Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites.

BACKGROUND: Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated. RESULTS: The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms. CONCLUSIONS: Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.

Limitations of the Food Compass Nutrient Profiling System.

Nutrient Profiling Systems provide frameworks to assess the healthfulness of foods based on food composition and are intended as inputs into strategies to improve diets. Many Nutrient Profiling Systems are founded on a reductionist assumption that the healthfulness of foods is determined by the sum of their individual nutrients, with no consideration for the extent and purpose of processing and its health implications. A novel Nutrient Profiling System called Food Compass attempted to address existing gaps and provide a more holistic assessment of the healthfulness of foods. We propose that the chosen algorithm is not well justified and produces results that fail to discriminate for common shortfall nutrients, exaggerate the risks associated with animal-source foods, and underestimate the risks associated with ultraprocessed foods. We caution against the use of Food Compass in its current form to inform consumer choices, policies, programs, industry reformulations, and investment decisions.

Atomistic Description of Interdroplet Ice-Bridge Formation during Condensation Frosting.

The propagation of frost in an assembly of supercooled dew droplets takes place by the formation of ice protrusions that bridge ice particles and still-liquid droplets. In this work, we develop a Kinetic Monte Carlo (KMC) model to study the formation kinetics of the ice protrusions. The KMC simulations reproduce well the experimental results reported in the literature. The elongation speed of the ice protrusions does not depend on the droplet size but increases when the interdroplet distance decreases, the temperature increases, or the substrate wettability increases. While 2D diffusion of the water molecules on the substrate surface is sufficient to explain the process kinetics, high 3D (vapor) water-molecule concentration can lead to the development of 3D lateral branches on the ice protrusions. A 1D analytical model based on the water-molecule concentration gradient between a droplet and a nearby ice particle reproduces well the simulation results and highlights the relation between the protrusion elongation kinetics and parameters like the interdroplet distance, the water diffusivity, and the concentration gradient. The bridge-formation time has a quadratic dependence on the droplet-ice distance. Comparing the simulations, the analytical model, and the experimental results of the literature, we conclude that the propagation of frost on a flat substrate in an assembly of supercooled dew droplets with interdroplet spacing larger than about 1 µm is limited by water-molecule diffusivity.

Genome-Based Characterization of a Plasmid-Associated Micrococcin P1 Biosynthetic Gene Cluster and Virulence Factors in Mammaliicoccus sciuri IMDO-S72.

Analysis of the de novo assembled genome of Mammaliicoccus sciuri IMDO-S72 revealed the genetically encoded machinery behind its earlier reported antibacterial phenotype and gave further insight into the repertoire of putative virulence factors of this recently reclassified species. A plasmid-encoded biosynthetic gene cluster was held responsible for the antimicrobial activity of M. sciuri IMDO-S72, comprising genes involved in thiopeptide production. The compound encoded by this gene cluster was structurally identified as micrococcin P1. Further examination of its genome highlighted the ubiquitous presence of innate virulence factors mainly involved in surface colonization. Determinants contributing to aggressive virulence were generally absent, with the exception of a plasmid-associated ica cluster. The native antibiotic resistance genes sal(A) and mecA were detected within the genome, among others, but were not consistently linked with a resistance phenotype. While mobile genetic elements were identified within the genome, such as an untypeable staphylococcal cassette chromosome (SCC) element, they proved to be generally free of virulence- and antibiotic-related genes. These results further suggest a commensal lifestyle of M. sciuri and indicate the association of antibiotic resistance determinants with mobile genetic elements as an important factor in conferring antibiotic resistance, in addition to their unilateral annotation. IMPORTANCEMammaliicoccus sciuri has been put forward as an important carrier of virulence and antibiotic resistance genes, which can be transmitted to clinically important staphylococcal species such as Staphylococcus aureus. As a common inhabitant of mammal skin, this species is believed to have a predominant commensal lifestyle, although it has been reported as an opportunistic pathogen in some cases. This study provides an extensive genome-wide description of its putative virulence potential taking into consideration the genomic context in which these genes appear, an aspect that is often overlooked during virulence analysis. Additional genome and biochemical analysis linked M. sciuri with the production of micrococcin P1, gaining further insight into the extent to which these biosynthetic gene clusters are distributed among different related species. The frequent plasmid-associated character hints that these traits can be horizontally transferred and might confer a competitive advantage to its recipient within its ecological niche.

Should dietary guidelines recommend low red meat intake?

Mainstream dietary recommendations now commonly advise people to minimize the intake of red meat for health and environmental reasons. Most recently, a major report issued by the EAT-Lancet Commission recommended a planetary reference diet mostly based on plants and with no or very low (14 g/d) consumption of red meat. We argue that claims about the health dangers of red meat are not only improbable in the light of our evolutionary history, they are far from being supported by robust scientific evidence.

Raw meat quality and salt levels affect the bacterial species diversity and community dynamics during the fermentation of pork mince.

Acidification level and temperature modulate the beneficial consortia of lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS) during meat fermentation. Less is known about the impact of other factors, such as raw meat quality and salting. These could for instance affect the growth of the pathogen Staphylococcus aureus or of Enterobacterales species, potentially indicative of poor fermentation practice. Therefore, pork batters from either normal or borderline quality (dark-firm-dry, DFD) were compared at various salt concentrations (0-4%) in meat fermentation models. Microbial ecology of the samples was investigated with culture-dependent techniques and (GTG)5-PCR fingerprinting of genomic DNA. Whilst Lactobacillus sakei governed the fermentation of normal meat, Lactobacillus curvatus was more prominent in the fermentation of the DFD meat variant. CNS were favoured during fermentation at rising salt concentrations without much effects on species diversity, consisting mostly of Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus. During fermentation of DFD meat, S. saprophyticus was less manifest than during that of normal meat. Enterobacterales mainly emerged in DFD meat during fermentation at low salt concentrations. The salt hurdle was insufficient to prevent Enterobacterales when acidification and initial pH were favourable for their growth.

High-Throughput DNA sequencing of ancient wood.

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.

Molecular dynamics analysis of the influence of Coulomb and van der Waals interactions on the work of adhesion at the solid-liquid interface.

We investigated the solid-liquid work of adhesion of water on a model silica surface by molecular dynamics simulations, where a methodology previously developed to determine the work of adhesion through thermodynamic integration was extended to a system with long-range electrostatic interactions between solid and liquid. In agreement with previous studies, the work of adhesion increased when the magnitude of the surface polarity was increased. On the other hand, we found that when comparing two systems with and without solid-liquid electrostatic interactions, which were set to have approximately the same total solid-liquid interfacial energy, former had a significantly smaller work of adhesion and a broader distribution in the interfacial energies, which has not been previously reported in detail. This was explained by the entropy contribution to the adhesion free energy; i.e., the former with a broader energy distribution had a larger interfacial entropy than the latter. While the entropy contribution to the work of adhesion has already been known, as a work of adhesion itself is free energy, these results indicate that, contrary to common belief, wetting behavior such as the contact angle is not only governed by the interfacial energy but also significantly affected by the interfacial entropy. Finally, a new interpretation of interfacial entropy in the context of solid-liquid energy variance was offered, from which a fast way to qualitatively estimate the work of adhesion was also presented.

Meat in the post-truth era: Mass media discourses on health and disease in the attention economy.

The debate on meat's role in health and disease is a rowdy and dissonant one. This study uses the health section of the online version of The Daily Mail as a case study to carry out a quantitative and qualitative reflection on the related discourses in mass media during the first fifteen years of the 21st century. This period ranged from the fall-out of the bovine spongiform encephalopathy (BSE) crisis and its associated food safety anxieties, over the Atkins diet-craze in 2003 and the avian flu episode in 2007, to the highly influential publication of the report on colon cancer by the International Agency for Research on Cancer (IARC) in 2015. A variety of conflicting news items was discernible, whereby moments of crisis, depicting the potential hazards of meat eating, seemed to generate reassuring counter-reactions stressing the benefits of meat as a rich source of nutrients. In contrast, when the popularity of meat-rich diets was on the rise due to diets stressing the role of protein in weight control, several warnings were issued. Meat's long-standing and semiotic connotations of vitality, strength, and fertility were either confirmed, rejected or inverted. Often this was achieved through scientification or medicalisation, with references to nutritional studies. The holistic role of meat within human diets and health was thus mostly reduced to a focus on specific food components and isolated biological mechanisms. The narratives were often histrionic and displayed serious contradictions. Since several interests were at play, involving a variety of input from dieticians, (health) authorities, the food industry, vegan or vegetarian movements, and celebrities, the overall discourse was highly heterogeneous.

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail.

Sliced cooked poultry products are susceptible to bacterial spoilage, notwithstanding their storage under modified-atmosphere packaging (MAP) in the cold chain. Although the prevailing bacterial communities are known to be mostly consisting of lactic acid bacteria (LAB), more information is needed about the potential variation in species diversity within national markets. In the present study, a total of 42 different samples of sliced cooked poultry products were collected in the Belgian retail and their bacterial communities were analysed at expiration date. A total of 629 isolates from four different culture media, including plate count agar for the total microbiota and de Man-Rogosa-Sharpe (MRS), modified MRS, and M17 agar as three selective agar media for LAB, were subjected to (GTG)5-PCR fingerprinting and identification by gene sequencing. Overall, Carnobacterium, Lactobacillus, and Leuconostoc were the dominant genera. Within each genus, the most encountered isolates were Carnobacterium divergens, Lactobacillus sakei, and Leuconostoc carnosum. When comparing samples from chicken origin with samples from turkey-derived products, a higher dominance of Carnobacteria spp. was found in the latter group. Also, an association between the dominance of lactobacilli and the presence of added plant material and lactate salts was found.

Effect of temperature and pH on the community dynamics of coagulase-negative staphylococci during spontaneous meat fermentation in a model system.

Coagulase-negative staphylococci (CNS) contribute to the product quality of fermented meats. In spontaneously fermented meats, CNS communities are variable and difficult to predict, as their compositions depend on a superposed combination of different processing factors. To partially disentangle this superposition, a meat model system was used to study the influence of temperature and pH on the CNS community dynamics. Therefore, cured pork mince was prepared that was divided into three batches of different initial acidity levels, namely pH 5.7, pH 5.5, and pH 5.3. These three batches were incubated at three different temperatures, namely 23 °C, 30 °C, and 37 °C. Hence, the experimental set-up resulted in nine combinations of different temperature and initial pH values. Samples were analysed after 3 and 14 days to monitor pH, colony counts, and species diversity of the CNS communities, based on mannitol-salt-phenol-red agar (MSA) medium. At conditions of mild acidity (pH 5.7) and low temperature (23 °C), as often encountered during artisan-type meat fermentations, a co-prevalence of Staphylococcus xylosus, Staphylococcus equorum, and Staphylococcus saprophyticus occurred. At the same initial pH but higher incubation temperatures (30 °C and 37 °C), Staphylococcus lugdunensis became the prevailing CNS species, besides S. saprophyticus (30 °C) and the coagulase-positive species Staphylococcus aureus (37 °C). When the initial pH was set at 5.5, S. saprophyticus was the prevailing CNS species at both 23 °C and 30 °C, but it was replaced by Staphylococcus epidermidis and Staphylococcus simulans at 37 °C after 3 and 14 days, respectively. At the most acidic conditions (pH 5.3), CNS counts declined and many of the MSA isolates were of non-staphylococcal nature. Among others, Staphylococcus carnosus (23 °C), Staphylococcus warneri (30 °C), and S. epidermidis (37 °C) were found. Overall, the results of the present study indicated that the processing factors temperature and pH had a clear impact on the shaping of staphylococcal communities during meat fermentation.

Solid-Liquid Interface Thermal Resistance Affects the Evaporation Rate of Droplets from a Surface: A Study of Perfluorohexane on Chromium Using Molecular Dynamics and Continuum Theory.

We study the role of solid-liquid interface thermal resistance (Kapitza resistance) on the evaporation rate of droplets on a heated surface by using a multiscale combination of molecular dynamics (MD) simulations and analytical continuum theory. We parametrize the nonbonded interaction potential between perfluorohexane (C6F14) and a face-centered-cubic solid surface to reproduce the experimental wetting behavior of C6F14 on black chromium through the solid-liquid work of adhesion (quantity directly related to the wetting angle). The thermal conductances between C6F14 and (100) and (111) solid substrates are evaluated by a nonequilibrium molecular dynamics approach for a liquid pressure lower than 2 MPa. Finally, we examine the influence of the Kapitza resistance on evaporation of droplets in the vicinity of a three-phase contact line with continuum theory, where the thermal resistance of liquid layer is comparable with the Kapitza resistance. We determine the thermodynamic conditions under which the Kapitza resistance plays an important role in correctly predicting the evaporation heat flux.

Microbial Ecology and Process Technology of Sourdough Fermentation.

From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.

Discovery of benzophosphadiazine drug candidate IDX375: A novel hepatitis C allosteric NS5B RdRp inhibitor.

Hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells, and as a consequence is an attractive target for selective inhibition. This paper describes the discovery of a novel family of HCV NS5B non-nucleoside inhibitors inspired by the bioisosterism between sulfonamide and phosphonamide. Systematic structural optimization in this new series led to the identification of IDX375, a potent non-nucleoside inhibitor that is selective for genotypes 1a and 1b. The structure and binding domain of IDX375 were confirmed by X-ray co-crystalisation study.

Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces.

In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.

Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?

Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer graphene with interactions ranging from hydrophobic to mildly hydrophilic. By design the water models employed yield similar liquid layer structures on the graphene surfaces. Moreover, they share common vibration properties close to the surfaces and thus couple with the vibrations of graphene in a similar way. These common properties explain why they yield similar Kapitza conductance values despite their bulk thermal conductivity differing by more than a factor of two.

Formation of coffee-stain patterns at the nanoscale: The role of nanoparticle solubility and solvent evaporation rate.

When droplets of nanoparticle suspension evaporate from surfaces, they leave behind a deposit of nanoparticles. The mechanism of evaporation-induced pattern formation in the deposit is studied by molecular dynamics simulations for sessile nanodroplets. The influence of the interaction between nanoparticles and liquid molecules and the influence of the evaporation rate on the final deposition pattern are addressed. When the nanoparticle-liquid interaction is weaker than the liquid-liquid interaction, an interaction-driven or evaporation-induced layer of nanoparticles appears at the liquid-vapor interface and eventually collapses onto the solid surface to form a uniform deposit independently of the evaporation rate. When the nanoparticle-liquid and liquid-liquid interactions are comparable, the nanoparticles are dispersed inside the droplet and evaporation takes place with the contact line pinned at a surface defect. In such a case, a pattern with an approximate ring-like shape is found with fast evaporation, while a more uniform distribution is observed with slower evaporation. When the liquid-nanoparticle interaction is stronger than the liquid-liquid interaction, evaporation always occurs with receding contact line. The final deposition pattern changes from volcano-like to pancake-like with decreasing evaporation rate. These findings might help to design nanoscale structures like nanopatterns or nanowires on surface through controlled solvent evaporation.

Yogurt's flexible image during its rise in popularity in post-war Belgium.

The consumption of yogurt in Western countries has risen for over a century, first slowly, then more rapidly. The purpose of the present study was to investigate this prolonged phase of growth, by examining the popularity and the projected image of yogurt. A particular focus was on the way these aspects were reflected in consumption patterns and media representations. The data showed how during its period of rapid popularization, yogurt's visibility in the media greatly increased. It was concluded that the product's image was highly flexible in post-war decades, evidenced by the multi-pronged approach taken by marketers. Yogurt was not only advertised as both tasty and healthy, but also as natural and convenient, a strategy that appears to have been informed by consumers' preferences and existing cultural values. This demonstrates how a high degree of product differentiation and diversification during a product's growth stage can result in a heterogeneous image, allowing for a broad range of marketing strategies.

Effects of glucose and oxygen on arginine metabolism by coagulase-negative staphylococci.

Coagulase-negative staphylococci (CNS) are not only part of the desirable microbiota of fermented meat products but also commonly inhabit skin and flesh wounds. Their proliferation depends on the versatility to use energy sources and the adaptation to fluctuating environmental parameters. In this study, the conversion of the amino acid arginine by two strains with arginine deiminase (ADI) activity (Staphylococcus carnosus 833 and S. pasteuri αs3-13) and a strain with nitric oxide synthase (NOS) activity (S. haemolyticus G110) was modelled as a function of glucose and oxygen availability. Both factors moderately inhibited the ADI-based conversion kinetics, never leading to full repression. However, for NOS-driven conversion of arginine by S. haemolyticus G110, oxygen was an absolute requirement. When changing from microaerobic conditions to aerobiosis, a switch from homolactic fermentation to a combined formation of lactic acid, acetic acid, and acetoin was found in all cases, after which lactic acid and acetic acid were used as substrates. The kinetic model proposed provided a suitable description of the data of glucose and arginine co-metabolism as a function of oxygen levels and may serve as a tool to further analyse the behaviour of staphylococci in different ecosystems or when applying specific food processing conditions.