Background Over the past two decades, the clinical evidence supporting the beneficial effects of probiotics in consumer's health and wellness has increased. Hence, the food and pharmaceutical industries have encouraged the production of different probiotic foods and probiotic strains. So far, nearly all marketed probiotics are from animal (dairy and human subjects) origin; however, other sources are increasingly being reported as promising reservoirs of new potential probiotics. In this last regard, before any possible application, probiotic candidates must be characterized by comprehensive trials. Scope and approach This review aims to provide a contemporary perspective in the evaluation and characterization of probiotics under the “probiogenomics” context. Key findings and conclusions Typically, probiotic candidates are selected after several in vitro and in vivo trials aimed to determine their suitable resistance to physiological barriers such as simulated digestive conditions, sensitive inhibition of pathogens, adherence to mucus and hemolytic potential, among other properties. However, there is a need for additional research to further clarify the knowledge of their metabolic capabilities, key features of adaptation, and their physiological functions, including their safety and the molecular mechanism underlaying their functional activities. Thus, different genomics-based approaches, known as “probiogenomics”, have been successfully applied to facilitate the study of current probiotics and new potential candidates, including their health-promoting and safety properties.

Genomics-based approaches to identify and predict the health-promoting and safety activities of promising probiotic strains – A probiogenomics review

The market of probiotic foods and supplements is growing rapidly but frequently the commercialized products are not compliant with their labels in terms of claimed probiotic strain(s) and labeled number of viable probiotic cells, thus mining the authenticity of these probiotic productsIn this review, we provide an up-to-date overview of: (i) the current regulatory aspects, (ii) the consistency of probiotic foods and supplements with their labels, (iii) the implications of mislabeling on the quality, safety and functionality of these products and (iv) the available and most promising methods to assess the authenticity of these products, taking into account the need to discriminate among the different physiological states probiotics might be in the carrier matrices It arises that authenticity of probiotic foods and supplements is an urgent issue, of industrial and legislation relevance, that need to be addressed A plethora of methods are available to reach this goal, each with its own advantages and disadvantages Protocols that combine the use of propidium monoazide (PMA) with metagenomics or polyphasic approaches including the PMA real time PCR or flow cytometry (for the viability assessment) and the whole genome sequence analysis (for the identification and typing of the probiotic strain) are the most promising that should be standardized and used by producers and regulators

Authenticity of probiotic foods and dietary supplements: A pivotal issue to address

Genomes of 21 strains of lactic acid bacteria isolated from Slovakian traditional cheeses were sequenced on an Illumina MiSeq platform. Subsequently, they were analysed regarding taxonomic classification, presence of genes encoding defence systems, antibiotic resistance and production of biogenic amines. Thirteen strains were found to carry genes encoding at least one bacteriocin, 18 carried genes encoding at least one restriction-modification system, all strains carried 1-6 prophages and 9 strains had CRISPR-Cas systems. CRISPR-Cas type II-A was the most common, containing 0-24 spacers. Only 10% spacers were found to be homological to known bacteriophage or plasmid sequences in databases. Two Enterococcus faecium strains and a Lactococcus lactis strain carried antibiotic resistance genes. Genes encoding for ornithine decarboxylase were detected in four strains and genes encoding for agmatine deiminase were detected in four strains. Lactobacillus paraplantarum 251 L appeared to be the most interesting strain, as it contained genes encoding for two bacteriocins, a restriction-modification system, two CRISPR-Cas systems, four prophages and no genes connected with antibiotic resistance or production of biogenic amines.

Genome analysis of lactic acid bacterial strains selected as potential starters for traditional Slovakian bryndza cheese.

Milk is a source of many valuable nutrients, including minerals, vitamins and proteins, with an important role in adult health. Milk and dairy products naturally containing or with added probiotics have healthy functional food properties. Indeed, probiotic microorganisms, which beneficially affect the host by improving the intestinal microbial balance, are recognized to affect the immune response and other important biological functions. In addition to macronutrients and micronutrients, biologically active peptides (BPAs) have been identified within the amino acid sequences of native milk proteins; hydrolytic reactions, such as those catalyzed by digestive enzymes, result in their release. BPAs directly influence numerous biological pathways evoking behavioral, gastrointestinal, hormonal, immunological, neurological, and nutritional responses. The addition of BPAs to food products or application in drug development could improve consumer health and provide therapeutic strategies for the treatment or prevention of diseases. Herein, we review the scientific literature on probiotics, BPAs in milk and dairy products, with special attention to milk from minor species (buffalo, sheep, camel, yak, donkey, etc.); safety assessment will be also taken into consideration. Finally, recent advances in foodomics to unveil the probiotic role in human health and discover novel active peptide sequences will also be provided.

Milk and Its Derivatives as Sources of Components and Microorganisms with Health-Promoting Properties: Probiotics and Bioactive Peptides

Lactic acid bacteria (LAB) are widely used in the food industry, but little is known about their population genomics, hindering our understanding of their genetic background and evolution. To better understand the evolution of LAB and their potential applications to related food production, we conducted a scoping review of the literature focusing on genomic issues related to LAB. The research progress of LAB population and functional genomics was summarized by sorting the literature of LAB genomics research in the last 10–15 years. According to the existing evidence, the formation mechanism of characteristics of LAB and their habitat adaptive evolution directed by genome decay and horizontal gene transfer were elucidated. The major evolutionary driving forces of LAB are mutations and horizontal gene transfer (HGT) events with or without the involvement of mobile genetic elements instead of recombination. We also underline the application of LAB genome in food safety and properties. Collectively, this review paper provides up‐to‐date information of the population and functional genomics of LAB, current challenges in the field, and suggestions for improving the exploitation and application of LAB resources.

Population and functional genomics of lactic acid bacteria, an important group of food microorganism: Current knowledge, challenges, and perspectives

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Genomic Characterisation of Starter Cultures and Probiotic Bacteria

Culture-independent microbial techniques in dairy microbiology: the state of the art.

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Genomic Characterisation of Starter Cultures and Probiotic Bacteria

Culture-independent microbial techniques in dairy microbiology: the state of the art.