1
|
Mongruel ACB, Medici EP, Canena ADC, Calchi AC, Machado RZ, André MR. Expanding the Universe of Hemoplasmas: Multi-Locus Sequencing Reveals Putative Novel Hemoplasmas in Lowland Tapirs ( Tapirus terrestris), the Largest Land Mammals in Brazil. Microorganisms 2022; 10:614. [PMID: 35336189 PMCID: PMC8950906 DOI: 10.3390/microorganisms10030614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/25/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
The lowland tapir (Tapirus terrestris) is the largest land mammal in Brazil and classified as a vulnerable species, according to the assessment of the risk of extinction. The present study aimed at investigating the occurrence and genetic diversity of hemoplasmas in free-ranging T. terrestris from the Brazilian Pantanal and Cerrado biomes. Blood samples were collected from 94 living and eight road-killed tapirs, totalizing 125 samples Conventional PCR targeting four different genes (16S rRNA, 23S rRNA, RNAse P, and dnaK) were performed, and the obtained sequences were submitted for phylogenetic, genotype diversity, and distance analyses. The association between hemoplasma positivity and possible risk variables (age, gender, and origin) was assessed. Out of 122 analyzed samples, 41 (41/122; 33.61% CI: 25.84-42.38%) were positive in the 16S rRNA-based PCR assay for hemoplasmas. Positivity for hemoplasmas did not differ between tapirs' gender and age. Tapirs from Pantanal were 5.64 times more likely to present positive results for hemoplasmas when compared to tapirs sampled in Cerrado. BLASTn, phylogenetic, genotype diversity, and distance analyses performed herein showed that the sampled lowland tapirs might be infected by two genetically distinct hemoplasmas, namely 'Candidatus Mycoplasma haematoterrestris' and 'Candidatus Mycoplasma haematotapirus'. While the former was positioned into "Mycoplasma haemofelis group" and closely related to 'Candidatus Mycoplasma haematoparvum, the latter was positioned into "Mycoplasma suis group" and closely related to 'Candidatus Mycoplasma haematobos'. The impact of both putative novel species on tapir health status should be investigated.
Collapse
Affiliation(s)
- Anna Claudia Baumel Mongruel
- Immunoparasitology Laboratory, Department of Pathology, Theriogenology, and One Health, School of Agricultural and Veterinary Sciences, São Paulo State University, UNESP, Jaboticabal 14884-900, SP, Brazil; (A.C.B.M.); (A.C.C.); (R.Z.M.)
| | - Emília Patrícia Medici
- Iniciativa Nacional para a Conservação da Anta Brasileira (INCAB), Instituto de Pesquisas Ecológicas (IPÊ), Campo Grande 79046-150, MS, Brazil; (E.P.M.); (A.d.C.C.)
- Escola Superior de Conservação Ambiental e Sustentabilidade (ESCAS/IPÊ), Nazaré Paulista 12960-000, SP, Brazil
- Tapir Specialist Group (TSG), International Union for Conservation of Nature (IUCN SSC), Campo Grande 79046-150, MS, Brazil
| | - Ariel da Costa Canena
- Iniciativa Nacional para a Conservação da Anta Brasileira (INCAB), Instituto de Pesquisas Ecológicas (IPÊ), Campo Grande 79046-150, MS, Brazil; (E.P.M.); (A.d.C.C.)
| | - Ana Cláudia Calchi
- Immunoparasitology Laboratory, Department of Pathology, Theriogenology, and One Health, School of Agricultural and Veterinary Sciences, São Paulo State University, UNESP, Jaboticabal 14884-900, SP, Brazil; (A.C.B.M.); (A.C.C.); (R.Z.M.)
| | - Rosangela Zacarias Machado
- Immunoparasitology Laboratory, Department of Pathology, Theriogenology, and One Health, School of Agricultural and Veterinary Sciences, São Paulo State University, UNESP, Jaboticabal 14884-900, SP, Brazil; (A.C.B.M.); (A.C.C.); (R.Z.M.)
| | - Marcos Rogério André
- Immunoparasitology Laboratory, Department of Pathology, Theriogenology, and One Health, School of Agricultural and Veterinary Sciences, São Paulo State University, UNESP, Jaboticabal 14884-900, SP, Brazil; (A.C.B.M.); (A.C.C.); (R.Z.M.)
| |
Collapse
|
2
|
Phylogenetic tree and Submission of Staphylococcus aureus Isolate from Skin Infection. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
3
|
Berg JA, Merrill BD, Breakwell DP, Hope S, Grose JH. A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl Environ Microbiol 2018; 84:e01886-18. [PMID: 30217838 PMCID: PMC6210111 DOI: 10.1128/aem.01886-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/01/2018] [Indexed: 12/18/2022] Open
Abstract
Paenibacillus larvae and Brevibacillus laterosporus are two bacteria that are members of the Paenibacillaceae family. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Here, we discuss the likely mischaracterization of three 16S rRNA sequences previously published as P. larvae and provide the phylogenetic evidence that supported the GenBank reassignment of the sequences as B. laterosporus We explore the issues that arise by using only 16S rRNA or other single-gene analyses to distinguish between these bacteria. We also present three sets of molecular markers, two sets that distinguish P. larvae from B. laterosporus and other closely related species within the Paenibacillus genus and a third set that distinguishes B. laterosporus from P. larvae and other closely related species within the Brevibacillus genus. These molecular markers provide a tool for proper identification of these oft-mistaken species.IMPORTANCE 16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA sequence similarity of some published strains of P. larvae and B. laterosporus, as well as possible horizontal gene transfer events within their shared ecological niche, complicates the use of 16S rRNA sequence as an effective molecular marker for differentiating these two species. Additionally, shared characteristics of these bacteria limit the effectiveness of using traditional phenotypic identification assays, such as the catalase test. The results from this study provide PCR methods to quickly differentiate between these two genera and will be useful when studying Brevibacillus, Paenibacillus, and other disease-relevant bacteria commonly found in beehives.
Collapse
Affiliation(s)
- Jordan A Berg
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| |
Collapse
|
4
|
Zhou Z, Wei Q, Yang Y, Li M, Gu JD. Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples. Appl Microbiol Biotechnol 2018; 102:5859-5871. [PMID: 29802476 DOI: 10.1007/s00253-018-9078-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/07/2018] [Indexed: 01/21/2023]
Abstract
Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH4+ and NO2- biochemically to form N2 gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.
Collapse
Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Qiaoyan Wei
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, People's Republic of China.
| |
Collapse
|
5
|
Raz N, Danin-Poleg Y, Hayman RB, Bar-On Y, Linetsky A, Shmoish M, Sanjuán E, Amaro C, Walt DR, Kashi Y. Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3. PLoS One 2014; 9:e114576. [PMID: 25526263 PMCID: PMC4272304 DOI: 10.1371/journal.pone.0114576] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/11/2014] [Indexed: 12/18/2022] Open
Abstract
Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.
Collapse
Affiliation(s)
- Nili Raz
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Danin-Poleg
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Ryan B. Hayman
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Yudi Bar-On
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Alex Linetsky
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Michael Shmoish
- Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Eva Sanjuán
- Department of Microbiology, Faculty of Biology, University of Valencia, Valencia, Spain
| | - Carmen Amaro
- Department of Microbiology, Faculty of Biology, University of Valencia, Valencia, Spain
| | - David R. Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
6
|
Lee KH, Wang YF, Zhang GX, Gu JD. Distribution patterns of ammonia-oxidizing bacteria and anammox bacteria in the freshwater marsh of Honghe wetland in Northeast China. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:1930-1942. [PMID: 25139035 DOI: 10.1007/s10646-014-1333-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/09/2014] [Indexed: 06/03/2023]
Abstract
Community characteristics of aerobic ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria in Honghe freshwater marsh, a Ramsar-designated wetland in Northeast China, were analyzed in this study. Samples were collected from surface and low layers of sediments in the Experimental, Buffer, and Core Zones in the reserve. Community structures of AOB were investigated using both 16S rRNA and amoA (encoding for the α-subunit of the ammonia monooxygenase) genes. Majority of both 16S rRNA and amoA gene-PCR amplified sequences obtained from the samples in the three zones affiliated with Nitrosospira, which agreed with other wetland studies. A relatively high richness of β-AOB amoA gene detected in the freshwater marsh might suggest minimal external pressure was experienced, providing a suitable habitat for β-AOB communities. Anammox bacteria communities were assessed using both 16S rRNA and hzo (encoding for hydrazine oxidoreductase) genes. However, PCR amplification of the hzo gene in all samples failed, suggesting that the utilization of hzo biomarker for detecting anammox bacteria in freshwater marsh might have serious limitations. Results with 16S rRNA gene showed that Candidatus Kuenenia was detected in only the Experimental Zone, whereas Ca. Scalindua including different lineages was observed in both the Buffer and Experimental Zones but not the Core Zone. These results indicated that both AOB and anammox bacteria have specific distribution patterns in the ecosystem corresponding to the extent of anthropogenic impact.
Collapse
Affiliation(s)
- Kwok-Ho Lee
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | | | | | | |
Collapse
|
7
|
Zimmermann J, Portillo MC, Serrano L, Ludwig W, Gonzalez JM. Acidobacteria in freshwater ponds at Doñana National Park, Spain. MICROBIAL ECOLOGY 2012; 63:844-855. [PMID: 22167078 DOI: 10.1007/s00248-011-9988-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/23/2011] [Indexed: 05/31/2023]
Abstract
The Acidobacteria show a widespread distribution in natural ecosystems. In this study, we analyzed the presence of Acidobacteria in freshwater ponds at Doñana National Park (southwestern Spain). Nucleic acid sequence analysis, quantitative, real-time RT-PCR, and fluorescence in situ hybridization (FISH) were carried out. Acidobacteria in these aquatic environments were investigated using their 16S and 23S rDNA sequences and acidobacterial specific primer pairs through phylogenetic approaches. The presence of up to five subdivisions of Acidobacteria was detected during this study. The analyzed ponds exhibited distinctive patterns of acidobacterial clades. In order to detect their role in ecosystem functions, metabolically active Acidobacteria were detected based upon rRNA analyses. Quantitative, real-time RT-PCR showed a low percentage of metabolically active Acidobacteria at suboxic zones within the water column covered by surface Fe-rich films. Oxygen-saturated areas showed around 4% of total bacterial RNA belonging to Acidobacteria both in the water column and the sediment surface. The morphology of the most abundant Acidobacteria was revealed by FISH as cocci generally in pairs or chains. Enrichment cultures were also obtained and indicated a putative metabolism based on aerobic and heterotrophic characteristics likely taking advantage of the abundant organic matter present at the investigated sites. These results represent a significant contribution toward understanding the distribution and ecological role of the phylum Acidobacteria in natural ecosystems, specifically at Doñana National Park freshwater ponds.
Collapse
Affiliation(s)
- Johannes Zimmermann
- Instituto de Recursos Naturales y Agrobiologia, CSIC, Avda. Reina Mercedes 10, Seville, Spain
| | | | | | | | | |
Collapse
|
8
|
Song B, Tobias CR. Molecular and Stable Isotope Methods to Detect and Measure Anaerobic Ammonium Oxidation (Anammox) in Aquatic Ecosystems. Methods Enzymol 2011; 496:63-89. [DOI: 10.1016/b978-0-12-386489-5.00003-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
9
|
Li H, Chen S, Mu BZ, Gu JD. Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs. MICROBIAL ECOLOGY 2010; 60:771-83. [PMID: 20740282 PMCID: PMC2974184 DOI: 10.1007/s00248-010-9733-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 06/12/2010] [Indexed: 05/21/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis. High concentration (5.31-39.2 mg l(-1)) of ammonium was detected in the production water from these oilfields with temperatures between 55°C and 75°C. Both 16S rRNA and hzo molecular biomarkers indicated the occurrence of anammox bacteria in nine out of 17 samples. Most of 16S rRNA gene phylotypes are closely related to the known anammox bacterial genera Candidatus Brocadia, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia, while hzo gene phylotypes are closely related to the genera Candidatus Anammoxoglobus, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia. The total bacterial and anammox bacterial densities were 6.4 ± 0.5 × 10(3) to 2.0 ± 0.18 × 10(6) cells ml(-1) and 6.6 ± 0.51 × 10(2) to 4.9 ± 0.36 × 10(4) cell ml(-1), respectively. The cluster I of 16S rRNA gene sequences showed distant identity (<92%) to the known Candidatus Scalindua species, inferring this cluster of anammox bacteria to be a new species, and a tentative name Candidatus "Scalindua sinooilfield" was proposed. The results extended the existence of anammox bacteria to the high-temperature oil reservoirs.
Collapse
Affiliation(s)
- Hui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237 People’s Republic of China
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Shuo Chen
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, 200237 People’s Republic of China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, 200237 People’s Republic of China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
- Swire Institute of Marine Science, The University of Hong Kong, Shek O, Cape d’Aguilar, Hong Kong SAR, People’s Republic of China
| |
Collapse
|
10
|
Pradella S, Päuker O, Petersen J. Genome organisation of the marine Roseobacter clade member Marinovum algicola. Arch Microbiol 2009; 192:115-26. [PMID: 20039020 DOI: 10.1007/s00203-009-0535-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 11/10/2009] [Accepted: 12/09/2009] [Indexed: 11/30/2022]
Abstract
The Roseobacter clade, belonging to the family Rhodobacteraceae of the class Alphaproteobacteria, is one of the major bacterial groups in marine environments. A remarkable wealth of diverse large plasmids has been detected in members of this lineage. Here, we analysed the genome structure and extrachromosomal DNA content of four strains of the roseobacter species Marinovum algicola by pulsed-field gel electrophoresis. They were originally isolated from toxic dinoflagellates and possess multireplicon genomes with sizes between 5.20 and 5.35 Mb. In addition to the single circular chromosomes (3.60-3.74 Mb), whose organisation seem to be conserved, 9 to 12 extrachromosomal replicons have been detected for each strain. This number is unprecedented for roseobacters and proposes a sophisticated regulation of replication and partitioning to ensure stable maintenance. The plasmid lengths range from 7 to 477 kb and our analyses document a circular conformation for all but one of them, which might represent a linear plasmid-like prophage. In striking contrast to other roseobacters, up to one-third of the genomic information (1.75 Mb) is plasmid borne in Marinovum algicola. The plasmid patterns of some strains are conspicuously different, indicating that recombination and conjugative gene transfer are dominant mechanisms for microevolution within the Roseobacter clade.
Collapse
Affiliation(s)
- Silke Pradella
- German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany.
| | | | | |
Collapse
|
11
|
Dale OR, Tobias CR, Song B. Biogeographical distribution of diverse anaerobic ammonium oxidizing (anammox) bacteria in Cape Fear River Estuary. Environ Microbiol 2009; 11:1194-207. [DOI: 10.1111/j.1462-2920.2008.01850.x] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Rinke C, Schmitz-Esser S, Loy A, Horn M, Wagner M, Bright M. High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont âCandidatus Thiobios zoothamnicoliâ. FEMS Microbiol Ecol 2009; 67:229-41. [DOI: 10.1111/j.1574-6941.2008.00628.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
13
|
Woebken D, Lam P, Kuypers MMM, Naqvi SWA, Kartal B, Strous M, Jetten MSM, Fuchs BM, Amann R. A microdiversity study of anammox bacteria reveals a novelCandidatusScalindua phylotype in marine oxygen minimum zones. Environ Microbiol 2008; 10:3106-19. [DOI: 10.1111/j.1462-2920.2008.01640.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Meisinger DB, Zimmermann J, Ludwig W, Schleifer KH, Wanner G, Schmid M, Bennett PC, Engel AS, Lee NM. In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA). Environ Microbiol 2007; 9:1523-34. [PMID: 17504489 DOI: 10.1111/j.1462-2920.2007.01271.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lower Kane Cave, Wyoming (USA), has hydrogen sulfide-bearing springs that discharge into the cave passage. The springs and cave stream harbour white filamentous microbial mats dominated by Epsilonproteobacteria. Recently, novel 16S rRNA gene sequences from the phylum Acidobacteria, subgroup 7, were found in these cave mats. Although Acidobacteria are ubiquitously distributed in many terrestrial and marine habitats, little is known about their ecophysiology. To investigate this group in Lower Kane Cave in more detail, a full-cycle rRNA approach was applied based on 16S and 23S rRNA gene clone libraries and the application of novel probes for fluorescence in situ hybridization. The 16S and 23S rRNA gene clone libraries yielded seven and six novel acidobacterial operational taxonomic units (OTUs) respectively. The majority of the OTUs were affiliated with subgroups 7 and 8. One OTU was affiliated with subgroup 6, and one OTU could not be assigned to any of the present acidobacterial subgroups. Fluorescence in situ hybridization distinguished two morphologically distinct, rod-shaped cells of the acidobacterial subgroups 7 and 8. Although the ecophysiology of Acidobacteria from Lower Kane Cave will not be fully resolved until cultures are obtained, acidobacterial cells were always associated with the potentially chemolithoautotrophic epsilon- or gammaproteobacterial filaments, suggesting perhaps a lifestyle based on heterotrophy or chemoorganotrophy.
Collapse
Affiliation(s)
- Daniela B Meisinger
- Microbial Systems Ecology Division, Department of Microbiology, Technische Universität München, D-85350 Freising, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Vannini C, Pöckl M, Petroni G, Wu QL, Lang E, Stackebrandt E, Schrallhammer M, Richardson PM, Hahn MW. Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environ Microbiol 2007; 9:347-59. [PMID: 17222133 DOI: 10.1111/j.1462-2920.2006.01144.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial strains affiliated to the phylogenetically shallow subcluster C (PnecC) of the Polynucleobacter cluster, which is characterized by a minimal 16S rRNA gene sequence similarity of approximately 98.5%, have been reported to occur as obligate endosymbionts of ciliates (Euplotes spp.), as well as to occur as free-living cells in the pelagic zone of freshwater habitats. We investigated if these two groups of closely related bacteria represent strains fundamentally differing in lifestyle, or if they simply represent different stages of a facultative endosymbiotic lifestyle. The phylogenetic analysis of 16S rRNA gene and 16S-23S ITS sequences of five endosymbiont strains from two different Euplotes species and 40 pure culture strains demonstrated host-species-specific clustering of the endosymbiont sequences within the PnecC subcluster. The sequences of the endosymbionts showed characteristics indicating an obligate endosymbiotic lifestyle. Cultivation experiments revealed fundamental differences in physiological adaptations, and determination of the genome sizes indicated a slight size reduction in endosymbiotic strains. We conclude that the two groups of PnecC bacteria represent obligately free-living and obligately endosymbiotic strains, respectively, and do not represent different stages of the same complex life cycle. These closely related strains occupy completely separated ecological niches. To our best knowledge, this is the closest phylogenetic relationship between obligate endosymbionts and obligately free-living bacteria ever revealed.
Collapse
Affiliation(s)
- Claudia Vannini
- Department of Biology-Protistology and Zoology Unit, University of Pisa, Via A. Volta 4/6, I-56126 Pisa, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Haaijer SCM, Van der Welle MEW, Schmid MC, Lamers LPM, Jetten MSM, Op den Camp HJM. Evidence for the involvement of betaproteobacterial Thiobacilli in the nitrate-dependent oxidation of iron sulfide minerals. FEMS Microbiol Ecol 2006; 58:439-48. [PMID: 17117988 DOI: 10.1111/j.1574-6941.2006.00178.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The Thiobacilli are an important group of autotrophic bacteria occurring in nature linking the biogeochemical cycles of sulfur and nitrogen. Betaproteobacterial Thiobacilli are very likely candidates for mediating the process of nitrate-dependent anoxic iron sulfide mineral oxidation in freshwater wetlands. A Thiobacillus denitrificans-like bacterium was present in an enrichment on thiosulfate and nitrate, derived from an iron-sulfide- and nitrate-rich freshwater environment. Preliminary FISH analysis showed that the 16S rRNA gene-based bacterial probe mix showed great variation in intensity under different culture conditions. Furthermore, the widely applied 23S rRNA gene-based probe set BET42a/GAM42a incorrectly identified the T. denitrificans-like bacterium as a member of the Gammaproteobacteria. To circumvent these problems, the 23S rRNA genes of two T. denitrificans strains were partially sequenced and a new 23S rRNA gene-based probe (Betthio 1001) specific for betaproteobacterial Thiobacilli was designed. Use of this new probe Betthio 1001, combined with field measurements, indicates the involvement of Thiobacilli in the process of nitrate-dependent iron sulfide mineral oxidation.
Collapse
Affiliation(s)
- Suzanne C M Haaijer
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | | | | | | | | |
Collapse
|
17
|
Taddei A, Rodríguez MJ, Márquez-Vilchez E, Castelli C. Isolation and identification of Streptomyces spp. from Venezuelan soils: Morphological and biochemical studies. I. Microbiol Res 2006; 161:222-31. [PMID: 16765838 DOI: 10.1016/j.micres.2005.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2005] [Indexed: 10/25/2022]
Abstract
The genus Streptomyces is represented in nature by the largest number of species and varieties among the family Actinomycetaceae. They differ greatly in their morphology, physiology, and biochemical activities, producing the majority of known antibiotics. The morphological and biochemical characteristics of 71 Streptomyces spp. isolated from soil samples collected at different places of Venezuela, are presented. A comparative analysis using the statistical software Minitab shows that 67 of these isolates are presumably new strains, since they possess a very low percentage of similarity with other reported species. Only four isolates shared 100% identity with one, two or three reported Streptomyces spp.
Collapse
Affiliation(s)
- Antonieta Taddei
- Departamento de Biología Celular, Universidad Simón Bolívar, USB, Apartado 89.000, Caracas 1080-A, Venezuela.
| | | | | | | |
Collapse
|
18
|
Jin DZ, Wen SY, Chen SH, Lin F, Wang SQ. Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays. Mol Cell Probes 2006; 20:337-47. [PMID: 16730943 DOI: 10.1016/j.mcp.2006.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 03/26/2006] [Accepted: 03/30/2006] [Indexed: 11/26/2022]
Abstract
The detection and identification of intestinal pathogens is critical for clinical patient diagnosis and antimicrobial therapy. No currently available assays with DNA microarrays can simultaneously detect and identify multiple intestinal pathogens, because there is no appropriate method for choosing target probes. To solve the problem we have experimented for facilitating screening of specific probes and developed a rapid (<3h) and reliable assay for simultaneous detection of intestinal pathogens using two universal PCR primers to amplify two variable regions of bacterial 16S and 23S ribosomal DNA (rDNA) genes, and then applied to DNA microarrays, hybridization between probes and amplicons occurred. Through this idea for screening of probes the assay was successful in discriminating 15 genera or species of intestinal pathogens. The limit of detection was approximately 10(3)CFU/mL for one species of pathogen and 10(5)CFU/mL for six species pathogens existing simultaneously in stool. When this assay was applied directly to identify 99 clinical specimens, 80(80.8%) were correctly analyzed, including four with mixed pathogens; 8(8.08%) received negative results due to no corresponding probes in this array and 11(11.11%) belonging to our targets were misidentified due to low-level pathogens and other factors. This approach is also convenient to obtain specific and proper probes while establishing assays for the applications in other aspects using DNA microarrays. In addition, the more species may be added to this system easily and endlessly by screening of candidate target probes in order to increase the power of simultaneous detection.
Collapse
Affiliation(s)
- Da-Zhi Jin
- Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Beijing, China
| | | | | | | | | |
Collapse
|
19
|
Maré L, Wolfaardt GM, Dicks LMT. Adhesion of Lactobacillus plantarum 423 and Lactobacillus salivarius 241 to the intestinal tract of piglets, as recorded with fluorescent in situ hybridization (FISH), and production of plantaricin 423 by cells colonized to the ileum. J Appl Microbiol 2006; 100:838-45. [PMID: 16553740 DOI: 10.1111/j.1365-2672.2006.02835.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AIMS To determine which intestinal section of pre and postweaned piglets are colonized by Lactobacillus plantarum 423 and Lactobacillus salivarius 241, and follow production of plantaricin 423 in a gastro-intestinal model. METHODS AND RESULTS Lactobacillus plantarum 423 and Lact. salivarius 241, single or in combination, were administered to 1-, 14- and 28-day-old (postweaned) piglets. According to results obtained by fluorescent in situ hybridization (FISH), Lact. plantarum 423 adhered strongly to the ileum and posterior colon and Lact. salivarius 241 to the duodenum in preweaned piglets. High numbers of strain 241 were recorded in the duodenum and posterior colon of postweaned piglets, whereas strain 423 remained localized to the ileum. Lowering in Enterococcus faecalis cell numbers were recorded when preweaned piglets were challenged with strain 241. Plantaricin 423 was produced for 96 h in the ileum section of a gastro-intestinal model. CONCLUSIONS Lactobacillus plantarum 423 and Lact. salivarius 241 adhere to different sections of the intestinal tract, depending on the piglet's age. Ent. faecalis were inhibited in vivo, probably by plantaricin 423. SIGNIFICANCE AND IMPACT OF THE STUDY Fluorescent in situ hybridization proved valuable in the detection of probiotic bacteria adhered to the intestine. This is the first report of bacteriocin production in a model simulating the porcine gastro-intestinal tract.
Collapse
Affiliation(s)
- L Maré
- Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa
| | | | | |
Collapse
|
20
|
Hunt DE, Klepac-Ceraj V, Acinas SG, Gautier C, Bertilsson S, Polz MF. Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol 2006; 72:2221-5. [PMID: 16517676 PMCID: PMC1393206 DOI: 10.1128/aem.72.3.2221-2225.2006] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 12/19/2005] [Indexed: 11/20/2022] Open
Abstract
The availability of a diverse set of 23S rRNA gene sequences enabled evaluation of the specificity of 39 previously published and 4 newly designed primers specific for bacteria. An extensive clone library constructed using an optimized primer pair resulted in similar gene richness but slightly differing coverage of some phylogenetic groups, compared to a 16S rRNA gene library from the same environmental sample.
Collapse
Affiliation(s)
- Dana E Hunt
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 48-421, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | | | | | | | | | | |
Collapse
|
21
|
Stakenborg T, Vicca J, Butaye P, Maes D, Minion FC, Peeters J, De Kruif A, Haesebrouck F. Characterization of In Vivo Acquired Resistance of Mycoplasma hyopneumoniae to Macrolides and Lincosamides. Microb Drug Resist 2005; 11:290-4. [PMID: 16201934 DOI: 10.1089/mdr.2005.11.290] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Macrolides and related antibiotics are used to control mycoplasma infections in the pig industry worldwide. Some porcine mycoplasmas, however, survive these treatments by acquiring resistance. The mechanism of acquired resistance to macrolides and lincosamides was studied in more detail for Mycoplasma hyopneumoniae by comparing both the phenotype and genotype of a resistant field isolate to five susceptible isolates. The MICs were significantly higher for the resistant strain for all antibiotics tested. The MICs for the 16-membered macrolide tylosin ranged from 8 to 16 microg for the resistant strain and from 0.03 to 0.125 microg/ml for the five susceptible strains. The MICs for the 15-membered macrolides and lincosamides were higher than 64 microg/ml for the resistant strain while only 0.06 to 0.5 microg/ml for the susceptible strains. Mycoplasma hyopneumoniae strains are intrinsically resistant to the 14-membered macrolides due to a G 2057 A transition (E. coli numbering) in their 23S rDNA. Therefore, high MICs were observed for all strains, although the MICs for the resistant strain were clearly increased. An additional, acquired A 2058 G point mutation was found in the 23S rRNA gene of the resistant strain. No differences linked to resistance were found in the ribosomal proteins L4 and L22. The present study showed that 23S rRNA mutations resulting in resistance to macrolides and lincosamides as described in other Mycoplasma spp. also occur under field conditions in M. hyopneumoniae.
Collapse
Affiliation(s)
- Tim Stakenborg
- Veterinary and Agrochemical Research Centre, Brussels, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Wu CM, Wu H, Ning Y, Wang J, Du X, Shen J. Induction of macrolide resistance inMycoplasma gallisepticumin vitro and its resistance-related mutations within domain V of 23S rRNA. FEMS Microbiol Lett 2005; 247:199-205. [PMID: 15936901 DOI: 10.1016/j.femsle.2005.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2005] [Revised: 05/03/2005] [Accepted: 05/04/2005] [Indexed: 11/21/2022] Open
Abstract
Antibiotic-resistant mutants of Mycoplasma gallisepticum were selected in vitro from the susceptible strains S6 and BG44T by serial passages in stepwise concentrations of erythromycin, tylosin, or tilmicosin. High resistance to erythromycin or tilmicosin developed readily, whereas resistance to tylosin developed only after greater numbers of passages. Three mutants selected by each selector antibiotic were cloned and detected, and all cloned mutants exhibited cross-resistance to the three selector antibiotics as well as to lincomycin. Portions of the genes encoding domain V of 23S rRNA of the cloned mutants were amplified by PCR, and their nucleotide sequences were compared to those of the susceptible parent strains. Five of the six mutants selected by erythromycin harbored an A2058G (Escherichia coli numbering) mutation in one of the two 23S rRNA. One of the six mutants selected by erythromycin harbored a G2057A mutation and an A2059G mutation in the other 23S rRNA. In tilmicosin-selected mutants, two mutations, A2058G and A2503U, occurred in one of the two 23S rRNA. No mutation was detected in the two 23S rRNA of tylosin-selected mutants with low-level resistance. Mutations at homologous locations in the 23S rRNA of other macrolide-resistant bacteria indicate that the phenotype of macrolide resistance occurring in M. gallisepticum is strongly associated with point mutations in domain V of 23S rRNA.
Collapse
Affiliation(s)
- Cong-Ming Wu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, China
| | | | | | | | | | | |
Collapse
|
23
|
Jetten M, Schmid M, van de Pas-Schoonen K, Sinninghe Damsté J, Strous M. Anammox Organisms: Enrichment, Cultivation, and Environmental Analysis. Methods Enzymol 2005; 397:34-57. [PMID: 16260284 DOI: 10.1016/s0076-6879(05)97003-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Anaerobic ammonium oxidation (anammox) is the microbial oxidation of ammonium with nitrite to dinitrogen gas under strict anoxic conditions mediated by planctomycete-like bacteria. Anammox is not only important in the oceanic nitrogen cycle, but can also contribute substantially to nitrogen removal in municipal and industrial wastewater treatment. This chapter addresses the enrichment and cultivation of anammox bacteria in a sequencing batch reactor (SBR) and a gas lift reactor. The reactors can be operated anoxically as an anammox reactor or as an oxygen-limited "completely autotrophic nitrogen removal over nitrite" (CANON) system. Pure cultures of anammox organisms have not yet been obtained, but anammox cells can be purified to more than 99.5% using a Percoll density gradient centrifugation protocol. Furthermore, we show how anammox communities in natural and man-made ecosystems can be identified and characterized using molecular methods such as fluorescence in situ hybridization (FISH) or Planctomycetes/anammox-specific polymerase chain reaction (PCR). Both techniques are based on retrieved 16S rRNA gene sequences. In addition to 16S rRNA, unique anammox ladderane lipids can also serve as biomarkers to determine the abundance of anammox organisms in environmental samples.
Collapse
Affiliation(s)
- Mike Jetten
- Department of Microbiology, Institute for Water & Wetland Research, Radboud University Nijmegen, The Netherlands
| | | | | | | | | |
Collapse
|
24
|
Peplies J, Glöckner FO, Amann R, Ludwig W. Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton. Syst Appl Microbiol 2004; 27:573-80. [PMID: 15490559 DOI: 10.1078/0723202041748172] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Almost complete 23S rRNA gene sequences were obtained from 11 Alphaproteobacteria isolated from marine surface water of the German Bight. Five of the strains belong to the "marine alpha" group, a phylogenetic cluster which encompasses members of the genus Roseobacter and closely related bacteria. Phylogenetic sequence analysis based on 52 published as well as unpublished complete 23S rDNA sequences from Alphaproteobacteria including the newly obtained was in general consistent with the 16S rRNA gene sequence-derived phylogeny. 16S and 23S rRNA based phylogenies both showed a distinct cluster for strains associated with the "marine alpha" group. The suitability of both markers for the design of oligonucleotide probes targeting selected groups of Alphaproteobacteria was systematically evaluated and compared in silico. Six clusters of sequences covering different phylogenetic levels as well as two strains were selected in a case study. To compensate for the quantitative difference in the two data sets, the 16S rRNA dataset was truncated to sequences with an equivalent in the 23S rRNA data set. Our results show, that the overall number of phylogenetically redundant probes available could be more than doubled by extending probe design to the 23S rRNA. For small clusters of high sequence similarity and single strains, up to 8 times more discriminating binding sites were provided by the 23S rRNA.
Collapse
MESH Headings
- Alphaproteobacteria/classification
- Alphaproteobacteria/genetics
- Alphaproteobacteria/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Germany
- Molecular Sequence Data
- North Sea
- Oligonucleotide Probes/genetics
- Phylogeny
- Plankton
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Roseobacter/classification
- Seawater/microbiology
- Sensitivity and Specificity
- Sequence Analysis, DNA
- Water Microbiology
Collapse
Affiliation(s)
- Jörg Peplies
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | | | | | | |
Collapse
|
25
|
Helander IM, Haikara A, Sadovskaya I, Vinogradov E, Salkinoja-Salonen MS. Lipopolysaccharides of anaerobic beer spoilage bacteria of the genusPectinatus– lipopolysaccharides of a Gram-positive genus. FEMS Microbiol Rev 2004; 28:543-52. [PMID: 15539073 DOI: 10.1016/j.femsre.2004.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Revised: 04/07/2004] [Accepted: 05/11/2004] [Indexed: 11/18/2022] Open
Abstract
Bacteria of the genus Pectinatus emerged during the seventies as contaminants and spoilage organisms in packaged beer. This genus comprises two species, Pectinatus cerevisiiphilus and Pectinatus frisingensis; both are strict anaerobes. On the basis of genomic properties the genus is placed among low GC Gram-positive bacteria (phylum Firmicutes, class Clostridia, order Clostridiales, family Acidaminococcaceae). Despite this assignment, Pectinatus bacteria possess an outer membrane and lipopolysaccharide (LPS) typical of Gram-negative bacteria. The present review compiles the structural and compositional studies performed on Pectinatus LPS. These lipopolysaccharides exhibit extensive heterogeneity, i.e. several macromolecularly and structurally distinct LPS molecules are produced by each strain. Whereas heterogeneity is a common property in lipopolysaccharides, Pectinatus LPS have been shown to contain exceptional carbohydrate structures, consisting of a fairly conserved core region that carries a large non-repetitive saccharide that probably replaces the O-specific chain. Such structures represent a novel architectural principle of the LPS molecule.
Collapse
Affiliation(s)
- Ilkka M Helander
- Division of Microbiology, Department of Applied Chemistry and Microbiology, University of Helsinki, Finland.
| | | | | | | | | |
Collapse
|
26
|
Shin JH, Joo HS, Lee WH, Seok HB, Calsamig M, Pijoan C, Molitor TW. Identification and characterization of cytopathogenic Mycoplasma hyorhinis from swine farms with a history of abortions. J Vet Med Sci 2003; 65:501-9. [PMID: 12736433 DOI: 10.1292/jvms.65.501] [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: 11/22/2022] Open
Abstract
A virus-like cytopathic agent isolated from swine farms with a history of recurrent abortion episodes was investigated. We employed a differential display reverse transcription-polymerase chain reaction (ddRT-PCR) to obtain genetic information of the cytopathic agent. Partial nucleotide sequence (527 bp) obtained from differentially displayed PCR fragments showed 88.7% similarity with the 23S rRNA gene of Mycoplasma hyopneumoniae. Unexpectedly, the 5' portion (1-333 bp) of the sequence shared 96.1% similarity with 5' untranslated region (UTR) of human prostate tumor inducing gene 1 (PTI-1). Cytopathic effects and extranuclear DNA fluorescence were no longer observed when BM-cyclin was added in the culture medium, suggesting that BM-cyclin sensitive mycoplasma-like organisms caused the cell death. Further evidence supporting the cytopathic agent as a mycoplasma-like organism was obtained by the capability of (3)H-thymidine and (3)H-uridine incorporation, a single peak in buoyant density gradient profile (1.20-1.24 g/ml), and ultrastructural morphology. Unlike M. hyopneumoniae, the organism was not propagated in Friis medium. Nucleotide sequence of 16S rRNA obtained from the cytopathic agent showed 0.8-1.0% divergences with other M. hyorhinis strains, suggesting that the newly isolated cytopathogenic swine mycoplasma was a variant form of M. hyorhinis. Striking homology between a portion of the 23S rRNA gene of M. hyorhinis and 5' UTR of human PTI-1 implicated that M. hyorhinis might potentially be related to the evolution of human PTI-1.
Collapse
Affiliation(s)
- Jin Ho Shin
- Department of Clinical and Population Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul 55108, USA
| | | | | | | | | | | | | |
Collapse
|
27
|
Uchino Y, Hamada T, Yokota A. Proposal of Pseudorhodobacter ferrugineus gen nov, comb nov, for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter. J GEN APPL MICROBIOL 2002; 48:309-19. [PMID: 12682869 DOI: 10.2323/jgam.48.309] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The marine gram-negative non-photosynthetic bacterium, Agrobacterium ferrugineum IAM 12616(T) forms one cluster with the species of the photosynthetic genus Rhodobacter in phylogenetic trees based on molecules of 16S rRNA, 23S rRNA and DNA gyrases. Agrobacterium ferrugineum and Rhodobacter species are similar in that growth occurs without NaCl in the culture medium (optimal NaCl concentration for growth of P. ferrugineus is 1%) and their major hydroxy fatty acid compositions are 3-hydroxy decanoic acids (3-OH 10:0) and 3-hydroxy tetradecanoic acids (3-OH 14:1). However, A. ferrugineum differs from Rhodobacter species in G+C content (58 mol% in A. ferrugineum versus 64-73 mol% in Rhodobacter species), in having an insertion in its 16S rRNA gene sequence, and in lacking photosynthetic abilities, bacteriochlorophyll a and intracytoplasmic membrane systems. Furthermore, experiments using PCR and Southern hybridization show that A. ferrugineum does not have puhA gene and puf genes localized near the opposite ends of the photosynthesis gene cluster of Rhodobacter capsulatus. It suggests that A. ferrugineum may not have any genes for photosynthesis. We propose the transfer of A. ferrugineum IAM 12616(T) to the genus Pseudorhodobacter gen. nov. as Pseudorhodobacter ferrugineus comb. nov. Although Pseudorhodobacter ferrugineus disturbs the phylogenetic monophyly of the genus Rhodobacter, this taxonomic proposal seems adequate until it has been clarified whether P. ferrugineus possesses an incomplete photosynthetic apparatus.
Collapse
Affiliation(s)
- Yoshihito Uchino
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| | | | | |
Collapse
|
28
|
Pereyre S, Gonzalez P, De Barbeyrac B, Darnige A, Renaudin H, Charron A, Raherison S, Bébéar C, Bébéar CM. Mutations in 23S rRNA account for intrinsic resistance to macrolides in Mycoplasma hominis and Mycoplasma fermentans and for acquired resistance to macrolides in M. hominis. Antimicrob Agents Chemother 2002; 46:3142-50. [PMID: 12234836 PMCID: PMC128781 DOI: 10.1128/aac.46.10.3142-3150.2002] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms of intrinsic resistance of Mycoplasma hominis to 14- and 15-membered macrolides were investigated in comparison with those of M. pneumoniae, which is naturally susceptible to macrolides. Radiolabeled erythromycin was not accumulated by M. hominis PG21, but addition of an ABC transporter inhibitor increased the level of erythromycin uptake more than two times, suggesting the existence of an active efflux process. The affinity of [(14)C]erythromycin to ribosomes isolated from M. hominis was dramatically reduced relative to that to ribosomes isolated from M. pneumoniae. The nucleotide sequences of 23S rRNA of both ribosomal operons rrnA and rrnB and ribosomal proteins L4 and L22 of M. hominis were obtained. Compared to the sequence of M. pneumoniae, M. hominis harbored a G2057A transition in its 23S rRNA sequence, as did M. fermentans, another mycoplasma that is erythromycin resistant. An additional C2610U change was also found in the sequence of M. hominis. Moreover, two M. hominis clinical isolates with acquired resistance to 16-membered macrolides were examined for mutations in domain II and domain V of 23S rRNA and in ribosomal proteins L4 and L22. Compared to the sequence of reference strain PG21, one isolate harbored a A2059G transition and a C2611U transition in one of the two rrn operons, while the other one was mutated only at position 2059, also on the same operon. No mutation was found in the two ribosomal protein sequences. Overall, the present study is an exhaustive characterization of the intrinsic resistance of M. hominis to 14- and 15-membered macrolides and the first description of mycoplasma clinical isolates resistant to macrolide, lincosamide, and streptogramin antibiotics harboring a mutation at position 2611 in the 23S rRNA.
Collapse
Affiliation(s)
- S Pereyre
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, 33076 Bordeaux Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Bogado I, Limansky A, Sutich E, Marchiaro P, Marzi M, Putero J, Viale A. Molecular characterization of methicillin-resistant coagulase-negative staphylococci from a neonatal intensive care unit. Infect Control Hosp Epidemiol 2002; 23:447-51. [PMID: 12186210 DOI: 10.1086/502083] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To evaluate clonal dissemination of methicillin-resistant coagulase-negative staphylococci (CNS). SETTING Neonatal intensive care unit of a 180-bed, university-affiliated general hospital. PATIENTS Neonates admitted to the neonatal intensive care unit between March 1999 and October 2000, from whom CNS were isolated as a unique pathogen. Patients from other wards from whom epidemiologically unrelated staphylococci strains were obtained served as control-patients. METHODS Conventional methods were used for phenotypic characterization of CNS. Methicillin resistance was determined by mecA polymerase chain reaction (PCR) amplification. Genotypic characterization was done by random amplification of DNA with degenerated primers (RAPD) and repetitive element sequence-based PCR (rep-PCR). RESULTS Forty methicillin-resistant CNS isolates obtained from neonates were characterized as Staphylococcus epidermidis (33), S. hominis (5), S. warneri (1), and S. auricularis (1). Both RAPD and rep-PCR indicated the presence of 4 different clones among the 33 S. epidermidis isolates. In turn, the 4 randomly selected, epidemiologically unrelated methicillin-resistant CNS strains obtained from control-patients showed 3 new profiles by RAPD and 2 by rep-PCR, which differed from the corresponding patterns mentioned earlier. Persistence of S. hominis in a neonate could be assessed by both genotypic techniques. CONCLUSIONS The molecular characterization of the methicillin-resistant CNS studied indicated dissemination of one particular methicillin-resistant CNS clone among the neonates in the ward studied. Although RAPD showed a superior power to discriminate among methicillin-resistant CNS isolates, both RAPD and rep-PCR detected intraspecific and interspecific genomic diversity.
Collapse
Affiliation(s)
- Isabel Bogado
- Institute of Cellular and Molecular Biology of Rosario, School of Biochemistry and Pharmacy, National University of Rosario, Argentina
| | | | | | | | | | | | | |
Collapse
|
30
|
Okazaki N, Narita M, Yamada S, Izumikawa K, Umetsu M, Kenri T, Sasaki Y, Arakawa Y, Sasaki T. Characteristics of macrolide-resistant Mycoplasma pneumoniae strains isolated from patients and induced with erythromycin in vitro. Microbiol Immunol 2002; 45:617-20. [PMID: 11592636 DOI: 10.1111/j.1348-0421.2001.tb01293.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Some patients with Mycoplasma pneumoniae infection are clinically resistant to antibiotics such as erythromycin, clarithromycin, or clindamycin. We isolated M. pneumoniae from such patients and found that one of three isolates showed a point mutation in the 23S rRNA gene. Furthermore, 141 EM-sensitive clinical isolates of M. pneumoniae were cultured in broth medium containing 100 microg/ml of erythromycin (EM). Among 11 EM-resistant strains that grew in the medium, point mutations in the 23S rRNA were found in 3 strains at A2063G, 5 strains at A2064G and 3 strains at A2064C. The relationship between the point mutation pattern of these EM-resistant strains and their resistance phenotypes to several macrolide antibiotics was investigated.
Collapse
Affiliation(s)
- N Okazaki
- Department of Bacteriology and Pathology, Kanagawa Prefectural Public Health Laboratories, Yokohama, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Application of PCR for Selection of Gram-Positive Bacteria with High DNA G+C Content among New Isolates. ACTA ACUST UNITED AC 2002. [DOI: 10.3209/saj.16_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
32
|
Frahm E, Heiber I, Ludwig W, Obst U. Rapid parallel detection of hygienically relevant microorganisms in water samples by PCR and specific hybridization in microtiter plates. Syst Appl Microbiol 2001; 24:423-9. [PMID: 11822680 DOI: 10.1078/0723-2020-00056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A molecular biological test protocol for the parallel detection of enterococci and Pseudomonas aeruginosa in drinking water was developed. Amplicons labelled with digoxigenin during PCR were hybridized to specific 23S rDNA targeted oligonucleotide probes immobilized in microtiter plates. Detection was performed by addition of anti-digoxigenin-peroxidase-conjugate and chromogenic substrate. Specificity of the probes was evaluated by using pure cultures. First evaluation data with natural water samples in comparison to conventional microbiological analysis according to the German Drinking Water Regulation showed good agreement. Its feasible and rapid performance should be advantageous for use in routine drinking water quality control. Further comparative evaluation studies need to be undertaken to determine the true applicability for routine testing of water samples.
Collapse
Affiliation(s)
- E Frahm
- Forschungszentrum Karlsruhe GmbH, ITC-WGT, Abt. Umweltmikrobiologie, Germany
| | | | | | | |
Collapse
|
33
|
Bogado I, Sutich E, Krapp A, Marchiaro P, Marzi M, Putero J, Carrillo N. Methicillin resistance study in clinical isolates of coagulase-negative staphylococci and determination of their susceptibility to alternative antimicrobial agents. J Appl Microbiol 2001; 91:344-50. [PMID: 11473600 DOI: 10.1046/j.1365-2672.2001.01400.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To achieve reliable detection of methicillin resistance in clinical isolates of coagulase-negative staphylococci. METHODS AND RESULTS Strains (105) were evaluated by normatized antimicrobial susceptibility methods, and for the presence of the methicillin resistance-determining mecA gene, using the polymerase chain reaction. Correlation between phenotypic and genotypic methods was obtained in 87.6% of the samples. Six strains, classified as methicillin-susceptible by phenotypic assays, revealed the presence of the mecA gene, indicating that methicillin resistance expression was probably repressed. Another seven isolates failed to show mecA amplification after displaying methicillin resistance in phenotypic evaluations. The susceptibility of the methicillin-resistant isolates to other antimicrobial agents was variable. CONCLUSION Genotypic determination of the mecA gene proved to be the most reliable method for detection of methicillin resistance. SIGNIFICANCE AND IMPACT OF THE STUDY Correct assessment of methicillin resistance, such as that attained through genotyping, is essential for defining therapeutic strategies, particularly when treating severely compromised patients.
Collapse
Affiliation(s)
- I Bogado
- Department of Microbiology, School of Biochemistry and Pharmacy, National University of Rosario, Rosario, Argentina.
| | | | | | | | | | | | | |
Collapse
|
34
|
Schmid M, Schmitz-Esser S, Jetten M, Wagner M. 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ Microbiol 2001; 3:450-9. [PMID: 11553235 DOI: 10.1046/j.1462-2920.2001.00211.x] [Citation(s) in RCA: 199] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recently, anaerobic ammonium-oxidizing bacteria (AAOB) were identified by comparative 16S rDNA sequence analysis as a novel, deep-branching lineage within the Planctomycetales. This lineage consists currently of only two, not yet culturable bacteria which have been provisionally described as Candidatus 'Brocadia anammoxidans' and Candidatus 'Kuenenia stuttgartiensis'. In this study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2 000 bases of the 23S rDNA, was polymerase chain reaction (PCR) amplified, cloned and sequenced from both AAOB. The retrieved 16S rDNA sequences of both species contain an insertion at helix 9 with a previously overlooked pronounced secondary structure (new subhelices 9a and 9b). This insertion, which is absent in all other known prokaryotes, is detectable by fluorescence in situ hybridization (FISH) and thus present in the mature 16S rRNA. In contrast with the genera Pirellula, Planctomyces and Gemmata that possess unlinked 16S and 23S rRNA genes, both AAOB have the respective genes linked together by an ISR of approximately 450 bp in length. Phylogenetic analysis of the obtained 23S rRNA-genes confirmed the deep branching of the AAOB within the Planctomycetales and allowed the design of additional specific FISH probes. Remarkably, the ISR of the AAOB also could be successfully detected by FISH via simultaneous application of four monolabelled oligonucleotide probes. Quantitative FISH experiments with cells of Candidatus 'Brocadia anammoxidans' that were inhibited by exposure to oxygen for different time periods demonstrated that the concentration of transcribed ISR reflected the activity of the cells more accurately than the 16S or 23S rRNA concentration. Thus the developed ISR probes might become useful tools for in situ monitoring of the activity of AAOB in their natural environment.
Collapse
MESH Headings
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- In Situ Hybridization, Fluorescence
- Molecular Sequence Data
- Nucleic Acid Conformation
- Oligonucleotide Probes
- Oxidation-Reduction
- Phylogeny
- Quaternary Ammonium Compounds/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Terminology as Topic
- rRNA Operon
Collapse
Affiliation(s)
- M Schmid
- Lehrstuhl für Mikrobiologie, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany
| | | | | | | |
Collapse
|
35
|
Turgeon N, Moineau S. Isolation and characterization of a Streptococcus thermophilus plasmid closely related to the pMV158 family. Plasmid 2001; 45:171-83. [PMID: 11407913 DOI: 10.1006/plas.2001.1517] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Twenty-two Streptococcus thermophilus strains used for milk fermentations were analyzed for their plasmid content and 13 of them (59%) were found to contain one or two plasmids. Fifteen S. thermophilus plasmids were divided into four groups using DNA homology. Ten plasmids were classified within group A and they shared homologies with all the previously sequenced S. thermophilus plasmids. Three plasmids (group B) hybridized with each other and two plasmids only hybridized with themselves (groups C and D). Single-stranded DNA was detected within strains containing plasmids of groups A, C, and D, indicating that they replicate via a rolling-circle mode. The only plasmid of group C, named pSMQ172, was further characterized. This 4230-bp plasmid replicates in Escherichia coli, Lactococcus lactis, and Streptococcus salivarius and does not confer phage resistance. Comparisons with databases showed that pSMQ172 was related to pMV158 of Streptococcus agalactiae and to pSSU1 of Streptococcus suis. These results suggest that genetic exchanges may have occurred between pathogenic and nonpathogenic streptococci.
Collapse
Affiliation(s)
- N Turgeon
- Department of Biochemistry and Microbiology, Université Laval, Québec, G1K 7P4, Canada
| | | |
Collapse
|
36
|
Ho KC, Tsai CC, Chung TL. Organization of ribosomal RNA genes from a Loofah witches' broom phytoplasma. DNA Cell Biol 2001; 20:115-22. [PMID: 11244569 DOI: 10.1089/104454901750070328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using the technique of integrative mapping with three vectors carrying chromosomal rDNA sequences, one of two rRNA operons of loofah witches' broom (LfWB) phytoplasma was constructed. This is the first complete rRNA operon of a phytoplasma to be reported. The operon has a context of 5'-16S-23S-5S-3' with a tRNA(Ile) gene in the ITS and tRNA(Val) and tRNA(Asn) genes downstream from the 5S rRNA gene. Although the other operon has not been cloned, the DNA sequence of a PCR-amplified product shows that it has no tRNA(Ile) gene in the ITS region. The complete nucleotide sequences of 16S, 23S, and 5S rDNA are 1538, 2864, and 113 bp, respectively. Five -10-like sequences, but no -35 sequences, were found within a 494-bp leader region. There was a TG dinucleotide two nucleotides upstream from each -10-like sequence. The existence of a TG dinucleotide at this position has been reported to enhance the efficiency of a promoter without a -35 region. The regions immediately flanking the 5' and 3' ends of 16S and 23S rDNA can form long basepaired stems that contain sites for processing by RNase III. No obvious sequence for a rho-dependent or rho-independent termination site was found downstream from the tRNA(Asn) gene. The transcription may stop within a pyrimidine-rich region, as has been reported for several polypeptide-encoding genes and rRNA operons of archaeobacteria. The presence of the tRNA genes downstream from the 5S rRNA gene in the rRNA operon of LfWB phytoplasma further supports the hypothesis that phytoplasmas are phylogenetically closer to acholeplasmas than to mycoplasmas. The phylogenetic relatedness of LfWB phytoplasma to other phytoplasmas is discussed on the basis of the nucleotide sequence of rRNA genes and ITS.
Collapse
MESH Headings
- 3' Untranslated Regions/analysis
- 5' Untranslated Regions/analysis
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- DNA, Ribosomal Spacer/analysis
- Gene Dosage
- Gene Order
- Genes, Bacterial
- Molecular Sequence Data
- Mycoplasma/genetics
- Operon
- Plants/microbiology
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/isolation & purification
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- K C Ho
- Department of Botany, National Taiwan University, Taipei, Taiwan
| | | | | |
Collapse
|
37
|
Deasy BM, Rea MC, Fitzgerald GF, Cogan TM, Beresford TP. A rapid PCR based method to distinguish between Lactococcus and Enterococcus. Syst Appl Microbiol 2000; 23:510-22. [PMID: 11249021 DOI: 10.1016/s0723-2020(00)80025-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phenotypic characterisation of Lactococcus and Enterococcus species remains unreliable as strains of both genera have been isolated which do not conform to the traditional criteria for separation of these genera. A bank of 131 isolates was phenotypically characterised by three methods: (a) traditional broth tests, (b) API Rapid ID 32 Strep and (c) BBL Crystal ID kits. Differences in genus designation between commercial kits were evident for 12 strains (9%), while 7 strains (5%) remained unidentified by either kit. Published 16S rRNA sequences were aligned and used to design genus-specific primers which, when used in separate PCR reactions, were capable of distinguishing all type strains of Lactococcus and Enterococcus. These primers did not react with known species of Streptococcus, Pediococcus, Lactobacillus, Leuconostoc or Tetragenococcus. Isolates which could not be identified by phenotype were assigned to either genus on the basis of the gene primers.
Collapse
Affiliation(s)
- B M Deasy
- Dairy Products Research Centre, Fermoy, Co. Cork, Ireland
| | | | | | | | | |
Collapse
|
38
|
Behr T, Koob C, Schedl M, Mehlen A, Meier H, Knopp D, Frahm E, Obst U, Schleifer K, Niessner R, Ludwig W. A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization. Syst Appl Microbiol 2000; 23:563-72. [PMID: 11249027 DOI: 10.1016/s0723-2020(00)80031-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Complete 23S and almost complete 16S rRNA gene sequences were determined for the type strains of the validly described Enterococcus species, Melissococcus pluton and Tetragenococcus halophilus. A comprehensive set of rRNA targeted specific oligonucleotide hybridization probes was designed according to the multiple probe concept. In silico probe design and evaluation was performed using the respective tools of the ARB program package in combination with the ARB databases comprising the currently available 16S as well as 23S rRNA primary structures. The probes were optimized with respect to their application for reverse hybridization in microplate format. The target comprising 16S and 23S rDNA was amplified and labeled by PCR (polymerase chain reaction) using general primers targeting a wide spectrum of bacteria. Alternatively, amplification of two adjacent rDNA fragments of enterococci was performed by using specific primers. In vitro evaluation of the probe set was done including all Enterococcus type strains, and a selection of other representatives of the gram-positive bacteria with a low genomic DNA G+C content. The optimized probe set was used to analyze enriched drinking water samples as well as original samples from waste water treatment plants.
Collapse
MESH Headings
- Base Sequence
- DNA Probes
- Enterococcus/classification
- Enterococcus/genetics
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- T Behr
- Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Hébert A, Sayasith K, Sénéchal S, Dubreuil P, Lagacé J. Demonstration of intracellular Staphylococcus aureus in bovine mastitis alveolar cells and macrophages isolated from naturally infected cow milk. FEMS Microbiol Lett 2000; 193:57-62. [PMID: 11094279 DOI: 10.1111/j.1574-6968.2000.tb09402.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Numerous in vitro studies have demonstrated that Staphylococcus aureus may be internalized and survive in a bovine mammary epithelial cell line. We report here the presence of internalized and living S. aureus in alveolar cells and macrophages in milk samples of bovine mastitis. We used fluorochrome labeled monoclonal antibodies, specifically recognizing surface cell markers of bovine alveolar cells and macrophages, to isolate these two types of cells using fluorescence activated cell sorting. Extracellular bacteria and DNA were previously eliminated to exclude possible contamination. In order to detect intracellular bacterial DNA inside the isolated cells, we used PCR amplification of bacterial DNA and the PCR products were analyzed by Southern blot with a specific probe for Staphylococcus. The results showed the presence of Staphylococcus DNA inside the two isolated populations of cells, confirming that S. aureus could penetrate alveolar cells and macrophages. The demonstration of the presence of intracellular living S. aureus was determined by bacteriological culture of positive samples plated onto blood agar plates and by its further identification. Our results showed for the first time that living S. aureus and its DNA are present in both alveolar cells and macrophages in chronically infected cow milk.
Collapse
Affiliation(s)
- A Hébert
- Department of Microbiology and Immunology, Faculty of Medicine, University of Montreal, Centre-Ville, Montreal, Que., Canada
| | | | | | | | | |
Collapse
|
40
|
Anthony RM, Brown TJ, French GL. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 2000; 38:781-8. [PMID: 10655385 PMCID: PMC86203 DOI: 10.1128/jcm.38.2.781-788.2000] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/1999] [Accepted: 10/29/1999] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of bacteria in blood cultures and other clinical specimens is important for patient management and antimicrobial therapy. We describe a rapid (<4 h) detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 23S ribosomal DNA, followed by reverse hybridization of the products to a panel of oligonucleotides. This procedure was successful in discriminating a range of bacteria in pure cultures. When this procedure was applied directly to 158 unselected positive blood culture broths on the day when growth was detected, 125 (79.7%) were correctly identified, including 4 with mixed cultures. Nine (7.2%) yielded bacteria for which no oligonucleotide targets were present in the oligonucleotide panel, and 16 culture-positive broths (10.3%) produced no PCR product. In seven of the remaining eight broths, streptococci were identified but not subsequently grown, and one isolate of Staphylococcus aureus was misidentified as a coagulase-negative staphylococcus. The accuracy, range, and discriminatory power of the assay can be continually extended by adding further oligonucleotides to the panel without significantly increasing complexity or cost.
Collapse
Affiliation(s)
- R M Anthony
- Department of Microbiology, King's College St. Thomas' Campus, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | | | | |
Collapse
|
41
|
Schmidt G, Hertel C, Hammes WP. Molecular characterisation of the dnaK operon of Lactobacillus sakei LTH681. Syst Appl Microbiol 1999; 22:321-8. [PMID: 10553284 DOI: 10.1016/s0723-2020(99)80039-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The use of lactobacilli as starter organisms in food fermentation processes requires thorough knowledge of their reaction to the multitude of ecological factors including their response to stress. We have characterised the dnaK gene region of Lactobacillus sakei LTH681. Two chromosomal EcoRI fragments of 2.5 and 4.0 kb were identified using a homologous dnaK probe generated by PCR. The sequence analysis of the cloned fragments showed that the dnaK gene region consists of four heat shock genes with the organisation hrcA-grpE-dnaK-dnaJ. Comparison of the deduced amino acid sequences revealed high similarity to the corresponding heat shock proteins of Gram-positive bacteria. An upstream located orfY was found which exhibited substantial similarity (41.5%) to the chloramphenicol acetyltransferase of Enterobacter aerogenes. Northern hybridisation analysis revealed that the transcription of the genes is induced by heat shock (42 degrees C) as well as salt (6%) or ethanol (10%) stress. Several transcripts were detected including a polycistronic mRNA of 4.9 kb which represents the transcript of the complete dnaK gene region indicating a tetracistronic organisation of the dnaK operon. The other RNA fragments were identified as shorter transcripts (3.7 and 1.3 kb) or cleavage products of the polycistronic mRNAs. The transcription start sites of the dnaK operon were determined under inducing and non-inducing conditions. The site varied with the applied stress condition. A regulatory CIRCE element was identified located between the transcription and translation start site. The promoter region including CIRCE was transcriptionally fused to the beta-glucuronidase reporter gene gusA and expressed in L. sakei LTH681. The kinetics of transcriptional induction of gusA by heat shocking were identical to those of the dnaK operon confirming the involvement of the CIRCE element in regulation of gene expression.
Collapse
Affiliation(s)
- G Schmidt
- Institut für Lebensmitteltechnologie, Universität Hohenheim, Stuttgart, Germany
| | | | | |
Collapse
|
42
|
Back W, Bohak I, Ehrmann M, Ludwig W, Pot B, Kersters K, Schleifer KH. Lactobacillus perolens sp. nov., a soft drink spoilage bacterium. Syst Appl Microbiol 1999; 22:354-9. [PMID: 10553287 DOI: 10.1016/s0723-2020(99)80042-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Lactic acid bacteria that are able to spoil soft drinks with low pH comprise a limited number of acidotolerant or acidophilic species of the genera Lactobacillus, Leuconostoc and Weissella. Various Gram-positive rods causing turbidity and off-flavour were isolated from orange lemonades. Physiological and biochemical studies including SDS-PAGE whole-cell protein analysis showed a homogeneous group of organisms. The 16S rRNA gene sequence analysis of two representatives revealed that they formed a phylogenetically distinct line within the genus Lactobacillus. All strains were facultatively heterofermentative, producing L-lactic acid. Based on the data presented a new species L. perolens is proposed. The name refers to the off-flavour caused by high amounts of diacetyl. The type strain of L. perolens is DSM 12744 (LMG 18936). A rRNA targeted oligonucleotide probe was designed that allows a fast and reliable identification of L. perolens.
Collapse
Affiliation(s)
- W Back
- Lehrstuhl für Technologie der Brauerei I, Technische Universität München-Weihenstephan, Freising, Germany
| | | | | | | | | | | | | |
Collapse
|
43
|
Loessner MJ, Gaeng S, Scherer S. Evidence for a holin-like protein gene fully embedded out of frame in the endolysin gene of Staphylococcus aureus bacteriophage 187. J Bacteriol 1999; 181:4452-60. [PMID: 10419939 PMCID: PMC103572 DOI: 10.1128/jb.181.15.4452-4460.1999] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have cloned, sequenced, and characterized the genes encoding the lytic system of the unique Staphylococcus aureus phage 187. The endolysin gene ply187 encodes a large cell wall-lytic enzyme (71.6 kDa). The catalytic site, responsible for the hydrolysis of staphylococcal peptidoglycan, was mapped to the N-terminal domain of the protein by the expression of defined ply187 domains. This enzymatically active N terminus showed convincing amino acid sequence homology to an N-acetylmuramoyl-L-alanine amidase, whereas the C-terminal part, whose function is unknown, revealed striking relatedness to major staphylococcal autolysins. An additional reading frame was identified entirely embedded out of frame (+1) within the 5' region of ply187 and was shown to encode a small, hydrophobic protein of holin-like function. The hol187 gene features a dual-start motif, possibly enabling the synthesis of two products of different lengths (57 and 55 amino acids, respectively). Overproduction of Hol187 in Escherichia coli resulted in growth retardation, leakiness of the cytoplasmic membrane, and loss of de novo ATP synthesis. Compared to other holins identified to date, Hol187 completely lacks the highly charged C terminus. The secondary structure of the polypeptide is predicted to consist of two small, antiparallel, hydrophobic, transmembrane helices. These are supposed to be essential for integration into the membrane, since site-specific introduction of negatively charged amino acids into the first transmembrane domain (V7D G8D) completely abolished the function of the Hol187 polypeptide. With antibodies raised against a synthetic 18-mer peptide representing a central part of the protein, it was possible to detect Hol187 in the cytoplasmic membrane of phage-infected S. aureus cells. An important indication that the protein actually functions as a holin in vivo was that the gene (but not the V7D G8D mutation) was able to complement a phage lambda Sam mutation in a nonsuppressing E. coli HB101 background. Plaque formation by lambdagt11::hol187 indicated that both phage genes have analogous functions. The data presented here indicate that a putative holin is encoded on a different reading frame within the enzymatically active domain of ply187 and that the holin is synthesized during the late stage of phage infection and found in the cytoplasmic membrane, where it causes membrane lesions which are thought to enable access of Ply187 to the peptidoglycan of phage-infected Staphylococcus cells.
Collapse
Affiliation(s)
- M J Loessner
- Institut für Mikrobiologie, Forschungszentrum für Milch und Lebensmittel Weihenstephan, Technische Universität München, D-85350 Freising, Germany
| | | | | |
Collapse
|
44
|
Bourgoin F, Pluvinet A, Gintz B, Decaris B, Guédon G. Are horizontal transfers involved in the evolution of the Streptococcus thermophilus exopolysaccharide synthesis loci? Gene 1999; 233:151-61. [PMID: 10375631 DOI: 10.1016/s0378-1119(99)00144-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A 32.5kb variable locus of the Streptococcus thermophilus CNRZ368 chromosome, the eps locus, contains 25 ORF and seven insertion sequences (IS). The putative products of 17 ORF are related to proteins involved in the synthesis of polysaccharides in various bacteria. The two distal regions and a small central region of the eps locus are constant and present in all or almost all of the S. thermophilus strains tested. The other regions are variable and present in only some S. thermophilus strains tested, particularly in the closely related strains CNRZ368 and A054. A 13.6kb variable region of the eps locus of S. thermophilus CNRZ368 contains two ORF that are almost identical to epsL and orfY of the eps locus of Lactococcus lactis NIZOB40 and seven IS belonging to four different families, ISS1, IS981, IS1193 and IS1194. Five of these sequences were probably acquired by horizontal transfer from L. lactis (Bourgoin, F., et al., 1996. Gene 178, 15-23). Three probes of this 13.6kb region hybridized with the DNA of several L. lactis strains tested. A specific probe for another sequence within the S. thermophilus eps locus, epsF, hybridized with the DNA of one of the L. lactis strains tested. Sequence comparisons also suggest that five ORF of the eps locus have a mosaic structure and probably result from recombinations between sequences that are 10 to 50% divergent. The chimeric structure of the eps locus suggests a very complex evolution. This evolution probably involves both the acquisition of the 13.6kb region from L. lactis by horizontal transfer and exchanges within the S. thermophilus species.
Collapse
Affiliation(s)
- F Bourgoin
- Laboratoire de Génétique et Microbiologie, UA INRA 952, Université Henri Poincaré Nancy I, Faculté des Sciences, BP 239, 54506, Vandoeuvre-lès-Nancy, France.
| | | | | | | | | |
Collapse
|
45
|
Abstract
We have developed a new, cultivation-independent, fast and flexible method for the rRNA-targeted probe-based enrichment of bacteria. The target cells were labelled by in situ hybridization with biotinylated polyribonucleotide probes. These probes were generated by in vitro transcription of amplified rDNA of a variable region in domain III of the 23S rRNA molecules. The probes were about 300 nucleotides in length and were labelled by incorporation of biotin-UTP during the transcription. Probes were hybridized with bacterial cells and incubated with paramagnetic streptavidin-coated particles. The labelled target cells can be separated in a column filled with steel wool inserted into the field of a permanent magnet. Unlabelled, non-target cells pass through the column, whereas labelled cells are retained. They were eluted from the column after removal of the magnetic field. Up to now, the method has been tested with mixtures of different pure cultures. For the first time, transcript probes have been used for the labelling of the target cells and for their specific separation. The enrichment of the target cells can be monitored by a streptavidin-fluorescein staining of the biotinylated target cells and/or by a subsequent in situ hybridization with fluorescently labelled oligonucleotide probes. Enrichment rates of up to 90-fold, depending on the original abundance of the cells of interest, could be determined. To demonstrate that the sorted cells were amenable to molecular analysis, we amplified and sequenced a part of the tuf gene of enriched Acinetobacter calcoaceticus cells.
Collapse
Affiliation(s)
- M Stoffels
- Lehrstuhl für Mikrobiologie, Technische Universität München, Munich, Germany.
| | | | | |
Collapse
|
46
|
Meier H, Amann R, Ludwig W, Schleifer KH. Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content. Syst Appl Microbiol 1999; 22:186-96. [PMID: 10390869 DOI: 10.1016/s0723-2020(99)80065-4] [Citation(s) in RCA: 264] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Almost one thousand 16S rRNA sequences of Gram-positive bacteria with a low DNA G + C content from public databases were analyzed using the ARB software package. A signature region was identified between positions 354 and 371 (E. coli numbering) for the Bacillus sub-branch of the Gram-positive bacteria with a low DNA G + C content, the former orders Bacillales and Lactobacillales. Three oligonucleotide probes, namely LGC354A, LGC354B, and LGC354C, were designed to target this diagnostic site. Their fluorescent derivatives were suitable for whole cell detection by fluorescence in situ hybridization (FISH). Hybridization conditions were adjusted for differentiation of target and related non-target reference species. When applying FISH to whole bacterial cells in a sample of activated sludge from a communal wastewater treatment plant, members of the Bacillus sub-branch were detected at levels from 0.01% of cells in samples fixed with paraformaldehyde to over 8 percent in the same samples fixed with ethanol and treated with lysozyme. The problems of quantitative in situ analysis of Gram-positive bacteria with a low DNA G + C content in biofilm flocs are discussed and recommendations made. Members of the Bacillus sub-branch were detected in different abundances in activated sludge samples from different wastewater plants.
Collapse
Affiliation(s)
- H Meier
- Technische Universität München, Germany
| | | | | | | |
Collapse
|
47
|
Bauernfeind A, Schneider I, Jungwirth R, Roller C. Discrimination of Burkholderia multivorans and Burkholderia vietnamiensis from Burkholderia cepacia genomovars I, III, and IV by PCR. J Clin Microbiol 1999; 37:1335-9. [PMID: 10203482 PMCID: PMC84768 DOI: 10.1128/jcm.37.5.1335-1339.1999] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a PCR procedure for identification of Burkholderia cepacia, Burkholderia multivorans, and Burkholderia vietnamiensis. 16S and 23S ribosomal DNAs (rDNAs) of B. multivorans and B. vietnamiensis were sequenced and aligned with published sequences for definition of species-specific 18-mer oligonucleotide primers. Specific antisense 16S rDNA primers (for B. cepacia, 5'-AGC ACT CCC RCC TCT CAG-3'; for B. multivorans, 5'-AGC ACT CCC GAA TCT CTT-3') and 23S rDNA primers (for B. vietnamiensis, 5'-TCC TAC CAT GCG TGC AA-3') were paired with a general sense primer of 16S rDNAs (5'-AGR GTT YGA TYM TGG CTC AG-3') or with a sense primer of 23S rDNA (5'-CCT TTG GGT CAT CCT GGA-3'). PCR with these primers under optimized conditions is appropriate to specifically and rapidly identify B. multivorans, B. vietnamiensis, and B. cepacia (genomovars I, III, and IV are not discriminated). In comparison with the polyphasic taxonomic analyses presently necessary for species and genomovar identification within the B. cepacia complex, our procedure is more rapid and easier to perform and may contribute to clarifying the clinical significance of individual members of the complex in cystic fibrosis.
Collapse
|
48
|
Schulze R, Spring S, Amann R, Huber I, Ludwig W, Schleifer KH, Kämpfer P. Genotypic diversity of Acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp. nov. Syst Appl Microbiol 1999; 22:205-14. [PMID: 10390871 DOI: 10.1016/s0723-2020(99)80067-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence in situ hybridization of activated sludge samples from a municipal wastewater treatment plant using oligonucleotide probes specific for Acidovorax demonstrated that these bacteria are highly abundant in this environment. For the targeted cultivation of representatives belonging to this genus, isolates grown on agar plates after serial dilution were screened by whole-cell hybridization with specific probes. The obtained strains clustered in two phylogenetic groups as determined by 16S rRNA gene sequence analyses. The isolates of one cluster were phylogenetically and genotypically closely related to A. delafieldii. In contrast, the strains of the other cluster were genotypically and phenotypically distinct from the hitherto known Acidovorax species. Therefore, a new species, Acidovorax defluvii sp. nov., was proposed for these strains. The main characteristics of the newly defined species are as follows: Gram-negative, motile or non-motile rods with rounded ends, often with large polyhydroxybutyrate granules. In broth cultures flocs are formed. Test for cytochrome oxidase is positive with all strains. The majority of strains is catalase positive and reduces nitrate. All strains are metabolically inactive against most carbohydrates and organic acids. Fatty acid patterns are typical for the genus Acidovorax. The guanine-plus-cytosine content of DNAs varies between 62 and 64 mol%. The type strain of A. defluvii is BSB411T (DSM 12644). A new 16S rRNA-targeted oligonucleotide probe reacting by in situ hybridization with all known Acidovorax species, including A. defluvii sp. nov., was designed.
Collapse
Affiliation(s)
- R Schulze
- Technische Universität München, Germany
| | | | | | | | | | | | | |
Collapse
|
49
|
Tremblay DM, Moineau S. Complete genomic sequence of the lytic bacteriophage DT1 of Streptococcus thermophilus. Virology 1999; 255:63-76. [PMID: 10049822 DOI: 10.1006/viro.1998.9525] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Streptococcus thermophilus lytic bacteriophage DT1, isolated from a mozzarella whey, was characterized at the microbiological and molecular levels. Phage DT1 had an isometric head of 60 nm and a noncontractile tail of 260 x 8 nm, two major structural proteins of 26 and 32 kDa, and a linear double-stranded DNA genome with cohesive ends at its extremities. The host range of phage DT1 was limited to 5 of the 21 S. thermophilus strains tested. Using S. thermophilus SMQ-301 as a host, phage DT1 had a burst size of 276 +/- 36 and a latent period of 25 min. The genome of phage DT1 contained 34,820 bp with a GC content of 39.1%. Forty-six open reading frames (ORFs) of more than 40 codons were found and putative functions were assigned to 20 ORFs, mostly in the late region of phage DT1. Comparative genomic analysis of DT1 with the completely sequenced S. thermophilus temperate phage O1205 revealed two large homologous regions interspersed by two heterologous segments. The homologous regions consisted of the early replication genes, the late morphogenesis genes, and the lysis cassette. The divergent segments contained the DNA packaging machinery, the major structural proteins, and remnants of a lysogeny module.
Collapse
Affiliation(s)
- D M Tremblay
- Faculté de Médecine Dentaire, Université Laval, Québec, G1K 7P4, Canada
| | | |
Collapse
|
50
|
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
|