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Collins C, Hall M, Bruno D, Sokolowska J, Duncan L, Yuecel R, McCarthy U, Fordyce MJ, Pert CC, McIntosh R, MacKay Z. Generation of Paramoeba perurans clonal cultures using flow cytometry and confirmation of virulence. JOURNAL OF FISH DISEASES 2017; 40:351-365. [PMID: 27524425 DOI: 10.1111/jfd.12517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 06/06/2023]
Abstract
Amoebic gill disease (AGD) in farmed Atlantic salmon is caused by the amoeba Paramoeba perurans. The recent establishment of in vitro culture techniques for P. perurans has provided a valuable tool for studying the parasite in detail. In this study, flow cytometry was used to generate clonal cultures from single-sorted amoeba, and these were used to successfully establish AGD in experimental Atlantic salmon. The clonal cultures displayed differences in virulence, based on gill scores. The P. perurans load on gills, determined by qPCR analysis, showed a positive relationship with gill score, and with clonal virulence, indicating that the ability of amoebae to proliferate and/or remain attached on gills may play a role in virulence. Gill scores based on gross signs and histopathological analysis were in agreement. No association between level of gill score and specific gill arch was observed. It was found that for fish with lower gill scores based on histopathological examination, gross examination and qPCR analysis of gills from the same fish were less successful in detecting lesions and amoebae, respectively.
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Affiliation(s)
- C Collins
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - M Hall
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - D Bruno
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - J Sokolowska
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - L Duncan
- Iain Fraser Cytometry Centre, Institute of Medical Sciences, School of Medicine & Dentistry, University of Aberdeen, Aberdeen, UK
| | - R Yuecel
- Iain Fraser Cytometry Centre, Institute of Medical Sciences, School of Medicine & Dentistry, University of Aberdeen, Aberdeen, UK
| | - U McCarthy
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - M J Fordyce
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - C C Pert
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - R McIntosh
- Marine Laboratory, Marine Scotland, Aberdeen, UK
| | - Z MacKay
- Marine Laboratory, Marine Scotland, Aberdeen, UK
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2
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Bruder LM, Dörkes M, Fuchs BM, Ludwig W, Liebl W. Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes. Syst Appl Microbiol 2016; 39:464-475. [DOI: 10.1016/j.syapm.2016.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 01/19/2023]
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3
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Lemonnier H, Lantoine F, Courties C, Guillebault D, Nézan E, Chomérat N, Escoubeyrou K, Galinié C, Blockmans B, Laugier T. Dynamics of phytoplankton communities in eutrophying tropical shrimp ponds affected by vibriosis. MARINE POLLUTION BULLETIN 2016; 110:449-459. [PMID: 27334725 DOI: 10.1016/j.marpolbul.2016.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/30/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
Tropical shrimp aquaculture systems in New Caledonia regularly face major crises resulting from outbreaks of Vibrio infections. Ponds are highly dynamic and challenging environments and display a wide range of trophic conditions. In farms affected by vibriosis, phytoplankton biomass and composition are highly variable. These conditions may promote the development of harmful algae increasing shrimp susceptibility to bacterial infections. Phytoplankton compartment before and during mortality outbreaks was monitored at a shrimp farm that has been regularly and highly impacted by these diseases. Combining information from flow cytometry, microscopy, pigment and phylogenetic analysis, the presence of Picocyanobacteria, Prasinophyceae and Diatomophyceae were detected as dominant phytoplankton groups and Cryptophyceae, Prymnesiophyceae and Dinophyceae as minor components. At the onset of the first shrimp mortalities, Bacillariophyceae increased while Cyanobacteria, Prymnesiophyceae and Dinophyceae decreased in the water column, followed by proliferation of Prasinophyceae. Several taxa were identified as potential harmful algae (Cyanobacteria, dinoflagellates and Phaeocystis).
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Affiliation(s)
- Hugues Lemonnier
- IFREMER LEAD, BP 2059, 98846 Nouméa cedex, New Caledonia, France.
| | - François Lantoine
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8222, LECOB, Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Claude Courties
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8222, LECOB, Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Delphine Guillebault
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8222, LECOB, Observatoire Océanologique, F-66650 Banyuls/mer, France; Microbia Environnement, Observatoire Océanologique de Banyuls, 66650 Banyuls-sur mer, France
| | - Elizabeth Nézan
- IFREMER, LER BO, Station de Biologie Marine, Place de la Croix, BP 40537, 29185 Concarneau Cedex, France
| | - Nicolas Chomérat
- IFREMER, LER BO, Station de Biologie Marine, Place de la Croix, BP 40537, 29185 Concarneau Cedex, France
| | - Karine Escoubeyrou
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Plate-forme Bio2Mar, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Christian Galinié
- GFA, Groupement des Fermes Aquacoles, ORPHELINAT, 1 rue Dame Lechanteur, 98800 Nouméa cedex, New Caledonia, France
| | - Bernard Blockmans
- GFA, Groupement des Fermes Aquacoles, ORPHELINAT, 1 rue Dame Lechanteur, 98800 Nouméa cedex, New Caledonia, France
| | - Thierry Laugier
- IFREMER LEAD, BP 2059, 98846 Nouméa cedex, New Caledonia, France
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Bettarel Y, Thanh MC, Patrice G, Antoinette A, Nadège KN, Bui VN, Thierry B. Flow cytometric enumeration of bacterial in the coral surface mucus layer. J Microbiol Methods 2016; 128:16-19. [DOI: 10.1016/j.mimet.2016.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
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5
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Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 2013; 152:39-50. [PMID: 23332745 DOI: 10.1016/j.cell.2012.10.052] [Citation(s) in RCA: 559] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 09/12/2012] [Accepted: 10/29/2012] [Indexed: 01/03/2023]
Abstract
The human gut contains trillions of microorganisms that influence our health by metabolizing xenobiotics, including host-targeted drugs and antibiotics. Recent efforts have characterized the diversity of this host-associated community, but it remains unclear which microorganisms are active and what perturbations influence this activity. Here, we combine flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the gut contains a distinctive set of active microorganisms, primarily Firmicutes. Short-term exposure to a panel of xenobiotics significantly affected the physiology, structure, and gene expression of this active gut microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding antibiotic resistance, drug metabolism, and stress response pathways. These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics, and suggest that attempts at personalized medicine should consider interindividual variations in the active human gut microbiome.
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Affiliation(s)
- Corinne Ferrier Maurice
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
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Budin G, Chung HJ, Lee H, Weissleder R. A magnetic Gram stain for bacterial detection. Angew Chem Int Ed Engl 2012; 51:7752-5. [PMID: 22744868 PMCID: PMC3496380 DOI: 10.1002/anie.201202982] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Indexed: 11/10/2022]
Abstract
Magnetizing: Bacteria are often classified into gram-positive and gram-negative strains by staining with crystal violet (CV). The described bioorthogonal modification of CV with trans-cyclooctene (TCO) can be used to render gram-positive bacteria magnetic with tetrazine-functionalized magnetic nanoparticles (MNP-Tz). This method allows class-specific automated magnetic detection and magnetic separation.
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Affiliation(s)
- Ghyslain Budin
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
| | - Hyun Jung Chung
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, (USA)
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Budin G, Chung HJ, Lee H, Weissleder R. A Magnetic Gram Stain for Bacterial Detection. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202982] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Development of defined microbial population standards using fluorescence activated cell sorting for the absolute quantification of S. aureus using real-time PCR. Mol Biotechnol 2012; 50:62-71. [PMID: 21611910 DOI: 10.1007/s12033-011-9417-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this article, four types of standards were assessed in a SYBR Green-based real-time PCR procedure for the quantification of Staphylococcus aureus (S. aureus) in DNA samples. The standards were purified S. aureus genomic DNA (type A), circular plasmid DNA containing a thermonuclease (nuc) gene fragment (type B), DNA extracted from defined populations of S. aureus cells generated by Fluorescence Activated Cell Sorting (FACS) technology with (type C) or without purification of DNA by boiling (type D). The optimal efficiency of 2.016 was obtained on Roche LightCycler(®) 4.1. software for type C standards, whereas the lowest efficiency (1.682) corresponded to type D standards. Type C standards appeared to be more suitable for quantitative real-time PCR because of the use of defined populations for construction of standard curves. Overall, Fieller Confidence Interval algorithm may be improved for replicates having a low standard deviation in Cycle Threshold values such as found for type B and C standards. Stabilities of diluted PCR standards stored at -20°C were compared after 0, 7, 14 and 30 days and were lower for type A or C standards compared with type B standards. However, FACS generated standards may be useful for bacterial quantification in real-time PCR assays once optimal storage and temperature conditions are defined.
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