Contribution of Farm Level Milk Sourcing on Non-Starter Lactic Acid Bacteria (NSLAB) in Cheddar, and the Assessment of High Resolution Melt Analysis used for Species Identification Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/hx11xk21j

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  • Non-starter lactic acid bacteria (NSLAB) are found at low levels in fresh raw milk and are important to the dairy industry because of their potential impact on the flavor and texture of yogurt, sour cream, and cheese. The purpose of this study was to evaluate three methods for the identification of NSLAB and investigate NSLAB contribution from raw milk sourced from different farms on the microbiological profile of Cheddar cheese during aging. Three methods were evaluated: P1V1/P2V1 PCR with HRM analysis, 16s rDNA sequencing using MicroSEQ® 500, and API 50 CHL. HRM analysis and API 50 CHL were evaluated using NSLAB reference strains which included Lb. paracasei, Lb. casei, Lb. plantarum, Lb. rhamnosus, and L. lactis subsp. lactis. In addition, 16s rDNA sequencing and HRM analysis of the P1V1/P2V1 amplicon were used for the identification of unknown isolates from raw milk and 6.5 mo aged Cheddar cheese. Five out of seven reference strains were correctly identified using API 50 CHL. HRM analysis was in agreement with 16s rDNA sequencing 75% and 66% of the time for L. lactis and Lb. paracasei, respectively. Melt curves of isolates identified as Lb. paracasei and L. lactis subps. lactis by 16s rDNA sequencing showed a significant amount of overlap. Farm level contribution of NSLAB was investigated by making Cheddar cheeses using a standardized recipe with raw milk sourced from dairies on the Oregon Coast and in the Willamette Valley and aged. Isolates were selected for preliminary speciation using HRM analysis and further subtyped using a second HRM repetitive sequence-based polymerase chain reaction (rep-PCR). Lb. paracasei/L. lactis were identified in raw milk and cheeses sourced from the Oregon Coast and from the Willamette Valley. Lb. curvatus was only identified in raw milk samples. Species diversity decreased throughout aging in all cheeses with the exception of cheese made from milk sourced from the southern Oregon Coast. After 6.5 mo of aging, the predominant species across all cheeses was Lb. paracasei/L. lactis (70.79% of isolates). Strain diversity was highest in milk sourced from the northern Oregon Coast. 16S rDNA sequencing identified additional species not reported using HRM analysis which included Lb. brevis, L. lactis cremoris, E. saccharolyticus, E. faecalis, S. bovis, S. chromogenes, Leuc. lactis, and W. paramesenteroides. Based on comparison to 16s rDNA identification, HRM analysis of the P1V1/P2V1 amplicon is not suitable for unknown NSLAB identification. For NSLAB contribution, evidence suggests that milk sourcing at the farm level contributes to the strain diversity of NSLAB present in raw milk and Cheddar cheese. This information can help larger producers understand the contribution their farmers have on their product and steps they may need to take to mitigate it or potentially capitalize on the differences in a small batch capacity.
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  • description.provenance : Made available in DSpace on 2017-01-05T00:15:53Z (GMT). No. of bitstreams: 2 BairdChristopherS2017.pdf: 5471043 bytes, checksum: e00534e64c57292b88e6619c65ec0e7a (MD5) license_rdf: 1223 bytes, checksum: d127a3413712d6c6e962d5d436c463fc (MD5) Previous issue date: 2016-12-12
  • description.provenance : Approved for entry into archive by Julie Kurtz(julie.kurtz@oregonstate.edu) on 2016-12-30T16:33:59Z (GMT) No. of bitstreams: 2 BairdChristopherS2017.pdf: 5471043 bytes, checksum: e00534e64c57292b88e6619c65ec0e7a (MD5) license_rdf: 1223 bytes, checksum: d127a3413712d6c6e962d5d436c463fc (MD5)
  • description.provenance : Submitted by Christopher Baird (bairdc@oregonstate.edu) on 2016-12-30T05:51:13Z No. of bitstreams: 2 BairdChristopherS2017.pdf: 5471043 bytes, checksum: e00534e64c57292b88e6619c65ec0e7a (MD5) license_rdf: 1223 bytes, checksum: d127a3413712d6c6e962d5d436c463fc (MD5)
  • description.provenance : Submitted by Christopher Baird (bairdc@oregonstate.edu) on 2016-12-13T01:36:05Z No. of bitstreams: 2 license_rdf: 1223 bytes, checksum: d127a3413712d6c6e962d5d436c463fc (MD5) BairdChristopherS2017.pdf: 5469638 bytes, checksum: 7a3fdf63e3b721d848d6285e26d01f84 (MD5)
  • description.provenance : Approved for entry into archive by Laura Wilson(laura.wilson@oregonstate.edu) on 2017-01-05T00:15:53Z (GMT) No. of bitstreams: 2 BairdChristopherS2017.pdf: 5471043 bytes, checksum: e00534e64c57292b88e6619c65ec0e7a (MD5) license_rdf: 1223 bytes, checksum: d127a3413712d6c6e962d5d436c463fc (MD5)
  • description.provenance : Rejected by Julie Kurtz(julie.kurtz@oregonstate.edu), reason: Hi Christopher, Rejecting for the following reasons. I also printed out some of the pretext pages and noted revisions which I will email you - 1) The title on the Abstract page doesn't match the title of the Title page exactly. Abstract has ...Cheddar, and the Assessment... on the Title page - ...Cheddar Cheese, and the... 2) Abstract page - move Joy Waite-Cusic so her name appears under the same line. 3) Title page - bottom, remove the word "Defense" so it reads - Presented December 12, 2016 4) Approval page - Change date from June 17, 2016 to December 12, 2016. Also remove all the names so the first & second signature line reads - Co-Major Professor, representing Food Science and Technology. Third line - Head of the Department of Food Science and Technology 5) Table of Contents - since you have more than 5 appendices a separate list of appendices should be added to appear after the List of Tables. 6) There's a number with the page numbering, after page 5, 6 it starts again 5, 6 - to the end. Renumber after the first page 6 Everything else looks good. Once revised, log back into ScholarsArchive and go to the upload page. Replace the attached file with the revised PDF and resubmit. Thanks, Julie on 2016-12-22T19:30:55Z (GMT)

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