Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese

The role of fermentation with lactic acid bacteria in quality and health effects of plant-based dairy analogues

The modern food industry is undergoing a rapid change with the trend of production of plant-based food products that are more sustainable and have less impact on nature. Plant-based dairy analogues have been increasingly popular due to their suitability for individuals with milk protein allergy or lactose intolerance and those preferring a plant-based diet. Nevertheless, plant-based products still have insufficient nutritional quality, undesirable structure, and earthy, green, and bean-like flavor compared to dairy products. In addition, most plant-based foods contain lesser amounts of essential nutrients, antinutrients limiting the bioavailability of some nutrients, and allergenic proteins. Novel processing technologies can be applied to have a homogeneous and stable structure. On the other hand, fermentation of plant-based matrix with lactic acid bacteria can provide a solution to most of these problems. Additional nutrients can be produced and antinutrients can be degraded by bacterial metabolism, thereby increasing nutritional value. Allergenic proteins can be hydrolyzed reducing their immunoreactivity. In addition, fermentation has been found to reduce undesired flavors and to enhance various bioactivities of plant foods. However, the main challenge in the production of fermented plant-based dairy analogues is to mimic familiar dairy-like flavors by producing the major flavor compounds other than organic acids, yielding a flavor profile similar to those of fermented dairy products. Further studies are required for the improvement of the flavor of fermented plant-based dairy analogues through the selection of special microbial cultures and formulations.

Transcriptome Analysis Reveals the Role of Sucrose in the Production of Latilactobacillus sakei L3 Exopolysaccharide

Latilactobacillus (L.) sakei is a species of lactic acid bacteria (LAB) mostly studied according to its application in food fermentation. Previously, L. sakei L3 was isolated by our laboratory and possessed the capability of high exopolysaccharide (EPS) yield during sucrose-added fermentation. However, the understanding of sucrose promoting EPS production is still limited. Here, we analyzed the growth characteristics of L. sakei L3 and alterations of its transcriptional profiles during sucrose-added fermentation. The results showed that L. sakei L3 could survive between pH 4.0 and pH 9.0, tolerant to NaCl (<10%, w/v) and urea (<6%, w/v). Meanwhile, transcriptomic analysis showed that a total of 426 differentially expressed genes and eight non-coding RNAs were identified. Genes associated with sucrose metabolism were significantly induced, so L. sakei L3 increased the utilization of sucrose to produce EPS, while genes related to uridine monophosphate (UMP), fatty acids and folate synthetic pathways were significantly inhibited, indicating that L. sakei L3 decreased self-growth, substance and energy metabolism to satisfy EPS production. Overall, transcriptome analysis provided valuable insights into the mechanisms by which L. sakei L3 utilizes sucrose for EPS biosynthesis. The study provided a theoretical foundation for the further application of functional EPS in the food industry.

Potential of Cheese-Associated Lactic Acid Bacteria to Metabolize Citrate and Produce Organic Acids and Acetoin

Lactic acid bacteria (LAB) are pivotal in shaping the technological, sensory, and safety aspects of dairy products. The evaluation of proteolytic activity, citrate utilization, milk pH reduction, and the production of organic compounds, acetoin, and diacetyl by cheese associated LAB strains was carried out, followed by Principal Component Analysis (PCA). Citrate utilization was observed in all Leuconostoc (Le.) mesenteroides, Le. citreum, Lactococcus (Lc.) lactis, Lc. garvieae, and Limosilactobacillus (Lm.) fermentum strains, and in some Lacticaseibacillus (Lact.) casei strains. Most strains exhibited proteolytic activity, reduced pH, and generated organic compounds. Multivariate PCA revealed Le. mesenteroides as a prolific producer of acetic, lactic, formic, and pyruvic acids and acetoin at 30 °C. Enterococcus sp. was distinguished from Lact. casei based on acetic, formic, and pyruvic acid production, while Lact. casei primarily produced lactic acid at 37 °C. At 42 °C, Lactobacillus (L.) helveticus and some L. delbrueckii subsp. bulgaricus strains excelled in acetoin production, whereas L. delbrueckii subsp. bulgaricus and Streptococcus (S.) thermophilus strains primarily produced lactic acid. Lm. fermentum stood out with its production of acetic, formic, and pyruvic acids. Overall, cheese-associated LAB strains exhibited diverse metabolic capabilities which contribute to desirable aroma, flavor, and safety of dairy products.

Selection of lactic acid bacteria as biopreservation agents and optimization of their mode of application for the control of Listeria monocytogenes in ready-to-eat cooked meat products

In order to meet consumers´ demands for more natural foods and to find new methods to control foodborne pathogens in them, research is currently being focused on alternative preservation approaches, such as biopreservation with lactic acid bacteria (LAB). Here, a collection of lactic acid bacteria (LAB) isolates was characterized to identify potential biopreservative agents. Six isolates (one Lactococcus lactis, one Lacticaseibacillus paracasei and four Lactiplantibacillus plantarum) were selected based on their antimicrobial activity in in vitro assays. Whole genome sequencing showed that none of the six LAB isolates carried known virulence factors or acquired antimicrobial resistance genes, and that the L. lactis isolate was potentially a nisin Z producer. Growth of L. monocytogenes was successfully limited by L. lactis ULE383, L. paracasei ULE721 and L. plantarum ULE1599 throughout the shelf-life of cooked ham, meatloaf and roasted pork shoulder. These LAB isolates were also applied individually or as a cocktail at different inoculum concentrations (4, 6 and 8 log10 CFU/g) in challenge test studies involving cooked ham, showing a stronger anti-Listerial activity when a cocktail was used at 8 log10 CFU/g. Thus, a reduction of up to ~5.0 log10 CFU/g in L. monocytogenes growth potential was attained in cooked ham packaged under vacuum, modified atmosphere packaging or vacuum followed by high pressure processing (HPP). Only minor changes in color and texture were induced, although there was a significant acidification of the product when the LAB cultures were applied. Remarkably, this acidification was delayed when HPP was applied to the LAB inoculated batches. Metataxonomic analyses showed that the LAB cocktail was able to grow in the cooked ham and outcompete the indigenous microbiota, including spoilage microorganisms such as Brochothrix. Moreover, none of the batches were considered unacceptable in a sensory evaluation. Overall, this study shows the favourable antilisterial activity of the cocktail of LAB employed, with the combination of HPP and LAB achieving a complete inhibition of the pathogen with no detrimental effects in physico-chemical or sensorial evaluations, highlighting the usefulness of biopreservation approaches involving LAB for enhancing the safety of cooked meat products.

Lactococcus lactis, a bacterium with probiotic functions and pathogenicity

Lactococcus lactis (L. lactis) is the primary organism for lactic acid bacteria (LAB) and is a globally recognized safe microorganism for the regulation of the intestinal micro-ecological balance of animals and improving the immune performance of the host. L. lactis is known to play a commercially important role in feed fortification, milk fermentation, and vaccine production, but pathogenic L. lactis has been isolated from many clinical cases in recent years, such as the brain of silver carp with Lactococcosis, the liver and spleen of diseased waterfowl, milk samples and padding materials with cow mastitis, and blood and urine from human patients with endocarditis. In dairy farming, where L. lactis has been used as a probiotic in the past, however, some studies have found that L. lactis can cause mastitis in cows, but the lack of understanding of the pathogenesis of mastitis in cows caused by L. lactis has become a new problem. The main objective of this review is to analyze the increasingly serious clinical mastitis caused by L. lactis and combined with the wide application of L. lactis as probiotics, to comprehensively discuss the characteristics and diversity of L. lactis.

An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota

The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes’ authenticity and cheese quality.

Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes

Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.

A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application

The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties.

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages

Metagenomics is a powerful tool to study and understand the microbial dynamics that occur during food fermentation and allows to close the link between microbial diversity and final sensory characteristics. Each food matrix can be colonized by different microbes, but also by different strains of the same species. In this study, using an innovative integrated approach combining culture-dependent method with a shotgun sequencing, we were able to show how strain-level biodiversity could influence the quality characteristics of the final product. The attention was placed on a model food fermentation process: Salame Piemonte, a Protected Geographical Indication (PGI) Italian fermented sausage. Three independent batches produced in February, March and May 2018 were analysed. The sausages were manufactured, following the production specification, in a local meat factory in the area of Turin (Italy) without the use of starter cultures. A pangenomic approach was applied in order to identify and evaluate the lactic acid bacteria (LAB) population driving the fermentation process. It was observed that all batches were characterized by the presence of few LAB species, namely Pediococcus pentosaceus, Latilactobacillus curvatus and Latilactobacillus sakei. Sausages from the different batches were different when the volatilome was taken into consideration, and a strong association between quality attributes and strains present was determined. In particular, different strains of L. sakei, showing heterogeneity at genomic level, colonized the meat at the beginning of each production and deeply influenced the fermentation process by distinctive metabolic pathways that affected the fermentation process and the final sensory aspects.

Lifestyle, metabolism and environmental adaptation in Lactococcus lactis

Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.