Thermus and the Pink Discoloration Defect in Cheese

Lisa Quigley; Daniel J O'Sullivan; David Daly; Orla O'Sullivan; Zuzana Burdikova; Rostislav Vana; Tom P Beresford; R Paul Ross; Gerald F Fitzgerald; Paul L H McSweeney; Linda Giblin; Jeremiah J Sheehan; Paul D Cotter

doi:10.1128/mSystems.00023-16

Thermus and the Pink Discoloration Defect in Cheese

mSystems. 2016 Jun 14;1(3):e00023-16. doi: 10.1128/mSystems.00023-16. eCollection 2016 May-Jun.

Affiliations

¹ Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
² Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.
³ Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
⁴ Tescan Orsay Holding, Brno, Czech Republic.
⁵ APC Microbiome Institute, Cork, Ireland; College of Science, Engineering and Food Science, University College Cork, Cork, Ireland.
⁶ School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Institute, Cork, Ireland.
⁷ School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.
⁸ Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; APC Microbiome Institute, Cork, Ireland.

Abstract

A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses. Prompted by this finding and data confirming the pink discoloration to be associated with the presence of a carotenoid, a culture-based approach was employed, and Thermus thermophilus was successfully cultured from defect-containing cheeses. The link between Thermus and the pinking phenomenon was then established through the cheese defect equivalent of Koch's postulates when the defect was recreated by the reintroduction of a T. thermophilus isolate to a test cheese during the manufacturing process. IMPORTANCE Pink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In this study, a combined 16S rRNA, whole-genome sequencing, and quantitative PCR approach was taken. This resulted in the identification of Thermus, a carotenoid-producing thermophile, in defect-associated cheeses and the recreation of the problem in cheeses to which Thermus was added. This finding has the potential to lead to new strategies to eliminate this defect, and our method represents an approach that can be employed to investigate the role of microbes in other food defects of unknown origin.

Keywords: Thermus; carotenoid; cheese; microbiota; pinking.

Grants and funding

This work was funded by Teagasc Walsh Fellowships and by the Department of Agriculture, Food and the Marine's Food Institutional Research Measure, through the 'Cheeseboard 2015' project.