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Díaz-Díaz M, Antón-Domínguez BI, Raya MC, Bernal-Cabrera A, Medina-Marrero R, Trapero A, Agustí-Brisach C. Streptomyces spp. Strains as Potential Biological Control Agents against Verticillium Wilt of Olive. J Fungi (Basel) 2024; 10:138. [PMID: 38392810 PMCID: PMC10890128 DOI: 10.3390/jof10020138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Verticillium wilt of olive (VWO) caused by Verticillium dahliae is considered a major olive (Olea europaea) disease in Mediterranean-type climate regions. The lack of effective chemical products against VWO makes it necessary to search for alternatives such as biological control. The main goal of this study was to evaluate the effect of six Streptomyces spp. strains as biological control agents (BCAs) against VWO. All of them were molecularly characterized by sequencing 16S or 23S rRNA genes and via phylogenetic analysis. Their effect was evaluated in vitro on the mycelial growth of V. dahliae (isolates V004 and V323) and on microsclerotia (MS) viability using naturally infested soils. Bioassays in olive plants inoculated with V. dahliae were also conducted to evaluate their effect against disease progress. In all the experiments, the reference BCAs Fusarium oxysporum FO12 and Aureobasidium pullulans AP08 were included for comparative purposes. The six strains were identified as Streptomyces spp., and they were considered as potential new species. All the BCAs, including Streptomyces strains, showed a significant effect on mycelial growth inhibition for both V. dahliae isolates compared to the positive control, with FO12 being the most effective, followed by AP08, while the Streptomyces spp. strains showed an intermediate effect. All the BCAs tested also showed a significant effect on the inhibition of germination of V. dahliae MS compared to the untreated control, with FO12 being the most effective treatment. Irrigation treatments with Streptomyces strain CBQ-EBa-21 or FO12 were significantly more effective in reducing disease severity and disease progress in olive plants inoculated with V. dahliae compared to the remaining treatments. This study represents the first approach to elucidating the potential effect of Streptomyces strains against VWO.
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Affiliation(s)
- Miriam Díaz-Díaz
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Begoña I Antón-Domínguez
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - María Carmen Raya
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Alexander Bernal-Cabrera
- Centro de Investigaciones Agropecuarias (CIAP), Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
- Departamento de Agronomía, Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Ricardo Medina-Marrero
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Antonio Trapero
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Carlos Agustí-Brisach
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
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2
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Chen Y, Zhang Q, Feng X, Wojnowska M, O'Hagan D. Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 are producers of the antibiotic nucleocidin and 4'-fluoroadenosine is identified as a co-product. Org Biomol Chem 2021; 19:10081-10084. [PMID: 34779476 DOI: 10.1039/d1ob01898a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genome homology and the presence of a putative biosynthetic gene cluster identified Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 as candidate producers of the antibiotic nucleocidin 1. Indeed when these bacterial strains were cultured in a medium supplemented with fluoride (4 mM) they each produced nucleocidin 1 and the previously identified 4'-fluoro-3'-O-β-glucosylated adenosine 2 and its sulfamylated derivative 3. In both of these cases 4'-fluoroadenosine 9 is also identified as a natural product although it has never been observed during fermentations of Streptomyces calvus, the original source of nucleocidin 1. The identity of 4'-fluoroadenosine 9 was confirmed by a total synthesis as well as by its in vitro enzymatic conversion to metabolite 2 using the glucosyl transferase enzyme, NucGT.
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Affiliation(s)
- Yawen Chen
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Qingzhi Zhang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Xuan Feng
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Marta Wojnowska
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - David O'Hagan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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3
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Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. PLoS One 2014; 9:e88645. [PMID: 24670812 PMCID: PMC3966736 DOI: 10.1371/journal.pone.0088645] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/08/2014] [Indexed: 01/09/2023] Open
Abstract
The microbiota of the human lower intestinal tract helps maintain healthy host physiology, for example through nutrient acquisition and bile acid recycling, but specific positive contributions of the oral microbiota to host health are not well established. Nitric oxide (NO) homeostasis is crucial to mammalian physiology. The recently described entero-salivary nitrate-nitrite-nitric oxide pathway has been shown to provide bioactive NO from dietary nitrate sources. Interestingly, this pathway is dependent upon oral nitrate-reducing bacteria, since humans lack this enzyme activity. This pathway appears to represent a newly recognized symbiosis between oral nitrate-reducing bacteria and their human hosts in which the bacteria provide nitrite and nitric oxide from nitrate reduction. Here we measure the nitrate-reducing capacity of tongue-scraping samples from six healthy human volunteers, and analyze metagenomes of the bacterial communities to identify bacteria contributing to nitrate reduction. We identified 14 candidate species, seven of which were not previously believed to contribute to nitrate reduction. We cultivated isolates of four candidate species in single- and mixed-species biofilms, revealing that they have substantial nitrate- and nitrite-reduction capabilities. Colonization by specific oral bacteria may thus contribute to host NO homeostasis by providing nitrite and nitric oxide. Conversely, the lack of specific nitrate-reducing communities may disrupt the nitrate-nitrite-nitric oxide pathway and lead to a state of NO insufficiency. These findings may also provide mechanistic evidence for the oral systemic link. Our results provide a possible new therapeutic target and paradigm for NO restoration in humans by specific oral bacteria.
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Wings S, Müller H, Berg G, Lamshöft M, Leistner E. A study of the bacterial community in the root system of the maytansine containing plant Putterlickia verrucosa. PHYTOCHEMISTRY 2013; 91:158-64. [PMID: 22795602 DOI: 10.1016/j.phytochem.2012.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/07/2012] [Accepted: 06/18/2012] [Indexed: 05/16/2023]
Abstract
Maytansinoid compounds are ansa antibiotics occurring in the bacterium Actinosynnema pretiosum, in mosses and in higher plants such as Putterlickia verrucosa (E. Meyer ex Sonder) Szyszyl. The disjunct occurrence of maytansinoids has led to the consideration that plant-associated bacteria may be responsible for the presence of maytansinoids in P. verrucosa plants. Investigation of the bacterial community of this plant by molecular methods led to the observation that A. pretiosum, a maytansine-producing bacterium, is likely to be an inhabitant of the rhizosphere and the endorhiza of P. verrucosa.
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Affiliation(s)
- Susanne Wings
- Institut fuer Pharmazeutische Biologie, Rheinische Friedrich Wilhelms-Universität, Bonn, Germany
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5
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Kim W, Park HK, Hwang WJ, Shin HS. Simultaneous detection of Streptococcus pneumoniae, S. mitis, and S. oralis by a novel multiplex PCR assay targeting the gyrB gene. J Clin Microbiol 2013; 51:835-40. [PMID: 23269740 PMCID: PMC3592088 DOI: 10.1128/jcm.02920-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/17/2012] [Indexed: 01/05/2023] Open
Abstract
A multiplex PCR (mPCR) protocol was developed for simultaneous detection of the gyrB gene in Streptococcus pneumoniae, Streptococcus mitis, and Streptococcus oralis, and the specificity was evaluated using 141 coccus strains. Genomic DNAs purified from S. pneumoniae, S. mitis, and S. oralis strains were efficiently detected with size differences, whereas no PCR products were amplified from any of the reference strains tested. A pilot study of 47 human oral swab specimens was conducted in parallel, and the mPCR assay identified S. pneumoniae in 1 sample, S. mitis in 8 samples, and S. oralis in 2 samples, providing a powerful means for characterization at the level of species compared with traditional culture analysis. Our results suggest that the mPCR protocol presented here is a sensitive and promising tool for the rapid detection and discrimination of S. pneumoniae, S. mitis, and S. oralis from clinical specimens.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hee Kuk Park
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Woo-Jin Hwang
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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6
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Bakker MG, Bradeen JM, Kinkel LL. Effects of plant host species and plant community richness on streptomycete community structure. FEMS Microbiol Ecol 2012; 83:596-606. [PMID: 23013423 DOI: 10.1111/1574-6941.12017] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/22/2012] [Accepted: 09/23/2012] [Indexed: 01/18/2023] Open
Abstract
We investigated soil streptomycete communities associated with four host plant species (two warm season C4 grasses: Andropogon gerardii, Schizachyrium scoparium and two legumes: Lespedeza capitata, Lupinus perennis), grown in plant communities varying in species richness. We used actinobacteria-selective PCR coupled with pyrosequencing to characterize streptomycete community composition and structure. The greatest pairwise distances between communities were observed in contrasts between monocultures of different plant species, indicating that plant species exert distinct selective effects on soil streptomycete populations. Increasing plant richness altered the composition and structure of streptomycete communities associated with each host plant species. Significant relationships between plant community characteristics, soil edaphic characteristics, and streptomycete community structure suggest that host plant effects on soil microbial communities may be mediated through changes to the soil environment. Co-occurring streptomycete taxa also shared consistent relationships with soil edaphic properties, providing further indication of the importance of habitat preference for taxon occurrence. Physical distance between sampling points had a significant influence on streptomycete community similarity. This work provides a detailed characterization of soil streptomycete populations across a field scale and in relation to plant host identity and plant community richness.
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Affiliation(s)
- Matthew G Bakker
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
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Loch TP, Kumar R, Xu W, Faisal M. Carnobacterium maltaromaticum infections in feral Oncorhynchus spp. (Family Salmonidae) in Michigan. J Microbiol 2011; 49:703-13. [DOI: 10.1007/s12275-011-0527-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/27/2011] [Indexed: 11/29/2022]
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8
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Kim W, Park HK, Thanh HD, Lee BY, Shin JW, Shin HS. Comparative genome analysis of Lactococcus garvieae using a suppression subtractive hybridization library: discovery of novel DNA signatures. FEMS Microbiol Lett 2011; 325:77-84. [PMID: 22092865 DOI: 10.1111/j.1574-6968.2011.02414.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/04/2011] [Accepted: 09/06/2011] [Indexed: 12/01/2022] Open
Abstract
Lactococcus garvieae, the pathogenic species in the genus Lactococcus, is recognized as an emerging pathogen in fish, animals, and humans. Despite the widespread distribution and emerging clinical significance of L. garvieae, little is known about the genomic content of this microorganism. Suppression subtractive hybridization was performed to identify the genomic differences between L. garvieae and Lactococcus lactis ssp. lactis, its closest phylogenetic neighbor, and the type species of the genus Lactococcus. Twenty-seven clones were specific to L. garvieae and were highly different from Lactococcus lactis in their nucleotide and protein sequences. Lactococcus garvieae primer sets were subsequently designed for two of these clones corresponding to a pyrH gene and a novel DNA signature for application in the specific detection of L. garvieae. The primer specificities were evaluated relative to three previously described 16S rRNA gene-targeted methods using 32 Lactococcus and closely related strains. Both newly designed primer sets were highly specific to L. garvieae and performed better than did the existing primers. Our findings may be useful for developing more stable and accurate tools for the discrimination of L. garvieae from other closely related species.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Korea
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9
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Identification and characterization of a Streptomyces sp. isolate exhibiting activity against multidrug-resistant coagulase-negative Staphylococci. Vet Res Commun 2011; 35:477-86. [DOI: 10.1007/s11259-011-9491-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2011] [Indexed: 11/25/2022]
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10
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Park HK, Lee SJ, Yoon JW, Shin JW, Shin HS, Kook JK, Myung SC, Kim W. Identification of the cpsA gene as a specific marker for the discrimination of Streptococcus pneumoniae from viridans group streptococci. J Med Microbiol 2010; 59:1146-1152. [PMID: 20616191 DOI: 10.1099/jmm.0.017798-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae, the aetiological agent of pneumonia and non-gonococcal urethritis, shares a high degree of DNA sequence identity with the viridans group of streptococci, particularly Streptococcus mitis and Streptococcus oralis. Although their clinical and pathological manifestations are different, discrimination between S. pneumoniae and its close viridans cocci relatives is still quite difficult. Suppression subtractive hybridization was performed to identify the genomic differences between S. pneumoniae and S. mitis. Thirty-four resulting S. pneumoniae-specific clones were examined by sequence determination and comparative DNA sequence analysis using blast. S. pneumoniae-specific primers were subsequently designed from one of the clonal DNA sequences containing the cps gene (coding for capsular polysaccharide biosynthesis). The primer specificities were evaluated using 49 viridans streptococci including 26 S. pneumoniae, 54 other streptococci, 14 Lactococcus species, 14 Enterococcus species and three Vagococcus species, and compared with the specificities of previously described autolysin (lytA), pneumolysin (ply), Spn9802 and Spn9828 primers. The newly designed cpsA-specific primer set was highly specific to S. pneumoniae and was even better than the existing primers. These findings may help improve the rapid identification and differentiation of S. pneumoniae from closely related members of the viridans group streptococci.
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Affiliation(s)
- Hee Kuk Park
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Sang-Jae Lee
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan 570-749, Republic of Korea
| | - Jang Won Yoon
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jong Wook Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan 570-749, Republic of Korea
| | - Joong-Ki Kook
- Department of Biochemistry, Chosun University College of Dentistry, Gwangju 501-825, Republic of Korea
| | - Soon Chul Myung
- Department of Urology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Wonyong Kim
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
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11
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Salamoni SP, Mann MB, Campos FS, Franco AC, Germani JC, Van Der Sand ST. Preliminary characterization of some Streptomyces species isolated from a composting process and their antimicrobial potential. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0366-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Park HK, Yoon JW, Shin JW, Kim JY, Kim W. rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 2010; 305:58-64. [DOI: 10.1111/j.1574-6968.2010.01913.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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SEMBIRING LANGKAH. Molecular Phylogenetic Classification of Streptomycetes Isolated from the Rhizosphere of Tropical Legume (Paraserianthes falcataria) (L.) Nielsen. HAYATI JOURNAL OF BIOSCIENCES 2009. [DOI: 10.4308/hjb.16.3.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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14
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Manteca A, Pelaez AI, del Mar Garcia-Suarez M, Hidalgo E, Lopez S, Mendez FJ. A rare case of silicone mammary implant infection by Streptomyces spp. in a patient with breast reconstruction after mastectomy: taxonomic characterization using molecular techniques. Diagn Microbiol Infect Dis 2009; 63:390-3. [PMID: 19302925 DOI: 10.1016/j.diagmicrobio.2008.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/09/2008] [Accepted: 12/15/2008] [Indexed: 10/21/2022]
Abstract
A Streptomyces sp. isolated from a patient who had had breast reconstruction after a mastectomy was identified at the species level by comparative sequence analysis of 16S ribosomal DNA (rDNA) and the hypervariable alpha-region of the 16S rDNA.
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Affiliation(s)
- Angel Manteca
- Departamento de Biologia Funcional, Instituto Universitario de Biotecnologia de Asturias, Universidad de Oviedo, Oviedo, Asturias, Spain.
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15
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Bramwell PA, Wiener P, Akkermans ADL, Wellington EMH. Phenotypic, genotypic and pathogenic variation among streptomycetes implicated in common scab disease. Lett Appl Microbiol 2008. [DOI: 10.1046/j.1472-765x.1998.00439.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- P. A. Bramwell
- Department of Biological Sciences, University of Warwick, Coventry, UK, and
| | - P. Wiener
- Department of Biological Sciences, University of Warwick, Coventry, UK, and
| | - A. D. L. Akkermans
- Department of Microbiology, Agricultural University, Wageningen, The Netherlands
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Manteca A, Pelaez AI, del Mar Garcia-Suarez M, Hidalgo E, del Busto B, Mendez FJ. A rare case of lung coinfection by Streptomyces cinereoruber and Haemophilus influenzae in a patient with severe chronic obstructive pulmonary disease: characterization at species level using molecular techniques. Diagn Microbiol Infect Dis 2007; 60:307-11. [PMID: 18061387 DOI: 10.1016/j.diagmicrobio.2007.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2007] [Revised: 10/02/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
Abstract
Streptomyces cinereoruber isolated from a patient with severe respiratory failure that could not be identified by culture was correctly identified at the species level by comparative sequence analysis of 16S rDNA and the hypervariable alpha-region of 16S rDNA. Restriction fragment length polymorphism, morphologic, and biochemical characteristics have confirmed their identity.
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Affiliation(s)
- Angel Manteca
- Area de Microbiologia, Departamento de Biologia Funcional, Instituto Universitario de Biotecnologia de Asturias (IUBA), Universidad de Oviedo, 33006 Oviedo, Asturias, Spain.
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17
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Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 2007; 69:330-9. [PMID: 17391789 PMCID: PMC2562909 DOI: 10.1016/j.mimet.2007.02.005] [Citation(s) in RCA: 665] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 01/31/2007] [Accepted: 02/05/2007] [Indexed: 10/23/2022]
Abstract
Bacterial 16S ribosomal RNA (rRNA) genes contain nine "hypervariable regions" (V1-V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations. No single region can differentiate among all bacteria; therefore, systematic studies that compare the relative advantage of each region for specific diagnostic goals are needed. We characterized V1-V8 in 110 different bacterial species including common blood borne pathogens, CDC-defined select agents and environmental microflora. Sequence similarity dendrograms were created for hypervariable regions V1-V8, and for selected combinations of regions or short segments within individual hypervariable regions that might be appropriate for DNA probing and real-time PCR. We determined that V1 best differentiated among Staphylococcus aureus and coagulase negative Staphylococcus sp. V2 and V3 were most suitable for distinguishing all bacterial species to the genus level except for closely related enterobacteriaceae. V2 best distinguished among Mycobacterium species and V3 among Haemophilus species. The 58 nucleotides-long V6 could distinguish among most bacterial species except enterobacteriaceae. V6 was also noteworthy for being able to differentiate among all CDC-defined select agents including Bacillus anthracis, which differed from B. cereus by a single polymorphism. V4, V5, V7 and V8 were less useful targets for genus or species-specific probes. The hypervariable sequence-specific dendrograms and the "MEGALIGN" files provided online will be highly useful tools for designing specific probes and primers for molecular assays to detect pathogenic bacteria, including select agents.
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Affiliation(s)
- Soumitesh Chakravorty
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, New Jersey
| | - Danica Helb
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, New Jersey
| | - Michele Burday
- Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, New Jersey
| | - Nancy Connell
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, New Jersey
| | - David Alland
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, New Jersey
- *Corresponding author: Division of Infectious Disease, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, MSB A920C, Newark NJ 07103. E-mail: . Phone: (973) 972-2179. Fax: (973) 972-0713
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Thangapand V, Ponmurugan P, Ponmurugan K. Actinomycetes Diversity in the Rhizosphere Soils of Different Medicinal Plants in Kolly Hills-Tamilnadu, India, for Secondary Metabolite Production. ACTA ACUST UNITED AC 2006. [DOI: 10.3923/ajps.2007.66.70] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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MacGregor BJ, Amann R. Single-stranded conformational polymorphism for separation of mixed rRNAS (rRNA-SSCP), a new method for profiling microbial communities. Syst Appl Microbiol 2006; 29:661-70. [PMID: 16460898 DOI: 10.1016/j.syapm.2006.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Indexed: 10/25/2022]
Abstract
We show that non-denaturing gel electrophoresis, or single-stranded conformational polymorphism (SSCP), can be used to separate mixtures of full-length rRNAs. Individual bands can then be excised for identification by RT-PCR and sequencing. This has the advantage over profiling methods such as DGGE and T-RFLP that no PCR amplification is involved prior to sequencing; thus, extraction biases aside, it should yield a quantitative picture of community composition in terms of ribosome content. To simplify banding patterns, RNA subsamples (e.g. bacterial 16S rRNA) can first be isolated by magnetic bead capture hybridization. Alternatively, oligonucleotide-directed ribonuclease H (RNase H) digestion can be used to identify bands of interest by running digested samples in parallel to undigested ones. We illustrate the use of this technique to identify a potentially predominant species in a hypersaline microbial mat. We anticipate that rRNA-SSCP will be useful for community profiling; for clone library construction by directed cloning of individual rRNAs; and for following incorporation of radiolabeled substrates at the species level, by gel autoradiography, without advance information or guesswork about which species might be active and abundant.
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Affiliation(s)
- Barbara J MacGregor
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany.
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Olivier A, Lee HY, Côté JC. Study of the heterogeneity of 16S rRNA genes in gamma-proteobacteria: implications for phylogenetic analysis. J GEN APPL MICROBIOL 2006; 51:395-405. [PMID: 16474200 DOI: 10.2323/jgam.51.395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Audrey Olivier
- Département de Génie Biologique, Institut Universitaire de Technologie, Université d'Angers, France
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21
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Salazar O, Valverde A, Genilloud O. Real-time PCR for the detection and quantification of geodermatophilaceae from stone samples and identification of new members of the genus blastococcus. Appl Environ Microbiol 2006; 72:346-52. [PMID: 16391063 PMCID: PMC1352205 DOI: 10.1128/aem.72.1.346-352.2006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR (RT-PCR) technology was used for the specific detection and quantification of members of the family Geodermatophilaceae in stone samples. Differences in the nucleotide sequences of the 16S rRNA gene region were used to design a pair of family-specific primers that were used to detect and quantify by RT-PCR DNA from members of this family in stone samples from different geographical origins in Spain. These primers were applied later to identify by PCR-specific amplification new members of the family Geodermatophilaceae isolated from the same stone samples. The diversity and taxonomic position of the wild-type strains identified from ribosomal sequence analysis suggest the presence of a new lineage within the genus Blastococcus.
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Affiliation(s)
- Oscar Salazar
- Centro de Investigación Básica de España, Merck Research Laboratories, Merck Sharp and Dohme de España S.A., Josefa Valcárcel 38, E-28027 Madrid, Spain.
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22
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Park HS, Kilbane JJ. Rapid detection and high-resolution discrimination of the genus Streptomyces based on 16S-23S rDNA spacer region and denaturing gradient gel electrophoresis. J Ind Microbiol Biotechnol 2005; 33:289-97. [PMID: 16315072 DOI: 10.1007/s10295-005-0060-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Accepted: 09/28/2005] [Indexed: 10/25/2022]
Abstract
As the leading source of antibiotics, Streptomyces species are the subject of widespread investigation. Many approaches have been tried to aid in the classification of Streptomyces isolates to the genus, species, and strain levels. Genetic methods are more rapid and convenient than classification methods based on phenotypic characteristics, but a method that is universal in detecting all Streptomyces yet selective in detecting only Streptomyces is needed. The highly conserved nature of the 16S rRNA gene (16S rDNA) combined with the need to discriminate between closely related strains results in analyses of ribosomal intergenic spacer (RIS) regions being more productive than analyses of 16S rRNA genes. PCR primers were designed to amplify the RIS region as well as a sufficient length of the 16S rRNA gene to enable phylogenetic analyses of Streptomyces. Improved selectivity and specificity for the amplification of RIS sequences from Streptomyces with environmental samples was demonstrated. The use of RIS-PCR and denaturing gradient gel electrophoresis (DGGE) was shown to be a convenient means to obtain unique genetic "fingerprints" of Streptomyces cultures allowing them to be accurately identified at species, and even strain classification levels. These RIS-PCR and DGGE approaches show potential for the rapid characterization of environmental Streptomyces populations.
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MESH Headings
- Base Sequence
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Electrophoresis, Polyacrylamide Gel/methods
- Molecular Sequence Data
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Species Specificity
- Streptomyces/classification
- Streptomyces/genetics
- Streptomyces/isolation & purification
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Affiliation(s)
- Ho-Shin Park
- Kim Laboratories Inc., 60 Hazelwood Dr., Champaign, IL 61820, USA
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23
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Molinari F, Romano D, Gandolfi R, Kroppenstedt RM, Marinelli F. Newly isolated Streptomyces spp. as enantioselective biocatalysts: hydrolysis of 1,2-O-isopropylidene glycerol racemic esters. J Appl Microbiol 2005; 99:960-7. [PMID: 16162249 DOI: 10.1111/j.1365-2672.2005.02655.x] [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: 11/28/2022]
Abstract
AIMS To identify microbial strains with esterase activity able to enantioselectively hydrolyse esters of (R,S)-1,2-O-isopropylidene glycerol. METHODS AND RESULTS The microbial hydrolysis of various racemic esters of 1,2-O-isopropylidene glycerol (IPG) was attempted by screening among Streptomyces spp. previously selected on the basis of their carboxylesterase activity. The best results were observed in the hydrolysis of butyrate ester and two strains appeared promising as they showed opposite enantioselectivity: Streptomyces sp. 90852 gave predominantly (S)-IPG, while strain 90930 mostly gave the R-alcohol. Streptomyces sp. 90930 was identified as Streptomyces violaceusniger, whereas Streptomyces sp. 90852 is a new species belonging to the Streptomyces violaceus taxon. The carboxylesterase belonging to strain 90852 gave a maximum value of enantiomeric ratio (E) of 14-16. This strain was lyophilized and used as dry mycelium for catalysing the synthesis of isopropylidene glycerol butyrate in heptane showing reaction rate and enantioselectivity (E = 6.6) lower than what observed for the hydrolysis. CONCLUSIONS A new esterase with enantioselective activity towards (R,S)-IPG butyrate has been selected. The best enantioselectivity is similar or even better than the highest reported value in the literature with commercial enzymes. The enzyme is produced by a new species belonging to the S. violaceus taxon. SIGNIFICANCE AND IMPACT OF THE STUDY New esterases from streptomycetes can be employed for the enantioselective hydrolysis of chiral esters derived from primary alcohols, not efficiently resolved with commercial enzymes.
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Affiliation(s)
- F Molinari
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, Milan, Italy.
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24
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Gaylarde PM, Crispim CA, Neilan BA, Gaylarde CC. Cyanobacteria from Brazilian building walls are distant relatives of aquatic genera. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2005; 9:30-42. [PMID: 15805777 DOI: 10.1089/omi.2005.9.30] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The 16S-rDNA from 22 cyanobacteria isolated from biofilms on walls of modern and historic buildings in Brazil was partially sequenced (approximately 350 bp) using specific primers. The cyanobacteria with the closest matching sequences were found using the BLAST tool. The sequences were combined with 52 other cyanobacterial sequences already deposited in public data banks and a dendrogram constructed, after deletion from each sequence of one of the variable 16S rDNA regions (VI). The newly sequenced organisms fitted well within their respective families, but their similarities to other members of the groups were generally low, less than 96%. Close matches were found only with one other terrestrial (hot dry desert) cyanobacterium, Microcoleus sociatus, and with Anabaena variabilis. Phylogenetic analysis suggested that the deletion of the hypervariable regions in the RNA structure is essential for meaningful evolutionary studies. The results support the standard phylogenetic tree based on morphology, but suggest that these terrestrial cyanobacteria are distant relatives of their equivalent aquatic genera and are, indeed, a distinct population.
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25
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Martín MC, Manteca A, Castillo ML, Vázquez F, Méndez FJ. Streptomyces albus isolated from a human actinomycetoma and characterized by molecular techniques. J Clin Microbiol 2004; 42:5957-60. [PMID: 15583353 PMCID: PMC535254 DOI: 10.1128/jcm.42.12.5957-5960.2004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 06/06/2004] [Accepted: 08/28/2004] [Indexed: 11/20/2022] Open
Abstract
A Streptomyces albus forearm actinomycetoma that could not be identified by culture was properly identified at the species level by study of an internal fragment of the heat shock protein gene, comparative sequence analysis of 16S ribosomal DNA (rDNA), and the hypervariable gamma-region of the 16S rDNA.
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Affiliation(s)
- Maria Cruz Martín
- Instituto de Productos Lácteos de Asturias (CSIC), Villaviciosa, Oviedo, Spain
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26
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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.
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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
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Affiliation(s)
- Jörg Peplies
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
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27
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Davelos AL, Xiao K, Samac DA, Martin AP, Kinkel LL. Spatial variation in Streptomyces genetic composition and diversity in a prairie soil. MICROBIAL ECOLOGY 2004; 48:601-612. [PMID: 15696393 DOI: 10.1007/s00248-004-0031-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 05/28/2004] [Indexed: 05/24/2023]
Abstract
Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m2). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.
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Affiliation(s)
- A L Davelos
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
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28
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Urzì C, La Cono V, Stackebrandt E. Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using fluorescence in situ hybridization (FISH). Environ Microbiol 2004; 6:678-85. [PMID: 15186346 DOI: 10.1111/j.1462-2920.2004.00619.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Bacteria of the family of Geodermatophilaceae are actively involved in the decay processes [Urzì, C. and Realini, M. (1998) Int Biodeterior Biodegrad 42: 45-54; Urzì, C., Salamone, P., Schumann, P., and Stackebrandt, E. (2000) Int J Syst Evol Microbiol 50: 529-536] of stone monuments. Characterization of isolates includes phenotypic, chemotaxonomic and genetic analysis often requiring long-term procedures. The use of specific probes for members of Geodermatophilaceae family could be useful for the easy detection of those strains colonizing rock surfaces and involved in the biodeterioration. Two 16S rRNA-targeted oligonucleotide probes were designed for the specific detection of members of the family Geodermatophilaceae using fluorescence in situ hybridization (FISH); one probe specific for members of the two genera Geodermatophilus/Blastococcus and the second for members of the genus Modestobacter.
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Affiliation(s)
- Clara Urzì
- Department of Microbiological, Genetic and Molecular Sciences, University of Messina, Salita Sperone, 31, I-98166 Messina, Italy.
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29
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Davelos AL, Xiao K, Flor JM, Kinkel LL. Genetic and phenotypic traits of streptomycetes used to characterize antibiotic activities of field-collected microbes. Can J Microbiol 2004; 50:79-89. [PMID: 15052309 DOI: 10.1139/w03-107] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although antibiotic production may contribute significantly to microbial fitness, there is limited information on the ecology of antibiotic-producing microbial populations in soil. Indeed, quantitative information on the variation in frequency and intensity of specific antibiotic inhibitory and resistance abilities within soil microbial communities is lacking. Among the streptomycetes, antibiotic production is highly variable and resistance to antibiotics is highly specific to individual microbial strains. The objective of this work was to genetically and phenotypically characterize a reference collection of streptomycetes for use in distinguishing inhibition and resistance phenotypes of field-collected microbes. Specifically, we examined inhibition and resistance abilities of all isolates in all possible pairwise combinations, genetic relatedness using BOX-PCR and 16S rDNA sequence analyses, nutrient utilization profiles, and antibiotic induction among all possible three-way combinations of isolates. Each streptomycete isolate possessed a unique set of phenotypic and genetic characteristics. However, there was little correspondence between phenotypic and genetic traits. This collection of reference isolates provides the potential for distinguishing 1024 inhibition and resistance phenotypes in field-collected microbes. Relationships between the genetic and phenotypic characteristics examined may provide preliminary insight into the distinct strategies that microbes use in optimizing their fitness in natural environments.Key words: antibiotic inhibition, resistance, nutrient utilization, BOX-PCR, 16S rDNA.
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MESH Headings
- Anti-Bacterial Agents/biosynthesis
- Anti-Bacterial Agents/pharmacology
- Antibiosis
- Bacterial Typing Techniques
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Drug Resistance, Bacterial
- Genes, rRNA/genetics
- Genotype
- Microbial Sensitivity Tests
- Molecular Sequence Data
- Phenotype
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Genetic
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Streptomycetaceae/drug effects
- Streptomycetaceae/genetics
- Streptomycetaceae/isolation & purification
- Streptomycetaceae/physiology
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Affiliation(s)
- Anita L Davelos
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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30
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La Cono V, Urzì C. Fluorescent in situ hybridization applied on samples taken with adhesive tape strips. J Microbiol Methods 2003; 55:65-71. [PMID: 14499996 DOI: 10.1016/s0167-7012(03)00115-5] [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: 11/18/2022]
Abstract
Fluorescent in situ hybridization (FISH), applied directly on samples taken with adhesive tape, is proposed as method to detect and identify microorganisms from the surfaces of valuable objects without being destructive. Results of tests carried out in laboratory conditions as well on samples taken from deteriorated surfaces of Roman Catacombs showed the feasibility of FISH when applied on adhesive tape. The potential as well as the limits of the technique were also discussed.
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Affiliation(s)
- V La Cono
- Department of Microbiological, Genetic and Molecular Sciences, University of Messina, Salita Sperone 31, 98166, Messina, Italy
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31
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Rintala H, Nevalainen A, Suutari M. Diversity of streptomycetes in water-damaged building materials based on 16S rDNA sequences. Lett Appl Microbiol 2002; 34:439-43. [PMID: 12028426 DOI: 10.1046/j.1472-765x.2002.01120.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The diversity of streptomycetes in two different types of water-damaged building materials was investigated. METHODS AND RESULTS Direct PCR amplification of 16S rDNA from DNA isolated from building materials, cloning of the fragments and sequence analysis were used. In the phylogenetic analysis of the variable gamma region of the PCR amplification products, the sequences affiliated with five groups. CONCLUSIONS Several different sequences were found in both materials, suggesting the presence of several species. Also, previously unknown sequences were detected, although all the sequences clustered together with sequences of known species. SIGNIFICANCE AND IMPACT OF THE STUDY Streptomycetes are known as indicators for moisture and mould damage in buildings and potential health risk, but their diversity in indoor environments is still unknown.
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Affiliation(s)
- H Rintala
- National Public Health Institute (KTL), Laboratory of Environmental Microbiology, Kuopio, Finland.
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32
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Rintala H, Nevalainen A, Rönkä E, Suutari M. PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes. Mol Cell Probes 2001; 15:337-47. [PMID: 11851377 DOI: 10.1006/mcpr.2001.0379] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Streptomycetes are filamentous actinobacteria commonly found in soil and biotechnically important, but they also have adverse effects on human health. In this work, two primer pairs, StrepB/StrepE and StrepB/StrepF combined with Bst YI restriction endonuclease digestion, targeting the 16S rRNA gene of streptomycetes were designed. The specificity of the primers was determined by polymerase chain reaction (PCR) amplification from Streptomyces strains and near relatives. All streptomycetes tested positive and non-streptomycetes were not amplified except three strains that, however, gave Bst YI restriction endonuclease digestion results distinct from streptomycetes. Moreover, both primer pairs gave an amplification product of the expected size only when Streptomyces VTT E-99-1334 DNA was present in the template DNA mixture isolated from six bacterial and three fungal strains. The primers were further successfully used to amplify from DNA isolated from two soil and two building material samples. The 40 sequenced amplification products obtained with the primer pair StrepB/StrepE showed greater than 96.1% similarity to streptomycete 16S rRNA sequences. Seventy PCR amplification products obtained with the primers StrepB/StrepF were analysed by sequencing and restriction analysis. All 54 PCR products having >95.7% similarity to streptomycete sequences were cleaved with Bst YI. No false-positive results were achieved. Both primer sets proved to be specific for streptomycetes, and applicable for the detection of streptomycetes in environmental samples.
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Affiliation(s)
- H Rintala
- National Public Health Institute, Department of Environmental Health, 70701 Kuopio, Finland.
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Roberts MA, Crawford DL. Use of randomly amplified polymorphic DNA as a means of developing genus- and strain-specific Streptomyces DNA probes. Appl Environ Microbiol 2000; 66:2555-64. [PMID: 10831438 PMCID: PMC110581 DOI: 10.1128/aem.66.6.2555-2564.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have analyzed 20 randomly amplified polymorphic DNA (RAPD) primers against 36 Streptomyces strains, including 17 taxonomically undefined strains, 25 nonstreptomycete actinomycetes, and 12 outgroups consisting of gram-positive and -negative species. Most of the primers were useful in identifying unique DNA polymorphisms of all strains tested. We have used RAPD techniques to develop a genus-specific probe, one not necessarily targeting the ribosomal gene, for Streptomyces, and a strain-specific probe for the biological control agent Streptomyces lydicus WYEC108. In the course of these investigations, small-scale DNA isolations were also developed for efficiently isolating actinomycete DNA. Various modifications of isolation procedures for soil DNA were compared, and the reliability and specificity of the RAPD methodology were tested by specifically detecting the S. lydicus WYEC108 in DNA isolated from soil.
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Affiliation(s)
- M A Roberts
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, Idaho 83844-3052, USA
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34
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Kreuze JF, Suomalainen S, Paulin L, Valkonen JP. Phylogenetic Analysis of 16S rRNA Genes and PCR Analysis of the nec1 Gene from Streptomyces spp. Causing Common Scab, Pitted Scab, and Netted Scab in Finland. PHYTOPATHOLOGY 1999; 89:462-469. [PMID: 18944717 DOI: 10.1094/phyto.1999.89.6.462] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT The sequences of the 16S rRNA genes (nucleotides 29 to 1,521) from various Streptomyces strains pathogenic to potato were compared. These included 10 pathogenic Streptomyces strains isolated from potato scab lesions in Finland, the type strains of S. aureofaciens NRRL 2209(T) and S. lydicus ATCC 25470(T), 'S. griseus subsp. scabies' ATCC 10246, and two S. griseus strains that were originally deposited to the collection as pathogens. The nucleotide sequence (>94.5% sequence identity [SI]) and length (1,469 to 1,481 nucleotides) of the analyzed region varied. Phylogenetic analysis of 16S rRNA genes placed Finnish strains into three species, supported by previously characterized morphological and physiological traits. Six Finnish strains, including two strains that deviated from the others in one trait (no spiral sporophores or D-xylose utilization), had identical 16S rRNA genes and were identified as S. scabies (99.9% SI to S. scabies ATCC 49173). Three Finnish strains were identified as S. turgidiscabies, a species previously described only in Japan (99.9% SI to S. turgidiscabies ATCC 700248). Finnish strain 317 and S. aureofaciens NRRL 2209 (99.8% SI) were placed in a distinct phylogenetic cluster together with Kitosatospora spp., which suggests that S. aureofaciens may belong to the recently revived genus Kitosatospora. In pathogenicity tests, S. scabies caused characteristic symptoms of common scab, S. turgidiscabies caused mainly pitted scab, and S. aureofaciens caused netted scab and necrotic lesions on stolons of potato cultivars Bintje and Matilda in the greenhouse. The nec1 gene and the intergenic region between nec1 and the 5' transposase pseudogene ORFtnp were successfully amplified by polymerase chain reaction from S. scabies ATCC 49173 and the pathogenic Finnish strains of S. scabies, but not from a nonpathogenic strain of S. scabies, three pathogenic and two nonpathogenic strains of S. turgidiscabies, and S. aureofaciens.
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35
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Sponga F, Cavaletti L, Lazzarini A, Borghi A, Ciciliato I, Losi D, Marinelli F. Biodiversity and potentials of marine-derived microorganisms. J Biotechnol 1999. [DOI: 10.1016/s0168-1656(99)00059-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Biodiversity and potentials of marine-derived microorganisms. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0079-6352(99)80099-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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37
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Ueda K, Seki T, Kudo T, Yoshida T, Kataoka M. Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 1999; 181:78-82. [PMID: 9864315 PMCID: PMC103534 DOI: 10.1128/jb.181.1.78-82.1999] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable alpha region of the 16S rRNA gene from 475 Streptomyces strains. Display of the direct sequencing patterns revealed the existence of 136 heterogeneous loci among a total of 33 strains. The heterogeneous loci were detected only in the stem region designated helix 10. All of the substitutions conserved the relevant secondary structure. The 33 strains were divided into two groups: one group, including 22 strains, had less than two heterogeneous bases; the other group, including 11 strains, had five or more heterogeneous bases. The two groups were different in their combinations of heterogeneous bases. The former mainly contained transitional substitutions, and the latter was mainly composed of transversional substitutions, suggesting that at least two mechanisms, possibly misincorporation during DNA replication and horizontal gene transfer, cause rRNA heterogeneity.
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Affiliation(s)
- K Ueda
- International Center for Biotechnology, Osaka University, Yamada-oka, Suita, Osaka 565, Japan
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38
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Heuer H, Krsek M, Baker P, Smalla K, Wellington EM. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 1997; 63:3233-41. [PMID: 9251210 PMCID: PMC168621 DOI: 10.1128/aem.63.8.3233-3241.1997] [Citation(s) in RCA: 782] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A group-specific primer, F243 (positions 226 to 243, Escherichia coli numbering), was developed by comparison of sequences of genes encoding 16S rRNA (16S rDNA) for the detection of actinomycetes in the environment with PCR and temperature or denaturing gradient gel electrophoresis (TGGE or DGGE, respectively). The specificity of the forward primer in combination with different reverse ones was tested with genomic DNA from a variety of bacterial strains. Most actinomycetes investigated could be separated by TGGE and DGGE, with both techniques giving similar results. Two strategies were employed to study natural microbial communities. First, we used the selective amplification of actinomycete sequences (E. coli positions 226 to 528) for direct analysis of the products in denaturing gradients. Second, a nested PCR providing actinomycete-specific fragments (E. coli positions 226 to 1401) was used which served as template for a PCR when conserved primers were used. The products (E. coli positions 968 to 1401) of this indirect approach were then separated by use of gradient gels. Both approaches allowed detection of actinomycete communities in soil. The second strategy allowed the estimation of the relative abundance of actinomycetes within the bacterial community. Mixtures of PCR-derived 16S rDNA fragments were used as model communities consisting of five actinomycetes and five other bacterial species. Actinomycete products were obtained over a 100-fold dilution range of the actinomycete DNA in the model community by specific PCR; detection of the diluted actinomycete DNA was not possible when conserved primers were used. The methods tested for detection were applied to monitor actinomycete community changes in potato rhizosphere and to investigate actinomycete diversity in different soils.
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Affiliation(s)
- H Heuer
- Federal Biological Research Center for Agriculture and Forestry, Institute for Biochemistry and Plant Virology, Braunschweig, Germany
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39
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de León P, Mellado RP. Ribosomal RNA synthesis in Streptomyces lividans under heat shock conditions. Gene X 1997; 194:125-32. [PMID: 9266681 DOI: 10.1016/s0378-1119(97)00183-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Clones containing rRNA genes were isolated from a gene library of Streptomyces lividans when RNA produced under heat shock conditions was used as a probe. Two of the clones carried entire rRNA operons rrnA and rrnF, respectively, the expression of both operons being under the control of four different promoters. At least two of the promoters were fully functional when the temperature increased from 30 to 45 degrees C, ensuring transcription of the rRNA genes under the heat shock. A third clone carried a partial rRNA operon in which expression was controlled by a main promoter that was functional at both 30 and 45 degrees C.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- Consensus Sequence
- Gene Library
- Genes, Bacterial
- Heat-Shock Response
- Molecular Sequence Data
- Open Reading Frames
- Promoter Regions, Genetic
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- Regulatory Sequences, Nucleic Acid
- Restriction Mapping
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Species Specificity
- Streptomyces/genetics
- Streptomyces/physiology
- Temperature
- Transcription, Genetic
- rRNA Operon
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Affiliation(s)
- P de León
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, Madrid, Spain
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40
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Conrads G, Gharbia SE, Gulabivala K, Lampert F, Shah HN. The use of a 16s rDNA directed PCR for the detection of endodontopathogenic bacteria. J Endod 1997; 23:433-8. [PMID: 9587296 DOI: 10.1016/s0099-2399(97)80297-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The study evaluates a 16S rDNA directed polymerase chain reaction (PCR) to detect and differentiate bacteria in necrotic root canal samples. The examination focused on species that are fastidious concerning culture or are difficult to differentiate after culturing by biochemical methods. In the described PCR assay, a universal 16S rDNA directed forward primer in combination with a highly specific reversed one was used to amplify taxon specific gene fragments of 230 to 950 bp length. A similar PCR reaction using a universal 16S rDNA reversed primer was also established to demonstrate bacteria in root canal specimens in general. A first application of this method revealed the presence of Actinomycetales-species, Fusobacterium nucleatum, "Streptococcus milleri," and, presumably for the first time described in infected root canals, Bacteroides forsythus. The identity of amplificons was confirmed by generating sequence information and comparison to gene databanks.
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Affiliation(s)
- G Conrads
- Clinic of Conservative & Preventive Dentistry and Periodontology, University Aachen, Germany
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41
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Kataoka M, Ueda K, Kudo T, Seki T, Yoshida T. Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces. FEMS Microbiol Lett 1997; 151:249-55. [PMID: 9244758 DOI: 10.1111/j.1574-6968.1997.tb12578.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Partial nucleotide sequences (120 bp) of the 16S rRNA gene (rDNA) containing a variable alpha region were compared in 89 strains of the genus Streptomyces belonging to eight major clusters of category I in Bergey's Manual of Systematic Bacteriology. Fifty-seven kinds of partial 16S rDNA sequences were observed among the 89 strains. Forty-three of the strains were grouped into 11 'identity groups', based on the fact that the strains in each group shared an identical sequence in the 120-bp region. The results of a phylogenetic analysis based on the 16S rDNA 120-bp sequences revealed that 60 of the 89 strains could be categorized into seven clusters, each consisting of four or more strains. Based on these observations it was concluded that short nucleotide sequences bearing the variable alpha region are useful for Streptomyces species identification.
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Affiliation(s)
- M Kataoka
- The International Center for Biotechnology, Osaka University, Japan
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42
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Huddleston AS, Cresswell N, Neves MC, Beringer JE, Baumberg S, Thomas DI, Wellington EM. Molecular detection of streptomycin-producing streptomycetes in Brazilian soils. Appl Environ Microbiol 1997; 63:1288-97. [PMID: 9097426 PMCID: PMC168423 DOI: 10.1128/aem.63.4.1288-1297.1997] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Actinomycetes were isolated from soybean rhizosphere soil collected as two field sites in Brazil. All the isolates were identified as Streptomyces species and were screened for streptomycin production and the presence of two genes, strA and strB1, known to be involved in streptomycin biosynthesis in Streptomyces griseus. Antibiotic resistance profiles were determined for 53 isolates from cultivated and uncultivated sites, and approximately half the strains were streptomycin resistance. Clustering by the unweighted pair group method with averages indicated the presence of two major clusters, with the majority of resistant strains from cultivated sites being placed in cluster 1. Only representatives from this cluster contained strA. Streptomycetes containing strA and strB1 were phenotypically diverse, and only half could be assigned to known species. Sequence comparison of 16S rRNA and trpBA (tryptophan synthetase) genes revealed that streptomycin- producing streptomycetes were phylogenetically diverse. It appeared that a population of streptomycetes had colonized the rhizosphere and that a proportion of these were capable of streptomycin production.
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Affiliation(s)
- A S Huddleston
- Department of Biological Sciences, University of Warwick, Coventry, West Midlands, United Kingdom
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43
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Christova K, Sholeva Z, Chipeva V, Najdenova M, Todorova D. Differentiation of Streptomyces Strains by Multilocus Enzyme Electrophoresis. BIOTECHNOL BIOTEC EQ 1997. [DOI: 10.1080/13102818.1997.10818929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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44
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Busse HJ, Denner EB, Lubitz W. Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J Biotechnol 1996; 47:3-38. [PMID: 8782421 DOI: 10.1016/0168-1656(96)01379-x] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Most of the bacterial species are still unknown. Consequently, our knowledge about bacterial ecology is poor and expectations about specialized species with novel enzymatic functions or new products are high. Thus, bacterial identification is a growing field of interest within microbiology. In this review, suitability of developments for identification based on miniaturized biochemical and physiological investigations of bacteria are evaluated. Special emphasis is given to chemotaxonomic methods such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, peptidoglycan diaminoacids, as well as analytical fingerprinting methods and cellular protein patterning. 16S rDNA sequencing introduced to investigate the phylogenetic relationships of bacteria, nucleic acids hybridization techniques and G + C content determination are discussed as well as restriction fragment length polymorphism (RFLP), macrorestriction analysis and random amplified polymorphic DNA (RAPD). The importance of the different approaches in classification and identification of bacteria according to phylogenetic relationships are demonstrated on selected examples.
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Affiliation(s)
- H J Busse
- Institute of Microbiology and Genetics, University of Vienna, Austria.
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45
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Oh CH, Ahn MH, Kim JH. Use of electrophoretic enzyme patterns for streptomycete systematics. FEMS Microbiol Lett 1996. [DOI: 10.1111/j.1574-6968.1996.tb08307.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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46
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Wang GC, Wang Y. Rapid differentiation of bacterial species with multiple probes of different lengths in a single slot blot hybridization. Appl Environ Microbiol 1995; 61:4269-73. [PMID: 8534094 PMCID: PMC167738 DOI: 10.1128/aem.61.12.4269-4273.1995] [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: 01/31/2023] Open
Abstract
We describe a highly efficient method for dot and slot blot hybridizations with multiple oligonucleotide probes for high throughput identification of organisms and studies of microbial community structures. Several probes with distinct specificities were designed to have the same melting temperature but unique lengths by adding different numbers of nonspecific nucleotides to one end. All of the probes were mixed, labelled with 32P, and hybridized to one piece of membrane on which genes coding for 16S rRNAs from different bacterial species had been immobilized. After hybridization, the bound probes were eluted and resolved on a denaturing polyacrylamide gel and the identities of the genes coding for 16S rRNAs were read from an autoradiograph of the gel. The results from the application of this technique to pure actinomycete cultures are reported here.
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Affiliation(s)
- G C Wang
- Microbial Collection and Screen Laboratory, National University of Singapore, Singapore
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47
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Moran MA, Rutherford LT, Hodson RE. Evidence for indigenous Streptomyces populations in a marine environment determined with a 16S rRNA probe. Appl Environ Microbiol 1995; 61:3695-700. [PMID: 7487005 PMCID: PMC167668 DOI: 10.1128/aem.61.10.3695-3700.1995] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A 16S rRNA genus-specific probe was used to determine whether Streptomyces populations are an indigenous component of marine sediment bacterial communities. Previous debates have suggested that marine Streptomyces isolates are derived not from resident populations but from spores of terrestrial species which have been physically transported to marine ecosystems but remain dormant until isolation. Rigorously controlled hybridization of rRNA extracted from coastal marsh sediments with the genus-specific probe indicated that Streptomyces rRNA accounted for 2 to 5% of the sediment community rRNA and that spores are not the source of the hybridization signal. Streptomyces populations must therefore be at least the 26th most abundant genus-level source of bacterial rRNA. the relative amounts of rRNAs from Streptomyces spp. and members of the Bacteria (69 to 79%) and Archaea (4 to 7%) domains were highly consistent in these marine sediments throughout an annual cycle, indicating that the species composition of sediment bacterial communities may be more stable than recent studies suggest for marine planktonic bacterial communities. Laboratory studies designed to investigate the possible functional roles of Streptomyces populations in coastal sediments demonstrated that population levels of this genus changed relatively rapidly (within a time frame of 6 weeks) in response to manipulation of substrate availability. Amendments of intact sediment cores with two compounds (vanillic acid and succinic acid) consistently resulted in Streptomyces populations contributing an increased percentage of rRNA (6 to 15%) to the total bacterial rRNA pool.
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Affiliation(s)
- M A Moran
- Department of Marine Sciences, University of Georgia, Athens 30602-2206, USA
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48
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Fulton TR, Losada MC, Fluder EM, Chou GT. rRNA operon restriction derived taxa for Streptomyces (RiDiTS). FEMS Microbiol Lett 1995; 125:149-58. [PMID: 7875562 DOI: 10.1111/j.1574-6968.1995.tb07351.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: 01/27/2023] Open
Abstract
A method for grouping Streptomyces strains by fingerprints of their rRNA operons is described. In polyacrylamide gels, multicopy rRNA operon fragments in Streptomyces genomic MseI fingerprints produced intense bands which are well resolved from the less conspicuous low copy fragments interspersed between them. The high intensity multicopy rRNA bands are easily distinguished from the low intensity bands, eliminating the need for Southern blot hybridization to visualize the rRNA fragments. Direct evidence that the high-intensity bands in these polyacrylamide gels originated from rRNA operons was provided by a 'differential' Southern blot technique. We have used this method to assign 98 strains to 11 rRNA fingerprint type groups. This clustering method may be applicable to any prokaryote with a high G+C content genome.
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49
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Canhos VP, Manfio GP, Blaine LD. Software tools and databases for bacterial systematics and their dissemination via global networks. Antonie Van Leeuwenhoek 1994; 64:205-29. [PMID: 8085786 DOI: 10.1007/bf00873083] [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: 01/28/2023]
Abstract
The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic 'Authority Files' are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.
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Affiliation(s)
- V P Canhos
- Tropical Data Base (BDT), Campinas, SP, Brazil
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50
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The distribution of antibiotic resistance patterns within streptomycetes and their use in secondary metabolite screening. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf01569663] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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