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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


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          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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          Author and article information

          Role: Editor
          Appl Environ Microbiol
          Appl. Environ. Microbiol
          Applied and Environmental Microbiology
          American Society for Microbiology (1752 N St., N.W., Washington, DC )
          28 July 2017
          15 September 2017
          1 October 2017
          : 83
          : 19
          [a ]Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
          [b ]Department of Biology, University of Copenhagen, Copenhagen, Denmark
          [c ]Department of Environmental Science, Aarhus University, Roskilde, Denmark
          [d ]Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
          [e ]School of Microbiology, University College Cork, Cork, Ireland
          [f ]APC Microbiome Institute, University College Cork, Cork, Ireland
          Rutgers, The State University of New Jersey
          Author notes
          Address correspondence to Finn K. Vogensen, fkv@ 123456food.ku.dk .

          Citation Muhammed MK, Kot W, Neve H, Mahony J, Castro-Mejía JL, Krych L, Hansen LH, Nielsen DS, Sørensen SJ, Heller KJ, van Sinderen D, Vogensen FK. 2017. 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 83:e00888-17. https://doi.org/10.1128/AEM.00888-17.

          PMC5601343 PMC5601343 5601343 00888-17
          Copyright © 2017 American Society for Microbiology.

          All Rights Reserved.

          Page count
          supplementary-material: 1, Figures: 2, Tables: 4, Equations: 0, References: 69, Pages: 15, Words: 10883
          Funded by: The Danish Council for Independent Research I Technology and Production Sciences
          Award ID: 0602-022170B
          Award Recipient : Dennis S. Nielsen Award Recipient : Søren Johannes Sørensen Award Recipient : Knut J. Heller Award Recipient : Douwe van Sinderen Award Recipient : Finn K. Vogensen Award Recipient : Musemma Kedir Muhammed Award Recipient : Witold Kot Award Recipient : Horst Neve Award Recipient : Jennifer Mahony Award Recipient : Lars Hestbjerg Hansen
          Funded by: Starting Investigator Research Grant
          Award ID: 15/SIRG/3430
          Award Recipient : Jennifer Mahony
          Funded by: CALM
          Award Recipient : Josué L. Castro-Mejía
          Funded by: Principal Investigator Award
          Award ID: 13/IA/1953
          Award Recipient : Douwe van Sinderen
          Custom metadata
          October 2017

          Leuconostoc ,mesophilic,metavirome, Siphoviridae ,starter culture,whey,abundance,bacteriophages, Caudovirales ,dairy,diversity, Lactococcus lactis


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