1
|
Miller WG, Lopes BS, Ramjee M, Jay-Russell MT, Chapman MH, Williams TG, Wood DF, Gruntar I, Papić B, Forbes KJ. Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids. Int J Syst Evol Microbiol 2024; 74. [PMID: 38842428 DOI: 10.1099/ijsem.0.006405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.
Collapse
Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Bruno S Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
- National Horizons Centre, Teesside University, Darlington, UK
| | - Meenakshi Ramjee
- Wolfson Wohl Cancer Research Centre, Glasgow. The University of Glasgow, Glasgow, UK
| | | | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Tina G Williams
- Bioproducts Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Delilah F Wood
- Bioproducts Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Igor Gruntar
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Bojan Papić
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Ken J Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| |
Collapse
|
2
|
The ribosomal RNA operon ( rrn ) of Campylobacter concisus supports molecular typing to genomospecies level. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
3
|
Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. Sci Rep 2016; 6:34362. [PMID: 27681823 PMCID: PMC5041132 DOI: 10.1038/srep34362] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022] Open
Abstract
Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial dark matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.
Collapse
|
4
|
Kaneko J, Yamada-Narita S, Abe N, Onodera T, Kan E, Kojima S, Miyazaki T, Yamamoto Y, Oguchi A, Ankai A, Ichikawa N, Nakazawa H, Fukui S, Takahashi M, Yamazaki S, Fujita N, Kamio Y. Complete genome sequence of Selenomonas ruminantium subsp. lactilytica will accelerate further understanding of the nature of the class Negativicutes. FEMS Microbiol Lett 2015; 362:fnv050. [PMID: 25837814 DOI: 10.1093/femsle/fnv050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2015] [Indexed: 01/14/2023] Open
Abstract
Selenomonas ruminantium subsp. lactilytica, a strictly anaerobic ruminal bacterium, possesses typical Gram-negative cell surface structure comprising cytoplasmic membrane, peptidoglycan layer and outer membrane, whereas its 16S rRNA-based taxonomy shows that the bacteria belongs to Gram-positive Firmicutes. Complete genome analysis showed that genes or gene clusters involved in Gram-negative cell structure were scattered in the S. ruminantium genome, and might provide the new insight of phylogenetic relationship between the bacterium and other bacterial species.
Collapse
Affiliation(s)
- Jun Kaneko
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Sachiko Yamada-Narita
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Naoki Abe
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Tomoko Onodera
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Eiichiro Kan
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Seiji Kojima
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Takao Miyazaki
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Yuji Yamamoto
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 23-35-1 Higashi, Towada 034-8628, Japan
| | - Akio Oguchi
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Akiho Ankai
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Natsuko Ichikawa
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Hidekazu Nakazawa
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Shigehiro Fukui
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Mikio Takahashi
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Syuji Yamazaki
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Nobuyuki Fujita
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Yoshiyuki Kamio
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan Department of Human Health and Nutrition, Graduate School of Comprehensive Human Sciences, Shokei Gakuin University, 4-10-1 Yurigaoka, Natori 981-1295, Japan
| |
Collapse
|
5
|
Oporto B, Hurtado A. Emerging thermotolerant Campylobacter species in healthy ruminants and swine. Foodborne Pathog Dis 2011; 8:807-13. [PMID: 21438765 DOI: 10.1089/fpd.2010.0803] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Campylobacters other than Campylobacter jejuni or C. coli were isolated in 35% of 343 farms recently analyzed in northern Spain. This study was aimed at identifying at the species level the 120 isolates collected (21 ovine, 52 beef cattle, 44 dairy cattle, and 3 porcine) by species-specific polymerase chain reaction and 16S rRNA gene sequencing analysis. Thus, five species were identified: Campylobacter hyointestinalis (90 isolates), Campylobacter lanienae (12), Campylobacter fetus subsp. fetus (10), Campylobacter lari (1), and Campylobacter sputorum (1). Ambiguous results were obtained for six isolates. Phylogenetic analyses of the 16S rRNA gene sequence placed three of them (cattle isolates) as an intermediate clade between C. hyointestinalis subsp. hyointestinalis and C. fetus, two ovine isolates formed a new clade clustering with Campylobacter concisus despite sharing higher similarity with Campylobacter mucosalis, and one porcine isolate shared similarly high homology with C. lanienae and C. hyointestinalis subsp. lawsonii. C. hyointestinalis was the predominant species, particularly in cattle, but it was also isolated from sheep and swine. C. lanienae was only found in sheep, C. fetus in cattle and sheep, and C. lari in a single dairy cattle farm. Although previously reported, the isolation of C. lari from cattle is not common, and this is the first report of C. lanienae and C. hyointestinalis in sheep. This study demonstrated the wide distribution in livestock of several emerging zoonotic Campylobacter species and provided valuable information on their host animal reservoirs.
Collapse
Affiliation(s)
- Beatriz Oporto
- Department of Animal Health, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio, Bizkaia, Spain
| | | |
Collapse
|
6
|
Smuts HEM, Lastovica AJ. Molecular Characterization of the 16S rRNA Gene of Helicobacter fennelliae Isolated from Stools and Blood Cultures from Paediatric Patients in South Africa. J Pathog 2010; 2011:217376. [PMID: 22567323 PMCID: PMC3335488 DOI: 10.4061/2011/217376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/27/2010] [Accepted: 10/04/2010] [Indexed: 11/20/2022] Open
Abstract
Forty strains of H. fennelliae collected from paediatric blood and stool samples over an 18 year period at a children's hospital in Cape Town, South Africa, were amplified by PCR of the 16S rRNA. Two distinct genotypes of H. fennelliae were identified based on the phylogenetic analysis. This was confirmed by sequencing a portion of the beta subunit of the RNA polymerase (rpoB) gene. All isolates from South Africa clustered with a proposed novel
Helicobacter strain (accession number AF237612) isolated in Australia, while three H. fennelliae type strains from the northern hemisphere, NCTC 11612, LMG 7546 and CCUG 18820, formed a separate branch. A large (355bp) highly conserved intervening sequence (IVS) in the 16S rRNA was found in all isolates. Predicted secondary structures of the IVS from the 16S rRNA and 23S rRNA were characterised by a primary stem structure formed by base pairing of the 3′ and 5′ ends and internal loops and stems. This phylogenetic analysis is the largest undertaken of H. fennelliae. The South African H. fennelliae isolates are closely related to an Australian isolate previously reported to be a possible novel species of Helicobacter. This study suggests that the latter is strain of H. fennelliae.
Collapse
Affiliation(s)
- Heidi E M Smuts
- Division of Medical Virology/National Health Laboratory Service, Department of Clinical Laboratory Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | | |
Collapse
|
7
|
Meinersmann RJ, Phillips RW, Ladely SR. Inter- and intra-genomic heterogeneity of the intervening sequence in the 23S ribosomal RNA gene of Campylobacter jejuni and Campylobacter coli. Syst Appl Microbiol 2009; 32:91-100. [PMID: 19201124 DOI: 10.1016/j.syapm.2008.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 12/15/2008] [Accepted: 12/22/2008] [Indexed: 11/30/2022]
Abstract
An intervening sequence (IVS) can be present or absent in the 23S rRNA of Campylobacter jejuni and Campylobacter coli. As part of a survey, we used a polymerase chain reaction (PCR) assay to detect the presence of the IVS in 43 isolates of C. coli and 82 isolates of C. jejuni. An IVS was present in 40 (93.0%) of the C. coli and only 34 (41.5%) of the C. jejuni isolates. Twelve (27.9%) of the C. coli isolates and seven (8.5%) of the C. jejuni isolates resulted in two polymerase chain reaction products, indicating heterogeneity in the presence of the 23S rRNA IVS. Fourteen of the isolates with two products were evaluated by pulse-field gel electrophoresis; 13 different patterns were observed. The total band size of one isolate was substantially greater than the expected 1.7 Mb, possibly indicating a mixed culture. Southern blot analyses demonstrated the expected three rRNA operons in all tested isolates. Nested PCR reactions with operon-specific primers followed by primers for the IVS confirmed that the strains of interest contained either one or two operons carrying the IVS and the remaining operon(s) did not. Sequence analysis of the IVS and flanking regions of the 23S rRNA genes did not discriminate C. jejuni and C. coli as distinct populations. These results indicate horizontal transfer of 23S rRNA genes or portions of the genes between C. jejuni and C. coli. Also, data showing sequence polymorphisms between the three 23S rRNA loci outside of the IVS region suggest that the isolates with intra-genomic heterogeneity appear to be members of clones that have an ancient defect in gene conversion mechanisms needed for concerted evolution of the ribosomal operons.
Collapse
Affiliation(s)
- R J Meinersmann
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA Agricultural Research Service, Athens, Richard J. Russell Research Center, P.O. Box 5677, Athens, GA 30604, USA.
| | | | | |
Collapse
|
8
|
MacGregor BJ, Amann R. Single-stranded conformational polymorphism for separation of mixed rRNAS (rRNA-SSCP), a new method for profiling microbial communities. Syst Appl Microbiol 2006; 29:661-70. [PMID: 16460898 DOI: 10.1016/j.syapm.2006.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Indexed: 10/25/2022]
Abstract
We show that non-denaturing gel electrophoresis, or single-stranded conformational polymorphism (SSCP), can be used to separate mixtures of full-length rRNAs. Individual bands can then be excised for identification by RT-PCR and sequencing. This has the advantage over profiling methods such as DGGE and T-RFLP that no PCR amplification is involved prior to sequencing; thus, extraction biases aside, it should yield a quantitative picture of community composition in terms of ribosome content. To simplify banding patterns, RNA subsamples (e.g. bacterial 16S rRNA) can first be isolated by magnetic bead capture hybridization. Alternatively, oligonucleotide-directed ribonuclease H (RNase H) digestion can be used to identify bands of interest by running digested samples in parallel to undigested ones. We illustrate the use of this technique to identify a potentially predominant species in a hypersaline microbial mat. We anticipate that rRNA-SSCP will be useful for community profiling; for clone library construction by directed cloning of individual rRNAs; and for following incorporation of radiolabeled substrates at the species level, by gel autoradiography, without advance information or guesswork about which species might be active and abundant.
Collapse
Affiliation(s)
- Barbara J MacGregor
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany.
| | | |
Collapse
|
9
|
Korczak BM, Stieber R, Emler S, Burnens AP, Frey J, Kuhnert P. Genetic relatedness within the genus Campylobacter inferred from rpoB sequences. Int J Syst Evol Microbiol 2006; 56:937-945. [PMID: 16627635 DOI: 10.1099/ijs.0.64109-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Campylobacter comprises 17 species, some of which are important animal and human pathogens. To gain more insight into the genetic relatedness of this genus and to improve the molecular tools available for diagnosis, a universal sequencing approach was established for the gene encoding the beta-subunit of RNA polymerase (rpoB) for the genus Campylobacter. A total of 59 strains, including the type strains of currently recognized species as well as field isolates, were investigated in the study. A primer set specific for Campylobacter species enabled straightforward amplification and sequencing of a 530 bp fragment of the rpoB gene. The 16S rRNA gene sequences of all of the strains were determined in parallel. A good congruence was obtained between 16S rRNA and rpoB gene sequence-based trees within the genus Campylobacter. The branching of the rpoB tree was similar to that of the 16S rRNA gene tree, even though a few discrepancies were observed for certain species. The resolution of the rpoB gene within the genus Campylobacter was generally much higher than that of the 16S rRNA gene sequence, resulting in a clear separation of most species and even some subspecies. The universally applicable amplification and sequencing approach for partial rpoB gene sequence determination provides a powerful tool for DNA sequence-based discrimination of Campylobacter species.
Collapse
Affiliation(s)
- Bożena M Korczak
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | - Regina Stieber
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | | | - André P Burnens
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| |
Collapse
|
10
|
Abstract
The exact knowledge on the ribosomal RNA (rRNA) structure is an important prerequisite for work with rRNA sequences in bioinformatic analyses and in experimental research. Most available rRNA sequences of bacteria are based on gene sequences and on similarity analyses using Escherichia coli rRNA as a standard. Therefore, it is often overlooked that many bacteria harbour mature rRNA 'in pieces'. In some cases, the processing steps during the fragmentation lead to the removal of rRNA segments that are usually found in the ribosome. In this review, the current knowledge on the mechanisms of rRNA fragmentation and on the occurrence of fragmented rRNA in bacteria is summarized, and the physiological implications of this phenomenon are discussed.
Collapse
Affiliation(s)
- Elena Evguenieva-Hackenberg
- Institut für Mikrobiologie und Molekularbiologie der Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| |
Collapse
|
11
|
Mandrell RE, Harden LA, Bates A, Miller WG, Haddon WF, Fagerquist CK. Speciation of Campylobacter coli, C. jejuni, C. helveticus, C. lari, C. sputorum, and C. upsaliensis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 2005; 71:6292-307. [PMID: 16204551 PMCID: PMC1265991 DOI: 10.1128/aem.71.10.6292-6307.2005] [Citation(s) in RCA: 120] [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
Multiple strains of Campylobacter coli, C. jejuni, C. helveticus, C. lari, C. sputorum, and C. upsaliensis isolated from animal, clinical, or food samples have been analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Whole bacterial cells were harvested from colonies or confluent growth on agar and transferred directly into solvent and then to a spot of dried 3-methoxy-4-hydroxycinnamic acid (matrix). Multiple ions in the 5,000- to 15,000-Da mass range were evident in spectra for each strain; one or two ions in the 9,500- to 11,000-Da range were consistently high intensity. "Species-identifying" biomarker ions (SIBIs) were evident from analyses of multiple reference strains for each of the six species, including the genome strains C. jejuni NCTC 11168 and C. jejuni RM1221. Strains grown on nine different combinations of media and atmospheres yielded SIBI masses within +/-5 Da with external instrument calibration. The highest-intensity C. jejuni SIBIs were cytosolic proteins, including GroES, HU/HCj, and RplL. Multiple intraspecies SIBIs, corresponding probably to nonsynonymous nucleotide polymorphisms, also provided some intraspecies strain differentiation. MALDI-TOF MS analysis of 75 additional Campylobacter strains isolated from humans, poultry, swine, dogs, and cats revealed (i) associations of SIBI type with source, (ii) strains previously speciated incorrectly, and (iii) "strains" composed of more than one species. MALDI-TOF MS provides an accurate, sensitive, and rapid method for identification of multiple Campylobacter species relevant to public health and food safety.
Collapse
|
12
|
Peix A, Rivas R, Velázquez E, Mateos PF, Martínez-Molina E, Muñoz-Herrera A, Gómez-Alonso A, Velázquez E. Application of horizontal staircase electrophoresis in agarose minigels to the random intergenic spacer analysis of clinical samples. Electrophoresis 2005; 26:4402-10. [PMID: 16315171 DOI: 10.1002/elps.200500357] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The random intergenic spacer analysis is a recently developed technique for the study of microbial populations. The bacterial intergenic spacer (ITS) is located between 16S rRNA and 23S rRNA genes and presents different length and sequence among bacterial species. Therefore, the amplicons can be separated by electrophoresis commonly performed at low voltage during several hours. Although this technique is especially useful for unculturable microorganisms, it has not been applied before to clinical sample analysis. As these samples have a limited number of bacterial species, the size of the gels may be reduced to facilitate their handling and to reduce the running time. To obtain maximum separation among the ITS bands, we analysed in this work different electrophoretical conditions including staircase electrophoresis, a technique based on the application of several voltage steps. The results obtained showed a different behaviour of the electrical resistance during the performance of submarine horizontal and vertical staircase electrophoresis. In the first case the resistance decreased during most of the running time whereas in the second case it increased. Here, we show that the performance of horizontal staircase electrophoresis reduces the running time more than 80% with respect to conventional electrophoresis at low voltages. This procedure was applied to the separation of ITS bands from bacterial DNA present in a tissue from a vocal cord biopsy. The sequencing of these bands allowed their identification. This new procedure may be very useful in the rapid diagnosis of bacteria present in human, animal and plant tissues.
Collapse
Affiliation(s)
- Alvaro Peix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Lentzsch P, Rieksneuwöhner B, Wieler LH, Hotzel H, Moser I. High-resolution genotyping of Campylobacter upsaliensis strains originating from three continents. J Clin Microbiol 2004; 42:3441-8. [PMID: 15297481 PMCID: PMC497571 DOI: 10.1128/jcm.42.8.3441-3448.2004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ninety-six Campylobacter upsaliensis strains that originated from Australia, Canada, and Europe (Germany) and that were isolated from humans, dogs, and cats were serotyped for their heat-stable surface antigens. All of them were genotyped by enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) profiling, and 83 strains were genotyped by macrorestriction analysis with the endonuclease XhoI. Eighty-four percent of the strains belonged to five different serotypes (serotypes OI, OII, OIII, OIV, and OVI), with the proportions of strains in each serotype being comparable among the groups of strains from all three continents. Two serotypes, OIII and OIV, were prevalent at rates of 35 to 40%. Serotypes OI, OII, and OVI were detected at rates of 1.5 to 15%. Between 10 and 17.7% of the strains did not react with the available antisera. Analysis of the ERIC-PCR profiles revealed two distinct genotypic clusters, which represented the German and the non-European strains, respectively. XhoI macrorestriction yielded two genotypic clusters; one of them contained 80.2% of the German strains and 34.6% of the non-European strains, and the second cluster consisted of 65.4% of the non-European strains and 19.8% of the German strains. Fourteen strains from all three continents were analyzed for their 16S rRNA gene sequences. Only two minor variations were detected in four of the strains. In conclusion, C. upsaliensis has undergone diverging processes of genome arrangement on different continents during evolution without segregating into different subspecies.
Collapse
Affiliation(s)
- P Lentzsch
- Centre for Agricultural Landscape and Land Use Research, Müncheberg, Germany
| | | | | | | | | |
Collapse
|
14
|
Hurtle W, Bode E, Kulesh DA, Kaplan RS, Garrison J, Bridge D, House M, Frye MS, Loveless B, Norwood D. Detection of the Bacillus anthracis gyrA gene by using a minor groove binder probe. J Clin Microbiol 2004; 42:179-85. [PMID: 14715750 PMCID: PMC321681 DOI: 10.1128/jcm.42.1.179-185.2004] [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
Identification of chromosomal markers for rapid detection of Bacillus anthracis is difficult because significant chromosomal homology exists among B. anthracis, Bacillus cereus, and Bacillus thuringiensis. We evaluated the bacterial gyrA gene as a potential chromosomal marker for B. anthracis. A real-time PCR assay was developed for the detection of B. anthracis. After analysis of the unique nucleotide sequence of the B. anthracis gyrA gene, a fluorescent 3' minor groove binding probe was tested with 171 organisms from 29 genera of bacteria, including 102 Bacillus strains. The assay was found to be specific for all 43 strains of B. anthracis tested. In addition, a test panel of 105 samples was analyzed to evaluate the potential diagnostic capability of the assay. The assay showed 100% specificity, demonstrating the usefulness of the gyrA gene as a specific chromosomal marker for B. anthracis.
Collapse
Affiliation(s)
- William Hurtle
- Clinical Research Management, North Royalton, Ohio 44133, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Baker BJ, Hugenholtz P, Dawson SC, Banfield JF. Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol 2003; 69:5512-8. [PMID: 12957940 PMCID: PMC194945 DOI: 10.1128/aem.69.9.5512-5518.2003] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2003] [Accepted: 06/11/2003] [Indexed: 11/20/2022] Open
Abstract
During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name "Candidatus Captivus acidiprotistae." To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.
Collapse
Affiliation(s)
- Brett J Baker
- Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, California 94720, USA.
| | | | | | | |
Collapse
|
16
|
Gorkiewicz G, Feierl G, Schober C, Dieber F, Köfer J, Zechner R, Zechner EL. Species-specific identification of campylobacters by partial 16S rRNA gene sequencing. J Clin Microbiol 2003; 41:2537-46. [PMID: 12791878 PMCID: PMC156541 DOI: 10.1128/jcm.41.6.2537-2546.2003] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species-specific identification of campylobacters is problematic, primarily due to the absence of suitable biochemical assays and the existence of atypical strains. 16S rRNA gene (16S rDNA)-based identification of bacteria offers a possible alternative when phenotypic tests fail. Therefore, we evaluated the reliability of 16S rDNA sequencing for the species-specific identification of campylobacters. Sequence analyses were performed by using almost 94% of the complete 16S rRNA genes of 135 phenotypically characterized Campylobacter strains, including all known taxa of this genus. It was shown that 16S rDNA analysis enables specific identification of most Campylobacter species. The exception was a lack of discrimination among the taxa Campylobacter jejuni and C. coli and atypical C. lari strains, which shared identical or nearly identical 16S rDNA sequences. Subsequently, it was investigated whether partial 16S rDNA sequences are sufficient to determine species identity. Sequence alignments led to the identification of four 16S rDNA regions with high degrees of interspecies variation but with highly conserved sequence patterns within the respective species. A simple protocol based on the analysis of these sequence patterns was developed, which enabled the unambiguous identification of the majority of Campylobacter species. We recommend 16S rDNA sequence analysis as an effective, rapid procedure for the specific identification of campylobacters.
Collapse
Affiliation(s)
- Gregor Gorkiewicz
- Institute of Molecular Biology, Biochemistry and Microbiology, Karl-Franzens University, Graz, Austria.
| | | | | | | | | | | | | |
Collapse
|
17
|
Teyssier C, Marchandin H, Siméon De Buochberg M, Ramuz M, Jumas-Bilak E. Atypical 16S rRNA gene copies in Ochrobactrum intermedium strains reveal a large genomic rearrangement by recombination between rrn copies. J Bacteriol 2003; 185:2901-9. [PMID: 12700269 PMCID: PMC154400 DOI: 10.1128/jb.185.9.2901-2909.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ochrobactrum intermedium is an opportunistic human pathogen belonging to the alpha 2 subgroup of proteobacteria. The 16S rDNA sequences of nine O. intermedium isolates from a collection of clinical and environmental isolates exhibited a 46-bp insertion at position 187, which was present in only one sequence among the 82 complete or partial 16S rDNA sequences of Ochrobactrum spp. available in data banks. Reverse transcription-PCR experiments showed that the 46-bp insertion remained in the 16S rRNA. The inserted sequence folded into a stem-loop structure, which took place in and prolonged helix H184 of the 16S rRNA molecule. Helix H184 has been described as conserved in length among eubacteria, suggesting the idiosyncratic character of the 46-bp insertion. Pulsed-field gel electrophoresis experiments showed that seven of the clinical isolates carrying the 46-bp insertion belonged to the same clone. Insertion and rrn copy numbers were determined by hybridization and I-CeuI digestion. In the set of clonal isolates, the loss of two insertion copies revealed the deletion of a large genomic fragment of 150 kb, which included one rrn copy; deletion occurred during the in vivo evolution of the clone. Determination of the rrn skeleton suggested that the large genomic rearrangement occurred during events involving homologous recombination between rrn copies. The loss of insertion copies suggested a phenomenon of concerted evolution among heterogeneous rrn copies.
Collapse
Affiliation(s)
- Corinne Teyssier
- Laboratoire de Bactériologie, Faculté de Pharmacie, Montpellier, France
| | | | | | | | | |
Collapse
|
18
|
Misawa N, Kawashima K, Kondo F, Kushima E, Kushima K, Vandamme P. Isolation and characterization of Campylobacter, Helicobacter, and Anaerobiospirillum strains from a puppy with bloody diarrhea. Vet Microbiol 2002; 87:353-64. [PMID: 12069772 DOI: 10.1016/s0378-1135(02)00086-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We carried out a microscopic examination of stools from a 2-month-old female puppy with bloody diarrhea, and this revealed large numbers of different spiral-shaped bacteria. To isolate these organisms, a rectal swab specimen was inoculated onto plates of Skirrow's agar and incubated at 37 degrees C for 6 days in a microaerobic atmosphere. Finally, a total of six different spiral-shaped bacteria (strains G1104, 94105, FR106, B0101, 3J102, and J2103) were isolated. Based on their morphology, biochemical traits, whole-cell protein profiles, and analysis of their 16S rDNA sequences, they were identified as Campylobacter upsaliensis, Helicobacter cinaedi, 'Flexispira rappini', two Anaerobiospirillum spp. with different morphologies, and Helicobacter sp., respectively. Analysis of 16S rRNA gene sequence data for strains 94150 (H. cinaedi) and FR106 (F. rappini) revealed that this approach has limitations when identifying isolates to the species level because of a high degree of sequence homology between these species (>99%) and considerable sequence variation among different isolates within these species. The dog was treated orally with amoxicillin for 3 days, which resolved the diarrhea. However, 1 day after the last dose the bloody diarrhea recurred but regarded to six more days amoxicillin treatment. This suggests a bacterial cause for the diarrhea. The approach to identification to microaerobic spiral-shaped bacteria in diarrheic dogs can be applied further to characterize their role in diarrhea illness.
Collapse
Affiliation(s)
- Naoaki Misawa
- Laboratory of Veterinary Public Health, Division of Veterinary Medicine, Faculty of Agriculture, Miyazaki University, Miyazaki, Japan.
| | | | | | | | | | | |
Collapse
|
19
|
On SL. Taxonomy of Campylobacter, Arcobacter, Helicobacter and related bacteria: current status, future prospects and immediate concerns. SYMPOSIUM SERIES (SOCIETY FOR APPLIED MICROBIOLOGY) 2001:1S-15S. [PMID: 11422556 DOI: 10.1046/j.1365-2672.2001.01349.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S L On
- Danish Veterinary Laboratory, Copenhagen, Denmark.
| |
Collapse
|
20
|
Moser I, Rieksneuwöhner B, Lentzsch P, Schwerk P, Wieler LH. Genomic heterogeneity and O-antigenic diversity of Campylobacter upsaliensis and Campylobacter helveticus strains isolated from dogs and cats in Germany. J Clin Microbiol 2001; 39:2548-57. [PMID: 11427567 PMCID: PMC88183 DOI: 10.1128/jcm.39.7.2548-2557.2001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A serotyping scheme based on heat-stable surface antigens was established for 101 Campylobacter upsaliensis and 10 Campylobacter helveticus strains isolated from 261 dogs and 46 cats of different ages originating from two geographically distinct regions in Germany. The prevalence of C. upsaliensis varied between 27.8% in juvenile dogs (<12 months of age) and 55.4% in adult dogs (P < 0.05). Of the cats, 19.6% harbored C. upsaliensis, whereas 21.7% carried C. helveticus. Of the C. upsaliensis isolates from both host species, 93.1% belonged to five different serogroups, two of them being prevalent at rates of 47.5 and 27.7%, with different frequencies in both regions. Six (54.6%) of the C. helveticus isolates also belonged to serotypes found among C. upsaliensis strains, whereas five (45.4%) possessed an O antigen unique for C. helveticus. In contrast, a considerable degree of genomic diversity of the isolates was assessed by macrorestriction analyses with the endonucleases SmaI and XhoI, using pulsed-field gel electrophoresis as well as enterobacterial repetitive intergenic consensus sequence PCR (ERIC PCR). Restriction with SmaI pointed towards the existence of clonal groups associated to some extent with serotypes, while restriction with XhoI disintegrated these groups to smaller noncoherent subgroups. Analysis of ERIC PCR profiles did not exhibit any associations with serotypes. In conclusion these data demonstrate the genomic heterogeneity among C. upsaliensis strains and indicate that the combination of SmaI restriction with serotyping is a useful tool to investigate the expansion of clonal groups of C. upsaliensis.
Collapse
MESH Headings
- Animals
- Antigenic Variation
- Base Sequence
- Campylobacter/classification
- Campylobacter/genetics
- Campylobacter/immunology
- Campylobacter/isolation & purification
- Campylobacter Infections/epidemiology
- Campylobacter Infections/microbiology
- Campylobacter Infections/veterinary
- Cat Diseases/epidemiology
- Cat Diseases/microbiology
- Cats
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- Dog Diseases/epidemiology
- Dog Diseases/microbiology
- Dogs
- Electrophoresis, Gel, Pulsed-Field
- Genetic Variation
- Germany/epidemiology
- Molecular Sequence Data
- O Antigens/genetics
- O Antigens/immunology
- Polymerase Chain Reaction/methods
- Polymorphism, Restriction Fragment Length
- Prevalence
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Serotyping
Collapse
Affiliation(s)
- I Moser
- Institut für Mikrobiologie und Tierseuchen, Freie Universität, Berlin, Germany.
| | | | | | | | | |
Collapse
|
21
|
Franklin RB, Garland JL, Bolster CH, Mills AL. Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments. Appl Environ Microbiol 2001; 67:702-12. [PMID: 11157234 PMCID: PMC92638 DOI: 10.1128/aem.67.2.702-712.2001] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.
Collapse
Affiliation(s)
- R B Franklin
- Laboratory of Microbial Ecology, Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia 22904, USA
| | | | | | | |
Collapse
|
22
|
Pabbaraju K, Sanderson KE. Sequence diversity of intervening sequences (IVSs) in the 23S ribosomal RNA in Salmonella spp. Gene 2000; 253:55-66. [PMID: 10925202 DOI: 10.1016/s0378-1119(00)00239-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Intervening sequences (IVSs) occur sporadically in the rrl (ribosomal RNA large) genes for 23S ribosomal RNA (rRNA) at helix-25 (base pair 550) and helix 45 (base pair 1170) in several bacterial genera, including Salmonella, Yersinia, Proteus, and Providencia, representing the Enterobacteriaceae, but are missing from other genera such as Escherichia. These sequences are transcribed, but later excised without re-ligation during RNaseIII processing of the rRNA, resulting in fragmented 23S rRNA. The IVSs from 22 strains of the SARB (Salmonella Reference Collection B) set were amplified by PCR and sequenced.IVSs with 90% or more sequence identity were placed in the same family; Salmonella has three families of IVSs in helix-25 (A, B, and C) and two in helix-45 (M and O). The rRNA secondary structure for the IVSs predicted from the mfold program reveals a primary stem of about 14bp, which is the postulated RNaseIII cleavage site, and a secondary region of stems and loops. The primary stem is considerably well conserved, with a high rate of compensatory mutations (positional covariants), confirming the reality of the secondary structure and indicating that removal of the IVSs exerts a positive selective pressure to retain the secondary structure. The pattern of possession and presence of families of IVSs was diverse and could not be related to the proposed ancestry of the strains as revealed by the multi-locus enzyme electrophoresis pattern of the strains, suggesting that the IVSs are transferred between strains by lateral transfer. Helix-25 IVSs from families A, B, and C of Salmonella and D of Proteus, which share almost identical primary stems, are placed in superfamily I, while the primary stems of other IVSs from Proteus and Providencia are unrelated to superfamily I and are thus placed into superfamily II; this indicates lateral transfer of members of superfamily I between Proteus and Salmonella, but an independent origin of IVSs of superfamily II in Proteus and Providencia.
Collapse
Affiliation(s)
- K Pabbaraju
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Calgary, Canada
| | | |
Collapse
|
23
|
Pabbaraju K, Miller WL, Sanderson KE. Distribution of intervening sequences in the genes for 23S rRNA and rRNA fragmentation among strains of the Salmonella reference collection B (SARB) and SARC sets. J Bacteriol 2000; 182:1923-9. [PMID: 10714998 PMCID: PMC101879 DOI: 10.1128/jb.182.7.1923-1929.2000] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) occur sporadically in several bacterial genera in the genes for 23S rRNA at relatively conserved locations. They are cleaved after transcription and lead to the presence of fragmented rRNA, which is incorporated into the ribosomes without religation but is nevertheless functional. The fragmentation of rRNA and the number of IVSs in all 72 strains of the Salmonella Reference Collection B set and 16 strains of the Salmonella Reference Collection C set, which have been established on the basis of multilocus enzyme electrophoresis (MLEE), were analyzed in the present study. Fragmentation of 23S rRNA was restricted to conserved cleavage sites located at bp 550 (helix 25) and bp 1170 (helix 45), locations where IVSs have been reported. Random cleavage at sites where IVSs could not be detected was not seen. Uncleaved IVSs were not detected in any case; thus, the IVSs invariably led to rRNA fragmentation, indicating a strong selection for maintenance of RNase III cleavage sites. The distribution of the number of IVSs carried by the different strains in the seven rrl genes is diverse, and the pattern of IVS possession could not be related to the MLEE pattern among the various Salmonella strains tested; this indicates that the IVSs are frequently exchanged between strains by lateral transfer. All eight subspecies of the genus Salmonella, including subspecies V represented by Salmonella bongori, have IVSs in both helix 25 and helix 45; this indicates that IVSs entered the genus after its divergence from Escherichia coli (more than 100 million years ago) but before separation of the genus Salmonella into many forms or that they were in the ancestor but have been lost from Escherichia.
Collapse
MESH Headings
- Base Pairing/genetics
- Biological Specimen Banks
- Conserved Sequence/genetics
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli Proteins
- Genes, Bacterial/genetics
- Genetic Variation/genetics
- Models, Genetic
- Molecular Weight
- Phylogeny
- Polymerase Chain Reaction
- RNA Processing, Post-Transcriptional/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Recombination, Genetic/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Regulatory Sequences, Nucleic Acid/physiology
- Ribonuclease III
- Salmonella/classification
- Salmonella/genetics
- rRNA Operon/genetics
Collapse
Affiliation(s)
- K Pabbaraju
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4.
| | | | | |
Collapse
|
24
|
Miller WL, Pabbaraju K, Sanderson KE. Fragmentation of 23S rRNA in strains of Proteus and Providencia results from intervening sequences in the rrn (rRNA) genes. J Bacteriol 2000; 182:1109-17. [PMID: 10648538 PMCID: PMC94388 DOI: 10.1128/jb.182.4.1109-1117.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) were originally identified in the rrl genes for 23S rRNA (rrl genes, for large ribosomal subunit, part of rrn operon encoding rRNA) of Salmonella enterica serovars Typhimurium LT2 and Arizonae. These sequences are transcribed but later removed during RNase III processing of the rRNA, resulting in fragmentation of the 23S species; IVSs are uncommon, but have been reported in at least 10 bacterial genera. Through PCR amplification of IVS-containing regions of the rrl genes we showed that most Proteus and Providencia strains contain IVSs similar to those of serovar Typhimurium in distribution and location in rrl genes. By extraction and Northern blotting of rRNA, we also found that these IVSs result in rRNA fragmentation. We report the first finding of two very different sizes of IVS (113 bp and 183 to 187 bp) in different rrl genes in the same strain, in helix 25 of Proteus and Providencia spp.; IVSs from helix 45 are 113 to 123 bp in size. Analysis of IVS sequence and postulated secondary structure reveals striking similarities of Proteus and Providencia IVSs to those of serovar Typhimurium, with the stems of the smaller IVSs from helix 25 being similar to those of Salmonella helix 25 IVSs and with both the stem and the central loop domain of helix 45 IVSs being similar. Thus, IVSs of related sequences are widely distributed throughout the Enterobacteriaceae, in Salmonella, Yersinia, Proteus, and Providencia spp., but we did not find them in Escherichia coli, Citrobacter, Enterobacter, Klebsiella, or Morganella spp.; the sporadic distribution of IVSs of related sequence indicates that lateral genetic transfer has occurred.
Collapse
Affiliation(s)
- W L Miller
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | | | | |
Collapse
|
25
|
García-Martínez J, Acinas SG, Antón AI, Rodríguez-Valera F. Use of the 16S--23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 1999; 36:55-64. [PMID: 10353800 DOI: 10.1016/s0167-7012(99)00011-1] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The description of microbial diversity by molecular culture-independent techniques most often involves the amplification of the 16S rRNA by PCR gene and either analysis of the diversity of amplified molecules (community fingerprinting) that allows the simultaneous study of many samples or the cloning and sequencing of a significant amount of amplification products. The fact that between the 16S and the 23S genes in the ribosomal operon there is a spacer extremely variable in both sequence and length provides an excellent tool to simplify both approaches. The spacer can be amplified almost as easily as the 16S rDNA taking advantage of conserved nucleotide stretches at the 5' end of the 23S gene and the amplicon can contain different amounts of the 16S rDNA choosing primers at the different conserved areas within this gene. Identified by the acronym RISA (rDNA internal spacer analysis), the spacer addition provides a marker of highly variable size allowing standard separation of the amplification products and the sequence of this hypervariable region is useful in the fine discrimination of operational taxonomic units.
Collapse
Affiliation(s)
- J García-Martínez
- Unidad de Microbiología, Centro de Biología Molecular y Celular, Universidad Miguel Hernández, Campus de San Juan, Alicante, Spain
| | | | | | | |
Collapse
|
26
|
Monstein HJ, Tiveljung A, Jonasson J. Non-random fragmentation of ribosomal RNA in Helicobacter pylori during conversion to the coccoid form. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1998; 22:217-24. [PMID: 9848682 DOI: 10.1111/j.1574-695x.1998.tb01209.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The integrity of DNA and ribosomal RNAs in exponentially growing (bacillary) and ageing stationary phase (coccoid) cultures of Helicobacter pylori type strain CCUG 17874 was investigated. Extensive non-random fragmentation of rRNAs was observed during the conversion to the coccoid form. Beside a small proportion of full-length 16S and 23S rRNA that was always present, the majority of both 16S and 23S rRNA molecules showed distinct highly specific fragmentation patterns. The 16S rRNA fragmentation was characterised in detail by means of Northern blot and primer extension analysis. One cleavage site was located within the highly conserved U5 region (position about 920). The results could not be attributed to the presence of intervening sequences in the 16S and 23S rRNA genes.
Collapse
MESH Headings
- Blotting, Northern
- Cloning, Molecular
- DNA Primers
- DNA, Bacterial/analysis
- DNA, Single-Stranded/analysis
- Helicobacter pylori/cytology
- Helicobacter pylori/genetics
- Helicobacter pylori/growth & development
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
Collapse
Affiliation(s)
- H J Monstein
- Division of Clinical Microbiology, Faculty of Health Sciences, University Hospital, Linköping, Sweden
| | | | | |
Collapse
|
27
|
Etoh Y, Yamamoto A, Goto N. Intervening sequences in 16S rRNA genes of Campylobacter sp.: diversity of nucleotide sequences and uniformity of location. Microbiol Immunol 1998; 42:241-3. [PMID: 9570291 DOI: 10.1111/j.1348-0421.1998.tb02278.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We found and sequenced intervening sequences (IVSs) in the PCR-amplicons of 16S rRNA genes of 3 strains of Campylobacter rectus, 2 strains of C. curvus and 2 strains of C. sputorum. The lengths of the IVSs were 140 to 233 bp. The IVSs of C. rectus were identical and had a sequence homology of 55 to 79% against those of C. curvus and C. helveticus. The IVSs of C. sputorum were 97.9-100% homologous but poorly homologous to the other IVSs. In spite of the diversities of the lengths and the nucleotide sequences, all of the IVSs were located at the same position in the 16S rRNA genes.
Collapse
Affiliation(s)
- Y Etoh
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan.
| | | | | |
Collapse
|
28
|
Pettersson B, Bölske G, Thiaucourt F, Uhlén M, Johansson KE. Molecular evolution of Mycoplasma capricolum subsp. capripneumoniae strains, based on polymorphisms in the 16S rRNA genes. J Bacteriol 1998; 180:2350-8. [PMID: 9573185 PMCID: PMC107175 DOI: 10.1128/jb.180.9.2350-2358.1998] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycoplasma capricolum subsp. capripneumoniae belongs to the so-called Mycoplasma mycoides cluster and is the causal agent of contagious caprine pleuropneumonia (CCPP). All members of the M. mycoides cluster have two rRNA operons. The sequences of the 16S rRNA genes of both rRNA operons from 20 strains of M. capricolum subsp. capripneumoniae of different geographical origins in Africa and Asia were determined. Nucleotide differences which were present in only one of the two operons (polymorphisms) were detected in 24 positions. The polymorphisms were not randomly distributed in the 16S rRNA genes, and some of them were found in regions of low evolutionary variability. Interestingly, 11 polymorphisms were found in all the M. capricolum subsp. capripneumoniae strains, thus defining a putative ancestor. A sequence length difference between the 16S rRNA genes in a poly(A) region and 12 additional polymorphisms were found in only one or some of the strains. A phylogenetic tree was constructed by comparative analysis of the polymorphisms, and this tree revealed two distinct lines of descent. The nucleotide substitution rate of strains within line II was up to 50% higher than within line I. A tree was also constructed from individual operonal 16S rRNA sequences, and the sequences of the two operons were found to form two distinct clades. The topologies of both clades were strikingly similar, which supports the use of 16S rRNA sequence data from homologous operons for phylogenetic studies. The strain-specific polymorphism patterns of the 16S rRNA genes of M. capricolum subsp. capripneumoniae may be used as epidemiological markers for CCPP.
Collapse
Affiliation(s)
- B Pettersson
- Department of Biochemistry and Biotechnology, The Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | | |
Collapse
|
29
|
von Wintzingerode F, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 1997; 21:213-29. [PMID: 9451814 DOI: 10.1111/j.1574-6976.1997.tb00351.x] [Citation(s) in RCA: 1054] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.
Collapse
MESH Headings
- Artifacts
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Environmental Microbiology
- Equipment Contamination
- False Negative Reactions
- False Positive Reactions
- Mutagenesis
- Polymerase Chain Reaction/instrumentation
- Polymerase Chain Reaction/methods
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal/genetics
- RNA, Ribosomal/isolation & purification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
Collapse
Affiliation(s)
- F von Wintzingerode
- Institut für Mikrobiologie und Hygiene, Universitätsklinikum Charité, Berlin, Germany
| | | | | |
Collapse
|
30
|
Linton D, Lawson AJ, Owen RJ, Stanley J. PCR detection, identification to species level, and fingerprinting of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples. J Clin Microbiol 1997; 35:2568-72. [PMID: 9316909 PMCID: PMC230012 DOI: 10.1128/jcm.35.10.2568-2572.1997] [Citation(s) in RCA: 381] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Three sets of primers were designed for PCR detection and differentiation of Campylobacter jejuni and Campylobacter coli. The first PCR assay was designed to coidentify C. jejuni and C. coli based on their 16S rRNA gene sequences. The second PCR assay, based on the hippuricase gene sequence, identified all tested reference strains of C. jejuni and also strains of that species which lack detectable hippuricase activity. The third PCR assay, based on the sequence of a cloned (putative) aspartokinase gene and the downstream open reading frame, identified all tested reference strains of C. coli. The assays will find immediate application in the rapid identification to species level of isolates. The assays combine with a protocol for purification of total DNA from fecal samples to allow reproducible PCR identification of campylobacters directly from stools. Of 20 clinical samples from which campylobacters had been cultured, we detected C. jejuni in 17, C. coli in 2, and coinfection of C. jejuni and Campylobacter hyointestinalis in 1. These results were concordant with culture and phenotypic identification to species level. Strain typing by PCR-restriction fragment length polymorphism of the flagellin (flaA) gene detected identical flaA types in fecal DNA and the corresponding campylobacter isolate. Twenty-five Campylobacter-negative stool samples gave no reaction with the PCR assays. These PCR assays can rapidly define the occurrence, species incidence, and flaA genotypes of enteropathogenic campylobacters.
Collapse
Affiliation(s)
- D Linton
- Virus Reference Division, Central Public Health Laboratory, London, United Kingdom
| | | | | | | |
Collapse
|
31
|
Hurtado A, Clewley JP, Linton D, Owen RJ, Stanley J. Sequence similarities between large subunit ribosomal RNA gene intervening sequences from different Helicobacter species. Gene X 1997; 194:69-75. [PMID: 9266674 DOI: 10.1016/s0378-1119(97)00158-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
When the 23S rRNA genes from several Helicobacter species were amplified by PCR and compared with similar amplicons derived from H. pylori, they were seen to be enlarged in size. Sequencing of these enlarged genes from H. mustelae, H. canis (two strains) and H. muridarum identified insertions of novel sequence (intervening sequences, IVSs) sized between 93 and 377 bp located at nt 545, in place of an 8-nt sequence in the conventionally sized H. pylori gene. These IVSs were not present elsewhere in the genome. All strains with such IVSs lacked intact 23S rRNA which was replaced by two fragment whose sizes were consistent with cleavage at either side of the particular IVS. The predicted secondary structures of the four IVSs were characterised by base pairing at the 5' and 3' ends to form a stem. The four IVSs exhibited significant sequence inter-relationships. Further relationships were also observed between them and similar elements in both small and large subunit rRNA genes of other Helicobacter and Campylobacter species. Alignment of each IVS with the other such elements identified blocks of related sequence consistent with insertion/deletion events, indicating possible evolutionary relationships.
Collapse
Affiliation(s)
- A Hurtado
- Laboratory of Enteric Pathogens, Central Public Health Laboratory, London, UK
| | | | | | | | | |
Collapse
|
32
|
Linton D, Owen RJ, Stanley J. Rapid identification by PCR of the genus Campylobacter and of five Campylobacter species enteropathogenic for man and animals. Res Microbiol 1996; 147:707-18. [PMID: 9296105 DOI: 10.1016/s0923-2508(97)85118-2] [Citation(s) in RCA: 261] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The nucleotide sequences for the 16S ribosomal RNA gene were compared for 33 species comprising the epsilon subdivision of the Proteobacteria (genera: Campylobacter, Helicobacter, Arcobacter and Wolinella). Regions specific for the genus Campylobacter and for five Campylobacter species important in human and/or veterinary medicine were identified. From these regions, PCR primer pairs were designed for use in species-specific identification. Primer pairs were validated against strains representing all taxa of campylobacter-like organisms. They did not amplify products other than from their five target species (C. upsaliensis, C. helveticus, C. fetus, C. hyointestinalis and C. lari), and they generated amplicons of defined size from large numbers of strains of those species. A primer pair suitable for identification of the genus Campylobacter was also identified and validated. This generated amplicons from all species of Campylobacter as well as from unnamed groups known to be within the genus, but not from any species or unnamed strains of Helicobacter, Arcobacter or Wolinella.
Collapse
Affiliation(s)
- D Linton
- Molecular Biology Unit, Central Public Health Laboratory, London
| | | | | |
Collapse
|
33
|
Latour X, Corberand T, Laguerre G, Allard F, Lemanceau P. The composition of fluorescent pseudomonad populations associated with roots is influenced by plant and soil type. Appl Environ Microbiol 1996; 62:2449-56. [PMID: 16535355 PMCID: PMC1388893 DOI: 10.1128/aem.62.7.2449-2456.1996] [Citation(s) in RCA: 184] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Populations of fluorescent pseudomonads isolated from an uncultivated soil and from the roots of two plant species were previously shown to differ (P. Lemanceau, T. Corberand, L. Gardan, X. Latour, G. Laguerre, J.-M. Boeufgras, and C. Alabouvette, Appl. Environ. Microbiol. 61:1004-1012, 1995). The diversities of fluorescent pseudomonads, from two uncultivated soils and from the roots of two plant species cultivated in these two soils, were compared. The phenotypic diversity of the bacterial isolates was characterized on the basis of biochemical and physiological tests and on the basis of their ability to utilize 147 different organic compounds. The genotypic diversity of the isolates was characterized on the basis of the types of 16S genes coding for rRNA (rDNA), their repetitive extragenic palindromic patterns by PCR, and plasmid profiles. Taxonomic identification of the isolates was achieved with both biochemical and physiological tests and by comparing their 16S rDNA types to those of reference and type strains of fluorescent Pseudomonas spp. Numerical analysis of phenotypic characteristics allowed the clustering of isolates that showed high levels of similarity. This analysis indicated that both soil type and host plant had an effect on the diversity of fluorescent pseudomonads. However, of the two factors studied, the soil was clearly the dominating one. Indeed, the populations associated with the roots of each plant species varied from one soil to the other. This variation could possibly be ascribed to the differences recorded between the phenotypically diverse populations of fluorescent pseudomonads from the two uncultivated soils. The plant selection was, at least partly, plant specific. It was not related to bacterial species and biovars or to the presence of plasmid DNA. The phenotypic clustering of isolates was well correlated with genotypic characterization by repetitive extragenic palindrome-PCR fingerprinting.
Collapse
|
34
|
On SL. Identification methods for campylobacters, helicobacters, and related organisms. Clin Microbiol Rev 1996; 9:405-22. [PMID: 8809468 PMCID: PMC172901 DOI: 10.1128/cmr.9.3.405] [Citation(s) in RCA: 220] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The organisms which are referred to as campylobacteria are associated with a diverse range of diseases and habitats and are important from both clinical and economic perspectives. Accurate identification of these organisms is desirable for deciding upon appropriate therapeutic measures, and also for furthering our understanding of their pathology and epidemiology. However, the identification process is made difficult because of the complex and rapidly evolving taxonomy, fastidious nature, and biochemical inertness of these bacteria. These problems have resulted in a proliferation of phenotypic and genotypic methods for identifying members of this group. The purpose of this review is to summarize the problems associated with identifying campylobacteria, critically appraise the methods that have been used for this purpose, and discuss prospects for improvements in this field.
Collapse
Affiliation(s)
- S L On
- Danish Veterinary Laboratory, Copenhagen V, Denmark.
| |
Collapse
|
35
|
Mattatall NR, Sanderson KE. Salmonella typhimurium LT2 possesses three distinct 23S rRNA intervening sequences. J Bacteriol 1996; 178:2272-8. [PMID: 8636028 PMCID: PMC177935 DOI: 10.1128/jb.178.8.2272-2278.1996] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The rrl genes for 23S rRNA of Salmonella typhimurium LT2 are known to carry intervening sequences (IVSs) at two sites, helix-25 and helix-45, which are excised by RNase III during rRNA maturation, resulting in rRNA which is fragmented but nevertheless functional. We isolated DNA fragments containing the seven rrl genes from BlnI, I-CeuI, and SpeI genomic digests following pulsed-field gel electrophoresis and used these DNA fragments as templates for PCRs utilizing primers upstream and downstream of helix-25 and helix-45. Variance in amplicon length and cycle sequencing indicated that rrlG and rrlH have IVSs in helix-25 of approximately 110 bp which are only 56% identical. rrnA, rrnB, rrnC, rrnD, rrnE, and rrnH have IVSs of approximately 90 bp in helix-45, and all have the same nucleotide sequence. Twenty-one independent wild-type strains of S. typhimurium from Salmonella Reference Collection A were analyzed for IVSs by using PCRs with genomic DNAs and by denaturing agarose electrophoresis of RNAs. Many strains resemble LT2, but some have no IVSs in helix-25 and others have IVSs in helix-45 in all seven rrl genes. However, the IVSs in individual wild-type lines are relatively stable, for several LT2 isolates separated over many years by many single-colony isolations are indistinguishable from one another, with the exception of line LB5010, which differs by one helix-25 IVS. We postulate that IVSs have entered strain LT2 by three independent lateral-transfer events and that the IVS in helix-45 was dispersed to and maintained in the same sequence in six of the seven rrl genes by the mechanism of gene conversion.
Collapse
Affiliation(s)
- N R Mattatall
- Salmonella Genetic Stock Centre, Uniersity of Calgary, Alberta, Canada.
| | | |
Collapse
|
36
|
Wesley IV, Schroeder-Tucker L, Baetz AL, Dewhirst FE, Paster BJ. Arcobacter-specific and Arcobacter butzleri-specific 16S rRNA-based DNA probes. J Clin Microbiol 1995; 33:1691-8. [PMID: 7545177 PMCID: PMC228251 DOI: 10.1128/jcm.33.7.1691-1698.1995] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The genus Arcobacter encompasses gram-negative, aerotolerant, spiral-shaped bacteria formerly designated Campylobacter cryaerophila. Two genus-specific 16S rRNA-based oligonucleotide DNA probes (23-mer and 27-mer) were developed. The probes hybridized with strains of Arcobacter butzleri (n = 58), Arcobacter cryaerophilus (n = 19), and Arcobacter skirrowii (n = 17). The probes did not cross-react with any of the reference strains of Campylobacter, Helicobacter, including "Flexispira rappini," or Wolinella. The 27-mer hybridized with 61 Arcobacter spp. field isolates originating from late-term aborted porcine (n = 54) and equine (n = 2) fetuses and humans with enteritis (n = 5). The species of Arcobacter isolates (n = 56) recovered from aborted livestock fetuses were determined by ribotyping and were as follows: A. cryaerophilus group 1A (11 of 56; 20%), A. cryaerophilus group 1B (37 of 56; 66%), A. butzleri (5 of 56; 9%), and unknown (3 of 56; 5%). The five human field strains were identified as A. butzleri. A species-specific DNA probe (24-mer) for A. butzleri was also developed since there is evidence that this organism may be a human pathogen. This probe hybridized with previously characterized strains of A. butzleri (n = 58), with 10 field strains identified as A. butzleri by ribotyping and with 2 strains having an indeterminate ribotype. The A. butzleri-specific probe did not cross-react with strains of A. skirrowii (n = 17) and A. cryaerophilus (n = 19).
Collapse
Affiliation(s)
- I V Wesley
- National Animal Disease Center, U.S. Department of Agriculture, Ames, Iowa 50010, USA
| | | | | | | | | |
Collapse
|
37
|
Farrelly V, Rainey FA, Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 1995; 61:2798-801. [PMID: 7618894 PMCID: PMC167554 DOI: 10.1128/aem.61.7.2798-2801.1995] [Citation(s) in RCA: 521] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In order to assess the effect of genome size and number of 16S rRNA genes (rDNAs) on the quantities of PCR-generated partial 16S rDNA fragments, equimolar amounts of DNA from pairs of different species for which these parameters are known were subjected to gene amplification. The experimentally determined ratio of PCR products obtained, as determined by image analysis of SYBR-Green I-stained amplification products, corresponded well with the predicted ratio calculated from the number of rrn genes per equimolar amounts of DNA in mixtures of Escherichia coli and "Thermus thermophilus" and of Pseudomonas aeruginosa and "T. thermophilus." The values for the pair of Bacillus subtilis and "T. thermophilus" showed greater deviations from the predicted value. The dependence of the amount of 16S rDNA amplification product on these two parameters makes it impossible to quantify the number of species represented in 16S rDNA clone libraries of environmental samples as long as these two parameters are unknown for the species present.
Collapse
Affiliation(s)
- V Farrelly
- DSM-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig
| | | | | |
Collapse
|
38
|
Linton D, Clewley JP, Burnens A, Owen RJ, Stanley J. An intervening sequence (IVS) in the 16S rRNA gene of the eubacterium Helicobacter canis. Nucleic Acids Res 1994; 22:1954-8. [PMID: 7518076 PMCID: PMC308106 DOI: 10.1093/nar/22.11.1954] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
PCR amplicons enlarged by approximately 250bp were generated from the 16S rRNA (rrs) genes of certain strains of the recently described Helicobacter species, H. canis. The DNA sequence of the rrs gene of one such strain was determined, and it was shown that an intervening sequence (IVS) of 235bp followed nucleotide 199 in the rrs sequence. In four other H. canis strains, identical or similar IVSs were found, always at the same location in the rrs gene. The secondary structures of the RNA transcripts of the IVSs were predicted. They were characterised by the presence of a conserved stem-loop structure, a potential recognition site for RNA processing enzymes. Ribosomal RNA was compared from a strain of H. canis with and without the IVS-containing rrs gene. In the former 16S rRNA appeared as two fragments, whose sizes were consistent with cleavage at either side of the IVS, and which were not subsequently religated. The IVS sequence was not represented elsewhere in the H. canis genome. Its evolutionary significance is discussed.
Collapse
Affiliation(s)
- D Linton
- National Collection of Type Cultures, Virus Reference Division, Central Public Health Laboratory, London, UK
| | | | | | | | | |
Collapse
|