Complete Genome Sequence of Bacillus bombysepticus, a Pathogen Leading to Bombyx mori Black Chest Septicemia

Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds

Seventeen bacterial strains able to suppress plant pathogens have been isolated from healthy Vietnamese crop plants and taxonomically assigned as members of the Bacillus cereus group. In order to prove their potential as biocontrol agents, we perform a comprehensive analysis that included the whole-genome sequencing of selected strains and the mining for genes and gene clusters involved in the synthesis of endo- and exotoxins and secondary metabolites, such as antimicrobial peptides (AMPs). Kurstakin, thumolycin, and other AMPs were detected and characterized by different mass spectrometric methods, such as MALDI-TOF-MS and LIFT-MALDI-TOF/TOF fragment analysis. Based on their whole-genome sequences, the plant-associated isolates were assigned to the following species and subspecies: B. cereus subsp. cereus (6), B. cereus subsp. bombysepticus (5), Bacillus tropicus (2), and Bacillus pacificus. These three isolates represent novel genomospecies. Genes encoding entomopathogenic crystal and vegetative proteins were detected in B. cereus subsp. bombysepticus TK1. The in vitro assays revealed that many plant-associated isolates enhanced plant growth and suppressed plant pathogens. Our findings indicate that the plant-associated representatives of the B. cereus group are a rich source of putative antimicrobial compounds with potential in sustainable agriculture. However, the presence of virulence genes might restrict their application as biologicals in agriculture.

Development of a high resolution melting method based on a novel molecular target for discrimination between Bacillus cereus and Bacillus thuringiensis

Delimitation within the Bacillus cereus group is confusing due to the highly similar genetic background of its constituent bacteria. This study aimed to develop a rapid and efficient method for the identification of Bacillus cereus and Bacillus thuringiensis, two closely related species within the B. cereus group. Using average nucleotide identity analysis (ANI) and ribosomal multilocus sequence typing (rMLST), the authenticity of the genomes of B. cereus and B. thuringiensis was determined. Emetic B. cereus and Bacillus bombysepticus were also included to provide novel genomic insights into the boundaries within the B. cereus group. Using pan-genome analysis, ispD, a novel core and single-copy molecular target, was identified for the differentiation between B. cereus and B. thuringiensis. Based on the single nucleotide polymorphism within ispD, a high resolution melting (HRM) method for the determination of B. cereus and B. thuringiensis was developed. This method can not only distinguish B. cereus and B. thuringiensis, but can also separate B. cereus from other foodborne pathogenic bacteria. The detection limit of this method could reach 1 pg of pure genomic DNA and 3.7 × 10² cfu/mL of pure culture. Moreover, this new method could effectively differentiate B. cereus and B. thuringiensis in spiked, mixed, and real food samples. Collectively, the established HRM method can provide a new reference paradigm for the sensitive and specific nucleic acid detection of pathogens with identical genomes.

Genomics and proteomics combined analysis revealed the toxicity response of silkworm Bombyx mori to the environmental pathogen Bacillus cereus ZJ-4

Bacterial contamination has caused a major public health problem worldwide. Bacillus cereus is a conditional environmental pathogenic bacteria that can cause food poisoning. Whether environmental pathogens can cause widespread transmission in the insect kingdom is unclear. In this study, a Bacillus cereus ZJ-4 was isolated from the hospital environment of Zhenjiang City, Jiangsu Province, China. It was fatal by injection into the silkworm hemolymph. To investigated the potential toxic factors of ZJ-4 and clarified the toxicity response mechanism of silkworm by the ZJ-4 infection. Then, the whole genome of ZJ-4 was sequenced, and the immune mechanism of silkworm fat body to ZJ-4 pathogen was studied by HE pathological section and proteomics. Bacterial genome sequencing indicated that ZJ-4 had 352 drug resistance genes and 6 virulence genes. After 36 h of subcutaneous puncture with ZJ-4 suspension, the pathological changes were obviously found in HE pathological sections of fat body tissue. Comparative proteomic results indicated that differentially expressed proteins are mainly involved in stress reactions, biological regulation, and innate immunity. The qRT-PCR analysis showed that the expressions of β-GRP, Spaetzle, MyD88, Tube and Dorsal genes in Toll pathway were up-regulated, while Pell and Cactus genes were down-regulated; in the antimicrobial peptide pathway, Glv2, Lzm, Mor, and Leb3 genes were up-regulated, while attacin1 and defensin genes were down-regulated; Sod gene was up-regulated, while Cat gene was down-regulated in the antioxidant pathway; Ldh, Sdh, and Mdh genes were down-regulated in glucose metabolism pathway. These results indicated that ZJ-4 can damage the innate immune pathway of silkworm, and also affect the normal immune function of fat body cells.

Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential

The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.

Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations

Bacillus cereus sensu lato comprises Gram-positive spore-forming bacteria producing toxins associated with foodborne diseases. Three pore-forming enterotoxins, nonhemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and cytotoxin K (CytK), are considered the primary factors in B. cereus sensu lato diarrhea. The aim of this study was to determine the potential risk of enterotoxicity among soil B. cereus sensu lato isolates representing diverse phylogroups and originated from different geographic locations with various climates (Burkina Faso, Kenya, Argentina, Kazakhstan, and Poland). While nheA- and hblA-positive isolates were present among all B. cereus sensu lato populations and distributed across all phylogenetic groups, cytK-2-positive strains predominated in geographic regions with an arid hot climate (Africa) and clustered together on a phylogenetic tree mainly within mesophilic groups III and IV. The highest in vitro cytotoxicity to Caco-2 and HeLa cells was demonstrated by the strains clustered within phylogroups II and IV. Overall, our results suggest that B. cereus sensu lato pathogenicity is a comprehensive process conditioned by many intracellular factors and diverse environmental conditions.IMPORTANCE This research offers a new route for a wider understanding of the dependency between pathogenicity and phylogeny of a natural bacterial population, specifically within Bacillus cereus sensu lato, that is widely distributed around the world and easily transferred into food products. Our study indicates differences in the phylogenetic and geographical distributions of potential enterotoxigenic B. cereus sensu lato strains. Hence, these bacilli possess a risk for human health, and rapid testing methods for their identification are greatly needed. In particular, the detection of the CytK enterotoxin should be a supporting strategy for the identification of pathogenic B. cereus sensu lato.

Phylogenetic Analysis of Bacillus cereus sensu lato Isolates from Commercial Bee Pollen Using tRNACys-PCR

Endospore-forming bacteria related to the Bacillus cereus group produce toxins that cause illnesses in organisms from invertebrates to mammals, including foodborne illnesses in humans. As commercial bee pollen can be contaminated with these bacteria, a comprehensive microbiological risk assessment of commercial bee pollen must be incorporated into the relevant regulatory requirements, including those that apply in Mexico. To facilitate detection of members of this group of bacteria, we have developed a PCR strategy that is based on the amplification of the single-copy tRNA^Cys gene and specific genes associated with tRNA^Cys to detect Bacillus cereus sensu lato (B. cereus s.l.). This tRNA^Cys-PCR-based approach was used to examine commercial bee pollen for endospore-forming bacteria. Our analysis revealed that 3% of the endospore-forming colonies isolated from a commercial source of bee pollen were related to B. cereus s.l., and this result was corroborated by phylogenetic analysis, bacterial identification via MALDI-TOF MS, and detection of enterotoxin genes encoding the HBL and NHE complexes. The results show that the isolated colonies are closely related phylogenetically to B. cereus, B. thuringiensis, and B. bombysepticus. Our results indicate that the tRNA^Cys-PCR, combined with other molecular tools, will be a useful approach for identifying B. cereus s.l. and will assist in controlling the spread of potential pathogens.

Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori

Bacillus bombyseptieus is a pathogen of Bombyx mori; it can cause bacterial septicemia in silkworm. One of the components of the parasporal crystal toxin of B. bombyseptieus, α-toxin, plays an important role in the process of infection in silkworm. In this study, we investigated the immune response of silkworm induced by α-toxin by using RNA-seq. We compared the changes in gene expression in the midgut, fatbody, and hemocytes of silkworm and in the B. mori embryonic cell line (BmE) after treatment with α-toxin and identified 952 differentially expressed genes and 353 differentially expressed long noncoding RNAs (lncRNAs). These regulated genes in different tissues were found to be enriched in different pathways. The upregulated genes in the midgut were mainly involved in peptidoglycan catabolic process and tyrosine kinase signaling pathway, whereas the downregulated genes were mainly involved in chitin metabolic pathways. The upregulated genes in fatbody were also involved in peptidoglycan catabolic process, but they were for a different peptidoglycan subtype. Further, genes encoding cecropins were enriched in the fatbody. The downregulated genes were mainly involved in the metabolic pathways of fundamental substances such as cellular protein metabolic process and nucleobase-containing compound metabolic process. These results suggest that α-toxin can induce various immune responses in silkworm, and further studies are warranted to understand the mechanism of α-toxin action in silkworm. Further, lncRNAs and differentially expressed genes were correlated using coexpression network analysis. Our findings revealed potential candidate genes and lncRNAs that might play important physiological functions in the immune response to α-toxins in silkworm.

Subterranean Mammals: Reservoirs of Infection or Overlooked Sentinels of Anthropogenic Environmental Soiling?

Global reports of emergent pathogens in humans have intensified efforts to identify wildlife reservoirs. Subterranean mammals, such as bathyergid mole rats, are largely overlooked, despite their high-level exposure to soil-dwelling microbes. Initial assessment of bathyergid reservoir potential was determined using a broad-range 16S rRNA PCR approach, which revealed an 83% PCR-positivity for the 234 bathyergid lung samples evaluated. The presence of the Bacillus cereus complex, a ubiquitous bacterial assemblage, containing pathogenic and zoonotic species, was confirmed through nucleotide sequencing, prior to group- and species-specific PCR sequencing. The latter allowed for enhanced placement and prevalence estimations of Bacillus in four bathyergid species sampled across a range of transformed landscapes in the Western Cape Province, South Africa. Two novel Bacillus strains (1 and 2) identified on the basis of the concatenated 16S rRNA-groEL-yeaC data set (2066 nucleotides in length), clustered with B. mycoides (ATCC 6462) and B. weihenstephanensis (WSBC 10204), within a well-supported monophyletic lineage. The levels of co-infection, evaluated with a groEL strain-specific assay, developed specifically for this purpose, were high (71%). The overall Bacillus presence of 17.95% (ranging from 0% for Georychus capensis to 45.35% for Bathyergus suillus) differed significantly between host species (χ² = 69.643; df = 3; P < 0.05), being significantly higher in bathyergids sampled near an urban informal settlement (χ² = 70.245; df = 3; P < 0.05). The results highlight the sentinel potential of soil-dwelling mammals for monitoring anthropogenically introduced, opportunistic pathogens and the threats they pose to vulnerable communities, particularly in the developing world.

Ribosomal background of the Bacillus cereus group thermotypes

In this study we reconstructed the architecture of Bacillus cereus sensu lato population based on ribosomal proteins, and identified a link between the ribosomal proteins’ variants and thermal groups (thermotypes) of the bacilli. The in silico phyloproteomic analysis of 55 ribosomal proteins (34 large and 21 small subunit r-proteins) of 421 strains, representing 14 well-established or plausible B. cereus sensu lato species, revealed several ribosomal clusters (r-clusters), which in general were well correlated with the strains’ affiliation to phylogenetic/thermal groups I–VII. However, a conformity and possibly a thermal characteristic of certain phylogenetic groups, e.g. the group IV, were not supported by a distribution of the corresponding r-clusters, and consequently neither by the analysis of cold-shock proteins (CSPs) nor by a content of heat shock proteins (HSPs). Furthermore, a preference for isoleucine and serine over valine and alanine in r-proteins along with a lack of HSP16.4 were recognized in non-mesophilic thermotypes. In conclusion, we suggest that the observed divergence in ribosomal proteins may be connected with an adaptation of B. cereus sensu lato members to various thermal niches.

Draft Genome Sequence of Bacillus thuringiensis INTA Fr7-4

We report here the complete annotated 6,035,547-bp draft genome sequence of Bacillus thuringiensis INTA Fr7-4. This strain contains three cry8 and two vip1 and vip2 insecticidal toxin genes.

Bacillus bombysepticus α-Toxin Binding to G Protein-Coupled Receptor Kinase 2 Regulates cAMP/PKA Signaling Pathway to Induce Host Death

Bacterial pathogens and their toxins target host receptors, leading to aberrant behavior or host death by changing signaling events through subversion of host intracellular cAMP level. This is an efficient and widespread mechanism of microbial pathogenesis. Previous studies describe toxins that increase cAMP in host cells, resulting in death through G protein-coupled receptor (GPCR) signaling pathways by influencing adenylyl cyclase or G protein activity. G protein-coupled receptor kinase 2 (GRK2) has a central role in regulation of GPCR desensitization. However, little information is available about the pathogenic mechanisms of toxins associated with GRK2. Here, we reported a new bacterial toxin-Bacillus bombysepticus (Bb) α-toxin that was lethal to host. We showed that Bb α-toxin interacted with BmGRK2. The data demonstrated that Bb α-toxin directly bound to BmGRK2 to promote death by affecting GPCR signaling pathways. This mechanism involved stimulation of G_αs, increase level of cAMP and activation of protein kinase A (PKA). Activated cAMP/PKA signal transduction altered downstream effectors that affected homeostasis and fundamental biological processes, disturbing the structural and functional integrity of cells, resulting in death. Preventing cAMP/PKA signaling transduction by inhibitions (NF449 or H-89) substantially reduced the pathogenicity of Bb α-toxin. The discovery of a toxin-induced host death specifically linked to GRK2 mediated signaling pathway suggested a new model for bacterial toxin action. Characterization of host genes whose expression and function are regulated by Bb α-toxin and GRK2 will offer a deeper understanding of the pathogenesis of infectious diseases caused by pathogens that elevate cAMP.

Interference with regulation of host signaling by pathogens can alter gene expression, leading to functional disarray in the host cells that causes abnormal division or death. Here, we propose a previously undescribed model for how bacterial toxins subvert host processes via interaction with GRK2 that influences cAMP/PKA signaling. Our findings provide new fundamental information about how bacterial pathogens regulate host signal transduction to cause death, which offers additional perspectives in host-pathogen systems. These findings will help to advance our understanding of bacteria pathogenic mechanism. Furthermore, these might extend to other microbial pathogenesis and assist in designing new or safer strategies against pathogens.

Identification and Characterization of Bacillus cereus SW7-1 in Bombyx mori (Lepidoptera: Bombycidae)

The bacterial diseases of silkworms cause significant reductions in sericulture and result in huge economic loss. This study aimed to identify and characterize a pathogen from diseased silkworm. SW7-1, a pathogenic bacterial strain, was isolated from the diseased silkworm. The strain was identified on the basis of its bacteriological properties and 16S rRNA gene sequence. The colony was round, slightly convex, opaque, dry, and milky on a nutrient agar medium, the colony also exhibited jagged edges. SW7-1 was Gram-positive, without parasporal crystal, and 0.8-1.2 by 2.6-3.4 µm in length, resembling long rods with rounded ends. The strain was positive to most of the physiological biochemical tests used in this study. The strain could utilize glucose, sucrose, and maltose. The results of its 16S rRNA gene sequence analysis revealed that SW7-1 shared the highest sequence identity (>99%) with Bacillus cereus strain 14. The bacterial strain was highly susceptible to gentamycin, streptomycin, erythromycin, norfloxacin, and ofloxacin and moderately susceptible to tetracycline and rifampicin. It exhibited resistance to other antibiotics. SW7-1 had hemolytic activity and could produce extracellular casease, lipase, and amylase. SW7-1 could reproduce septicemia-like symptoms with high mortality rate when re-fed to healthy silkworm. .The median lethal concentration (LC50) was 5.45 × 10(4) cfu/ml. Thus, SW7-1 was identified as B. cereus, which is a pathogen for silkworm and human infections are possible.

Chromosome-Directed PCR-Based Detection and Quantification of Bacillus cereus Group Members with Focus on B. thuringiensis Serovar israelensis Active against Nematoceran Larvae

Bacillus thuringiensis serovar israelensis is a wide-spread soil bacterium affiliated with the B. cereus group (Bcg) and is widely used in biocontrol products applied against mosquito and black fly larvae. For monitoring and quantification of applied B. thuringiensis serovar israelensis and its effect on indigenous B. thuringiensis serovar israelensis and Bcg assemblages, efficient and reliable tools are essential. The abundance and properties of B. thuringiensis serovar israelensis strains in the environment traditionally have been investigated with cultivation-dependent techniques, which are hampered by low sensitivity and the morphological similarity between B. cereus and B. thuringiensis. Currently available PCR-based detection and quantification tools target markers located on plasmids. In this study, a new cultivation-independent PCR-based method for efficient and specific quantification of B. thuringiensis serovar israelensis and Bcg is presented, utilizing two sets of PCR primers targeting the bacterial chromosome. Sequence database searches and empirical tests performed on target and nontarget species, as well as on bulk soil DNA samples, demonstrated that this diagnostic tool is specific for B. thuringiensis serovar israelensis and Bcg. The method will be useful for comparisons of Bcg and B. thuringiensis serovar israelensis abundances in the same samples. Moreover, the effect of B. thuringiensis serovar israelensis-based insecticide application on the total Bcg assemblages, including indigenous populations, can be investigated. This type of information is valuable in risk assessment and policy making for use of B. thuringiensis serovar israelensis in the environment.