Gene Transcription Patterns of pH- and Salt-Stressed Listeria monocytogenes Cells in Simulated Gastric and Pancreatic Conditions

A Listeria monocytogenes subgenomic array, targeting 54 genes involved in the adhesion, adaptation, intracellular life cycle, invasion, and regulation of the infection cycle was used to investigate the gene expression patterns of acid- and salt-stressed Listeria cells after exposure to conditions similar to those in gastric and pancreatic fluids. Three L. monocytogenes strains, one laboratory reference strain (EGDe) and two food isolates (wild strain 12 isolated from milk and wild strain 3 isolated from fermented sausage), were used during the studies. Differences in the expressed genes were observed between the gastric and pancreatic treatments and also between the serotypes. Increased transcripts were observed of the genes belonging to the adaptation and regulation group for serotype 4b (strain 12) and to the invasion and regulation group for serotype 1/2a (strain EGDe). Interestingly, no significantly differentially expressed genes were found for serotype 3c (strain 3) in most cases. The genes related to adaptation (serotype 1/2a) and to intracellular life cycle and invasion (serotype 4b) were down-regulated in order to cope with the hostile environment of the gastric and pancreatic fluids. These findings may provide experimental evidence for the dominance of serotypes 1/2a and 4b in clinical cases of listeriosis and for the sporadic occurrence of serotype 3c

Fermented Foods: New Concepts and Technologies for the Development of New Products, Quality Control

Fermentation has been of great interest for humans since antiquity and has been extensively used in all cultures worldwide [...

Comparative Genomic Analysis Reveals the Functional Traits and Safety Status of Lactic Acid Bacteria Retrieved from Artisanal Cheeses and Raw Sheep Milk

Lactic acid bacteria (LAB) are valuable for the production of fermented dairy products. We investigated the functional traits of LAB isolated from artisanal cheeses and raw sheep milk, assessed their safety status, and explored the genetic processes underlying the fermentation of carbohydrates. Lactiplantibacillus plantarum had the largest and more functional genome compared to all other LAB, while most of its protein-encoding genes had unknown functions. A key finding of our analysis was the overall absence of acquired resistance genes (RGs), virulence genes (VGs), and prophages, denoting that all LAB isolates fulfill safety criteria and can be used as starter or adjunct cultures. In this regard, the identified mobile genetic elements found in LAB, rather than enabling the integration of RGs or VGs, they likely facilitate the uptake of genes involved in beneficial functions and in the adaptation of LAB in dairy matrices. Another important finding of our study was that bacteriocins and CAZymes were abundant in LAB though each species was associated with specific genes, which in turn had different activity spectrums and identified applications. Additionally, all isolates were able to metabolize glucose, lactose, maltose, and sucrose, but Lactiplantibacillus plantarum was strongly associated with the fermentation of rhamnose, mannose, cellobiose, and trehalose whereas Levilactobacillus brevis with the utilization of arabinose and xylose. Altogether these results suggest that to fully exploit the beneficial properties of LAB, a combination of strains as food additives may be necessary. Interestingly, biological processes involved in the metabolism of carbohydrates that are not of direct interest for the dairy industry may yield valuable metabolites or activate pathways associated with beneficial health effects. Our results provide useful information for the development of new probiotic artisanal cheeses and probiotic starter cultures

Functional and Safety Characterization of <i>Weissella paramesenteroides</i> Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics

Strains belonging to the Weissella genus are frequently recovered from spontaneously fermented foods. Their functional, microbial-modulating, and probiotic traits enhance not only the sensorial properties but also the nutritional value, beneficial effects, and safety of fermented products. Sporadic cases of opportunistic pathogenicity and antibiotic resistance have deprived safety status from all Weissella species, which thus remain understudied. Our study increased the number of available high-quality and taxonomically accurate W. paramesenteroides genomes by 25% (9 genomes reported, leading to a total of 36 genomes). We conducted a phylogenetic and comparative genomic analysis of the most dominant Weissella species (W. cibaria, W. paramesenteroides, W. viridescens, W. soli, W. koreensis, W. hellenica and W. thailadensis). The phylogenetic tree corroborated species assignment but also revealed phylogenetic diversity within the Weissella species, which is likely related to the adaptation of Weissella in different niches. Using robust alignment criteria, we showed the overall absence of resistance and virulence genes in Weissella spp., except for one W. cibaria isolate carrying blaTEM-181. Enrichment analysis showed the association of Weissella species several CAZymes, which are essential for biotechnological applications. Additionally, the combination of CAZyme metabolites with probiotics can potentially lead to beneficial effects for hosts, such as the inhibition of inflammatory processes and the reduction of cholesterol levels. Bacteriocins and mobile genetic elements MGEs (Inc11 plasmid and ISS1N insertion sequence) were less abundant, however W. thailadensis and W. viridescens showed significant association with specific bacteriocin-encoding genes. Lastly, an analysis of phenotypic traits underlined the need to carefully evaluate W. cibaria strains before use as food additives and suggested the possibility of employing W. paramesenteroides and W. hellenica in the fermentation process of vegetable products. More studies providing high-resolution characterization of Weissella strains from various sources are necessary to elucidate the safety of Weissella spp. and exploit their beneficial characteristics

Whole-Genome Sequencing and Comparative Genomic Analysis of Enterococcus spp. Isolated from Dairy Products: Genomic Diversity, Functional Characteristics, and Pathogenic Potential

Enterococci are commensal organisms that have probiotic effects for their hosts and can be used as adjunct cultures in fermented dairy products. The dark side of Enterococci is manifested in E. faecium and E. faecalis, which are the causative agents of nosocomial infections, and thus Enterococci have not been granted a safety status as food additives. In this context, we aimed to assess the safety and functional profile of an Enterococci collection retrieved from traditional dairy products through a high-resolution genomic characterization and comparative genomic analysis. Analysis did not reveal major differences in the main cellular processes of Enterococci. Moreover, a diverse repertoire of resistance and virulence genes was present, though known hallmark pathogenicity factors were either absent or occurred rarely. The abundance of bacteriocins and CRISPR/Cas systems suggested the ability of the isolates to suppress pathogens and evade bacteriophages, respectively. Presence&ndash;absence patterns of genes suggested that dairy-originated E. faecium are not associated with pathogenicity factors, while those of human origin are strongly linked with notorious resistance and virulence determinants. Our comparative analysis provided some notable insights regarding the genomic composition of Enterococci in the context of their origin. However, their pathogenic lifestyle is likely to be explained by the interplay of multiple genomic factors

Whole-Genome Sequencing and Comparative Genomic Analysis of <i>Enterococcus</i> spp. Isolated from Dairy Products: Genomic Diversity, Functional Characteristics, and Pathogenic Potential

Enterococci are commensal organisms that have probiotic effects for their hosts and can be used as adjunct cultures in fermented dairy products. The dark side of Enterococci is manifested in E. faecium and E. faecalis, which are the causative agents of nosocomial infections, and thus Enterococci have not been granted a safety status as food additives. In this context, we aimed to assess the safety and functional profile of an Enterococci collection retrieved from traditional dairy products through a high-resolution genomic characterization and comparative genomic analysis. Analysis did not reveal major differences in the main cellular processes of Enterococci. Moreover, a diverse repertoire of resistance and virulence genes was present, though known hallmark pathogenicity factors were either absent or occurred rarely. The abundance of bacteriocins and CRISPR/Cas systems suggested the ability of the isolates to suppress pathogens and evade bacteriophages, respectively. Presence–absence patterns of genes suggested that dairy-originated E. faecium are not associated with pathogenicity factors, while those of human origin are strongly linked with notorious resistance and virulence determinants. Our comparative analysis provided some notable insights regarding the genomic composition of Enterococci in the context of their origin. However, their pathogenic lifestyle is likely to be explained by the interplay of multiple genomic factors