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Hoton FM, Fornelos N, N'guessan E, Hu X, Swiecicka I, Dierick K, Jääskeläinen E, Salkinoja-Salonen M, Mahillon J. Family portrait of Bacillus cereus and Bacillus weihenstephanensis cereulide-producing strains. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:177-83. [PMID: 23765791 DOI: 10.1111/j.1758-2229.2009.00028.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Two thousand Bacillus cereus sensu lato isolates from food and environmental matrices were screened by PCR for the presence of cereulide-producing strains. This survey identified 73 potential emetic strains, most of which originated from non-random food and clinical samplings. None of the 460 Bacillus thuringiensis, Bacillus mycoides and Bacillus pseudomycoides strains were PCR-positive for the cereulide genetic determinants. The chromosomal and extrachromosomal gene pool diversity of a subset of 30 cereulide-producing strains was then assessed using multilocus sequence typing, large plasmid gel electrophoresis and Southern blot hybridization. The strain toxicity on boar sperm and cereulide production were also analysed. The most striking observation was the identification of two distinct clusters of cereulide-producing strains, with members of the second group (cluster II) identified as psychrotolerant B. weihenstephanensis able to grow at 8°C. Moreover, the location of the cereulide genetic determinants was shown to vary depending on the strain, indicating a probable genomic mobility.
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Affiliation(s)
- Florence M Hoton
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud, 2/12, B-1348 Louvain-la-Neuve, Belgium. Department of Microbiology, University of Bialystok, 20B Swierkowa Street, PL15-950 Bialystok, Poland. Institute of Public Health, Bacteriology, 14 Rue Juliette Wijtsman, B-1050 Brussels, Belgium. Department of Applied Chemistry and Microbiology, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014 Helsinki, Finland
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Porwal S, Lal S, Cheema S, Kalia VC. Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One 2009; 4:e4438. [PMID: 19212464 PMCID: PMC2639701 DOI: 10.1371/journal.pone.0004438] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/18/2008] [Indexed: 11/18/2022] Open
Abstract
Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.
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Affiliation(s)
- Shalini Porwal
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
- Department of Biotechnology, University of Pune, Pune, India
| | - Sadhana Lal
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
| | - Simrita Cheema
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
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Manzano M, Giusto C, Iacumin L, Cantoni C, Comi G. Molecular methods to evaluate biodiversity in Bacillus cereus and Bacillus thuringiensis strains from different origins. Food Microbiol 2009; 26:259-64. [PMID: 19269566 DOI: 10.1016/j.fm.2008.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 12/29/2008] [Accepted: 12/30/2008] [Indexed: 10/21/2022]
Abstract
The spore-forming genus Bacillus includes species of industrial, clinical and environmental significance. The possibility of differentiating between Bacillus cereus and Bacillus thuringiensis, toxin producers associated with illness, is a real need in monitoring potentially contaminated foods to understand the real distribution of B. cereus/B. thuringiensis in different outbreak cases. As the use of DNA comparison obtains clearer results than classical microbiological methods in distinguishing B. cereus from B. thuringiensis in this work PCR-TTGE (Temporal Temperature Gradient gel Electrophoresis), rep-PCR and RAPD-PCR methods have been compared to assess the intra- and inter-specific variability of B. cereus and B. thuringiensis. 80 strains of B. cereus and B. thuringiensis isolated from food, patients and pesticides were analyzed using a gyrB gene DNA sequence in TTGE; primer M13 in the RAPD-PCR and primers REP1DT and REP2DT in the rep-PCR methods. A widespread distribution of the electrophoretic profiles was obtained either for B. cereus or for B. thuringiensis using TTGE. rep-PCR and RAPD-PCR were not always able to group strains from the same origin or belonging to the same species. The fingerprints obtained with the rep- and RAPD-PCR methods confirm the high intraspecific variability present in B. cereus and B. thuringiensis indicating the difficulty to discriminate between these two species in outbreak cases.
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Affiliation(s)
- Marisa Manzano
- Dipartimento di Scienze degli Alimenti, Facoltà di Agraria, Università di Udine, 33100 Udine, Italy.
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Wang DB, Bi LJ, Zhang ZP, Chen YY, Yang RF, Wei HP, Zhou YF, Zhang XE. Label-free detection of B. anthracis spores using a surface plasmon resonance biosensor. Analyst 2009; 134:738-42. [DOI: 10.1039/b813038h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Brusetti L, Malkhazova I, Gtari M, Tamagnini I, Borin S, Merabishvili M, Chanishvili N, Mora D, Cappitelli F, Daffonchio D. Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography. BMC Microbiol 2008; 8:220. [PMID: 19077307 PMCID: PMC2625358 DOI: 10.1186/1471-2180-8-220] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 12/15/2008] [Indexed: 11/30/2022] Open
Abstract
Background BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (Bacillus cereus; Escherichia coli; isolates of the family Geodermatophilaceae). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of Modestobacter multiseptatus isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of Streptococcus thermophilus isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia. Results Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (p < 0.004 and p < 0.00003) and in capillary electrophoresis (compared only with HEX, p < 2 × 10-7). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped M. multiseptatus strains according to the microsite of isolation and S. thermophilus strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used. Conclusion F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.
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Affiliation(s)
- Lorenzo Brusetti
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, Milan, Italy.
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Raddadi N, Belaouis A, Tamagnini I, Hansen BM, Hendriksen NB, Boudabous A, Cherif A, Daffonchio D. Characterization of polyvalent and safe Bacillus thuringiensis
strains with potential use for biocontrol. J Basic Microbiol 2008; 49:293-303. [DOI: 10.1002/jobm.200800182] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Brillard J, Susanna K, Michaud C, Dargaignaratz C, Gohar M, Nielsen-Leroux C, Ramarao N, Kolstø AB, Nguyen-the C, Lereclus D, Broussolle V. The YvfTU two-component system is involved in plcR expression in Bacillus cereus. BMC Microbiol 2008; 8:183. [PMID: 18925929 PMCID: PMC2588459 DOI: 10.1186/1471-2180-8-183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 10/16/2008] [Indexed: 11/30/2022] Open
Abstract
Background Most extracellular virulence factors produced by Bacillus cereus are regulated by the pleiotropic transcriptional activator PlcR. Among strains belonging to the B. cereus group, the plcR gene is always located in the vicinity of genes encoding the YvfTU two-component system. The putative role of YvfTU in the expression of the PlcR regulon was therefore investigated. Results Expression of the plcR gene was monitored using a transcriptional fusion with a lacZ reporter gene in a yvfTU mutant and in its B. cereus ATCC 14579 parental strain. Two hours after the onset of the stationary phase, a stage at which the PlcR regulon is highly expressed, the plcR expression in the yvfTU mutant was only 50% of that of its parental strain. In addition to the reduced plcR expression in the yvfTU mutant, a few members of the PlcR regulon showed a differential expression, as revealed by transcriptomic and proteomic analyses. The virulence of the yvfTU mutant in a Galleria mellonella insect model was slightly lower than that of the parental strain. Conclusion The YvfTU two-component system is not required for the expression of most of the virulence factors belonging to the PlcR regulon. However, YvfTU is involved in expression of plcR, a major regulator of virulence in B. cereus.
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Affiliation(s)
- Julien Brillard
- UMR408, Sécurité et Qualité des Produits d'Origine Végétale, INRA, Université d'Avignon, F-84000 Avignon, France.
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Zhou WW, Zhang LX, Zhang B, Wang F, Liang ZH, Niu TG. Isolation and characterization of ZH14 with antiviral activity againstTobacco mosaic virus. Can J Microbiol 2008; 54:441-9. [DOI: 10.1139/w08-026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A large number of bacteria were isolated from plant samples and screened for antiviral activity against the Tobacco mosaic virus (TMV). The bacterium ZH14, which was isolated from Chinese Anxi oolong tea, secreted the antiviral substances, having 94.2% virus inhibition when the bacterial culture filtrate and TMV extract were mixed at a ratio of 1:1. The ZH14 strain is a gram-positive, spore-forming rod and has the ability to degrade ribonucleic acid. Based on its effectiveness on virus inhibition, ZH14 was selected for characterization and was identified as a strain of the Bacillus cereus group based on phenotypic tests and comparative analysis of its 16S rDNA sequence. At the same time, we determined the antiviral product of ZH14 as an extracellular protein with high molecular mass, having an optimum temperature of 15–60 °C and an optimum pH of 6–10. Hence, the ZH14 strain and its culture filtrate have potential application in controlling plant diseases caused by TMV.
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Affiliation(s)
- Wen-Wen Zhou
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Li-Xiang Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Bin Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Fei Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Zhi-Hong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Tian-Gui Niu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
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Bizzarri MF, Prabhakar A, Bishop AH. Multiple-locus sequence typing analysis of Bacillus thuringiensis recovered from the phylloplane of clover (Trifolium hybridum) in vegetative form. MICROBIAL ECOLOGY 2008; 55:619-25. [PMID: 17682816 DOI: 10.1007/s00248-007-9305-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 06/18/2007] [Accepted: 07/15/2007] [Indexed: 05/16/2023]
Abstract
Abstract The chromosomal genotype, as judged by multi locus sequence typing, and the episomal genotype, as judged by plasmid profile and cry gene content, were analyzed for a collection of strains of Bacillus thuringiensis. These had been recovered in vegetative form over a period of several months from the leaves of a small plot of clover (Trifolium hybridum). A clonal population structure was indicated, although greater variation in sequence types (STs) was discovered than in previous collections of B. cereus/B. thuringiensis. Isolates taken at the same time had quite different genotypes, whereas those of identical genotypes were recovered at different times. The profiles of plasmid content and cry genes generally bore no relation to each other nor to the STs. Evidently, although relatively little recombination was occurring in the seven chromosomal genes analyzed, a great deal of conjugal transfer, and perhaps recombination, was occurring involving plasmids. A clinical diarrheal isolate of B. cereus and the commercial biopesticide strain HD-1 of B. thuringiensis, both included as out-groups, were found to have very similar STs. This further emphasizes the role of episomal elements in the characteristics and differentiation of these two species.
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Affiliation(s)
- M F Bizzarri
- School of Science, University of Greenwich, Chatham Maritime ME4 4TB, UK
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60
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Gtari M, Brusetti L, Cherif A, Boudabous A, Daffonchio D. Heteroduplex structures in 16S-23S rRNA intergenic transcribed spacer PCR products reveal ribosomal interoperonic polymorphisms within single Frankia strains. J Appl Microbiol 2008; 103:1031-40. [PMID: 17897207 DOI: 10.1111/j.1365-2672.2007.03329.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Detection of polymorphisms in intergenic transcribed spacer (ITS) 16S-23S rRNA within single Frankia strains. METHODS AND RESULTS Polymorphisms in the 16S-23S rRNA ITS were investigated in single-colony subcultures of seven Frankia isolates. Multiple ITS-polymerase chain reaction (PCR) bands were detected solely in isolates BMG5.5 and BMG5.11. The slow-migrating bands in the ITS-PCR agarose gel electrophoresis profiles of the isolates were revealed to be heteroduplexes on the basis of their migration shift in different electrophoretic matrices, southern hybridization and the single-strand DNA mung bean endonuclease digestion. Laser-scanned capillary electrophoresis detected two ITS-PCR fragments differing in length by three and six nucleotide insertions/deletions in strains BMG5.5 and BMG5.11, respectively. Sequence analysis of the cloned ITS showed that in strain BMG5.5 the two ITS differed by the presence of three to four copies of the 3-bp tandem repeat 5'-TGG-3'. In strain BMG5.11, the two ITS differed by the presence of two to three copies of the 6-bp tandem repeat 5'-CTTGGG-3'. CONCLUSIONS We demonstrate the occurrence of ITS 16S-23S rRNa polymorphisms within single Frankia strains. SIGNIFICANCE AND IMPACT OF THE STUDY We reported the occurrence of ITS 16S-23S rRNA polymorphisms within single Frankia strains from Elaeagnus host group recognized as the more flexible strains within Frankia genus. Furthermore, we underscored the applied interest of strains BMG5.11 and BMG5.5 in future ecological studies using ITS 16S-23S rRNA as molecular marker.
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Affiliation(s)
- M Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Département de Biologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 Tunis, Tunisia.
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Callahan C, Castanha ER, Fox KF, Fox A. The Bacillus cereus containing sub-branch most closely related to Bacillus anthracis, have single amino acid substitutions in small acid-soluble proteins, while remaining sub-branches are more variable. Mol Cell Probes 2008; 22:207-11. [PMID: 18439962 DOI: 10.1016/j.mcp.2007.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 11/21/2007] [Indexed: 10/22/2022]
Abstract
Hoffmaster et al. [Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, Marston CK, et al. Identification of anthrax toxin genes in Bacillus cereus associated with illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 2004;101:8449-54; Hoffmaster AR, Hill KK, Gee JE, Marston CK, De BK, Popovic T, et al. Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol 2006;44:3352-60] phylogenetically divided Bacillus cereus strains into 10 branches by amplified fragment length polymorphism (AFLP) with Branch F including all Bacillus anthracis strains and pneumonia-causing strains of B. cereus. There are four sub-branches within Branch F, referred to here as F1-A, F1-B, F2-A and F2-B. The B. anthracis strains are found within sub-branch F1-B. Concerning, the currently available B. cereus pneumonia-causing isolates, one was found to categorize within sub-branch F1-B and two within F2-B. In the following work the sequence variation between B. cereus strains was determined by MALDI-TOF MS and MS-MS for each strain of B. cereus in Branch F. ESI-MS was performed on selected strains for confirmation. Small acid-soluble proteins (SASPs) of B. cereus strains found in F1-B showed a single amino acid substitution, while strains in the other three sub-branches were more variable generally showing one or two amino acid substitutions. The single substitutions always occurred in the C-terminus. Double substitutions occurred in both N and C termini. Of the pneumonia-causing strains, one exhibited a single amino acid substitution, while the other two exhibited a two amino acid substitution.
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Affiliation(s)
- Courtney Callahan
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, 6311 Garners Ferry Road, Columbia, SC 29208, USA.
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Bavykin SG, Mikhailovich VM, Zakharyev VM, Lysov YP, Kelly JJ, Alferov OS, Gavin IM, Kukhtin AV, Jackman J, Stahl DA, Chandler D, Mirzabekov AD. Discrimination of Bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray. Chem Biol Interact 2008; 171:212-35. [PMID: 17950718 PMCID: PMC3188417 DOI: 10.1016/j.cbi.2007.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 08/23/2007] [Accepted: 09/03/2007] [Indexed: 10/22/2022]
Abstract
Analysis of 16S rRNA sequences is a commonly used method for the identification and discrimination of microorganisms. However, the high similarity of 16S and 23S rRNA sequences of Bacillus cereus group organisms (up to 99-100%) and repeatedly failed attempts to develop molecular typing systems that would use DNA sequences to discriminate between species within this group have resulted in several suggestions to consider B. cereus and B. thuringiensis, or these two species together with B. anthracis, as one species. Recently, we divided the B. cereus group into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, based on 16S rRNA, 23S rRNA and gyrB gene sequences and identified subgroup-specific makers in each of these three genes. Here we for the first time demonstrated discrimination of these seven subgroups, including subgroup Anthracis, with a 3D gel element microarray of oligonucleotide probes targeting 16S and 23S rRNA markers. This is the first microarray enabled identification of B. anthracis and discrimination of these seven subgroups in pure cell cultures and in environmental samples using rRNA sequences. The microarray bearing perfect match/mismatch (p/mm) probe pairs was specific enough to discriminate single nucleotide polymorphisms (SNPs) and was able to identify targeted organisms in 5min. We also demonstrated the ability of the microarray to determine subgroup affiliations for B. cereus group isolates without rRNA sequencing. Correlation of these seven subgroups with groupings based on multilocus sequence typing (MLST), fluorescent amplified fragment length polymorphism analysis (AFLP) and multilocus enzyme electrophoresis (MME) analysis of a wide spectrum of different genes, and the demonstration of subgroup-specific differences in toxin profiles, psychrotolerance, and the ability to harbor some plasmids, suggest that these seven subgroups are not based solely on neutral genomic polymorphisms, but instead reflect differences in both the genotypes and phenotypes of the B. cereus group organisms.
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MESH Headings
- Bacillus anthracis/genetics
- Bacillus anthracis/isolation & purification
- Base Sequence
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Polymorphism, Single Nucleotide
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/genetics
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- Sergei G Bavykin
- Center for Environmental and Security Science and Technology, Argonne National Laboratory, Argonne, IL 60439, USA.
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Bacillus thuringiensis beyond insect biocontrol: plant growth promotion and biosafety of polyvalent strains. ANN MICROBIOL 2007. [DOI: 10.1007/bf03175344] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Effects of wildfire and harvest disturbances on forest soil bacterial communities. Appl Environ Microbiol 2007; 74:216-24. [PMID: 18024684 DOI: 10.1128/aem.01355-07] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH(4)(+) and NO(3)(-) due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.
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Cherif A, Ettoumi B, Raddadi N, Daffonchio D, Boudabous A. Genomic diversity and relationship of Bacillus thuringiensis and Bacillus cereus by multi-REP-PCR fingerprinting. Can J Microbiol 2007; 53:343-50. [PMID: 17538643 DOI: 10.1139/w06-129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomic diversity and relationship among 56 Bacillus thuringiensis and Bacillus cereus type strains were investigated by multi-REP-PCR fingerprinting consisting of three PCR reactions targeting the enterobacterial ERIC1 and ERIC2 and the streptococcal BOXA1R consensus sequences. A total of 113 polymorphic bands were generated in the REP-PCR profiles that allowed tracing of a single dendrogram with three major groups. Bacillus cereus strains clustered together in the A and B groups. Most of the B. thuringiensis strains clustered in group C, which included groups of serovars with a within-group similarity higher than 40% as follows: darmstadiensis, israelensis, and morrisoni; aizawai, kenyae, pakistani, and thompsoni; canadensis, entomocidus, galleriae, kurstaki, and tolworthi; alesti, dendrolimus, and kurstaki; and finitimus, sotto, and thuringiensis. Multi-REP-PCR fingerprinting clustered B. thuringiensis serovars in agreement with previously developed multilocus sequence typing schemes, indicating that it represents a rapid shortcut for addressing the genetic relationship of unknown strains with the major known serovars.
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Affiliation(s)
- Ameur Cherif
- Laboratoire miroorganismes et biomolécules actives, Faculté des sciences de Tunis, Campus Universitaire, 2092 Tunis, Tunisia.
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Characterization of a small PlcR-regulated gene co-expressed with cereolysin O. BMC Microbiol 2007; 7:52. [PMID: 17555563 PMCID: PMC1913518 DOI: 10.1186/1471-2180-7-52] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 06/07/2007] [Indexed: 11/22/2022] Open
Abstract
Background In the human pathogen Bacillus cereus, the expression of most extracellular virulence factors is controlled by the transcriptional activator PlcR. Among these virulence factors, cereolysin O (Clo) is an haemolysin belonging to the cholesterol-dependant cytolysins, a protein family extensively studied in Gram-positive bacteria. Results In the genomes of bacteria belonging to the B. cereus group, including Bacillus anthracis and Bacillus thuringiensis, a small gene encoding a 26-amino acid peptide was present in multicopy. One copy was always found upstream from the gene encoding Clo. In B. cereus ATCC 14579, the small gene and the clo gene are co-transcribed. Transcriptional fusions showed that the three paralogues identified in this strain were expressed in a PlcR-dependent manner. We propose to name these peptides Spp for small PlcR-regulated peptides. We show that a synthetic peptide corresponding to the deduced product of the spp genes displayed antibacterial activity. Conclusion The co-expression of spp, a small PlcR-regulated multicopy gene with clo suggests a yet unidentified relationship between Spp and the cholesterol-dependent cytolysin in bacteria belonging to the B.cereus group.
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68
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Vilas-Bôas GT, Peruca APS, Arantes OMN. Biology and taxonomy ofBacillus cereus,Bacillus anthracis, andBacillus thuringiensis. Can J Microbiol 2007; 53:673-87. [PMID: 17668027 DOI: 10.1139/w07-029] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three species of the Bacillus cereus group (Bacillus cereus, Bacillus anthracis , and Bacillus thuringiensis ) have a marked impact on human activity. Bacillus cereus and B. anthracis are important pathogens of mammals, including humans, and B. thuringiensis is extensively used in the biological control of insects. The microbiological, biochemical, and genetic characteristics of these three species are reviewed, together with a discussion of several genomic studies conducted on strains of B. cereus group. Using bacterial systematic concepts, we speculate that to understand the taxonomic relationship within this group of bacteria, special attention should be devoted also to the ecology and the population genetics of these species.
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Affiliation(s)
- G T Vilas-Bôas
- Departamento de Biologia Geral, CCB, UEL, CP 6001, Londrina/PR, 86051-990, Brazil.
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69
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Castanha ER, Vestal M, Hattan S, Fox A, Fox KF, Dickinson D. Bacillus cereus strains fall into two clusters (one closely and one more distantly related) to Bacillus anthracis according to amino acid substitutions in small acid-soluble proteins as determined by tandem mass spectrometry. Mol Cell Probes 2007; 21:190-201. [PMID: 17197155 DOI: 10.1016/j.mcp.2006.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 11/10/2006] [Accepted: 11/10/2006] [Indexed: 10/23/2022]
Abstract
Small acid-soluble proteins (SASPs) are located in the core region of Bacillus spores and have been previously demonstrated as reliable biomarkers for differentiating Bacillus anthracis and Bacillus cereus. Using MS and MS-MS analysis of SASPs further phylogenetic correlations among B. anthracis and B. cereus strains are described here. ESI was demonstrated to be a more comprehensive method, allowing for the analysis of intact proteins in both MS and MS-MS mode, thus providing molecular weight (MW) and sequence information in a single analysis, and requiring almost no sample preparation. MALDI MS was used for determination of MW of intact proteins; however, MS-MS analysis can only be achieved after enzymatic digestion of these proteins. It was demonstrated that the combination of the two different approaches provides confirmatory and complementary information, allowing for unambiguous protein characterization and sequencing. This study established that B. cereus strains fall into two clusters (one closely and one more distantly related) to B. anthracis as exhibited by amino acid substitutions. The closely related cluster was characterized by a beta-SASP with a single amino acid substitution, localized either close to the C terminus (phenylalanine-->tyrosine, 16 masses change) or close to the N terminus (serine-->alanine serine, also 16 masses change). The more distantly related cluster displayed both amino acid substitutions (32 masses change). One strain of B. cereus isolated from a patient with severe pneumonia (an anthrax-like disease) fell into the more distantly related cluster implying that pathogenicity and phylogenicity are not necessarily correlated features. Unlike PCR and DNA sequencing, protein sequence variation assessed by ESI MS-MS, essentially occurs in real-time, and involves simply extracting the protein and injecting into the instrument for analysis.
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Affiliation(s)
- Elisangela R Castanha
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
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70
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Halpern M, Raats D, Lev-Yadun S. Plant biological warfare: thorns inject pathogenic bacteria into herbivores. Environ Microbiol 2007; 9:584-92. [PMID: 17298359 DOI: 10.1111/j.1462-2920.2006.01174.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Thorns, spines and prickles are among the rich arsenal of antiherbivore defence mechanisms that plants have evolved. Many of these thorns are aposematic, that is, marked by various types of warning coloration. This coloration was recently proposed to deter large herbivores. Yet, the mechanical defence provided by thorns against large herbivores might be only the tip of the iceberg in a much more complicated story. Here we present evidence that thorns harbour an array of pathogenic bacteria that are much more dangerous to herbivores than the painful mechanical wounding by the thorns. Pathogenic bacteria like Clostridium perfringens, the causative agent of the life-threatening gas gangrene, and others, were isolated and identified from date palm (with green-yellow-black aposematic spines) and common hawthorn (with red aposematic thorns). These thorn-inhabiting bacteria have a considerable potential role in antiherbivory, and may have uniquely contributed to the common evolution of aposematism (warning coloration) in thorny plants.
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Affiliation(s)
- Malka Halpern
- Department of Biology, Faculty of Science and Science Education, University of Haifa - Oranim, Tivon 36006, Israel.
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71
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Zhong W, Shou Y, Yoshida TM, Marrone BL. Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis by using pulsed-field gel electrophoresis. Appl Environ Microbiol 2007; 73:3446-9. [PMID: 17400781 PMCID: PMC1907107 DOI: 10.1128/aem.02478-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A pulsed-field gel electrophoresis (PFGE) method was developed for discriminating Bacillus anthracis from B. cereus and B. thuringiensis. A worldwide collection of 25 B. anthracis isolates showed high-profile homology, and these isolates were unambiguously distinguished from B. cereus and B. thuringiensis isolates by cluster analysis of the whole-genome macrorestriction enzyme digestion patterns generated by NotI.
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Affiliation(s)
- Wenwan Zhong
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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72
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Esterase electrophoretic polymorphism ofBacillus thuringiensis andBacillus cereus reference strains. ANN MICROBIOL 2007. [DOI: 10.1007/bf03175045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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73
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Sue D, Hoffmaster AR, Popovic T, Wilkins PP. Capsule production in Bacillus cereus strains associated with severe pneumonia. J Clin Microbiol 2006; 44:3426-8. [PMID: 16954292 PMCID: PMC1594739 DOI: 10.1128/jcm.00873-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified three encapsulated Bacillus cereus strains, isolated from patients with severe pneumonia, in a collection of B. cereus isolates associated with human illness. We found that the extent of capsule expression was influenced by culturing conditions. Our findings highlight consequent clinical and laboratory diagnostic challenges posed by such isolates.
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Affiliation(s)
- David Sue
- Bacterial Zoonoses Branch, Division of Foodborne, Bacterial and Mycotic Diseases, National Center for Zoonotic Vector-borne and Enteric Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia 30333, USA
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74
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Merabishvili M, Natidze M, Rigvava S, Brusetti L, Raddadi N, Borin S, Chanishvili N, Tediashvili M, Sharp R, Barbeschi M, Visca P, Daffonchio D. Diversity of Bacillus anthracis strains in Georgia and of vaccine strains from the former Soviet Union. Appl Environ Microbiol 2006; 72:5631-6. [PMID: 16885320 PMCID: PMC1538727 DOI: 10.1128/aem.00440-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the Bacillus anthracis strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.
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Affiliation(s)
- Maya Merabishvili
- The G.Eliava Institute of Bacteriophage, Microbiology and Virology, 0160 Tbilisi, Georgia
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75
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de Been M, Francke C, Moezelaar R, Abee T, Siezen RJ. Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis. Microbiology (Reading) 2006; 152:3035-3048. [PMID: 17005984 DOI: 10.1099/mic.0.29137-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Members of the Bacillus cereus group are ubiquitously present in the environment and can adapt to a wide range of environmental fluctuations. In bacteria, these adaptive responses are generally mediated by two-component signal transduction systems (TCSs), which consist of a histidine kinase (HK) and its cognate response regulator (RR). With the use of in silico techniques, a complete set of HKs and RRs was recovered from eight completely sequenced B. cereus group genomes. By applying a bidirectional best-hits method combined with gene neighbourhood analysis, a footprint of these proteins was made. Around 40 HK-RR gene pairs were detected in each member of the B. cereus group. In addition, each member contained many HK and RR genes not encoded in pairs (‘orphans’). Classification of HKs and RRs based on their enzymic domains together with the analysis of two neighbour-joining trees of these domains revealed putative interaction partners for most of the ‘orphans’. Putative biological functions, including involvement in virulence and host–microbe interactions, were predicted for the B. cereus group HKs and RRs by comparing them with those of B. subtilis and other micro-organisms. Remarkably, B. anthracis appeared to lack specific HKs and RRs and was found to contain many truncated, putatively non-functional, HK and RR genes. It is hypothesized that specialization of B. anthracis as a pathogen could have reduced the range of environmental stimuli to which it is exposed. This may have rendered some of its TCSs obsolete, ultimately resulting in the deletion of some HK and RR genes.
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Affiliation(s)
- Mark de Been
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University, PO Box 9101, 6500 HB Nijmegen, The Netherlands
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
| | - Christof Francke
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University, PO Box 9101, 6500 HB Nijmegen, The Netherlands
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
| | - Roy Moezelaar
- Food Technology Centre, Wageningen University and Research Centre, Wageningen, The Netherlands
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
| | - Roland J Siezen
- NIZO food research BV, Ede, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University, PO Box 9101, 6500 HB Nijmegen, The Netherlands
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
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76
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Swiecicka I, Mahillon J. Diversity of commensal Bacillus cereus sensu lato isolated from the common sow bug (Porcellio scaber, Isopoda). FEMS Microbiol Ecol 2006; 56:132-40. [PMID: 16542411 DOI: 10.1111/j.1574-6941.2006.00063.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although Bacillus cereus sensu lato are important both from an ecological and an economical point of view, little is known about their population structure, ecology, and relationships with other organisms. In the present work, the genotypic similarity of arthropod-borne B. cereus s.l. isolates, and their symbiotic relationship with the host are assessed. Bacilli of this group were recovered from the digestive tracts of sow bugs (Porcellio scaber) collected in three closely located sites. Their genotypic diversity was investigated using pulse-field gel electrophoresis (PFGE) following the whole-genome DNA digestions with NotI and AscI, and PCR amplification of virulence genes. The majority of the sow-bug Bacillus cereus sensu stricto isolates originating from the same but also from different sites displayed identical PFGE patterns, virulence gene content and enterotoxicity, indicating strong genetic and genomic relationships. The sow-bug Bacillus mycoides/Bacillus pseudomycoides strains displayed a higher diversity. The isopod-B. cereus s.l. relationship was also evaluated using antibiotic-resistant derivatives of B. cereus s.s., B. mycoides/B. pseudomycoides and Bacillus thuringiensis reintroduced into sow bugs. Both spores and vegetative cells of B. cereus s.l. were recovered from sow bugs over a 30-day period, strongly suggesting that these bacteria are natural residents of terrestrial isopods.
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Affiliation(s)
- Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland.
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77
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Sorokin A, Candelon B, Guilloux K, Galleron N, Wackerow-Kouzova N, Ehrlich SD, Bourguet D, Sanchis V. Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains. Appl Environ Microbiol 2006; 72:1569-78. [PMID: 16461712 PMCID: PMC1392946 DOI: 10.1128/aem.72.2.1569-1578.2006] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used multilocus sequence typing (MLST) to characterize phylogenetic relationships for a collection of Bacillus cereus group strains isolated from forest soil in the Paris area during a mild winter. This collection contains multiple strains isolated from the same soil sample and strains isolated from samples from different sites. We characterized 115 strains of this collection and 19 other strains based on the sequences of the clpC, dinB, gdpD, panC, purF, and yhfL loci. The number of alleles ranged from 36 to 53, and a total of 93 allelic profiles or sequence types were distinguished. We identified three major strain clusters-C, T, and W-based on the comparison of individual gene sequences or concatenated sequences. Some less representative clusters and subclusters were also distinguished. Analysis of the MLST data using the concept of clonal complexes led to the identification of two, five, and three such groups in clusters C, T, and W, respectively. Some of the forest isolates were closely related to independently isolated psychrotrophic strains. Systematic testing of the strains of this collection showed that almost all the strains that were able to grow at a low temperature (6 degrees C) belonged to cluster W. Most of these strains, including three independently isolated strains, belong to two clonal complexes and are therefore very closely related genetically. These clonal complexes represent strains corresponding to the previously identified species Bacillus weihenstephanensis. Most of the other strains of our collection, including some from the W cluster, are not psychrotrophic. B. weihenstephanensis (cluster W) strains appear to comprise an effectively sexual population, whereas Bacillus thuringiensis (cluster T) and B. cereus (cluster C) have clonal population structures.
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Affiliation(s)
- Alexei Sorokin
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France.
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78
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Daffonchio D, Raddadi N, Merabishvili M, Cherif A, Carmagnola L, Brusetti L, Rizzi A, Chanishvili N, Visca P, Sharp R, Borin S. Strategy for identification of Bacillus cereus and Bacillus thuringiensis strains closely related to Bacillus anthracis. Appl Environ Microbiol 2006; 72:1295-301. [PMID: 16461679 PMCID: PMC1392923 DOI: 10.1128/aem.72.2.1295-1301.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus cereus strains that are genetically closely related to B. anthracis can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these "near neighbors" are of great interest for the study of B. anthracis virulence mechanisms, as well as to prevent the use of such strains for B. anthracis-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of B. anthracis based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of B. anthracis. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of B. anthracis was screened in 126 B. cereus group strains of different origin. Two B. cereus strains and one B. thuringiensis strain showed RSI-PCR profiles identical to that of B. anthracis. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to B. anthracis. The strict relationship with B. anthracis was confirmed by multilocus sequence typing (MLST) of four other independent loci: cerA, plcR, AC-390, and SG-749. The relationship to B. anthracis of the three strains described by MLST was comparable and even higher to that of four B. cereus strains associated with periodontitis in humans and previously reported as the closest known strains to B. anthracis. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to B. anthracis.
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Affiliation(s)
- Daniele Daffonchio
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy.
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79
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Raddadi N, Cherif A, Mora D, Brusetti L, Borin S, Boudabous A, Daffonchio D. The autolytic phenotype of the Bacillus cereus group. J Appl Microbiol 2006; 99:1070-81. [PMID: 16238737 DOI: 10.1111/j.1365-2672.2005.02713.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM To determine the autolytic phenotype of five species in the Bacillus cereus group. METHODS AND RESULTS The autolytic rate of 96 strains belonging to five species in the B. cereus group was examined under starvation conditions at pH 6, 6.5 and 8.5 in different buffers. The autolytic rate was strain-dependent with a wide variability at pH 6, but higher and more uniform at pH 6.5. At pH 8.5, and respect to the extent of autolysis at pH 6.5, it was relatively low for most of the strains with the lowest values between 13 and 52% in Bacillus mycoides and Bacillus pseudomycoides. Peptidoglycan hydrolase patterns evaluated by renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis using cells of Bacillus thuringiensis ssp. tolworthi HD125 as an indicator, revealed complex profiles with lytic bands of about 90, 63, 46, 41, 38, 32, 28 and 25 kDa in B. cereus, B. thuringiensis and Bacillus weihenstephanensis. Bacillus mycoides and B. pseudomycoides had simpler profiles with lytic bands of 63, 46 and 38 kDa. Changes in the autolytic pattern were observed for cells harvested at the stationary phase of growth (72 h) showing an increase in the intensity of the 25 kDa band in the case of B. cereus, B. thuringiensis and B. weihenstephanensis, while no changes were observed for B. mycoides. Using Micrococcus lysodeicticus and Listeria monocytogenes as indicators lytic activity was retained by proteins of 63, 46, 38, 32 and 25 kDa and a new one of about 20 kDa in B. mycoides. Growth in the different media did not affect the autolytic pattern. NaCl abolished the activity of all the peptidoglycan hydrolases except for those of B. mycoides and B. weihenstephanensis. Lytic activity was retained in the presence of MgCl(2), MnCl(2) and EDTA and increased at basic pH. CONCLUSIONS Bacillus cereus/B. thuringiensis/B. weihenstephanensis showed a high extent of autolysis around neutral pH, even though they presented relatively complex autolysin profiles at alkaline pH. Bacillus mycoides/B. pseudomycoides had a higher extent of autolysis at acidic pH and a simpler autolysin pattern. SIGNIFICANCE AND IMPACT OF THE STUDY Information on the autolytic phenotype expand the phenotypic characterization of the different species in the B. cereus group.
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Affiliation(s)
- N Raddadi
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi, Milano, Italy
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80
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Zolock RA, Li G, Bleckmann C, Burggraf L, Fuller DC. Atomic force microscopy of Bacillus spore surface morphology. Micron 2005; 37:363-9. [PMID: 16376084 DOI: 10.1016/j.micron.2005.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2005] [Revised: 11/03/2005] [Accepted: 11/04/2005] [Indexed: 12/01/2022]
Abstract
Bacillus spore surface morphology was imaged with atomic force microscopy (AFM) to determine if characteristic surface features could be used to distinguish between four closely related species; Bacillus anthracis Sterne strain, Bacillus thuringiensis var. kurstaki, Bacillus cereus strain 569, and Bacillus globigii var. niger. AFM surface height images showed an irregular topography across the curved upper surface of the spores. Phase images showed a superficial grain structure with different levels of phase contrast and significant differences in average surface morphologies among the four species. Although spores of the same species showed similarities, there was significant variability within each species. Overall, AFM revealed that spore surface morphology is rich with information, which can be used to distinguish a sample of about 20 spores from a similar number of spores of closely related species. Statistical analysis of spore morphology from a combination of amplitude and phase images for a small sample allows differentiation between, B. anthracis and its close relatives.
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Affiliation(s)
- Ruth A Zolock
- Department of Systems and Engineering Management, Air Force Institute of Technology, 2950 Hobson Way, Bldg 640, Wright-Patterson AFB, OH 45433-7765, USA
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81
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Edwards KA, Clancy HA, Baeumner AJ. Bacillus anthracis: toxicology, epidemiology and current rapid-detection methods. Anal Bioanal Chem 2005; 384:73-84. [PMID: 16283259 DOI: 10.1007/s00216-005-0090-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 08/18/2005] [Accepted: 08/18/2005] [Indexed: 01/27/2023]
Abstract
B. anthracis, the causative agent for anthrax, has been well studied for over 150 years. Due to the genetic similarities among various Bacillus species, as well as its existence in both a spore form and a vegetative state, the detection and specific identification of B. anthracis have been proven to require complex techniques and/or laborious methods. With the heightened interest in the organism as a potential biological threat agent, a large number of interesting detection technologies have recently been developed, including methods involving immunological and nucleic acid-based assay formats. The technologies range from culture-based methods to portable Total Analysis Systems based on real-time PCR. This review with 170 references provides a brief background on the toxicology and epidemiology of B. anthracis, discusses challenges associated with its detection related to genetic similarities to other species, and reviews immunological and, with greater emphasis, nucleic acid-based detection systems.
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Affiliation(s)
- Katie A Edwards
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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83
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Yasuda M, Shiaris MP. Differentiation of bacterial strains by thermal gradient gel electrophoresis using non-GC-clamped PCR primers for the 16S-23S rDNA intergenic spacer region. FEMS Microbiol Lett 2005; 243:235-42. [PMID: 15668024 DOI: 10.1016/j.femsle.2004.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 12/06/2004] [Accepted: 12/09/2004] [Indexed: 10/26/2022] Open
Abstract
The method for DNA fingerprinting of the 16S-23S rDNA intergenic spacer region was modified to increase resolution of bacterial strains by thermal gradient gel electrophoresis (TGGE) analysis. By utilizing the high melting temperature region of the tRNA gene located in the middle of the 16S-23S rDNA intergenic spacer region as an internal clamp for TGGE, multiple melting domain problems were solved. PCR primers lacking a stretch of GC-rich sequences (GC-clamp) amplified the intergenic spacer region more efficiently than GC-clamped primers. Therefore, PCR artifacts were avoided by using low, 17-cycle, PCR. The method was successfully applied to diverse bacterial species for strain differentiation by TGGE without requiring a special PCR primer set.
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Affiliation(s)
- Michie Yasuda
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA.
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84
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Rasko DA, Altherr MR, Han CS, Ravel J. Genomics of theBacillus cereusgroup of organisms. FEMS Microbiol Rev 2005. [DOI: 10.1016/j.fmrre.2004.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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85
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Rueckert A, Ronimus RS, Morgan HW. Development of a rapid detection and enumeration method for thermophilic bacilli in milk powders. J Microbiol Methods 2005; 60:155-67. [PMID: 15590090 DOI: 10.1016/j.mimet.2004.09.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Revised: 09/09/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
Thermophilic strains of Geobacillus, Anoxybacillus and Bacillus that are able to grow at 55 degrees C and above are recognized as commonly occurring contaminants during the production of milk powders. In particular, Anoxybacillus flavithermus strain C and Bacillus licheniformis strain F are often the most prevalent. We describe here the development of a TaqMan-based real-time-PCR assay using a small amplicon of the ribosomal 16S rRNA gene for the selective and quantitative detection of thermophilic bacilli in milk powders. We further present an effective, rapid and inexpensive method for the isolation of total bacterial DNA from milk powder for quantitative PCR analysis within 20 min. With this method, the detection of thermophilic bacilli in milk powder can be accomplished within 1 h. The detection limit for reconstituted and inoculated milk was 8 vegetative cfu ml(-1) and 64 spores ml(-1), respectively.
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Affiliation(s)
- Andreas Rueckert
- Thermophile Research Unit, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton 2001, New Zealand.
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86
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Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A. Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. J Clin Microbiol 2004; 42:3711-30. [PMID: 15297521 PMCID: PMC497648 DOI: 10.1128/jcm.42.8.3711-3730.2004] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species in the B. cereus group. We also analyzed 30 gyrB sequences for B. cereus group strains with published 16S rRNA sequences. Our findings indicated that the three most common species of the B. cereus group, B. cereus, Bacillus thuringiensis, and Bacillus mycoides, were each heterogeneous in all three gene sequences, while all analyzed strains of Bacillus anthracis were found to be homogeneous. Based on analysis of 16S and 23S rRNA sequence variations, the microorganisms within the B. cereus group were divided into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, and these seven subgroups were further organized into two distinct clusters. This classification of the B. cereus group conflicts with current taxonomic groupings, which are based on phenotypic traits. The presence of B. cereus strains in six of the seven subgroups and the presence of B. thuringiensis strains in three of the subgroups do not support the proposed unification of B. cereus and B. thuringiensis into one species. Analysis of the available phenotypic data for the strains included in this study revealed phenotypic traits that may be characteristic of several of the subgroups. Finally, our results demonstrated that rRNA and gyrB sequences may be used for discriminating B. anthracis from other microorganisms in the B. cereus group.
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Affiliation(s)
- Sergei G Bavykin
- BioChip Technology Center, Argonne National Laboratory, Argonne, IL 60439, USA.
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87
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Brillard J, Lereclus D. Comparison of cytotoxin cytK promoters from Bacillus cereus strain ATCC 14579 and from a B. cereus food-poisoning strain. Microbiology (Reading) 2004; 150:2699-2705. [PMID: 15289566 DOI: 10.1099/mic.0.27069-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The cytotoxin CytK produced by Bacillus cereus is believed to be involved in food-borne diseases. The transcriptional activity of the cytK promoter region in a food-poisoning strain was studied using a reporter gene and compared with that in the reference B. cereus strain ATCC 14579. In the food-poisoning strain, cytK is more strongly transcribed, possibly explaining the pathogenicity. The global regulator PlcR in B. cereus controls several putative virulence factors. It was found that PlcR regulates cytK in this clinical strain despite a mismatch in the PlcR recognition site, as currently defined. This suggests that the PlcR box consensus should be reconsidered and that the PlcR regulon might be larger than suspected. It is also shown that the high level of cytK transcription is not caused by a modification in the PlcR recognition site.
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Affiliation(s)
- Julien Brillard
- Institut Pasteur, Génétique et Physiologie des Bacillus Pathogènes, Département de Microbiologie Fondamentale et Médicale, 25 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Didier Lereclus
- INRA, Unité Génétique Microbienne et Environnement, La Minière, 78285 Guyancourt cedex, France
- Institut Pasteur, Génétique et Physiologie des Bacillus Pathogènes, Département de Microbiologie Fondamentale et Médicale, 25 rue du Dr Roux, 75724 Paris cedex 15, France
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88
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Volokhov D, Pomerantsev A, Kivovich V, Rasooly A, Chizhikov V. Identification of Bacillus anthracis by multiprobe microarray hybridization. Diagn Microbiol Infect Dis 2004; 49:163-71. [PMID: 15246505 DOI: 10.1016/j.diagmicrobio.2004.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 03/22/2004] [Indexed: 11/19/2022]
Abstract
We have developed a rapid assay based on microarray analysis of amplified genetic markers for reliable identification of Bacillus anthracis and its discrimination from other closely related bacterial species of the Bacillus cereus group. By combining polymerase chain reaction (PCR) amplification of six B. anthracis-specific genes (plasmid-associated genes encoding virulence factors (cyaA, pagA, lef, and capA, capB, capC) and one chromosomal marker BA-5449) with analysis of amplicons by microarray hybridization, we were able to unambiguously identify and discriminate B. anthracis among other closely related species. Bacillus identification relied on hybridization with multiple individual microarray oligonucleotide probes (oligoprobes) specific to each target B. anthracis gene. Evaluation of the assay was conducted using several B. anthracis strains (with or without pXO1 and pXO2 plasmids) as well as over 50 other species phylogenetically related to B. anthracis, including B. cereus, B. thuringiensis, B. mycoides, and B. subtilis. The developed microarray analysis of amplified genetic markers protocol provides an efficient method for (i) unambiguous identification and discrimination of B. anthracis from other Bacillus species and (ii) distinguishing between plasmid-containing and plasmid-free Bacillus anthracis strains.
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Affiliation(s)
- Dmitriy Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, Kensington, MD 20895, USA
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89
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Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, Marston CK, De BK, Sacchi CT, Fitzgerald C, Mayer LW, Maiden MCJ, Priest FG, Barker M, Jiang L, Cer RZ, Rilstone J, Peterson SN, Weyant RS, Galloway DR, Read TD, Popovic T, Fraser CM. Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 2004; 101:8449-54. [PMID: 15155910 PMCID: PMC420414 DOI: 10.1073/pnas.0402414101] [Citation(s) in RCA: 391] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by the presence of plasmids pXO1 and pXO2, which encode the lethal toxin complex and the poly-gamma-d-glutamic acid capsule, respectively. This work describes a non-B. anthracis isolate that possesses the anthrax toxin genes and is capable of causing a severe inhalation anthrax-like illness. Although initial phenotypic and 16S rRNA analysis identified this isolate as B. cereus, the rapid generation and analysis of a high-coverage draft genome sequence revealed the presence of a circular plasmid, named pBCXO1, with 99.6% similarity with the B. anthracis toxin-encoding plasmid, pXO1. Although homologues of the pXO2 encoded capsule genes were not found, a polysaccharide capsule cluster is encoded on a second, previously unidentified plasmid, pBC218. A/J mice challenged with B. cereus G9241 confirmed the virulence of this strain. These findings represent an example of how genomics could rapidly assist public health experts responding not only to clearly identified select agents but also to novel agents with similar pathogenic potentials. In this study, we combined a public health approach with genome analysis to provide insight into the correlation of phenotypic characteristics and their genetic basis.
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Affiliation(s)
- Alex R Hoffmaster
- Epidemiologic Investigations Laboratory, Meningitis and Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G34, Atlanta, GA 30333, USA
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90
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Candelon B, Guilloux K, Ehrlich SD, Sorokin A. Two distinct types of rRNA operons in the Bacillus cereus group. MICROBIOLOGY-SGM 2004; 150:601-611. [PMID: 14993309 DOI: 10.1099/mic.0.26870-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Bacillus cereus group includes insecticidal bacteria (B. thuringiensis), food-borne pathogens (B. cereus and B. weihenstephanensis) and B. anthracis, the causative agent of anthrax. The precise number of rRNA operons in 12 strains of the B. cereus group was determined. Most of the tested strains possess 13 operons and the tested psychrotolerant strains contain 14 operons, the highest number ever found in bacteria. The separate clustering of the tested psychrotolerant strains was confirmed by partial sequencing of several genes distributed over the chromosomes. Analysis of regions downstream of the 23S rRNA genes in the type strain B. cereus ATCC 14579 indicates that the rRNA operons can be divided into two classes, I and II, consisting respectively of eight and five operons. Class II operons exhibit multiple tRNA genes downstream of the 5S rRNA gene and a putative promoter sequence in the 23S-5S intergenic region, suggesting that 5S rRNA and the downstream tRNA genes can be transcribed independently of the 16S and 23S genes. Similar observations were made in the recently sequenced genome of B. anthracis strain Ames. The existence of these distinct types of rRNA operons suggests an unknown mechanism for regulation of rRNA and tRNA synthesis potentially related to the pool of amino acids available for protein synthesis.
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MESH Headings
- Bacillus cereus/classification
- Bacillus cereus/genetics
- Base Sequence
- DNA, Bacterial/genetics
- Genes, Bacterial
- Molecular Sequence Data
- Operon
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Ribotyping
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Benjamin Candelon
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
| | - Kévin Guilloux
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
| | - S Dusko Ehrlich
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
| | - Alexei Sorokin
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
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91
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Won YJ, Hallam SJ, O'Mullan GD, Pan IL, Buck KR, Vrijenhoek RC. Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus bathymodiolus. Appl Environ Microbiol 2004; 69:6785-92. [PMID: 14602641 PMCID: PMC262266 DOI: 10.1128/aem.69.11.6785-6792.2003] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deep-sea Bathymodiolus mussels, depending on species and location, have the capacity to host sulfur-oxidizing (thiotrophic) and methanotrophic eubacteria in gill bacteriocytes, although little is known about the mussels' mode of symbiont acquisition. Previous studies of Bathymodiolus host and symbiont relationships have been based on collections of nonoverlapping species across wide-ranging geographic settings, creating an apparent model for vertical transmission. We present genetic and cytological evidence for the environmental acquisition of thiotrophic endosymbionts by vent mussels from the Mid-Atlantic Ridge. Open pit structures in cell membranes of the gill surface revealed likely sites for endocytosis of free-living bacteria. A population genetic analysis of the thiotrophic symbionts exploited a hybrid zone where two Bathymodiolus species intergrade. Northern Bathymodiolus azoricus and southern Bathymodiolus puteoserpentis possess species-specific DNA sequences that identify both their symbiont strains (internal transcribed spacer regions) and their mitochondria (ND4). However, the northern and southern symbiont-mitochondrial pairs were decoupled in the hybrid zone. Such decoupling of symbiont-mitochondrial pairs would not occur if the two elements were transmitted strictly vertically through the germ line. Taken together, these findings are consistent with an environmental source of thiotrophic symbionts in Bathymodiolus mussels, although an environmentally "leaky" system of vertical transmission could not be excluded.
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Affiliation(s)
- Yong-Jin Won
- Monterey Bay Aquarium Research Institute, Moss Landing, California 95039-0628, USA
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92
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Rasko DA, Ravel J, Økstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV, Kolonay J, Nelson WC, Kolstø AB, Fraser CM, Read TD. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 2004; 32:977-88. [PMID: 14960714 PMCID: PMC373394 DOI: 10.1093/nar/gkh258] [Citation(s) in RCA: 256] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of capsule carbohydrate and flagella surface structures were identified. Bacillus cereus ATCC 10987 contains a single large plasmid (pBc10987), of approximately 208 kb, that is similar in gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk.
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Affiliation(s)
- David A Rasko
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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93
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Hurtle W, Bode E, Kaplan RS, Garrison J, Kearney B, Shoemaker D, Henchal E, Norwood D. Use of denaturing high-performance liquid chromatography to identify Bacillus anthracis by analysis of the 16S-23S rRNA interspacer region and gyrA gene. J Clin Microbiol 2004; 41:4758-66. [PMID: 14532217 PMCID: PMC254356 DOI: 10.1128/jcm.41.10.4758-4766.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Denaturing high-performance liquid chromatography (DHPLC) was evaluated as a method for identifying Bacillus anthracis by analyzing two chromosomal targets, the 16S-23S intergenic spacer region (ISR) and the gyrA gene. The 16S-23S ISR was analyzed by this method with 42 strains of B. anthracis, 36 strains of Bacillus cereus, and 12 strains of Bacillus thuringiensis; the gyrA gene was analyzed by this method with 33 strains of B. anthracis, 27 strains of B. cereus, and 9 strains of B. thuringiensis. Two blind panels of 45 samples each were analyzed to evaluate the potential diagnostic capability of this method. Our results show that DHPLC is an efficient method for the identification of B. anthracis.
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Affiliation(s)
- William Hurtle
- Clinical Research Management, North Royalton, Ohio 44133, USA
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94
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Daffonchio D, Cherif A, Brusetti L, Rizzi A, Mora D, Boudabous A, Borin S. Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera. Appl Environ Microbiol 2003; 69:5128-37. [PMID: 12957895 PMCID: PMC194986 DOI: 10.1128/aem.69.9.5128-5137.2003] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intergenic transcribed spacers (ITS) between the 16S and 23S rRNA genetic loci are frequently used in PCR fingerprinting to discriminate bacterial strains at the species and intraspecies levels. We investigated the molecular nature of polymorphisms in ITS-PCR fingerprinting of low-G+C-content spore-forming bacteria belonging to the genera Bacillus, Brevibacillus, Geobacillus, and Paenibacillus: We found that besides the polymorphisms in the homoduplex fragments amplified by PCR, heteroduplex products formed during PCR between amplicons from different ribosomal operons, with or without tRNA genes in the ITS, contribute to the interstrain variability in ITS-PCR fingerprinting patterns obtained in polyacrylamide-based gel matrices. The heteroduplex nature of the discriminating bands was demonstrated by fragment separation in denaturing polyacrylamide gels, by capillary electrophoresis, and by cloning, sequencing, and recombination of purified short and tRNA gene-containing long ITS. We also found that heteroduplex product formation is enhanced by increasing the number of PCR cycles. Homoduplex-heteroduplex polymorphisms (HHP) in a conserved region, such as the 16S and 23S rRNA gene ITS, allowed discrimination of closely related strains and species undistinguishable by other methods, indicating that ITS-HHP analysis is an easy and reproducible additional tool for strain typing.
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Affiliation(s)
- Daniele Daffonchio
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi, 20133 Milan, Italy.
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95
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Cherif A, Brusetti L, Borin S, Rizzi A, Boudabous A, Khyami-Horani H, Daffonchio D. Genetic relationship in the 'Bacillus cereus group' by rep-PCR fingerprinting and sequencing of a Bacillus anthracis-specific rep-PCR fragment. J Appl Microbiol 2003; 94:1108-19. [PMID: 12752821 DOI: 10.1046/j.1365-2672.2003.01945.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To evaluate the genetic relationship in the Bacillus cereus group by rep-PCR fingerprinting. METHODS AND RESULTS A collection of 112 strains of the six species of the B. cereus group was analysed by rep-PCR fingerprinting using the BOX-A1R primer. A relative genetic distinctness was found among the species. Cluster analysis of the rep-PCR patterns showed clusters of B. thuringiensis strains quite separate from those of B. cereus strains. The B. anthracis strains represented an independent lineage in a B. cereus cluster. The B. mycoides, B. pseudomycoides and B. weihenstephanensis strains were clustered into three groups at some distance from the other species. Comparison of sequences of AC-390, a typical B. anthracis rep-PCR fragment, from 27 strains of B. anthracis, B. cereus, B. thuringiensis and B. weihenstephanensis, representative of different clusters identified by rep-PCR fingerprinting, confirmed that B. anthracis diverges from its related species. CONCLUSIONS The genetic relationship deduced from the rep-PCR patterns indicates a relatively clear separation of the six species, suggesting that they can indeed be considered as separate units. SIGNIFICANCE AND IMPACT OF THE STUDY rep-PCR fingerprinting can make a contribution in the clarification of the genetic relationships between the species of the B. cereus group.
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Affiliation(s)
- A Cherif
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi, via Celoria 2, 20133, Milano, Italy
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96
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Abstract
Bacillus cereus sensu lato, the species group comprising Bacillus anthracis, Bacillus thuringiensis and B. cereus (sensu stricto), has previously been scrutinized regarding interspecies genetic correlation and pathogenic characteristics. So far, little attention has been paid to analysing the biological and ecological properties of the three species in their natural environments. In this review, we describe the B. cereus sensu lato living in a world on its own; all B. cereus sensu lato can grow saprophytically under nutrient-rich conditions, which are only occasionally found in the environment, except where nutrients are actively collected. As such, members of the B. cereus group have recently been discovered as common inhabitants of the invertebrate gut. We speculate that all members disclose symbiotic relationships with appropriate invertebrate hosts and only occasionally enter a pathogenic life cycle in which the individual species infects suitable hosts and multiplies almost unrestrained.
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Affiliation(s)
- G B Jensen
- National Institute of Occupational Health, Lersø Parkalle 105, 2100 Copenhagen, Denmark.
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97
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Chang YH, Shangkuan YH, Lin HC, Liu HW. PCR assay of the groEL gene for detection and differentiation of Bacillus cereus group cells. Appl Environ Microbiol 2003; 69:4502-10. [PMID: 12902235 PMCID: PMC169126 DOI: 10.1128/aem.69.8.4502-4510.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2002] [Accepted: 05/08/2003] [Indexed: 11/20/2022] Open
Abstract
Strains of species in the Bacillus cereus group are potentially enterotoxic. Thus, the detection of all B. cereus group strains is important. As 16S ribosomal DNA sequence analysis cannot adequately differentiate species of the B. cereus group, we explored the potential of the groEL gene as a phylogenetic marker. A phylogenetic analysis of the groEL sequences of 78 B. cereus group strains revealed that the B. cereus group strains were split into two major clusters, one including six B. mycoides and one B. pseudomycoides (cluster II) and the other including two B. mycoides and the rest of the B. cereus group strains (cluster I). Cluster I was further differentiated into two subclusters, Ia and Ib. The sodA gene sequences of representative strains from different clusters were also compared. The phylogenetic tree constructed from the sodA sequences showed substantial similarity to the tree constructed from the groEL sequences. Based on the groEL sequences, a PCR assay for detection and identification of B. cereus group strains was developed. Subsequent restriction fragment length polymorphism (RFLP) analysis verified the PCR amplicons and the differentiation of the B. cereus group strains. RFLP with MboI was identical for all the B. cereus group strains analyzed, while RFLP with MfeI or PstI classified all B. cereus and B. thuringiensis strains into two groups. All cluster II B. mycoides and B. pseudomycoides strains could be discriminated from other B. cereus group bacteria by restriction analysis with TspRI.
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Affiliation(s)
- Yu-Hsiu Chang
- Division of Bacteriology, Institute of Preventive Medicine, National Defense Medical Center, Sanhsia, Taipei, Taiwan 237, Republic of China
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98
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Merrill L, Richardson J, Kuske CR, Dunbar J. Fluorescent heteroduplex assay for monitoring Bacillus anthracis and close relatives in environmental samples. Appl Environ Microbiol 2003; 69:3317-26. [PMID: 12788732 PMCID: PMC161496 DOI: 10.1128/aem.69.6.3317-3326.2003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Accepted: 03/05/2003] [Indexed: 11/20/2022] Open
Abstract
A fluorescent heteroduplex method was developed to assess the presence of 16S rRNA gene (rDNA) sequences from Bacillus anthracis and close relatives in PCR-amplified 16S rDNA sequence mixtures from environmental samples. The method uses a single-stranded, fluorescent DNA probe, 464 nucleotides in length, derived from a B. anthracis 16S rRNA gene. The probe contains a unique, engineered deletion such that all probe-target duplexes are heteroduplexes with an unpaired G at position 343 (deltaG343). Heteroduplex profiles of sequences >/=85% similar to the probe were produced using an ABI 377 sequencer in less than 3 h. The method divides strains of the Bacillus cereus-Bacillus thuringiensis-B. anthracis group into two subgroups. Each subgroup is defined by a specific 16S rRNA gene sequence type. Sequence type A, containing one mismatch with the probe, occurs in B. anthracis and a small number of closely related clonal lineages represented mostly by food-borne pathogenic isolates of B. cereus and B. thuringiensis. Sequence type B, containing two mismatches with the probe, is found in the majority of B. cereus and B. thuringiensis strains examined to date. Sequence types A and B, when hybridized to the probe, generate two easily differentiated heteroduplexes. Thus, from heteroduplex profiles, the presence of B. cereus-B. thuringiensis-B. anthracis subgroups in environmental samples can be inferred unambiguously. The results show that fluorescent heteroduplex analysis is an effective profiling technique for detection and differentiation of sequences representing small phylogenetic or functional groups in environmental samples.
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Affiliation(s)
- Lori Merrill
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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99
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Fedhila S, Gohar M, Slamti L, Nel P, Lereclus D. The Bacillus thuringiensis PlcR-regulated gene inhA2 is necessary, but not sufficient, for virulence. J Bacteriol 2003; 185:2820-5. [PMID: 12700261 PMCID: PMC154399 DOI: 10.1128/jb.185.9.2820-2825.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously reported that Bacillus thuringiensis strain 407 Cry 32(-) secretes a zinc-requiring metalloprotease, InhA2, that is essential for virulence in orally infected insects. Analysis of the inhA2-lacZ transcriptional fusion showed that inhA2 expression is repressed in a PlcR(-) background. Using DNase I footprinting experiments, we demonstrated that PlcR activates inhA2 transcription directly by binding to a DNA sequence showing a one-residue mismatch with the previously reported PlcR box. It was previously reported that PlcR is essential for B. thuringiensis virulence in oral infection by contributing to the synergistic properties of the spores on the insecticidal activity of the Cry1C protein. We used complementation experiments to investigate whether the PlcR(-) phenotype was due to the absence of InhA2. The results indicated that overexpression of inhA2 in the (Delta)plcR strain did not restore the wild-type phenotype. However, virulence was fully restored in the (Delta)inhA2 complemented mutant. Thus, inhA2 is the first example of a PlcR-regulated gene found to be directly involved in virulence. However, it is not sufficient for pathogenicity when the other members of the PlcR regulon are lacking. This suggests that InhA2 may act in concert with other PlcR-regulated gene products to provide virulence.
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Affiliation(s)
- Sinda Fedhila
- Unité Génétique Microbienne et Environnement, Institut National de la Recherche Agronomique, La Minière, 78285 Guyancourt Cedex, France.
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Hurtado LA, Mateos M, Lutz RA, Vrijenhoek RC. Coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam Calyptogena magnifica. Appl Environ Microbiol 2003; 69:2058-64. [PMID: 12676683 PMCID: PMC154811 DOI: 10.1128/aem.69.4.2058-2064.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. This symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. If symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if coupled to the host's maternally inherited mitochondrial DNA. This coupling would be obscured, however, with low rates of horizontal or environmental transfers, the equivalent of recombination between host lineages. Population genetic analyses of C. magnifica clams and associated symbionts from eastern Pacific hydrothermal vents clearly supported the hypothesis of strictly maternal cotransmission. Host mitochondrial and symbiont DNA sequences were coupled in a clam population that was polymorphic for both genetic markers. These markers were not similarly coupled with sequence variation at a nuclear gene locus, as expected for a randomly mating sexual population. Phylogenetic analysis of the two cytoplasmic genes also revealed no evidence for recombination. The tight association between vesicomyid clams and their vertically transmitted bacterial endosymbionts is phylogenetically very young (<50 million years) and may serve as a model for the origin and evolution of eukaryotic organelles.
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Affiliation(s)
- Luis A Hurtado
- Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, USA.
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