Genomics landscape of 185 Streptococcus thermophilus and identification of fermentation biomarkers

Development of a single nucleotide polymorphism-based strain-identified method for Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 using pan-genomics analysis

The health benefits conferred by probiotics is specific to individual probiotic strains, highlighting the importance of identifying specific strains for research and production purposes. Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 are exceedingly valuable for commercial use with an excellent mixed-culture fermentation. To differentiate these 2 strains from other S. thermophilus and L. delbrueckii ssp. bulgaricus, a specific, sensitive, accurate, rapid, convenient, and cost-effective method is required. In this study, we conducted a pan-genome analysis of S. thermophilus and L. delbrueckii ssp. bulgaricus to identify species-specific core genes, along with strain-specific SNPs. These genes were used to develop suitable PCR primers, and the conformity of sequence length and unique SNPs was confirmed by sequencing for qualitative identification at the strain level. The results demonstrated that SNPs analysis of PCR products derived from these primers could distinguish CICC 6038 and CICC 6047 accurately and reproducibly from the other strains of S. thermophilus and L. delbrueckii ssp. bulgaricus, respectively. The strain-specific PCR method based on SNPs herein is universally applicable for probiotics identification. It offers valuable insights into identifying probiotics at the strain level that is fit-for-purpose in quality control and compliance assessment of commercial dairy products.

Substitution of Asp29 with Asn29 in the metallochaperone UreE of Streptococcus thermophilus DSM 20617T increases the urease activity and anticipates urea hydrolysis during milk fermentation

Urease operon is highly conserved within the species Streptococcus thermophilus and urease-negative strains are rare in nature. S. thermophilus MIMO1, isolated from commercial yogurt, was previously characterized as urease-positive Ni-dependent strain. Beside a mutation in ureQ, coding for a nickel ABC transporter permease, the strain MIMO1 showed a mutation in ureE gene which code for a metallochaperone involved in Ni delivery to the urease catalytic site. The single base mutation in ureE determined a substitution of Asp29 with Asn29 in the metallochaperone in a conserved protein region not involved in the catalytic activity. With the aim to investigate the role Asp29vs Asn29 substitution in UreE on the urease activity of S. thermophilus, ureE gene of the reference strain DSM 20617T (ureEDSM20617) was replaced by ureE gene of strain MIMO1 (ureEMIMO1) to obtain the recombinant ES3. In-gel detection of urease activity revealed that the substitution of Asp29 with Asn29 in UreE resulted in a higher stability of the enzyme complexes. Moreover, the recombinant ES3 showed higher level of urease activity compared to the wildtype without any detectable increase in the expression level of ureC gene, thus highlighting the role of UreE not only in Ni assembly but also on the level of urease activity. During the growth in milk, the recombinant ES3 showed an anticipated urease activity compared to the wildtype, and analogous milk fermentation performance. The overall data obtained by comparing urease-positive and urease-negative strains/mutants confirmed that urease activity strongly impacts on the milk fermentation process and specifically on the yield of the homolactic fermentation.

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem

Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.

Foodborne Microbial Communities as Potential Reservoirs of Antimicrobial Resistance Genes for Pathogens: A Critical Review of the Recent Literature

Antimicrobial resistance (AMR) is a global and increasing threat to human health. Several genetic determinants of AMR are found in environmental reservoirs, including bacteria naturally associated with widely consumed fermented foods. Through the food chain, these bacteria can reach the gut, where horizontal gene transfer (HGT) can occur within the complex and populated microbial environment. Numerous studies on this topic have been published over the past decades, but a conclusive picture of the potential impact of the non-pathogenic foodborne microbial reservoir on the spread of AMR to human pathogens has not yet emerged. This review critically evaluates a comprehensive list of recent experimental studies reporting the isolation of AMR bacteria associated with fermented foods, focusing on those reporting HGT events, which represent the main driver of AMR spread within and between different bacterial communities. Overall, our analysis points to the methodological heterogeneity as a major weakness impairing determination or a causal relation between the presence of AMR determinants within the foodborne microbial reservoir and their transmission to human pathogens. The aim is therefore to highlight the main gaps and needs to better standardize future studies addressing the potential role of non-pathogenic bacteria in the spread of AMR.

Milk fermentation by monocultures or co-cultures of Streptococcus thermophilus strains

Direct vat-set starter cultures are the key ingredient for the production of fermented dairy products. The characteristics of the strains used for fermentation determine the fermentation time, texture and flavor of the fermented milk products. In this study, a large-scale analysis of the acid production rate, texture, carbon source utilization characteristics of Streptococcus thermophilus strains was conducted. All 100 S. thermophilus strains were divided into six groups according to the acid production rate and into two groups according to the consistency texture. A universal medium, basing on the carbon sources metabolic properties were optimized (0.5% lactose and 3.5% glucose), to culture all of the tested strains. Among them 40 strains were used to test pH-controlled conditions using this universal culture medium. After 5-7 h of fermentation, the optical density (OD) values of all fermented products exceeded 10, suggesting the potential for high-density cultivation of S. thermophilus. Although the OD could be further increased by adding more glucose, this may have hindered subsequent lyophilization because of high residual lactic acid in the fermented product. Next, the application of Streptococcus thermophilus strains in fermented milk was studied. Monocultures and co-cultures of strains were evaluated and compared. The results revealed the existence of symbiotic or competitive relationships between different S. thermophilus strains. Based on the findings, the mixing ratio of three symbiotic S. thermophilus strains was optimized. A co-culture of these three strains yielded fermented milk with high viscosity, low post-acidification, good sensory properties and processability.

The fourth industrial revolution in the food industry-part II: Emerging food trends

The food industry has recently been under unprecedented pressure due to major global challenges, such as climate change, exponential increase in world population and urbanization, and the worldwide spread of new diseases and pandemics, such as the COVID-19. The fourth industrial revolution (Industry 4.0) has been gaining momentum since 2015 and has revolutionized the way in which food is produced, transported, stored, perceived, and consumed worldwide, leading to the emergence of new food trends. After reviewing Industry 4.0 technologies (e.g. artificial intelligence, smart sensors, robotics, blockchain, and the Internet of Things) in Part I of this work (Hassoun, Aït-Kaddour, et al. 2022. The fourth industrial revolution in the food industry-Part I: Industry 4.0 technologies. Critical Reviews in Food Science and Nutrition, 1-17.), this complimentary review will focus on emerging food trends (such as fortified and functional foods, additive manufacturing technologies, cultured meat, precision fermentation, and personalized food) and their connection with Industry 4.0 innovations. Implementation of new food trends has been associated with recent advances in Industry 4.0 technologies, enabling a range of new possibilities. The results show several positive food trends that reflect increased awareness of food chain actors of the food-related health and environmental impacts of food systems. Emergence of other food trends and higher consumer interest and engagement in the transition toward sustainable food development and innovative green strategies are expected in the future.