Genome-Scale Metabolic Modeling Combined with Transcriptome Profiling Provides Mechanistic Understanding of Streptococcus thermophilus CH8 Metabolism.

Streptococcus thermophilus is a lactic acid bacterium adapted toward growth in milk and is a vital component of starter cultures for milk fermentation. Here, we combine genome-scale metabolic modeling and transcriptome profiling to obtain novel metabolic insights into this bacterium. Notably, a refined genome-scale metabolic model (GEM) accurately representing S. thermophilus CH8 metabolism was developed. Modeling the utilization of casein as a nitrogen source revealed an imbalance in amino acid supply and demand, resulting in growth limitation due to the scarcity of specific amino acids, in particular sulfur amino acids. Growth experiments in milk corroborated this finding. A subtle interdependency of the redox balance and the secretion levels of the key metabolites lactate, formate, acetoin, and acetaldehyde was furthermore identified with the modeling approach, providing a mechanistic understanding of the factors governing the secretion product profile. As a potential effect of high expression of arginine biosynthesis genes, a moderate secretion of ornithine was observed experimentally, augmenting the proposed hypothesis of ornithine/putrescine exchange as part of the protocooperative interaction between S. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in yogurt. This study provides a foundation for future community modeling of food fermentations and rational development of starter strains with improved functionality. IMPORTANCE Streptococcus thermophilus is one the main organisms involved in the fermentation of milk and, increasingly, also in the fermentation of plant-based foods. The construction of a functional high-quality genome-scale metabolic model, in conjunction with in-depth transcriptome profiling with a focus on metabolism, provides a valuable resource for the improved understanding of S. thermophilus physiology. An example is the model-based prediction of the most significant route of synthesis for the characteristic yogurt flavor compound acetaldehyde and identification of metabolic principles governing the synthesis of other flavor compounds. Moreover, the systematic assessment of amino acid supply and demand during growth in milk provides insights into the key challenges related to nitrogen metabolism that is imposed on S. thermophilus and any other organism associated with the milk niche.

Effect of Lactobacillus rhamnosus on Physicochemical Properties of Fermented Plant-Based Raw Materials.

To overcome texture and flavor challenges in fermented plant-based product development, the potential of microorganisms is generating great interest in the food industry. This study examines the effect of Lactobacillus rhamnosus on physicochemical properties of fermented soy, oat, and coconut. L. rhamnosus was combined with different lactic acid bacteria strains and Bifidobacterium. Acidification, titratable acidity, and viability of L. rhamnosus and Bifidobacterium were evaluated. Oscillation and flow tests were performed to characterize rheological properties of fermented samples. Targeted and untargeted volatile organic compounds in fermented samples were assessed, and sensory evaluation with a trained panel was conducted. L. rhamnosus reduced fermentation time in soy, oat, and coconut. L. rhamnosus and Bifidobacterium grew in all fermented raw materials above 107 CFU/g. No significant effect on rheological behavior was observed when L. rhamnosus was present in fermented samples. Acetoin levels increased and acetaldehyde content decreased in the presence of L. rhamnosus in all three bases. Diacetyl levels increased in fermented oat and coconut samples when L. rhamnosus was combined with a starter culture containing Streptococcus thermophilus and with another starter culture containing S. thermophilus, L. bulgaricus and Bifidobacterium. In all fermented oat samples, L. rhamnosus significantly enhanced fermented flavor notes, such as sourness, lemon, and fruity taste, which in turn led to reduced perception of base-related attributes. In fermented coconut samples, gel firmness perception was significantly improved with L. rhamnosus. The findings suggest that L. rhamnosus can improve fermentation time and sensory perception of fermented plant-based products.

Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis.

Lactococcus lactis cheese starter cultures typically contain a mix of many strains and may include variants that produce and/or tolerate the antimicrobial bacteriocin nisin. Nisin is well-established as an effective agent against several undesirable Gram-positive bacteria in cheese and various other foods. In the current study, we have examined the effect of nisin on 710 individual L. lactis strains during milk fermentations. Changes in milk acidification profiles with and without nisin exposure, ranging from unaltered acidification to loss of acidification, could be largely explained by the type(s) and variants of nisin immunity and nisin degradation genes present, but surprisingly, also by genotypic lineage (L. lactis ssp. cremoris vs. ssp. lactis). Importantly, we identify that nisin degradation by NSR is frequent among L. lactis and therefore likely the main mechanism by which dairy-associated L. lactis strains tolerate nisin. Insights from this study on the strain-specific effect of nisin tolerance and degradation during milk acidification is expected to aid in the design of nisin-compatible cheese starter cultures.