Genomic insights into the taxonomic status of the Bacillus cereus group

Bacillus cereus Group Bacteriophage Flapjack Genome Sequence

The Bacillus cereus group bacteriophage Flapjack, a double-stranded DNA (dsDNA) Myoviridae isolate collected from soil collected in Washington, DC, is a member of cluster C3 and encodes an intramolecular chaperone-containing tail fiber protein previously found in Podoviridae and Siphoviridae but not annotated in the Myoviridae.

Pan-genome and phylogeny of Bacillus cereus sensu lato

BACKGROUND

Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., "pan-GWAS" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered.

METHODS

A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes.

RESULTS

The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are "core" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering.

CONCLUSIONS

All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers

Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection) are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes). The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.

Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae

Three double-stranded DNA phi29-like Bacillus cereus group bacteriophages, BeachBum, Harambe, and SerPounce, were identified and characterized. BeachBum and Harambe are closely related but are remarkably different from previously identified phi29-like phages. SerPounce is substantially closer to other phi29-like phages, enabling the identification of its prohead RNA (pRNA) gene.

Characterization of Enterotoxigenic Bacillus cereus sensu lato and Staphylococcus aureus Isolates and Associated Enterotoxin Production Dynamics in Milk or Meat-Based Broth

Bacillus cereus sensu lato species, as well as Staphylococcus aureus, are important pathogenic bacteria which can cause foodborne illness through the production of enterotoxins. This study characterised enterotoxin genes of these species and examined growth and enterotoxin production dynamics of isolates when grown in milk or meat-based broth. All B. cereus s. l. isolates harboured nheA, hblA and entFM toxin genes, with lower prevalence of bceT and hlyII. When grown at 16 °C, toxin production by individual B. cereus s. l. isolates varied depending on the food matrix; toxin was detected at cell densities below 5 log₁₀(CFU/mL). At 16 °C no staphylococcal enterotoxin C (SEC) production was detected by S. aureus isolates, although low levels of SED production was noted. At 30 °C all S. aureus isolates produced detectable enterotoxin in the simulated meat matrix, whereas SEC production was significantly reduced in milk. Relative to B. cereus s. l. toxin production, S. aureus typically required reaching higher cell numbers to produce detectable levels of enterotoxin. Phylogenetic analysis of the sec and sel genes suggested population evolution which correlated with animal host adaptation, with subgroups of bovine isolates or caprine/ovine isolates noted, which were distinct from human isolates. Taken together, this study highlights the marked differences in the production of enterotoxins both associated with different growth matrices themselves, but also in the behaviour of individual strains when exposed to different food matrices.

A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species

A multilocus sequence analysis (MLSA) was established and performed on the genus Thioclava, including 23 strains isolated from diverse marine environments, with the aim of better differentiation of strains and species within this genus. The study was based on sequences of 16S rRNA gene and five protein-coding housekeeping genes, gyrB, rpoD, dnaK, trpB, and recA. In contrast to 16S rRNA gene-based tree that was unable to separate some species within this genus, each tree based on a single housekeeping gene and MLSA had consistently defined seven clades, corresponding to the five established ones and two novel ones. The digital DNA-DNA hybridization and average nucleotide identity analyses based on genome sequences of the representative strains reconfirmed the validity of the MLSA analysis, and recommended a 97.3% MLSA similarity as the soft species threshold and nine species representing the five known and four putative novel species. Two of the four new species were identified as Thioclava sediminum sp. nov. (type strain TAW-CT134^T = MCCC 1A10143^T = LMG 29615^T) and Thioclava marinus sp. nov. (type strain 11.10-0-13^T = MCCC 1A03502^T = LMG 29618^T) by using a polyphasic taxonomic approach. Taken together, the newly established MLSA in this study first described the variability and phylogeny of the genus Thioclava which contributes to better understanding its ecology and evolution.

A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies

The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics. In this manuscript, we review the most commonly used platforms and approaches for ortholog group analyses with a focus on their potential for phylogenetic and taxonomic research. Furthermore, we describe the latest improvements of the EDGAR platform for comparative genome analyses and present recent examples of its application for the phylogenomic analysis of different taxa. Finally, we illustrate the role of the EDGAR platform as part of the BiGi Center for Microbial Bioinformatics within the German network on Bioinformatics Infrastructure (de.NBI).

In defense of Bacillus thuringiensis, the safest and most successful microbial insecticide available to humanity - a response to EFSA

The Bacillus cereus group contains vertebrate pathogens such as B. anthracis and B. cereus and the invertebrate pathogen B. thuringiensis (Bt). Microbial biopesticides based on Bt are widely recognised as being among the safest and least environmentally damaging insecticidal products available. Nevertheless, a recent food-poisoning incident prompted a European Food Safety Authority review which argued that Bt poses a health risk equivalent to B. cereus, a causative agent of diarrhoea. However, a critical examination of available data, and this latest incident, provides no solid evidence that Bt causes diarrhoea. Although relatively high levels of B. cereus-like spores can occur in foods, genotyping demonstrates that these are predominantly naturally occurring strains rather than biopesticides. Moreover, MLST genotyping of >2000 isolates show that biopesticide genotypes have never been isolated from any clinical infection. MLST data demonstrate that B. cereus group is heterogeneous and formed of distinct clades with substantial differences in biology, ecology and host association. The group posing the greatest risk (the anthracis clade) is distantly related to the clade containing all biopesticides. These recent data support the long-held view that Bt and especially the strains used in Bt biopesticides are very safe for humans.

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.

Genetic diversity and population structure of the Bacillus cereus group bacteria from diverse marine environments

The phylogenetic diversity of marine bacteria belonged to the Bacillus cereus group has not been well investigated. Here, we present the genetic diversity and population structure of 71 bacteria from diverse marine environments, using a multilocus sequence typing (MLST) approach and the analyses of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) based on some representative genomic sequences. The MLST analysis demonstrated that these isolates were highly diverse and a wide distribution in marine environments and some of them showed niche specificity to some extent. They were assigned to 27 sequence types (STs) with 23 novel STs. Phylogenetic analysis of 82 bacteria containing 11 type strains based on MLST discriminated them as 20 clusters including 10 new ones. Both the dDDH and ANI results supported the proposition that each of 20 clusters represented one independent species, including 10 putative novel species. Values of 98.3% of MLST similarity and 96.2% of ANI were proposed as the standard for the species definition of this group. In summary, the first insight into the phylogenetic diversity of the group bacteria from marine environments will contribute to better understanding of their ecological role and evolution in contrast with terrestrial environments.

Prevalence, virulence factor genes and antibiotic resistance of Bacillus cereus sensu lato isolated from dairy farms and traditional dairy products

Background

B. cereus are of particular interest in food safety and public health because of their capacity to cause food spoilage and disease through the production of various toxins. The aim of this study was to determine the prevalence, virulence factor genes and antibiotic resistance profile of B. cereus sensu lato isolated from cattle grazing soils and dairy products in Ghana. A total of 114 samples made up of 25 soil collected from cattle grazing farm land, 30 raw milk, 28 nunu (yoghurt-like product) and 31 woagashie (West African soft cheese). Ninety-six B. cereus sensu lato isolates from 54 positive samples were screened by PCR for the presence of 8 enterotoxigenic genes (hblA, hblC, hblD, nheA, nheB, nheC, cytK and entFM), and one emetic gene (ces). Phenotypic resistance to 15 antibiotics were also determined for 96 B. cereus sensu lato isolates.

Results

About 72% (18 of 25 soil), 47% (14 of 30 raw milk), 35% (10 of 28 nunu) and 39% (12 of 31 woagashi) were positive for B. cereus sensu lato with mean counts (log₁₀ cfu/g) of 4.2 ± 1.8, 3.3 ± 2.0, 1.8 ± 1.4 and 2.6 ± 1.8 respectively. The distribution of enterotoxigenic genes revealed that 13% (12/96 isolates) harboured all three gene encoding for haemolytic enterotoxin HBL complex genes (hblA, hblC and hblD), 25% (24/96 isolates) possessed no HBL gene, whereas 63% (60/96 isolates) possessed at least one of the three HBL genes. All three genes encoding for non-haemolytic enterotoxin (nheA, nheB and nheC) were detected in 60% (57/96) isolates, 14% (13/96) harboured only one gene, 19% (18/96) whereas 8% possessed none of the NHE genes. The detection rates of cytk, entFM, and ces genes were 75, 67 and 9% respectively. Bacillus cereus s. l. isolates were generally resistant to β-lactam antibiotics such as ampicillin (98%), oxacillin (92%), penicillin (100%), amoxicillin (100%), and cefepime (100%) but susceptible to other antibiotics tested.

Conclusions

Bacillus cereus s. l. is prevalent in soil, raw milk and dairy products in Ghana. However, loads are at levels considered to be safe for consumption. Various enterotoxin genes associated with virulence of B. cereus are widespread among the isolates.

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibrio strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANIb) and MUMmer (ANIm), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.

Complete Genome Sequences of Bacillus Phages DirtyBetty and Kida

We report here the genome sequences of two bacteriophages of the Bacillus cereus group, DirtyBetty and Kida. These bacteriophages are double-stranded DNA-containing Myoviridae isolated from soil samples using Bacillus thuringiensis subsp. kurstaki as their host bacteria.

Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group

Bacteria from the Bacillus cereus group exhibit genetic and physiological diversity through different ecotypes. Here, we present the draft genome sequences of 20 bacterial strains belonging to the contrasted psychrotolerant and thermotolerant ecotypes.

Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products

With the abolition of milk quotas in the European Union in 2015, several member states including Ireland, Luxembourg, and Belgium have seen year on year bi-monthly milk deliveries to dairies increase by up to 35%. Milk production has also increased outside of Europe in the past number of years. Unsurprisingly, there has been a corresponding increased focus on the production of dried milk products for improved shelf life. These powders are used in a wide variety of products, including confectionery, infant formula, sports dietary supplements and supplements for health recovery. To ensure quality and safety standards in the dairy sector, strict controls are in place with respect to the acceptable quantity and species of microorganisms present in these products. A particular emphasis on spore-forming bacteria is necessary due to their inherent ability to survive extreme processing conditions. Traditional microbiological detection methods used in industry have limitations in terms of time, efficiency, accuracy, and sensitivity. The following review will explore the common spore-forming bacterial contaminants of milk powders, will review the guidelines with respect to the acceptable limits of these microorganisms and will provide an insight into recent advances in methods for detecting these microbes. The various advantages and limitations with respect to the application of these diagnostics approaches for dairy food will be provided. It is anticipated that the optimization and application of these methods in appropriate ways can ensure that the enhanced pressures associated with increased production will not result in any lessening of safety and quality standards.

The Identification of Intrinsic Chloramphenicol and Tetracycline Resistance Genes in Members of the Bacillus cereus Group (sensu lato)

Bacillus toyonensis strain BCT-7112T (NCIMB 14858T) has been widely used as an additive in animal nutrition for more than 30 years without reports of adverse toxigenic effects. However, this strain is resistant to chloramphenicol and tetracycline and it is generally considered inadvisable to introduce into the food chain resistance determinants capable of being transferred to other bacterial strains, thereby adding to the pool of such determinants in the gastro-enteric systems of livestock species. We therefore characterized the resistance phenotypes of this strain and its close relatives to determine whether they were of recent origin, and therefore likely to be transmissible. To this end we identified the genes responsible for chloramphenicol (catQ) and tetracycline (tetM) resistance and confirmed the presence of homologs in other members of the B. toyonensis taxonomic unit. Unexpectedly, closely related strains encoding these genes did not exhibit chloramphenicol and tetracycline resistance phenotypes. To understand the differences in the behaviors, we cloned and expressed the genes, together with their upstream regulatory regions, into Bacillus subtilis. The data showed that the genes encoded functional proteins, but were expressed inefficiently from their native promoters. B. toyonensis is a taxonomic unit member of the Bacillus cereus group (sensu lato). We therefore extended the analysis to determine the extent to which homologous chloramphenicol and tetracycline resistance genes were present in other species within this group. This analysis revealed that homologous genes were present in nearly all representative species within the B. cereus group (sensu lato). The absence of known transposition elements and the observations that they are found at the same genomic locations, indicates that these chloramphenicol and tetracycline resistance genes are of ancient origin and intrinsic to this taxonomic group, rather than recent acquisitions. In this context we discuss definitions of what are and are not intrinsic genes, an issue that is of fundamental importance to both Regulatory Authorities, and the animal feed and related industries.

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.

Detection of the cryptic prophage-like molecule pBtic235 in Bacillus thuringiensis subsp. israelensis

Bacillus thuringiensis has long been recognized to carry numerous extrachromosomal molecules. Of particular interest are the strains belonging to the B. thuringiensis subsp. israelensis lineage, as they can harbor at least seven extrachromosomal molecules. One of these elements seems to be a cryptic molecule that may have been disregarded in strains considered plasmid-less. Therefore, this work focused on this cryptic molecule, named pBtic235. Using different approaches that included transposition-tagging, large plasmid gel electrophoresis and Southern blotting, conjugation and phage-induction experiments, in combination with bioinformatics analyses, it was found that pBtic235 is a hybrid molecule of 235,425 bp whose genome displays potential plasmid- and phage-like modules. The sequence of pBtic235 has been identified in all sequenced genomes of B. thuringiensis subsp. israelensis strains. Here, the pBtic235 sequence was considered identical to that of plasmid pBTHD789-2 from strain HD-789. Despite the fact that the pBtic235 genome possesses 240 putative CDSs, many of them have no homologs in the databases. However, CDSs coding for potential proteins involved in replication, genome packaging and virion structure, cell lysis, regulation of lytic-lysogenic cycles, metabolite transporters, stress and metal resistance, were identified. The candidate plasmidial prophage pBtic235 exemplifies the notable diversity of the extrachromosomal realm found in B. thuringiensis.

Gene content dissimilarity for subclassification of highly similar microbial strains

Background

Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgnisms to different taxonomic levels, and it is still not clear that to what extent genomic fluidity should occur to form a microbial taxonomic group.

Results

By taking advantage of the eggNOG database for orthologous groups, we calculated gene content dissimilarity among different microbial strains based on the orthologous gene profiles and tested the possibility of applying gene content dissimilarity as a quantitative index in classifying microbial taxonomic groups, as well as its potential application in subclassification of highly similar microbial strains. Evaluation of gene content dissimilarity to completed microbial genomes at different taxonomic levels suggested that cutoffs of 0.2 and 0.4 can be respectively used for species and family delineation, and that 0.2 gene content dissimilarity cutoff approximately corresponded to 98 % 16S rRNA gene identity and 94 % ANI for microbial species delineation. Furthermore, application of gene content dissimilarity to highly similar microbial strains suggested it as an effective approach in classifying closely related microorganisms into subgroups.

Conclusions

This approach is especially useful in identifying pathogens from commensals in clinical microbiology. It also provides novel insights into how genomic fluidity is linked with microbial taxonomy.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2991-9) contains supplementary material, which is available to authorized users.

Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments

A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA-DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).

Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade

BACKGROUND

Bacillus cereus group isolates that produce diarrheal or emetic toxins are frequently isolated from raw milk and, in spore form, can survive pasteurization. Several species within the B. cereus group are closely related and cannot be reliably differentiated by established taxonomical criteria. While B. cereus is traditionally recognized as the principal causative agent of foodborne disease in this group, there is a need to better understand the distribution and expression of different toxin and virulence genes among B. cereus group food isolates to facilitate reliable characterization that allows for assessment of the likelihood of a given isolate to cause a foodborne disease.

RESULTS

We performed whole genome sequencing of 22 B. cereus group dairy isolates, which represented considerable genetic diversity not covered by other isolates characterized to date. Maximum likelihood analysis of these genomes along with 47 reference genomes representing eight validly published species revealed nine phylogenetic clades. Three of these clades were represented by a single species (B. toyonensis -clade V, B. weihenstephanensis - clade VI, B. cytotoxicus - VII), one by two dairy-associated isolates (clade II; representing a putative new species), one by two species (B. mycoides, B. pseudomycoides - clade I) and four by three species (B. cereus, B. thuringiensis, B. anthracis - clades III-a, b, c and IV). Homologues of genes encoding a principal diarrheal enterotoxin (hemolysin BL) were distributed across all, except the B. cytotoxicus clade. Using a lateral flow immunoassay, hemolysin BL was detected in 13 out of 18 isolates that carried hblACD genes. Isolates from clade III-c (which included B. cereus and B. thuringiensis) consistently did not carry hblACD and did not produce hemolysin BL. Isolates from clade IV (B. cereus, B. thuringiensis) consistently carried hblACD and produced hemolysin BL. Compared to others, clade IV was significantly (p = 0.0001) more likely to produce this toxin. Isolates from clade VI (B. weihenstephanensis) carried hblACD homologues, but did not produce hemolysin BL, possibly due to amino acid substitutions in different toxin-encoding genes.

CONCLUSIONS

Our results demonstrate that production of diarrheal enterotoxin hemolysin BL is neither inclusive nor exclusive to B. cereus sensu stricto, and that phylogenetic classification of isolates may be better than taxonomic identification for assessment of B. cereus group isolates risk for causing a diarrheal foodborne disease.

Complete Genome Sequences of Nine Bacillus cereus Group Phages

We report the sequences of nine novel Bacillus cereus group bacteriophages: DIGNKC, Juglone, Nemo, Nigalana, NotTheCreek, Phrodo, SageFayge, Vinny, and Zuko. These bacteriophages are double-stranded DNA-containing Myoviridae isolated from soil samples using B. thuringiensis subsp. kurstaki as the host bacterium.

Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317^T = CCUG 68412^T), Burkholderia hypogeia sp. nov. (type strain LMG 29322^T = CCUG 68407^T), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326^T = CCUG 68403^T), Burkholderia glebae sp. nov. (type strain LMG 29325^T = CCUG 68404^T), Burkholderia pedi sp. nov. (type strain LMG 29323^T = CCUG 68406^T), Burkholderia arationis sp. nov. (type strain LMG 29324^T = CCUG 68405^T), Burkholderia fortuita sp. nov. (type strain LMG 29320^T = CCUG 68409^T), Burkholderia temeraria sp. nov. (type strain LMG 29319^T = CCUG 68410^T), Burkholderia calidae sp. nov. (type strain LMG 29321^T = CCUG 68408^T), Burkholderia concitans sp. nov. (type strain LMG 29315^T = CCUG 68414^T), Burkholderia turbans sp. nov. (type strain LMG 29316^T = CCUG 68413^T), Burkholderia catudaia sp. nov. (type strain LMG 29318^T = CCUG 68411^T) and Burkholderia peredens sp. nov. (type strain LMG 29314^T = CCUG 68415^T). Furthermore, we present emended descriptions of the species Burkholderia sordidicola, Burkholderia zhejiangensis and Burkholderia grimmiae. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and gyrB gene sequences determined in this study are LT158612-LT158624 and LT158625-LT158641, respectively.

Draft Genome Sequences of Four Plant Probiotic Bacillus Strains

Here, we report the whole-genome sequences of four Bacillus strains that exhibit plant probiotic activities. Three of them are the type strains of Bacillus endophyticus, “Bacillus gaemokensis,” and Bacillus trypoxylicola, and the other, Bacillus sp. strain KCTC 13219, should be reclassified into a species belonging to the genus Lysinibacillus.

Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a Potential Biocontrol Agent against Phytopathogens

Bacillus thuringiensis is the most widely known microbial pesticide used in agricultural applications. Herein, we report a draft genome sequence of the endophytic bacterium Bacillus thuringiensis strain KB1, which exhibits antagonism against phytopathogens.