Transcriptomic analysis of food-related microorganisms : Cheese microbiota, food spoilage lactic acid bacteria, and foodborne pathogens

Food products produced by humans are usually not sterile and typically contain several types of microorganisms. While there are beneficial microorganisms that are used in production and preservation of food, there are also microorganisms that cause food spoilage and foodborne illness. This study investigated the gene-expression profiles of three types of food-related bacteria during food processes. Mesophilic lactic acid bacteria and Propionibacterium that are added in milk during Maasdam cheese production were examined in Chapter I. Metagenomic analysis suggested that Maasdam cheese microbiota mainly consisted of Lc. lactis, Lb. helveticus, Lb. rhamnosus, and Propionibacterium. Lc. lactis was the most dominant species. Metatranscriptome analysis during transition from the warm room to the cold room showed that flavor-production and central-metabolism genes were downregulated at cold-room temperatures for all species except Lc. lactis. Cold-shock and heat-shock gene expression of psychrotrophic spoilage lactic acid bacteria (LAB) was investigated in Chapter II. Psychrotrophic LAB are the dominant taxa in cold-stored modified-atmosphere packaged meat products. Their metabolic activities are responsible for meat spoilage. Transcriptomic analysis revealed that spoilage-related genes were upregulated in Le. gelidum at cold-shock temperatures. Moreover, cold-shock also caused upregulation of slime-production genes in Lc. piscium, and Plb. oligofermentans. Gene network analysis suggested that rRNA modification and efflux MFS transporter genes were part of the cold-shock response. At the heat-shock temperature Chaperone and Clp family genes were upregulated in all three species. L. monocytogenes is a foodborne pathogen and is the focus of Chapter III. High-pressure processing (HPP) is one of the common methods that inactivate L. monocytogenes in food products. However, L. monocytogenes can still recover from HPP. This study investigated the gene-expression response of L. monocytogenes during HPP recovery. It was predicted that HPP stress was activated by sigma factor B. The data indicated that sRNA Rli47, cobalamin biosynthesis genes, heat-shock genes and cell-wall-related genes were upregulated after HPP. Further downstream analysis using pbp2A mutants confirmed that among cell-wall-related genes, pbp2A played a significant role in HPP recovery. In conclusion, this thesis extends current knowledge of the role of microorganisms in food, ranging from food fermentations (cheese), towards spoilage (in meat) and foodborne pathogens.Ihmisen tuottamat elintarvikkeet eivät yleensä ole steriilejä, vaan ne sisältävät monenlaisia mikro-organismeja. Mikro-organismeja käytetään sekä elintarvikkeiden valmistukseen että säilöntään, mutta osa mikro-organismeista voi myös aiheuttaa elintarvikkeiden pilaantumista ja johtaa ruokamyrkytykseen. Tässä tutkimuksessa perehdytään kolmenlaisten elintarvikevälitteisten bakteerien geenien ilmentymisen profiileihin elintarviketuotannossa. Tulokset lisäävät nykyistä tietoa mikro-organismien roolista elintarvikkeissa, (juuston) fermentaatiosta (lihan) pilaantumiseen ja elintarvikevälitteisiin patogeeneihin