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Herasimovich A, Akhremchuk A, Valentovich L, Sidarenka A. Whole genome analysis, thermal and UV-tolerance of Lactococcus phage BIM BV-114 isolated from cheese brine. Res Microbiol 2024; 175:104203. [PMID: 38685370 DOI: 10.1016/j.resmic.2024.104203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Lactococcus phages that belong to the genus Ceduovirus are among the three most frequently isolated phage groups infecting Lactococcus lactis starter strains in dairy plants. In this study, we characterized virulent Lactococcus phage BIM BV-114 isolated from industrial cheese brine in Belarus and identified as Ceduovirus. The bacteriophage demonstrated a relatively short lytic cycle (latent period of 23 ± 5 min, lysis time of 90 ± 5 min), high thermal stability (inactivation after 7 min at 95 °C in skimmed milk) and tolerance to UV radiation (inactivation time - 15 min), indicating adaptation for better persistence in dairy facilities. The genome of the phage BIM BV-114 (21 499 bp; 37 putative open reading frames) has a similar organization to that of other Ceduovirus phages. RLf1_00140 and RLf_00050 gene products, found in the early genes region, may be involved in the sensitivity of phage to the lactococcal abortive infection mechanisms AbiV and AbiQ, respectively. Furthermore, nucleotide deletion, observed in the middle region of the gene encoding putative tape measure protein (RLf1_00300), is possibly responsible for increased thermal tolerance of phage BIM BV-114. Together, these findings will contribute to a better knowledge of virulent Lactococcus phages and the development of effective methods of their control for dairy technologies.
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Affiliation(s)
- Aliaksandra Herasimovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich str., 2, 220084, Minsk, Belarus.
| | - Artur Akhremchuk
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich str., 2, 220084, Minsk, Belarus.
| | - Leonid Valentovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich str., 2, 220084, Minsk, Belarus.
| | - Anastasiya Sidarenka
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich str., 2, 220084, Minsk, Belarus.
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2
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Makete G, Mamphogoro TP. De novo genome assembly of a probiotic Lacticaseibacillus rhamnosus ISO20, isolated from raw milk in South Africa. Microbiol Resour Announc 2024; 13:e0122723. [PMID: 38376337 DOI: 10.1128/mra.01227-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Lactic acid bacteria are known to exhibit probiotic properties through various mechanisms including production of antimicrobial substances and bile salts tolerance. Here, we report a draft genome sequence of Lacticaseibacillus rhamnosus ISO20, a lactic acid bacterium isolated from raw goat's milk to provide genomic insight into its strategies as probiotic strain.
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Affiliation(s)
- Goitsemang Makete
- Gastro-Intestinal Microbiology and Biotechnology Unit, Agricultural Research Council-Animal Production, Irene, Pretoria, South Africa
| | - Tshifhiwa Paris Mamphogoro
- Gastro-Intestinal Microbiology and Biotechnology Unit, Agricultural Research Council-Animal Production, Irene, Pretoria, South Africa
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Goulet A, Joos R, Lavelle K, Van Sinderen D, Mahony J, Cambillau C. A structural discovery journey of streptococcal phages adhesion devices by AlphaFold2. Front Mol Biosci 2022; 9:960325. [PMID: 36060267 PMCID: PMC9437275 DOI: 10.3389/fmolb.2022.960325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 12/04/2022] Open
Abstract
Successful bacteriophage infection starts with specific recognition and adhesion to the host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limits their structural analyses by experimental approaches such as X-ray crystallography and electron microscopy. However, the protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of whole adhesion devices of five representative siphophages infecting Streptococcus thermophilus, one of the main lactic acid bacteria used in dairy fermentations. The predictions highlight the mosaic nature of these devices that share functional domains for which active sites and residues could be unambiguously identified. Such AlphaFold2 analyses of phage-encoded host adhesion devices should become a standard method to characterize phage-host interaction machineries and to reliably annotate phage genomes.
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Affiliation(s)
- Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix-Marseille Université, UMR7255, Marseille, France
- *Correspondence: Adeline Goulet, ; Jennifer Mahony, ; Christian Cambillau,
| | - Raphaela Joos
- School of Microbiology, University College Cork, Cork, Ireland
| | - Katherine Lavelle
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe Van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- *Correspondence: Adeline Goulet, ; Jennifer Mahony, ; Christian Cambillau,
| | - Christian Cambillau
- School of Microbiology, University College Cork, Cork, Ireland
- AlphaGraphix, Formiguères, France
- *Correspondence: Adeline Goulet, ; Jennifer Mahony, ; Christian Cambillau,
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Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production. Appl Microbiol Biotechnol 2021; 105:8575-8592. [PMID: 34694447 DOI: 10.1007/s00253-021-11509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022]
Abstract
The widespread existence of bacteriophage has been of great interest to the biological research community and ongoing investigations continue to explore their diversity and role. They have also attracted attention and in-depth research in connection to fermented food processing, in particular from the dairy and wine industries. Bacteriophage, mostly oenophage, may in fact be a 'double edged sword' for winemakers: whilst they have been implicated as a causal agent of difficulties with malolactic fermentation (although not proven), they are also beginning to be considered as alternatives to using sulphur dioxide to prevent wine spoilage. Investigation and characterisation of oenophage of Oenococcus oeni, the main species used in winemaking, are still limited compared to lactococcal bacteriophage of Lactococcus lactis and Lactiplantibacillus plantarum (formally Lactobacillus plantarum), the drivers of most fermented dairy products. Interestingly, these strains are also being used or considered for use in winemaking. In this review, the genetic diversity and life cycle of phage, together with the debate on the consequent impact of phage predation in wine, and potential control strategies are discussed. KEY POINTS: • Bacteriophage detected in wine are diverse. • Many lysogenic bacteriophage are found in wine bacteria. • Phage impact on winemaking can depend on the stage of the winemaking process. • Bacteriophage as potential antimicrobial agents against spoilage organisms.
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Lavelle K, Goulet A, McDonnell B, Spinelli S, van Sinderen D, Mahony J, Cambillau C. Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages. Microb Biotechnol 2020; 13:1765-1779. [PMID: 32525270 PMCID: PMC7533335 DOI: 10.1111/1751-7915.13593] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 Å resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP- or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.
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Affiliation(s)
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | | | - Silvia Spinelli
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | - Douwe van Sinderen
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Jennifer Mahony
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Christian Cambillau
- School of MicrobiologyUniversity College CorkCorkIreland
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
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Mutant and Recombinant Phages Selected from In Vitro Coevolution Conditions Overcome Phage-Resistant Listeria monocytogenes. Appl Environ Microbiol 2020; 86:AEM.02138-20. [PMID: 32887717 DOI: 10.1128/aem.02138-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteriophages (phages) are currently available for use by the food industry to control the foodborne pathogen Listeria monocytogenes Although phage biocontrols are effective under specific conditions, their use can select for phage-resistant bacteria that repopulate phage-treated environments. Here, we performed short-term coevolution experiments to investigate the impact of single phages and a two-phage cocktail on the regrowth of phage-resistant L. monocytogenes and the adaptation of the phages to overcome this resistance. We used whole-genome sequencing to identify mutations in the target host that confer phage resistance and in the phages that alter host range. We found that infections with Listeria phages LP-048, LP-125, or a combination of both select for different populations of phage-resistant L. monocytogenes bacteria with different regrowth times. Phages isolated from the end of the coevolution experiments were found to have gained the ability to infect phage-resistant mutants of L. monocytogenes and L. monocytogenes strains previously found to be broadly resistant to phage infection. Phages isolated from coinfected cultures were identified as recombinants of LP-048 and LP-125. Interestingly, recombination events occurred twice independently in a locus encoding two proteins putatively involved in DNA binding. We show that short-term coevolution of phages and their hosts can be utilized to obtain mutant and recombinant phages with adapted host ranges. These laboratory-evolved phages may be useful for limiting the emergence of phage resistance and for targeting strains that show general resistance to wild-type (WT) phages.IMPORTANCE Listeria monocytogenes is a life-threatening bacterial foodborne pathogen that can persist in food processing facilities for years. Phages can be used to control L. monocytogenes in food production, but phage-resistant bacterial subpopulations can regrow in phage-treated environments. Coevolution experiments were conducted on a Listeria phage-host system to provide insight into the genetic variation that emerges in both the phage and bacterial host under reciprocal selective pressure. As expected, mutations were identified in both phage and host, but additionally, recombination events were shown to have repeatedly occurred between closely related phages that coinfected L. monocytogenes This study demonstrates that in vitro evolution of phages can be utilized to expand the host range and improve the long-term efficacy of phage-based control of L. monocytogenes This approach may also be applied to other phage-host systems for applications in biocontrol, detection, and phage therapy.
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Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020; 18:e3000877. [PMID: 33048924 PMCID: PMC7553319 DOI: 10.1371/journal.pbio.3000877] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
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Affiliation(s)
- Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
| | - Benjamin A. Adler
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Harneet S. Rishi
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Denish Piya
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Crystal Zhong
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Britt Koskella
- Department of Integrative Biology, University of California – Berkeley, Berkeley, California, United States of America
| | | | - Richard Calendar
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
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8
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Scanlan JG, Hall AR, Scanlan PD. Impact of bile salts on coevolutionary dynamics between the gut bacterium Escherichia coli and its lytic phage PP01. INFECTION GENETICS AND EVOLUTION 2019; 73:425-432. [DOI: 10.1016/j.meegid.2019.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/21/2019] [Accepted: 05/29/2019] [Indexed: 01/21/2023]
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Bergsveinson J, Ziola B. Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates. Can J Microbiol 2017; 63:970-983. [PMID: 28977764 DOI: 10.1139/cjm-2017-0405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.
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Affiliation(s)
- Jordyn Bergsveinson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada.,Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada.,Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
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Abstract
Among other fermentation processes, lactic acid fermentation is a valuable process which enhances the safety, nutritional and sensory properties of food. The use of starters is recommended compared to spontaneous fermentation, from a safety point of view but also to ensure a better control of product functional and sensory properties. Starters are used for dairy products, sourdough, wine, meat, sauerkraut and homemade foods and beverages from dairy or vegetal origin. Among lactic acid bacteria, Lactobacillus, Lactococcus, Leuconostoc, Streptococcus and Pediococcus are the majors genera used as starters whereas Weissella is not. Weissella spp. are frequently isolated from spontaneous fermented foods and participate to the characteristics of the fermented product. They possess a large set of functional and technological properties, which can enhance safety, nutritional and sensory characteristics of food. Particularly, Weissella cibaria and Weissella confusa have been described as high producers of exo-polysaccharides, which exhibit texturizing properties. Numerous bacteriocins have been purified from Weissella hellenica strains and may be used as bio-preservative. Some Weissella strains are able to decarboxylate polymeric phenolic compounds resulting in a better bioavailability. Other Weissella strains showed resistance to low pH and bile salts and were isolated from healthy human feces, suggesting their potential as probiotics. Despite all these features, the use of Weissella spp. as commercial starters remained non-investigated. Potential biogenic amine production, antibiotic resistance pattern or infection hazard partly explains this neglecting. Besides, Weissella spp. are not recognized as GRAS (Generally Recognized As Safe). However, Weissella spp. are potential powerful starters for food fermentation as well as Lactococcus, Leuconostoc or Lactobacillus species.
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Sert D, Mercan E, Dertli E. Characterization of lactic acid bacteria from yogurt-like product fermented with pine cone and determination of their role on physicochemical, textural and microbiological properties of product. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2016.12.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Survey on the phage resistance mechanisms displayed by a dairy Lactobacillus helveticus strain. Food Microbiol 2017; 66:110-116. [PMID: 28576359 DOI: 10.1016/j.fm.2017.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/20/2017] [Accepted: 04/23/2017] [Indexed: 11/20/2022]
Abstract
In this study the presence and functionality of phage defence mechanisms in Lactobacillus helveticus ATCC 10386, a strain of dairy origin which is sensitive to ΦLh56, were investigated. After exposure of ATCC 10386 to ΦLh56, the whole-genome sequences of ATCC 10386 and of a phage-resistant derivative (LhM3) were compared. LhM3 showed deletions in the S-layer protein and a higher expression of the genes involved in the restriction/modification (R/M) system. Genetic data were substantiated by measurements of bacteriophage adsorption rates, efficiency of plaquing, cell wall protein size and by gene expression analysis. In LhM3 two phage resistance mechanisms, the inhibition of phage adsorption and the upregulation of Type I R/M genes, take place and explain its resistance to ΦLh56. Although present in both ATCC 10386 and LhM3 genomes, the CRISPR machinery did not seem to play a role in the phage resistance of LhM3. Overall, the natural selection of phage resistant strains resulted successful in detecting variants carrying multiple phage defence mechanisms in L. helveticus. The concurrent presence of multiple phage-resistance systems should provide starter strains with increased fitness and robustness in dairy ecosystems.
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Millen AM, Romero DA. Genetic determinants of lactococcal C2viruses for host infection and their role in phage evolution. J Gen Virol 2016; 97:1998-2007. [PMID: 27389474 PMCID: PMC5156332 DOI: 10.1099/jgv.0.000499] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lactococcus lactis is an industrial starter culture used for the production of fermented dairy products. Pip (phage infection protein) bacteriophage-insensitive mutant (BIM) L. lactis DGCC11032 was isolated following challenge of parental strain DGCC7271 with C2viruses. Over a period of industrial use, phages infecting DGCC11032 were isolated from industrial whey samples and identified as C2viruses. Although Pip is reported to be the receptor for many C2viruses including species type phage c2, a similar cell-membrane-associated protein, YjaE, was recently reported as the receptor for C2virus bIL67. Characterization of DGCC7271 BIMs following challenge with phage capable of infecting DGCC11032 identified mutations in yjaE, confirming YjaE to be necessary for infection. DGCC7271 YjaE mutants remained sensitive to the phages used to generate pip variant DGCC11032, indicating a distinction in host phage determinants. We will refer to C2viruses requiring Pip as c2-type andC2viruses that require YjaE as bIL67-type. Genomic comparisons of two c2-type phages unable to infect pip mutant DGCC11032 and four bIL67-type phages isolated on DGCC11032 confirmed the segregation of each group based on resemblance to prototypical phages c2 and bIL67, respectively. The distinguishing feature is linked to three contiguous late-expressed genes: l14-15-16 (c2) and ORF34-35-36 (bIL67). Phage recombinants in which the c2-like l14-15-16 homologue gene set was exchanged with corresponding bIL67 genes ORF34-35-36 were capable of infecting a pip mutated host. Together, these results correlate the phage genes corresponding to l14-15-16 (c2) and ORF34-35-36 (bIL67) to host lactococcal phage determinants Pip and YjaE, respectively.
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Affiliation(s)
- Anne M Millen
- DuPont Nutrition and Health, Madison, Wisconsin, USA
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14
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Ceapa C, Davids M, Ritari J, Lambert J, Wels M, Douillard FP, Smokvina T, de Vos WM, Knol J, Kleerebezem M. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires. Genome Biol Evol 2016; 8:1889-905. [PMID: 27358423 PMCID: PMC4943194 DOI: 10.1093/gbe/evw123] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.
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Affiliation(s)
- Corina Ceapa
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, the Netherlands
| | - Jarmo Ritari
- RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland
| | - Jolanda Lambert
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands
| | | | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, the Netherlands RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland Department of Veterinary Biosciences, University of Helsinki, Finland
| | - Jan Knol
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
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15
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Casey A, Jordan K, Neve H, Coffey A, McAuliffe O. A tail of two phages: genomic and functional analysis of Listeria monocytogenes phages vB_LmoS_188 and vB_LmoS_293 reveal the receptor-binding proteins involved in host specificity. Front Microbiol 2015; 6:1107. [PMID: 26500641 PMCID: PMC4598591 DOI: 10.3389/fmicb.2015.01107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/25/2015] [Indexed: 12/16/2022] Open
Abstract
The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these phages were identified to be highly conserved when compared to other serovar 4-specific Listeria phages. Spontaneous mutants of each of these phages with broadened host specificities were generated. Their late tail gene sequences were compared with their wild-type counterparts resulting in the putative identification of the products of ORF 19 of vB_LmoS_188 and ORF 20 of vB_LmoS_293 as the receptor binding proteins of these phages. The research findings also indicate that conserved baseplate architectures and host interaction mechanisms exist for Listeria siphoviruses with differing host-specificities, and further contribute to the current knowledge of phage-host interactions with regard to Listeria phages.
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Affiliation(s)
- Aidan Casey
- Teagasc Food Research Centre Fermoy, Ireland ; Department of Biological Sciences, Cork Institute of Technology Bishopstown, Ireland
| | | | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food Kiel, Germany
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology Bishopstown, Ireland
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16
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Identification, typing and functional characterization of dominant lactic acid bacteria strains from Iranian traditional yoghurt. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2562-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Cambillau C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial phage A118. Virology 2015; 484:86-92. [PMID: 26074066 DOI: 10.1016/j.virol.2015.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/10/2015] [Accepted: 05/21/2015] [Indexed: 12/22/2022]
Abstract
Each phage infects its specific bacterial host strain through highly specific interactions between the baseplate-associated receptor binding protein (RBP) at the tip of the phage tail and the receptor at the host surface. Baseplates incorporate structural core modules, Dit and Tal, largely conserved among phages, and peripheral modules anchoring the RBPs. Exploiting structural information from the HHpred program and EM data from the Bielmann et al. (2015) paper, a molecular model of the A118 phage baseplate was generated from different building blocks. This model implies the occurrence of baseplate module reshuffling and suggests that listerial phage A118 may have been derived from lactococcal phage TP901-1 through host species exchange. With the increase of available viral module structures, modelling phage baseplates will become easier and more reliant, and will provide insightful information on the nature of the phage host receptor and its mode of recognition.
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Affiliation(s)
- Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS, France; AFMB, Aix-Marseille University, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.
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18
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Passerini D, Vuillemin M, Ufarté L, Morel S, Loux V, Fontagné-Faucher C, Monsan P, Remaud-Siméon M, Moulis C. Inventory of the GH70 enzymes encoded byLeuconostoc citreumNRRL B-1299 - identification of three novel α-transglucosylases. FEBS J 2015; 282:2115-30. [DOI: 10.1111/febs.13261] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Delphine Passerini
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
| | - Marlène Vuillemin
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
| | - Lisa Ufarté
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
| | - Sandrine Morel
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
| | - Valentin Loux
- Institut National de la Recherche Agronomique; UMR1077 Mathématique; Informatique et Génome; Jouy-en-Josas France
| | - Catherine Fontagné-Faucher
- Laboratoire de Biologie Appliquée à l'Agroalimentaire et à l'Environnement; Institut Universitaire de Technologie - Université Paul Sabatier; Auch France
| | - Pierre Monsan
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
| | - Magali Remaud-Siméon
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
| | - Claire Moulis
- Université de Toulouse; Institut National des Sciences Appliquées (INSA); Université Paul Sabatier (UPS); Institut National Polytechnique (INP); Laboratoire d'Ingénierie des Systémes biologiques et des Procédés (LISBP); Toulouse France
- Centre National de la Recherche Scientifique; UMR5504; Toulouse France
- Institut National de la Recherche Agronomique; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; Toulouse France
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19
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20
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Mahony J, van Sinderen D. Novel strategies to prevent or exploit phages in fermentations, insights from phage-host interactions. Curr Opin Biotechnol 2014; 32:8-13. [PMID: 25300036 DOI: 10.1016/j.copbio.2014.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/19/2014] [Accepted: 09/23/2014] [Indexed: 12/26/2022]
Abstract
Phages infecting lactic acid bacteria (LAB) provide some of the most advanced model systems for (tailed) phage-host interactions. In particular the identification of receptor molecules of representative lactococcal phages combined with the elucidation of the structure of the receptor-binding protein has permitted crucial insights into the early stages of infection. Dairy and biotechnological fermentations are persistently marred by the destructive activities of phages. Here, we discuss how recent advances in our knowledge on LAB phage-host interactions have provided a basis for the next generation anti-phage strategies. Furthermore, the significant increase in genomic data has furthered our understanding of the genetics of these phages, thereby permitting the exploitation of phage-derived components for food safety and biotechnological applications.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland; Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
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21
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Hoffmann J, Altenbuchner J. Hyaluronic acid production with Corynebacterium glutamicum: effect of media composition on yield and molecular weight. J Appl Microbiol 2014; 117:663-78. [PMID: 24863652 DOI: 10.1111/jam.12553] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/19/2014] [Accepted: 05/19/2014] [Indexed: 02/02/2023]
Abstract
AIMS Corynebacterium glutamicum was tested as an alternative host for heterologous production of hyaluronic acid (HA). METHODS AND RESULTS A set of expression vectors containing hasA, encoding HA synthase from Streptococcus equi subsp. zooepidemicus, alone or in combination with genes encoding enzymes for HA precursor production (hasB, hasC, glmU from Pseudomonas putida KT2440) or bacterial haemoglobin (vgb from Vitreoscilla sp.) was constructed. Recombinant Coryne. glutamicum strains were cultivated in two different minimal media, CGXII and MEK700. HA was isolated from the culture broth by ethanol precipitation or ultrafiltration. Analyses of the isolated HA revealed that overall production was higher in CGXII medium (1241 mg l(-1)) than in MEK700 medium (363 mg l(-1)), but molecular weight of the product was higher in MEK700 (>1·4 MDa) than in CGXII (<270 kDa). Coexpression of hasB, hasC or glmU had no effect on HA yield and did not improve molecular weight of the product. Coexpression of vgb lowered HA yield about 1·5-fold and did not affect molecular weight of the product. Microscopy of negative-stained cultures revealed that Coryne. glutamicum produces no distinct HA capsule. CONCLUSIONS Regulation of cell growth and gene expression level of hasA are reasonable starting points for controlling the molecular weight of HA produced by Coryne. glutamicum. SIGNIFICANCE AND IMPACT OF THE STUDY Corynebacterium glutamicum has a great potential as an alternative production host for HA. The fact that Coryne. glutamicum produces no distinct HA capsule facilitates HA isolation and improves overall yield.
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Affiliation(s)
- J Hoffmann
- Institute of Industrial Genetics, University of Stuttgart, Stuttgart, Germany
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22
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Chirico D, Gorla A, Verga V, Pedersen PD, Polgatti E, Cava A, Dal Bello F. Bacteriophage-insensitive mutants for high quality Crescenza manufacture. Front Microbiol 2014; 5:201. [PMID: 24834065 PMCID: PMC4018529 DOI: 10.3389/fmicb.2014.00201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 04/16/2014] [Indexed: 12/13/2022] Open
Abstract
Streptococcus thermophilus is a thermophilic lactic acid bacterium used as starter culture for the manufacture of fermented dairy products. For the production of Crescenza and other soft cheeses, Sacco has developed and provides dairies with three different defined blends of S. thermophilus strains. Each blend contains two different S. thermophilus strains. The strains were selected based on their unique technological properties as well as different phage profiles. Analysis of 133 whey samples collected in 2009–2010 from Italian dairies showed a high prevalence (about 50%) of bacteriophage attacks on the blend ST020. More specifically, the strain S. thermophilus ST1A was found to be the preferred target of the bacteriophages. A bacteriophage insensitive mutant (BIM5) of the phage-sensitive strain ST1A was successfully developed and used to substitute strain ST1A in the Crescenza starter culture ST020. The strain BIM5 showed identical technological and industrial traits as those of the phage-sensitive strain ST1A. The improved resistance of the modified Crescenza starter culture ST020R was confirmed at Italian dairies, and its effectiveness monitored on 122 whey samples collected in 2011–2012. Compared to the previous values (2009–2010), the use of the phage-hardened blend ST020R allowed reducing of frequency of phage attacks from about 50 to less than 5% of the whey samples investigated.
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Affiliation(s)
- Donatella Chirico
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
| | - Arianna Gorla
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
| | - Viola Verga
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
| | - Per D Pedersen
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
| | - Eliseo Polgatti
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
| | - Antonio Cava
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
| | - Fabio Dal Bello
- Clerici-Sacco Group, Caglificio Clerici S.p.A. and Sacco S.r.l., Cadorago Italy
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23
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Differences in lactococcal cell wall polysaccharide structure are major determining factors in bacteriophage sensitivity. mBio 2014; 5:e00880-14. [PMID: 24803515 PMCID: PMC4010823 DOI: 10.1128/mbio.00880-14] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Analysis of the genetic locus encompassing a cell wall polysaccharide (CWPS) biosynthesis operon of eight strains of Lactococcus lactis, identified as belonging to the same CWPS type C genotype, revealed the presence of a variable region among the strains examined. The results allowed the identification of five subgroups of the C type named subtypes C1 to C5. This variable region contains genes encoding glycosyltransferases that display low or no sequence homology between the subgroups. In this study, we purified an acidic polysaccharide from the cell wall of L. lactis 3107 (subtype C2) and confirmed that it is structurally different from the previously established CWPS of subtype C1L. lactis MG1363. The CWPS of L. lactis 3107 is composed of pentasaccharide repeating units linked by phosphodiester bonds with the structure 6-α-Glc-3-β-Galf-3-β-GlcNAc-2-β-Galf-6-α-GlcNAc-1-P. Combinations of genes from the variable region of subtype C2 were introduced into a mutant of subtype C1L. lactis NZ9000 deficient in CWPS biosynthesis. The resulting recombinant mutant synthesized a polysaccharide with a composition characteristic of that of subtype C2L. lactis 3107 and not wild-type C1L. lactis NZ9000. By challenging the recombinant mutant with various lactococcal phages, we demonstrated that CWPS is the host cell surface receptor of tested bacteriophages of both the P335 and 936 groups and that differences between the CWPS structures play a crucial role in determining phage host range. Despite the efforts of nearly 80 years of lactococcal phage research, the precise nature of the cell surface receptors of the P335 and 936 phage group receptors has remained elusive. This work demonstrates the molecular nature of a P335 group receptor while bolstering the evidence of its role in host recognition by phages of the 936 group and at least partially explains why such phages have a very narrow host range. The information generated will be instrumental in understanding the molecular mechanisms of how phages recognize specific saccharidic receptors located on the surface of their bacterial host.
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24
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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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25
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Bull M, Plummer S, Marchesi J, Mahenthiralingam E. The life history ofLactobacillus acidophilusas a probiotic: a tale of revisionary taxonomy, misidentification and commercial success. FEMS Microbiol Lett 2013; 349:77-87. [DOI: 10.1111/1574-6968.12293] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/30/2013] [Accepted: 10/02/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Matthew Bull
- Organisms and Environment Division; Cardiff School of Biosciences; Cardiff University; Cardiff UK
| | | | - Julian Marchesi
- Organisms and Environment Division; Cardiff School of Biosciences; Cardiff University; Cardiff UK
- Department of Hepatology and Gastroenterology; St Mary's Hospital; Imperial College London; London UK
| | - Eshwar Mahenthiralingam
- Organisms and Environment Division; Cardiff School of Biosciences; Cardiff University; Cardiff UK
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26
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Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13. Appl Environ Microbiol 2013; 79:4401-9. [PMID: 23666331 DOI: 10.1128/aem.00832-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcal dairy starter strains are under constant threat from phages in dairy fermentation facilities, especially by members of the so-called 936, P335, and c2 species. Among these three phage groups, members of the P335 species are the most genetically diverse. Here, we present the complete genome sequences of two P335-type phages, Q33 and BM13, isolated in North America and representing a novel lineage within this phage group. The Q33 and BM13 genomes exhibit homology, not only to P335-type, but also to elements of the 936-type phage sequences. The two phage genomes also have close relatedness to phages infecting Enterococcus and Clostridium, a heretofore unknown feature among lactococcal P335 phages. The Q33 and BM13 genomes are organized in functionally related clusters with genes encoding functions such as DNA replication and packaging, morphogenesis, and host cell lysis. Electron micrographic analysis of the two phages highlights the presence of a baseplate more reminiscent of the baseplate of 936 phages than that of the majority of members of the P335 group, with the exception of r1t and LC3.
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