1
|
Fukushi M, Mino S, Tanaka H, Nakagawa S, Takai K, Sawabe T. Biogeochemical Implications of N 2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov. iScience 2020; 23:101462. [PMID: 32866828 PMCID: PMC7476070 DOI: 10.1016/j.isci.2020.101462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/21/2020] [Accepted: 08/12/2020] [Indexed: 01/02/2023] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.
Collapse
Affiliation(s)
- Muneyuki Fukushi
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Hirohisa Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| |
Collapse
|
2
|
Shakir SM, Powers-Fletcher MV, Slechta ES, Fisher MA. Helicobacter canis bacteraemia and cellulitis in a patient with end-stage renal disease. JMM Case Rep 2017; 4:e005126. [PMID: 29255610 PMCID: PMC5729898 DOI: 10.1099/jmmcr.0.005126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022] Open
Abstract
Introduction. Invasive infections by Helicobacter canis are uncommon and occur primarily in immunocompromised patients. Here, we describe a case of H. canis bacteraemia and cellulitis in a patient with end-stage renal disease (ESRD). Case presentation. A 49-year-old male with ESRD on haemodialysis presented to an emergency department with cellulitis overlying his left upper extremity arteriovenous fistula for 3 days without constitutional symptoms. Mild leucocytosis and thrombocytopenia was noted on initial laboratory work up. The patient received a dose of vancomycin initially, and then transitioned to oral doxycycline prior to discharge 3 days later. Blood cultures drawn on admission were positive with curved Gram-negative rods at day 5. Routine sub-cultures initially failed to isolate the organism; however, small, tan colonies were observed on sheep blood agar incubated under microaerobic conditions. H. canis was identified by 16S rRNA sequencing. Antimicrobial-susceptibility testing was not performed due to poor growth and lack of interpretive guidelines. The patient was ultimately treated successfully with amoxicillin/clavulanic acid. Conclusion. This case illustrates the importance of recognizing H. canis infections in immunocompromised patients, especially in those with recent pet exposure. In addition, this case highlights the need for improved laboratory diagnostics for H. canis as isolation and identification of this fastidious organism is challenging.
Collapse
Affiliation(s)
- Salika M. Shakir
- Department of Pathology, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
- *Correspondence: Salika M. Shakir,
| | | | - E. Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Mark A. Fisher
- Department of Pathology, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| |
Collapse
|
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
|
Kawamura Y, Tomida J, Miyoshi-Akiyama T, Okamoto T, Narita M, Hashimoto K, Cnockaert M, Vandamme P, Morita Y, Sawa T, Akaike T. Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter cinaedi, isolated from canines. Syst Appl Microbiol 2016; 39:307-12. [PMID: 27381809 DOI: 10.1016/j.syapm.2016.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 01/27/2023]
Abstract
During the course of our taxonomic investigation of Helicobacter cinaedi, it was realized that the strains isolated from dogs, which have been identified as H. cinaedi, showed different biochemical traits than did the isolates obtained from humans. None of the three dog isolates could reduce nitrate to nitrite, whereas all of the human H. cinaedi isolates could do so. The dog isolates showed a strong positive alkaline phosphatase reaction and could grow at 42°C, however the human isolates showed negative to very weak responses to those tests. The GyrA protein based phylogenetic analysis showed that the three isolates from dogs formed a slightly distinct cluster from the human isolate cluster. Phylogenetic analysis of the 16S rRNA, 23S rRNA, gyrB, and hsp60 gene sequences further confirmed that the dog isolates differed from the human H. cinaedi isolate cluster. The whole-genome in silico DNA similarities of each isolate based on their full genome sequences revealed that the isolates from dogs shared more than 94.9% ANIb (average nucleotide identity based on BLAST), while 94.0% ANIb were found between the isolates from dogs and the humans, including the H. cinaedi type strain ATCC BAA-847(T) (=CCUG 18818(T)). From these data, we propose a new species, 'H. canicola' sp. nov., for the isolates from dogs. The type strain is PAGU 1410(T) (CCUG 33887(T)=LMG 29580(T)).
Collapse
Affiliation(s)
- Yoshiaki Kawamura
- Department of Microbiology, Aichi Gakuin University, School of Pharmacy, 1-100 Kusumoto-cho, Nagoya, Aichi 464-8650, Japan.
| | - Junko Tomida
- Department of Microbiology, Aichi Gakuin University, School of Pharmacy, 1-100 Kusumoto-cho, Nagoya, Aichi 464-8650, Japan.
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan.
| | - Tatsuya Okamoto
- Intensive Care Unit, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan.
| | - Masashi Narita
- Division of Infectious Diseases, Department of Medicine, Okinawa Chubu Hospital, 281 Miyazato, Uruma, Okinawa 902-2293, Japan.
| | - Katsuhiko Hashimoto
- Emergency, Critical Care and Anesthesia, Ohta General Hospital Foundation, Ohta Nishinouchi Hospital, 2-5-20, Nishinouchi, Koriyama, Fukushima 963-8558, Japan.
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
| | - Yuji Morita
- Department of Microbiology, Aichi Gakuin University, School of Pharmacy, 1-100 Kusumoto-cho, Nagoya, Aichi 464-8650, Japan.
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjou, Kumamoto, Kumamoto 860-8556, Japan.
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba, Sendai, Miyagi 980-8575, Japan.
| |
Collapse
|
5
|
Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria. Proc Natl Acad Sci U S A 2012; 109:4203-8. [PMID: 22371583 DOI: 10.1073/pnas.1120192109] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gene encoding the small subunit rRNA serves as a prominent tool for the phylogenetic analysis and classification of Bacteria and Archaea owing to its high degree of conservation and its fundamental function in living organisms. Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis, regularly contain numerous self-splicing introns of variable length. The 16S rRNA genes can thus be enlarged to up to 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although they are the most frequently sequenced genes today. This may be caused in part by a bias during the PCR amplification step that discriminates against longer homologs, as we show experimentally. Such length heterogeneity of 16S rRNA genes has so far never been considered when constructing 16S rRNA-based clone libraries, even though an elongation of rRNA genes due to intervening sequences has been reported previously. The detection of elongated 16S rRNA genes has profound implications for common methods in molecular ecology and may cause systematic biases in several techniques. In this study, catalyzed reporter deposition-fluorescence in situ hybridization on both ribosomes and rRNA precursor molecules as well as in vitro splicing experiments were performed and confirmed self-splicing of the introns. Accordingly, the introns do not inhibit the formation of functional ribosomes.
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
|
The internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the Campylobacter genus. Appl Environ Microbiol 2010; 76:3071-81. [PMID: 20348308 DOI: 10.1128/aem.02551-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Campylobacter genus consists of a number of important human and animal pathogens. Although the 16S rRNA gene has been used extensively for detection and identification of Campylobacter species, there is currently limited information on the 23S rRNA gene and the internal transcribed spacer (ITS) region that lies between the 16S and 23S rRNA genes. We examined the potential of the 23S rRNA gene and the ITS region to be used in species differentiation and delineation of systematic relationships for 30 taxa within the Campylobacter genus. The ITS region produced the highest mean pairwise percentage difference (35.94%) compared to the 16S (5.34%) and 23S (7.29%) rRNA genes. The discriminatory power for each region was further validated using Simpson's index of diversity (D value). The D values were 0.968, 0.995, and 0.766 for the ITS region and the 23S and 16S rRNA genes, respectively. A closer examination of the ITS region revealed that Campylobacter concisus, Campylobacter showae, and Campylobacter fetus subsp. fetus harbored tRNA configurations not previously reported for other members of the Campylobacter genus. We also observed the presence of strain-dependent intervening sequences in the 23S rRNA genes. Neighbor-joining trees using the ITS region revealed that Campylobacter jejuni and Campylobacter coli strains clustered in subgroups, which was not observed in trees derived from the 16S or 23S rRNA gene. Of the three regions examined, the ITS region is by far the most cost-effective region for the differentiation and delineation of systematic relationships within the Campylobacter genus.
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
|
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
|
10
|
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
|
11
|
Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, Paster BJ, Fox JG. Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J Bacteriol 2005; 187:6106-18. [PMID: 16109952 PMCID: PMC1196133 DOI: 10.1128/jb.187.17.6106-6118.2005] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.
Collapse
Affiliation(s)
- Floyd E Dewhirst
- Department of Molecular Genetics, The Forsyth Institute, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Hänninen ML, Kärenlampi RI, Koort JMK, Mikkonen T, Björkroth KJ. Extension of the species Helicobacter bilis to include the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Finnish canine and feline flexispira strains. Int J Syst Evol Microbiol 2005; 55:891-898. [PMID: 15774681 DOI: 10.1099/ijs.0.63245-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The evolution and taxonomy of enterohepatic Helicobacter species with flexispira morphology were studied by a polyphasic approach including phenotypic characterization, analysis of 16S rRNA and ureB gene sequences and dot-blot DNA-DNA hybridization of whole genomic DNA. In addition, available phylogenetic data on the HSP60 gene were used in the analysis. The study included 14 Finnish canine and feline flexispira strains, the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Helicobacter bilis ATCC 51630(T). Phenotypically, all canine and feline strains were similar to H. bilis. Analysis of 16S rRNA gene sequences of these strains revealed a similarity of 97-99.5 %. Similarity of ureB nucleotide and amino acid sequences within the studied flexispira group was 97-100 % and 99-100 %, respectively, revealing close relatedness. ureB sequences of Helicobacter hepaticus had only 64-66 % similarity to the flexispira group. The similarity to Helicobacter trogontum was 81.5-82.1 %. High levels of DNA-DNA hybridization between the strains were found in dot-blot tests. Polyphasic analysis of the phenotypic and genotypic characteristics of the Finnish flexispira strains and the reference strains of taxa 2, 3 and 8 showed that they differed from other Helicobacter species and are members of the previously described species H. bilis. In addition, canine strain F56 differed in all phylogenetic analyses from the H. bilis group and probably represents a novel Helicobacter species.
Collapse
Affiliation(s)
- M-L Hänninen
- Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Helsinki University, PO Box 66, FI-00014 Helsinki, Finland
| | - R I Kärenlampi
- Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Helsinki University, PO Box 66, FI-00014 Helsinki, Finland
| | - J M K Koort
- Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Helsinki University, PO Box 66, FI-00014 Helsinki, Finland
| | - T Mikkonen
- Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Helsinki University, PO Box 66, FI-00014 Helsinki, Finland
| | - K J Björkroth
- Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Helsinki University, PO Box 66, FI-00014 Helsinki, Finland
| |
Collapse
|
13
|
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
|
14
|
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
|
15
|
Beier CL, Horn M, Michel R, Schweikert M, Görtz HD, Wagner M. The genus Caedibacter comprises endosymbionts of Paramecium spp. related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria). Appl Environ Microbiol 2002; 68:6043-50. [PMID: 12450827 PMCID: PMC134415 DOI: 10.1128/aem.68.12.6043-6050.2002] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Obligate bacterial endosymbionts of paramecia able to form refractile inclusion bodies (R bodies), thereby conferring a killer trait upon their ciliate hosts, have traditionally been grouped into the genus CAEDIBACTER: Of the six species described to date, only the Paramecium caudatum symbiont Caedibacter caryophilus has been phylogenetically characterized by its 16S rRNA gene sequence, and it was found to be a member of the Alphaproteobacteria related to the RICKETTSIALES: In this study, the Caedibacter taeniospiralis type strain, an R-body-producing cytoplasmatic symbiont of Paramecium tetraurelia strain 51k, was investigated by comparative 16S rRNA sequence analysis and fluorescence in situ hybridization with specific oligonucleotide probes. C. taeniospiralis is not closely related to C. caryophilus (80% 16S rRNA sequence similarity) but forms a novel evolutionary lineage within the Gammaproteobacteria with the family Francisellaceae as a sister group (87% 16S rRNA sequence similarity). These findings demonstrate that the genus Caedibacter is polyphyletic and comprises at least two phylogenetically different bacterial species belonging to two different classes of the PROTEOBACTERIA: Comparative phylogenetic analysis of C. caryophilus, five closely related Acanthamoeba endosymbionts (including one previously uncharacterized amoebal symbiont identified in this study), and their hosts suggests that the progenitor of the alphaproteobacterial C. caryophilus lived within acanthamoebae prior to the infection of paramecia.
Collapse
Affiliation(s)
- Cora L Beier
- Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany
| | | | | | | | | | | |
Collapse
|
16
|
Iten A, Graf S, Egger M, Täuber M, Graf J. Helicobacter sp. flexispira bacteremia in an immunocompetent young adult. J Clin Microbiol 2001; 39:1716-20. [PMID: 11325980 PMCID: PMC88015 DOI: 10.1128/jcm.39.5.1716-1720.2001] [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
A young immunocompetent patient was admitted for a febrile illness with malaise, arthralgias, painful leg swelling, and polyserositis. Shortly prior to becoming ill, the patient had traveled to the Northern African desert. The symptoms disappeared during treatment with antibiotics (doxycycline and ceftriaxone) but recurred twice after stopping therapy. A motile gram-negative fusiform rod was isolated from a blood culture taken on the first admission. Analysis of the 16S rRNA gene of the blood culture isolate revealed close similarity with Helicobacter sp. flexispira taxon 8 (99.9% identity), a species that was previously reported as "Flexispira rappini." This is the first reported case of a recurrent Helicobacter sp. flexispira bacteremia in an adult, immunocompetent patient.
Collapse
Affiliation(s)
- A Iten
- University Hospital Insel, University of Berne, Friedbühlstr. 51, CH-3010 Berne, Switzerland
| | | | | | | | | |
Collapse
|
17
|
Vaneechoutte M, Heyndrickx M. Application and Analysis of ARDRA Patterns in Bacterial Identification, Taxonomy and Phylogeny. NEW APPROACHES FOR THE GENERATION AND ANALYSIS OF MICROBIAL TYPING DATA 2001:211-247. [DOI: 10.1016/b978-044450740-2/50010-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
18
|
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
|
19
|
Han S, Schindel C, Genitsariotis R, Märker-Hermann E, Bhakdi S, Maeurer MJ. Identification of a unique Helicobacter species by 16S rRNA gene analysis in an abdominal abscess from a patient with X-linked hypogammaglobulinemia. J Clin Microbiol 2000; 38:2740-2. [PMID: 10878075 PMCID: PMC87015 DOI: 10.1128/jcm.38.7.2740-2742.2000] [Citation(s) in RCA: 21] [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
A unique Helicobacter species, MZ640285, was isolated from a patient with X-linked hypogammaglobulinemia suffering from recurrent abdominal abscesses and was identified by 16S rRNA gene sequence analysis. In the phylogenetic tree, the isolate fell into a cluster which included Flexispira rappini, Helicobacter bilis, and Helicobacter sp. strain Mainz. Helicobacters are being increasingly recognized as pathogens in immunocompromised hosts. These fastidious bacteria are not easily cultured in the routine diagnostic laboratory, and this is the first report of their identification by 16S rRNA gene sequencing performed directly from a clinical specimen.
Collapse
Affiliation(s)
- S Han
- Department of Medical Microbiology, Johannes Gutenberg University, Mainz, Germany
| | | | | | | | | | | |
Collapse
|
20
|
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
|
21
|
Foley JE, Marks SL, Munson L, Melli A, Dewhirst FE, Yu S, Shen Z, Fox JG. Isolation of Helicobacter canis from a colony of bengal cats with endemic diarrhea. J Clin Microbiol 1999; 37:3271-5. [PMID: 10488191 PMCID: PMC85546 DOI: 10.1128/jcm.37.10.3271-3275.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
On the basis of biochemical, phenotypic, and 16S rRNA analyses, Helicobacter canis was isolated from Bengal cats with and without chronic diarrhea. Because the cats were coinfected with other potential pathogens, including Campylobacter helveticus, and because H. canis was isolated from nondiarrheic cats, the causal role of H. canis in producing the diarrhea could not be proven. Histologically, the colons of the four affected cats were characterized by mild to moderate neutrophilic, plasmacytic, and histocytic infiltrates in the lamina propria. Rare crypt abscesses were also noted for three cats but were a more prominent feature of the colonic lesions noted for the fourth cat. This is the first observation of H. canis in cats and raises the possibility that H. canis, like H. hepaticus and H. bilis in mice, can cause inflammation of the colon, particularly in hosts with immune dysregulation. Further studies are needed to determine the importance of H. canis as a primary enteric pathogen in cats and the role of cats in the possible zoonotic spread of H. canis to humans.
Collapse
Affiliation(s)
- J E Foley
- Department of Medicine and Epidemiology, Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis 95616, USA
| | | | | | | | | | | | | | | |
Collapse
|
22
|
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
|
23
|
Naimi A, Beck G, Monique M, Lefèbvre G, Branlanti C. Determination of the nucleotide sequence of the 23S ribosomal RNA and flanking spacers of an Enterococcus faecium strain, reveals insertion-deletion events in the ribosomal spacer 1 of enterococci. Syst Appl Microbiol 1999; 22:9-21. [PMID: 10188274 DOI: 10.1016/s0723-2020(99)80023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The usefulness of 16S-23S (ITS1) and 23S-5S (ITS2) ribosomal spacer nucleotide sequence determination, as a complementary approach to the biochemical tests traditionally used for enterococcal species identification, is shown by its application to the identification of a strain, E27, isolated from a natural bacteria mixture used for cheese production. Using combined approaches we showed, unambiguously, that strain E27 belongs to the Enterococcus faecium species. However, its ITS1 region has an interesting peculiarity. In our previous study of ITS1s from various enterococcal species (NAIMI et al., 1997, Microbiology 143, 823-834), the ITS1s of the two E. faecium strains studied, were found to contain an additional 115-nt long stem-loop structure as compared to the ITS1s of other enterococci, only one out of the 3 ITS1s of E. hirae ATCC 9790, was found to contain a similar 107-nt long stem-loop structure. The ITS1 of strain E27 is 100% identical to that of E. faecium ATCC 19434T, except that the 115-nt additional fragment is absent. This strongly suggests the existence of lateral DNA transfer or DNA recombination events at a hot spot position of the ITS1s from E. faecium and E. hirae. Small and large ITS1 nucleotide sequence determination for strain E27 generalized the notion of two kinds of ITSs in enterococci: one with a tRNA(Ala) gene, one without tRNA gene. To complete strain E27 characterization, its 23S rRNA sequence was established. This is the first complete 23S rRNA nucleotide sequence determined for an enterococcal species.
Collapse
Affiliation(s)
- A Naimi
- Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-Université Henri Poincaré, Vandoeuvre-Lès-Nancy, France
| | | | | | | | | |
Collapse
|
24
|
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
|
25
|
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
|
26
|
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
|
27
|
Malarkey DE, Ton TV, Hailey JR, Devereux TR. A PCR-RFLP method for the detection of Helicobacter hepaticus in frozen or fixed liver from B6C3F1 mice. Toxicol Pathol 1997; 25:606-12. [PMID: 9437806 DOI: 10.1177/019262339702500611] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Establishing the diagnosis of Helicobacter hepaticus infection in mouse liver has recently become important for the interpretation of rodent carcinogenicity bioassays. A seminested primer polymerase chain reaction (PCR) amplification of the bacterial 16S ribosomal RNA gene in combination with a restriction fragment length polymorphism (RFLP) assay was designed to identify and distinguish H. hepaticus from H. muridarum and H. bilis in mouse liver. The PCR-RFLP assay was applied to formalin-fixed, paraffin-embedded and, when available, corresponding frozen liver tissues from male and female B6C3F1 mice with or without histologic evidence of infection from various National Toxicology Program 2-yr bioassay studies. PCR products consistent with H. hepaticus were detected in 10-80% of livers from mice in studies with other evidence of infection that were frozen or fixed for less than 24 hr but not in liver fixed for several weeks. The sensitivity of the PCR-RFLP assay for H. hepaticus on formalin-fixed, paraffin-embedded mouse liver varied between studies from markedly decreased when compared to the results from frozen liver or histologic evaluation to nearly equivalent or more sensitive than histologic evaluation. The PCR-RFLP results appeared dependent on the duration of fixation and bacterial load but not on the presence of hepatitis, sampling from neoplastic or nonneoplastic liver, or sex of the mouse.
Collapse
Affiliation(s)
- D E Malarkey
- Department of Microbiology, Pathology, and Parasitology, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA.
| | | | | | | |
Collapse
|
28
|
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
|
29
|
Fox JG, Drolet R, Higgins R, Messier S, Yan L, Coleman BE, Paster BJ, Dewhirst FE. Helicobacter canis isolated from a dog liver with multifocal necrotizing hepatitis. J Clin Microbiol 1996; 34:2479-82. [PMID: 8880504 PMCID: PMC229299 DOI: 10.1128/jcm.34.10.2479-2482.1996] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
On the basis of biochemical, phenotypic, and 16S rRNA analysis, a novel gram-negative bacterium, isolated from normal and diarrheic dogs as well as humans with gastroenteritis, has been recently named Helicobacter canis. A 2-month-old female crossbred puppy was submitted to necropsy with a history of weakness and vomiting for several hours prior to death. The liver had multiple and slightly irregular yellowish foci up to 1.5 cm in diameter. Histologically, the liver parenchyma contained randomly distributed, occasionally coalescing hepatocellular necrosis, often accompanied by large numbers of mononuclear cells and neutrophils. Sections of liver stained by the Warthin-Starry silver impregnation technique revealed spiral- to curve-shaped bacteria predominantly located in bile canaliculi and occasionally in bile ducts. Aerobic culture of liver was negative, whereas small colonies were noted on Campylobacter selective media after 5 days of microaerobic incubation. The bacteria were gram negative and oxidase positive but catalase, urease, and indoxyl acetate negative; nitrate was not reduced to nitrite, and the organism did not hydrolyze hippurate. The bacteria were also resistant to 1.5% bile. Electron microscopy revealed spiral-shaped bacteria with bipolar sheathed flagella. By 16S rRNA analysis, the organism was determined to be H. canis. This is the first observation of H. canis in active hepatitis in a dog and correlates with recent findings of Helicobacter hepaticus- and Helicobacter bilis-related hepatic disease in mice. Further studies are clearly warranted to ascertain whether H. canis-associated hepatitis is more widespread in canines as well as a cause of previously classified idiopathic liver disease in humans.
Collapse
Affiliation(s)
- J G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. Prokaryotic introns and inteins: a panoply of form and function. J Bacteriol 1995; 177:3897-903. [PMID: 7608058 PMCID: PMC177115 DOI: 10.1128/jb.177.14.3897-3903.1995] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- M Belfort
- Molecular Genetics Program, Wadsworth Center and School of Public Health, State University of New York at Albany 12201-2002, USA
| | | | | | | |
Collapse
|
31
|
Abstract
The analysis of information in nucleotide and amino acid sequence data from an investigator's own laboratory, or from the ever-growing worldwide databases, is critically dependent on well planned and written software. Although the most powerful packages previously have been confined to workstations, there has been a dramatic increase over the last few years in the sophistication of the programs available for personal computers, as the speed and power of these have increased. A wide choice of software is available for the Macintosh, including the LaserGene suite of programs from DNAStar. This review assesses the strengths and weaknesses of LaserGene and concludes that it provides a useful and comprehensive range of sequence analysis tools.
Collapse
Affiliation(s)
- J P Clewley
- Virus Reference Division, Central Public Health Laboratory, London, UK
| |
Collapse
|