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Gutiérrez Santana JC, Coria Jiménez VR. Burkholderia cepacia complex in cystic fibrosis: critical gaps in diagnosis and therapy. Ann Med 2024; 56:2307503. [PMID: 38261606 PMCID: PMC10810671 DOI: 10.1080/07853890.2024.2307503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024] Open
Abstract
Burkholderia cepacia complex (Bcc) is a bacterial group with 'natural' multi-antimicrobial resistance. This complex has generated epidemic outbreaks across the world. In people with cystic fibrosis (CF), Bcc can cause severe lung infections that lead to accelerated lung damage, which can be complicated by necrotizing pneumonia accompanied by high fevers, leucocytosis, and bacteraemia, which commonly causes fatal outcomes. Specifically, infection by Burkholderia cenocepacia is considered an exclusion criterion for lung transplantation. The species of Bcc exhibit both genetic and phenotypic hypervariability that complicate their accurate microbiological identification. Automated methods such as MALDI-TOF can err in the determination of species. Their slow growth even in selective agars and the absence of international consensuses on the optimal conditions for their isolation make early diagnosis a difficult challenge to overcome. The absence of correlations between antibiograms and clinical results has resulted in the absence of standardized cut-off values of antimicrobial susceptibility, a fact that brings a latent risk since incorrect antibiotic therapy can induce the selection of more aggressive variants that worsen the clinical picture of the host, added to the absence of a clear therapeutic guide for the eradication of pulmonary infections by Bcc in patients with CF, resulting in frequently ineffective treatments. There is an urgent need to standardize methods and diagnostic tools that would allow an early and accurate diagnosis, as well as to perform clinical studies of the effectiveness of available antibiotics to eradicate Bcc infections, which would allow us to establish standardized therapeutic schemes for Bcc-infected patients.
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Semenzato G, Faddetta T, Falsini S, Del Duca S, Esposito A, Padula A, Greco C, Mucci N, Zaccaroni M, Puglia AM, Papini A, Fani R. Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds. Microorganisms 2022; 10:microorganisms10102086. [PMID: 36296360 PMCID: PMC9612275 DOI: 10.3390/microorganisms10102086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field.
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Affiliation(s)
- Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Sara Falsini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Antonia Esposito
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Alessio Papini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
- Correspondence:
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Endophytic Bacteria and Essential Oil from Origanum vulgare ssp. vulgare Share Some VOCs with an Antibacterial Activity. Microorganisms 2022; 10:microorganisms10071424. [PMID: 35889143 PMCID: PMC9320186 DOI: 10.3390/microorganisms10071424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/02/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Medicinal aromatic plants’ essential oils (EOs) are mixtures of volatile compounds showing antimicrobial activity, which could be exploited to face the emerging problem of multi-drug resistance. Their chemical composition can depend on the interactions between the plant and its endophytic microbiota, which is known to synthesize volatile organic compounds (VOCs). However, it is still not clear whether those volatile metabolites can contribute to the composition of the aroma profile of plants’ EOs. The aims of this study were to characterize medicinal plant O. vulgare ssp. vulgare bacterial endophyte VOCs, evaluating their ability to antagonize the growth of opportunistic human pathogens belonging to the Burkholderia cepacia complex (Bcc) and compare them with O. vulgare EO composition. Many of the tested endophytic strains showed (i) a bactericidal and/or bacteriostatic activity against most of Bcc strains and (ii) the production of VOCs with widely recognized antimicrobial properties, such as dimethyl disulfide, dimethyl trisulfide, and monoterpenes. Moreover, these monoterpenes were also detected in the EOs extracted from the same O. vulgare plants from which endophytes were isolated. Obtained results suggest that endophytes could also play a role in the antibacterial properties of O. vulgare ssp. vulgare and, potentially, in determining its aromatic composition.
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Zhang L, Gao W, Yin Y, Wang Z. Discrimination of Burkholderia gladioli pv. alliicola and B. cepacia complex using the gyrB gene of B. gladioli pv. alliicola. Exp Ther Med 2019; 17:1870-1876. [PMID: 30783462 DOI: 10.3892/etm.2018.7137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/22/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the efficiency of the gyrB gene derived from Burkholderia gladioli pv.Alliicola (Bga) on the identification of Bga from the B. cepacia complex (Bcc) based on the COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy. A set of primers used for the specific amplification of the gyrB gene in Bga were designed according to the CODEHOP principle. A total of 1,644 bp of the gyrB gene sequence of Bga were acquired by CODEHOP amplification. The sequence was blasted in GenBank and it revealed an average of 86% similarity with the gyrB gene of nine genomovars of Bcc. A phylogenetic tree was constructed using the gyrB gene sequences. The microarray method was adopted to discriminate Bga from Bcc based on the specific probes designed upon the gyrB gene, and five genomovars of Bcc demonstrated a good discrimination from Bga on the microarray chip. CODEHOP strategy succeeded in amplification of the gyrB gene of Bga, which made it possible for the identification of Bga from five genomovars of Bcc.
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Affiliation(s)
- Lun Zhang
- School of Life Sciences, Chongqing University, Shapingba, Chongqing 400030, P.R. China
| | - Wenna Gao
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing 100026, P.R. China
| | - Youping Yin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing 400030, P.R. China
| | - Zhongkang Wang
- School of Life Sciences, Chongqing University, Shapingba, Chongqing 400030, P.R. China
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Perrin E, Maggini V, Maida I, Gallo E, Lombardo K, Madarena MP, Buroni S, Scoffone VC, Firenzuoli F, Mengoni A, Fani R. Antimicrobial activity of six essential oils against Burkholderia cepacia complex: insights into mechanism(s) of action. Future Microbiol 2018; 13:59-67. [DOI: 10.2217/fmb-2017-0121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate the activity and mechanisms of action of six essential oils (EOs) against Burkholderia cepacia complex, opportunistic human pathogens highly resistant to antibiotics. Materials & methods: Minimal inhibitory concentration of EOs alone, plus antibiotics or efflux pump inhibitors was determined. Results: Origanum vulgare, Thymus vulgaris and Eugenia caryophyllata EOs resulted to be more active than the other EOs. EOs did not enhance antibiotic activity against the model strain B. cenocepacia J2315. EOs resulted more active in the presence of an efflux pump inhibitor acting on Resistance-Nodulation Cell Division efflux pumps and against B. cenocepacia J2315 Resistance-Nodulation Cell Division knocked-out mutants. Conclusion: EOs showed intracellular mechanisms of action and, thus, the efflux pumps inhibitor addition could boost their activity.
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Affiliation(s)
- Elena Perrin
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
| | - Valentina Maggini
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
- Department of Experimental & Clinical Medicine, University of Florence, I-50134, Florence, Italy
- Center for Integrative Medicine, Careggi University Hospital, University of Florence, I-50134, Florence, Italy
| | - Isabel Maida
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
| | - Eugenia Gallo
- Department of Experimental & Clinical Medicine, University of Florence, I-50134, Florence, Italy
- Center for Integrative Medicine, Careggi University Hospital, University of Florence, I-50134, Florence, Italy
| | - Katia Lombardo
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
| | - Maria Pia Madarena
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
| | - Silvia Buroni
- Department of Biology & Biotechnology, University of Pavia, Via Ferrata 1, I-27100, Pavia, Italy
| | - Viola Camilla Scoffone
- Department of Biology & Biotechnology, University of Pavia, Via Ferrata 1, I-27100, Pavia, Italy
| | - Fabio Firenzuoli
- Center for Integrative Medicine, Careggi University Hospital, University of Florence, I-50134, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino I-50019, Florence, Italy
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Simonetti E, Roberts IN, Montecchia MS, Gutierrez-Boem FH, Gomez FM, Ruiz JA. A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth. Microbiol Res 2017; 206:50-59. [PMID: 29146260 DOI: 10.1016/j.micres.2017.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 09/07/2017] [Accepted: 09/20/2017] [Indexed: 02/05/2023]
Abstract
Fusaric acid (FA) is a fungal metabolite produced by several Fusarium species responsible for wilts and root rot diseases of a great variety of plants. Bacillus spp. and Pseudomonas spp. have been considered as promising biocontrol agents against phytopathogenic Fusarium spp., however it has been demonstrated that FA negatively affects growth and production of some antibiotics in these bacteria. Thus, the capability to degrade FA would be a desirable characteristic in bacterial biocontrol agents of Fusarium wilt. Taking this into account, bacteria isolated from the rhizosphere of barley were screened for their ability to use FA as sole carbon and energy source. One strain that fulfilled this requirement was identified according to sequence analysis of 16S rRNA, gyrB and recA genes as Burkholderia ambifaria. This strain, designated T16, was able to grow with FA as sole carbon, nitrogen and energy source and also showed the ability to detoxify FA in barley seedlings. This bacterium also exhibited higher growth rate, higher cell densities, longer survival, higher levels of indole-3-acetic acid (IAA) production, enhanced biofilm formation and increased resistance to different antibiotics when cultivated in Luria Bertani medium at pH 5.3 compared to pH 7.3. Furthermore, B. ambifaria T16 showed distinctive plant growth-promoting features, such as siderophore production, phosphate-solubilization, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, in vitro antagonism against Fusarium spp. and improvement of grain yield when inoculated to barley plants grown under greenhouse conditions. This strain might serve as a new source of metabolites or genes for the development of novel FA-detoxification systems.
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Affiliation(s)
- Ester Simonetti
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Irma N Roberts
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Marcela S Montecchia
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Flavio H Gutierrez-Boem
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico M Gomez
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jimena A Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina.
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7
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A gyrB oligonucleotide microarray for the specific detection of pathogenic Legionella and three Legionella pneumophila subsp. Antonie van Leeuwenhoek 2017; 110:1515-1525. [PMID: 28695408 DOI: 10.1007/s10482-017-0903-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 10/19/2022]
Abstract
Among the 50 species and 70 serogroups of Legionella identified, Legionella pneumophila, comprising three subsp. (subsp. pneumophila, subsp. fraseri, and subsp. pasculleii), is recognized as the major cause of epidemic legionellosis. Rapid and reliable assays to identify pathogenic Legionella spp., and the three L. pneumophila subsp. in particular, are in great demand. In this study, we analyzed the gyrB genes of eleven Legionella spp. and subsp., comprising L. anisa, L. bozemanii, L. dumoffii, L. feeleii, L. gormanii, L. longbeachae, L. micdadei, L. waltersii, L. pneumophila subsp. pneumophila, L. pneumophila subsp. fraseri, and L. pneumophila subsp. pasculleii. We developed a rapid oligonucleotide microarray detection technique to identify accurately these common pathogenic Legionella spp. and L. pneumophila subsp. To detect multiple Legionella species with high specificity, 31 reproducible probes were designed in the array. Sixty-one strains were analyzed in total, including 37 target pathogens and 24 non-target bacterial species used to validate the microarray. The sensitivity of the detection was 1.0 ng using genomic DNA of three Legionella spp., L. anisa, L. dumoffii, and L. waltersii, or 13 CFU/100 mL using the cultured L. pneumophila subsp. pneumophila. Eight isolated strains were tested using the microarray with 100% accuracy. The data indicated that the technique is an efficient method to diagnose and detect Legionella spp. and subsp. in basic microbiology, clinical diagnosis, epidemiological surveillance, and food safety applications. In addition, a phylogenetic study based on the gyrB gene revealed the genetic relationship among the different Legionella spp. and subsp.
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Chiellini C, Maida I, Maggini V, Bosi E, Mocali S, Emiliani G, Perrin E, Firenzuoli F, Mengoni A, Fani R. Preliminary data on antibacterial activity of Echinacea purpurea-associated bacterial communities against Burkholderia cepacia complex strains, opportunistic pathogens of Cystic Fibrosis patients. Microbiol Res 2016; 196:34-43. [PMID: 28164789 DOI: 10.1016/j.micres.2016.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/17/2016] [Accepted: 12/03/2016] [Indexed: 12/22/2022]
Abstract
Burkholderia cepacia complex bacteria (Bcc) represent a serious threat for immune-compromised patient affected by Cystic Fibrosis (CF) since they are resistant to many substances and to most antibiotics. For this reason, the research of new natural compounds able to inhibit the growth of Bcc strains has raised new interest during the last years. A source of such natural compounds is represented by medicinal plants and, in particular, by bacterial communities associated with these plants able to produce molecules with antimicrobial activity. In this work, a panel of 151 (endophytic) bacteria isolated from three different compartments (rhizospheric soil, roots, and stem/leaves) of the medicinal plant Echinacea purpurea were tested (using the cross-streak method) for their ability to inhibit the growth of 10 Bcc strains. Data obtained revealed that bacteria isolated from the roots of E. purpurea are the most active in the inhibition of Bcc strains, followed by bacteria isolated from the rhizospheric soil, and endophytes from stem/leaf compartment. At the same time, Bcc strains of environmental origin showed a higher resistance toward inhibition than the Bcc strains with clinical (i.e. CF patients) origin. Differences in the inhibition activity of E. purpurea-associated bacteria are mainly linked to the environment -the plant compartment- rather than to their taxonomical position.
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Affiliation(s)
- Carolina Chiellini
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Isabel Maida
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Valentina Maggini
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy; Center for Integrative Medicine, Careggi University Hospital, University of Florence, Florence, Italy.
| | - Emanuele Bosi
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Stefano Mocali
- CREA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, centro di ricerca per l'Agrobiologia e la Pedologia, Via di Lanciola 12A, Cascine del Riccio, 50125 Florence (FI), Italy.
| | - Giovanni Emiliani
- Tree and Timber Institute National Research Council, Via Madonna del Piano, 10 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Fabio Firenzuoli
- Center for Integrative Medicine, Careggi University Hospital, University of Florence, Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
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Jeong SE, Lee HJ, Jia B, Jeon CO. Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000. Int J Syst Evol Microbiol 2016; 66:3524-3530. [PMID: 27267599 DOI: 10.1099/ijsem.0.001229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells were motile rods with a single polar flagellum, showing catalase- and oxidase-positive reactions. Growth was observed at 10-40 °C (optimum, 30 °C), pH 4.0-10.0 (optimum, pH 7.0-7.5) and with 0-4.0 % (w/v) NaCl (optimum, 0-2 %). Only ubiquinone-8 was detected as the isoprenoid quinone, and C16 : 0, C17 : 0 cyclo, C19 : 1ω8c cyclo and summed feature 2 (comprising C12 : 0 aldehyde and/or unknown) were found to be the major fatty acids. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. Putrescine and 2-hydroxyputrescine were the predominant polyamines. The DNA G+C content was 61.0 mol%. Phylogenetic analyses based on 16S rRNA and DNA gyrase B gene sequences revealed that strain SE-S21T formed a phyletic lineage within the genus Pandoraea. Strain SE-S21T was most closely related to Pandoraea faecigallinarum KOxT and Pandoraea pnomenusa CCUG 38742T with 98.8 % and 98.7 % 16S rRNA gene sequence similarities, respectively. However, the DNA-DNA relatedness values between strain SE-S21T and the type strains of P. faecigallinarum and P. pnomenusa were 26.6±5.7 % and 20.5±3.7 %, respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SE-S21T clearly represents a novel species of the genus Pandoraea, for which the name Pandoraea terrae sp. nov. is proposed. The type strain is SE-S21T (=KACC 18127T=JCM 30137T). An emended description of the genus Pandoraea is also proposed.
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Affiliation(s)
- Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyo Jung Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Identification, origin, and evolution of leaf nodulating symbionts of Sericanthe (Rubiaceae). J Microbiol 2011; 49:935-41. [DOI: 10.1007/s12275-011-1163-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 07/20/2011] [Indexed: 10/14/2022]
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Lemaire B, Vandamme P, Merckx V, Smets E, Dessein S. Bacterial leaf symbiosis in angiosperms: host specificity without co-speciation. PLoS One 2011; 6:e24430. [PMID: 21915326 PMCID: PMC3168474 DOI: 10.1371/journal.pone.0024430] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 08/09/2011] [Indexed: 11/25/2022] Open
Abstract
Bacterial leaf symbiosis is a unique and intimate interaction between bacteria and flowering plants, in which endosymbionts are organized in specialized leaf structures. Previously, bacterial leaf symbiosis has been described as a cyclic and obligate interaction in which the endosymbionts are vertically transmitted between plant generations and lack autonomous growth. Theoretically this allows for co-speciation between leaf nodulated plants and their endosymbionts. We sequenced the nodulated Burkholderia endosymbionts of 54 plant species from known leaf nodulated angiosperm genera, i.e. Ardisia, Pavetta, Psychotria and Sericanthe. Phylogenetic reconstruction of bacterial leaf symbionts and closely related free-living bacteria indicates the occurrence of multiple horizontal transfers of bacteria from the environment to leaf nodulated plant species. This rejects the hypothesis of a long co-speciation process between the bacterial endosymbionts and their host plants. Our results indicate a recent evolutionary process towards a stable and host specific interaction confirming the proposed maternal transmission mode of the endosymbionts through the seeds. Divergence estimates provide evidence for a relatively recent origin of bacterial leaf symbiosis, dating back to the Miocene (5-23 Mya). This geological epoch was characterized by cool and arid conditions, which may have triggered the origin of bacterial leaf symbiosis.
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Affiliation(s)
- Benny Lemaire
- Laboratory of Plant Systematics, K.U.Leuven, Leuven, Belgium.
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Sahin N, Tani A, Kotan R, Sedláček I, Kimbara K, Tamer AU. Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int J Syst Evol Microbiol 2011; 61:2247-2253. [DOI: 10.1099/ijs.0.026138-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five isolates, designated TA2, TA4, TA25T, KOxT and NS15T were isolated in previous studies by enrichment in mineral medium with potassium oxalate as the sole carbon source and were characterized using a polyphasic approach. The isolates were Gram-reaction-negative, aerobic, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA and DNA gyrase B subunit (gyrB) gene sequences confirmed that the isolates belonged to the genus Pandoraea and were most closely related to Pandoraea sputorum and Pandoraea pnomenusa (97.2–99.7 % 16S rRNA gene sequence similarity). The isolates could be differentiated from their closest relatives on the basis of several phenotypic characteristics. The major cellular fatty acid profiles of the isolates comprised C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). On the basis of DNA–DNA hybridization studies and phylogenetic analyses, the isolates represent three novel species within the genus Pandoraea, for which the names Pandoraea oxalativorans sp. nov. (TA25T = NBRC 106091T = CCM 7677T = DSM 23570T), Pandoraea faecigallinarum sp. nov. (KOxT = NBRC 106092T = CCM 2766T = DSM 23572T) and Pandoraea vervacti sp. nov. (NS15T = NBRC 106088T = CCM 7667T = DSM 23571T) are proposed.
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Affiliation(s)
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Recep Kotan
- Department of Plant Protection, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kazuhide Kimbara
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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PCR methods for the rapid detection and identification of four pathogenic Legionella spp. and two Legionella pneumophila subspecies based on the gene amplification of gyrB. Appl Microbiol Biotechnol 2011; 91:777-87. [DOI: 10.1007/s00253-011-3283-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/25/2011] [Accepted: 03/26/2011] [Indexed: 10/18/2022]
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14
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Genetic diversity and plant-growth related features of Burkholderia spp. from sugarcane roots. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0364-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Ferri L, Perrin E, Campana S, Tabacchioni S, Taccetti G, Cocchi P, Ravenni N, Dalmastri C, Chiarini L, Bevivino A, Manno G, Mentasti M, Fani R. Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: the Burkholderia cepacia complex case. J Microbiol Methods 2010; 80:251-6. [PMID: 20079386 DOI: 10.1016/j.mimet.2010.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 01/06/2010] [Indexed: 10/20/2022]
Abstract
Burkholderia cepacia complex (BCC) is characterized by a complex taxonomy constituted by seventeen closely related species of both biotechnological and clinical importance. Several molecular methods have been developed to accurately identify BCC species but simpler and effective strategies for BCC classification are still needed. A single nucleotide primer extension (SNuPE) assay using gyrB as a target gene was developed to identify bacteria belonging to the B. cepacia (BCC) complex. This technique allows the successful detection and distinction of single nucleotide polymorphisms (SNPs) and is effectively applied in routine medical diagnosis since it permits to analyze routinely many samples in a few times. Seven SNuPE primers were designed analyzing the conserved regions of the BCC gyrB sequences currently available in databases. The specificity of the assay was evaluated using reference strains of some BCC species. Data obtained enabled to discriminate bacteria belonging to the species B. multivorans, B. cenocepacia (including bacteria belonging to recA lineages III-A, III-C, and III-D), B. vietnamiensis, B. dolosa, B. ambifaria, B. anthina and B. pyrrocinia. Conversely, identification failed for B. cepacia, B. cenocepacia III-B and B. stabilis. This study demonstrates the efficacy of SNuPE technique for the identification of bacteria characterized by a complex taxonomical organization as BCC bacteria.
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Affiliation(s)
- L Ferri
- Department of Evolutionary Biology, University of Florence, Via Romana 17-19, I-50125 Florence, Italy
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16
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Papaleo MC, Russo E, Fondi M, Emiliani G, Frandi A, Brilli M, Pastorelli R, Fani R. Structural, evolutionary and genetic analysis of the histidine biosynthetic “core” in the genus Burkholderia. Gene 2009; 448:16-28. [DOI: 10.1016/j.gene.2009.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/25/2009] [Accepted: 08/05/2009] [Indexed: 11/28/2022]
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17
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Rezzonico F, Smits THM, Montesinos E, Frey JE, Duffy B. Genotypic comparison of Pantoea agglomerans plant and clinical strains. BMC Microbiol 2009; 9:204. [PMID: 19772624 PMCID: PMC2764716 DOI: 10.1186/1471-2180-9-204] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 09/22/2009] [Indexed: 11/10/2022] Open
Abstract
Background Pantoea agglomerans strains are among the most promising biocontrol agents for a variety of bacterial and fungal plant diseases, particularly fire blight of apple and pear. However, commercial registration of P. agglomerans biocontrol products is hampered because this species is currently listed as a biosafety level 2 (BL2) organism due to clinical reports as an opportunistic human pathogen. This study compares plant-origin and clinical strains in a search for discriminating genotypic/phenotypic markers using multi-locus phylogenetic analysis and fluorescent amplified fragment length polymorphisms (fAFLP) fingerprinting. Results Majority of the clinical isolates from culture collections were found to be improperly designated as P. agglomerans after sequence analysis. The frequent taxonomic rearrangements underwent by the Enterobacter agglomerans/Erwinia herbicola complex may be a major problem in assessing clinical associations within P. agglomerans. In the P. agglomerans sensu stricto (in the stricter sense) group, there was no discrete clustering of clinical/biocontrol strains and no marker was identified that was uniquely associated to clinical strains. A putative biocontrol-specific fAFLP marker was identified only in biocontrol strains. The partial ORF located in this band corresponded to an ABC transporter that was found in all P. agglomerans strains. Conclusion Taxonomic mischaracterization was identified as a major problem with P. agglomerans, and current techniques removed a majority of clinical strains from this species. Although clear discrimination between P. agglomerans plant and clinical strains was not obtained with phylogenetic analysis, a single marker characteristic of biocontrol strains was identified which may be of use in strain biosafety determinations. In addition, the lack of Koch's postulate fulfilment, rare retention of clinical strains for subsequent confirmation, and the polymicrobial nature of P. agglomerans clinical reports should be considered in biosafety assessment of beneficial strains in this species.
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Affiliation(s)
- Fabio Rezzonico
- Agroscope Changins-Wädenswil ACW, Plant Protection Division, CH-8820 Wädenswil, Switzerland.
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Time-resolved metabolic footprinting for nonlinear modeling of bacterial substrate utilization. Appl Environ Microbiol 2009; 75:2453-63. [PMID: 19218401 DOI: 10.1128/aem.01742-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Untargeted profiling of small-molecule metabolites from microbial culture supernatants (metabolic footprinting) has great potential as a phenotyping tool. We used time-resolved metabolic footprinting to compare one Escherichia coli and three Pseudomonas aeruginosa strains growing on complex media and show that considering metabolite changes over the whole course of growth provides much more information than analyses based on data from a single time point. Most strikingly, there was pronounced selectivity in metabolite uptake, even when the bacteria were growing apparently exponentially, with certain groups of metabolites not taken up until others had been entirely depleted from the medium. In addition, metabolite excretion showed some complex patterns. Fitting nonlinear equations (four-parameter sigmoids) to individual metabolite data allowed us to model these changes for metabolite uptake and visualize them by back-projecting the curve-fit parameters onto the original growth curves. These "uptake window" plots clearly demonstrated strain differences, with the uptake of some compounds being reversed in order between different strains. Comparison of an undefined rich medium with a defined complex medium designed to mimic cystic fibrosis sputum showed many differences, both qualitative and quantitative, with a greater proportion of excreted to utilized metabolites in the defined medium. Extending the strain comparison to a more closely related set of isolates showed that it was possible to discriminate two species of the Burkholderia cepacia complex based on uptake dynamics alone. We believe time-resolved metabolic footprinting could be a valuable tool for many questions in bacteriology, including isolate comparisons, phenotyping deletion mutants, and as a functional complement to taxonomic classifications.
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