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When selecting microbial strains for the production of fermented foods, various microbial phenotypes need to be taken into account to achieve target product characteristics, such as biosafety, flavor, texture, and health-promoting effects. Through continuous advances in sequencing technologies, microbial whole-genome sequences of increasing quality can now be obtained both cheaper and faster, which increases the relevance of genome-based characterization of microbial phenotypes. Prediction of microbial phenotypes from genome sequences makes it possible to quickly screen large strain collections in silico to identify candidates with desirable traits. Several microbial phenotypes relevant to the production of fermented foods can be predicted using knowledge-based approaches, leveraging our existing understanding of the genetic and molecular mechanisms underlying those phenotypes. In the absence of this knowledge, data-driven approaches can be applied to estimate genotype-phenotype relationships based on large experimental datasets. Here, we review computational methods that implement knowledge- and data-driven approaches for phenotype prediction, as well as methods that combine elements from both approaches. Furthermore, we provide examples of how these methods have been applied in industrial biotechnology, with special focus on the fermented food industry.

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Bacteriophages (or phages) represent a persistent threat to the success and reliability of food fermentation processes. Recent reports of phages that infect Streptococcus thermophilus have highlighted the diversification of phages of this species. Phages of S. thermophilus typically exhibit a narrow range, a feature that is suggestive of diverse receptor moieties being presented on the cell surface of the host. Cell wall polysaccharides, including rhamnose-glucose polysaccharides and exopolysaccharides have been implicated as being involved in the initial interactions with several phages of this species. Following internalization of the phage genome, the host presents several defences, including CRISPR-Cas and restriction and modification systems to limit phage proliferation. This review provides a current and holistic view of the interactions of phages and their S. thermophilus host cells and how this has influenced the diversity and evolution of both entities.

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Lactobacillaceae are among the major fermentation organisms in most food fermentations but the metabolic pathways for conversion of (poly)phenolic compounds by lactobacilli have been elucidated only in the past two decades. Hydroxycinnamic and hydroxybenzoic acids are metabolized by separate enzymes which include multiple esterases, decarboxylases and hydroxycinnamic acid reductases. Glycosides of phenolic compounds including flavonoids are metabolized by glycosidases, some of which are dedicated to glycosides of plant phytochemicals rather than oligosaccharides. Metabolism of phenolic compounds in food fermentations often differs from metabolism in vitro, likely reflecting the diversity of phenolic compounds and the unknown stimuli that induce expression of metabolic genes. Current knowledge will facilitate fermentation strategies to achieve improved food quality by targeted conversion of phenolic compounds.

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Bacteriophages (or phages) represent one of the most persistent threats to food fermentations, particularly large-scale commercial dairy fermentations. Phages infecting lactic acid bacteria (LAB) that are used as starter cultures in dairy fermentations are well studied, and in recent years there have been significant advances in defining the driving forces of LAB-phage coevolution. The means by which different starter bacterial species defend themselves against phage predation and the chromosomal or plasmid location of the genes encoding these defense mechanisms have dictated the technological approaches for the development of robust starter cultures. In this review, we highlight recent advances in defining phage-host interactions and how phage resistance occurs in different bacterial species. Furthermore, we discuss how these insights continue to transform the dairy fermentation industry and how they also are anticipated to guide food fermentations involving plant-based alternatives in the future.

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