrated into the bacterial chromosome. Most prophage genes are silent but those that are expressed can provide unexpected properties to their host. Using as a model E. coli K-12 that carries 9 defective prophages in its genome, we aimed at highlighting the impact of genes encoded by prophages on host physiology. We focused our work on AppY, a transcriptional regulator encoded on the DLP12 prophage. By performing RNA-Seq experiments, we showed that AppY production modulates the expression of more than 200 genes. Among them, 11 were identified by ChIP-Seq as direct AppY targets. AppY directly and positively regulates several genes involved in the acid stress response including the master regulator gene gadE but also nhaR and gadY, two genes important for biofilm formation. Moreover, AppY indirectly and negatively impacts bacterial motility by favoring the degradation of FlhDC, the master regulator of the flagella biosynthesis. As a consequence of these regulatory effects, AppY increases acid stress resistance and biofilm formation while also causing a strong defect in motility. Our research shed light on the importance to consider the genetic interactions occurring between prophages and bacteria to fully understand bacterial physiology. It also highlights how a prophage-encoded transcriptional regulator integrates in a complex manner into the host regulatory network and how it benefits its host, allowing it to cope with changing environmental conditions.
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Affiliation(s)
- Naoual Derdouri
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Nicolas Ginet
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Yann Denis
- Aix Marseille Université, Centre National de la Recherche Scientifique, Plateforme Transcriptome, Institut de Microbiologie de la Méditerranée-, Marseille, France
| | - Mireille Ansaldi
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Aurélia Battesti
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
- * E-mail:
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33
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Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage. Appl Environ Microbiol 2023; 89:e0197322. [PMID: 36656039 PMCID: PMC9973029 DOI: 10.1128/aem.01973-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.
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34
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Davies MR, Keller N, Brouwer S, Jespersen MG, Cork AJ, Hayes AJ, Pitt ME, De Oliveira DMP, Harbison-Price N, Bertolla OM, Mediati DG, Curren BF, Taiaroa G, Lacey JA, Smith HV, Fang NX, Coin LJM, Stevens K, Tong SYC, Sanderson-Smith M, Tree JJ, Irwin AD, Grimwood K, Howden BP, Jennison AV, Walker MJ. Detection of Streptococcus pyogenes M1 UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA. Nat Commun 2023; 14:1051. [PMID: 36828918 PMCID: PMC9951164 DOI: 10.1038/s41467-023-36717-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
A new variant of Streptococcus pyogenes serotype M1 (designated 'M1UK') has been reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase in invasive infections, and exhibiting enhanced expression of the superantigen SpeA. The progenitor S. pyogenes 'M1global' and M1UK clones can be differentiated by 27 SNPs and 4 indels, yet the mechanism for speA upregulation is unknown. Here we investigate the previously unappreciated expansion of M1UK in Australia, now isolated from the majority of serious infections caused by serotype M1 S. pyogenes. M1UK sub-lineages circulating in Australia also contain a novel toxin repertoire associated with epidemic scarlet fever causing S. pyogenes in Asia. A single SNP in the 5' transcriptional leader sequence of the transfer-messenger RNA gene ssrA drives enhanced SpeA superantigen expression as a result of ssrA terminator read-through in the M1UK lineage. This represents a previously unappreciated mechanism of toxin expression and urges enhanced international surveillance.
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Affiliation(s)
- Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia M Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bodie F Curren
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen V Smith
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Ning-Xia Fang
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martina Sanderson-Smith
- Illawarra Health and Medical Research Institute and Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia.,Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, QLD, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amy V Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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35
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Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming. mBio 2023; 14:e0300922. [PMID: 36786571 PMCID: PMC10127799 DOI: 10.1128/mbio.03009-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.
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36
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Wang B, Ma B, Stirling E, He Z, Zhang H, Yan Q. Freshwater trophic status mediates microbial community assembly and interdomain network complexity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120690. [PMID: 36403871 DOI: 10.1016/j.envpol.2022.120690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Freshwater microorganisms and their interactions are important drivers of nutrient cycling that are in turn affected by nutrient status, causing shifts in microbial community diversity, composition, and interactions. However, the impact of water trophic status on bacterial-archaeal interdomain interactions remains poorly understood. This study focused on the impact of trophic status, as characterized by trophic state index (TSI), on the interdomain interactions of freshwater microbial communities from 45 ponds in Hangzhou. Our results showed that the mesotrophic wetland bordering on lightly eutrophic (Hemu: TSI of 49; lightly eutrophic is defined as 50 ≤ TSI <60) harbored a much more complex bacterial-archaeal interdomain network, which showed significantly (P < 0.05) higher connectivity than the wetlands with lower (TSI of 38) or higher (TSI of 57) trophic levels. Notably, light eutrophication strengthened the network modules' negative associations with organic carbon through some network hubs, which could trigger carbon loss in wetlands. We also detected a non-linear response of interdomain network complexity to the increasing of nutrients with a turning point of approximately TSI 50. Quantitative estimates of community assembly processes and structural equation modelling analysis indicated that chlorophyll-a, total nitrogen, and total phosphorus could regulate interdomain network complexity (50% of the variation explanation rate) by driving microbial community assembly. This study demonstrates that microbial interdomain network complexity could be used as a bioindicator for ecological changes, which would helpful for improving ecological assessment of the freshwater eutrophication.
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Affiliation(s)
- Binhao Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China; Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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37
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Khan T, Raza S. Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review. Curr Top Med Chem 2023; 23:1640-1663. [PMID: 36725827 DOI: 10.2174/1568026623666230201144522] [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: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
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38
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Leung KY, Wang Q, Zheng X, Zhuang M, Yang Z, Shao S, Achmon Y, Siame BA. Versatile lifestyles of Edwardsiella: Free-living, pathogen, and core bacterium of the aquatic resistome. Virulence 2022; 13:5-18. [PMID: 34969351 PMCID: PMC9794015 DOI: 10.1080/21505594.2021.2006890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Edwardsiella species in aquatic environments exist either as individual planktonic cells or in communal biofilms. These organisms encounter multiple stresses, include changes in salinity, pH, temperature, and nutrients. Pathogenic species such as E. piscicida, can multiply within the fish hosts. Additionally, Edwardsiella species (E. tarda), can carry antibiotic resistance genes (ARGs) on chromosomes and/or plasmids, that can be transmitted to the microbiome via horizontal gene transfer. E. tarda serves as a core in the aquatic resistome. Edwardsiela uses molecular switches (RpoS and EsrB) to control gene expression for survival in different environments. We speculate that free-living Edwardsiella can transition to host-living and vice versa, using similar molecular switches. Understanding such transitions can help us understand how other similar aquatic bacteria switch from free-living to become pathogens. This knowledge can be used to devise ways to slow down the spread of ARGs and prevent disease outbreaks in aquaculture and clinical settings.
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Affiliation(s)
- Ka Yin Leung
- Biotechnology and Food Engineering Program, Guangdong Technion – Israel Institute of Technology, Shantou, China,Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa, Israel,CONTACT Ka Yin Leung
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China,Shanghai Engineering Research Center of Marine Cultured Animal Vaccines, Shanghai, China,Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Xiaochang Zheng
- Biotechnology and Food Engineering Program, Guangdong Technion – Israel Institute of Technology, Shantou, China
| | - Mei Zhuang
- Biotechnology and Food Engineering Program, Guangdong Technion – Israel Institute of Technology, Shantou, China,Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Zhiyun Yang
- Biotechnology and Food Engineering Program, Guangdong Technion – Israel Institute of Technology, Shantou, China,Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yigal Achmon
- Biotechnology and Food Engineering Program, Guangdong Technion – Israel Institute of Technology, Shantou, China,Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Bupe A. Siame
- Department of Biology, Trinity Western University, Langley, British Columbia, Canada,Bupe A. Siame
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39
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Wang Y, Deng J, Ren J, Liang L, Li J, Niu S, Wu X, Zhao Y, Gao S, Yan F, Liu Y, Ma H, Tian WX, Yan Y. RAP44 phage integrase-guided 50K genomic island integration in Riemerella anatipestifer. Front Vet Sci 2022; 9:961354. [PMID: 36524231 PMCID: PMC9745183 DOI: 10.3389/fvets.2022.961354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 11/08/2022] [Indexed: 07/27/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria. Bacteria and bacteriophages have been fighting for survival. Over time, the evolution of both populations has been affected. Pathogenic Flavobacteriaceae species including Riemerella anatipestifer mainly infects ducklings, geese, and turkeys. However, it does not infect humans, rats, or other mammals, and is a suitable and safe research object in the laboratory. Our previous study showed that there is a 10K genomic island in R. anatipestiferIn this study, we found another integrated 50K genomic islands and focused on the relationship between R. anatipestifer genomic islands and the RAP44 phage genome. The phage RAP44 genome was integrated into R. anatipestifer chromosome, and an evolutionary relationship was evident between them in our comparative analysis. Furthermore, the integrated defective RAP44 phage sequence had the function of integration, excision, and cyclization automatically. Integrases are important integration elements. The integrative function of integrase was verified in R. anatipestifer. The integrase with the attP site can be integrated stably at the attB locus of the R. anatipestifer genome. A recombinant strain can stably inherit and express the exogenous gene. By studying the integration between host bacterium and phage, we have provided evidence for the evolution of the genomes in R. anatipestifer.
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Affiliation(s)
- Ying Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jianfeng Deng
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jianle Ren
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Libin Liang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Junping Li
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Sheng Niu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Xingchen Wu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yujun Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Shimin Gao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Fang Yan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yuqing Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haili Ma
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Wen-xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yi Yan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
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40
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Almeida A. Editorial: Insights in phage biology: 2021. Front Microbiol 2022; 13:1052366. [DOI: 10.3389/fmicb.2022.1052366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
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41
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Pan X, Zhou Z, Liu B, Wu Z. A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases. Front Microbiol 2022; 13:1037389. [DOI: 10.3389/fmicb.2022.1037389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a “reservoir” of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.
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42
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Haudiquet M, de Sousa JM, Touchon M, Rocha EPC. Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210234. [PMID: 35989606 PMCID: PMC9393566 DOI: 10.1098/rstb.2021.0234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Jorge Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Marie Touchon
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
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43
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Nishikawa Y, Kogawa M, Hosokawa M, Wagatsuma R, Mineta K, Takahashi K, Ide K, Yura K, Behzad H, Gojobori T, Takeyama H. Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater. ISME COMMUNICATIONS 2022; 2:92. [PMID: 37938694 PMCID: PMC9723564 DOI: 10.1038/s43705-022-00179-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 04/26/2023]
Abstract
Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1-25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.
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Affiliation(s)
- Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Ryota Wagatsuma
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Katsuhiko Mineta
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kai Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Keigo Ide
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kei Yura
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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Grouzdev D, Gaisin V, Lunina O, Krutkina M, Krasnova E, Voronov D, Baslerov R, Sigalevich P, Savvichev A, Gorlenko V. Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota. FEMS Microbiol Ecol 2022; 98:6693937. [PMID: 36073352 DOI: 10.1093/femsec/fiac103] [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: 05/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022] Open
Abstract
Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.
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Affiliation(s)
- Denis Grouzdev
- SciBear OU, 10115 Tallinn, Estonia.,School of Marine and Atmospheric Sciences, Stony Brook University, 11794, Stony Brook, USA
| | - Vasil Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.,Current affiliation: Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Olga Lunina
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | | | - Elena Krasnova
- Pertsov White Sea Biological Station, 184042, Republic Karelia, Russia
| | - Dmitry Voronov
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia
| | - Roman Baslerov
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Pavel Sigalevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Alexander Savvichev
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Vladimir Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
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45
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Van Cauwenberghe J, Santamaría RI, Bustos P, González V. Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium. Front Microbiol 2022; 13:990394. [PMID: 36177468 PMCID: PMC9512667 DOI: 10.3389/fmicb.2022.990394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/19/2022] [Indexed: 11/27/2022] Open
Abstract
This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3–6 kb genomes in size and GC 59–60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensional models of the major capsid protein (MCP) showed a conserved β-barrel structural “jelly-roll” fold. A variable-length loop in the MCPs distinguished three Rhizobium microvirus groups. Microviridae subfamilies were consistent with viral clusters determined by the protein-sharing network. All viral clusters, except for Bullavirinae, included mostly microviruses identified in metagenomes from distinct ecosystems. Two Rhizobium microvirus clusters, chaparroviruses, and chicoviruses, were included within large viral unknown clusters with microvirus genomes identified in diverse metagenomes. A third Rhizobium microvirus cluster belonged to the subfamily Amoyvirinae. Phylogenetic analysis of the MCP confirms the divergence of the Rhizobium microviruses into separate clades. The phylogeny of the bacterial hosts matches the microvirus MCP phylogeny, suggesting a coevolutionary history between the phages and their bacterial host. This study provided essential biological information on cultivated microvirus for understanding the evolution and ecological diversification of the Microviridae family in diverse microbial ecosystems.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
- Department of Integrative Biology, University of California, Berkeley, CA, United States
- *Correspondence: Jannick Van Cauwenberghe,
| | - Rosa I. Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
- Víctor González,
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46
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Shehreen S, Birkholz N, Fineran P, Brown C. Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Res 2022; 50:8615-8625. [PMID: 35947749 PMCID: PMC9410906 DOI: 10.1093/nar/gkac674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/06/2022] [Accepted: 07/25/2022] [Indexed: 12/24/2022] Open
Abstract
Many bacteria use CRISPR-Cas systems to defend against invasive mobile genetic elements (MGEs). In response, MGEs have developed strategies to resist CRISPR-Cas, including the use of anti-CRISPR (Acr) proteins. Known acr genes may be followed in an operon by a putative regulatory Acr-associated gene (aca), suggesting the importance of regulation. Although ten families of helix-turn-helix (HTH) motif containing Aca proteins have been identified (Aca1-10), only three have been tested and shown to be transcriptional repressors of acr-aca expression. The AcrIIA1 protein (a Cas9 inhibitor) also contains a functionally similar HTH containing repressor domain. Here, we identified and analysed Aca and AcrIIA1 homologs across all bacterial genomes. Using HMM models we found aca-like genes are widely distributed in bacteria, both with and without known acr genes. The putative promoter regions of acr-aca operons were analysed and members of each family of bacterial Aca tested for regulatory function. For each Aca family, we predicted a conserved inverted repeat binding site within a core promoter. Promoters containing these sites directed reporter expression in E. coli and were repressed by the cognate Aca protein. These data demonstrate that acr repression by Aca proteins is widely conserved in nature.
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Affiliation(s)
- Saadlee Shehreen
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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47
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Modin O, Fuad N, Abadikhah M, I'Ons D, Ossiansson E, Gustavsson DJ, Edefell E, Suarez C, Persson F, Wilén BM. A relationship between phages and organic carbon in wastewater treatment plant effluents. WATER RESEARCH X 2022; 16:100146. [PMID: 35761925 PMCID: PMC9233278 DOI: 10.1016/j.wroa.2022.100146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/27/2022] [Accepted: 06/15/2022] [Indexed: 06/10/2023]
Abstract
With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.
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Affiliation(s)
- Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Nafis Fuad
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Department of Civil and Environmental Engineering, University of Connecticut, USA
| | - Marie Abadikhah
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | | | - Elin Ossiansson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- VA SYD, P.O. Box 191, Malmö SE-2021, Sweden
| | - David J.I. Gustavsson
- VA SYD, P.O. Box 191, Malmö SE-2021, Sweden
- Sweden Water Research, c/o Ideon Science Park, Scheelevägen 15, Lund SE-223 70, Sweden
| | - Ellen Edefell
- Sweden Water Research, c/o Ideon Science Park, Scheelevägen 15, Lund SE-223 70, Sweden
- Department of Chemical Engineering, Lund University, PO Box 124, Lund SE-221 00, Sweden
| | - Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Box 118, Lund SE-221 00, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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Ribeiro HG, Nilsson A, Melo LDR, Oliveira A. Analysis of intact prophages in genomes of Paenibacillus larvae: An important pathogen for bees. Front Microbiol 2022; 13:903861. [PMID: 35923395 PMCID: PMC9341999 DOI: 10.3389/fmicb.2022.903861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious and worldwide spread bacterial disease that affects honeybee brood. In this study, all complete P. larvae genomes available on the NCBI database were analyzed in order to detect presence of prophages using the PHASTER software. A total of 55 intact prophages were identified in 11 P. larvae genomes (5.0 ± 2.3 per genome) and were further investigated for the presence of genes encoding relevant traits related to P. larvae. A closer look at the prophage genomes revealed the presence of several putative genes such as metabolic and antimicrobial resistance genes, toxins or bacteriocins, potentially influencing host performance. Some of the coding DNA sequences (CDS) were present in all ERIC-genotypes, while others were only found in a specific genotype. While CDS encoding toxins and antitoxins such as HicB and MazE were found in prophages of all bacterial genotypes, others, from the same category, were provided by prophages particularly to ERIC I (enhancin-like toxin), ERIC II (antitoxin SocA) and ERIC V strains (subunit of Panton-Valentine leukocidin system (PVL) LukF-PV). This is the first in-depth analysis of P. larvae prophages. It provides better knowledge on their impact in the evolution of virulence and fitness of P. larvae, by discovering new features assigned by the viruses.
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Affiliation(s)
- Henrique G. Ribeiro
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Anna Nilsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luís D. R. Melo
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- *Correspondence: Luís D. R. Melo,
| | - Ana Oliveira
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- Ana Oliveira,
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Abstract
Alteromonas is an opportunistic marine bacterium that persists in the global ocean and has important ecological significance. However, current knowledge about the diversity and ecology of alterophages (phages that infect Alteromonas) is lacking. Here, three similar phages infecting Alteromonas macleodii ATCC 27126T were isolated and physiologically characterized. Transmission electron microscopy revealed Siphoviridae morphology, with an oblate icosahedral head and a long noncontractile tail. Notably, these members displayed a small burst size (15–19 plaque-forming units/cell) yet an extensively broad host spectrum when tested on 175 Alteromonas strains. Such unique infection kinetics are potentially associated with discrepancies in codon usage bias from the host tRNA inventory. Phylogenetic analysis indicated that the three phages are closely evolutionarily related; they clustered at the species level and represent a novel genus. Three auxiliary metabolic genes with roles in nucleotide metabolism and putative biofilm dispersal were found in these phage genomes, which revealed important biogeochemical significance of these alterophages in marine ecosystems. Our isolation and characterization of these novel phages expand the current understanding of alterophage diversity, evolution, and phage–host interactions. IMPORTANCE The marine bacterium Alteromonas is prevalent in the global ocean with crucial ecological significance; however, little is known about the diversity and evolution of its bacteriophages that profoundly affect the bacterial communities. Our study characterized a novel genus of three newly isolated Alteromonas phages that exhibited a distinct infection strategy of broad host spectrum and small burst size. This strategy is likely a consequence of the viral trade-off between virulence and lysis profiles during phage–host coevolution, and our work provides new insight into viral evolution and infection strategies.
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50
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Mutuku C, Gazdag Z, Melegh S. Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches. World J Microbiol Biotechnol 2022; 38:152. [PMID: 35781751 PMCID: PMC9250919 DOI: 10.1007/s11274-022-03334-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/10/2022] [Indexed: 12/14/2022]
Abstract
Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.
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Affiliation(s)
- Christopher Mutuku
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Ifjúság u. 6, Pecs, 7624, Hungary.
| | - Zoltan Gazdag
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Ifjúság u. 6, Pecs, 7624, Hungary
| | - Szilvia Melegh
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7622, Pecs, Hungary
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