Abstract
Lactic acid fermentation is an ancient-origin process based on the growth and metabolic activities of microorganisms for the preservation and transformation of food materials. Nowadays, there is a renewed interest in fermented food products, mainly driven by their professed health benefits. Lactic acid fermentation has traditionally been a spontaneous process driven by the inherent microbial consortia of the food matrix. Hence, a loss of control during the fermentation process may occur, leading to undesired outcomes. For this reason, the tendency during the past years moved towards starter-driven fermentations based on the accurate selection of strains with specific metabolic traits to achieve safe fermented products with desirable organoleptic properties. This may drive the efficient exploitation of food by-products through lactic acid bacteria bioprocessing. Because of metabolic traits rely directly on phenotype expression, the recent introduction of phenomics as a novel -omic technique may revolutionize starter selection. In addition, advances in the study of lactic acid bacteria (LAB) established novel groups and outlined contrasting lifestyles with appealing metabolic activities for the application in certain food products, such fructophilic lactic acid bacteria (FLAB) and as nomadic lactobacilli, respectively. Thus, the aim of this thesis is to investigate metabolic capabilities of lactic acid bacteria for food fermentations, its exploitation in novel applications and by-product re-cycling. A novel R pipeline for automated phenomics data analysis was developed integrating the latest data analysis approaches in the literature. In addition, phenotype switching approach within phenomics was outlined. This approach was applied in the starter selection for the exploitation of brewers’ spent grain (BSG), the most abundant by-product generated in the beer-brewing process. The metabolic capabilities of three strains of Lactiplantibacillus plantarum (PU1, H46 and WCFS1) and Leuconostoc pseudomesenteroides DSM 20193 were characterized under BSG model medium in contrast to MRS. Phenotype profiles of L. plantarum clustered depending on the culture media, reflecting its nomadic lifestyle. Nevertheless, in-depth bayesian phenotypic approach unveiled L. plantarum PU1 as the strain with the highest metabolic flexibility, which was further validated by metabolomics and gene expression analyses. The metabolism drift of the above-mentioned strains cultured in a second type of BSG model media was further investigated. We observed higher metabolic activity towards gentiobiose, cellobiose and β-glucoside conjugates of phenolic compounds during BSG fermentation. Gene expression analysis confirmed the importance of cellobiose metabolism, while a release of monolignol aglycones was found during BSG fermentation. Although L. plantarum strains follow similar metabolic strategies under the same environmental pressure, the mode of action to pursue such strategies is strain dependent. Free amino acid catabolism gene expression of three L. plantarum strains in response to stressor levels commonly found during cheese ripening, was modelled using a factorial statistical design. CB5 strain, a dairy isolate, showed a distinctive response from the other two strains and the highest metabolic flexibility in response to such stressors. Despite their nomadic lifestyle, an underpinning adaptation capacity might be unveiled in the mode of action to pursue a metabolic strategy. Although only recently discovered, FLAB already deserve a marked interest for their potential applications in food and pharmaceutical industries. This interest relies on the preferential consumption of fructose and the capability to colonize uncommon niches. Fermentable Oligo-, Di-, Mono-saccharides And Polyols (FODMAPs) are certainly responsible for Irritable bowel syndrome and non-celiac gluten sensitivity. We carried out a proof-of-concept study to show the potential of FLAB in FODMAPs consumption during sourdough fermentation, exploiting the metabolic capabilities of this newly discovered LAB group.