Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach

Study on the inactivation effect and mechanism of EGCG disinfectant on Bacillus subtilis

The widespread use of chlorine-based disinfectants in drinking water treatment has led to the proliferation of chlorine-resistant bacteria and the risk of disinfection byproducts (DBPs), posing a serious threat to public health. This study aims to explore the effectiveness and potential applications of epigallocatechin gallate (EGCG) against chlorine-resistant Bacillus and its spores in water, providing new insights for the control of chlorine-resistant bacteria and improving the biological stability of distribution systems. The inactivation effects of EGCG on Bacillus subtilis (B. subtilis) and its spores were investigated using transmission electron microscopy, ATP measurement, and transcriptome sequencing analysis to determine changes in surface structure, energy metabolism, and gene expression levels, thereby elucidating the inactivation mechanism. The results demonstrate the potential application of EGCG in continuously inhibiting chlorine-resistant B. subtilis in water, effectively improving the biological stability of the distribution system. However, EGCG is not suitable for treating raw water with high spore content and is more suitable as a supplementary disinfectant for processes with strong spore removal capabilities, such as ozone, ultraviolet, or ultrafiltration. EGCG exhibits a disruptive effect on the morphological structure and energy metabolism of B. subtilis and suppresses the synthesis of substances, energy metabolism, and normal operation of the antioxidant system by inhibiting the expression of multiple genes, thereby achieving the inactivation of B. subtilis.

Microbial risk assessment of dairy products from retail marketplaces in Basrah province, Iraq

Background

Milk-borne bacteria cause degradation of milk products and constitute a significant risk to public health.

Aim

The objectives of the present study are to determine the microbiological quality of dairy products and to investigate pathogenic microorganisms.

Methods

A total of 60 samples of raw milk, homemade cheese, and yogurt were randomly selected from different retail marketplaces in Basrah. The bacteriological and biochemical tests were utilized to identify the pathogens in dairy samples, as well as the molecular technique was used as an accurate diagnostic test.

Results

The prevalence of contamination of milk products with various isolates was estimated as 50% (95% Cl: 36.8-63.2). The mean of total bacteria count for cheese was 7.29 ± 2.70, raw milk 4.62 ± 2.86, and yogurt 2.87 ± 1.05, with a significant p-value (p = 0.001). The mean count of aerobic spore-forming (ASF) contaminated raw milk was analyzed as 3.77 ± 1.18 and less contamination detected in the yogurt samples with mean of ASF was estimated as 2.52 ± 1.47 SD log 10 CFU/ml. A range of important microorganisms to human health were identified by employing the VITEK_2 system and sequencing 16S rDNA gene, including Staphylococcus aureus, Escherichia coli, Pseudomonas aerogenosa, and Bacillus cereus.

Conclusion

The study indicates that there is a high level of bacterial contamination in dairy products with different bacteria species, which is medically important. Therefore, food safety management must be implemented to reduce biological risks carried by dairy products and ensure healthy food for consumers.

Changes in the Spore Proteome of Bacillus cereus in Response to Introduction of Plasmids

Fluorescent fusion proteins were expressed in Bacillus cereus to visualize the germinosome by introducing a plasmid that carries fluorescent fusion proteins of germinant receptor GerR subunits or germinosome scaffold protein GerD. The effects of plasmid insertion and recombinant protein expression on the spore proteome were investigated. Proteomic analysis showed that overexpression of the target proteins had negligible effects on the spore proteome. However, plasmid-bearing spores displayed dramatic abundance changes in spore proteins involved in signaling and metabolism. Our findings indicate that the introduction of a plasmid alone alters the spore protein composition dramatically, with 993 proteins significantly down-regulated and 415 proteins significantly up-regulated among 3323 identified proteins. This shows that empty vector controls are more appropriate to compare proteome changes due to plasmid-encoded genes than is the wild-type strain, when using plasmid-based genetic tools. Therefore, researchers should keep in mind that molecular cloning techniques can alter more than their intended targets in a biological system, and interpret results with this in mind.

Transcriptome analysis reveals the molecular mechanisms of the novel Lactobacillus pentosus pentocin against Bacillus cereus

The objective of this study was to investigate the antibacterial effect and mechanism of Lactobacillus pentosus pentocin against Bacillus cereus. The dynamic growth of B. cereus showed that the pentocin had strong antibacterial activity against the strain. The antibacterial mechanism focused on cytomembrane destruction, biofilms formation, DNA replication and protein synthesis of B. cereus. The scanning electron microscopy, transmission electron microscopy and flow cytometry analysis illustrated that the cytomembranes were destroyed, causing the leakage of internal cellular components. Transcriptome sequencing indicated that the genes (KinB, KinC and Spo0B) in two component systems signal pathway were down-regulated, which resulted in the inhibition of the spores and biofilms formation of B. cereus. The phosphorylation and autoinducer-2 import were inhibited by down-regulating the expression levels of LuxS and LsrB genes in quorum sensing signal pathway, which also suppressed biofilms formation of B. cereus. The K⁺ leakage activated the K⁺ transport channels by up-relating the genes (KdpA, KdpB and KdpC), promoting the entry of K⁺ from the extracellular. In addition, the pentocin interfered DNA replication and protein synthesis by regulating the genes associated with DNA replication (dnaX and holB), RNA degradation (cshA, rho, rnj, deaD, rny, dnaK, groEL and hfq) and ribosome function (rpsA, rpsO and rplS). In this article, we provide some novel insights into the molecular mechanism responsible for high antibacterial activity of the L. pentosus pentocin against B. cereus. And the pentocin might be a very promising natural preservative for controlling the B. cereus contaminations in foods.

Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS)

By reporting the molar abundance of proteins, absolute quantification determines their stoichiometry in complexes, pathways, or networks. Typically, absolute quantification relies either on protein-specific isotopically labeled peptide standards or on a semiempirical calibration against the average abundance of peptides chosen from arbitrarily selected proteins. In contrast, a generic protein standard FUGIS (fully unlabeled generic internal standard) requires no isotopic labeling, chemical synthesis, or external calibration and is applicable to quantifying proteins of any organismal origin. The median intensity of the peptide peaks produced by the tryptic digestion of FUGIS is used as a single-point calibrant to determine the molar abundance of any codigested protein. Powered by FUGIS, median-based absolute quantification (MBAQ) outperformed other methods of untargeted proteome-wide absolute quantification.

The Membrane Proteome of Spores and Vegetative Cells of the Food-Borne Pathogen Bacillus cereus

Membrane proteins are fascinating since they play an important role in diverse cellular functions and constitute many drug targets. Membrane proteins are challenging to analyze. The spore, the most resistant form of known life, harbors a compressed inner membrane. This membrane acts not only as a barrier for undesired molecules but also as a scaffold for proteins involved in signal transduction and the transport of metabolites during spore germination and subsequent vegetative growth. In this study, we adapted a membrane enrichment method to study the membrane proteome of spores and cells of the food-borne pathogen Bacillus cereus using quantitative proteomics. Using bioinformatics filtering we identify and quantify 498 vegetative cell membrane proteins and 244 spore inner membrane proteins. Comparison of vegetative and spore membrane proteins showed there were 54 spore membrane-specific and 308 cell membrane-specific proteins. Functional characterization of these proteins showed that the cell membrane proteome has a far larger number of transporters, receptors and proteins related to cell division and motility. This was also reflected in the much higher expression level of many of these proteins in the cellular membrane for those proteins that were in common with the spore inner membrane. The spore inner membrane had specific expression of several germinant receptors and spore-specific proteins, but also seemed to show a preference towards the use of simple carbohydrates like glucose and fructose owing to only expressing transporters for these. These results show the differences in membrane proteome composition and show us the specific proteins necessary in the inner membrane of a dormant spore of this toxigenic spore-forming bacterium to survive adverse conditions.

Removal efficacy of opportunistic pathogen gene markers in drinking water supply systems: an in situ and large-scale molecular investigation

The prevalence and interactions with biofilm and disinfectant of opportunistic pathogens in drinking water supply systems (DWSSs) have been extensively interpreted. In contrast, the large geographical distribution and in situ removal of opportunistic pathogens are overlooked aspects. Here, paired source and tap water samples of 36 parallel DWSSs across China were collected, with five common waterborne pathogens characterized by qPCR. From source to tap, the removal of bacterial biomass (16S rRNA gene copy number) was 1.10 log, and gene marker removal of five opportunistic pathogens ranged from 0.66 log to 2.27 log, with the order of Escherichia coli > Mycobacterium spp. > Clostridium perfringens > Bacillus cereus > Aeromonas hydrophila. Different with bacterial community, geographical location and source water types (river or reservoir) were not key contributor to variation of opportunistic pathogens. Gene marker removal efficacies of E. coli, Mycobacterium spp., and C. perfringens from source to tap were restricted to removal efficacy of overall bacterial biomass, while abundance of B. cereus in tap water linked to the input of B. cereus from source water. Although culture-dependent approach is important for pathogen enumeration in drinking water, qPCR-based molecular survey shows advantages of quantifiable high-throughput and easy operation, providing abundant and timely information on pathogen occurrence in water. This study provides the in situ, molecular-level evidence toward differential propagation features of multiple opportunistic pathogens in DWSSs and suggests the source protection and early warning of treatment-resistant pathogens.

Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics

Mass spectrometry for rapid identification of microorganisms is expanding over the last years because this approach is quick. This methodology provides a decisive interest to fight against bioterrorism as it is applicable whatever the pathogen to be considered and often allows subtyping which may be crucial for confirming a massive and widespread attack with biological agents. Here, we present a methodology based on next-generation proteomics and tandem mass spectrometry for discovering numerous protein biomarkers allowing the discrimination of spores and vegetative cells of Bacillus atrophaeus, a biowarfare simulant. We propose a global quantitative evaluation of the two groups of discriminant biomarkers based on their aggregated normalized spectral abundance factors.

Structural, Metabolic and Evolutionary Comparison of Bacterial Endospore and Exospore Formation

Sporulation is a specialized developmental program employed by a diverse set of bacteria which culminates in the formation of dormant cells displaying increased resilience to stressors. This represents a major survival strategy for bacteria facing harsh environmental conditions, including nutrient limitation, heat, desiccation, and exposure to antimicrobial compounds. Through dispersal to new environments via biotic or abiotic factors, sporulation provides a means for disseminating genetic material and promotes encounters with preferable environments thus promoting environmental selection. Several types of bacterial sporulation have been characterized, each involving numerous morphological changes regulated and performed by non-homologous pathways. Despite their likely independent evolutionary origins, all known modes of sporulation are typically triggered by limited nutrients and require extensive membrane and peptidoglycan remodeling. While distinct modes of sporulation have been observed in diverse species, two major types are at the forefront of understanding the role of sporulation in human health, and microbial population dynamics and survival. Here, we outline endospore and exospore formation by members of the phyla Firmicutes and Actinobacteria, respectively. Using recent advances in molecular and structural biology, we point to the regulatory, genetic, and morphological differences unique to endo- and exospore formation, discuss shared characteristics that contribute to the enhanced environmental survival of spores and, finally, cover the evolutionary aspects of sporulation that contribute to bacterial species diversification.

Ozone disinfection of chlorine-resistant bacteria in drinking water

The wide application of chlorine disinfectant for drinking water treatment has led to the appearance of chlorine-resistant bacteria, which pose a severe threat to public health. This study was performed to explore the physiological-biochemical characteristics and environmental influence (pH, temperature, and turbidity) of seven strains of chlorine-resistant bacteria isolated from drinking water. Ozone disinfection was used to investigate the inactivation effect of bacteria and spores. The DNA concentration and cell surface structure variations of typical chlorine-resistant spores (Bacillus cereus spores) were also analysed by real-time qPCR, flow cytometry, and scanning electron microscopy to determine their inactivation mechanisms. The ozone resistance of bacteria (Aeromonas jandaei < Vogesella perlucida < Pelomonas < Bacillus cereus < Aeromonas sobria) was lower than that of spores (Bacillus alvei < Lysinibacillus fusiformis < Bacillus cereus) at an ozone concentration of 1.5 mg/L. More than 99.9% of Bacillus cereus spores were inactivated by increasing ozone concentration and treatment duration. Moreover, the DNA content of Bacillus cereus spores decreased sharply, but approximately 1/4 of the target genes remained. The spore structure exhibited shrinkage and folding after ozone treatment. Both cell structures and gene fragments were damaged by ozone disinfection. These results showed that ozone disinfection is a promising method for inactivating chlorine-resistant bacteria and spores in drinking water.

Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores

Bacterial spores are ubiquitous in nature and can withstand both chemical and physical stresses. Spores can survive food preservation processes and upon outgrowth cause food spoilage as well as safety risks. The heterogeneous germination and outgrowth behavior of isogenic spore populations exacerbates this risk. A major unknown factor of spores is likely to be the inherently heterogeneous spore protein composition. The proteomics methods discussed here help in broadening the knowledge about spore structure and identification of putative target proteins from spores of different spore formers. Approaches to synchronize Bacillus subtilis spore formation, and to analyze spore proteins as well as the physiology of spore germination and outgrowth are also discussed. Live-imaging and fluorescence microscopy techniques discussed here allow analysis, at single cell level, of the 'germinosome', the process of spore germination itself, spore outgrowth and the spore intracellular pH dynamics. For the latter, a recently published improved pHluorin (IpHluorin) under control of the ptsG promoter is applicable. While the data obtained from such tools offers novel insight in the mechanisms of bacterial spore awakening, it may also be used to probe candidate antimicrobial compounds for inhibitory effects on spore germination and strengthen microbial risk assessment.