Differentiation of Bacillus thuringiensis From Bacillus cereus Group Using a Unique Marker Based on Real-Time PCR

Characterization of toxigenic genes of Bacillus cereus strains isolated from different spices sold in Algeria

Many cooked foods are prepared with spices and dried herbs; these can be contaminated by several types of microorganisms, including aerobic spore-forming bacteria. The Bacillus cereus group is very widespread in nature and is known among the common food contaminants. They are involved in food poisoning, causing two types of syndromes, diarrheal and emetic. The aims of the present work were to determine the prevalence of toxigenic Bacillus cereus spores in spices and herbs marketed in the Laghouat area and to identify their toxigenic genes via PCR. Among the 191 samples, 14.13% were determined to be B. cereus, with concentrations ranging from 2.52 to 5.82 log cfu/g, where the highest level of contamination was observed in allspice and ginger. Moreover, entFM (100%), nhe (88.23%) and cytK (70.58%) were the most frequently identified toxin genes, whereas hbl (23.52%) was less common, and no emetic toxin-encoding gene (cesB) was found in any of the samples. Considering the results of the present study, the B. cereus microbial load and toxin gene profiles of spices show that spices have potential for public health in Algeria. In this context, it is crucial to guarantee the microbiological safety of spices by respecting good hygiene practices, eliminating bacterial spores and toxin production via sterilization and using appropriate packaging for these products.

Aerobic spore-forming bacteria associated with ropy bread: Identification, characterization and spoilage potential assessment

Aerobic spore-forming (ASF) bacteria have been reported to cause ropiness in bread. Sticky and stringy degradation, discoloration, and an odor reminiscent of rotting fruit are typical characteristics of ropy bread spoilage. In addition to economic losses, ropy bread spoilage may lead to health risks, as virulent strains of ASF bacteria are not uncommon. However, the lack of systematic approaches to quantify physicochemical spoilage characteristics makes it extremely difficult to assess rope formation in bread. To address this problem, the aim of this study was to identify, characterize and objectively assess the spoilage potential of ASF bacteria associated with ropy bread. Hence, a set of 82 ASF bacteria, including isolates from raw materials and bakery environments as well as strains from international culture collections, were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and their species identity confirmed by 16S rRNA and gyrA or panC gene sequencing. A standardized approach supported by objective colorimetric measurements was developed to assess the rope-inducing potential (RIP) of a strain by inoculating autoclaved bread slices with bacterial spores. In addition, the presence of potential virulence factors such as swarming motility or hemolysis was investigated. This study adds B. velezensis, B. inaquosorum and B. spizizenii to the species potentially implicated of causing ropy bread spoilage. Most importantly, this study introduces a standardized classification protocol for assessing the RIP of a bacterial strain. Colorimetric measurements are used to objectively quantify the degree of breadcrumb discoloration. Furthermore, our results indicate that strains capable of inducing rope spoilage in bread often exhibit swarming motility and virulence factors such as hemolysis, raising important food quality considerations.

The use of antigens derived from Bacillus thuringiensis bacteria for further differentiation

This study is devoted to studying Bacillus thuringiensis antigens and their insecticide activity as critical features in bacterial differentiation. Indeed, 190 samples were examined for flagellar antigenicity as well as the insecticidal activity exhibited. From a serological perspective, 122 isolates (64.2 %) were attributed to 8 H-serogroups, including 3 non-typeable and 65 unverified. The dominant serotype was H3abc (82 % frequency); H6 was less frequent (8.5 %). The other 6 serotypes accounted for a low frequency of occurrence (up to 1.5 %). Of the 190 isolates tested, 125 (65.8 %) formed bipyramidal, and 63 (33.2 %) represented spherical inclusions. All H3abc isolates contained bipyramidal inclusions. The same applied to H8ab and H7 isolates. Insecticide activity was noted in 70.1 % of the population. In general, 128 samples were toxic to both species (Bombyx mori, Aedes sp.). Another 3 samples were toxic only to B. mori, and 2 for Aedes sp. Among the samples exhibiting toxicity to both species, 97.6 % belonged to bipyramidal paraspore inclusions (H3abc). All H7 samples were toxic to two insect species. Monotoxic B. thuringiensis against Aedes sp. were found only among organisms producing spherical parasporal inclusions in the cell. Examples of such microorganisms include an isolate of the H4ab/43 serotype.

Early Growth Patterns of Bacillus cereus on Potato Substrate in the Presence of Low Densities of Black Soldier Fly Larvae

Bacillus cereus is a common and ubiquitous bacterium that can cause foodborne illnesses in humans and other animals. Common methods of contact between foodborne pathogens and their victims include exposure through contaminated food or food containment products. Using larvae of black soldier flies, Hermetia illucens, for biological conversion of wastes into components of animal feeds is a rapidly growing technology. However, contamination of larval biomass with pathogenic microorganisms may challenge its use on an industrial scale. We conducted laboratory experiments to test the effects of the black soldier fly larvae developing on simulated potato waste substrate on B. cereus abundance. We observed a general increase in the number of colony-forming units and concentration of hblD - gene when the larvae were present in the substrate, although the effect was modulated by larval densities and time since inoculation. It is possible that starch breakdown by black soldier fly larvae may provide a beneficial environment for B. cereus. Our results differ from the suppression in the presence by black soldier fly larvae reported for several other bacterial species and highlight the importance of taking proper food safety measures when using this technology.

Retrospective Screening of Anthrax-like Disease Induced by Bacillus tropicus str. JMT from Chinese Soft-Shell Turtles in Taiwan

Bacillus cereus is ubiquitous in the environment and a well-known causative agent of foodborne disease. Surprisingly, more and more emerging strains of atypical B. cereus have been identified and related to severe disease in humans and mammals such as chimpanzees, apes, and bovine. Recently, the atypical B. cereus isolates, which mainly derive from North America and Africa, have drawn great attention due to the potential risk of zoonosis. The cluster of B. cereus carries several anthrax-like virulent genes that are implicated in lethal disease. However, in non-mammals, the distribution of atypical B. cereus is still unknown. In this study, we conducted a retrospective screening of the 32 isolates of Bacillus spp. from diseased Chinese soft-shelled turtles from 2016 to 2020. To recognize the causative agent, we used various methods, such as sequencing analysis using PCR-amplification of the 16S rRNA gene, multiplex PCR for discriminating, and colony morphology by following previous studies. Furthermore, the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated, respectively, below the 70 and 96% cutoff to define species boundaries. According to the summarized results, the pathogen is taxonomically classified as Bacillus tropicus str. JMT (previous atypical Bacillus cereus). Subsequently, analyses such as targeting the unique genes using PCR and visual observation of the bacteria under various staining techniques were implemented in our study. Our findings show that all (32/32, 100%) isolates in this retrospective screening share similar phenotypical properties and carry the protective antigen (PA), edema factor (EF), hyaluronic acid (HA), and exopolysaccharide (Bps) genes on their plasmids. In this study, the results indicate that the geographic distribution and host range of B. tropicus were previously underestimated.

DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species

Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for "opening up" the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10-23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of B. thuringiensis 16S rRNA at fluorescein and B. mycoides at Cy5 channels with a limit of detection of 30 × 10³ and 35 × 10³ CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification.

Bacillus predominates in the Ophiocordyceps pseudolloydii-infected ants, and it potentially improves protection and utilization of the host cadavers

The bacterial communities that colonize the cadaver environment of insects infected and killed by parasitic fungi can be selected by the sympatric fungi and provide novel impacts. In this study, we found that Bacillus cereus/thuringiensis predominate the bacterial community in Dolichoderus thoracicus ant cadavers colonized by O. pseudolloydii. The most predominant bacterial strains in these ant cadavers were hemolytic and able to produce hydrolytic enzymes for digesting the ant tissue. A relatively intense lethal effect on the co-cultured nematode was displayed by a hemolytic strain. Moreover, the antagonistic effect against pathogenic fungi detected in the bacteria sympatric with O. pseudolloydii was reported here. Naphthoquinones have been shown to confer antibacterial activities and produced by the ant-pathogenic Ophiocordyceps fungi. However, our results did not show the naphthoquinone tolerance we expected to be detected in the bacteria from the ant infected by O. pseudolloydii. The bacterial diversity in the samples associated with O. pseudolloydii infected ants as revealed in this study will be a step forward to the understanding of the roles playing by the microbial community in the native habitats of O. pseudolloydii.

Prevalence and characterization of toxigenic Bacillus cereus group isolated from low-moisture food products

The present study was conducted to determine the occurrence of B. cereus group members in low-moisture food products by phenotypic and genetic assessment and to evaluate the toxigenic potential of B. cereus group isolates. According to the results of their morphological shape, growth temperature range, strain-specific gene distribution, 79.5% and 20.5% among 112 isolates were identified as B. cereus sensu stricto (s.s.) and B. thuringiensis, respectively and other toxigenic B. cereus group members was not found. All B. cereus group isolates possessed nheABC, hblACD, cytK, entFM genes, and the most frequent gene was nheA. Only three B. cereus s. s. isolates exhibited as emetic toxin gene-harboring B. cereus group. Several B. cereus s.s. and B. thuringiensis isolates from a low-moisture food products were moderate biofilm formers and showed resistance to rifampicin, tetracycline, or clindamycin. The existence of B. cereus s.s. and B. thuringiensis in low-moisture food products indicates the possible risk of foodborne infections due to their virulence potential.

Differentiation of Bacillus cereus and Bacillus thuringiensis Using Genome-Guided MALDI-TOF MS Based on Variations in Ribosomal Proteins

Bacillus cereus and B. thuringiensis are closely related species that are relevant to foodborne diseases and biopesticides, respectively. Unambiguous differentiation of these two species is crucial for bacterial taxonomy. As genome analysis offers an objective but time-consuming classification of B. cereus and B. thuringiensis, in the present study, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used to accelerate this process. By combining in silico genome analysis and MALDI-TOF MS measurements, four species-specific peaks of B. cereus and B. thuringiensis were screened and identified. The species-specific peaks of B. cereus were m/z 3211, 6427, 9188, and 9214, and the species-specific peaks of B. thuringiensis were m/z 3218, 6441, 9160, and 9229. All the above peaks represent ribosomal proteins, which are conserved and consistent with the phylogenetic relationship between B. cereus and B. thuringiensis. The specificity of the peaks was robustly verified using common foodborne pathogens. Thus, we concluded that genome-guided MALDI-TOF MS allows high-throughput differentiation of B. cereus and B. thuringiensis and provides a framework for differentiating other closely related species.

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.

Possible impacts of the predominant Bacillus bacteria on the Ophiocordyceps unilateralis s. l. in its infected ant cadavers

Animal hosts infected and killed by parasitoid fungi become nutrient-rich cadavers for saprophytes. Bacteria adapted to colonization of parasitoid fungi can be selected and can predominate in the cadavers, actions that consequently impact the fitness of the parasitoid fungi. In Taiwan, the zombie fungus, Ophiocordyceps unilateralis sensu lato (Clavicipitaceae: Hypocreales), was found to parasitize eight ant species, with preference for a principal host, Polyrhachis moesta. In this study, ant cadavers grew a fungal stroma that was predominated by Bacillus cereus/thuringiensis. The bacterial diversity in the principal ant host was found to be lower than the bacterial diversity in alternative hosts, a situation that might enhance the impact of B. cereus/thuringiensis on the sympatric fungus. The B. cereus/thuringiensis isolates from fungal stroma displayed higher resistance to a specific naphthoquinone (plumbagin) than sympatric bacteria from the environment. Naphthoquinones are known to be produced by O. unilateralis s. l., and hence the resistance displayed by B. cereus/thuringiensis isolates to these compounds suggests an advantage to B. cereus/thuringiensis to grow in the ant cadaver. Bacteria proliferating in the ant cadaver inevitably compete for resources with the fungus. However, the B. cereus/thuringiensis isolates displayed in vitro capabilities of hemolysis, production of hydrolytic enzymes, and antagonistic effects to co-cultured nematodes and entomopathogenic fungi. Thus, co-infection with B. cereus/thuringiensis offers potential benefits to the zombie fungus in killing the host under favorable conditions for reproduction, digesting the host tissue, and protecting the cadaver from being taken over by other consumers. With these potential benefits, the synergistic effect of B. cereus/thuringiensis on O. unilateralis infection is noteworthy given the competitive relationship of these two organisms sharing the same resource.

Genotype and virulence gene analyses of Bacillus cereus group clinical isolates from the Chinese softshell turtle (Pelodiscus sinensis) in Taiwan

Chinese softshell turtles (Pelodiscus sinensis) (CST) are susceptible to infections by bacteria belonging to the Bacillus cereus group (Bcg). Bcg includes several closely related species, two of which, B. cereus and B. thuringiensis, are pathogens of aquatic animals or insects. In the present study, we collected 57 Bcg isolates obtained from diseased CST from 2016 to 2019 in Kaohsiung and Pingtung, the areas with the most CST farms in Taiwan. All isolates were divided into four genotypes with two restriction enzymes, SmaI and NotI, by pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). Representative isolates from each genotype were subjected to phylogenetic tree analysis using 16S rDNA and pyruvate carboxylase genes as phylogenetic markers, and these CST isolates appeared in different clades. PCR was performed targeting six selected virulence genes, four of which were detected in CST isolates, including cytotoxin K (1/57), hblC of the haemolysin BL complex (46/57), nheA of the non-haemolytic enterotoxin complex (52/57) and enterotoxin FM (57/57), whereas cereulide synthetase and cereulide peptide synthase-like genes were not detected in any isolates.

Isolation, molecular characterization and pathogenicity of native Bacillus thuringiensis, from Ethiopia, against the tomato leafminer, Tuta absoluta: Detection of a new high lethal phylogenetic group

Tuta absoluta (tomato leafminer) is one of the devastating agricultural pest that attack mainly tomatoes. The continuous use of chemical pesticides is not affordable and poses a collateral damage to human and environmental health. This requires integrated pest management to reduce chemical pesticides. B. thuringiensis is a cosmopolitan, antagonistic soil bacterium used to control agricultural pests. In this study, effective Bt strains were screened from different sample sources based on their lepidopteran specific cry genes and larvicidal efficacy against tomato leafminer, T. absoluta under laboratory conditions. Of the 182 bacterial isolates, 55 (30 %) of isolates harbored parasporal protein crystals. Out of these, 34 (62 %) isolates possess one or more lepidopteran specific cry genes: 20 % of isolates positive for cry2, 18.2 % for cry9, 3.6 % for cry1, 16.4 % for cry2 + cry9, 1.8 % for cry1 + cry9, and 1.8 % for cry1 + cry2 + cry9. However, 21 (38.2 %) isolates did not show any lepidopteran specific cry genes. Isolates positive for cry genes showed 36.7-75 % and 46.7-98.3 % mortality against second and third instar larvae of the T. absoluta at the concentration of 10⁸ colony forming units (CFUs) ml^-1. Cry1 and cry1 plus other cry gene positive isolates were relatively more pathogenic against T. absoluta. However, third instar larvae of the T. absoluta was more susceptible than second instar larvae. Two of the isolates, AAUF6 and AAUMF9 were effective and scored LT₅₀ values of 2.3 and 2.7 days and LC₅₀ values of 3.4 × 10³ and 4.15 × 10³ CFUs ml^-1 against the third instar larvae, respectively. The phylogenetic studies showed some congruence of groups with cry gene profiles and lethality level of isolates and very interestingly, we have detected a putative new phylogenetic group of Bt from Ethiopia.

Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control

Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders. In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer, our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen, since there is no efficient chemical or biological control method for this pest. Therefore, endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid, central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil. The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus. The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%). BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract, while the B. cereus group remained very closely clustered in the dendrogram. According to XRE biomarker analysis, eleven strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) correspond to B. thuringiensis species. Additional studies using conserved genes (glp, gmk, pta, and tpi) indicated that most of these strains were phylogenetically closely related to B. thuringiensis and may be considered different subspecies. In conclusion, this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time. These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B. thuringiensis species.

Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials

The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the tested five organic agricultural materials, a total of seven distinct bacterial colonies (A-1, B-1, C-1, D-1, E-1, E-2, and E-3) were isolated and processed for sequential identification utilizing HiCrome™ Bacillus agar, biochemical tests with API CHB50, 16S rRNA gene analysis, random amplified polymorphic DNA (RAPD), and species-specific PCR analysis. All the isolated microorganisms were Gram-positive rods and spore former belonging to Bacillus group and appeared as a differential characteristic feature on HiCrome™ Bacillus agar. All isolates showed high-percentage similarities with the different members of Bacillus species in biochemical testing and 16S rRNA gene analysis. The collective identification results revealed isolates, A-1, B-1, and C-1, close to B. velezensis. Further RAPD-PCR and species-specific PCR discriminated and provided confirmatory evidence for D-1 as B. thuringiensis and E-1, E-2, and E-3 as B. licheniformis, respectively. In addition, presence of B. thuringiensis was also confirmed by toxin crystal protein staining. In conclusion, the species-specific primers could be used as a rapid and accurate identification tool to discriminate closely related Bacillus species such as B. subtilis, B. licheniformis, and B. thuringiensis.