Comparative genomic and metabolic analysis of three Lactobacillus paracasei cheese isolates reveals considerable genomic differences in strains from the same niche

peer-reviewedBackground Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities. Results Genome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident. Conclusions The findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche

Lactobacillus paracasei: an evaluation of the flavour diversification potential of the species through genomics, metabolomics and applications

Strains of Lactobacillus paracasei are commonly isolated from numerous and diverse niches, such as dairy products, plant materials and reproductive and gastrointestinal tracts of humans and animals. In cheese, strains of L. paracasei belong predominantly to the non-starter microbiota, which is often considered to be immensely important for the development of flavour. In this project, the genetic and phenotypic diversity of L. paracasei strains and their application as adjunct cultures to support the development of flavour compounds was assessed. The bank of 310 strains investigated in this study consisted of isolates originating from cheese, yoghurt and sourdough. After genomic profiling, 99 strains were selected for future examination. The phenotypic characterisation included in vitro assessment of the key proteolytic enzyme activities, the most important factor contributing to the flavour compound development. The activities of the examined enzymes significantly differed among the analysed strains. Ten strains showing different enzyme activities were selected to compare their ability for flavour compounds production in two cheese model systems. The volatile profiles of the strains differed in both model systems, and according to the all generated results, three strains (DPC2071, DPC4206 and DPC4536) were selected as adjunct cultures for Cheddar cheese manufacture. The cheese analysis showed that although some differences existed, they were minimal and cheeses were of similar flavour characteristics. Finally, to identify and characterise specific genes that may contribute to the overall differentiation of the selected strains, genome sequencing and assembly and comparative genome analysis were performed on the three strains used in the cheese production, and a considerable level of genetic heterogeneity was observed

Symposium review: Genomic investigations of flavor formation by dairy microbiota

peer-reviewedFlavor is one of the most important attributes of any fermented dairy product. Dairy consumers are known to be willing to experiment with different flavors; thus, many companies producing fermented dairy products have looked at culture manipulation as a tool for flavor diversification. The development of flavor is a complex process, originating from a combination of microbiological, biochemical, and technological aspects. A key driver of flavor is the enzymatic activities of the deliberately inoculated starter cultures, in addition to the environmental or “nonstarter” microbiota. The contribution of microbial metabolism to flavor development in fermented dairy products has been exploited for thousands of years, but the availability of the whole genome sequences of the bacteria and yeasts involved in the fermentation process and the possibilities now offered by next-generation sequencing and downstream “omics” technologies is stimulating a more knowledge-based approach to the selection of desirable cultures for flavor development. By linking genomic traits to phenotypic outputs, it is now possible to mine the metabolic diversity of starter cultures, analyze the metabolic routes to flavor compound formation, identify those strains with flavor-forming potential, and select them for possible commercial application. This approach also allows for the identification of species and strains not previously considered as potential flavor-formers, the blending of strains with complementary metabolic pathways, and the potential improvement of key technological characteristics in existing strains, strains that are at the core of the dairy industry. An in-depth knowledge of the metabolic pathways of individual strains and their interactions in mixed culture fermentations can allow starter blends to be custom-made to suit industry needs. Applying this knowledge to starter culture research programs is enabling research and development scientists to develop superior starters, expand flavor profiles, and potentially develop new products for future market expansion

Draft Genome Sequences of Three Lactobacillus paracasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese

peer-reviewedLactobacillus paracasei strains are common members of the nonstarter microbiota present in various types of cheeses. The draft genome sequences of three strains isolated from mature cheddar cheeses are reported here

Advances in the genomics and metabolomics of dairy lactobacilli: A review

The Lactobacillus genus represents the largest and most diverse genera of all the lactic acid bacteria (LAB), encompassing species with applications in industrial, biotechnological and medical fields. The increasing number of available Lactobacillus genome sequences has allowed understanding of genetic and metabolic potential of this LAB group. Pangenome and core genome studies are available for numerous species, demonstrating the plasticity of the Lactobacillus genomes and providing the evidence of niche adaptability. Advancements in the application of lactobacilli in the dairy industry lie in exploring the genetic background of their commercially important characteristics, such as flavour development potential or resistance to the phage attack. The integration of available genomic and metabolomic data through the generation of genome scale metabolic models has enabled the development of computational models that predict the behaviour of organisms under specific conditions and present a route to metabolic engineering. Lactobacilli are recognised as potential cell factories, confirmed by the successful production of many compounds. In this review, we discuss the current knowledge of genomics, metabolomics and metabolic engineering of the prevalent Lactobacillus species associated with the production of fermented dairy foods. In-depth understanding of their characteristics opens the possibilities for their future knowledge-based applications

Genetic, enzymatic and metabolite profiling of the Lactobacillus casei group reveals strain biodiversity and potential applications for flavour diversification

Aims: The Lactobacillus casei group represents a widely explored group of lactic acid bacteria, characterized by a high level of biodiversity. In this study, the genetic and phenotypic diversity of a collection of more than 300 isolates of the Lact. casei group and their potential to produce volatile metabolites important for flavour development in dairy products, was examined. Methods and Results: Following confirmation of species by 16S rRNA PCR, the diversity of the isolates was determined by pulsed-field gel electrophoresis. The activities of enzymes involved in the proteolytic cascade were assessed and significant differences among the strains were observed. Ten strains were chosen based on the results of their enzymes activities and they were analysed for their ability to produce volatiles in media with increased concentrations of a representative aromatic, branched chain and sulphur amino acid. Volatiles were assessed using gas chromatography coupled with mass spectrometry. Strain-dependent differences in the range and type of volatiles produced were evident. Conclusions: Strains of the Lact. casei group are characterized by genetic and metabolic diversity which supports variability in volatile production. Significance and Impact of the Study: This study provides a screening approach for the knowledge-based selection of strains potentially enabling flavour diversification in fermented dairy products

Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy

Abstract Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections

Strains of the Lactobacillus casei group show diverse abilities for the production of flavor compounds in 2 model systems

peer-reviewedCheese flavor development is directly connected to the metabolic activity of microorganisms used during its manufacture, and the selection of metabolically diverse strains represents a potential tool for the production of cheese with novel and distinct flavor characteristics. Strains of Lactobacillus have been proven to promote the development of important cheese flavor compounds. As cheese production and ripening are long-lasting and expensive, model systems have been developed with the purpose of rapidly screening lactic acid bacteria for their flavor potential. The biodiversity of 10 strains of the Lactobacillus casei group was evaluated in 2 model systems and their volatile profiles were determined by gas chromatography-mass spectrometry. In model system 1, which represented a mixture of free AA, inoculated cells did not grow. In total, 66 compounds considered as flavor contributors were successfully identified, most of which were aldehydes, acids, and alcohols produced via AA metabolism by selected strains. Three strains (DPC2071, DPC3990, and DPC4206) had the most diverse metabolic capacities in model system 1. In model system 2, which was based on processed cheese curd, inoculated cells increased in numbers over incubation time. A total of 47 compounds were identified, and they originated not only from proteolysis, but also from glycolytic and lipolytic processes. Tested strains produced ketones, acids, and esters. Although strains produced different abundances of volatiles, diversity was less evident in model system 2, and only one strain (DPC4206) was distinguished from the others. Strains identified as the most dissimilar in both of the model systems could be more useful for cheese flavor diversification

Evaluation of the Potential of Lactobacillus paracasei Adjuncts for Flavor Compounds Development and Diversification in Short-Aged Cheddar Cheese

peer-reviewedThe non-starter microbiota of Cheddar cheese mostly comprises mesophilic lactobacilli, such as Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus plantarum. These bacteria are recognized for their potential to improve Cheddar cheese flavor when used as adjunct cultures. In this study, three strains of L. paracasei (DPC2071, DPC4206, and DPC4536) were evaluated for their contribution to the enhancement and diversification of flavor in short-aged Cheddar cheese. The strains were selected based on their previously determined genomic diversity, variability in proteolytic enzyme activities and metabolic capability in cheese model systems. The addition of adjunct cultures did not affect the gross composition or levels of lipolysis of the cheeses. The levels of free amino acids (FAA) in cheeses showed a significant increase after 28 days of ripening. However, the concentrations of individual amino acids in the cheeses did not significantly differ except for some amino acids (aspartic acid, threonine, serine, and tryptophan) at Day 14. Volatile profile analysis revealed that the main compounds that differentiated the cheeses were of lipid origin, such as long chain aldehydes, acids, ketones, and lactones. This study demonstrated that the adjunct L. paracasei strains contributed to the development and diversification of compounds related to flavor in short-aged Cheddar cheeses

CLINTON VS TRUMP : An investigation of how the leadership of US presidential candidates is being designed discursively in Metro and Dagens Nyheter

Abstract Title:CLINTON VS TRUMP -An investigation of how the leadership of US presidential candidates is being designed discursively in Metro and Dagens Nyheter Author: Ewelina Bosak & Sandra Stefanovic In 2016 a man and a woman competed for the first time in history in becoming the President of the United States. In 2016 one could read about the American presidential election every day in any newspaper. With this in mind, we want to examine the leadership being applied to the candidates by the news sources Metro and Dagens Nyheter. As leadership traditionally is considered a masculine feature, we apply a gender perspective to this study. The questions we intend to answer: - What discourse is construed by Metro and Dagens Nyheter regarding the leadership of Clinton and Trump? - How are Clinton and Trump being portrayed from a gender perspective? We used the method of discourse analysis, as it advocates the principle of language being the primary tool in shaping our realities. The theoretical framework we use to interpret and explain our results is based on discourse theory as well as the social construction of age and gender. Our research shows that Trump is generally being portrayed in a way not considered to be "right" in accordance to the leadership- or age norm. The discourse of Trump presents him as an inexperienced, dishonest and attempted leader with an childish behaviour. Trump is also often described through typically considered feminine features. Clinton, being perceived as almost invisible and often depicted in comparison to Trump or other male leaders, is at the same time portrayed as a successful, experienced, driven and intelligent leader. However, we have discovered that in spite of Clinton’s described leadership features she is constantly also criticised for being cold and not evoking any feelings or engagement. Clinton is not only being questioned on the basis of the masculine leadership norms, but also on the lack characteristics in line with the feminine norm