Detection of putative new mutacins by bioinformatic analysis using available web tools

In order to characterise new bacteriocins produced by Streptococcus mutans we perform a complete bioinformatic analyses by scanning the genome sequence of strains UA159 and NN2025. By searching in the adjacent genomic context of the two-component signal transduction system we predicted the existence of many putative new bacteriocins' maturation pathways and some of them were only exclusive to a group of Streptococcus. Computational genomic and proteomic analysis combined to predictive functionnal analysis represent an alternative way for rapid identification of new putative bacteriocins as well as new potential antimicrobial drugs compared to the more traditional methods of drugs discovery using antagonism tests

Contribution of Exogenous Genetic Elements to the Group A Streptococcus Metagenome

Variation in gene content among strains of a bacterial species contributes to biomedically relevant differences in phenotypes such as virulence and antimicrobial resistance. Group A Streptococcus (GAS) causes a diverse array of human infections and sequelae, and exhibits a complex pathogenic behavior. To enhance our understanding of genotype-phenotype relationships in this important pathogen, we determined the complete genome sequences of four GAS strains expressing M protein serotypes (M2, M4, and 2 M12) that commonly cause noninvasive and invasive infections. These sequences were compared with eight previously determined GAS genomes and regions of variably present gene content were assessed. Consistent with the previously determined genomes, each of the new genomes is ∼1.9 Mb in size, with ∼10% of the gene content of each encoded on variably present exogenous genetic elements. Like the other GAS genomes, these four genomes are polylysogenic and prophage encode the majority of the variably present gene content of each. In contrast to most of the previously determined genomes, multiple exogenous integrated conjugative elements (ICEs) with characteristics of conjugative transposons and plasmids are present in these new genomes. Cumulatively, 242 new GAS metagenome genes were identified that were not present in the previously sequenced genomes. Importantly, ICEs accounted for 41% of the new GAS metagenome gene content identified in these four genomes. Two large ICEs, designated 2096-RD.2 (63 kb) and 10750-RD.2 (49 kb), have multiple genes encoding resistance to antimicrobial agents, including tetracycline and erythromycin, respectively. Also resident on these ICEs are three genes encoding inferred extracellular proteins of unknown function, including a predicted cell surface protein that is only present in the genome of the serotype M12 strain cultured from a patient with acute poststreptococcal glomerulonephritis. The data provide new information about the GAS metagenome and will assist studies of pathogenesis, antimicrobial resistance, and population genomics

Prospects for the development of probiotics and prebiotics for oral applications

There has been a paradigm shift towards an ecological and microbial community-based approach to understanding oral diseases. This has significant implications for approaches to therapy and has raised the possibility of developing novel strategies through manipulation of the resident oral microbiota and modulation of host immune responses. The increased popularity of using probiotic bacteria and/or prebiotic supplements to improve gastrointestinal health has prompted interest in the utility of this approach for oral applications. Evidence now suggests that probiotics may function not only by direct inhibition of, or enhanced competition with, pathogenic micro-organisms, but also by more subtle mechanisms including modulation of the mucosal immune system. Similarly, prebiotics could promote the growth of beneficial micro-organisms that comprise part of the resident microbiota. The evidence for the use of pro or prebiotics for the prevention of caries or periodontal diseases is reviewed, and issues that could arise from their use, as well as questions that still need to be answered, are raised. A complete understanding of the broad ecological changes induced in the mouth by probiotics or prebiotics will be essential to assess their long-term consequences for oral health and disease

Yeast epigenetics and its potential applications in biotechnology

Epigenetic changes in the genome provide phenotypic plasticity without alteration of the DNA sequence. We show that benzoic acid, a common food additive and known histone deacetylase inhibitor (HDACi), has an epigenetic effect on Saccharomyces cerevisiae. Benzoic acid stimulated formation of epigenetic histone marks H3K4Me2, H3K27Me2, H3K18ac and H3Ser10p in yeast and altered their phenotypic behaviour, resulting in increased production of phenylethyl alcohol and ester compounds during alcoholic fermentation. Our study also demonstrates the HDACi activity of certain dietary compounds such as sodium butyrate, curcumin and anacardic acid, suggesting a potential use of these dietary compounds in altering yeast phenotypes without altering host-cell DNA. This study highlights the potential to use common dietary compounds to exploit epigenetic modifications for various fermentation and biotechnology applications as an alternative to genetic modification. Furthermore, we observed that H3K27me3 mark was downregulated and GCN4 gene was upregulated by benzoic acid. Both, downregulation of H3K27me3 mark and upregulation of GCN4 are known to play a crucial role in life span extension of Caenorhabditis elegans and S.cerevisiae respectively, indicating potential application of dietary HDACi in ageing science. Further research including the dissection of the epigenome of yeast cells treated with dietary HDACi using multiomics approach

Weibull-based methodology for condition assessment of cast iron water mains and its application

A qualitative and quantitative understanding of how cast iron water distribution pipes fail in service would facilitate a targeted approach to the management of rehabilitation in the water industry. This paper proposes a technique for assessing the condition of pipes, based on strength characteristics obtained from small samples; this offers an alternative way of estimating the likelihood of failure to current methodologies based on pit-depth measurements. Examination of recovered pipe samples indicates that the strength of the cast iron pipe reduces over time as a result of corrosion, although other time-dependent processes, such as fatigue, may also contribute to this degradation. Taken with previous work, this paper suggests that the variation in strength of small samples removed from cast iron water distribution pipes can be characterized using Weibull methods. It is argued that the Weibull modulus provides a useful indicator of the condition of the pipe. Using scaling arguments, inherent in the Weibull methodology, it is then possible to use data from small samples to predict the likely strength characteristics of water distribution pipes in the ground, which is reasoned to be a good measure of the potential performance of the pipe in service. The Weibull approach is applied to a number of different data sets obtained from testing samples extracted from a range of pipes, which have seen service at various locations in the Thames Water region. One of these data sets was from locations where failure had occurred in service. It is shown that the use of Weibull analysis can identify pipes in the network that have degraded the most significantly. A methodology is suggested whereby this information taken with other performance indicators can be used to identify the local regions where rehabilitation is required most urgently. Alternatively, it can be used to identify those regions of the network, which are in good condition and unlikely to need repair or replacement work

Nutrifermentics: Pioneering next generation fermented products

Nutrifermentics” is a new concept we have developed to describe an approach to fermentation focused on understanding how specific dietary compounds impact on the epigenetic regulation of microbial strains. We use this knowledge to develop microbial strains for food and beverage production without resorting to genetic modification. Our innovative approach, rooted in epigenetics, allows us to modify the metabolomic profile of fermented products without directly altering the DNA of the involved microbes. This cutting-edge technique has already shown promising results in alcohol fermentation and wine production. Here, we investigated the epigenetic responses (changes in DNA methylation levels) of the probiotic gut bacteria Lactobacillus acidophilus, which is widely used in yogurt making, to dietary epigenetically-active compounds such as genistein. These epigenetic changes altered the metabolomic profile and produced beneficial primary and secondary metabolites, including antimicrobial compounds like 3-phenyllactic acid and health-promoting substances like trehalose. Moreover, this study demonstrated that individual genes or loci, such as those responsible for melibiose production which was upregulated 8 fold, can be altered without resorting to genetic modification methods such as CRISPR, thus highlighting the plethora of biotechnology applications for this technology. This in-depth multiomic analysis of the effect of certain dietary compounds on epigenetics, transcriptomics, and metabolomics in the probiotic gut bacteria Lactobacillus acidophilus, provides useful insights into the role of dietary compounds on the fermentative capability of bacteria. Furthermore, this study has shown that dietary epigenetic compounds can be used to alter the microbes used in the fermentation process, ultimately leading to the development of sustainable and non-GMO fermented products

Epigenetic modifications impact metabolite production and lifespan in yeast

Epigenetics have been shown to play a crucial role in regulating gene expression during the aging and immune response processes, with changes in epigenetic marks being linked to age-related diseases and inflammatory responses. Recently it has been revealed that S-adenosyl-l-homocysteine can extend the lifespan of the budding yeast Saccharomyces cerevisiae by mimicking caloric restriction. In this present study, we aimed to activate the production of S-adenosyl-l-homocysteine by S. cerevisiae through introducing epigenetic changes as a result of exposure to benzoic acid, a known epigenetic modifier. The impact of this on metabolite production was evaluated using LC-MS/MS. The study successfully activated and measured an overproduction of S-adenosyl-l-homocysteine (SAH) in yeast previously exposed to benzoic acid and led to lifespan extension. The link between the aging process and immune responses in yeast was further explored in the study. The production of SAH was downregulated while several inflammatory response metabolites were upregulated in aging cells. The upregulation of inflammatory response metabolites with their inherent anti-viral and antimicrobial activities could potentially be valuable for use in human health applications. By contrast, in cells with higher lifespans these inflammatory metabolites were downregulated. This finding supports the concept that aging leads to higher levels of histone methylation and acetylation, which in turn cause the production of immune response metabolites and inflammation. By contrast, it appears that lower levels of histone methylation and acetylation as seen in healthy cells, can increase production of metabolites responsible for lifespan extension, such as SAH. In summary, this study provides insights into the molecular mechanisms involved in lifespan extension and the role of metabolites in regulating aging in yeast. The research sheds light on the interplay between metabolism, epigenetics, immunity and aging and contributes to the growing field of metabolomics

Epigenetic changes in Saccharomyces cerevisiae alters the aromatic profile in alcoholic fermentation

Epigenetic changes in genomics provide phenotypic modification without DNA sequence alteration. This study shows that benzoic acid, a common food additive and known histone deacetylase inhibitor (HDACi), has an epigenetic effect on Saccharomyces cerevisiae. Benzoic acid stimulated formation of epigenetic histone marks H3K4Me2, H3K27Me2, H3K18ac and H3Ser10p in S. cerevisiae and altered their phenotypic behavior, resulting in increased production of phenylethyl alcohol and ester compounds during alcoholic fermentation. Our study demonstrates the HDACi activity of certain dietary compounds such as sodium butyrate, curcumin and anacardic acid, suggests the potential use of these dietary compounds in altering S. cerevisiae phenotypes without altering host-cell DNA. This study highlights the potential to use common dietary compounds to exploit epigenetic modifications for various fermentation and biotechnology applications as an alternative to genetic modification. These findings indicate that benzoic acid and other food additives may have potential epigenetic effects on human gut microbiota, in which several yeast species are involved

Epigenetic changes in Saccharomyces cerevisiae alters the aromatic profile in alcoholic fermentation

Epigenetic changes in genomics provide phenotypic modification without DNA sequence alteration. This study shows that benzoic acid, a common food additive and known histone deacetylase inhibitor (HDACi), has an epigenetic effect on Saccharomyces cerevisiae. Benzoic acid stimulated formation of epigenetic histone marks H3K4Me2, H3K27Me2, H3K18ac, and H3Ser10p in S. cerevisiae and altered their phenotypic behavior, resulting in increased production of phenylethyl alcohol and ester compounds during alcoholic fermentation using wine as a representative model system. Our study demonstrates the HDACi activity of certain dietary compounds such as sodium butyrate, curcumin and anacardic acid, suggests the potential use of these dietary compounds in altering S. cerevisiae phenotypes without altering host-cell DNA. This study highlights the potential to use common dietary compounds to exploit epigenetic modifications for various fermentation and biotechnology applications as an alternative to genetic modification. These findings indicate that benzoic acid and other food additives may have potential epigenetic effects on human gut microbiota, in which several yeast species are involved. IMPORTANCE The manuscript investigates and reports for the first time utilizing a non-GMO approach to alter the fermentation process of Pinot Noir wines. We have experimentally demonstrated that certain dietary compounds possess histone deacetylase (HDAC) inhibiting activity and can alter the wine characteristics by potentially altering yeast gene transcription, which was resulted from epigenetic effects. We have previously proposed the term “nutrifermentics” to represent this newly proposed field of research that provides insights on the effect of certain dietary compounds on microbial strains and their potential application in fermentation. This technological approach is a novel way to manipulate microorganisms for innovative food and beverage production with quality attributes catering for consumer’s needs. Using a multidisciplinary approach with an emphasis on food fermentation and biotechnology, this study will be substantially useful and of broad interest to food microbiologists and biotechnologists who seek for innovative concepts with real-world application potential