1
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Parlindungan E, McDonnell B, Lugli GA, Ventura M, van Sinderen D, Mahony J. Dairy streptococcal cell wall and exopolysaccharide genome diversity. Microb Genom 2022; 8. [PMID: 35442186 PMCID: PMC9453073 DOI: 10.1099/mgen.0.000803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The large-scale and high-intensity application of
Streptococcus thermophilus
species in milk fermentation processes is associated with a persistent threat of (bacterio)phage infection. Phage infection of starter cultures may cause inconsistent, slow or even failed fermentations with consequent diminished product quality and/or output. The phage life cycle commences with the recognition of, and binding to, a specific host-encoded and surface-exposed receptor, which in the case of
S. thermophilus
can be the rhamnose-glucose polysaccharide (RGP; specified by the rgp gene cluster) or exopolysaccharide (EPS; specified by the eps gene cluster). The genomic diversity of 23
S
.
thermophilus
strains isolated from unpasteurized dairy products was evaluated, including a detailed analysis of the rgp and eps loci. In the present study, five novel eps genotypes were identified while variations of currently recognized rgp gene cluster types were also observed. Furthermore, the diversity of rgp genotypes amongst retrieved isolates positively correlated with phage diversity based on phageome analysis of eight representative dairy products. Our findings therefore substantially expand our knowledge on S. thermophilus’ strain and phage diversity in (artisanal) dairy products and highlight the merit of phageome analysis of artisanal and traditional fermented foods as a sensitive marker of dominant microbiota involved in the fermentation.
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Affiliation(s)
- Elvina Parlindungan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Brian McDonnell
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
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2
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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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3
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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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4
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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: 1] [Impact Index Per Article: 0.3] [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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5
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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: 25] [Impact Index Per Article: 8.3] [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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6
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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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7
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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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8
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Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization. Appl Environ Microbiol 2020; 86:AEM.00227-20. [PMID: 32303549 DOI: 10.1128/aem.00227-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is a lactic acid bacterium commonly used for the manufacture of yogurt and specialty cheeses. Virulent phages represent a major risk for milk fermentation processes worldwide, as they can inactivate the added starter bacterial cells, leading to low-quality fermented dairy products. To date, four genetically distinct groups of phages infecting S. thermophilus have been described. Here, we describe a fifth group. Phages P738 and D4446 are virulent siphophages that infect a few industrial strains of S. thermophilus The genomes of phages P738 and D4446 were sequenced and found to contain 34,037 and 33,656 bp as well as 48 and 46 open reading frames, respectively. Comparative genomic analyses revealed that the two phages are closely related to each other but display very limited similarities to other S. thermophilus phages. In fact, these two novel S. thermophilus phages share similarities with streptococcal phages of nondairy origin, suggesting that they emerged recently in the dairy environment.IMPORTANCE Despite decades of research and adapted antiphage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide, as they can cause manufacturing failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the food-grade Gram-positive bacterial species Streptococcus thermophilus These two related viruses represent a fifth group of S. thermophilus phages, as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting nondairy streptococci, suggesting their recent emergence and probable coexistence in dairy environments. These findings highlight the necessity of phage surveillance programs as the phage population evolves in response to the application of antiphage strategies.
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9
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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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10
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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: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [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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11
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Inactivation of Dairy Bacteriophages by Thermal and Chemical Treatments. Viruses 2019; 11:v11050480. [PMID: 31130656 PMCID: PMC6563197 DOI: 10.3390/v11050480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/22/2019] [Indexed: 11/16/2022] Open
Abstract
This article provides information on the characteristics of diverse phages of lactic acid bacteria and highlights the incidence of their presence in different dairy fermentations. As it is known, thermal treatments on raw milk and use of sanitizers in the disinfection of surfaces and equipment are strategies usually applied in dairy to prevent bacteriophage infections. In this sense, this review mainly focuses on the existing data about the resistance against thermal treatments and sanitizers usually used in the dairy industry worldwide, and the differences found among bacteriophages of diverse genera are remarked upon. Also, we provide information concerning the problems that have arisen as a consequence of the potential presence of bacteriophages in cheese whey powder and derivatives when they are added in fermented dairy product manufacturing. Finally, some important conclusions on each topic are marked and checkpoints to be considered are suggested.
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12
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Cha Y, Chun J, Son B, Ryu S. Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity. Viruses 2019; 11:v11010054. [PMID: 30642091 PMCID: PMC6356323 DOI: 10.3390/v11010054] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 h of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.
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Affiliation(s)
- Yoyeon Cha
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
| | - Jihwan Chun
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
- Center for Food and Bioconvergence4, Seoul National University, Seoul 08826, Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Center for Food and Bioconvergence4, Seoul National University, Seoul 08826, Korea.
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13
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da Silva Duarte V, Giaretta S, Campanaro S, Treu L, Armani A, Tarrah A, Oliveira de Paula S, Giacomini A, Corich V. A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496. Viruses 2018; 11:v11010007. [PMID: 30583530 PMCID: PMC6356513 DOI: 10.3390/v11010007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.
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Affiliation(s)
- Vinícius da Silva Duarte
- Department of Microbiology, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa-MG 36570-900, Brazil.
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Sabrina Giaretta
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Laura Treu
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, 35129 Padova, Italy.
| | - Armin Tarrah
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
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14
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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: 23] [Impact Index Per Article: 3.8] [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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15
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Hynes AP, Rousseau GM, Agudelo D, Goulet A, Amigues B, Loehr J, Romero DA, Fremaux C, Horvath P, Doyon Y, Cambillau C, Moineau S. Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nat Commun 2018; 9:2919. [PMID: 30046034 PMCID: PMC6060171 DOI: 10.1038/s41467-018-05092-w] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/13/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are bacterial anti-viral systems, and bacterial viruses (bacteriophages, phages) can carry anti-CRISPR (Acr) proteins to evade that immunity. Acrs can also fine-tune the activity of CRISPR-based genome-editing tools. While Acrs are prevalent in phages capable of lying dormant in a CRISPR-carrying host, their orthologs have been observed only infrequently in virulent phages. Here we identify AcrIIA6, an Acr encoded in 33% of virulent Streptococcus thermophilus phage genomes. The X-ray structure of AcrIIA6 displays some features unique to this Acr family. We compare the activity of AcrIIA6 to those of other Acrs, including AcrIIA5 (also from S. thermophilus phages), and characterize their effectiveness against a range of CRISPR-Cas systems. Finally, we demonstrate that both Acr families from S. thermophilus phages inhibit Cas9-mediated genome editing of human cells.
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Affiliation(s)
- Alexander P Hynes
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Daniel Agudelo
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Beatrice Amigues
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Dennis A Romero
- DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA
| | | | - Philippe Horvath
- DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, 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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16
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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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17
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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: 30] [Impact Index Per Article: 5.0] [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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18
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Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) loci, which provide a specific immunity against exogenous elements, are hypervariable among distinct prokaryotes. Based on previous researches, this review focuses on concluding systematical genome editing protocols in Streptococcus thermophilus. Firstly, its protocols and optimized conditions in gene editing are introduced. What’s more, classification and diversity analyses of S. thermophilus CRISPR-Cas benefit the further understanding of evolution relationship among Streptococcus. Ability of its foreign segment integration and spacer source analyses also indicate a new direction of phage resistance. Above all, all of these point out its potential to be regarded as another model system other than type II CRISPR-Cas in Streptococcus pyogenes.
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Affiliation(s)
- Mengyuan Hao
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yanhua Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, China
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19
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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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20
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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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21
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Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species. Appl Environ Microbiol 2017; 83:AEM.02748-16. [PMID: 28039135 PMCID: PMC5311409 DOI: 10.1128/aem.02748-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/12/2016] [Indexed: 12/03/2022] Open
Abstract
Bacteriophages are the main cause of fermentation failures in dairy plants. The majority of Streptococcus thermophilus phages can be divided into either cos- or pac-type phages and are additionally characterized by examining the V2 region of their antireceptors. We screened a large number of S. thermophilus phages from the Chr. Hansen A/S collection, using PCR specific for the cos- or pac-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had shorter tails than the traditional S. thermophilus phages. The third phage, CHPC1151, had a tail size similar to those of the cos- or pac-type phages, but it displayed a different baseplate structure. Sequencing analysis revealed the genetic similarity of CHPC577 and CHPC926 with a subgroup of Lactococcus lactis P335 phages. Phage CHPC1151 was closely related to the atypical S. thermophilus phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of S. thermophilus and L. lactis strains, we revealed the possibility of cross-interactions. Our data indicated that the use of S. thermophilus together with L. lactis, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among S. thermophilus phage populations requires that a new classification of the group be proposed. IMPORTANCEStreptococcus thermophilus is a component of thermophilic starter cultures commonly used for cheese and yogurt production. Characterizing streptococcal phages, understanding their genetic relationships, and studying their interactions with various hosts are the necessary steps for preventing and controlling phage attacks that occur during dairy fermentations.
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22
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Wagner N, Brinks E, Samtlebe M, Hinrichs J, Atamer Z, Kot W, Franz CMAP, Neve H, Heller KJ. Whey powders are a rich source and excellent storage matrix for dairy bacteriophages. Int J Food Microbiol 2016; 241:308-317. [PMID: 27835774 DOI: 10.1016/j.ijfoodmicro.2016.10.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/26/2016] [Accepted: 10/30/2016] [Indexed: 10/20/2022]
Abstract
Thirteen whey powders and 5 whey powder formulations were screened for the presence of dairy bacteriophages using a representative set of 8 acid-producing Lactococcus lactis and 5 Streptococcus thermophilus, and 8 flavour-producing Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides strains. Lytic L. lactis phages were detected in all samples, while S. thermophilus and Leuconostoc phages were present in 50% or 40% of the samples, respectively. Maximal phage titers were 6×107 plaque-forming units (pfu)/g of whey powder for L. lactis phages, 1×107pfu/g for Leuconostoc phages and 1×105pfu/g for S. thermophilus phages. In total, 55 phages were isolated and characterized. Thirty one of the 33 lactococcal phages tested belonged to the wide-spread 936 phage group. In the course of this study, a PCR detection method for Leuconostoc phages (Ali et al., 2013) was adapted to new phage isolates. Furthermore, a remarkably high stability of phages in whey powder samples was documented during a long-term storage period of 4 years.
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Affiliation(s)
- Natalia Wagner
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Meike Samtlebe
- Department of Soft Matter and Dairy Technology, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstraße 21, 70593 Stuttgart, Germany
| | - Jörg Hinrichs
- Department of Soft Matter and Dairy Technology, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstraße 21, 70593 Stuttgart, Germany
| | - Zeynep Atamer
- Department of Soft Matter and Dairy Technology, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstraße 21, 70593 Stuttgart, Germany
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej, 399, 4000 Roskilde, Denmark
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Hermann-Weigmann-Str. 1, 24103 Kiel, Germany.
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
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23
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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: 48] [Impact Index Per Article: 6.0] [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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24
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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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25
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Acar-Soykut E, Tunail N. Classification of S
treptococcus thermophilus
Phages Originating from Turkey. J Food Saf 2015. [DOI: 10.1111/jfs.12226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Esra Acar-Soykut
- Food Research Center; Hacettepe University; Beytepe Ankara 06800 Turkey
| | - Nezihe Tunail
- Food Engineering Department; Ankara University; Ankara Turkey
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Biodiversity ofLactobacillus helveticusbacteriophages isolated from cheese whey starters. J DAIRY RES 2015; 82:242-7. [DOI: 10.1017/s0022029915000151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Twenty-oneLactobacillus helveticusbacteriophages, 18 isolated from different cheese whey starters and three from CNRZ collection, were phenotypically and genetically characterised. A biodiversity between phages was evidenced both by host range and molecular (RAPD-PCR) typing. A more detailed characterisation of six phages showed similar structural protein profiles and a relevant genetic biodiversity, as shown by restriction enzyme analysis of total DNA. Latent period, burst time and burst size data evidenced that phages were active and virulent. Overall, data highlighted the biodiversity ofLb. helveticusphages isolated from cheese whey starters, which were confirmed to be one of the most common phage contamination source in dairy factories. More research is required to further unravel the ecological role ofLb. helveticusphages and to evaluate their impact on the dairy fermentation processes where whey starter cultures are used.
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Adriaenssens EM, Edwards R, Nash JHE, Mahadevan P, Seto D, Ackermann HW, Lavigne R, Kropinski AM. Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology 2014; 477:144-154. [PMID: 25466308 DOI: 10.1016/j.virol.2014.10.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/08/2014] [Accepted: 10/17/2014] [Indexed: 11/26/2022]
Abstract
Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.
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Affiliation(s)
- Evelien M Adriaenssens
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa
| | - Rob Edwards
- Geology, Mathematics, and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - John H E Nash
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4
| | | | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Hans-Wolfgang Ackermann
- Département de Microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada G1K 7P4
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, KasteelparkArenberg 21 - b2462, Heverlee 3001, Belgium.
| | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2A1.
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29
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Abstract
This review highlights the main strategies available to control phage infection during large-scale milk fermentation by lactic acid bacteria. The topics that are emphasized include the factors influencing bacterial activities, the sources of phage contamination, the methods available to detect and quantify phages, as well as practical solutions to limit phage dispersion through an adapted factory design, the control of air flow, the use of adequate sanitizers, the restricted used of recycled products, and the selection and growth of bacterial cultures.
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Mahony J, Bottacini F, van Sinderen D, Fitzgerald GF. Progress in lactic acid bacterial phage research. Microb Cell Fact 2014; 13 Suppl 1:S1. [PMID: 25185514 PMCID: PMC4155818 DOI: 10.1186/1475-2859-13-s1-s1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Research on lactic acid bacteria (LAB) has advanced significantly over the past number of decades and these developments have been driven by the parallel advances in technologies such as genomics, bioinformatics, protein expression systems and structural biology, combined with the ever increasing commercial relevance of this group of microorganisms. Some of the more significant and impressive outputs have been in the domain of bacteriophage-host interactions which provides a prime example of the cutting-edge model systems represented by LAB research. Here, we present a retrospective overview of the key advances in LAB phage research including phage-host interactions and co-evolution. We describe how in many instances this knowledge can be pivotal in creating real improvements in the application of LAB cultures in commercial practice.
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Ishlimova D, Urshev Z. Evolution of CRISPR1 and CRISPR3 in Spontaneous Phage-Resistant Mutants ofStreptococcus ThermophilusStrain LBB.A. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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32
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Ishlimova D, Urshev Z, Stoyancheva G, Petrova P, Minkova S, Doumanova L. Genetic Diversity of Bacteriophages Highly Specific forStreptococcus ThermophilusStrain Lbb.A. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10817666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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33
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Ma C, Pan N, Chen Z, Liu Z, Gong G, Ma A. Geographical diversity of Streptococcus thermophilus phages in Chinese yoghurt plants. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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34
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Campagna C, Villion M, Labrie SJ, Duchaine C, Moineau S. Inactivation of dairy bacteriophages by commercial sanitizers and disinfectants. Int J Food Microbiol 2014; 171:41-7. [DOI: 10.1016/j.ijfoodmicro.2013.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/01/2013] [Accepted: 11/11/2013] [Indexed: 01/14/2023]
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35
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Mahony J, van Sinderen D. Current taxonomy of phages infecting lactic acid bacteria. Front Microbiol 2014; 5:7. [PMID: 24478767 PMCID: PMC3900856 DOI: 10.3389/fmicb.2014.00007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/07/2014] [Indexed: 01/29/2023] Open
Abstract
Phages infecting lactic acid bacteria have been the focus of significant research attention over the past three decades. Through the isolation and characterization of hundreds of phage isolates, it has been possible to classify phages of the dairy starter and adjunct bacteria Lactococus lactis, Streptococcus thermophilus, Leuconostoc spp., and Lactobacillus spp. Among these, phages of L. lactis have been most thoroughly scrutinized and serve as an excellent model system to address issues that arise when attempting taxonomic classification of phages infecting other LAB species. Here, we present an overview of the current taxonomy of phages infecting LAB genera of industrial significance, the methods employed in these taxonomic efforts and how these may be employed for the taxonomy of phages of currently underrepresented and emerging phage species.
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Affiliation(s)
- Jennifer Mahony
- Department of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology, University College Cork Cork, Ireland ; Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland
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36
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Abstract
Due to their crucial role in pathogenesis and virulence, phages of Staphylococcus aureus have been extensively studied. Most of them encode and disseminate potent staphylococcal virulence factors. In addition, their movements contribute to the extraordinary versatility and adaptability of this prominent pathogen by improving genome plasticity. In addition to S. aureus, phages from coagulase-negative Staphylococci (CoNS) are gaining increasing interest. Some of these species, such as S. epidermidis, cause nosocomial infections and are therefore problematic for public health. This review provides an overview of the staphylococcal phages family extended to CoNS phages. At the morphological level, all these phages characterized so far belong to the Caudovirales order and are mainly temperate Siphoviridae. At the molecular level, comparative genomics revealed an extensive mosaicism, with genes organized into functional modules that are frequently exchanged between phages. Evolutionary relationships within this family, as well as with other families, have been highlighted. All these aspects are of crucial importance for our understanding of evolution and emergence of pathogens among bacterial species such as Staphylococci.
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Affiliation(s)
- Marie Deghorain
- Author to whom correspondence should be addressed; (L.V.M.); (M.D.); Tel.: +32-2-650-97-76 (M.D.); +32-2-650-97-78 (L.V.M.); Fax: +32-2-650-97-70
| | - Laurence Van Melderen
- Author to whom correspondence should be addressed; (L.V.M.); (M.D.); Tel.: +32-2-650-97-76 (M.D.); +32-2-650-97-78 (L.V.M.); Fax: +32-2-650-97-70
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37
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Mahony J, Ainsworth S, Stockdale S, van Sinderen D. Phages of lactic acid bacteria: the role of genetics in understanding phage-host interactions and their co-evolutionary processes. Virology 2012; 434:143-50. [PMID: 23089252 DOI: 10.1016/j.virol.2012.10.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/12/2012] [Accepted: 10/01/2012] [Indexed: 12/26/2022]
Abstract
Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.
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Affiliation(s)
- Jennifer Mahony
- Department of Microbiology, University College Cork, Western Road, Cork, Ireland.
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38
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Abstract
M102AD is the new designation for a Streptococcus mutans phage described in 1993 as phage M102. This change was necessitated by the genome analysis of another S. mutans phage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed that S. mutans phage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains of S. mutans. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3'-overhang cos site that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship between S. mutans phages M102AD and M102 as well as with Streptococcus thermophilus phages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.
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Mills S, Griffin C, O’Sullivan O, Coffey A, McAuliffe O, Meijer W, Serrano L, Ross R. A new phage on the ‘Mozzarella’ block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages. Int Dairy J 2011. [DOI: 10.1016/j.idairyj.2011.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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40
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Gao Y, Luo L. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method. Gene 2011; 492:309-14. [PMID: 22100880 DOI: 10.1016/j.gene.2011.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 09/19/2011] [Accepted: 11/01/2011] [Indexed: 12/25/2022]
Abstract
Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification.
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Affiliation(s)
- Yang Gao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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41
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42
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Zinno P, Janzen T, Bennedsen M, Ercolini D, Mauriello G. Characterization of Streptococcus thermophilus lytic bacteriophages from mozzarella cheese plants. Int J Food Microbiol 2009; 138:137-44. [PMID: 20060612 DOI: 10.1016/j.ijfoodmicro.2009.12.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 12/02/2009] [Accepted: 12/05/2009] [Indexed: 11/17/2022]
Abstract
Phage infection still represents the main cause of fermentation failure during the mozzarella cheese manufacturing, where Streptococcus thermophilus is widely employed as starter culture. Thereby, the success of commercial lactic starter cultures is closely related to the use of strains with low susceptibility to phage attack. The characterization of lytic S. thermophilus bacteriophages is an important step for the selection and use of starter cultures. The aim of this study was to characterize 26 bacteriophages isolated from mozzarella cheese plants in terms of their host range, DNA restriction profile, DNA packaging mechanism, and the variable region VR2 of the antireceptor gene. The DNA restriction analysis was carried out by using the restriction enzymes EcoRV, PstI, and HindIII. The bacteriophages were distinguished into two main groups of S. thermophilus phages (cos- and pac-type) using a multiplex PCR method based on the amplification of conserved regions in the genes coding for the major structural proteins. All the phages belonged to the cos-type group except one, phage 1042, which gave a PCR fragment distinctive of pac-type group. Furthermore, DNA sequencing of the variable region VR2 of the antireceptor gene allowed to classify the phages and examine the correlation between typing profile and host range. Finally, bacterial strains used in this study were investigated for the presence of temperate phages by induction with mitomycin C and only S. thermophilus CHCC2070 was shown to be lysogenic.
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Affiliation(s)
- P Zinno
- Dipartimento di Scienza degli Alimenti, Università degli Studi di Napoli Federico II, Portici, Italy
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43
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Guglielmotti DM, Deveau H, Binetti AG, Reinheimer JA, Moineau S, Quiberoni A. Genome analysis of two virulent Streptococcus thermophilus phages isolated in Argentina. Int J Food Microbiol 2009; 136:101-9. [DOI: 10.1016/j.ijfoodmicro.2009.09.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 08/31/2009] [Accepted: 09/06/2009] [Indexed: 11/30/2022]
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44
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Streptococcus thermophilus phage monitoring in a cheese factory: Phage characteristics and starter sensitivity. Int Dairy J 2009. [DOI: 10.1016/j.idairyj.2009.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Mills S, Griffin C, Coffey A, Meijer WC, Hafkamp B, Ross RP. CRISPR analysis of bacteriophage-insensitive mutants (BIMs) of industrial Streptococcus thermophilus--implications for starter design. J Appl Microbiol 2009; 108:945-955. [PMID: 19709335 DOI: 10.1111/j.1365-2672.2009.04486.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AIMS An efficient approach for generation of bacteriophage-insensitive mutants (BIMs) of Streptococcus thermophilus starters was described in our laboratory [Mills et al. (2007) J Microbiol Methods70, 159-164]. The aim of this study was to analyse the phage resistance mechanism responsible for BIM formation. METHODS AND RESULTS Three clustered regularly interspaced short palindromic repeat (CRISPR) regions have been identified in Strep. thermophilus, and Strep. thermophilus can integrate novel spacers into these loci in response to phage attack. Characterization of three sets of BIMs indicated that two sets had altered CRISPR1 and/or CRISPR3 loci. A range of BIMs of yoghurt starter CSK938 were generated with the same phage in different phage challenge experiments, and each acquired unique spacer regions ranging between one and four new spacers in CRISPR1. In addition, the BIM that acquired only one new spacer in CRISPR1 also acquired an additional spacer in CRISPR3. A fourth BIM, generated with a different phage, had two spacers deleted from CRISPR1 but acquired two spacers in CRISPR3. Analysis of the Mozzarella starter CSK939 and its associated BIMs indicated that formation of second generation BIMs does not lead to increases in spacer number but to alterations in spacer regions. BIMs of an exopolysaccharide (EPS)-producing strain that lost the ability to produce EPS did not harbour an altered CRISPR, suggesting that phage sensitivity may be related to the EPS-producing phenotype. CONCLUSIONS Acquisition/deletion of new spacers in CRISPR loci in response to phage attack generates distinctly individual variants. It also demonstrates that other modifications may be responsible for the phage resistance of Strep. thermophilus BIMs. SIGNIFICANCE AND IMPACT OF THE STUDY Isolation of individual BIMs that have unique spacers towards the leader region of the CRISPR locus may be a very useful approach for rotation strategies with the same starter backbone. Upon phage infection, BIMs 'in reserve' can be slotted into the rotation scheme.
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Affiliation(s)
- S Mills
- Teagasc, Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland., CSK Food Enrichment, Ede, the Netherlands
| | - C Griffin
- Teagasc, Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland., CSK Food Enrichment, Ede, the Netherlands
| | - A Coffey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - W C Meijer
- CSK Food Enrichment, Ede, the Netherlands
| | - B Hafkamp
- CSK Food Enrichment, Ede, the Netherlands
| | - R P Ross
- Teagasc, Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland., Alimentary Pharmabiotic Centre, Cork, Ireland
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Ahn SI, Azzouny RA, Huyen TTT, Kwak HS. The Characteristics, Detection and Control of Bacteriophage in Fermented Dairy Products. Korean J Food Sci Anim Resour 2009. [DOI: 10.5851/kosfa.2009.29.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Multiplex fast real-time PCR for quantitative detection and identification of cos- and pac-type Streptococcus thermophilus bacteriophages. Appl Environ Microbiol 2008; 74:4779-81. [PMID: 18539804 DOI: 10.1128/aem.00295-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fermentation of milk by Streptococcus thermophilus is a widespread industrial process that is susceptible to bacteriophage attack. In this work, a preventive fast real-time PCR method for the detection, quantification, and identification of types of S. thermophilus phages in 30 min is described.
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Quiberoni A, Tremblay D, Ackermann HW, Moineau S, Reinheimer JA. Diversity of Streptococcus thermophilus phages in a large-production cheese factory in Argentina. J Dairy Sci 2008; 89:3791-9. [PMID: 16960053 DOI: 10.3168/jds.s0022-0302(06)72420-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Phage infections still represent a serious risk to the dairy industry, in which Streptococcus thermophilus is used in starter cultures for the manufacture of yogurt and cheese. The goal of the present study was to analyze the biodiversity of the virulent S. thermophilus phage population in one Argentinean cheese plant. Ten distinct S. thermophilus phages were isolated from cheese whey samples collected in a 2-mo survey. They were then characterized by their morphology, host range, and restriction patterns. These phages were also classified within the 2 main groups of S. thermophilus phages (cos- and pac-type) using a newly adapted multiplex PCR method. Six phages were classified as cos-type phages, whereas the 4 others belonged to the pac-type group. This study illustrates the phage diversity that can be found in one factory that rotates several cultures of S. thermophilus. Limiting the number of starter cultures is likely to reduce phage biodiversity within a fermentation facility.
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Affiliation(s)
- A Quiberoni
- Instituto de Lactología Industrial, Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe, Argentina.
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49
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated genes are linked to a mechanism of acquired resistance against bacteriophages. Bacteria can integrate short stretches of phage-derived sequences (spacers) within CRISPR loci to become phage resistant. In this study, we further characterized the efficiency of CRISPR1 as a phage resistance mechanism in Streptococcus thermophilus. First, we show that CRISPR1 is distinct from previously known phage defense systems and is effective against the two main groups of S. thermophilus phages. Analyses of 30 bacteriophage-insensitive mutants of S. thermophilus indicate that the addition of one new spacer in CRISPR1 is the most frequent outcome of a phage challenge and that the iterative addition of spacers increases the overall phage resistance of the host. The added new spacers have a size of between 29 to 31 nucleotides, with 30 being by far the most frequent. Comparative analysis of 39 newly acquired spacers with the complete genomic sequences of the wild-type phages 2972, 858, and DT1 demonstrated that the newly added spacer must be identical to a region (named proto-spacer) in the phage genome to confer a phage resistance phenotype. Moreover, we found a CRISPR1-specific sequence (NNAGAAW) located downstream of the proto-spacer region that is important for the phage resistance phenotype. Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.
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50
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Fortier LC, Moineau S. Morphological and genetic diversity of temperate phages in Clostridium difficile. Appl Environ Microbiol 2007; 73:7358-66. [PMID: 17890338 PMCID: PMC2168219 DOI: 10.1128/aem.00582-07] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Eight temperate phages were characterized after mitomycin C induction of six Clostridium difficile isolates corresponding to six distinct PCR ribotypes. The hypervirulent C. difficile strain responsible for a multi-institutional outbreak (NAP1/027 or QCD-32g58) was among these prophage-containing strains. Observation of the crude lysates by transmission electron microscopy (TEM) revealed the presence of three phages with isometric capsids and long contractile tails (Myoviridae family), as well as five phages with long noncontractile tails (Siphoviridae family). TEM analyses also revealed the presence of a significant number of phage tail-like particles in all the lysates. Southern hybridization experiments with restricted prophage DNA showed that C. difficile phages belonging to the family Myoviridae are highly similar and most likely related to previously described prophages phiC2, phiC5, and phiCD119. On the other hand, members of the Siphoviridae phage family are more genetically divergent, suggesting that they originated from distantly related ancestors. Our data thus suggest that there are at least three genetically distinct groups of temperate phages in C. difficile; one group is composed of highly related myophages, and the other two groups are composed of more genetically heterogeneous siphophages. Finally, no gene homologous to genes encoding C. difficile toxins or toxin regulators could be identified in the genomes of these phages using DNA hybridization. Interestingly, each unique phage restriction profile correlated with a specific C. difficile PCR ribotype.
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Affiliation(s)
- Louis-Charles Fortier
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4.
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