The Complete Genome Sequence of
            <i>Bacillus thuringiensis</i>
            Al Hakam

Challacombe, Jean F.; Altherr, Michael R.; Xie, Gary; Bhotika, Smriti S.; Brown, Nancy; Bruce, David; Campbell, Connie S.; Campbell, Mary L.; Chen, Jin; Chertkov, Olga; Cleland, Cathy; Dimitrijevic, Mira; Doggett, Norman A.; Fawcett, John J.; Glavina, Tijana; Goodwin, Lynne; Green, Lance D.; Han, Cliff; Hill, Karen K.; Hitchcock, P J; Jackson, Paul J.; Keim, Paul; Kewalramani, Avinash Ramesh; Longmire, Jon; Lucas, Susan; Malfatti, Stephanie; Martínez, Diego; McMurry, Kim; Meincke, Linda; Misra, Monica; Moseman, Bernice L.; Mundt, Mark; Munk, A. Christine; Okinaka, Richard T.; Parson-Quintana, B.; Reilly, Lee Philip; Richardson, Paul; Robinson, Donna L.; Saunders, Elizabeth; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Ticknor, Lawrence O.; Wills, Patti L.; Gilna, Paul; Brettin, Thomas

doi:10.1128/jb.00241-07

Cited by 70 publications

(40 citation statements)

References 2 publications

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“…The whole-genome phylogenies of B. cereus agreed well with those from previous studies based on MLST (Priest et al 2004;Tourasse and Kolstø 2008), and we grouped the strains into clades, using the naming scheme of the first published B. cereus MLST description (Table 2; Priest et al 2004). Clade 1 contained B. anthracis, as well as several previously sequenced pathogens and other strains linked to virulence (G924 [Hoffmaster et al 2004], BACI [Klee et al 2010], BALH [Challacombe et al 2007], and BCZK [Rasko et al 2005]). The phylogeny confirmed that the pXO1 plasmid had been acquired on three separate occasions within clade 1 (Klee et al 2010).…”

Section: Resultssupporting

confidence: 70%

Genomic characterization of theBacillus cereussensu lato species: Backdrop to the evolution ofBacillus anthracis

Zwick¹,

Joseph²,

Didelot³

et al. 2012

Genome Res.

151

139

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The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diversity within the species based on the existing multilocus sequence typing scheme. From the resulting data, we called more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees. Although B. anthracis has undergone an ecological shift within the species, its chromosome does not appear to be exceptional on a macroscopic scale compared with close relatives.

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Section: Resultssupporting

confidence: 70%

Genomic characterization of theBacillus cereussensu lato species: Backdrop to the evolution ofBacillus anthracis

Zwick¹,

Joseph²,

Didelot³

et al. 2012

Genome Res.

151

139

View full text Add to dashboard Cite

show abstract

“…Five ORFs encoding putative inosine-preferring NHs have been found in the genomes of B. cereus strain ATCC 14579 and four ORFs have been found in B. cereus strain ATCC 10987 (Ivanova et al, 2003;Rasko et al, 2004). This number is similar to that found in the genome of B. thuringiensis (Challacombe et al, 2007). The disruption of iunH eliminates inosine hydrolase activity in spores and promotes inosine-initiated germination of B. thuringiensis.…”

Section: Discussionsupporting

confidence: 63%

The role of a purine-specific nucleoside hydrolase in spore germination of Bacillus thuringiensis

Liang

Liu

et al. 2008

Microbiology

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A homologous gene (iunH) of a putative nucleoside hydrolase (NH), which had been identified from the exosporia of Bacillus cereus and Bacillus anthracis spores, was cloned from Bacillus thuringiensis subsp. kurstaki. Disruption of iunH did not affect the vegetative growth and sporulation of Bacillus thuringiensis, but promoted both inosine-and adenosine-induced spore germination. The inosine-or adenosine-induced germination rate decreased when the wild-type iunH gene was overexpressed in Bacillus thuringiensis. The iunH gene product was characterized as a purine-specific NH. The kinetic parameters of IunH with inosine as substrate were K m 5399±115 mM, k cat 548.9±8.5 s "1 and k cat /K m 51.. The optimal pH and temperature for IunH were found to be pH 6 and 80 6C. Meanwhile, the specific activity of inosine hydrolase in intact spores of the wild-type strain with inosine as substrate was 2.89±0.23¾10"2 mmol min "1 (mg dry wt). These results indicate that IunH is important in moderating inosine-or adenosine-induced germination of Bacillus thuringiensis spores.

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“…DNA concentrations were measured on a Qubit (Invitrogen, Carlsbad, CA). Based on the reported genome size and number of 16S rRNA genes from B. thuringiensis (18,19) and C. glutamicum (20,21), the DNA extracts were diluted to the same number of 16S rRNA gene copies per unit volume. To estimate the sensitivity of the HRM analysis, the 16S rRNA genes from the two bacteria were mixed in different ratios (see Fig.…”

Section: Soilmentioning

confidence: 99%

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

Hjelmsø

Hansen

Bælum

et al. 2014

Appl Environ Microbiol

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In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.T he increased availability of sequencing facilities and the relative reduction in sequencing costs have made nucleotide sequencing a common tool in research. Despite this, the costs of sequencing and subsequent bioinformatic analyses still represent a substantive expense in many project budgets. A cheap and efficient initial screening of samples before sequencing is therefore an attractive way to discriminate samples and thus potentially reduce costs by focusing the effort on the most interesting ones. Traditional fingerprinting methods such as denaturing gradient gel electrophoresis (DGGE) (1) or terminal restriction fragment length polymorphism (T-RFLP) have previously been used extensively to study diversity changes in complex environmental samples. However, these methods require considerable technical experience and are laborious and time-consuming (2). An alternative to these gel-based methods is desirable, and we suggest here that high-resolution melt (HRM) analysis (3) as a screening tool could provide a superior alternative. The thermal stability of a PCR product is determined by its GC content, sequence length, and primary structure (4). This stability is used in melt curve analysis, in which specific PCR products are denatured under tightly controlled conditions and their melting behavior observed. Melt curve analysis of a PCR product was initially developed in conjunction with the quantitative PCR (qPCR) approach for quantifying a particular amplicon product (4). With this method it is possible to identify nonspecific PCR products or primer dimers. To examine PCR products in further detail, HRM analysis was developed (5). T...

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The Complete Genome Sequence of Bacillus thuringiensis Al Hakam

Cited by 70 publications

References 2 publications

Genomic characterization of theBacillus cereussensu lato species: Backdrop to the evolution ofBacillus anthracis

Genomic characterization of theBacillus cereussensu lato species: Backdrop to the evolution ofBacillus anthracis

The role of a purine-specific nucleoside hydrolase in spore germination of Bacillus thuringiensis

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

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