title: Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness.
abstract: BACKGROUND
  Lactococcus lactis is industrially employed to manufacture various fermented dairy products. The most cost-effective method for the preservation of L. lactis starter cultures is spray drying, but during this process cultures encounter heat and oxidative stress, typically resulting in low survival rates. However, viability of starter cultures is essential for their adequate contribution to milk fermentation, supporting the ambition to better understand and improve their robustness phenotypes.
  
  
  RESULTS
  This study describes a transcriptome-phenotype matching approach in which the starter L. lactis MG1363 was fermented under a variety of conditions that differed in the levels of oxygen and/or salt, as well as the fermentation pH and temperature. Samples derived from these fermentations in the exponential phase of bacterial growth were analyzed by full-genome transcriptomics and the assessment of heat and oxidative stress phenotypes. Variations in the fermentation conditions resulted in up to 1000-fold differences in survival during heat and oxidative stress. More specifically, aeration during fermentation induced protection against heat stress, whereas a relatively high fermentation temperature resulted in enhanced robustness towards oxidative stress. Concomitantly, oxygen levels and fermentation temperature induced differential expression of markedly more genes when compared with the other fermentation parameters. Correlation analysis of robustness phenotypes and gene expression levels revealed transcriptome signatures for oxidative and/or heat stress survival, including the metC-cysK operon involved in methionine and cysteine metabolism. To validate this transcriptome-phenotype association we grew L. lactis MG1363 in the absence of cysteine which led to enhanced robustness towards oxidative stress.
  
  
  CONCLUSIONS
  Overall, we demonstrated the importance of careful selection of fermentation parameters prior to industrial processing of starter cultures. Furthermore, established stress genes as well as novel genes were associated with robustness towards heat and/or oxidative stress. Assessment of the expression levels of this group of genes could function as an indicator for enhanced selection of fermentation parameters resulting in improved robustness during spray drying. The increased robustness after growth without cysteine appeared to confirm the role of expression of the metC-cysK operon as an indicator of robustness and suggests that sulfur amino acid metabolism plays a pivotal role in oxidative stress survival.
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, Delft, GA, The Netherlands. annereinou.dijkstra@nizo.com.|NIZO food research, P.O. Box 20, 6710, Ede, BA, The Netherlands. annereinou.dijkstra@nizo.com.|Universiteit van Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098, Amsterdam, XH, The Netherlands. annereinou.dijkstra@nizo.com.
authors.forename: Annereinou R
authors.initials: AR
authors.lastname: Dijkstra
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, Delft, GA, The Netherlands. wynand.alkema@nizo.com.|NIZO food research, P.O. Box 20, 6710, Ede, BA, The Netherlands. wynand.alkema@nizo.com.|Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, P.O. Box 9101, 6500, Nijmegen, HB, The Netherlands. wynand.alkema@nizo.com.
authors.forename: Wynand
authors.initials: W
authors.lastname: Alkema
authors.affiliation: NIZO food research, P.O. Box 20, 6710, Ede, BA, The Netherlands. marjo.starrenburg@nizo.com.
authors.forename: Marjo J C
authors.initials: MJ
authors.lastname: Starrenburg
authors.affiliation: Universiteit van Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098, Amsterdam, XH, The Netherlands. jeroen.hugenholtz@corbion.com.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Hugenholtz
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, Delft, GA, The Netherlands. sacha.vanhijum@nizo.com.|NIZO food research, P.O. Box 20, 6710, Ede, BA, The Netherlands. sacha.vanhijum@nizo.com.|Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, P.O. Box 9101, 6500, Nijmegen, HB, The Netherlands. sacha.vanhijum@nizo.com.|TI Food & Nutrition, Nieuwe Kanaal 9A, 6709, Wageningen, PA, The Netherlands. sacha.vanhijum@nizo.com.
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, Delft, GA, The Netherlands. peter.bron@nizo.com.|NIZO food research, P.O. Box 20, 6710, Ede, BA, The Netherlands. peter.bron@nizo.com.|TI Food & Nutrition, Nieuwe Kanaal 9A, 6709, Wageningen, PA, The Netherlands. peter.bron@nizo.com.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Bron
mesh_terms: D003611:Dairy Products; D006358:Hot Temperature; D013294:Lactococcus lactis / Q000235:genetics* / Q000378:metabolism*; D050296:Microbial Viability / Q000235:genetics*; D018384:Oxidative Stress / Q000502:physiology*; D010641:Phenotype