Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations

Jiménez, Gloria Gallego; Urdiain, Mercedes; Cifuentes, Ana; López-López, Aránzazu; Blanch, Anicet R.; Tamames, Javier; Kämpfer, Peter; Kolstø, Anne‐Brit; Ramón, Daniel; Martínez, Juan F.; Codoñer, Francisco M.; Rosselló‐Móra, Ramon

doi:10.1016/j.syapm.2013.04.008

Cited by 215 publications

(178 citation statements)

References 38 publications

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“…The latter is used extensively as a biological pesticide and is generally not considered harmful for humans. B. anthracis and B. thuringiensis are both members of the B. cereus group and genetically very similar, with most of the disease and host specificity being attributable to their plasmid content (40,41). It has even been suggested that all members of the B. cereus group should be considered to be B. cereus and only subsequently be differentiated by their plasmids (42).…”

Section: Discussionmentioning

confidence: 99%

Benchmarking of Methods for Genomic Taxonomy

et al. 2014

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One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is-that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.

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Section: Discussionmentioning

confidence: 99%

Benchmarking of Methods for Genomic Taxonomy

et al. 2014

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“…Sequences were assembled by using SOAP denovo2.0, and gap filling was performed by using GapCloser 1.05 (Luo et al, 2012). The average nucleotide identity (ANI) values among the strain YIC4027 T and closely related reference strains were calculated using JSpecies software (Richter & Rosselló-Móra, 2009;Jimenez et al, 2013;Saw et al, 2013). Genes were predicted using Glimmer software version 3.0 (Delcher et al, 2007); genes encoding tRNA were predicted by tRNAscan-SE (Lowe & Eddy, 1997); and rRNA genes were predicted by RNAmmer version 1.2 (Lagesen et al, 2007 with E. saheli LMG 7837 T and 81.8 % with E. glycinis 23380 T , which were much lower than the species threshold of 95 % (Goris et al, 2007).…”

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confidence: 99%

Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils

Yan

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A group of Sesbania cannabina rhizobia belonging to four recA genotypes of a novel group was further characterized in comparison with the related Ensifer species. They showed 98.2 to 99.9 % similarities among themselves and 92.9 to 93.3 % similarities with the most related strain Ensifer sojae CCBAU 05684 T in multilocus sequence analysis of recA, atpD and glnII. The genome average nucleotide identity values between representative strain YIC4027 T and the type strains of its closely related species were 81.6 to 88.9 %. Identical symbiotic gene (nodA, nodC and nifH) sequences highly similar with those in other Sesbania-nodulating strains (Rhizobium sp. SIN-1, Neorhizobium huautlense S02 T , Ensifer saheli ORS609 T and Rhizobium sp. IRBG74) were detected. The representative strain YIC4027 T could form effective nodules on its original host Sesbania cannabina, but not on Sophora flavescens, Trifolium repens, Glycine max, Glycyrrhiza uralensis, Phaseolus vulgaris or Medicago sativa. The use of lactulose as sole carbon source, possession of C 13 : 0 2-OH, C 13 : 1 at 12-13, C 15 : 1 iso !9c, C 17 : 0 anteiso and C 18 : 0 iso and absence of C 14 : 0 anteiso, C 15 : 0 anteiso and C 18 : 0 3-OH in fatty acids distinguished the strain YIC4027 T from the type strains of its closely related species. Based on all the analyses mentioned above, we propose a novel species Ensifer alkalisoli sp. nov. and designate YIC4027 T (=HAMBI 3655 T =LMG 29286 T ) as the type strain. The genome size of YIC4027 T is 5.97 Mbp, comprising 5588 predicted genes, and the DNA G+C content is 62.2 mol%.

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“…To begin with, the size and GϩC content of the B. subtilis B7-S genome are 5. (37)(38)(39)(40). Although these novel Bacillus species have been proposed to belong to the Bcg, valid species descriptions still are missing.…”

Section: Discussionmentioning

confidence: 99%

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

Schneider

Hendriksen

Melin

et al. 2015

Appl Environ Microbiol

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e 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. The bacterium Bacillus thuringiensis (Bt) is one of the grand successes in microbial pest control (1). After its first discovery in 1901 and description by Berliner in 1911, the first biocontrol product based on Bt, Sporein, for control of the European corn borer (Ostrinia nubilalis), was commercially available already in 1938 (1). The crystalline, proteinaceous ␦-endotoxins of Bt are formed during sporulation, and their lethal effect is manifested only after larval ingestion of spores or free crystals (2, 3). Bt is a member of the Bacillus cereus group (Bcg), which consists of the Gram-positive rod-shaped spore-forming bacterial species B. cereus, Bt, B. anthracis, B. mycoides, B. pseudomycoides, and B. weihenstephanensis (4,5). However, a multidatatype phylogenetic analysis of Bcg strains isolated from various sample types, including environmental, clinical, food, and diary sources, did not reflect current Bcg taxonomy well. This finding indicated that the phylogeny of this bacterial group is more complicated than reflected by the division into the current six species (6).The bacterium B. thuringiensis serovar israelensis produces toxins active against nematoceran larvae and has been widely used for biocontrol of mosquitoes and black flies (3). B. thuringiensis serovar israelensis was described in 1976 (7) and has been shown to have ...

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Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations

Cited by 215 publications

References 38 publications

Benchmarking of Methods for Genomic Taxonomy

Benchmarking of Methods for Genomic Taxonomy

Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils

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

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