Metagenomic analysis of dairy bacteriophages: Extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter cultures

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dc.contributor.authorMuhammed, Musemma K.
dc.contributor.authorKot, Witold
dc.contributor.authorNeve, Horst
dc.contributor.authorMahony, Jennifer
dc.contributor.authorCastro-Mejía, Josué L.
dc.contributor.authorKrych, Lukasz
dc.contributor.authorHansen, Lars H.
dc.contributor.authorNielsen, Dennis S.
dc.contributor.authorSørensen, Søren J
dc.contributor.authorHeller, Knut J.
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.authorVogensen, Finn K.
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderKøbenhavns Universiteten
dc.date.accessioned2021-08-23T14:33:47Z
dc.date.available2021-08-23T14:33:47Z
dc.date.issued2017-10-01
dc.date.updated2021-08-23T13:51:10Z
dc.description.abstractDespite 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.en
dc.description.sponsorshipKøbenhavns Universitet (FTP Project number 0602-022170B MetaPhageLAB project; Ph.D. stipend; Counteracting Age-related Loss of Skeletal Muscle Mass (CALM) project)en
dc.description.statusPeer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide00888-17en
dc.identifier.citationMuhammed, M. K., Kot, W., Neve, H., Mahony, J., Castro-Mejía, J. L., Krych, L., Hansen, L. H., Nielsen, D. S., Sørensen, S. J., Heller, K. J. van Sinderen, D. and Vogensen, F. K. (2017) 'Metagenomic analysis of dairy bacteriophages: Extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter cultures', Applied and Environmental Microbiology, 83(19), e00888-17 (15pp). doi: 10.1128/AEM.00888-17en
dc.identifier.doi10.1128/AEM.00888-17en
dc.identifier.eissn1098-5336
dc.identifier.endpage15en
dc.identifier.issn0099-2240
dc.identifier.issued19en
dc.identifier.journaltitleApplied and Environmental Microbiologyen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/11773
dc.identifier.volume83en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Starting Investigator Research Grant (SIRG)/15/SIRG/3430/IE/Phage-host interactome of the dairy bacterium Streptococcus thermophilus (PHIST)/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Investigator Programme/13/IA/1953/IE/Functional analysis of the host adsorption and DNA injection processes of a lactococcal bacteriophage/en
dc.rights© 2017, American Society for Microbiology. All Rights Reserved.en
dc.subjectabundance, bacteriophages, Caudovirales, dairy, diversity, Lactococcus lactisen
dc.subjectLeuconostocen
dc.subjectMesophilicen
dc.subjectMetaviromeen
dc.subjectSiphoviridaeen
dc.subjectStarter cultureen
dc.subjectWheyen
dc.titleMetagenomic analysis of dairy bacteriophages: Extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter culturesen
dc.typeArticle (peer-reviewed)en
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