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Abstract
Bacteriophages represent the main microbiological threat for the manufacture of fermented foods. The dairy industry is the most affected by this problem, as phages are naturally present in raw milk, surfaces, vats, tanks, floors, and distributed by air displacements. Cheese whey may also contain high phage concentrations. Prophages harbored by lysogenic strains could be induced, generating new lytic phages. In this context, where phages cannot be eradicated from dairies, methods of phage monitoring are mandatory. These are mainly based in microbiological features, like classical methods, that are the most used, economic and simple to carry out. Phage DNA detection and quantification by PCR and qPCR, more complex and expensive, are faster, although not able to discern between viable and non-viable virions. Electron microscopy allows direct visualization and characterization of phage morphology, but the apparatus is expensive. Alternative methods based in other phage traits also exist, though less studied and not applicable on a daily basis. Recognition of contamination sources and correct phage monitoring in dairy factories allow a correct application of control measures. These include general measures such as proper factory design, efficient programs of sanitization, good treatment of raw materials, especially milk, and careful handling of by-products. Additionally, the use of starts cultures should be adequate, with application of rotation schemes when possible. Finally, the selection of bacteriophage insensitive mutants (BIM) is essential, and can be achieved simply and empirically, though the study of CRISPR-Cas and other newly discovered mechanisms provide a more rational basis to obtain BIMs with optimized features.
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Maske BL, de Melo Pereira GV, da Silva Vale A, Marques Souza DS, De Dea Lindner J, Soccol CR. Viruses in fermented foods: are they good or bad? Two sides of the same coin. Food Microbiol 2021; 98:103794. [PMID: 33875222 PMCID: PMC7992106 DOI: 10.1016/j.fm.2021.103794] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/21/2021] [Indexed: 12/23/2022]
Abstract
The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.
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Affiliation(s)
- Bruna Leal Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | | | - Alexander da Silva Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Doris Sobral Marques Souza
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil; Applied Virology Laboratory, UFSC, Florianópolis, SC, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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3
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Kyrkou I, Carstens AB, Ellegaard-Jensen L, Kot W, Zervas A, Djurhuus AM, Neve H, Franz CMAP, Hansen M, Hansen LH. Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus". Sci Rep 2020; 10:8763. [PMID: 32472049 PMCID: PMC7260188 DOI: 10.1038/s41598-020-65366-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus "Silenusvirus".
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Affiliation(s)
- Ifigeneia Kyrkou
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Alexander Byth Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
| | - Amaru Miranda Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark.
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark.
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Briggiler Marcó MB, Quiberoni A, Suárez V. Virulence of Leuconostoc phages: Influence of stress conditions associated to dairy processes on their host-phage interactions. Int J Food Microbiol 2019; 303:26-31. [PMID: 31128387 DOI: 10.1016/j.ijfoodmicro.2019.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/15/2019] [Accepted: 05/12/2019] [Indexed: 01/17/2023]
Abstract
In this work, we assessed the impact of technological cell stress conditions, commonly present in industrial dairy processes, on the host strain-phage interactions in Leuconostoc. Adsorption and burst size of LDG (Leuconostoc pseudomesenteroides) and Ln-9 (Leuconostoc mesenteroides) phages were evaluated under the following conditions: i) MRS broth, 30 °C; ii) MRS broth at pH 5.5, 30 °C (acidic stress); iii) MRS broth added of NaCl at 4% w/v, 30 °C (osmotic stress) and iv) MRS broth, 10 °C (cold stress). Experiences were performed with the host strains growing both in MRS broth (30 °C) and under stress conditions. On the other hand, the effect of diverse levels of NaCl, KCl, saccharose and glucose on the adsorption for LDG phage was evaluated. Acidic and cold conditions did not significantly affect the adsorption rates for any phage. However, adsorption rate of phage LDG was highly reduced under osmotic stress (NaCl), except when the host strain previously grew in presence of the salt. LDG phage adsorption was not modified by addition of saccharides, but it drastically decreased in presence of salts. Acidic conditions did not affect the burst size for LDG phage, but Ln-9 phage diminished this parameter (61 phage particles/infected cell). Latency time showed a lengthening of 10 min for both phages, while the burst time remained unaltered for LDG and it was delayed 10 min for Ln-9. LDG phage did not propagate under osmotic conditions, but Ln-9 phage released phage particles with an important increase of its latent period and burst time. No phage particles were released within 90 min after the adsorption step under cold stress. This is the first report about this subject. Under certain conditions of technological stress (osmotic and cold) associated to dairy processes, phage infections on the two systems studied in this work could be delayed/inhibited.
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Affiliation(s)
- Mariángeles Briggiler Briggiler Marcó
- Instituto de Lactología Industrial, Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe, Argentina.
| | - Andrea Quiberoni
- Instituto de Lactología Industrial, Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe, Argentina
| | - Viviana Suárez
- Instituto de Lactología Industrial, Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe, Argentina
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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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Pujato SA, Quiberoni A, Mercanti DJ. Bacteriophages on dairy foods. J Appl Microbiol 2018; 126:14-30. [PMID: 30080952 DOI: 10.1111/jam.14062] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/29/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023]
Abstract
This review focuses on the impact of bacteriophages on the manufacture of dairy foods. Firstly, the impact of phages of lactic acid bacteria in the dairy industry, where they are considered enemies, is discussed. The sources of phage contamination in dairy plants are detailed, with special emphasis on the rise of phage infections related to the growing use of cheese whey as ingredient. Other topics include traditional and new methods of phage detection, quantification and monitoring, and strategies of phage control in dairy plants, either of physical, chemical or biological nature. Finally, the use of phages or purified phage enzymes as allies to control pathogenic bacteria in the food industry is reviewed.
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Affiliation(s)
- S A Pujato
- Facultad de Ingeniería Química, Instituto de Lactología Industrial (Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas), Santa Fe, Argentina
| | - A Quiberoni
- Facultad de Ingeniería Química, Instituto de Lactología Industrial (Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas), Santa Fe, Argentina
| | - D J Mercanti
- Facultad de Ingeniería Química, Instituto de Lactología Industrial (Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas), Santa Fe, Argentina
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Muhammed MK, Olsen ML, Kot W, Neve H, Castro-Mejía JL, Janzen T, Hansen LH, Nielsen DS, Sørensen SJ, Heller KJ, Vogensen FK. Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches. Int J Food Microbiol 2018. [PMID: 29529425 DOI: 10.1016/j.ijfoodmicro.2018.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To investigate the notion that starter cultures can be a reservoir of bacteriophages (phages) in the dairy environment, strains of three DL-starters (undefined mesophilic mixed-strain starters containing Lactococcus lactis subsp. lactis biovar. diacetylactis and Leuconostoc species) were selected and induced by mitomycin C, and the whole starters were induced spontaneously as well as by mitomycin C. Frequency of induction of 17%, 26% and 12% was estimated among the isolates of the three starters, with majority of the induced phages mostly showing morphological similarity to known P335 phages, and with a fraction of them showing atypical features. Sequences of P335 quasi-species phages were found to be the most frequent entities in almost all metaviromes derived from the induced lysates. However, sequences of Sk1virus phages (previously 936 phages) were emerged as the predominant entities following spontaneous induction of one of the starters, suggesting a phage-carrier state. Sequences of other phages such as 949, 1706, C2virus (previously c2 phages) and Leuconostoc species could also be observed but with a lower relative frequency. Taken together, the majority of the P335 quasi-species phages could represent the induced viral community of the starters and the remaining phage groups mainly represent the background ambient viral community.
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Affiliation(s)
- Musemma K Muhammed
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Mette L Olsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Witold Kot
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark; Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str. 1, D-24103 Kiel, Germany
| | - Josué L Castro-Mejía
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Thomas Janzen
- Cultures and Enzyme Division, Chr. Hansen A/S, Boege Alle 10-12, DK-2970 Hoersholm, Denmark
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str. 1, D-24103 Kiel, Germany
| | - Finn K Vogensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark.
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Pujato SA, Quiberoni A, Guglielmotti DM. Technological performance of spontaneous phage-resistant derivatives of Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides during milk fermentation. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures. Appl Environ Microbiol 2017; 83:AEM.00888-17. [PMID: 28754704 DOI: 10.1128/aem.00888-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023] Open
Abstract
Despite being potentially highly useful for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows the removal of the bulk protein from whey and milk samples with losses of less than 50% of spiked phages. The protocol was applied to extract phages from whey in order to test the notion that members of Lactococcus lactis 936 (now Sk1virus), P335, c2 (now C2virus) and Leuconostoc phage groups are the most frequently encountered in the dairy environment. The relative abundance and diversity of phages in eight and four whey mixtures from dairies using undefined mesophilic mixed-strain cultures containing Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc species (i.e., DL starter cultures) and defined cultures, respectively, were assessed. Results obtained from transmission electron microscopy and high-throughput sequence analyses revealed the dominance of Lc. lactis 936 phages (order Caudovirales, family Siphoviridae) in dairies using undefined DL starter cultures and Lc. lactis c2 phages (order Caudovirales, family Siphoviridae) in dairies using defined cultures. The 936 and Leuconostoc phages demonstrated limited diversity. Possible coinduction of temperate P335 prophages and satellite phages in one of the whey mixtures was also observed.IMPORTANCE The method optimized in this study could provide an important basis for understanding the dynamics of the phage community (abundance, development, diversity, evolution, etc.) in dairies with different sizes, locations, and production strategies. It may also enable the discovery of previously unknown phages, which is crucial for the development of rapid molecular biology-based methods for phage burden surveillance systems. The dominance of only a few phage groups in the dairy environment signifies the depth of knowledge gained over the past decades, which served as the basis for designing current phage control strategies. The presence of a correlation between phages and the type of starter cultures being used in dairies might help to improve the selection and/or design of suitable, custom, and cost-efficient phage control strategies.
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Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides bacteriophages: Genomics and cross-species host ranges. Int J Food Microbiol 2017. [PMID: 28651078 DOI: 10.1016/j.ijfoodmicro.2017.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Unveiling virus-host interactions are relevant for understanding the biology and evolution of microbes globally, but in particular, it has also a paramount impact on the manufacture of fermented dairy products. In this study, we aim at characterizing phages infecting the commonly used heterofermentative Leuconostoc spp. on the basis of host range patterns and genome analysis. Host range of six Leuconostoc phages was investigated using three methods (efficiency of plaquing, spot and turbidity tests) against Ln. mesenteroides and Ln. pseudomesenteroides strains. Complete genome sequencing from four out of the six studied Leuconostoc phages were obtained in this work, while the remaining two have been sequenced previously. According to our results, cross-species host specificity was demonstrated, as all phages tested were capable of infecting both Ln. pseudomesenteroides and Ln. mesenteroides strains, although with different efficiency of plaquing (EOP). Phage adsorption rates and ability of low-EOP host strains to propagate phages by crossing the Leuconostoc species' barrier confirm results. At the genome level, phages CHA, CHB, Ln-7, Ln-8 and Ln-9 revealed high similarity with previously characterized phages infecting mostly Ln. mesenteroides strains, while phage LDG was highly similar to phages infecting Ln. pseudomesenteroides. Additionally, correlation between receptor binding protein (RBP) and host range patterns allowed us to unveil a finer clustering of Leuconostoc phages studied into four groups. This is the first report of overlapped phage host ranges between Leuconostoc species.
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Wagner N, Samtlebe M, Franz CM, Neve H, Heller KJ, Hinrichs J, Atamer Z. Dairy bacteriophages isolated from whey powder: Thermal inactivation and kinetic characterisation. Int Dairy J 2017. [DOI: 10.1016/j.idairyj.2016.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Muhammed MK, Krych L, Nielsen DS, Vogensen FK. A high-throughput qPCR system for simultaneous quantitative detection of dairy Lactococcus lactis and Leuconostoc bacteriophages. PLoS One 2017; 12:e0174223. [PMID: 28339484 PMCID: PMC5365131 DOI: 10.1371/journal.pone.0174223] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 03/05/2017] [Indexed: 11/20/2022] Open
Abstract
Simultaneous quantitative detection of Lactococcus (Lc.) lactis and Leuconostoc species bacteriophages (phages) has not been reported in dairies using undefined mixed-strain DL-starters, probably due to the lack of applicable methods. We optimized a high-throughput qPCR system that allows simultaneous quantitative detection of Lc. lactis 936 (now SK1virus), P335, c2 (now C2virus) and Leuconostoc phage groups. Component assays are designed to have high efficiencies and nearly the same dynamic detection ranges, i.e., from ~1.1 x 105 to ~1.1 x 101 phage genomes per reaction, which corresponds to ~9 x 107 to ~9 x 103 phage particles mL-1 without any additional up-concentrating steps. The amplification efficiencies of the corresponding assays were 100.1±2.6, 98.7±2.3, 101.0±2.3 and 96.2±6.2. The qPCR system was tested on samples obtained from a dairy plant that employed traditional mother-bulk-cheese vat system. High levels of 936 and P335 phages were detected in the mother culture and the bulk starter, but also in the whey samples. Low levels of phages were detected in the cheese milk samples.
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Affiliation(s)
- Musemma K. Muhammed
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Dennis S. Nielsen
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Finn K. Vogensen
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
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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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Mahony J, Stockdale SR, Collins B, Spinelli S, Douillard FP, Cambillau C, van Sinderen D. Lactococcus lactis phage TP901-1 as a model for Siphoviridae virion assembly. BACTERIOPHAGE 2016; 6:e1123795. [PMID: 27144086 DOI: 10.1080/21597081.2015.1123795] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/28/2022]
Abstract
Phages infecting Lactococcus lactis pose a serious threat to the dairy fermentation sector. Consequently, they are among the most thoroughly characterized Gram positive-infecting phages. The majority of lactococcal phages belong to the tailed family of phages named the Siphoviridae. The coliphage lambda and the Bacillus subtilis phage SPP1 have been the predominant comparators for emerging siphophages both genomically and structurally and both phages recognize a membrane protein receptor. In contrast, the lactococcal P335 group phage TP901-1 attaches to cell wall surface polysaccharides. It is a typical "lambdoid" siphophage possessing a long non-contractile tail and a genomic architecture reminiscent of lambda and SPP1 despite low or undetectable sequence homology in many of its encoded products, especially those involved in host recognition. A functional analysis of the structural components of TP901-1 was undertaken based on the characterization of a series of mutants in the region encoding the capsid and tail morphogenetic elements. Through this analysis, it was possible to deduce that, despite the lack of sequence homology, the overall genomic architecture of Siphoviridae phages typified by functional synteny is conserved. Furthermore, a model of the TP901-1 assembly pathway was developed with potential implications for many tailed phages.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology, University College Cork , Cork, Ireland
| | - Stephen R Stockdale
- School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Barry Collins
- School of Microbiology, University College Cork , Cork, Ireland
| | - Silvia Spinelli
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy , Marseille Cedex, France
| | | | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille Cedex, France; Centre National de la Recherche Scientifique, AFMB, Campus de Luminy, Marseille Cedex, France
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
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15
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Draft Genome Sequence of Three Antibiotic-Resistant Leuconostoc mesenteroides Strains of Dairy Origin. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01018-15. [PMID: 26358600 PMCID: PMC4566182 DOI: 10.1128/genomea.01018-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Leuconostoc mesenteroides is a lactic acid bacterium (LAB) commonly associated with fermented foods. Here, we report the genome sequence of three selected dairy strains, showing atypical antibiotic resistances (AR). Genome analysis provided a better understanding of the genetic bases of AR in Leuconostoc and its potential transferability among foodborne bacteria.
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16
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Pujato SA, Mercanti DJ, Guglielmotti DM, Rousseau GM, Moineau S, Reinheimer JA, Quiberoni ADL. Phages of dairy Leuconostoc mesenteroides: Genomics and factors influencing their adsorption. Int J Food Microbiol 2015; 201:58-65. [DOI: 10.1016/j.ijfoodmicro.2015.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 02/05/2015] [Accepted: 02/16/2015] [Indexed: 10/24/2022]
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17
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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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18
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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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19
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Pujato SA, Guglielmotti DM, Ackermann HW, Patrignani F, Lanciotti R, Reinheimer JA, Quiberoni A. Leuconostoc bacteriophages from blue cheese manufacture: long-term survival, resistance to thermal treatments, high pressure homogenization and chemical biocides of industrial application. Int J Food Microbiol 2014; 177:81-8. [DOI: 10.1016/j.ijfoodmicro.2014.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/12/2014] [Accepted: 02/15/2014] [Indexed: 12/27/2022]
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20
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Kot W, Neve H, Heller KJ, Vogensen FK. Bacteriophages of leuconostoc, oenococcus, and weissella. Front Microbiol 2014; 5:186. [PMID: 24817864 PMCID: PMC4009412 DOI: 10.3389/fmicb.2014.00186] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
Leuconostoc (Ln.), Weissella, and Oenococcus form a group of related genera of lactic acid bacteria, which once all shared the name Leuconostoc. They are associated with plants, fermented vegetable products, raw milk, dairy products, meat, and fish. Most of industrially relevant Leuconostoc strains can be classified as either Ln. mesenteroides or Ln. pseudomesenteroides. They are important flavor producers in dairy fermentations and they initiate nearly all vegetable fermentations. Therefore, bacteriophages attacking Leuconostoc strains may negatively influence the production process. Bacteriophages attacking Leuconostoc strains were first reported in 1946. Since then, the majority of described Leuconostoc phages was isolated from either dairy products or fermented vegetable products. Both lytic and temperate phages of Leuconostoc were reported. Most of Leuconostoc phages examined using electron microscopy belong to the Siphoviridae family and differ in morphological details. Hybridization and comparative genomic studies of Leuconostoc phages suggest that they can be divided into several groups, however overall diversity of Leuconostoc phages is much lower as compared to, e.g., lactococcal phages. Several fully sequenced genomes of Leuconostoc phages have been deposited in public databases. Lytic phages of Leuconostoc can be divided into two host species-specific groups with similarly organized genomes that shared very low nucleotide similarity. Phages of dairy Leuconostoc have rather limited host-ranges. The receptor binding proteins of two lytic Ln. pseudomesenteroides phages have been identified. Molecular tools for detection of dairy Leuconostoc phages have been developed. The rather limited data on phages of Oenococcus and Weissella show that (i) lysogeny seems to be abundant in Oenococcus strains, and (ii) several phages infecting Weissella cibaria are also able to productively infect strains of other Weissella species and even strains of the genus Lactobacillus.
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Affiliation(s)
- Witold Kot
- Department of Biology, Faculty of Science, University of Copenhagen Copenhagen, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Finn K Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen Frederiksberg, Denmark
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21
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Han JH, Wang MS, Das J, Sudheendra L, Vonasek E, Nitin N, Kennedy IM. Capture and detection of T7 bacteriophages on a nanostructured interface. ACS APPLIED MATERIALS & INTERFACES 2014; 6:4758-65. [PMID: 24650205 PMCID: PMC3985741 DOI: 10.1021/am500655r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/20/2014] [Indexed: 05/25/2023]
Abstract
A highly ordered array of T7 bacteriophages was created by the electrophoretic capture of phages onto a nanostructured array with wells that accommodated the phages. Electrophoresis of bacteriophages was achieved by applying a positive potential on an indium tin oxide electrode at the bottom of the nanowells. Nanoscale arrays of phages with different surface densities were obtained by changing the electric field applied to the bottom of the nanowells. The applied voltage was shown to be the critical factor in generating a well-ordered phage array. The number of wells occupied by a phage, and hence the concentration of phages in a sample solution, could be quantified by using a DNA intercalating dye that rapidly stains the T7 phage. The fluorescence signal was enhanced by the intrinsic photonic effect made available by the geometry of the platform. It was shown that the quantification of phages on the array was 6 orders of magnitude better than could be obtained with a fluorescent plate reader. The device opens up the possibility that phages can be detected directly without enrichment or culturing, and by detecting phages that specifically infect bacteria of interest, rapid pathogen detection becomes possible.
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Affiliation(s)
- Jin-Hee Han
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Min S. Wang
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Jayanti Das
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
| | - L. Sudheendra
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Erica Vonasek
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Nitin Nitin
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Ian M. Kennedy
- Department of Mechanical and Aerospace Engineering, Food Science and Technology, and Biological and
Agricultural Engineering, University of
California, Davis, Davis, California 95616, United States
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22
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Kot W, Hansen LH, Neve H, Hammer K, Jacobsen S, Pedersen PD, Sørensen SJ, Heller KJ, Vogensen FK. Sequence and comparative analysis of Leuconostoc dairy bacteriophages. Int J Food Microbiol 2014; 176:29-37. [PMID: 24561391 DOI: 10.1016/j.ijfoodmicro.2014.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/24/2014] [Accepted: 01/29/2014] [Indexed: 01/21/2023]
Abstract
Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc mesenteroides or Leuconostoc pseudomesenteroides strains. The phages have dsDNA genomes with sizes ranging from 25.7 to 28.4 kb. Comparative genomics analysis helped classify the 9 phages into two classes, which correlates with the host species. High percentage of similarity within the classes on both nucleotide and protein levels was observed. Genome comparison also revealed very high conservation of the overall genomic organization between the classes. The genes were organized in functional modules responsible for replication, packaging, head and tail morphogenesis, cell lysis and regulation and modification, respectively. No lysogeny modules were detected. To our knowledge this report provides the first comparative genomic work done on Leuconostoc dairy phages.
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Affiliation(s)
- Witold Kot
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg, Denmark
| | - Lars H Hansen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark; Department of Environmental Science, Aarhus University, Frederiksborgvej, 399, Roskilde, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, D-24103 Kiel, Germany
| | - Karin Hammer
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Susanne Jacobsen
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Per D Pedersen
- Clerici-Sacco Group, Via Manzoni 29, I-22071 Cadorago, Italy
| | - Søren J Sørensen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, D-24103 Kiel, Germany
| | - Finn K Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg, Denmark.
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23
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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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