1
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Edwards KF, Hayward C. The dimensionality of infection networks among viruses infecting microbial eukaryotes and bacteria. Ecol Lett 2024; 27:e14383. [PMID: 38344874 DOI: 10.1111/ele.14383] [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: 09/14/2023] [Revised: 11/15/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024]
Abstract
Diverse viruses and their hosts are interconnected through complex networks of infection, which are thought to influence ecological and evolutionary processes, but the principles underlying infection network structure are not well understood. Here we focus on network dimensionality and how it varies across 37 networks of viruses infecting eukaryotic phytoplankton and bacteria. We find that dimensionality is often strikingly low, with most networks being one- or two-dimensional, although dimensionality increases with network richness, suggesting that the true dimensionality of natural systems is higher. Low-dimensional networks generally exhibit a mixture of host partitioning among viruses and nestededness of host ranges. Networks of bacteria-infecting and eukaryote-infecting viruses possess comparable distributions of dimensionality and prevalence of nestedness, indicating that fundamentals of network structure are similar among domains of life and different viral lineages. The relative simplicity of many infection networks suggests that coevolutionary dynamics are often driven by a modest number of underlying mechanisms.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Colleen Hayward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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2
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Wu M, Zhu Y, Yang Y, Gong Y, Chen Z, Liao B, Xiong Y, Zhou X, Li Y. SVep1, a temperate phage of human oral commensal Streptococcus vestibularis. Front Microbiol 2023; 14:1256669. [PMID: 37779698 PMCID: PMC10536254 DOI: 10.3389/fmicb.2023.1256669] [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: 07/11/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Bacteriophages play a vital role in the human oral microbiome, yet their precise impact on bacterial physiology and microbial communities remains relatively understudied due to the limited isolation and characterization of oral phages. To address this gap, the current study aimed to isolate and characterize novel oral phages. Methods To achieve this, oral bacteria were isolated using a culture-omics method from 30 samples collected from healthy individuals. These bacteria were then cultured in three different types of media under both aerobic and anaerobic conditions. The samples were subsequently subjected to full-length 16S rRNA gene sequencing for analysis. Subsequently, we performed the isolation of lytic and lysogenic phages targeting all these bacteria. Results In the initial step, a total of 75 bacterial strains were successfully isolated, representing 30 species and 9 genera. Among these strains, Streptococcus was found to have the highest number of species. Using a full-length 16S rRNA gene similarity threshold of 98.65%, 14 potential novel bacterial species were identified. In the subsequent phase, a temperate phage, which specifically targets the human oral commensal bacterium S. vestibularis strain SVE8, was isolated. The genome of S. vestibularis SVE8 consists of a 1.96-megabase chromosome, along with a 43,492-base pair prophage designated as SVep1. Annotation of SVep1 revealed the presence of 62 open reading frames (ORFs), with the majority of them associated with phage functions. However, it is worth noting that no plaque formation was observed in S. vestibularis SVE8 following lytic induction using mitomycin C. Phage particles were successfully isolated from the supernatant of mitomycin C-treated cultures of S. vestibularis SVE8, and examination using transmission electron microscopy confirmed that SVep1 is a siphovirus. Notably, phylogenetic analysis suggested a common ancestral origin between phage SVep1 and the cos-type phages found in S. thermophilus. Discussion The presence of SVep1 may confer immunity to S. vestibularis against infection by related phages and holds potential for being engineered as a genetic tool to regulate oral microbiome homeostasis and oral diseases.
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Affiliation(s)
- Miaomiao Wu
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yanpeng Zhu
- Department of Oral and Maxillofacial Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yuhui Yang
- School of Nursing, Army Medical University, Chongqing, China
| | - Yali Gong
- State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University, Chongqing, China
| | - Zongyue Chen
- School of Nursing, Army Medical University, Chongqing, China
| | - Binyou Liao
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yu Xiong
- Department of Oral and Maxillofacial Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xia Zhou
- State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University, Chongqing, China
- Department of Stomatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Yan Li
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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3
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Hosseini N, Paquet VE, Marcoux PÉ, Alain CA, Paquet MF, Moineau S, Charette SJ. MQM1, a bacteriophage infecting strains of Aeromonas salmonicida subspecies salmonicida carrying Prophage 3. Virus Res 2023; 334:199165. [PMID: 37385348 PMCID: PMC10410586 DOI: 10.1016/j.virusres.2023.199165] [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: 04/06/2023] [Revised: 05/30/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
Aeromonas salmonicida subsp. salmonicida is a Gam-negative bacterium responsible for furunculosis in fish. Because this aquatic bacterial pathogen has a rich reservoir of antibiotic-resistant genes, it is essential to investigate antibacterial alternatives, including the use of phages. Yet, we have previously demonstrated the inefficiency of a phage cocktail designed against A. salmonicida subsp. salmonicida strains due to a phage resistance phenotype associated to a prophage, namely Prophage 3. To bypass this resistance, one of the solutions is to isolate novel phages capable of infecting Prophage 3-bearing strains. Here we report on the isolation and characterization of the new virulent phage vB_AsaP_MQM1 (or MQM1), which is highly specific to A. salmonicida subsp. salmonicida strains. Phage MQM1 inhibited the growth of 01-B516, a strain carrying Prophage 3, including when combined to the previous phage cocktail. MQM1 infected 26 out of the 30 (87%) Prophage 3-bearing strains tested. Its linear dsDNA genome contains 63,343 bp, with a GC content of 50.2%. MQM1 genome can encode 88 proteins and 8 tRNAs, while no integrase or transposase-encoding genes were found. This podophage has an icosahedral capsid and a non-contractile short tail. We suggest that MQM1 may be a good addition to future phage cocktails against furunculosis to resolve the Prophage 3-resistance issue.
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Affiliation(s)
- Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada..
| | - Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Pierre-Étienne Marcoux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Charles-Antoine Alain
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Maude F Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada..
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4
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Garrett SC, Philippe C, Kim JG, Wei Y, Johnson KA, Olson S, Graveley BR, Terns MP. Investigation of CRISPR-Independent Phage Resistance Mechanisms Reveals a Role for FtsH in Phage Adsorption to Streptococcus thermophilus. J Bacteriol 2023; 205:e0048222. [PMID: 37255445 PMCID: PMC10294649 DOI: 10.1128/jb.00482-22] [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: 01/06/2023] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
Prokaryotes are under constant pressure from phage infection and thus have evolved multiple means of defense or evasion. While CRISPR-Cas constitutes a robust immune system and appears to be the predominant means of survival for Streptococcus thermophilus when facing lytic phage infection, other forms of phage resistance coexist in this species. Here, we show that S. thermophilus strains with deleted CRISPR-Cas loci can still give rise to phage-resistant clones following lytic phage challenge. Notably, non-CRISPR phage-resistant survivors had multiple mutations which would truncate or recode a membrane-anchored host protease, FtsH. Phage adsorption was dramatically reduced in FtsH mutants, implicating this protein in phage attachment. Phages were isolated which could bypass FtsH-based resistance through mutations predicted to alter tape measure protein translation. Together, these results identify key components in phage propagation that are subject to mutation in the molecular arms race between phage and host cell. IMPORTANCE Streptococcus thermophilus is an important organism for production of cultured dairy foods, but it is susceptible to lytic phages which can lead to failed products. Consequently, mechanisms for phage resistance are an active area of research. One such mechanism is CRISPR-Cas, and S. thermophilus is a model organism for the study of this form of adaptive immunity. Here, we expand on known mechanisms with our finding that spontaneous mutations in ftsH, a gene encoding a membrane-anchored protease, protected against phage infection by disrupting phage adsorption. In turn, mutations in phage tail protein genes allowed phages to overcome ftsH-based resistance. Our results identified components in phage propagation that are subject to mutation in the molecular arms race between phage and host.
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Affiliation(s)
- Sandra C. Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Cecile Philippe
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Jenny G. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Katie A. Johnson
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Michael P. Terns
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
- Department of Genetics, University of Georgia Athens, Athens, Georgia, USA
- Department of Microbiology, University of Georgia Athens, Athens, Georgia, USA
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5
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Elois MA, da Silva R, Pilati GVT, Rodríguez-Lázaro D, Fongaro G. Bacteriophages as Biotechnological Tools. Viruses 2023; 15:349. [PMID: 36851563 PMCID: PMC9963553 DOI: 10.3390/v15020349] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.
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Affiliation(s)
- Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Raphael da Silva
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - David Rodríguez-Lázaro
- Microbiology Division, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain
- Research Centre for Emerging Pathogens and Global Health, University of Burgos, 09001 Burgos, Spain
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
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6
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Costa SP, Nogueira CL, Cunha AP, Lisac A, Carvalho CM. Potential of bacteriophage proteins as recognition molecules for pathogen detection. Crit Rev Biotechnol 2022:1-18. [PMID: 35848817 DOI: 10.1080/07388551.2022.2071671] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bacterial pathogens are leading causes of infections with high mortality worldwide having a great impact on healthcare systems and the food industry. Gold standard methods for bacterial detection mainly rely on culture-based technologies and biochemical tests which are laborious and time-consuming. Regardless of several developments in existing methods, the goal of achieving high sensitivity and specificity, as well as a low detection limit, remains unaccomplished. In past years, various biorecognition elements, such as antibodies, enzymes, aptamers, or nucleic acids, have been widely used, being crucial for the pathogens detection in different complex matrices. However, these molecules are usually associated with high detection limits, demand laborious and costly production, and usually present cross-reactivity. (Bacterio)phage-encoded proteins, especially the receptor binding proteins (RBPs) and cell-wall binding domains (CBDs) of endolysins, are responsible for the phage binding to the bacterial surface receptors in different stages of the phage lytic cycle. Due to their remarkable properties, such as high specificity, sensitivity, stability, and ability to be easily engineered, they are appointed as excellent candidates to replace conventional recognition molecules, thereby contributing to the improvement of the detection methods. Moreover, they offer several possibilities of application in a variety of detection systems, such as magnetic, optical, and electrochemical. Herein we provide a review of phage-derived bacterial binding proteins, namely the RBPs and CBDs, with the prospect to be employed as recognition elements for bacteria. Moreover, we summarize and discuss the various existing methods based on these proteins for the detection of nosocomial and foodborne pathogens.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Catarina L Nogueira
- International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Alexandra P Cunha
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Ana Lisac
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Braga, Portugal
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7
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White K, Yu JH, Eraclio G, Dal Bello F, Nauta A, Mahony J, van Sinderen D. Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods. MICROBIOME RESEARCH REPORTS 2022; 1:3. [PMID: 38089066 PMCID: PMC10714293 DOI: 10.20517/mrr.2021.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 02/19/2024]
Abstract
Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Jun-Hyeok Yu
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | | | | | - Arjen Nauta
- FrieslandCampina, Amersfoort 3800 BN, The Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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8
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Hsu CL, Duan Y, Fouts DE, Schnabl B. Intestinal virome and therapeutic potential of bacteriophages in liver disease. J Hepatol 2021; 75:1465-1475. [PMID: 34437908 PMCID: PMC8929164 DOI: 10.1016/j.jhep.2021.08.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022]
Abstract
Humans harbour a large quantity of microbes in the intestinal tract and have evolved symbiotic relationships with many of them. However, several specific bacterial pathobionts are associated with liver disease pathogenesis. Although bacteriophages (phages) and eukaryotic viruses (collectively known as "the virome") outnumber bacteria and fungi in the intestine, little is known about the intestinal virome in patients with liver disease. As natural predators of bacteria, phages can precisely edit the bacterial microbiota. Hence, there is interest in using them to target bacterial pathobionts in several diseases, including those of the liver. Herein, we will summarise changes in the faecal virome associated with fatty liver diseases and cirrhosis, and describe the therapeutic potential of phages and potential challenges to their clinical application.
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Affiliation(s)
- Cynthia L Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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9
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Brussowvirus SW13 requires a cell surface-associated polysaccharide to recognise its Streptococcus thermophilus host. Appl Environ Microbiol 2021; 88:e0172321. [PMID: 34669424 PMCID: PMC8752142 DOI: 10.1128/aem.01723-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Four bacteriophage-insensitive mutants (BIMs) of the dairy starter bacterium Streptococcus thermophilus UCCSt50 were isolated following challenge with Brussowvirus SW13. The BIMs displayed an altered sedimentation phenotype. Whole-genome sequencing and comparative genomic analysis of the BIMs uncovered mutations within a family 2 glycosyltransferase-encoding gene (orf06955UCCSt50) located within the variable region of the cell wall-associated rhamnose-glucose polymer (Rgp) biosynthesis locus (designated the rgp gene cluster here). Complementation of a representative BIM, S. thermophilus B1, with native orf06955UCCSt50 restored phage sensitivity comparable to that of the parent strain. Detailed bioinformatic analysis of the gene product of orf06955UCCSt50 identified it as a functional homolog of the Lactococcus lactispolysaccharide pellicle (PSP) initiator WpsA. Biochemical analysis of cell wall fractions of strains UCCSt50 and B1 determined that mutations within orf06955UCCSt50 result in the loss of the side chain decoration from the Rgp backbone structure. Furthermore, it was demonstrated that the intact Rgp structure incorporating the side chain structure is essential for phage binding through fluorescence labeling studies. Overall, this study confirms that the rgp gene cluster of S. thermophilus encodes the biosynthetic machinery for a cell surface-associated polysaccharide that is essential for binding and subsequent infection by Brussowviruses, thus enhancing our understanding of S. thermophilus phage-host dynamics. IMPORTANCEStreptococcus thermophilus is an important starter culture bacterium in global dairy fermentation processes, where it is used for the production of various cheeses and yogurt. Bacteriophage predation of the species can result in substandard product quality and, in rare cases, complete fermentation collapse. To mitigate these risks, it is necessary to understand the phage-host interaction process, which commences with the recognition of, and adsorption to, specific host-encoded cell surface receptors by bacteriophage(s). As new groups of S. thermophilus phages are being discovered, the importance of underpinning the genomic elements that specify the surface receptor(s) is apparent. Our research identifies a single gene that is critical for the biosynthesis of a saccharidic moiety required for phage adsorption to its S. thermophilus host. The acquired knowledge provides novel insights into phage-host interactions for this economically important starter species.
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10
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Engineered Bacteriophage as a Delivery Vehicle for Antibacterial Protein, SASP. Pharmaceuticals (Basel) 2021; 14:ph14101038. [PMID: 34681262 PMCID: PMC8538823 DOI: 10.3390/ph14101038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
The difficulties in developing novel classes of antibacterials is leading to a resurgence of interest in bacteriophages as therapeutic agents, and in particular engineered phages that can be optimally designed. Here, pre-clinical microbiology assessment is presented of a Staphylococcus aureus phage engineered to deliver a gene encoding an antibacterial small acid soluble spore protein (SASP) and further, rendered non-lytic to give product SASPject PT1.2. PT1.2 has been developed initially for nasal decolonisation of S. aureus, including methicillin-resistant S. aureus. Time-kill curve assays were conducted with PT1.2 against a range of staphylococcal species, and serial passaging experiments were conducted to investigate the potential for resistance to develop. SASPject PT1.2 demonstrates activity against 100% of 225 geographically diverse S. aureus isolates, exquisite specificity for S. aureus, and a rapid speed of kill. The kinetics of S. aureus/PT1.2 interaction is examined together with demonstrating that PT1.2 activity is unaffected by the presence of human serum albumin. SASPject PT1.2 shows a low propensity for resistance to develop with no consistent shift in sensitivity in S. aureus cells passaged for up to 42 days. SASPject PT1.2 shows promise as a novel first-in-class antibacterial agent and demonstrates potential for the SASPject platform.
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11
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Hanemaaijer L, Kelleher P, Neve H, Franz CMAP, de Waal PP, van Peij NNME, van Sinderen D, Mahony J. Biodiversity of Phages Infecting the Dairy Bacterium Streptococcus thermophilus. Microorganisms 2021; 9:microorganisms9091822. [PMID: 34576718 PMCID: PMC8470116 DOI: 10.3390/microorganisms9091822] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus-infecting phages represent a major problem in the dairy fermentation industry, particularly in relation to thermophilic production systems. Consequently, numerous studies have been performed relating to the biodiversity of such phages in global dairy operations. In the current review, we provide an overview of the genetic and morphological diversity of these phages and highlight the source and extent of genetic mosaicism among phages infecting this species through comparative proteome analysis of the replication and morphogenesis modules of representative phages. The phylogeny of selected phage-encoded receptor binding proteins (RBPs) was assessed, indicating that in certain cases RBP-encoding genes have been acquired separately to the morphogenesis modules, thus highlighting the adaptability of these phages. This review further highlights the significant advances that have been made in defining emergent genetically diverse groups of these phages, while it additionally summarizes remaining knowledge gaps in this research area.
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Affiliation(s)
| | - Philip Kelleher
- School of Microbiology and APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Centre of Nutrition and Food, 24103 Kiel, Germany; (H.N.); (C.M.A.P.F.)
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Centre of Nutrition and Food, 24103 Kiel, Germany; (H.N.); (C.M.A.P.F.)
| | | | | | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
- Correspondence: (D.v.S.); (J.M.); Tel.: +353-20-4901365 (D.v.S.); +353-21-4902730 (J.M.)
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
- Correspondence: (D.v.S.); (J.M.); Tel.: +353-20-4901365 (D.v.S.); +353-21-4902730 (J.M.)
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12
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Romero DA, Magill D, Millen A, Horvath P, Fremaux C. Dairy lactococcal and streptococcal phage-host interactions: an industrial perspective in an evolving phage landscape. FEMS Microbiol Rev 2021; 44:909-932. [PMID: 33016324 DOI: 10.1093/femsre/fuaa048] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
Almost a century has elapsed since the discovery of bacteriophages (phages), and 85 years have passed since the emergence of evidence that phages can infect starter cultures, thereby impacting dairy fermentations. Soon afterward, research efforts were undertaken to investigate phage interactions regarding starter strains. Investigations into phage biology and morphology and phage-host relationships have been aimed at mitigating the negative impact phages have on the fermented dairy industry. From the viewpoint of a supplier of dairy starter cultures, this review examines the composition of an industrial phage collection, providing insight into the development of starter strains and cultures and the evolution of phages in the industry. Research advances in the diversity of phages and structural bases for phage-host recognition and an overview of the perpetual arms race between phage virulence and host defense are presented, with a perspective toward the development of improved phage-resistant starter culture systems.
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Affiliation(s)
- Dennis A Romero
- DuPont Nutrition and Biosciences, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Damian Magill
- DuPont Nutrition and Biosciences, CS 10010, Dangé-Saint-Romain 86220, France
| | - Anne Millen
- DuPont Nutrition and Biosciences, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Philippe Horvath
- DuPont Nutrition and Biosciences, CS 10010, Dangé-Saint-Romain 86220, France
| | - Christophe Fremaux
- DuPont Nutrition and Biosciences, CS 10010, Dangé-Saint-Romain 86220, France
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13
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Philippe C, Moineau S. The endless battle between phages and CRISPR-Cas systems in Streptococcus thermophilus. Biochem Cell Biol 2021; 99:397-402. [PMID: 33534660 DOI: 10.1139/bcb-2020-0593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This review describes the contribution of basic research on phage-bacteria interactions to the understanding of CRISPR-Cas systems and their various applications. It focuses on the natural function of CRISPR-Cas systems as adaptive defense mechanisms against mobile genetic elements such as bacteriophage genomes and plasmids. Some of the advances in the characterization of the type II-A CRISPR-Cas system of Streptococcus thermophilus and Streptococcus pyogenes led to the development of the CRISPR-Cas9 genome-editing technology. We mostly discuss the 3 stages of the CRISPR-Cas system in S. thermophilus, namely the adaptation stage, which is unique to this resistance mechanism; the CRISPR RNA biogenesis; and the DNA-cutting activity in the interference stage to protect bacteria against phages. Finally, we look into applications of CRISPR-Cas in microbiology, including overcoming limitations in genome editing.
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Affiliation(s)
- Cécile Philippe
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, QC G1V 0A6, Canada
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14
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Lavelle K, Goulet A, McDonnell B, Spinelli S, van Sinderen D, Mahony J, Cambillau C. Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages. Microb Biotechnol 2020; 13:1765-1779. [PMID: 32525270 PMCID: PMC7533335 DOI: 10.1111/1751-7915.13593] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 Å resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP- or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.
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Affiliation(s)
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | | | - Silvia Spinelli
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | - Douwe van Sinderen
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Jennifer Mahony
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Christian Cambillau
- School of MicrobiologyUniversity College CorkCorkIreland
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
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15
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Evseev PV, Lukianova AA, Shneider MM, Korzhenkov AA, Bugaeva EN, Kabanova AP, Miroshnikov KK, Kulikov EE, Toshchakov SV, Ignatov AN, Miroshnikov KA. Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches. Microorganisms 2020; 8:E1707. [PMID: 33142811 PMCID: PMC7693777 DOI: 10.3390/microorganisms8111707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/25/2023] Open
Abstract
Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | - Anna A. Lukianova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail M. Shneider
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | | | - Eugenia N. Bugaeva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Anastasia P. Kabanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Eugene E. Kulikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Alexander N. Ignatov
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Konstantin A. Miroshnikov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
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16
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Abstract
Antibiotic-resistant bacteria infections pose a threat to public health. Considering the difficulty in developing new antibiotics, it is an urgent need to develop alternative therapies against bacterial pathogens. Bacteriophages (phages) are evaluated as potential substitutes or adjuncts of antibiotics because they are abundant in nature and could specifically lyse bacteria. In this review, we briefly introduce phage therapy and its advantages compared with traditional antibiotic therapy. We also summarize new emerging phage technologies, such as CRISPR-Cas, synthetic phages, etc., and discuss some possible obstacles and potential risks in the application process. We believe that, with the advancement in synthetic biology and delivery technology, phage therapy has broad prospects in the future.
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17
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Characterization and pre-industrial validation of Streptococcus thermophilus strains to be used as starter cultures for Crescenza, an Italian soft cheese. Food Microbiol 2020; 92:103599. [PMID: 32950140 DOI: 10.1016/j.fm.2020.103599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/09/2020] [Accepted: 07/21/2020] [Indexed: 11/23/2022]
Abstract
The aim of this work was to search for new candidate strains to be included in a culture for Crescenza, a rindless soft cheese, today produced mainly at industrial level using selected starter cultures composed of S. thermophilus. Performance testing was applied to 29 pre-selected strains and a scoring approach was developed to identify the most suitable candidates to be employed in Crescenza cheesemaking. Eight S. thermophilus strains fulfilling most of the desired properties (e.g., high phage resistance, fast acidification rate, no growth below 20 °C, NaCl sensibility, no post acidification at 4 °C) were selected. These strains were grouped in pairs to design different starter culture formulations, which were preliminary tested for the production of Crescenza cheeses at laboratory scale. Two couples of binary cultures (designed Phage rotation 1 and Phage rotation 2) were finally designed and used as starters in pilot scale cheesemaking. The combinations, especially those designed in Phage rotation 1, appeared to be suitable for Crescenza production and showed mutual similarity in terms of strain characteristics, technological performance, and cheese quality. The selection method and ranking approach presented in this work may be adapted to other species of LAB showing traits of industrial interest.
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18
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Furfaro LL, Payne MS, Chang BJ. Host range, morphological and genomic characterisation of bacteriophages with activity against clinical Streptococcus agalactiae isolates. PLoS One 2020; 15:e0235002. [PMID: 32574197 PMCID: PMC7310703 DOI: 10.1371/journal.pone.0235002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/06/2020] [Indexed: 01/21/2023] Open
Abstract
Streptococcus agalactiae or Group B Streptococcus (GBS) is a leading cause of sepsis in neonates. As a preventative measure prophylactic antibiotic administration is common in pregnant women colonised with GBS, but antibiotic-resistance and adverse effects on neonatal microbiomes may result. Use of bacteriophages (phages) is one option for targeted therapy. To this end, four phages (LF1 –LF4) were isolated from wastewater. They displayed lytic activity in vitro against S. agalactiae isolates collected from pregnant women and neonates, with 190/246 isolates (77.2%) and 10/10 (100%) isolates susceptible to at least one phage, respectively. Phage genomes ranged from 32,205–44,768 bp and all phages were members of the Siphoviridae family. High nucleotide identity (99.9%) was observed between LF1 and LF4, which were closely related to a putative prophage of S. agalactiae. The genome organisation of LF2 differed, and it showed similarity to a different S. agalactiae prophage, while LF3 was more closely related to a Streptococcus pyogenes phage. Lysogenic gene presence (integrase, repressor and regulatory modules), was suggestive of temperate phages. In a therapeutic context, temperate phages are not ideal candidates, however, the broad host range activity of these phages observed on clinical isolates in vitro is promising for future therapeutic approaches including bioengineered phage or lysin applications.
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Affiliation(s)
- Lucy L. Furfaro
- The School of Medicine, Division of Obstetrics and Gynaecology, The University of Western Australia, Crawley, Australia
- * E-mail:
| | - Matthew S. Payne
- The School of Medicine, Division of Obstetrics and Gynaecology, The University of Western Australia, Crawley, Australia
| | - Barbara J. Chang
- The School of Biomedical Sciences, The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia
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19
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host. Front Microbiol 2020; 11:1241. [PMID: 32582130 PMCID: PMC7296060 DOI: 10.3389/fmicb.2020.01241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023] Open
Abstract
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Jose L. R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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20
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Mougari S, Chelkha N, Sahmi-Bounsiar D, Di Pinto F, Colson P, Abrahao J, La Scola B. A virophage cross-species infection through mutant selection represses giant virus propagation, promoting host cell survival. Commun Biol 2020; 3:248. [PMID: 32439847 PMCID: PMC7242381 DOI: 10.1038/s42003-020-0970-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/15/2020] [Indexed: 01/03/2023] Open
Abstract
Virus adaptation to new hosts is a major cause of infectious disease emergence. This mechanism has been intensively studied in the context of zoonotic virus spillover, due to its impact on global health. However, it remains unclear for virophages, parasites of giant viruses and potential regulators of microbial communities. Here, we present, for the first time to our knowledge, evidence of cross-species infection of a virophage. We demonstrated that challenging the native population of Guarani virophage with two previously unidentified giant viruses, previously nonpermissive to this virophage, allows the selection of a mutant genotype able to infect these giant viruses. We were able to characterize the potential genetic determinant (deletion) carried by the virophage with the expanded-host range. Our study also highlights the relevant biological impact of this host adaptation by demonstrating that coinfection with the mixture containing the mutant virophage abolishes giant virus production and rescues the host cell population from lysis.
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Affiliation(s)
- Said Mougari
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
| | - Nisrine Chelkha
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Dehia Sahmi-Bounsiar
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Fabrizio Di Pinto
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Jonatas Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, postal code 31270-901.
| | - Bernard La Scola
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
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21
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Goulet A, Spinelli S, Mahony J, Cambillau C. Conserved and Diverse Traits of Adhesion Devices from Siphoviridae Recognizing Proteinaceous or Saccharidic Receptors. Viruses 2020; 12:E512. [PMID: 32384698 PMCID: PMC7291167 DOI: 10.3390/v12050512] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 01/30/2023] Open
Abstract
Bacteriophages can play beneficial roles in phage therapy and destruction of food pathogens. Conversely, they play negative roles as they infect bacteria involved in fermentation, resulting in serious industrial losses. Siphoviridae phages possess a long non-contractile tail and use a mechanism of infection whose first step is host recognition and binding. They have evolved adhesion devices at their tails' distal end, tuned to recognize specific proteinaceous or saccharidic receptors on the host's surface that span a large spectrum of shapes. In this review, we aimed to identify common patterns beyond this apparent diversity. To this end, we analyzed siphophage tail tips or baseplates, evaluating their known structures, where available, and uncovering patterns with bioinformatics tools when they were not. It was thereby identified that a triad formed by three proteins in complex, i.e., the tape measure protein (TMP), the distal tail protein (Dit), and the tail-associated lysozyme (Tal), is conserved in all phages. This common scaffold may harbor various functional extensions internally while it also serves as a platform for plug-in ancillary or receptor-binding proteins (RBPs). Finally, a group of siphophage baseplates involved in saccharidic receptor recognition exhibits an activation mechanism reminiscent of that observed in Myoviridae.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland;
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
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22
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McDonnell B, Hanemaaijer L, Bottacini F, Kelleher P, Lavelle K, Sadovskaya I, Vinogradov E, Ver Loren van Themaat E, Kouwen T, Mahony J, van Sinderen D. A cell wall-associated polysaccharide is required for bacteriophage adsorption to the Streptococcus thermophilus cell surface. Mol Microbiol 2020; 114:31-45. [PMID: 32073719 DOI: 10.1111/mmi.14494] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 11/29/2022]
Abstract
Streptococcus thermophilus strain ST64987 was exposed to a member of a recently discovered group of S. thermophilus phages (the 987 phage group), generating phage-insensitive mutants, which were then characterized phenotypically and genomically. Decreased phage adsorption was observed in selected bacteriophage-insensitive mutants, and was partnered with a sedimenting phenotype and increased cell chain length or aggregation. Whole genome sequencing of several bacteriophage-insensitive mutants identified mutations located in a gene cluster presumed to be responsible for cell wall polysaccharide production in this strain. Analysis of cell surface-associated glycans by methylation and NMR spectroscopy revealed a complex branched rhamno-polysaccharide in both ST64987 and phage-insensitive mutant BIM3. In addition, a second cell wall-associated polysaccharide of ST64987, composed of hexasaccharide branched repeating units containing galactose and glucose, was absent in the cell wall of mutant BIM3. Genetic complementation of three phage-resistant mutants was shown to restore the carbohydrate and phage resistance profiles of the wild-type strain, establishing the role of this gene cluster in cell wall polysaccharide production and phage adsorption and, thus, infection.
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Affiliation(s)
- Brian McDonnell
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Francesca Bottacini
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Philip Kelleher
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Katherine Lavelle
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Irina Sadovskaya
- Équipe BPA, Université du Littoral Côte d'Opale, Institut Régional Charles Violette EA 7394, USC Anses-ULCO, Boulogne-sur-Mer, France
| | - Evgeny Vinogradov
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, ON, Canada
| | | | - Thijs Kouwen
- DSM Biotechnology Center, Delft, the Netherlands
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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23
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Identification of Novel Bacteriophages with Therapeutic Potential That Target Enterococcus faecalis. Infect Immun 2019; 87:IAI.00512-19. [PMID: 31451618 PMCID: PMC6803325 DOI: 10.1128/iai.00512-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022] Open
Abstract
The Gram-positive opportunistic pathogen Enterococcus faecalis is frequently responsible for nosocomial infections in humans and represents one of the most common bacteria isolated from recalcitrant endodontic (root canal) infections. E. faecalis is intrinsically resistant to several antibiotics routinely used in clinical settings (such as cephalosporins and aminoglycosides) and can acquire resistance to vancomycin (vancomycin-resistant enterococci). The resistance of E. faecalis to several classes of antibiotics and its capacity to form biofilms cause serious therapeutic problems. Here, we report the isolation of several bacteriophages that target E. faecalis strains isolated from the oral cavity of patients suffering root canal infections. All phages isolated were Siphoviridae with similar tail lengths (200 to 250 nm) and icosahedral heads. The genome sequences of three isolated phages were highly conserved with the exception of predicted tail protein genes that diverge in sequence, potentially reflecting the host range. The properties of the phage with the broadest host range (SHEF2) were further characterized. We show that this phage requires interaction with components of the major and variant region enterococcal polysaccharide antigen to engage in lytic infection. Finally, we explored the therapeutic potential of this phage and show that it can eradicate E. faecalis biofilms formed in vitro on a standard polystyrene surface but also on a cross-sectional tooth slice model of endodontic infection. We also show that SHEF2 cleared a lethal infection of zebrafish when applied in the circulation. We therefore propose that the phage described here could be used to treat a broad range of antibiotic-resistant E. faecalis infections.
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24
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Dunne M, Rupf B, Tala M, Qabrati X, Ernst P, Shen Y, Sumrall E, Heeb L, Plückthun A, Loessner MJ, Kilcher S. Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Rep 2019; 29:1336-1350.e4. [DOI: 10.1016/j.celrep.2019.09.062] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 09/19/2019] [Indexed: 01/08/2023] Open
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25
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Ekroth AKE, Rafaluk-Mohr C, King KC. Host genetic diversity limits parasite success beyond agricultural systems: a meta-analysis. Proc Biol Sci 2019; 286:20191811. [PMID: 31551053 DOI: 10.1098/rspb.2019.1811] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is evidence that human activities are reducing the population genetic diversity of species worldwide. Given the prediction that parasites better exploit genetically homogeneous host populations, many species could be vulnerable to disease outbreaks. While agricultural studies have shown the devastating effects of infectious disease in crop monocultures, the widespread nature of this diversity-disease relationship remains unclear in natural systems. Here, we provide broad support that high population genetic diversity can protect against infectious disease by conducting a meta-analysis of 23 studies, with a total of 67 effect sizes. We found that parasite functional group (micro- or macroparasite) affects the presence of the effect and study setting (field or laboratory-based environment) influences the magnitude. Our study also suggests that host genetic diversity is overall a robust defence against infection regardless of host reproduction, parasite host range, parasite diversity, virulence and the method by which parasite success was recorded. Combined, these results highlight the importance of monitoring declines of host population genetic diversity as shifts in parasite distributions could have devastating effects on at-risk populations in nature.
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Affiliation(s)
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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26
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Labrie SJ, Mosterd C, Loignon S, Dupuis MÈ, Desjardins P, Rousseau GM, Tremblay DM, Romero DA, Horvath P, Fremaux C, Moineau S. A mutation in the methionine aminopeptidase gene provides phage resistance in Streptococcus thermophilus. Sci Rep 2019; 9:13816. [PMID: 31554834 PMCID: PMC6761271 DOI: 10.1038/s41598-019-49975-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/31/2019] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is a lactic acid bacterium widely used by the dairy industry for the manufacture of yogurt and specialty cheeses. It is also a Gram-positive bacterial model to study phage-host interactions. CRISPR-Cas systems are one of the most prevalent phage resistance mechanisms in S. thermophilus. Little information is available about other host factors involved in phage replication in this food-grade streptococcal species. We used the model strain S. thermophilus SMQ-301 and its virulent phage DT1, harboring the anti-CRISPR protein AcrIIA6, to show that a host gene coding for a methionine aminopeptidase (metAP) is necessary for phage DT1 to complete its lytic cycle. A single mutation in metAP provides S. thermophilus SMQ-301 with strong resistance against phage DT1. The mutation impedes a late step of the lytic cycle since phage adsorption, DNA replication, and protein expression were not affected. When the mutated strain was complemented with the wild-type version of the gene, the phage sensitivity phenotype was restored. When this mutation was introduced into other S. thermophilus strains it provided resistance against cos-type (Sfi21dt1virus genus) phages but replication of pac-type (Sfi11virus genus) phages was not affected. The mutation in the gene coding for the MetAP induces amino acid change in a catalytic domain conserved across many bacterial species. Introducing the same mutation in Streptococcus mutans also provided a phage resistance phenotype, suggesting the wide-ranging importance of the host methionine aminopeptidase in phage replication.
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Affiliation(s)
- Simon J Labrie
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,SyntBioLab Inc., 4820-250, rue de la Pascaline, Lévis, G6W 0L9, Canada
| | - Cas Mosterd
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Stéphanie Loignon
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Marie-Ève Dupuis
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Philippe Desjardins
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Denise M Tremblay
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Dennis A Romero
- DuPont Nutrition and Biosciences, 3329 Agriculture Dr, Madison, WI, 53716, USA
| | - Philippe Horvath
- DuPont Nutrition and Biosciences, BP10, Dangé-Saint-Romain, 86220, France
| | - Christophe Fremaux
- DuPont Nutrition and Biosciences, BP10, Dangé-Saint-Romain, 86220, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
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27
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Paquet VE, Vincent AT, Moineau S, Charette SJ. Beyond the A-layer: adsorption of lipopolysaccharides and characterization of bacteriophage-insensitive mutants of Aeromonas salmonicida subsp. salmonicida. Mol Microbiol 2019; 112:667-677. [PMID: 31115938 DOI: 10.1111/mmi.14308] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2019] [Indexed: 12/28/2022]
Abstract
Aeromonas salmonicida subsp. salmonicida is a fish pathogen that causes furunculosis. Antibiotherapy used to treat furunculosis in fish has led to resistance. Virulent phages are increasingly seen as alternatives or complementary treatments against furunculosis in aquaculture environments. For phage therapy to be successful, it is essential to study the natural mechanisms of phage resistance in A. salmonicida subsp. salmonicida. Here, we generated bacteriophage-insensitive mutants (BIMs) of A. salmonicida subsp. salmonicida, using a myophage with broad host range and characterized them. Phage plaques were different depending on whether the A-layer surface array protein was expressed or not. The genome analysis of the BIMs helped to identify mutations in genes involved in the biogenesis of lipopolysaccharides (LPS) and on an uncharacterized gene (ASA_1998). The characterization of the LPS profile and gene complementation assays identified LPS as a phage receptor and confirmed the involvement of the uncharacterized protein ASA_1998 in phage infection. In addition, we confirmed that the presence of an A-layer at the bacterial surface could act as protection against phages. This study brings new elements into our understanding of the phage adsorption to A. salmonicida subsp. salmonicida cells.
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Affiliation(s)
- Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | | | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
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28
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Szymczak P, Rau MH, Monteiro JM, Pinho MG, Filipe SR, Vogensen FK, Zeidan AA, Janzen T. A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages. Sci Rep 2019; 9:7991. [PMID: 31142793 PMCID: PMC6541646 DOI: 10.1038/s41598-019-44481-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Comparative genomics has proven useful in exploring the biodiversity of phages and understanding phage-host interactions. This knowledge is particularly useful for phages infecting Streptococcus thermophilus, as they constitute a constant threat during dairy fermentations. Here, we explore the genetic diversity of S. thermophilus phages to identify genetic determinants with a signature for host specificity, which could be linked to the bacterial receptor genotype. A comparative genomic analysis was performed on 142 S. thermophilus phage genomes, 55 of which were sequenced in this study. Effectively, 94 phages were assigned to the group cos (DT1), 36 to the group pac (O1205), six to the group 5093, and six to the group 987. The core genome-based phylogeny of phages from the two dominating groups and their receptor binding protein (RBP) phylogeny corresponded to the phage host-range. A role of RBP in host recognition was confirmed by constructing a fluorescent derivative of the RBP of phage CHPC951, followed by studying the binding of the protein to the host strain. Furthermore, the RBP phylogeny of the cos group was found to correlate with the host genotype of the exocellular polysaccharide-encoding operon. These findings provide novel insights towards developing strategies to combat phage infections in dairies.
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Affiliation(s)
- Paula Szymczak
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Martin Holm Rau
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark
| | - João M Monteiro
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Mariana G Pinho
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Sérgio Raposo Filipe
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- Laboratory of Bacterial Cell Surfaces and Pathogenesis, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Finn Kvist Vogensen
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Ahmad A Zeidan
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark
| | - Thomas Janzen
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark.
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29
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Watson BNJ, Easingwood RA, Tong B, Wolf M, Salmond GPC, Staals RHJ, Bostina M, Fineran PC. Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spacers. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180090. [PMID: 30905290 PMCID: PMC6452268 DOI: 10.1098/rstb.2018.0090] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against genetic invaders, such as bacteriophages. The systems integrate short sequences from the phage genome into the bacterial CRISPR array. These 'spacers' provide sequence-specific immunity but drive natural selection of evolved phage mutants that escape the CRISPR-Cas defence. Spacer acquisition occurs by either naive or primed adaptation. Naive adaptation typically results in the incorporation of a single spacer. By contrast, priming is a positive feedback loop that often results in acquisition of multiple spacers, which occurs when a pre-existing spacer matches the invading phage. We predicted that single and multiple spacers, representative of naive and primed adaptation, respectively, would cause differing outcomes after phage infection. We investigated the response of two phages, ϕTE and ϕM1, to the Pectobacterium atrosepticum type I-F CRISPR-Cas system and observed that escape from single spacers typically occurred via point mutations. Alternatively, phages escaped multiple spacers through deletions, which can occur in genes encoding structural proteins. Cryo-EM analysis of the ϕTE structure revealed shortened tails in escape mutants with tape measure protein deletions. We conclude that CRISPR-Cas systems can drive phage genetic diversity, altering morphology and fitness, through selective pressures arising from naive and primed acquisition events. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- B. N. J. Watson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - R. A. Easingwood
- Otago Centre for Electron Microscopy, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - B. Tong
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M. Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology, Graduate University, Onna, Okinawa, Japan
| | - G. P. C. Salmond
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - R. H. J. Staals
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 HB Wageningen, The Netherlands
| | - M. Bostina
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Otago Centre for Electron Microscopy, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - P. C. Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
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30
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Engineering of receptor-binding proteins in bacteriophages and phage tail-like bacteriocins. Biochem Soc Trans 2019; 47:449-460. [PMID: 30783013 DOI: 10.1042/bst20180172] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 12/23/2022]
Abstract
Bacteriophages and phage tail-like bacteriocins (PTLBs) rely on receptor-binding proteins (RBPs) located in tail fibers or spikes for an initial and specific interaction with susceptible bacteria. Bacteriophages kill bacteria through a lytic, replicative cycle, whereas PTLBs kill the target through membrane depolarization in a single hit mechanism. Extensive efforts in the engineering of RBPs of both phages and PTLBs have been undertaken to obtain a greater understanding of the structural organization of RBPs. In addition, a major goal of engineering RBPs of phages and PTLBs is the production of antibacterials with a customized spectrum. Swapping of the RBP of phages and PTLBs results in a shift in activity spectrum in accordance with the spectrum of the new RBP. The engineering of strictly virulent phages with new RBPs required significant technical advances in the past decades, whereas the engineering of RBPs of PTLBs relied on the traditional molecular techniques used for the manipulation of bacteria and was thus relatively straightforward. While phages and PTLBs share their potential for specificity tuning, specific features of phages such as their lytic killing mechanism, their self-replicative nature and thus different pharmacokinetics and their potential to co-evolve are clear differentiators compared with PTLBs in terms of their antibacterial use.
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31
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Biodiversity of Streptococcus thermophilus Phages in Global Dairy Fermentations. Viruses 2018; 10:v10100577. [PMID: 30360457 PMCID: PMC6213268 DOI: 10.3390/v10100577] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus strains are among the most widely employed starter cultures in dairy fermentations, second only to those of Lactococcus lactis. The extensive application of this species provides considerable opportunity for the proliferation of its infecting (bacterio)phages. Until recently, dairy streptococcal phages were classified into two groups (cos and pac groups), while more recently, two additional groups have been identified (5093 and 987 groups). This highlights the requirement for consistent monitoring of phage populations in the industry. Here, we report a survey of 35 samples of whey derived from 27 dairy fermentation facilities in ten countries against a panel of S. thermophilus strains. This culminated in the identification of 172 plaque isolates, which were characterized by multiplex PCR, restriction fragment length polymorphism analysis, and host range profiling. Based on this characterisation, 39 distinct isolates representing all four phage groups were selected for genome sequencing. Genetic diversity was observed among the cos isolates and correlations between receptor binding protein phylogeny and host range were also clear within this phage group. The 987 phages isolated within this study shared high levels of sequence similarity, yet displayed reduced levels of similarity to those identified in previous studies, indicating that they are subject to ongoing genetic diversification.
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32
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Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol 2018; 3:1023-1031. [PMID: 30038310 PMCID: PMC6112176 DOI: 10.1038/s41564-018-0210-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/27/2018] [Indexed: 02/08/2023]
Abstract
The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbors a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are significantly altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease establishing a platform for investigating phage involvement in IBD.
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Affiliation(s)
- Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | | | - Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Brian Bushnell
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Brian Hassell
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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33
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Abstract
Phages of Streptococcus thermophilus present a major threat to the production of many fermented dairy products. To date, only a few studies have assessed the biodiversity of S. thermophilus phages in dairy fermentations. In order to develop strategies to limit phage predation in this important industrial environment, it is imperative that such studies are undertaken and that phage-host interactions of this species are better defined. The present study investigated the biodiversity and evolution of phages within an Irish dairy fermentation facility over an 11-year period. This resulted in the isolation of 17 genetically distinct phages, all of which belong to the so-called cos group. The evolution of phages within the factory appears to be influenced by phages from other dairy plants introduced into the factory for whey protein powder production. Modular exchange, primarily within the regions encoding lysogeny and replication functions, was the major observation among the phages isolated between 2006 and 2016. Furthermore, the genotype of the first isolate in 2006 was observed continuously across the following decade, highlighting the ability of these phages to prevail in the factory setting for extended periods of time. The proteins responsible for host recognition were analyzed, and carbohydrate-binding domains (CBDs) were identified in the distal tail (Dit), the baseplate proteins, and the Tail-associated lysin (Tal) variable regions (VR1 and VR2) of many isolates. This supports the notion that S. thermophilus phages recognize a carbohydrate receptor on the cell surface of their host.IMPORTANCE Dairy fermentations are consistently threatened by the presence of bacterial viruses (bacteriophages or phages), which may lead to a reduction in acidification rates or even complete loss of the fermentate. These phages may persist in factories for long periods of time. The objective of the current study was to monitor the progression of phages infecting the dairy bacterium Streptococcus thermophilus over a period of 11 years in an Irish dairy plant so as to understand how these phages evolve. A focused analysis of the genomic region that encodes host recognition functions highlighted that the associated proteins harbor a variety of carbohydrate-binding domains, which corroborates the notion that phages of S. thermophilus recognize carbohydrate receptors at the initial stages of the phage cycle.
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34
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Mahony J, Cambillau C, van Sinderen D. Host recognition by lactic acid bacterial phages. FEMS Microbiol Rev 2018; 41:S16-S26. [PMID: 28830088 DOI: 10.1093/femsre/fux019] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/05/2017] [Indexed: 02/07/2023] Open
Abstract
Bacteriophage infection of lactic acid bacteria (LAB) is one of the most significant causes of inconsistencies in the manufacture of fermented foods, affecting production schedules and organoleptic properties of the final product. Consequently, LAB phages, and particularly those infecting Lactococcus lactis, have been the focus of intensive research efforts. During the past decade, multidisciplinary scientific approaches have uncovered molecular details on the exquisite process of how a lactococcal phage recognises and binds to its host. Such approaches have incorporated genomic/molecular analyses and their partnership with phage structural analysis and host cell wall biochemical studies are discussed in this review, which will also provide our views on future directions of this research field.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.,APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, 13288 Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Marseille, 13288 Marseille, France
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.,APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland
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Fan F, Li X, Pang B, Zhang C, Li Z, Zhang L, Li J, Zhang J, Yan M, Liang W, Kan B. The outer-membrane protein TolC of Vibrio cholerae serves as a second cell-surface receptor for the VP3 phage. J Biol Chem 2017; 293:4000-4013. [PMID: 29259138 DOI: 10.1074/jbc.m117.805689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/14/2017] [Indexed: 12/17/2022] Open
Abstract
Receptor recognition is a key step in the initiation of phage infection. Previously, we found that VP3, the T7 family phage of the Vibrio cholerae serogroup O1 biotype El Tor, can adsorb the core oligosaccharide (OS) of lipopolysaccharides of V. cholerae However, some wildtype strains of V. cholerae possessing the intact OS gene cluster still have VP3 binding but are resistant to VP3 infection. Moreover, an OS gene-deletion mutant still exhibits weak VP3 binding, suggesting multiple factors are possibly involved in VP3 binding to V. cholerae Here, we report that the outer-membrane protein TolC of V. cholerae is involved in the host adsorption of VP3. We observed that TolC directly interacts with the VP3 tail fiber protein gp44 and its C-terminal domains, and we also found that three amino acid residues in the outside loops of TolC, at positions 78, 290, and 291, are critical for binding to gp44. Among the VP3-resistant wildtype V. cholerae strains, frequent amino acid residue mutations were observed in the loops around the sites 78, 290, and 291, which were predicted to be exposed to the cell surface. These findings reveal a co-receptor-binding mechanism for VP3 infection of V. cholerae and that both outer-membrane TolC and OS are necessary for successful VP3 infection of V. cholerae We conclude that mutations on the outside loops of the receptor may confer V. cholerae strains with VP3 phage resistance, enabling these strains to survive in environments containing VP3 or related phages.
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Affiliation(s)
- Fenxia Fan
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Xu Li
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Bo Pang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Cheng Zhang
- the National Institute of Biological Sciences, Beijing 102206, China
| | - Zhe Li
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Lijuan Zhang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Jie Li
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Jingyun Zhang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Meiying Yan
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Weili Liang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206.,the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, and
| | - Biao Kan
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, .,the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, and
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36
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Zolfaghari Emameh R, Purmonen S, Sukura A, Parkkila S. Surveillance and diagnosis of zoonotic foodborne parasites. Food Sci Nutr 2017; 6:3-17. [PMID: 29387356 PMCID: PMC5778216 DOI: 10.1002/fsn3.530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 12/16/2022] Open
Abstract
Foodborne parasites are a source of human parasitic infection. Zoonotic infections of humans arise from a variety of domestic and wild animals, including sheep, goats, cattle, camels, horses, pigs, boars, bears, felines, canids, amphibians, reptiles, poultry, and aquatic animals such as fishes and shrimp. Therefore, the implementation of efficient, accessible, and controllable inspection policies for livestock, fisheries, slaughterhouses, and meat processing and packaging companies is highly recommended. In addition, more attention should be paid to the education of auditors from the quality control (QC) and assurance sectors, livestock breeders, the fishery sector, and meat inspection veterinarians in developing countries with high incidence of zoonotic parasitic infections. Furthermore, both the diagnosis of zoonotic parasitic infections by inexpensive, accessible, and reliable identification methods and the organization of effective control systems with sufficient supervision of product quality are other areas to which more attention should be paid. In this review, we present some examples of successful inspection policies and recent updates on present conventional, serologic, and molecular diagnostic methods for zoonotic foodborne parasites from both human infection and animal‐derived foods.
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Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology Division of Industrial & Environmental Biotechnology National Institute of Genetic Engineering and Biotechnology (NIGEB) Tehran Iran
| | - Sami Purmonen
- Faculty of Medicine and Life Sciences University of Tampere Tampere Finland
| | - Antti Sukura
- Department of Veterinary Biosciences Faculty of Veterinary Medicine University of Helsinki Helsinki Finland
| | - Seppo Parkkila
- Faculty of Medicine and Life Sciences University of Tampere Tampere Finland.,Fimlab Laboratories Ltd and Tampere University Hospital Tampere Finland
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37
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McDonnell B, Mahony J, Hanemaaijer L, Neve H, Noben JP, Lugli GA, Ventura M, Kouwen TR, van Sinderen D. Global Survey and Genome Exploration of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. Front Microbiol 2017; 8:1754. [PMID: 28955321 PMCID: PMC5601072 DOI: 10.3389/fmicb.2017.01754] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/29/2017] [Indexed: 01/31/2023] Open
Abstract
Despite the persistent and costly problem caused by (bacterio)phage predation of Streptococcus thermophilus in dairy plants, DNA sequence information relating to these phages remains limited. Genome sequencing is necessary to better understand the diversity and proliferative strategies of virulent phages. In this report, whole genome sequences of 40 distinct bacteriophages infecting S. thermophilus were analyzed for general characteristics, genomic structure and novel features. The bacteriophage genomes display a high degree of conservation within defined groupings, particularly across the structural modules. Supporting this observation, four novel members of a recently discovered third group of S. thermophilus phages (termed the 5093 group) were found to be conserved relative to both phage 5093 and to each other. Replication modules of S. thermophilus phages generally fall within two main groups, while such phage genomes typically encode one putative transcriptional regulator. Such features are indicative of widespread functional synteny across genetically distinct phage groups. Phage genomes also display nucleotide divergence between groups, and between individual phages of the same group (within replication modules and at the 3′ end of the lysis module)—through various insertions and/or deletions. A previously described multiplex PCR phage detection system was updated to reflect current knowledge on S. thermophilus phages. Furthermore, the structural protein complement as well as the antireceptor (responsible for the initial attachment of the phage to the host cell) of a representative of the 5093 group was defined. Our data more than triples the currently available genomic information on S. thermophilus phages, being of significant value to the dairy industry, where genetic knowledge of lytic phages is crucial for phage detection and monitoring purposes. In particular, the updated PCR detection methodology for S. thermophilus phages is highly useful in monitoring particular phage group(s) present in a given whey sample. Studies of this nature therefore not only provide information on the prevalence and associated threat of known S. thermophilus phages, but may also uncover newly emerging and genomically distinct phages infecting this dairy starter bacterium.
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Affiliation(s)
- Brian McDonnell
- School of Microbiology, College of Science, Engineering and Food Science, University College CorkCork, Ireland
| | - Jennifer Mahony
- School of Microbiology, College of Science, Engineering and Food Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | | | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-InstitutKiel, Germany
| | - Jean-Paul Noben
- Biomedical Research Institute, Hasselt UniversityDiepenbeek, Belgium
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of ParmaParma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of ParmaParma, Italy
| | | | - Douwe van Sinderen
- School of Microbiology, College of Science, Engineering and Food Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
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38
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Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J, Turner C, Turner P, Bentley SD. Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 2017; 6:e26255. [PMID: 28742023 PMCID: PMC5576492 DOI: 10.7554/elife.26255] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/21/2017] [Indexed: 01/04/2023] Open
Abstract
Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.
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Affiliation(s)
- John A Lees
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Nicholas J Croucher
- Department of Infectious Disease EpidemiologySt. Mary’s Campus, Imperial College LondonLondonUnited Kingdom
| | - David Goldblatt
- Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Julian Parkhill
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Stephen D Bentley
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
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Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides bacteriophages: Genomics and cross-species host ranges. Int J Food Microbiol 2017. [PMID: 28651078 DOI: 10.1016/j.ijfoodmicro.2017.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Unveiling virus-host interactions are relevant for understanding the biology and evolution of microbes globally, but in particular, it has also a paramount impact on the manufacture of fermented dairy products. In this study, we aim at characterizing phages infecting the commonly used heterofermentative Leuconostoc spp. on the basis of host range patterns and genome analysis. Host range of six Leuconostoc phages was investigated using three methods (efficiency of plaquing, spot and turbidity tests) against Ln. mesenteroides and Ln. pseudomesenteroides strains. Complete genome sequencing from four out of the six studied Leuconostoc phages were obtained in this work, while the remaining two have been sequenced previously. According to our results, cross-species host specificity was demonstrated, as all phages tested were capable of infecting both Ln. pseudomesenteroides and Ln. mesenteroides strains, although with different efficiency of plaquing (EOP). Phage adsorption rates and ability of low-EOP host strains to propagate phages by crossing the Leuconostoc species' barrier confirm results. At the genome level, phages CHA, CHB, Ln-7, Ln-8 and Ln-9 revealed high similarity with previously characterized phages infecting mostly Ln. mesenteroides strains, while phage LDG was highly similar to phages infecting Ln. pseudomesenteroides. Additionally, correlation between receptor binding protein (RBP) and host range patterns allowed us to unveil a finer clustering of Leuconostoc phages studied into four groups. This is the first report of overlapped phage host ranges between Leuconostoc species.
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40
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YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I. Appl Environ Microbiol 2017; 83:AEM.03186-16. [PMID: 28062463 DOI: 10.1128/aem.03186-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/04/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended -10 element (p L ) and a σ70-like promoter (p R ) were mapped 5' to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5' rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p R , but not p L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.
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41
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Bosi E, Fondi M, Orlandini V, Perrin E, Maida I, de Pascale D, Tutino ML, Parrilli E, Lo Giudice A, Filloux A, Fani R. The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights. BMC Genomics 2017; 18:93. [PMID: 28095778 PMCID: PMC5240218 DOI: 10.1186/s12864-016-3382-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/06/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. RESULTS Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. CONCLUSIONS This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.
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Affiliation(s)
- Emanuele Bosi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy
| | - Valerio Orlandini
- Department of Clinical and Experimental Biomedical Science "Mario Serio", University of Florence, Viale Pieraccini, 6, I-50139, Florence, Italy
| | - Elena Perrin
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy
| | - Isabel Maida
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, I-80131, Naples, Italy
| | - Maria Luisa Tutino
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126, Naples, Italy
| | - Ermenegilda Parrilli
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126, Naples, Italy
| | - Angelina Lo Giudice
- Institute for the Coastal Marine Environment, National Research Council, Spianata San Raineri 86, I-98122, Messina, Italy
- Department of Biological and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, I-98166, Messina, Italy
| | - Alain Filloux
- Department of Life Sciences, Imperial College London, MRC Centre for Molecular Bacteriology and Infection, Flowers Building, 1st floor, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy.
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42
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The Presence of Two Receptor-Binding Proteins Contributes to the Wide Host Range of Staphylococcal Twort-Like Phages. Appl Environ Microbiol 2016; 82:5763-74. [PMID: 27422842 DOI: 10.1128/aem.01385-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/13/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Thanks to their wide host range and virulence, staphylococcal bacteriophages (phages) belonging to the genus Twortlikevirus (staphylococcal Twort-like phages) are regarded as ideal candidates for clinical application for Staphylococcus aureus infections due to the emergence of antibiotic-resistant bacteria of this species. To increase the usability of these phages, it is necessary to understand the mechanism underlying host recognition, especially the receptor-binding proteins (RBPs) that determine host range. In this study, we found that the staphylococcal Twort-like phage ΦSA012 possesses at least two RBPs. Genomic analysis of five mutant phages of ΦSA012 revealed point mutations in orf103, in a region unique to staphylococcal Twort-like phages. Phages harboring mutated ORF103 could not infect S. aureus strains in which wall teichoic acids (WTAs) are glycosylated with α-N-acetylglucosamine (α-GlcNAc). A polyclonal antibody against ORF103 also inhibited infection by ΦSA012 in the presence of α-GlcNAc, suggesting that ORF103 binds to α-GlcNAc. In contrast, a polyclonal antibody against ORF105, a short tail fiber component previously shown to be an RBP, inhibited phage infection irrespective of the presence of α-GlcNAc. Immunoelectron microscopy indicated that ORF103 is a tail fiber component localized at the bottom of the baseplate. From these results, we conclude that ORF103 binds α-GlcNAc in WTAs, whereas ORF105, the primary RBP, is likely to bind the WTA backbone. These findings provide insight into the infection mechanism of staphylococcal Twort-like phages. IMPORTANCE Staphylococcus phages belonging to the genus Twortlikevirus (called staphylococcal Twort-like phages) are considered promising agents for control of Staphylococcus aureus due to their wide host range and highly lytic capabilities. Although staphylococcal Twort-like phages have been studied widely for therapeutic purposes, the host recognition process of staphylococcal Twort-like phages remains unclear. This work provides new findings about the mechanisms of host recognition of the staphylococcal Twort-like phage ΦSA012. The details of the host recognition mechanism of ΦSA012 will allow us to analyze the mechanisms of infection and expand the utility of staphylococcal Twort-like phages for the control of S. aureus.
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Abstract
The human intestine harbors diverse communities of bacteria and bacteriophages. Given the specificity of phages for their bacterial hosts, there is growing interest in using phage therapies to combat the rising incidence of multidrug-resistant bacterial infections. A significant barrier to such therapies is the rapid development of phage-resistant bacteria, highlighting the need to understand how bacteria acquire phage resistance in vivo. Here we identify novel lytic phages in municipal raw sewage that kill Enterococcus faecalis, a Gram-positive opportunistic pathogen that resides in the human intestine. We show that phage infection of E. faecalis requires a predicted integral membrane protein that we have named PIPEF (for phage infection protein from E. faecalis). We find that PIPEF is conserved in E. faecalis and harbors a 160-amino-acid hypervariable region that determines phage tropism for distinct enterococcal strains. Finally, we use a gnotobiotic mouse model of in vivo phage predation to show that the sewage phages temporarily reduce E. faecalis colonization of the intestine but that E. faecalis acquires phage resistance through mutations in PIPEF. Our findings define the molecular basis for an evolutionary arms race between E. faecalis and the lytic phages that prey on them. They also suggest approaches for engineering E. faecalis phages that have altered host specificity and that can subvert phage resistance in the host bacteria. Bacteriophage therapy has received renewed attention as a potential solution to the rise in antibiotic-resistant bacterial infections. However, bacteria can acquire phage resistance, posing a major barrier to phage therapy. To overcome this problem, it is necessary to understand phage resistance mechanisms in bacteria. We have unraveled one such resistance mechanism in Enterococcus faecalis, a Gram-positive natural resident of the human intestine that has acquired antibiotic resistance and can cause opportunistic infections. We have identified a cell wall protein hypervariable region that specifies phage tropism in E. faecalis. Using a gnotobiotic mouse model of in vivo phage predation, we show that E. faecalis acquires phage resistance through mutations in this cell wall protein. Our findings define the molecular basis for lytic phage resistance in E. faecalis. They also suggest opportunities for engineering E. faecalis phages that circumvent the problem of bacterial phage resistance.
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Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. Appl Environ Microbiol 2016; 82:5153-65. [PMID: 27316953 DOI: 10.1128/aem.00835-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/09/2016] [Indexed: 01/18/2023] Open
Abstract
UNLABELLED We present the complete genome sequences of four members of a novel group of phages infecting Streptococcus thermophilus, designated here as the 987 group. Members of this phage group appear to have resulted from genetic exchange events, as evidenced by their "hybrid" genomic architecture, exhibiting DNA sequence relatedness to the morphogenesis modules of certain P335 group Lactococcus lactis phages and to the replication modules of S. thermophilus phages. All four identified members of the 987 phage group were shown to elicit adsorption affinity to both their cognate S. thermophilus hosts and a particular L. lactis starter strain. The receptor binding protein of one of these phages (as a representative of this novel group) was defined using an adsorption inhibition assay. The emergence of a novel phage group infecting S. thermophilus highlights the continuous need for phage monitoring and development of new phage control measures. IMPORTANCE Phage predation of S. thermophilus is an important issue for the dairy industry, where viral contamination can lead to fermentation inefficiency or complete fermentation failure. Genome information and phage-host interaction studies of S. thermophilus phages, particularly those emerging in the marketplace, are an important part of limiting the detrimental impact of these viruses in the dairy environment.
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45
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Li W, Bian X, Evivie SE, Huo GC. Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives. Curr Microbiol 2016; 73:393-400. [PMID: 27378131 DOI: 10.1007/s00284-016-1076-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/26/2016] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.
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Affiliation(s)
- Wan Li
- Key Laboratory of Dairy Science-Ministry of Education (KLDS-MOE), College of Food Sciences, Northeast Agricultural University (NEAU), Harbin, 150030, Heilongjiang Province, China
| | - Xin Bian
- Key Laboratory of Dairy Science-Ministry of Education (KLDS-MOE), College of Food Sciences, Northeast Agricultural University (NEAU), Harbin, 150030, Heilongjiang Province, China
| | - Smith Etareri Evivie
- Key Laboratory of Dairy Science-Ministry of Education (KLDS-MOE), College of Food Sciences, Northeast Agricultural University (NEAU), Harbin, 150030, Heilongjiang Province, China
| | - Gui-Cheng Huo
- Key Laboratory of Dairy Science-Ministry of Education (KLDS-MOE), College of Food Sciences, Northeast Agricultural University (NEAU), Harbin, 150030, Heilongjiang Province, China.
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46
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Li X, Koç C, Kühner P, Stierhof YD, Krismer B, Enright MC, Penadés JR, Wolz C, Stehle T, Cambillau C, Peschel A, Xia G. An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus. Sci Rep 2016; 6:26455. [PMID: 27212064 PMCID: PMC4876445 DOI: 10.1038/srep26455] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/28/2016] [Indexed: 01/26/2023] Open
Abstract
Despite the importance of phages in driving horizontal gene transfer (HGT) among pathogenic bacteria, the underlying molecular mechanisms mediating phage adsorption to S. aureus are still unclear. Phage ϕ11 is a siphovirus with a high transducing efficiency. Here, we show that the tail protein Gp45 localized within the ϕ11 baseplate. Phage ϕ11 was efficiently neutralized by anti-Gp45 serum, and its adsorption to host cells was inhibited by recombinant Gp45 in a dose-dependent manner. Flow cytometry analysis demonstrated that biotin-labelled Gp45 efficiently stained the wild-type S. aureus cell but not the double knockout mutant ΔtarM/S, which lacks both α- and β-O-GlcNAc residues on its wall teichoic acids (WTAs). Additionally, adsorption assays indicate that GlcNAc residues on WTAs and O-acetyl groups at the 6-position of muramic acid residues in peptidoglycan are essential components of the ϕ11 receptor. The elucidation of Gp45-involved molecular interactions not only broadens our understanding of siphovirus-mediated HGT, but also lays the groundwork for the development of sensitive affinity-based diagnostics and therapeutics for S. aureus infection.
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Affiliation(s)
- Xuehua Li
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Cengiz Koç
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076, Tübingen, Germany
| | - Petra Kühner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - York-Dieter Stierhof
- Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Mark C Enright
- School of Healthcare Sciences, Manchester Metropolitan University, Chester Street, Manchester, M1 5GD, United Kingdom
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076, Tübingen, Germany.,Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.,German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 6098, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Guoqing Xia
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Germany.,Institute of Inflammation &Repair, Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
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47
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Lai MJ, Chang KC, Huang SW, Luo CH, Chiou PY, Wu CC, Lin NT. The Tail Associated Protein of Acinetobacter baumannii Phage ΦAB6 Is the Host Specificity Determinant Possessing Exopolysaccharide Depolymerase Activity. PLoS One 2016; 11:e0153361. [PMID: 27077375 PMCID: PMC4831824 DOI: 10.1371/journal.pone.0153361] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/29/2016] [Indexed: 12/31/2022] Open
Abstract
Acinetobacter baumannii is a non-fermenting, gram-negative bacterium. In recent years, the frequency of A. baumannii infections has continued to increase, and multidrug-resistant strains are emerging in hospitalized patients. Therefore, as therapeutic options become limited, the potential of phages as natural antimicrobial agents to control infections is worth reconsidering. In our previous study, we isolated ten virulent double-stranded DNA A. baumannii phages, ϕAB1-9 and ϕAB11, and found that each has a narrow host range. Many reports indicate that receptor-binding protein of phage mediates host recognition; however, understanding of the specific interactions between A. baumannii and phages remains very limited. In this study, host determinants of A. baumannii phages were investigated. Sequence comparison of ϕAB6 and ϕAB1 revealed high degrees of conservation among their genes except the tail fiber protein (ORF41 in ϕAB1 and ORF40 in ϕAB6). Furthermore, we found that ORF40ϕAB6 has polysaccharide depolymerase activity capable of hydrolyzing the A. baumannii exopolysaccharide and is a component of the phage tail apparatus determining host specificity. Thus, the lytic phages and their associated depolymerase not only have potential as alternative therapeutic agents for treating A. baumannii infections but also provide useful and highly specific tools for studying host strain exopolysaccharides and producing glycoconjugate vaccines.
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Affiliation(s)
- Meng-Jiun Lai
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Shiuan-Wen Huang
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Cheng-Hung Luo
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Pei-Yu Chiou
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Chao-Chuan Wu
- Department of Surgery, Buddhist Tzu Chi General Hospital, Taipei, Taiwan
| | - Nien-Tsung Lin
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
- * E-mail:
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48
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Mahony J, McDonnell B, Casey E, van Sinderen D. Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria. Annu Rev Food Sci Technol 2016; 7:267-85. [PMID: 26735798 DOI: 10.1146/annurev-food-041715-033322] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cheese production is a global biotechnological practice that is reliant on robust and technologically appropriate starter and adjunct starter cultures to acidify the milk and impart particular flavor and textural properties to specific cheeses. To this end, lactic acid bacteria, including Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus and Leuconostoc spp., are routinely employed. However, these bacteria are susceptible to infection by (bacterio)phages. Over the past decade in particular, significant advances have been achieved in defining the receptor molecules presented by lactococcal host bacteria and in the structural analysis of corresponding phage-encoded receptor-binding proteins. These lactococcal model systems are expanding toward understanding phage-host interactions of other LAB species. Ultimately, such scientific efforts will uncover the mechanistic (dis)similarities among these phages and define how these phages recognize and infect their hosts. This review presents the current status of the LAB-phage interactome, highlighting the most recent and significant developments in this active research field.
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Affiliation(s)
| | | | | | - Douwe van Sinderen
- School of Microbiology;,APC Microbiome Institute, University College Cork, Western Road, Cork, Ireland;
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49
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Zolfaghari Emameh R, Kuuslahti M, Näreaho A, Sukura A, Parkkila S. Innovative molecular diagnosis of Trichinella species based on β-carbonic anhydrase genomic sequence. Microb Biotechnol 2015; 9:172-9. [PMID: 26639312 PMCID: PMC4767284 DOI: 10.1111/1751-7915.12327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/03/2015] [Accepted: 09/18/2015] [Indexed: 11/30/2022] Open
Abstract
Trichinellosis is a helminthic infection where different species of Trichinella nematodes are the causative agents. Several molecular assays have been designed to aid diagnostics of trichinellosis. These assays are mostly complex and expensive. The genomes of Trichinella species contain certain parasite‐specific genes, which can be detected by polymerase chain reaction (PCR) methods. We selected β‐carbonic anhydrase (β‐CA) gene as a target, because it is present in many parasites genomes but absent in vertebrates. We developed a novel β‐CA gene‐based method for detection of Trichinella larvae in biological samples. We first identified a β‐CA protein sequence from Trichinella spiralis by bioinformatic tools using β‐CAs from Caenorhabditis elegans and Drosophila melanogaster. Thereafter, 16 sets of designed primers were tested to detect β‐CA genomic sequences from three species of Trichinella, including T. spiralis, Trichinella
pseudospiralis and Trichinella
nativa. Among all 16 sets of designed primers, the primer set No. 2 efficiently amplified β‐CA genomic sequences from T. spiralis, T. pseudospiralis and T. nativa without any false‐positive amplicons from other parasite samples including Toxoplasma gondii, Toxocara cati and Parascaris equorum. This robust and straightforward method could be useful for meat inspection in slaughterhouses, quality control by food authorities and medical laboratories.
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Affiliation(s)
- Reza Zolfaghari Emameh
- School of Medicine, University of Tampere, FI-33520, Tampere, Finland.,BioMediTech, University of Tampere, FI-33520, Tampere, Finland.,Fimlab Laboratories Ltd and Tampere University Hospital, Biokatu 4, FI-33520, Tampere, Finland
| | | | - Anu Näreaho
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, FI-00014, Helsinki, Finland
| | - Antti Sukura
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, FI-00014, Helsinki, Finland
| | - Seppo Parkkila
- School of Medicine, University of Tampere, FI-33520, Tampere, Finland.,Fimlab Laboratories Ltd and Tampere University Hospital, Biokatu 4, FI-33520, Tampere, Finland
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50
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Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid. J Virol 2015; 89:10945-58. [PMID: 26311868 PMCID: PMC4621102 DOI: 10.1128/jvi.01353-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/10/2015] [Indexed: 01/21/2023] Open
Abstract
Relatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of the Sinorhizobium meliloti-infecting T4 superfamily phage ΦM9. This phage and its close relative Rhizobium phage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-like S. meliloti phages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble through interactions between one subunit and the adjacent E-loop insertion domain. Though genetically very distant from the cyanophages, the ΦM9 capsid closely resembles that of the T4 superfamily cyanophage Syn9. ΦM9 also has the same T=16 capsid architecture as the very distant phage SPO1 and the herpesviruses. Despite their overall lack of similarity at the genomic and structural levels, ΦM9 and S. meliloti phage ΦM12 have a small number of open reading frames in common that appear to encode structural proteins involved in interaction with the host and which may have been acquired by horizontal transfer. These proteins are predicted to encode tail baseplate proteins, tail fibers, tail fiber assembly proteins, and glycanases that cleave host exopolysaccharide. IMPORTANCE Despite recent advances in the phylogenetic and structural characterization of bacteriophages, only a small number of phages of plant-symbiotic nitrogen-fixing soil bacteria have been studied at the molecular level. The effects of phage predation upon beneficial bacteria that promote plant growth remain poorly characterized. First steps in understanding these soil bacterium-phage dynamics are genetic, molecular, and structural characterizations of these groups of phages. The T4 superfamily phages are among the most complex phages; they have large genomes packaged within an icosahedral head and a long, contractile tail through which the DNA is delivered to host cells. This phylogenetic and structural study of S. meliloti-infecting T4 superfamily phage ΦM9 provides new insight into the diversity of this family. The comparison of structure-related genes in both ΦM9 and S. meliloti-infecting T4 superfamily phage ΦM12, which comes from a completely different lineage of these phages, allows the identification of host infection-related factors.
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