Bacillus cereus cell response upon exposure to acid environment: toward the identification of potential biomarkers

Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.

Sporulation conditions influence the surface and adhesion properties of Bacillus subtilis spores

Spore-forming bacteria of the Bacillus subtilis group are responsible for recurrent contamination of processing lines in the food industry which can lead to food spoilage. The persistence of B. subtilis would be due to the high resistance of spores to extreme environmental condition and their propensity to contaminate surfaces. While it is well known that sporulation conditions modulate spore resistance properties, little is known about their effect on surface and adhesion properties. Here, we studied the impact of 13 sporulation conditions on the surface and adhesion properties of B. subtilis 168 spores. We showed that Ca2+ or Mg2+ depletion, lower oxygen availability, acidic pH as well as oxidative stresses during sporulation lead to the release of more hydrophobic and adherent spores. The consequences of these sporulation conditions on crust composition in carbohydrates and proteins were also evaluated. The crust glycans of spores produced in a sporulation medium depleted in Ca2+ or Mg2+ or oxygen-limited conditions were impaired and contained lower amounts of rhamnose and legionaminic acid. In addition, we showed that lower oxygen availability or addition of hydrogen peroxide during sporulation decreases the relative amount of two crust proteins (CgeA and CotY) and the changes observed in these conditions could be due to transcriptional repression of genes involved in crust synthesis in late stationary phase. The fact that sporulation conditions affect the ease with which spores can contaminate surfaces could explain the frequent and recurrent presence of B. subtilis spores in food processing lines.

Tuning the sensitivity of cell-based biosensors for the detection of biocides

The presence of biocides in wastewater can negatively impact the efficiency of wastewater treatment processes, particular the process of nitrification. In this paper, we describe the development of cell-based biosensors (CBBs) with tunable levels of sensitivity for rapidly detecting the presence and predicting the type and concentration of biocides. The CBB assay developed is performed by first exposing a panel of bacterial strains (E. coli, B. subtilis, B. cereus) to the sample being tested and to the control sample without biocide, and then adding a fluorescent dye (LIVE/DEAD BacLight). We then compare the fluorescence signals generated by the two samples, and the differences in the signals indicate the presence of a biocide, as previously reported in the literature. We found that the sensitivity of the CBB assay can be improved by tuning the type/salinity of the buffer used to suspend the cells, and by changing the number of cells used in the assay. These changes improved the level of detection (LOD) of the biocide Cetyltrimethylammonium bromide (CTAB) from 10 ppm to 0.625 ppm and the biocide Grotan® BK from 500 ppm to 7.8 ppm. With the optimized conditions for each strain, we also establish that the combined response from the panel of bacterial strains can be used to predict the type and concentration of biocide sample tested. Additionally, we provide evidence that the response of the tunable CBB assay can be quantitatively measured using a compact, commercially available fluorometer. Overall, the significance of this work will improve point-of-use testing and enable the discrimination between biocide-containing samples of similar toxicity and detection of lower toxicity samples, thereby improving the accuracy of the CBB assay.

SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus

BACKGROUND

The Bacillus cereus Sigma B (SigB) dependent general stress response is activated via the two-component RsbKY system, which involves a phosphate transfer from RsbK to RsbY. It has been hypothesized that the Hpr-like phosphocarrier protein (Bc1009) encoded by bc1009 in the SigB gene cluster may play a role in this transfer, thereby acting as a regulator of SigB activation. Alternatively, Bc1009 may be involved in the activation of a subset of SigB regulon members.

RESULTS

We first investigated the potential role of bc1009 to act as a SigB regulator but ruled out this possibility as the deletion of bc1009 did not affect the expression of sigB and other SigB gene cluster members. The SigB-dependent functions of Bc1009 were further examined in B. cereus ATCC14579 via comparative proteome profiling (backed up by transcriptomics) of wt, Δbc1009 and ΔsigB deletion mutants under heat stress at 42 °C. This revealed 284 proteins displaying SigB-dependent alterations in protein expression levels in heat-stressed cells, including a subgroup of 138 proteins for which alterations were also Bc1009-dependent. Next to proteins with roles in stress defense, newly identified SigB and Bc1009-dependent proteins have roles in cell motility, signal transduction, transcription, cell wall biogenesis, and amino acid transport and metabolism. Analysis of lethal stress survival at 50 °C after pre-adaptation at 42 °C showed intermediate survival efficacy of Δbc1009 cells, highest survival of wt, and lowest survival of ΔsigB cells, respectively. Additional comparative proteome analysis of non-stressed wt and mutant cells at 30 °C revealed 96 proteins with SigB and Bc1009-dependent differences in levels: 51 were also identified under heat stress, and 45 showed significant differential expression at 30 °C. This includes proteins with roles in carbohydrate/ion transport and metabolism. Overlapping functions at 30 °C and 42 °C included proteins involved in motility, and ΔsigB and Δbc1009 cells showed reduced motility compared to wt cells in swimming assays at both temperatures.

CONCLUSION

Our results extend the B. cereus SigB regulon to > 300 members, with a novel role of SigB-dependent Bc1009 in the activation of a subregulon of  > 180 members, conceivably via interactions with other transcriptional regulatory networks.

In vitro and in silico assessment of probiotic and functional properties of Bacillus subtilis DE111®

Bacillus subtilis DE111^® is a safe, well-tolerated commercially available spore-forming probiotic that has been clinically shown to support a healthy gut microbiome, and to promote digestive and immune health in both adults and children. Recently it was shown that this spore-forming probiotic was capable of germinating in the gastrointestinal tract as early as 3 h after ingestion. However, a better understanding of the mechanisms involved in the efficacy of DE111^® is required. Therefore, the present investigation was undertaken to elucidate the functional properties of DE111^® through employing a combination of in vitro functional assays and genome analysis. DE111^® genome mining revealed the presence of several genes encoding acid and stress tolerance mechanisms in addition to adhesion proteins required to survive and colonize harsh gastrointestinal environment including multi subunit ATPases, arginine deiminase (ADI) pathway genes (argBDR), stress (GroES/GroEL and DnaK/DnaJ) and extracellular polymeric substances (EPS) biosynthesis genes (pgsBCA). DE111^® harbors several genes encoding enzymes involved in the metabolism of dietary molecules (protease, lipases, and carbohyrolases), antioxidant activity and genes associated with the synthesis of several B-vitamins (thiamine, riboflavin, pyridoxin, biotin, and folate), vitamin K2 (menaquinone) and seven amino acids including five essential amino acids (threonine, tryptophan, methionine, leucine, and lysine). Furthermore, a combined in silico analysis of bacteriocin producing genes with in vitro analysis highlighted a broad antagonistic activity of DE111^® toward numerous urinary tract, intestinal, and skin pathogens. Enzymatic activities included proteases, peptidases, esterase's, and carbohydrate metabolism coupled with metabolomic analysis of DE111^® fermented ultra-high temperature milk, revealed a high release of amino acids and beneficial short chain fatty acids (SCFAs). Together, this study demonstrates the genetic and phenotypic ability of DE111^® for surviving harsh gastric transit and conferring health benefits to the host, in particular its efficacy in the metabolism of dietary molecules, and its potential to generate beneficial SCFAs, casein-derived bioactive peptides, as well as its high antioxidant and antimicrobial potential. Thus, supporting the use of DE111^® as a nutrient supplement and its pottential use in the preparation of functional foods.

iTRAQ-based proteomics analysis of Bacillus pumilus responses to acid stress and quorum sensing in a vitamin C fermentation system

Microbial consortia play a key role in human health, bioenergy, and food manufacturing due to their strong stability, robustness and versatility. One of the microbial consortia consisting of Ketogulonicigenium vulgare and Bacillus megaterium for the production of the vitamin C precursor, 2-keto-L-gulonic acid (2-KLG), has been widely used for large-scale industrial production. To further investigate the cell-cell communication in microbial consortia, a microbial consortium consisting of Ketogulonicigenium vulgare and Bacillus pumilus was constructed and the differences in protein expression at different fermentation time points (18 h and 40 h) were analyzed by iTRAQ-based proteomics. The results indicated that B. pumilus was subjected to acid shocks in the coculture fermentation system and responded to it. In addition, the quorum sensing system existed in the coculture fermentation system, and B. pumilus could secrete quorum-quenching lactonase (YtnP) to inhibit the signaling pathway of K. vulgare. This study offers valuable guidance for further studies of synthetic microbial consortia.

Transcriptome analysis reveals the molecular mechanism of cinnamaldehyde against Bacillus cereus spores in ready-to-eat beef

The purpose of this study was to investigate the antibacterial effect and mechanism of cinnamaldehyde on Bacillus cereus spores in ready-to-eat beef. The colour difference and texture of the ready-to-eat beef supplemented with cinnamaldehyde did not differ greatly from the colour and texture of the blank beef. However, cinnamaldehyde has an effective antibacterial effect on the total number of bacterial colonies and B. cereus spores in ready-to-eat beef. Transmission electron microscopy (TEM) analysis revealed that the cell membrane of B. cereus was disrupted by cinnamaldehyde, leading to leakage of intracellular components. Transcriptome sequencing (RNA-seq) indicated that the B. cereus spore resistance regulation system (sigB, sigW, rsbW, rsbV, yfkM and yflT) and phosphoenolpyruvate phosphotransferase system (PTS) (ptsH, ptsI and ptsG) respond positively to cinnamaldehyde in an adverse environment. Intracellular disorders due to damage to the cell membrane involve some transporters (copA, opuBA and opuD) and some oxidative stress systems (ywrO, scdA and katE) in the regulation of the body. However, downregulation of K⁺ transport channels (kdpD and kdpB), osmotic pressure regulation (opuE) and some oxidative stress (norR and srrA)-related genes may accelerate spore apoptosis. In addition, cinnamaldehyde also effectively inhibits the spore germination-related genes (smc, mreB and gerE). This study provides new insights into the molecular mechanism of the antibacterial effect of cinnamaldehyde on B. cereus spores in ready-to-eat beef.

Elucidation of Iron(III) Bioleaching Properties of Gram-Positive Bacteria

Microbial-based iron reduction is an emerging technology used as an alternative to conventional chemical-based iron reduction. The iron reduction in kaolin refinement is vital for enhancing its commercial value. Extensive studies on microbial-based iron reduction mainly focus on Gram-negative bacteria, whereas little is understood about Gram-positive bacteria's mechanism and potential application. This study aims to investigate the iron-reducing mechanism of two Gram-positive bacterial isolates, Bacillus cereus (B. cereus) and Staphylococcus aureus (S. aureus). By varying the growth environment of bacteria and monitoring the biochemical changes during the process of iron reduction, the results show that Gram-positive bacterial iron reduction performance depends on the medium composition, differing from Gram-negative bacteria-based reduction processes. Nitrogen-rich medium facilitates the microbial basification of the medium, where the alkaline conditions impact the microbial iron reduction process by altering the gene expression involved in intracellular pH homeostasis and microbial growth. This discovery will contribute to the mineral refining processes and promote the development of microbial-based bioprocesses for ore purification, while also laying the foundation for investigating other Gram-positive bacterial iron-reducing ability.

Genomic characterization of Bacillus cereus sensu stricto 3A ES isolated from eye shadow cosmetic products

BACKGROUND

The Bacillus cereus group, also known as B. cereus sensu lato (s.l.) contains ubiquitous spore-forming bacteria found in the environment including strains from the B. cereus sensu stricto (s.s.) species. They occur naturally in a wide range of raw materials and in consumer products. Characterizing isolates that have survived in consumer products allows us to better understand the mechanisms that permit spores to persist and potentially cause illness. Here we characterize the draft genome sequence of B. cereus s. s. 3A-ES, originally isolated from eye shadow and since investigated in several cosmetic studies and compared it to other top ten published complete genome sequences of B. cereus s.l. members.

RESULTS

The draft genome sequence of B. cereus s.s. 3A ES consisted of an average of 90 contigs comprising approximately 5,335,727 bp and a GC content of 34,988%, and with 5509 predicted coding sequences. Based on the annotation statistics and comparison to other genomes within the same species archived in the Pathosystems Resource Integration Center (PATRIC), this genome "was of good quality. Annotation of B. cereus s.s. 3A ES revealed a variety of subsystem features, virulence factors and antibiotic resistant genes. The phylogenetic analysis of ten B. cereus group members showed B. cereus s.s. 3A-ES to be a closely related homolog of B. cereus s.s. ATCC 14,579, an established reference strain that is not adapted for cosmetic microbiological studies. Survival of 3A-ES in eye shadow could be linked to predicted stress-response genes and strengthened by additional stress-response genes such as VanB-type, VanRB, CAT15/16, BcrA, BcrB, Lsa(B), and recA that are lacking in B. cereus s.s. ATCC 14,579.

CONCLUSION

Our genomic analysis of B. cereus s.s. 3A-ES revealed genes, which may allow this bacterium to withstand the action of preservatives and inhibitors in cosmetics, as well as virulence factors that could contribute to its pathogenicity. Having a well-characterized strain obtained from eye-shadow may be useful for establishing a reference strain for cosmetics testing.

The arginine deaminase system plays distinct roles in Borrelia burgdorferi and Borrelia hermsii

Borrelia species are amino acid auxotrophs that utilize di- and tri- peptides obtained through their oligopeptide transport system to supply amino acids for replicative growth during their enzootic cycles. However, Borrelia species from both the Lyme disease (LD) and relapsing fever (RF) groups harbor an amino acid transport and catabolism system, the Arginine Deiminase System (ADI), that could potentially augment intracellular L-arginine required for growth. RF spirochetes contain a “complete”, four gene ADI (arcA, B, D, and C) while LD spirochetes harbor arcA, B, and sometimes D but lack arcC (encoding carbamate kinase). In this study, we evaluated the role of the ADI system in bacterial survival and virulence and discovered important differences in RF and LD ADIs. Both in vitro and in a murine model of infection, B. hermsii cells significantly reduced extracellular L-arginine levels and that reduction was dependent on arginine deiminase expression. Conversely, B. burgdorferi did not reduce the concentration of L-arginine during in vitro growth experiments nor during infection of the mammalian host, suggesting a fundamental difference in the ability to directly utilize L-arginine compared to B. hermsii. Further experiments using a panel of mutants generated in both B. burgdorferi and B. hermsii, identified important differences in growth characteristics and ADI transcription and protein expression. We also found that the ADI system plays a key role in blood and spleen colonization in RF spirochetes. In this study we have identified divergent metabolic strategies in two closely related human pathogens, that ultimately impacts the host-pathogen interface during infection.

Reports of tick-borne diseases have been steadily increasing in the US and the number of Lyme disease cases caused by B. burgdorferi have tripled since the late 1990’s. Although less common, cases of tick-borne relapsing fever, caused by B. hermsii and B. turicatae in the US, have increased as well. While transmitted by different ticks and maintained in unique enzootic cycles, the closely related spirochetes B. burgdorferi and B. hermsii share numerous genetic features including a truncated and streamlined capacity for metabolic activity. In this study we combine genetic and biochemical assays to define the role of the ADI in the infective cycles of B. burgdorferi and B. hermsii. When we compared B. burgdorferi and B. hermsii, we identified important differences in their respective ADI’s including operon arrangement, sensitivity to L-arginine and L-ornithine levels, as well as gene and protein expression. In addition, we show that arginine deiminase is required to reduce host L-arginine levels during murine infection with B. hermsii. This study provides new insights into the metabolic activities of two medically relevant spirochetes and highlights the dynamic nature of host-pathogen interactions.

Lactiplantibacillus plantarum LRCC5314 includes a gene for serotonin biosynthesis via the tryptophan metabolic pathway

As the functions of probiotics within the same species may not be shared, it is important to analyze the genetic characteristics of strains to determine their safety and usefulness before industrial applications. Hence the present study was undertaken to determine functional genes, and beneficial activities of strain LRCC5314, a bacterial strain isolated from kimchi through comparative genomic analysis. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LRCC5314 was a member of the species L. plantarum. Whole genome size of strain LRCC5314 was sequence was 3.25 Mb long, with a G + C content of 44.5 mol% and 3,031 predicted genes. Strain LRCC5314 could metabolize hexoses through homofermentation, which produces only lactic acid from hexoses. According to gene annotation, strain LRCC-5314 contained genes of EPS production and CRISPR. Moreover, the strain contained genes that could encode a complete biosynthetic pathway for the production of tryptophan, which can be used as a precursor of serotonin. Notably, the tryptophan and serotonin activities strain LRCC5314 were higher than those of reference strains, L. plantarum ATCC 14917^T, DSM 20246, DSM 2601, and ATCC 8014, which reach tryptophan amount of 0.784 ± 0.045 μM/ml in MRS broth and serotonin concentration of 19.075 ± 0.295 ng/ml in HT-22 cells. These findings indicated that L. plantarum LRCC5314 could provide a source for serotonin production and could be used as a functional probiotic for stress regulation.

Combination treatment of peroxyacetic acid or lactic acid with UV-C to control Salmonella Enteritidis biofilms on food contact surface and chicken skin

The risk of salmonellosis is expected to increase with the rise in the consumption of poultry meat. The aim of this study was to investigate the combination treatment of peroxyacetic acid (PAA) or lactic acid (LA) with UV-C against Salmonella Enteritidis biofilms formed on food contact surface (stainless steel [SS], silicone rubber [SR], and ultra-high molecular weight polyethylene [UHMWPE]) and chicken skin. The biofilm on food contact surface and chicken skin was significantly decreased (P < 0.05) by combination treatment of PAA or LA with UV-C. Combination treatment of PAA (50-500 μg/mL) with UV-C (5 and 10 min) reduced 3.10-6.41 log CFU/cm² and LA (0.5-2.0%) with UV-C (5 and 10 min) reduced 3.35-6.41 log CFU/cm² of S. Enteritidis biofilms on food contact surface. Salmonella Enteritidis biofilms on chicken skin was reduced around 2 log CFU/g with minor quality changes in color and texture by combination treatment of PAA (500 μg/mL) or LA (2.0%) with UV-C (10 min). Additional reduction occurred on SS and UHMWPE by PAA or LA with UV-C, while only LA with UV-C caused additional reduction on chicken skin. Also, it was visualized that the biofilm on food contact surface and chicken skin was removed through field emission scanning electron microscopy (FESEM) and death of cells constituting the biofilm was confirmed through confocal laser scanning microscopy (CLSM). These results indicating that the combination treatment of PAA or LA with UV-C could be used for S. Enteritidis biofilm control strategy in poultry industry.

Genome assisted probiotic characterization and application of Bacillus velezensis ZBG17 as an alternative to antibiotic growth promoters in broiler chickens

The present study describes genome annotation and phenotypic characterization of Bacillus velezensis ZBG17 and evaluation of its performance as antibiotic growth promoter substitute in broiler chickens. ZBG17 comprises 3.89 Mbp genome with GC content of 46.5%. ZBG17 could tolerate simulated gastrointestinal juices prevalent in the animal gut. Some adhesion-associated genomic features of ZBG17 supported the experimentally determined cell surface hydrophobicity and cell aggregation results. ZBG17 encoded multiple secondary metabolite gene clusters correlating with its broad-spectrum antibacterial activity. Interestingly, ZBG17 completely inhibited Salmonella enterica and Escherichia coli within 6 h and 8 h in liquid co-culture assay, respectively. ZBG17 genome analysis did not reveal any genetic determinant associated with reported safety hazards for use as a poultry direct-fed microbial. Dietary supplementation of ZBG17 significantly improved feed utilization efficiency and humoral immune response in broiler chickens, suggesting its prospective application as a direct-fed microbial in broiler chickens.

Organic Acid Sanitizers for Natamycin and Other Fungicides in Recirculating Application Systems for Citrus Postharvest Decay Management

Natamycin is a new postharvest biofungicide for citrus and some other fruit crops in the United States that can be effectively used in recycling drench or flooder treatments. These applications necessitate sanitation of the fungicide solution to ensure that it remains free from contamination by bacteria that are potentially human pathogens. During in vitro experiments, heated (48°C) citric acid (1,100 or 2,200 μg/ml) amended with sodium dodecylbenzenesulfonate (SDBS) (60 or 120 μg/ml, respectively) significantly reduced the viability of a nonpathogenic strain of Escherichia coli in natamycin solutions by >5 log₁₀ compared with the control. During laboratory studies with Penicillium digitatum-inoculated lemon fruit, 1,000 μg/ml of natamycin mixed with 1,000 μg/ml of lactic acid or citric acid and with or without SDBS (55 μg/ml) effectively and significantly reduced green mold. Natamycin mixed with lactic acid at ≥2,000 μg/ml, however, caused fruit injury, resulting in browning and rind pitting. Natamycin was incompatible with peroxyacetic acid, resulting in reduced efficacy against green mold. Sodium hypochlorite mixed with natamycin lost its toxicity to E. coli; however, the performance of natamycin was not affected. With heated (average 49°C) drench treatments on an experimental packing line, natamycin (1,000 μg/ml), fludioxonil (300 μg/ml), or azoxystrobin (300 μg/ml) mixed with citric acid (1,000 μg/ml) and SDBS (55 μg/ml) were effective against green mold without fruit injury. At a pH between 3.6 and 3.8, citric acid-SDBS significantly reduced the viability of E. coli by approximately 4 log₁₀ in mixtures with fludioxonil or azoxystrobin, but not with natamycin. However, natamycin at 1,000 μg/ml mixed with 2,000 μg/ml of citric acid and SDBS (55 μg/ml) significantly reduced E. coli counts by >4 log₁₀ within 4 min when the pH was maintained between 3.0 and 3.3, and the efficacy of the fungicide was retained. The use of citric acid with a surfactant can be a viable alternative sanitation method for natamycin in citrus packinghouses utilizing heated recirculating fungicide systems.

A genome guided evaluation of the Lab4 probiotic consortium

In this study, we present the draft genome sequences of the Lab4 probiotic consortium using whole genome sequencing. Draft genome sequences were retrieved and deposited for each of the organisms; PRJNA559984 for B. bifidum CUL20, PRJNA482335 for Lactobacillus acidophilus CUL60, PRJNA482434 for Lactobacillus acid. Probiogenomic in silico analyses confirmed existing taxonomies and identified the presence putative gene sequences that were functionally related to the performance of each organism during in vitro assessments of bile and acid tolerability, adherence to enterocytes and susceptibility to antibiotics. Predictions of genomic stability identified no significant risk of horizontal gene transfer in any of the Lab4 strains and the absence of both antibiotic resistance and virulence genes. These observations were supported by the outcomes of acute phase and repeat dose tolerability studies in Wistar rats where challenge with high doses of Lab4 did not result in any mortalities, clinical/histopathological abnormalities nor indications of systemic toxicity. Detection of increased numbers of lactobacilli and bifidobacteria in the faeces of supplemented rats implied an ability to survive transit through the gastrointestinal tract and/or impact upon the intestinal microbiota composition. In summary, this study provides in silico, in vitro and in vivo support for probiotic functionality and the safety of the Lab4 consortium.

A pH-Dependent Gene Expression Enables Bacillus amyloliquefaciens MBNC to Adapt to Acid Stress

Acid tolerance response (ATR), a process by which bacteria optimize their growth conditions for cellular functions, is a well-characterized bacterial stress response. A bacterial isolate identified, as Bacillus amyloliquefaciens MBNC, was isolated from acidic soil and studied for its acid tolerance response under several range of acidic stress conditions imposed through inorganic acid, organic acid, acetate buffer, and soil extract. The ability of the B. amyloliquefaciens MBNC to tolerate extreme acidic conditions (pH 4.5) increased when exposed to moderate-acidic pH (pH 5.5). Along with ATR, the bacterial cell density was also critical to its ability to tolerate low pH as the cells of late log phase were more tolerant to low pH stress compared to the early log phase cells. A comparative expression study of 28 genes of B. amyloliquefaciens MBNC was assessed in cells grown in neutral (pH 7.0) and acidic condition (pH 4.5) through qRT-PCR. Among the 28 genes analyzed, 24 genes showed increased expression whereas the expression of 4 genes was downregulated under acid stress indicating to the involvement of the genes in acid stress response.

Nanotoxicity of 2D Molybdenum Disulfide, MoS2, Nanosheets on Beneficial Soil Bacteria, Bacillus cereus and Pseudomonas aeruginosa

Concerns arising from accidental and occasional releases of novel industrial nanomaterials to the environment and waterbodies are rapidly increasing as the production and utilization levels of nanomaterials increase every day. In particular, two-dimensional nanosheets are one of the most significant emerging classes of nanomaterials used or considered for use in numerous applications and devices. This study deals with the interactions between 2D molybdenum disulfide (MoS2) nanosheets and beneficial soil bacteria. It was found that the log-reduction in the survival of Gram-positive Bacillus cereus was 2.8 (99.83%) and 4.9 (99.9988%) upon exposure to 16.0 mg/mL bulk MoS2 (macroscale) and 2D MoS2 nanosheets (nanoscale), respectively. For the case of Gram-negative Pseudomonas aeruginosa, the log-reduction values in bacterial survival were 1.9 (98.60%) and 5.4 (99.9996%) for the same concentration of bulk MoS2 and MoS2 nanosheets, respectively. Based on these findings, it is important to consider the potential toxicity of MoS2 nanosheets on beneficial soil bacteria responsible for nitrate reduction and nitrogen fixation, soil formation, decomposition of dead and decayed natural materials, and transformation of toxic compounds into nontoxic compounds to adequately assess the environmental impact of 2D nanosheets and nanomaterials.

Elucidation of Gram-Positive Bacterial Iron(III) Reduction for Kaolinite Clay Refinement

Recently, microbial-based iron reduction has been considered as a viable alternative to typical chemical-based treatments. The iron reduction is an important process in kaolin refining, where iron-bearing impurities in kaolin clay affects the whiteness, refractory properties, and its commercial value. In recent years, Gram-negative bacteria has been in the center stage of iron reduction research, whereas little is known about the potential use of Gram-positive bacteria to refine kaolin clay. In this study, we investigated the ferric reducing capabilities of five microbes by manipulating the microbial growth conditions. Out of the five, we discovered that Bacillus cereus and Staphylococcus aureus outperformed the other microbes under nitrogen-rich media. Through the biochemical changes and the microbial behavior, we mapped the hypothetical pathway leading to the iron reduction cellular properties, and found that the iron reduction properties of these Gram-positive bacteria rely heavily on the media composition. The media composition results in increased basification of the media that is a prerequisite for the cellular reduction of ferric ions. Further, these changes impact the formation of biofilm, suggesting that the cellular interaction for the iron(III)oxide reduction is not solely reliant on the formation of biofilms. This article reveals the potential development of Gram-positive microbes in facilitating the microbial-based removal of metal contaminants from clays or ores. Further studies to elucidate the corresponding pathways would be crucial for the further development of the field.

Effects of spraying lactic acid and peroxyacetic acid on the quality and microbial community dynamics of vacuum skin-packaged chilled beef during storage

A long shelf life for fresh meat products is very important both to processors, retailers and consumers. In this work, the effect of repeat acid spraying on the shelf life of vacuum skin-packaged (VSP) chilled beef, as well as the quality and microbial community dynamics was evaluated. Carcasses were sprayed with 300 ppm peroxyacetic acid (PA) or 3% lactic acid (LA) three times during the chilling process, or one more time of LA spray before packaging (LLA). Quality, sensory attributes and microbial load of VSP beef during 32 days of storage at 4 °C were evaluated. The results showed that quality and sensory scores decreased over time for all treatments, but LLA treated samples were still above the rejection threshold at the end of the storage period. Moreover, the total volatile basic nitrogen value and the total viable counts were 15.0 mg/100 g and 7.2 log CFU/g for the control group, while acid treated groups remained below these two values until the end of the storage period. In particular LLA treated beef steaks exhibited the best preservation potential even at the end of storage. This is attributed to the reduction of Proteobacteria in LLA beef steaks shown by the bacterial diversity analysis via high-throughput sequencing, as well as the lower counts of B. thermosphacta and Enterobacteriaceae during storage. This indicates that LLA treatment has the potential to achieve a shelf life extension of VSP steaks without impacting on quality.

Genome analysis reveals probiotic propensities of Paenibacillus polymyxa HK4

The legislations on the usage of antibiotics as growth promoters and prophylactic agents have compelled to develop alternative tools to upsurge the animal protection and contain antibiotic usage. Probiotics have emerged as an effective antibiotic substitute in animal farming. The present study explores the probiotic perspective of Paenibacillus polymyxa HK4 interlinking the genotypic and phenotypic characteristics. The draft genome of HK4 revealed the presence of ORFs encoding the functions associated with tolerance to gastrointestinal stress and adhesion. The biosynthetic gene clusters encoding non-ribosomally synthesized peptides, polyketides and lanthipeptides such as fusaricidin, tridecaptin, polymyxin, paenilan and paenibacillin were annotated in HK4 genome. The strain harbored the chromosomal gene conferring the resistance to lincosamides. No functional gene encoding virulence or toxins could be identified in the genome of HK4. The genome analysis data was complemented by the in vitro experiments confirming its survival during gastrointestinal transit, antimicrobial potential and antibiotic sensitivity. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The draft-genome sequence of Paenibacillus polymyxa HK4 has been deposited as whole-genome shotgun project at GenBank under the accession number PRJNA603023.

Quantitative approach to assess the compliance to a performance objective (PO) of Campylobacter jejuni in poultry meat in France

Predictive modelling is used in microbiological risk assessment to quantify the growth and inactivation of microorganisms through the use of mathematical models. Campylobacter jejuni is one of the main foodborne pathogens and broiler meat is considered as the most important source of human campylobacteriosis. The purpose of this study was to assess the effects of heating and chilling during the poultry slaughter process on inactivation kinetics of Campylobacter jejuni during chilled storage in order to predict its contamination level prior to preparation and consumption in the consumer's home, and then to assess the compliance to a Performance Objective (PO). Three strains of C. jejuni were submitted to consecutive heat (54 °C for 3 min) and cold (3 °C for 2 h) stresses, mimicking the two main slaughtering steps, i.e. scalding and chilling, by inoculating chicken fillets with three different concentrations (4, 6 and 8 log₁₀ CFU/g). Fillets were then stored at 6 °C during 17 days under the modified atmosphere currently used by food processors (70% O₂/30% CO₂). For all strains, bacterial log reduction was the lowest when inoculated at 8 log₁₀ CFU/g. One strain showed an enhanced resistance during cold storage after application of stressing steps, suggesting an impact of the cell history on further bacterial resistance. Taking strain variability into account, after six days of storage, predictions showed compliance of ready-to-be-cooked chicken meat with a hypothetical PO of 2.55 log₁₀ CFU/g, value set before the meat enters the consumer's home by the ICMSF (International Commission on Microbiological Specifications for Foods). This study opens the path to assess the compliance to a PO of Campylobacter jejuni in poultry meat and more generally provides inputs to refine microbiological risk assessment by taking into account the cell history and more particularly the impact of stressful steps on the subsequent inactivation at consumer's home.

Potential of Cell-Free Supernatant from Lactobacillus plantarum NIBR97, Including Novel Bacteriocins, as a Natural Alternative to Chemical Disinfectants

The recent pandemic of coronavirus disease 2019 (COVID-19) has increased demand for chemical disinfectants, which can be potentially hazardous to users. Here, we suggest that the cell-free supernatant from Lactobacillus plantarum NIBR97, including novel bacteriocins, has potential as a natural alternative to chemical disinfectants. It exhibits significant antibacterial activities against a broad range of pathogens, and was observed by scanning electron microscopy (SEM) to cause cellular lysis through pore formation in bacterial membranes, implying that its antibacterial activity may be mediated by peptides or proteins and supported by proteinase K treatment. It also showed significant antiviral activities against HIV-based lentivirus and influenza A/H3N2, causing lentiviral lysis through envelope collapse. Furthermore, whole-genome sequencing revealed that NIBR97 has diverse antimicrobial peptides, and among them are five novel bacteriocins, designated as plantaricin 1 to 5. Plantaricin 3 and 5 in particular showed both antibacterial and antiviral activities. SEM revealed that plantaricin 3 causes direct damage to both bacterial membranes and viral envelopes, while plantaricin 5 damaged only bacterial membranes, implying different antiviral mechanisms. Our data suggest that the cell-free supernatant from L. plantarum NIBR97, including novel bacteriocins, is potentially useful as a natural alternative to chemical disinfectants.

In ovo inoculation of duck embryos with different strains of Bacillus cereus to analyse their synergistic post-hatch anti-allergic potentialities

BACKGROUND

Bacillus cereus is a Gram-positive, facultative anaerobic bacteria with few strains reported to be used as probiotics for animals and birds in recent times if the doses are formulated properly.

OBJECTIVES

To analyse the synergistic anti-allergic potentiality of different Bacillus cereus strains on experimental in ovo and in vitro duck model, as probiotic immune stimulant.

MATERIALS AND METHODS

Different strains of Bacillus cereus from 29 isolates were identified through 16S rRNA gene sequencing from the milk samples of buffalo breeds of South Asia. The probiotic properties were tested in aspects of gram staining, catalase test, coagulase, test, bile salt tolerance, pH tolerance and phenol tolerance test. MIC₅₀ and MIC₉₀ levels were profiled using nine different antibiotics, and antimicrobial activity against eight different enteric pathogens was assessed. Finally, the test strains of Bacillus cereus (Colony Forming Unit [CFU] 30X10¹¹ ) were combined-infused at different concentrations in embryonated duck eggs to assess the post-hatch anti-allergic effects against histamine-induced allergic reaction and their immunoglobulin E (IgE) level was tested.

RESULTS

Molecular identification confirmed the test strains as B. cereus HKS 1-1, B. cereus LOCK 1,002 and B. cereus BF2, which were all motile, spore-forming, catalase-positive and rod-shaped. All were 0.3% bile salt, 0.4% phenol and pH tolerant. Two-way ANOVA test P values revealed that B. cereus BF2 was statistically significant (p < .0014) in bile salt tolerance test. B. cereus HKS 1-1 was significant in phenol and pH tolerance at p < .0002 and p < .0489, respectively. Besides, the test strains showed antibiotic sensitivity and antimicrobial activity to different enteric pathogens. In vivo model referred the test strains as effective in partial allergy reduction at same CFU but at different concentrations with p < .0001 among the groups.

CONCLUSION

The isolated and characterized strains of B. cereus showed partial immune-stimulating potentiality against experimentally induced allergic reaction.

Aspects Determining the Dominance of Fomitopsis pinicola in the Colonization of Deadwood and the Role of the Pathogenicity Factor Oxalate

Carbon and mineral cycling in sustainable forest systems depends on a microbiome of basidiomycetes, ascomycetes, litter-degrading saprobes, ectomycorrhizal, and mycoparasitic fungi that constitute a deadwood degrading consortium. The brown rot basidiomycete Fomitopsis pinicola (Swartz: Fr.) P. Karsten (Fp), as an oxalate-producing facultative pathogen, is an early colonizer of wounded trees and fresh deadwood. It replaces basidiomycetous white rot fungi and non-basidiomycetous fungal phyla in the presence of its volatilome, but poorly in its absence. With the goal of determining its dominance over the most competitive basidiomycetes and its role in fungal successions within the forest microbiome in general, Fp was exposed to the white rot fungus Kuehneromyces mutabilis (Schaeff.: Fr.) Singer & Smith (Km) in aseptic dual culture established on fertilized 100 mm-long wood dust columns in glass tubes with the inclusion of their volatilomes. For the mycelia approaching from the opposite ends of the wood dust columns, the energy-generating systems of laccase and manganese peroxidase (MnP), the virulence factor oxalate, and the exhalation of terpenes were determined by spectrophotometry, High Pressure Liquid Chromatography (HPLC), and Gas Chromatography-Mass Spectrometry (GC-MS). Km mycelia perceived the approaching Fp over 20 mm of non-colonized wood dust, reduced the laccase activity to 25%, and raised MnP to 275%–500% by gaining energy and presumably by controlling oxalate, H2O2, and the dropping substrate pH caused by Fp. On mycelial contact, Km stopped Fp, secured its substrate sector with 4 mm of an impermeable barrier region during an eruption of antimicrobial bisabolenes, and dropped from the invasion mode of substrate colonization into the steady state mode of low metabolic and defensive activity. The approaching Fp raised the oxalate production throughout to >20 g kg−1 to inactivate laccase and caused, with pH 1.4–1.7, lethal conditions in its substrate sector whose physiological effects on Km could be reproduced with acidity conditions incited by HCl. After a mean lag phase of 11 days, Fp persisting in a state of high metabolic activity overgrew and digested the debilitated Km thallus and terminated the production of oxalate. It is concluded that the factors contributing to the competitive advantage of F. pinicola in the colonization of wounded trees and pre-infected deadwood are the drastic long-term acidification of the timber substrate, its own insensitivity to extremely low pH conditions, its efficient control of the volatile mono- and sesquiterpenes of timber and microbial origin, and the action of a undefined blend of terpenes and allelopathic substances.

A Rapid Assay to Assess Nitrification Inhibition Using a Panel of Bacterial Strains and Partial Least Squares Modeling

As a proof of concept, a rapid assay consisting of a cell-based biosensor (CBB) panel of pure bacterial strains, a fluorescent dye, and partial least squares (PLS) modeling was developed to assess the nitrification inhibition potential of industrial wastewater (WW) samples. The current standard method used to assess the nitrification inhibition potential is the specific nitrification rate (SNR) batch test, which requires approximately 4 h to complete under the watch of an experienced operator. In this study, we exposed the CBB panel of seven bacterial strains (nitrifying and non-nitrifying) to 28 different industrial WW samples and then probed both the membrane integrity and cellular activity using a commercially available "live/dead" fluorescent dye. The CBB panel response acts as a surrogate measurement for the performance of nitrification. Of the seven strains, four (Nitrospira, Escherichia coli, Bacillus subtilis, Bacillus cereus) were identified via the modeling technique to be the most significant contributors for predicting the nitrification inhibition potential. The key outcome from this work is that the CBB panel fluorescence data (collected in approximately 10 min) can accurately predict the outcome of an SNR batch test (that takes 4 h) when performed with the same WW samples and has a strong potential to approximate the chemical composition of these WW samples using PLS modeling. Overall, this is a powerful technique that can be used for point-of-use detection of nitrification inhibition.

Effect of lactic acid spray on microbial and quality parameters of buffalo meat

We evaluated the effect of lactic acid spray on micro-flora, instrumental color, shelf-life and sensory attributes of buffalo meat displayed under Modified Atmosphere Packaging. Buffalo calf carcasses (n = 12) were sliced into equal sagittal halves, n = 6 halves were randomly assigned to each of four treatments i.e. 2% LA, 4% LA, 6% LA and control. Afterwards, sirloin and tenderloin were vacuum packed and aged for 7 days. Later, steaks were packed in high-oxygen MAP. Microbial load, instrumental color, shelf-life and sensory attributes were evaluated at different days. Aerobic plate count of sprayed carcass and steaks was significantly lower than un-sprayed control. Similarly, though non-significant, redness and chroma value of sprayed carcass meat was found better than un-sprayed control. Lactic acid sprayed meat did not differ in terms of sensory attributes. It is concluded that spraying buffalo carcasses with 2-4% lactic acid after slaughter not only enhances microbial quality but it may also improve its instrumental color.

Bacillus cereus cshA Is Expressed during the Lag Phase of Growth and Serves as a Potential Marker of Early Adaptation to Low Temperature and pH

The spore-forming bacterium B. cereus is a major cause of foodborne outbreaks in Europe. Some B. cereus strains can grow at low temperatures and low pH in many processed foods. Modeling of the bacterial lag time is hampered by a lack of knowledge of the timing of events occurring during this phase. In this context, the identification of lag phase markers, not currently available, could be a real advance for the better prediction of lag time duration. Currently, no molecular markers of this phase are available. By determining that cshA was always expressed early during the lag phase, we provide a molecular marker of the early adaptation process of B. cereus cells when exposed to low temperature and pH.

Bacterial adaptation is characterized by a lag phase during which cells do not multiply or modify their physiology to cope with the constraints of their environment. Our aim was to determine a sequence of events during the lag phase of growth at low temperature and pH for three Bacillus cereus strains. The onsets of expression of two genes, one of which is essential for stress adaptation (cshA, coding for a RNA helicase) and one of which is involved in the transition between lag phase and exponential phase (abrB, coding for a transition regulator), were determined using fluorescent transcriptional reporter systems. Regardless of the stressing conditions and the tested strains, the cshA promoter was active very early, while the biomass increased and always did so before the first cell division. At 12°C and pH 7.0, the onset of cshA promoter activity occurred at between 3 h and 7 h, while the bacterial counts started to increase at between 12 h and 13 h. At pH 5.0 and at 20°C or 30°C, the onset of cshA promoter activity occurred before 1 h and earlier than at pH 7.0. In contrast, the onset of abrB promoter activity depended on the strain and the stressing conditions. In the ATCC 14579 strain, the onset of abrB promoter activity always started at between 30 min and 3 h, before biomass increased and cell division occurred. For the other strains, it took place along with the first cell division at 12°C but did so much later during growth under the other tested conditions.

IMPORTANCE The spore-forming bacterium B. cereus is a major cause of foodborne outbreaks in Europe. Some B. cereus strains can grow at low temperatures and low pH in many processed foods. Modeling of the bacterial lag time is hampered by a lack of knowledge of the timing of events occurring during this phase. In this context, the identification of lag phase markers, not currently available, could be a real advance for the better prediction of lag time duration. Currently, no molecular markers of this phase are available. By determining that cshA was always expressed early during the lag phase, we provide a molecular marker of the early adaptation process of B. cereus cells when exposed to low temperature and pH.

A quantitative model of Bacillus cereus ATCC 9634 growth inhibition by bifidobacteria for synbiotic effect evaluation

The present study is dedicated to the development of novel criteria for assessing the synbiotic effect of prebiotic and probiotic composition against a specific pathogen. These criteria were obtained from the quantitative model of Bifidobacterium adolescentis ATCC 15703 and Bacillus cereus ATCC 9634 (as a model food contaminant) competition in co-culture fermentation. The model is based on the hypothesis that probiotics can reduce the specific growth rate of non-probiotics by producing short-chain fatty acids. To define the relationship between the specific growth rate of non-probiotics and short-chain fatty acid yields, the inhibition constants were determined separately for each inhibitor produced by bifidobacteria (lactic, acetic and propionic acids) in a pure culture of bacilli. Two different equations based on the minimum inhibitor concentration (MIC) and inhibition constant (K_i) were used to connect the specific growth rate and concentrations of inhibitors. The yields of the inhibitors mentioned above were obtained from co-culture experiments. The experimental values and the values predicted by the model of Bacillus count did not differ significantly (R² not less than 0.83) in the competition experiments. Therefore, the general criterion of the synbiotic effect was derived from the model and presents the coefficient of non-probiotic specific growth rate reduction as a result of probiotic growth and inhibitor formation in the final co-culture fermentation. This criterion has been examined for different commercial prebiotics coupled with the Bifidobacterium adolescentis strain. The synergistic combination of inulin GR with bifidobacteria had the best effect against Bacillus cereus ATCC 9634.

Unraveling the role of the transcriptional regulator VirS in low pH-induced responses of Mycobacterium tuberculosis and identification of VirS inhibitors

The ability of Mycobacterium tuberculosis to respond and adapt to various stresses such as oxygen/nitrogen radicals and low pH inside macrophages is critical for the persistence of this human pathogen inside its host. We have previously shown that an AraC/XylS-type transcriptional regulator, VirS, which is induced in low pH, is involved in remodeling the architecture of the bacterial cell envelope. However, how VirS influences gene expression to coordinate these pH responses remains unclear. Here, using a genetic biosensor of cytoplasmic pH, we demonstrate that VirS is required for the intracellular pH maintenance in response to acidic stress and inside acidified macrophages. Furthermore, we observed that VirS plays an important role in blocking phagosomal-lysosomal fusions. Transcriptomics experiments revealed that VirS affects the expression of genes encoding metabolic enzymes, cell-wall envelope proteins, efflux pumps, ion transporters, detoxification enzymes, and transcriptional regulators expressed under low-pH stress. Employing electrophoretic mobility-shift assays, DNA footprinting, and in silico analysis, we identified a DNA sequence to which VirS binds and key residues in VirS required for its interaction with DNA. A significant role of VirS in M. tuberculosis survival in adverse conditions suggested it as a potential anti-mycobacterial drug target. To that end, we identified VirS inhibitors in a virtual screen; the top hit compounds inhibited its DNA-binding activity and also M. tuberculosis growth in vitro and inside macrophages. Our findings establish that VirS mediates M. tuberculosis responses to acidic stress and identify VirS-inhibiting compounds that may form the basis for developing more effective anti-mycobacterial agents.

The protective potential of selected lactic acid bacteria against the most common contaminants in various types of cheese in Egypt

Dairy products, especially cheeses have a great nutritional value and a high consumption level around the world. Considering a widespread consumption of cheeses, there is a growing concern regarding safety and microbiological quality. The current study was designed to conduct a recent evaluation of cheeses microbiological quality. Sixty cheese samples from retailing Egyptian markets were analyzed on different selective microbiological media and 64 bacteria, 35 yeasts and 8 molds were isolated. Out of 60 samples; 26.6% were contaminated with Escherichia coli, 73.3% with Staphylococcus scuiri, 3.33% with Bacillus cereus, 1.66% with Salmonella enterica, and 1.66% with Pseudomonas aeruginosa. The presence of such microorganisms in cheeses referred to the wrong management in cheese manufacturing. These organisms are significant from public health view as they have been associated with the base of human food poisoning. Promising antagonistic behavior was observed using the tested lactic acid bacteria (LAB) either single or in combinations toward the undesired isolates. Lactobacillus helveticus CNRZ 32 (Lb. helveticus) was the most potent culture; recording ≥95% reduction in undesired microbial counts.

Urease is an essential component of the acid response network of Staphylococcus aureus and is required for a persistent murine kidney infection

Staphylococcus aureus causes acute and chronic infections resulting in significant morbidity. Urease, an enzyme that generates NH₃ and CO₂ from urea, is key to pH homeostasis in bacterial pathogens under acidic stress and nitrogen limitation. However, the function of urease in S. aureus niche colonization and nitrogen metabolism has not been extensively studied. We discovered that urease is essential for pH homeostasis and viability in urea-rich environments under weak acid stress. The regulation of urease transcription by CcpA, Agr, and CodY was identified in this study, implying a complex network that controls urease expression in response to changes in metabolic flux. In addition, it was determined that the endogenous urea derived from arginine is not a significant contributor to the intracellular nitrogen pool in non-acidic conditions. Furthermore, we found that during a murine chronic renal infection, urease facilitates S. aureus persistence by promoting bacterial fitness in the low-pH, urea-rich kidney. Overall, our study establishes that urease in S. aureus is not only a primary component of the acid response network but also an important factor required for persistent murine renal infections.

Urease has been reported to be crucial to bacteria in environmental adaptation, virulence, and defense against host immunity. Although the function of urease in S. aureus is not clear, recent evidence suggests that urease is important for acid resistance in various niches. Our study deciphered a function of S. aureus urease both in laboratory conditions and during host colonization. Furthermore, we uncovered the major components of the regulatory system that fine-tunes the expression of urease. Collectively, this study established the dual function of urease which serves as a significant part of the S. aureus acid response while also serving as an enzyme required for persistent kidney infections and potential subsequent staphylococcal metastasis.

Resilience in the Face of Uncertainty: Sigma Factor B Fine-Tunes Gene Expression To Support Homeostasis in Gram-Positive Bacteria

Gram-positive bacteria are ubiquitous and diverse microorganisms that can survive and sometimes even thrive in continuously changing environments. The key to such resilience is the ability of members of a population to respond and adjust to dynamic conditions in the environment. In bacteria, such responses and adjustments are mediated, at least in part, through appropriate changes in the bacterial transcriptome in response to the conditions encountered. Resilience is important for bacterial survival in diverse, complex, and rapidly changing environments and requires coordinated networks that integrate individual, mechanistic responses to environmental cues to enable overall metabolic homeostasis. In many Gram-positive bacteria, a key transcriptional regulator of the response to changing environmental conditions is the alternative sigma factor σ(B) σ(B) has been characterized in a subset of Gram-positive bacteria, including the genera Bacillus, Listeria, and Staphylococcus Recent insight from next-generation-sequencing results indicates that σ(B)-dependent regulation of gene expression contributes to resilience, i.e., the coordination of complex networks responsive to environmental changes. This review explores contributions of σ(B) to resilience in Bacillus, Listeria, and Staphylococcus and illustrates recently described regulatory functions of σ(B).

Staphylococcus epidermidis: metabolic adaptation and biofilm formation in response to different oxygen concentrations

Staphylococcus epidermidis has become a major health hazard. It is necessary to study its metabolism and hopefully uncover therapeutic targets. Cultivating S. epidermidis at increasing oxygen concentration [O2] enhanced growth, while inhibiting biofilm formation. Respiratory oxidoreductases were differentially expressed, probably to prevent reactive oxygen species formation. Under aerobiosis, S. epidermidis expressed high oxidoreductase activities, including glycerol-3-phosphate dehydrogenase, pyruvate dehydrogenase, ethanol dehydrogenase and succinate dehydrogenase, as well as cytochromes bo and aa3; while little tendency to form biofilms was observed. Under microaerobiosis, pyruvate dehydrogenase and ethanol dehydrogenase decreased while glycerol-3-phosphate dehydrogenase and succinate dehydrogenase nearly disappeared; cytochrome bo was present; anaerobic nitrate reductase activity was observed; biofilm formation increased slightly. Under anaerobiosis, biofilms grew; low ethanol dehydrogenase, pyruvate dehydrogenase and cytochrome bo were still present; nitrate dehydrogenase was the main terminal electron acceptor. KCN inhibited the aerobic respiratory chain and increased biofilm formation. In contrast, methylamine inhibited both nitrate reductase and biofilm formation. The correlation between the expression and/or activity or redox enzymes and biofilm-formation activities suggests that these are possible therapeutic targets to erradicate S. epidermidis.

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.

Mechanisms of food processing and storage-related stress tolerance in Clostridium botulinum

Vegetative cultures of Clostridium botulinum produce the extremely potent botulinum neurotoxin, and may jeopardize the safety of foods unless sufficient measures to prevent growth are applied. Minimal food processing relies on combinations of mild treatments, primarily to avoid deterioration of the sensory qualities of the food. Tolerance of C. botulinum to minimal food processing is well characterized. However, data on effects of successive treatments on robustness towards further processing is lacking. Developments in genetic manipulation tools and the availability of annotated genomes have allowed identification of genetic mechanisms involved in stress tolerance of C. botulinum. Most studies focused on low temperature, and the importance of various regulatory mechanisms in cold tolerance of C. botulinum has been demonstrated. Furthermore, novel roles in cold tolerance were shown for metabolic pathways under the control of these regulators. A role for secondary oxidative stress in tolerance to extreme temperatures has been proposed. Additionally, genetic mechanisms related to tolerance to heat, low pH, and high salinity have been characterized. Data on genetic stress-related mechanisms of psychrotrophic Group II C. botulinum strains are scarce; these mechanisms are of interest for food safety research and should thus be investigated. This minireview encompasses the importance of C. botulinum as a food safety hazard and its central physiological characteristics related to food-processing and storage-related stress. Special attention is given to recent findings considering genetic mechanisms C. botulinum utilizes in detecting and countering these adverse conditions.