Acid stress in the food pathogen Bacillus cereus

Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis

Adaptation to sublethal amounts of ethanol enables Salmonella Enteritidis to survive under normally lethal ethanol conditions, which is referred to as the ethanol tolerance response (ETR). To uncover mechanisms underlying this adaptative response, RNA-seq and RT-qPCR techniques were employed to reveal global gene expression patterns in S. Enteritidis after sublethal ethanol treatment. It was observed that 811 genes were significantly differentially expressed in ethanol-treated cells compared with control cells, among which 328 were up-regulated and 483 were down-regulated. Functional analysis revealed that these genes were enriched in different pathways, including signal transduction, membrane transport, metabolism, transcription, translation, and cell motility. Specifically, a couple of genes encoding histidine kinases and response regulators in two-component systems were up-regulated to activate sensing and signaling pathways. Membrane function was also influenced by ethanol treatment since ABC transporter genes for transport of glutamate, phosphate, 2-aminoethylphosphonate, and osmoprotectant were up-regulated, while those for transport of iron complex, manganese, and ribose were down-regulated. Accompanied with this, diverse gene expression alterations related to the metabolism of amino acids, carbohydrates, vitamins, and nucleotides were observed, which suggested nutritional requirements for S. Enteritidis to mount the ETR. Furthermore, genes associated with ribosomal units, bacterial chemotaxis, and flagellar assembly were generally repressed as a possible energy conservation strategy. Taken together, this transcriptomic study indicates that S. Enteritidis employs multiple genes and adaptation pathways to develop the ETR.

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A total of 811 genes were involved in ethanol tolerance of Salmonella Enteritidis.

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Certain genes encoding two-component signaling systems were upregulated.

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Differential expression of many metabolism-related genes was observed.

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Bacterial chemotaxis and flagellar assembly were repressed by ethanol stress.

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Diverse membrane transport functions were influenced by ethanol stress.

Bacillus cereus food intoxication and toxicoinfection

Bacillus cereus is one of the leading etiological agents of toxin-induced foodborne diseases. Its omnipresence in different environments, spore formation, and its ability to adapt to varying conditions and produce harmful toxins make this pathogen a health hazard that should not be underestimated. Food poisoning by B. cereus can manifest itself as an emetic or diarrheal syndrome. The former is caused by the release of the potent peptide toxin cereulide, whereas the latter is the result of proteinaceous enterotoxins (e.g., hemolysin BL, nonhemolytic enterotoxin, and cytotoxin K). The final harmful effect is not only toxin and strain dependent, but is also affected by the stress responses, accessory virulence factors, and phenotypic properties under extrinsic, intrinsic, and explicit food conditions and host-related environment. Infamous portrait of B. cereus as a foodborne pathogen, as well as a causative agent of nongastrointestinal infections and even nosocomial complications, has inspired vast volumes of multidisciplinary research in food and clinical domains. As a result, extensive original data became available asking for a new, both broad and deep, multifaceted look into the current state-of-the art regarding the role of B. cereus in food safety. In this review, we first provide an overview of the latest knowledge on B. cereus toxins and accessory virulence factors. Second, we describe the novel taxonomy and some of the most pertinent phenotypic characteristics of B. cereus related to food safety. We link these aspects to toxin production, overall pathogenesis, and interactions with its human host. Then we reflect on the prevalence of different toxinotypes in foods opening the scene for epidemiological aspects of B. cereus foodborne diseases and methods available to prevent food poisoning including overview of the different available methods to detect B. cereus and its toxins.

Short communication: Modulation of fatty acid metabolism improves oxygen tolerance of Bifidobacterium animalis ssp. lactis Probio-M8

Bifidobacterium animalis ssp. lactis Probio-M8 is a potential probiotic strain that was isolated from human milk. Previously, we obtained an oxygen-resistant variant (Probio-M8o) of Probio-M8 by an adaptive evolution strategy. In the present study, a comparative transcriptomic analysis of Probio-M8o and Probio-M8 was carried out to reveal the cellular mechanism of the oxygen-resistant phenotype. Using RNA-seq, 210 and 217 differentially expressed genes were identified in Probio-M8o compared with Probio-M8 after oxygen exposure for 30 and 60 min, respectively. The oxygen treatment upregulated a set of genes that encoded proteins responsible for fatty acid biosynthesis. This observation was in good agreement with the composition change in fatty acids at the biochemical level. Our study showed that the oxygen-resistant phenotype could be related to adaptation of fatty acid metabolism.

Molecular identification of a Bacillus cereus strain from Murrah buffalo milk showed in vitro bioremediation properties on selective heavy metals

Objective:

This study aims for molecular identification of naturally growing Bacillus cereus strain from a unique source, able to survive, and alleviate heavy metals from the nature.

Materials and Methods:

Pure isolate from Murrah buffalo milk was prepared in B. cereus selective Polymyxin pyruvate egg-yolk mannitol–bromothymol blue agar (PEMBA) medium through a cascade of contamination free subcultures. The morphological and biochemical tests were done prior to 16S rRNA gene sequencing for strain identification and further physiological tests. The test strain was inoculated in both solid and suspension culture medium supplemented individually with Cd, Cu, Ag, and Zn to reveal the qualitative and quantitative heavy metal tolerance properties, respectively. Finally, the data collected from the in vitro assessment was statistically analyzed

Results:

Molecular analysis revealed that the test strain was B. cereus BF2, which was motile, catalase positive and Gram positive rod. B. cereus BF2 was found significant at 0.3% bile salt tolerance [two-way analysis of variance (ANOVA)—p value is < 0.0001] where, t-test p value is < 0.0002 between Control Group (CG) and TGR-1; p < 0.037 between TGR-1 and 2; p < 0.0014 between CG and TGR-2. Similarly, B. cereus BF2 was significant in pH tolerant up to 8.0 with p < 0.0115 (in scale p < 0.05). The heavy metal tolerance test revealed that the test metals could not stop the growth of B. cereus BF2 even after 24 h of incubation but partially suppressed the growth kinetics for letting into stationary phase. Among the four heavy metals, Cd and Zn showed partial antagonism to the growth of B. cereus BF2. The survivability was highly significant in the medium supplemented with Zn (p < 0.0001) and Ag (p < 0.018).

Conclusion:

Bacillus cereus BF2 can survive in selective heavy metals with metal resistance and biodegradation capacity.

Ethanol Adaptation Strategies in Salmonella enterica Serovar Enteritidis Revealed by Global Proteomic and Mutagenic Analyses

Salmonella enterica subsp. enterica serovar Enteritidis is able to adapt to sublethal concentrations of ethanol, which subsequently induce tolerance of this pathogen to normally lethal ethanol challenges. This work aims to elucidate the underlying ethanol adaptation mechanisms of S Enteritidis by proteomic and mutagenic analyses. The global proteomic response of S Enteritidis to ethanol adaptation (5% ethanol for 1 h) was determined by isobaric tags for relative and absolute quantification (iTRAQ), and it was found that a total of 138 proteins were differentially expressed in ethanol-adapted cells compared to nonadapted cells. A total of 56 upregulated proteins were principally associated with purine metabolism and as transporters for glycine betaine, phosphate, d-alanine, thiamine, and heme, whereas 82 downregulated proteins were mainly involved in enterobactin biosynthesis and uptake, the ribosome, flagellar assembly, and virulence. Moreover, mutagenic analysis further revealed the functions of two highly upregulated proteins belonging to purine metabolism (HiuH, 5-hydroxyisourate hydrolase) and glycine betaine transport (ProX, glycine betaine-binding periplasmic protein) pathways. Deletion of either hiuH or proX resulted in the development of a stronger ethanol tolerance response, suggesting negative regulatory roles in ethanol adaptation. Collectively, this work suggests that S Enteritidis employs multiple strategies to coordinate ethanol adaptation.IMPORTANCE Stress adaptation in foodborne pathogens has been recognized as a food safety concern since it may compromise currently employed microbial intervention strategies. While adaptation to sublethal levels of ethanol is able to induce ethanol tolerance in foodborne pathogens, the molecular mechanism underlying this phenomenon is poorly characterized. Hence, global proteomic analysis and mutagenic analysis were conducted in the current work to understand the strategies employed by Salmonella enterica subsp. enterica serovar Enteritidis to respond to ethanol adaptation. It was revealed that coordinated regulation of multiple pathways involving metabolism, ABC transporters, regulators, enterobactin biosynthesis and uptake, the ribosome, flagellar assembly, and virulence was responsible for the development of ethanol adaptation response in this pathogen. Such knowledge will undoubtedly contribute to the development and implementation of more-effective food safety interventions.

Silage review: Animal and human health risks from silage

Silage may contain several agents that are potentially hazardous to animal health, the safety of milk or other animal food products, or both. This paper reviews published literature about microbial hazards, plant toxins, and chemical hazards. Microbial hazards include Clostridium botulinum, Bacillus cereus, Listeria monocytogenes, Shiga toxin-producing Escherichia coli, Mycobacterium bovis, and various mold species. High concentrations of C. botulinum in silage have been associated with cattle botulism. A high initial concentration of C. botulinum spores in forage in combination with poor silage fermentation conditions can promote the growth of C. botulinum in silage. The elevated pH level that is generally associated with aerobic deterioration of silage is a major factor influencing concentrations of L. monocytogenes, Shiga toxin-producing E. coli, and molds in silage and may also encourage survival and growth of M. bovis, the bacterium that causes bovine tuberculosis. Soil is a major source of B. cereus spores in silage; growth of this bacterium in silage appears to be limited. Hazards from plant toxins include pyrrolizidine, tropane and tropolone alkaloids, phytoestrogens, prussic acid, and mimosine, compounds that exist naturally in certain plant species that may contaminate forages at harvesting. Another group of toxins belonging to this category are ergot alkaloids, which are produced by endophytic fungal species in forages such as tall fescue grass, sorghum, and ryegrass. Varying effects of ensiling on the degradation of these plant toxins have been reported. Chemical hazards include nitrate, nitrite, and toxic oxide gases of nitrogen produced from nitrate and high levels of butyric acid, biogenic amines, and ammonia. Chemical and microbiological hazards are associated with poorly fermented silages, which can be avoided by using proper silage-making practices and creating conditions that promote a rapid and sufficient reduction of the silage pH and prevent aerobic deterioration.

Microbial diversities and potential hazards of Korean turbid rice wines (makgeolli): Multivariate analyses

A number of makgeolli (Korean traditional turbid rice wine) products are commercially available in various forms. To date, there has been no comprehensive investigation of these products. Here, we collected samples of almost all of the makgeolli products that are currently commercially available (n = 167), recorded their manufacturing variables, and examined physiochemical parameters and microbial communities, using quantitative and qualitative methods. The aerobic plate count (APC) and counts of lactic acid bacteria (LAB), acetic acid bacteria (AAB), fungi, total coliforms, and Bacillus cereus were obtained, and the presence of Escherichia coli and eight foodborne pathogens was also examined. The data obtained were segmented and analyzed based on multiple variables associated with the manufacturing characteristics. Despite high ethanol contents (up to 16.0%) and high acidities (pH 3.3-4.5), the rice wine products examined here had diverse and abundant microbiotas (mean values: APC, 5.3; LAB,4.4; AAB,1.5; fungi, 3.8 log CFU/ml). In particular, LAB and fungi, which are used as co-starter cultures during rice wine manufacturing, accounted for the majority of the microbiotas. Bivariate analyses revealed significant positive correlations between the individual micro-organism counts (Pearson correlation coefficient = 0.668-0.947). Among the manufacturing variables considered in this study, only the pasteurization status had a significant effect on the microbial communities of rice wine products (p < 0.05). When examining the presence of foodborne pathogens, B. cereus was isolated from some of the rice wine products (58.1%) at low levels (<100 CFU/ml), and its detection rate was not significantly lower in the pasteurized products than the raw products. Overall, the results presented here provide a comprehensive overview of the microbiotas of commercially available turbid rice wines and their relationships to manufacturing variables. These data will help to direct future studies focusing on rice wine quality and safety control measures.

Soil microbial community responses to acid exposure and neutralization treatment

Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture. Hydrofluoric acid was more effectively neutralized by the soils, compared with sulfuric acid at the same normality. Gram-negative ß-Proteobacteria were shown to be the most acid-sensitive bacterial strains, while spore-forming Gram-positive Bacilli were the most acid-tolerant. The results of this study suggest that the Gram-positive to Gram-negative bacterial ratio may serve as an effective bio-indicator in assessing the impact of the acid shock on the microbial community. Neutralization treatments helped recover the ratio closer to their original values. The findings of this study show that microbial community changes as well as geochemical changes such as pH and dissolved ion concentrations need to be considered in estimating the impact of an acid spill, in selecting an optimal remediation strategy, and in deciding when to end remedial actions at the acid spill impacted site.

Proteomic Analysis of Vibrio parahaemolyticus Under Cold Stress

Vibrio parahaemolyticus is a kind of food-borne pathogenic bacterium, which can seriously infect food, especially seafood causing gastroenteritis and other disease. We studied the global proteome responses of V. parahaemolyticus under cold stress by nano-liquid chromatography-tandem mass spectrometry to improve the present understanding of V. parahaemolyticus proteomics events under cold stress. A total of 1151 proteins were identified and 101 proteins were differentially expressed, of which 69 were significantly up-regulated and 32 were downregulated. Functional categorization of these proteins revealed distinct differences between cold-stressed and control cells. These proteins were grouped into 21 functional categories by the clusters of orthologous groups (COG) analysis. The most of up-regulated proteins were functionally categorized as nucleotide transport and metabolism, transcription, function unknown, and defense mechanisms. These up-regulated proteins play an important role under cold stress.

Adaptation in Bacillus cereus: From Stress to Disease

Bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. After ingestion, B. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic pH in the stomach and changing oxygen conditions in the human intestine. B. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and minimizing damage to cellular infrastructure. As reviewed in this article, B. cereus adapts to acidic pH and changing oxygen conditions through diverse regulatory mechanisms and then exploits its metabolic flexibility to grow and produce enterotoxins. We then focus on the intricate link between metabolism, redox homeostasis, and enterotoxins, which are recognized as important contributors of food-borne disease.

Microbiological diversity and prevalence of spoilage and pathogenic bacteria in commercial fermented alcoholic beverages (beer, fruit wine, refined rice wine, and yakju)

The present study examined 469 commercially available fermented alcoholic beverages (FABs), including beer (draft, microbrewed, and pasteurized), fruit wine (grape and others), refined rice wine, and yakju (raw and pasteurized). Samples were screened for Escherichia coli and eight foodborne pathogens (Bacillus cereus, Campylobacter jejuni, Clostridium perfringens, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Yersinia enterocolitica), and the aerobic plate count, lactic acid bacteria, acetic acid bacteria, fungi, and total coliforms were also enumerated. Microbrewed beer contained the highest number of microorganisms (average aerobic plate count, 3.5; lactic acid bacteria, 2.1; acetic acid bacteria, 2.0; and fungi, 3.6 log CFU/ml), followed by draft beer and yakju (P < 0.05), whereas the other FABs contained , 25 CFU/25 ml microorganisms. Unexpectedly, neither microbial diversity nor microbial count correlated with the alcohol content (4.7 to 14.1%) or pH (3.4 to 4.2) of the product. Despite the harsh conditions, coliforms (detected in 23.8% of microbrewed beer samples) and B. cereus (detected in all FABs) were present in some products. B. cereus was detected most frequently in microbrewed beer (54.8% of samples) and nonpasteurized yakju (50.0%), followed by pasteurized yakju (28.8%), refined rice wine (25.0%), other fruit wines (12.3%), grape wine (8.6%), draft beer (5.6%), and pasteurized beer (2.2%) (P < 0.05). The finding that spore-forming B. cereus and coliform bacteria can survive the harsh conditions present in alcoholic beverages should be taken into account (alongside traditional quality indicators such as the presence of lactic acid-producing bacteria, acetic acid-producing bacteria, or both) when developing manufacturing systems and methods to prolong the shelf life of high-quality FAB products. New strategic quality management plans for various FABs are needed.

The effect of selected factors on the survival of Bacillus cereus in the human gastrointestinal tract

Bacillus cereus is a Gram-positive bacterium widely distributed in soil and vegetation. This bacterial species can also contaminate raw or processed foods. Pathogenic B. cereus strains can cause a range of infections in humans, as well as food poisoning of an emetic (intoxication) or diarrheal type (toxico-infection). Toxico-infections are due to the action of the Hbl toxin, Nhe toxin, and cytotoxin K produced by the microorganism in the gastrointestinal tract. This occurs once the spores or vegetative B. cereus cells survive the pH barrier of the stomach and reach the small intestine where they produce toxins in sufficient amounts. This article discusses the effect of various factors on the survival of B. cereus in the gastrointestinal tract, including low pH and the presence of digestive enzymes in the stomach, bile salts in the small intestine, and indigenous microflora in the lower parts of the gastrointestinal tract. Additional aspects also reported to affect B. cereus survival and virulence in the gastrointestinal tract include the interaction of the spores and vegetative cells with enterocytes. In vitro studies revealed that both vegetative B. cereus and spores can survive in the gastrointestinal tract suggesting that the biological form of the microorganism may have less influence on the occurrence of the symptoms of infection than was once believed. It is most likely the interaction between the pathogen and enterocytes that is necessary for the diarrheal form of B. cereus food poisoning to develop. The adhesion of B. cereus to the intestinal epithelium allows the bacterium to grow and produce enterotoxins in the proximity of the epithelium. Recent studies suggest that the human intestinal microbiota inhibits the growth of vegetative B. cereus cells considerably.

Adaptive responses of Bacillus cereus ATCC14579 cells upon exposure to acid conditions involve ATPase activity to maintain their internal pH

This study examined the involvement of ATPase activity in the acid tolerance response (ATR) of Bacillus cereus ATCC14579 strain. In the current work, B. cereus cells were grown in anaerobic chemostat culture at external pH (pH_e ) 7.0 or 5.5 and at a growth rate of 0.2 h^-1 . Population reduction and internal pH (pH_i ) after acid shock at pH 4.0 was examined either with or without ATPase inhibitor N,N'-dicyclohexylcarbodiimide (DCCD) and ionophores valinomycin and nigericin. Population reduction after acid shock at pH 4.0 was strongly limited in cells grown at pH 5.5 (acid-adapted cells) compared with cells grown at pH 7.0 (unadapted cells), indicating that B. cereus cells grown at low pH_e were able to induce a significant ATR and Exercise-induced increase in ATPase activity. However, DCCD and ionophores had a negative effect on the ability of B. cereus cells to survive and maintain their pH_i during acid shock. When acid shock was achieved after DCCD treatment, pH_i was markedly dropped in unadapted and acid-adapted cells. The ATPase activity was also significantly inhibited by DCCD and ionophores in acid-adapted cells. Furthermore, transcriptional analysis revealed that atpB (ATP beta chain) transcripts was increased in acid-adapted cells compared to unadapted cells before and after acid shock. Our data demonstrate that B. cereus is able to induce an ATR during growth at low pH. These adaptations depend on the ATPase activity induction and pH_i homeostasis. Our data demonstrate that the ATPase enzyme can be implicated in the cytoplasmic pH regulation and in acid tolerance of B. cereus acid-adapted cells.

Survival of Normal and Chlorine-Stressed Pathogenic and Non-Pathogenic Vibrio parahaemolyticus Under Adverse Conditions

Background:

Vibrio parahaemolyticus is an important human pathogen which can cause gastroenteritis when consumed in raw or partially-cooked seafood. The pathogenesis of V. parahaemolyticus is based on the presence of virulence factors: the thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), encoded by the tdh and trh genes, respectively.

Objectives:

The present study aimed to evaluate the survival of normal and chlorine-stressed cells of pathogenic and non-pathogenic V. parahaemolyticus under adverse conditions.

Materials and Methods:

Normal and chlorine-stressed cells of pathogenic and non-pathogenic V. parahaemolyticus were subjected to environmental stresses such as low storage temperature (4°C and -18°C), high incubation temperature (50°C) and high NaCl content (20%). Viable counts were then made at various time intervals by surface plating on TSA-2.0% NaCl, and the survival rates of the cells were determined and compared.

Results:

Findings of the current study revealed that the normal cells of pathogenic and non-pathogenic V. parahaemolyticus, as well as the chlorine-stressed cells of both strains behave similarly under adverse conditions. In addition, chlorine stress increased the susceptibility of pathogenic and non-pathogenic V. parahaemolyticus to incubation at 4°C, and the presence of high NaCl content in the medium. However, chlorine stress did not significantly affect the thermal tolerance of pathogenic and non-pathogenic V. parahaemolyticus, and the susceptibility to incubation at -18°C.

Conclusions:

Chlorine-stressed cells of V. parahaemolyticus were more susceptible to adverse conditions than the non-stressed ones. Pathogenic and non-pathogenic strains showed the same survival characteristics under the adverse conditions. These results should be considered in the development of food preservation measures.

Coping with low pH: molecular strategies in neutralophilic bacteria

As part of their life cycle, neutralophilic bacteria are often exposed to varying environmental stresses, among which fluctuations in pH are the most frequent. In particular, acid environments can be encountered in many situations from fermented food to the gastric compartment of the animal host. Herein, we review the current knowledge of the molecular mechanisms adopted by a range of Gram-positive and Gram-negative bacteria, mostly those affecting human health, for coping with acid stress. Because organic and inorganic acids have deleterious effects on the activity of the biological macromolecules to the point of significantly reducing growth and even threatening their viability, it is not unexpected that neutralophilic bacteria have evolved a number of different protective mechanisms, which provide them with an advantage in otherwise life-threatening conditions. The overall logic of these is to protect the cell from the deleterious effects of a harmful level of protons. Among the most favoured mechanisms are the pumping out of protons, production of ammonia and proton-consuming decarboxylation reactions, as well as modifications of the lipid content in the membrane. Several examples are provided to describe mechanisms adopted to sense the external acidic pH. Particular attention is paid to Escherichia coli extreme acid resistance mechanisms, the activity of which ensure survival and may be directly linked to virulence.

Catalase activity as a biomarker for mild-stress-induced robustness in Bacillus weihenstephanensis

Microorganisms are able to survive and grow in changing environments by activating stress adaptation mechanisms which may enhance bacterial robustness. Stress-induced enhanced robustness complicates the predictability of microbial inactivation. Using psychrotolerant Bacillus weihenstephanensis strain KBAB4 as a model, we investigated the impact of the culturing temperature on mild-oxidative-stress-induced (cross-)protection toward multiple stresses, including severe oxidative, heat, and acid stresses. Culturing at a refrigeration temperature (7°C) compared to the optimal growth temperature (30°C) affected both the robustness level of B. weihenstephanensis and the oxidative stress adaptive response. Scavengers of reactive oxygen species have a crucial role in adaptation to oxidative stresses, and this points to a possible predictive role in mild-oxidative-stress-induced robustness. Therefore, the catalase activity was determined upon mild oxidative stress treatment and was demonstrated to be significantly correlated with the robustness level of mild-stress-treated cells toward severe oxidative and heat stresses but not toward severe acid stress for cells grown at both refrigeration and optimal temperatures. The quantified correlations supported the predictive quality of catalase activity as a biomarker and also underlined that the predictive quality is stress specific. Biomarkers that are able to predict stress-induced enhanced robustness can be used to better understand stress adaptation mechanisms and might allow the design of effective combinations of hurdles to control microbial behavior.

Bacillus cereus responses to acid stress

Coping with acid environments is one of the prerequisites for the soil saprophytic and human pathogenic lifestyle of Bacillus cereus. This minireview highlights novel insights in the responses displayed by vegetative cells and germinating spores of B. cereus upon exposure to low pH as well as organic acids, including acetic acid, lactic acid and sorbic acid. Insights regarding the possible acid-inflicted damage, physiological responses and protective mechanisms have been compiled based on single cell fluorescence microscopy, flow cytometry and transcriptome analyses.

Short- and long-term biomarkers for bacterial robustness: a framework for quantifying correlations between cellular indicators and adaptive behavior

The ability of microorganisms to adapt to changing environments challenges the prediction of their history-dependent behavior. Cellular biomarkers that are quantitatively correlated to stress adaptive behavior will facilitate our ability to predict the impact of these adaptive traits. Here, we present a framework for identifying cellular biomarkers for mild stress induced enhanced microbial robustness towards lethal stresses. Several candidate-biomarkers were selected by comparing the genome-wide transcriptome profiles of our model-organism Bacillus cereus upon exposure to four mild stress conditions (mild heat, acid, salt and oxidative stress). These candidate-biomarkers--a transcriptional regulator (activating general stress responses), enzymes (removing reactive oxygen species), and chaperones and proteases (maintaining protein quality)--were quantitatively determined at transcript, protein and/or activity level upon exposure to mild heat, acid, salt and oxidative stress for various time intervals. Both unstressed and mild stress treated cells were also exposed to lethal stress conditions (severe heat, acid and oxidative stress) to quantify the robustness advantage provided by mild stress pretreatment. To evaluate whether the candidate-biomarkers could predict the robustness enhancement towards lethal stress elicited by mild stress pretreatment, the biomarker responses upon mild stress treatment were correlated to mild stress induced robustness towards lethal stress. Both short- and long-term biomarkers could be identified of which their induction levels were correlated to mild stress induced enhanced robustness towards lethal heat, acid and/or oxidative stress, respectively, and are therefore predictive cellular indicators for mild stress induced enhanced robustness. The identified biomarkers are among the most consistently induced cellular components in stress responses and ubiquitous in biology, supporting extrapolation to other microorganisms than B. cereus. Our quantitative, systematic approach provides a framework to search for these biomarkers and to evaluate their predictive quality in order to select promising biomarkers that can serve to early detect and predict adaptive traits.

Quantification of the effect of culturing temperature on salt-induced heat resistance of bacillus species

Short- and long-term exposure to mild stress conditions can activate stress adaptation mechanisms in pathogens, resulting in a protective effect toward otherwise lethal stresses. The mesophilic strains Bacillus cereus ATCC 14579 and ATCC 10987 and the psychrotolerant strain B. weihenstephanensis KBAB4 were cultured at 12 degrees C and 30 degrees C until the exponential growth phase (i) in the absence of salt, (ii) in the presence of salt, and (iii) with salt shock after they reached the exponential growth phase and subsequently heat inactivated. Both the first-order model and the Weibull model were fitted to the inactivation kinetics, and statistical indices were calculated to select for each condition the most appropriate model to describe the inactivation data. The third-decimal reduction times (which reflected the times needed to reduce the initial number of microorganisms by three decimal powers) were determined for quantitative comparison. The heat resistance of both mesophilic strains increased when cells were salt cultured and salt shocked at 30 degrees C, whereas these salt-induced effects were not significant for the psychrotolerant strain. In contrast, only the psychrotolerant strain showed salt-induced heat resistance when cells were cultured at 12 degrees C. Therefore, culturing temperature and strain diversity are important aspects to address when adaptive stress responses are quantified. The activated adaptive stress response had an even larger impact on the number of surviving microorganisms when the stress factor (i.e., salt) was still present during inactivation. These factors should be considered when stress-integrated predictive models are developed that can be used in the food industry to balance and optimize processing conditions of minimally processed foods.

Comparison of two optical-density-based methods and a plate count method for estimation of growth parameters of Bacillus cereus

Quantitative microbiological models predicting proliferation of microorganisms relevant for food safety and/or food stability are useful tools to limit the need for generation of biological data through challenge testing and shelf-life testing. The use of these models requires quick and reliable methods for the generation of growth data and estimation of growth parameters. Growth parameter estimation can be achieved using methods based on plate counting and methods based on measuring the optical density. This research compares the plate count method with two optical density methods, namely, the 2-fold dilution (2FD) method and the relative rate to detection (RRD) method. For model organism Bacillus cereus F4810/72, the plate count method and both optical density methods gave comparable estimates for key growth parameters. Values for the maximum specific growth rate (mu(max)) derived by the 2FD method and by the RRD method were of the same order of magnitude, but some marked differences between the two approaches were apparent. Whereas the 2FD method allowed the derivation of values for lag time (lambda) from the data, this was not possible with the RRD method. However, the RRD method gave many more data points per experiment and also gave more data points close to the growth boundary. This research shows that all three proposed methods can be used for parameter estimation but that the choice of method depends on the objectives of the research.

Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis

BACKGROUND

Bacillus subtilis encounters a wide range of environmental pH. The bacteria maintain cytoplasmic pH within a narrow range. Response to acid stress is a poorly understood function of external pH and of permeant acids that conduct protons into the cytoplasm.

METHODS AND PRINCIPAL FINDINGS

Cytoplasmic acidification and the benzoate transcriptome were observed in Bacillus subtilis. Cytoplasmic pH was measured with 4-s time resolution using GFPmut3b fluorimetry. Rapid external acidification (pH 7.5 to 6.0) acidified the B. subtilis cytoplasm, followed by partial recovery. Benzoate addition up to 60 mM at external pH 7 depressed cytoplasmic pH but left a transmembrane Delta pH permitting growth; this robust adaptation to benzoate exceeds that seen in E. coli. Cytoplasmic pH was depressed by 0.3 units during growth with 30 mM benzoate. The transcriptome of benzoate-adapted cells was determined by comparing 4,095 gene expression indices following growth at pH 7, +/- 30 mM benzoate. 164 ORFs showed > or = 2-fold up-regulation by benzoate (30 mM benzoate/0 mM), and 102 ORFs showed > or = 2-fold down-regulation. 42% of benzoate-dependent genes are regulated up or down, respectively, at pH 6 versus pH 7; they are candidates for cytoplasmic pH response. Acid-stress genes up-regulated by benzoate included drug resistance genes (yhbI, yhcA, yuxJ, ywoGH); an oligopeptide transporter (opp); glycine catabolism (gcvPA-PB); acetate degradation (acsA); dehydrogenases (ald, fdhD, serA, yrhEFG, yjgCD); the TCA cycle (citZ, icd, mdh, sucD); and oxidative stress (OYE-family yqjM, ohrB). Base-stress genes down-regulated by benzoate included malate metabolism (maeN), sporulation control (spo0M, spo0E), and the SigW alkali shock regulon. Cytoplasmic pH could mediate alkali-shock induction of SigW.

CONCLUSIONS

B. subtilis maintains partial pH homeostasis during growth, and withstands high concentrations of permeant acid stress, higher than for gram-negative neutralophile E. coli. The benzoate adaptation transcriptome substantially overlaps that of external acid, contributing to a cytoplasmic pH transcriptome.

Acid and base stress and transcriptomic responses in Bacillus subtilis

Acid and base environmental stress responses were investigated in Bacillus subtilis. B. subtilis AG174 cultures in buffered potassium-modified Luria broth were switched from pH 8.5 to pH 6.0 and recovered growth rapidly, whereas cultures switched from pH 6.0 to pH 8.5 showed a long lag time. Log-phase cultures at pH 6.0 survived 60 to 100% at pH 4.5, whereas cells grown at pH 7.0 survived <15%. Cells grown at pH 9.0 survived 40 to 100% at pH 10, whereas cells grown at pH 7.0 survived <5%. Thus, growth in a moderate acid or base induced adaptation to a more extreme acid or base, respectively. Expression indices from Affymetrix chip hybridization were obtained for 4,095 protein-encoding open reading frames of B. subtilis grown at external pH 6, pH 7, and pH 9. Growth at pH 6 upregulated acetoin production (alsDS), dehydrogenases (adhA, ald, fdhD, and gabD), and decarboxylases (psd and speA). Acid upregulated malate metabolism (maeN), metal export (czcDO and cadA), oxidative stress (catalase katA; OYE family namA), and the SigX extracytoplasmic stress regulon. Growth at pH 9 upregulated arginine catabolism (roc), which generates organic acids, glutamate synthase (gltAB), polyamine acetylation and transport (blt), the K(+)/H(+) antiporter (yhaTU), and cytochrome oxidoreductases (cyd, ctaACE, and qcrC). The SigH, SigL, and SigW regulons were upregulated at high pH. Overall, greater genetic adaptation was seen at pH 9 than at pH 6, which may explain the lag time required for growth shift to high pH. Low external pH favored dehydrogenases and decarboxylases that may consume acids and generate basic amines, whereas high external pH favored catabolism-generating acids.

Physiological response of Bacillus cereus vegetative cells to simulated food processing treatments

Vegetative cells of the spore-former Bacillus cereus were exposed to a number of treatments commonly used in commercial food preparation or during equipment cleaning and decontamination. Treated suspensions were then analyzed for reductions (CFU per milliliter) by plate counting and changes in levels of ATP and ADP released from cells with a bioluminescence-based assay. With the use of flow cytometry (FCM), the physiological status of individual cells before and after exposure to treatments was determined by staining of control and treated cells with three pairs of physiological dyes (SYTO 9/propidium iodide, carboxyfluorescein diacetate/Hoechst 33342, and C12-resazurin/SYTOX Green). Good agreement was found between plate counting and FCM. In general, treatments giving rise to the highest count reductions also had the greatest effects on cell membrane permeability (measured with the use of propidium iodide or SYTOX Green), esterase activity (measured with carboxyfluorescein diacetate), or redox activity (C12-resazurin). FCM data demonstrated the extent of heterogeneity of vegetative cell responses to treatments in, for example, the treatment with 5% H2O2, which caused a 6-log reduction in which approximately 95% of the population was composed of membrane-damaged cells (as reflected by their permeability to SYTOX Green), whereas in treatment with 0.09% (wt/vol) potassium sorbate, which caused only a 1-log reduction, not more than 40% of cells were membrane damaged. The approaches described in this work can be applied to gain a greater understanding of bacterial responses to food control measures, generate more accurate inactivation models, or screen novel prospective food control measures.

Population heterogeneity of Lactobacillus plantarum WCFS1 microcolonies in response to and recovery from acid stress

Within an isogenic microbial population in a homogenous environment, individual bacteria can still exhibit differences in phenotype. Phenotypic heterogeneity can facilitate the survival of subpopulations under stress. As the gram-positive bacterium Lactobacillus plantarum grows, it acidifies the growth medium to a low pH. We have examined the growth of L. plantarum microcolonies after rapid pH downshift (pH 2 to 4), which prevents growth in liquid culture. This acidification was achieved by transferring cells from liquid broth onto a porous ceramic support, placed on a base of low-pH MRS medium solidified using Gelrite. We found a subpopulation of cells that displayed phenotypic heterogeneity and continued to grow at pH 3, which resulted in microcolonies dominated by viable but elongated (filamentous) cells lacking septation, as determined by scanning electron microscopy and staining cell membranes with the lipophilic dye FM4-64. Recovery of pH-stressed cells from these colonies was studied by inoculation onto MRS-Gelrite-covered slides at pH 6.5, and outgrowth was monitored by microscopy. The heterogeneity of the population, calculated from the microcolony areas, decreased with recovery from pH 3 over a period of a few hours. Filamentous cells did not have an advantage in outgrowth during recovery. Specific regions within single filamentous cells were more able to form rapidly dividing cells, i.e., there was heterogeneity even within single recovering cells.

Modeling survival of Listeria monocytogenes in the traditional Greek soft cheese Katiki

In the present work, survival of Listeria monocytogenes in the traditional Greek soft, spreadable cheese Katiki was studied throughout the shelf life of the product. Samples of finished cheese were inoculated with a cocktail of five L. monocytogenes strains (ca. 6 log CFU g(-1)) and stored at 5, 10, 15, and 20 degrees C. Acid-stress adaptation or cross-protection to the same stress was also investigated by inoculation of acid-adapted cells in the product. The results showed that pathogen survival was biphasic. Various mathematical equations (Geeraerd, Cerf, Albert-Mafart, Whiting, Zwietering, and Baranyi models) were fitted to the experimental data. A thorough statistical analysis was performed to choose the best model. The Geeraerd model was finally selected, and the results revealed no acid tolerance acquisition (no significant differences, P > 0.05, in the survival rates of the non-acid-adapted and acid-adapted cells). Secondary modeling (second-order polynomial with a(0) = 0.8453, a(1) = -0.0743, and a(2) = 0.0059) of the survival rate (of sensitive population), and other parameters that were similar at all temperatures (fraction of initial population in the major population = 99.98%, survival rate of resistant population = 0.10 day(-1), and initial population = 6.29 log CFU g(-1)), showed that survival of the pathogen was temperature dependent with bacterial cells surviving for a longer period of time at lower temperatures. Finally, the developed predictive model was successfully validated at two independent temperatures (12 and 17 degrees C). This study underlines the usefulness of predictive modeling as a tool for realistic estimation and control of L. monocytogenes risk in food products. Such data are also useful when conducting risk assessment studies.

Low concentrations of bile salts induce stress responses and reduce motility in Bacillus cereus ATCC 14579 [corrected]

Tolerance to bile salts was investigated in forty Bacillus cereus strains, including 17 environmental isolates, 11 dairy isolates, 3 isolates from food poisoning outbreaks, and 9 other clinical isolates. Growth of all strains was observed at low bile salt concentrations, but no growth was observed on LB agar plates containing more than 0.005% bile salts. Preincubation of the B. cereus type strain, ATCC 14579, in low levels of bile salts did not increase tolerance levels. B. cereus ATCC 14579 was grown to mid-exponential growth phase and shifted to medium containing bile salts (0.005%). Global expression patterns were determined by hybridization of total cDNA to a 70-mer oligonucleotide microarray. A general stress response and a specific response to bile salts were observed. The general response was similar to that observed in cultures grown in the absence of bile salts but at a higher (twofold) cell density. Up-regulation of several putative multidrug exporters and transcriptional regulators and down-regulation of most motility genes were observed as part of the specific response. Motility experiments in soft agar showed that motility decreased following bile salts exposure, in accordance with the transcriptional data. Genes encoding putative virulence factors were either unaffected or down-regulated.

Quantitative analysis of population heterogeneity of the adaptive salt stress response and growth capacity of Bacillus cereus ATCC 14579

Bacterial populations can display heterogeneity with respect to both the adaptive stress response and growth capacity of individual cells. The growth dynamics of Bacillus cereus ATCC 14579 during mild and severe salt stress exposure were investigated for the population as a whole in liquid culture. To quantitatively assess the population heterogeneity of the stress response and growth capacity at a single-cell level, a direct imaging method was applied to monitor cells from the initial inoculum to the microcolony stage. Highly porous Anopore strips were used as a support for the culturing and imaging of microcolonies at different time points. The growth kinetics of cells grown in liquid culture were comparable to those of microcolonies grown upon Anopore strips, even in the presence of mild and severe salt stress. Exposure to mild salt stress resulted in growth that was characterized by a remarkably low variability of microcolony sizes, and the distributions of the log(10)-transformed microcolony areas could be fitted by the normal distribution. Under severe salt stress conditions, the microcolony sizes were highly heterogeneous, and this was apparently caused by the presence of both a nongrowing and growing population. After discriminating these two subpopulations, it was shown that the variability of microcolony sizes of the growing population was comparable to that of non-salt-stressed and mildly salt-stressed populations. Quantification of population heterogeneity during stress exposure may contribute to an optimized application of preservation factors for controlling growth of spoilage and pathogenic bacteria to ensure the quality and safety of minimally processed foods.

Gene expression analysis of Corynebacterium glutamicum subjected to long-term lactic acid adaptation

Corynebacteria form an important part of the red smear cheese microbial surface consortium. To gain a better understanding of molecular adaptation due to low pH induced by lactose fermentation, the global gene expression profile of Corynebacterium glutamicum adapted to pH 5.7 with lactic acid under continuous growth in a chemostat was characterized by DNA microarray analysis. Expression of a total of 116 genes was increased and that of 90 genes was decreased compared to pH 7.5 without lactic acid, representing 7% of the genes in the genome. The up-regulated genes encode mainly transcriptional regulators, proteins responsible for export, import, and metabolism, and several proteins of unknown function. As much as 45% of the up-regulated open reading frames code for hypothetical proteins. These results were validated using real-time reverse transcription-PCR. To characterize the functions of 38 up-regulated genes, 36 single-crossover disruption mutants were generated and analyzed for their lactic acid sensitivities. However, only a sigB knockout mutant showed a highly significant negative effect on growth at low pH, suggesting a function in organic-acid adaptation. A sigE mutant already displayed growth retardation at neutral pH but grew better at acidic pH than the sigB mutant. The lack of acid-sensitive phenotypes in 34 out of 36 disrupted genes suggests either a considerable redundancy in acid adaptation response or coincidental effects. Other up-regulated genes included genes for ion transporters and metabolic pathways, including carbohydrate and respiratory metabolism. The enhanced expression of the nrd (ribonucleotide reductase) operon and a DNA ATPase repair protein implies a cellular response to combat acid-induced DNA damage. Surprisingly, multiple iron uptake systems (totaling 15% of the genes induced >or=2-fold) were induced at low pH. This induction was shown to be coincidental and could be attributed to iron-sequestering effects in complex media at low pH.

Polyhydroxyalkanoates in Gram-positive bacteria: insights from the genera Bacillus and Streptomyces

Gram-positive bacteria, notably Bacillus and Streptomyces, have been used extensively in industry. However, these microorganisms have not yet been exploited for the production of the biodegradable polymers, polyhydroxyalkanoates (PHAs). Although PHAs have many potential applications, the cost of production means that medical applications are currently the main area of use. Gram-negative bacteria, currently the only commercial source of PHAs, have lipopolysaccharides (LPS) which co-purify with the PHAs and cause immunogenic reactions. On the other hand, Gram- positive bacteria lack LPS, a positive feature which justifies intensive investigation into their production of PHAs. This review summarizes currently available knowledge on PHA production by Gram- positive bacteria especially Bacillus and Streptomyces. We hope that this will form the basis of further research into developing either or both as a source of PHAs for medical applications.

EnterotoxigenicBacillus spp. DNA fingerprint revealed in naturally contaminated nonfat dry milk powder using rep-PCR

Dry milk powders and functional ingredients frequently contain high levels of viable bacterial spores, some of which may result in growth of toxigenic Bacillus spp. in reconstituted and temperature-abused foods. Samples from nonfat dry milk (NFDM), infant milk formula (IMF), coffee creamer, lecithin, and cocoa powder were subjected to a short heat treatment followed by enrichment in tryptone phosphate glucose yeast extract (TPGY) broth at 32 degrees C for 12-25 hours to obtain cell densities of 10(6) CFU ml(-1). DNA was extracted using a modification of established protocol, leading to the development of an optimized method for each food system. Purified DNA was amplified by rep-PCR using extragenic sequence-targeting primers and optimized for each food. PCR fingerprints from each food were analyzed electrophoretically for banding patterns earlier correlated to that of enterotoxigenic Bacillus spp. and Bacillus cereus positive control DNA fingerprints. Reverse passive latex agglutination (RPLA) and Bacillus Diarrhoeal Enterotoxin Enzyme Linked Immunosorbent Assay (Tecra Diagnostics) confirmed the presence of HBL and NHE enterotoxin production in NFDM, Coffee creamer, infant milk formula, and two lecithin samples but not in cocoa powder. These results demonstrate the utility of rep-PCR not only as a tool for bacterial genotyping, but a unique means of quality control and hygiene monitoring in food microbiology.