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Tanpradit N, Thongdee M, Sariya L, Paungpin W, Chaiwattanarungruengpaisan S, Sirimanapong W, Kasantikul T, Phonarknguen R, Punchukrang A, Lekcharoen P, Arya N. Epidemiology of Chlamydia sp. infection in farmed Siamese crocodiles (Crocodylus siamensis) in Thailand. Acta Vet Scand 2023; 65:50. [PMID: 38008768 PMCID: PMC10680321 DOI: 10.1186/s13028-023-00713-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Although Chlamydia sp. causes widespread disease outbreaks in juvenile crocodiles in Thailand, data regarding the epidemiology, and risk factors of such infections are limited. The aim of this study was to investigate the prevalence and possible risk factors associated with Chlamydia sp. infections on Siamese crocodile (Crocodylus siamensis) farms in Thailand. A cross-sectional study was conducted from July to December 2019. Samples were collected from 40 farms across six regions in Thailand. Conjunctival, pharyngeal, and cloacal swab samples were analyzed for Chlamydiaceae nucleic acids using semi-nested PCR followed by phylogenetic analysis based on the ompA gene fragment. Risk factors of infection were analyzed using chi-square and univariate regression to calculate odds ratios. RESULTS The prevalence of Chlamydia sp. infection across all regions was 65%. The ompA phylogenetic analysis showed that Chlamydia sp. detected in this study was genetically closely related to Chlamydia crocodili and Chlamydia caviae. The risk factors for infection were water source, reusing treated wastewater from the treatment pond, not disposing of leftover food, low frequency of water replacement in the enclosure of juvenile crocodiles, and lack of water replacement after the death of a crocodile. CONCLUSION The prevalence of Chlamydia sp. infection in farmed crocodiles in Thailand was 65% during the study period. Cloacal swabs were superior to conjunctival and pharyngeal swabs due to their higher sensitivity in detecting Chlamydia sp., as well as their lower invasiveness. Good management and biosecurity in crocodile farming can reduce the risk of Chlamydia sp. INFECTION
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Affiliation(s)
- Nae Tanpradit
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Metawee Thongdee
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Ladawan Sariya
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Weena Paungpin
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Somjit Chaiwattanarungruengpaisan
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Wanna Sirimanapong
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
- Faculty of Veterinary Science, The Veterinary Aquatic Animal Research Health Care Unit, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Michigan State University, East Lansing, USA
| | - Rassameepen Phonarknguen
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Apichart Punchukrang
- Faculty of Agricultural Technology, Songkhla Rajabhat University, Songkhla, 90000, Thailand
| | - Paisin Lekcharoen
- The Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nlin Arya
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Baccari O, Barkallah M, Elleuch J, Ben Ayed N, Chtourou A, Karray-Hakim H, Hammami A, Michaud P, Fendri I, Abdelkafi S. Development of a duplex q-PCR for the simultaneous detection of Parachlamydia acanthamoebae and Simkania negevensis in environmental and clinical samples. Anal Biochem 2023; 667:115080. [PMID: 36775111 DOI: 10.1016/j.ab.2023.115080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Parachlamydia acanthamoebae and Simkania negevensis, two Chlamydia-like bacteria, have been recently recognized as emerging human respiratory pathogens. The prevalence and frequency of these bacteria in the environment and among atypical pneumonia patients are still underestimated by classical cultures, immunohistochemistry and serology which are non-specific, long and tedious methods. This study aims to develop a new duplex probe-based q-PCR assay for the simultaneous detection and quantification of P. acanthamoebae and S. negevensis. The selected hydrolysis probes displayed no cross-reaction with the closely related Chlamydia or the other tested waterborne pathogens. The assay achieved a large dynamic range for quantification (from 5 × 106 to 5 DNA copies/reaction). Efficiencies of FAM and JOE label probes weren't affected when they were combined. They were close to 100%, indicating the linear amplification. The application of this diagnostic tool resulted in 9/47 (19%) and 4/47 (8.5%) positive water samples for P. acanthamoebae and S. negevensis, respectively. P. acanthamoebae was also covered from 2/78 (2.5%) respiratory specimens and only one case (1/200 = 0.5%) of P. acanthamoebae and SARS-CoV-2 co-infection was noticed. While S. negevensis wasn't detected in clinical samples, the developed duplex q-PCR was shown to be an accurate, highly sensitive, and robust diagnostic tool for the detection and quantification of P. acanthamoebae and S. negevensis.
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Affiliation(s)
- Olfa Baccari
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Nourelhouda Ben Ayed
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Amel Chtourou
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Héla Karray-Hakim
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Adenene Hammami
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Philippe Michaud
- Institut Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, F-63000, Clermont-Ferrand, France
| | - Imen Fendri
- Laboratoire de Biotechnologie Végétale Appliquée à l'Amélioration des Cultures, Faculté des Sciences de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia.
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Baccari O, Barkallah M, Elleuch J, Ben Ayed N, Chtourou A, Karray-Hakim H, Hammami A, Michaud P, Fendri I, Abdelkafi S. A new TaqMan real-time PCR assay to detect Parachlamydia acanthamoebae and to monitor its co-existence with SARS-COV-2 among COVID-19 patients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17564-17572. [PMID: 36195814 PMCID: PMC9532228 DOI: 10.1007/s11356-022-23227-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Human respiratory infections caused by a large variety of microbial pathogens are the most common diseases responsible for hospitalization, morbidity and mortality. Parachlamydia acanthamoebae, a Chlamydia-related bacterium, has been found to be potentially associated with these diseases. An early and accurate diagnosis of this pathogen could be useful to avoid the potential respiratory complications linked especially to COVID-19 patients and to set suitable outbreak control measures. A TaqMan-PCR assay was developed to detect and quantify Parachlamydia acanthamoebae in environmental and clinical samples from patients of all ages with COVID-19. The selected hydrolysis probe displayed no cross-reaction with the closely related Chlamydia or the other tested pathogens. This q-PCR achieved good reproducibility and repeatability with a detection limit of about 5 DNA copies per reaction. Using this q-PCR assay, Parachlamydia acanthamoebae was detected in 2/78 respiratory specimens and 9/47 water samples. Only one case (1.3%) of Parachlamydia acanthamoebae and SARS-COV-2 co-infection was noticed. To our knowledge, the combination of these two respiratory pathogens has not been described yet. This new TaqMan-PCR assay represents an efficient diagnostic tool to survey Parachlamydia acanthamoebae on a large-scale screening programs and also during outbreaks.
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Affiliation(s)
- Olfa Baccari
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Nourelhouda Ben Ayed
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Héla Karray-Hakim
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Adenene Hammami
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Philippe Michaud
- Institut Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, 63000, Clermont-Ferrand, France
| | - Imen Fendri
- Laboratoire de Biotechnologie Végétale Appliquée à l'Amélioration des Cultures, Faculté des Sciences de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia.
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Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains. mSystems 2022; 7:e0004122. [PMID: 35353006 PMCID: PMC9040591 DOI: 10.1128/msystems.00041-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe–metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.
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Arumugam K, Bessarab I, Haryono MAS, Liu X, Zuniga-Montanez RE, Roy S, Qiu G, Drautz-Moses DI, Law YY, Wuertz S, Lauro FM, Huson DH, Williams RBH. Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing. NPJ Biofilms Microbiomes 2021; 7:23. [PMID: 33727564 PMCID: PMC7966762 DOI: 10.1038/s41522-021-00196-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023] Open
Abstract
New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
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Affiliation(s)
- Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rogelio E Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue, University of California, Davis, CA, USA
| | - Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
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Rayamajhee B, Subedi D, Peguda HK, Willcox MD, Henriquez FL, Carnt N. A Systematic Review of Intracellular Microorganisms within Acanthamoeba to Understand Potential Impact for Infection. Pathogens 2021; 10:pathogens10020225. [PMID: 33670718 PMCID: PMC7922382 DOI: 10.3390/pathogens10020225] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
Acanthamoeba, an opportunistic pathogen is known to cause an infection of the cornea, central nervous system, and skin. Acanthamoeba feeds different microorganisms, including potentially pathogenic prokaryotes; some of microbes have developed ways of surviving intracellularly and this may mean that Acanthamoeba acts as incubator of important pathogens. A systematic review of the literature was performed in order to capture a comprehensive picture of the variety of microbial species identified within Acanthamoeba following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Forty-three studies met the inclusion criteria, 26 studies (60.5%) examined environmental samples, eight (18.6%) studies examined clinical specimens, and another nine (20.9%) studies analysed both types of samples. Polymerase chain reaction (PCR) followed by gene sequencing was the most common technique used to identify the intracellular microorganisms. Important pathogenic bacteria, such as E. coli, Mycobacterium spp. and P. aeruginosa, were observed in clinical isolates of Acanthamoeba, whereas Legionella, adenovirus, mimivirus, and unidentified bacteria (Candidatus) were often identified in environmental Acanthamoeba. Increasing resistance of Acanthamoeba associated intracellular pathogens to antimicrobials is an increased risk to public health. Molecular-based future studies are needed in order to assess the microbiome residing in Acanthamoeba, as a research on the hypotheses that intracellular microbes can affect the pathogenicity of Acanthamoeba infections.
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Affiliation(s)
- Binod Rayamajhee
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences (KRIBS), Lalitpur 44700, Nepal
- Correspondence: or
| | - Dinesh Subedi
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia;
| | - Hari Kumar Peguda
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
| | - Mark Duncan Willcox
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
| | - Fiona L. Henriquez
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland (UWS), Paisley PA1 2BE, UK;
| | - Nicole Carnt
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
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Meenatchi R, Brindangnanam P, Hassan S, Rathna K, Kiran GS, Selvin J. Diversity of a bacterial community associated with Cliona lobata Hancock and Gelliodes pumila (Lendenfeld, 1887) sponges on the South-East coast of India. Sci Rep 2020; 10:11558. [PMID: 32665602 PMCID: PMC7360593 DOI: 10.1038/s41598-020-67717-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 05/13/2020] [Indexed: 01/05/2023] Open
Abstract
Marine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay suffered from pollution due to the dumping of untreated domestic sewage, effluents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial-abundant sponge species, such as Gelliodes pumila and Cliona lobata, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3–V4 region-specific primers. In both C. lobata and G. pumila, there was an overwhelming dominance (98 and 99%) of phylum Candidatus Saccharibacteria and Proteobacteria, respectively. The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique to G. pumila and C. lobata, respectively; 15 shared OTUs). Alphaproteobacteria was the most abundant class in both the sponge species. Unclassified species of phylum Candidatus Saccharibacteria from C. lobata and Chelotivorans composti from G. pumila were the most abundant bacterial species. The predominance of Alphaproteobacteria also revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay. Studies on sponge microbiomes at various understudied geographical locations might be helpful in predicting the status of reef environments.
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Affiliation(s)
- Ramu Meenatchi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Pownraj Brindangnanam
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India.,Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Saqib Hassan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Kumarasamy Rathna
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - G Seghal Kiran
- Department of Food Science and Technology, School of Lifesciences, Pondicherry University, Puducherry, India
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India.
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Arumugam K, Bağcı C, Bessarab I, Beier S, Buchfink B, Górska A, Qiu G, Huson DH, Williams RBH. Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data. MICROBIOME 2019; 7:61. [PMID: 30992083 PMCID: PMC6469205 DOI: 10.1186/s40168-019-0665-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/11/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. RESULTS We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. CONCLUSIONS Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.
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Affiliation(s)
- Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551 Singapore
| | - Caner Bağcı
- Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076 Germany
- International Max Planck Research School From Molecules to Organisms, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Max-Planck-Ring 5, Tübingen, 72076 Germany
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Sina Beier
- Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076 Germany
| | - Benjamin Buchfink
- Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076 Germany
| | - Anna Górska
- Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076 Germany
- International Max Planck Research School From Molecules to Organisms, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Max-Planck-Ring 5, Tübingen, 72076 Germany
| | - Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551 Singapore
| | - Daniel H. Huson
- Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076 Germany
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Rohan B. H. Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
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Lefevre E, Redfern L, Cooper EM, Stapleton HM, Gunsch CK. Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:959-968. [PMID: 30625682 PMCID: PMC6481660 DOI: 10.1016/j.scitotenv.2018.11.403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 05/15/2023]
Abstract
The detection of increasing concentrations of tetrabromobisphenol A (TBBPA) in wastewater treatment plants is raising concerns as TBBPA has been identified as a potentially toxic flame retardant. The objectives of this study were to evaluate the effect of acetate biostimulation on TBBPA microbial reductive debromination, and the response of anaerobic sludge associated microbial communities repeatedly exposed to TBBPA. Results indicate that the bulk of the microbial community did not experience significant shifts as a result of TBBPA exposure, and that only a small fraction of the community responded to the presence of TBBPA. Taxa most likely responsible for TBBPA transformation affiliated to Clostridiales and the wastewater sludge group Blvii28. The biostimulating effect of acetate was only observed during reactor startup, when acetogenesis was likely not yet occurring. However, when acetate likely started to be microbially generated in the reactor, acetate addition resulted in a slight but significant inhibiting effect on TBBPA transformation. A significant increase of hydrogenotrophic methanogens in the TBBPA-spiked reactor overtime implies that TBBPA degraders were not in direct competition with methanogens for H2. These results strongly suggest that TBBPA degrading taxa might have been primarily using acetate as an electron donor for the reductive debromination of TBBPA.
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Affiliation(s)
- Emilie Lefevre
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA
| | - Lauren Redfern
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC 27710, USA
| | - Heather M Stapleton
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC 27710, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA.
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10
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Stringlis IA, Yu K, Feussner K, de Jonge R, Van Bentum S, Van Verk MC, Berendsen RL, Bakker PAHM, Feussner I, Pieterse CMJ. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci U S A 2018; 115:E5213-E5222. [PMID: 29686086 DOI: 10.1094/pbiomes-11-18-0050-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sietske Van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
- Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands;
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11
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Tsao HF, Scheikl U, Volland JM, Köhsler M, Bright M, Walochnik J, Horn M. 'Candidatus Cochliophilus cryoturris' (Coxiellaceae), a symbiont of the testate amoeba Cochliopodium minus. Sci Rep 2017; 7:3394. [PMID: 28611430 PMCID: PMC5469826 DOI: 10.1038/s41598-017-03642-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/02/2017] [Indexed: 11/09/2022] Open
Abstract
Free-living amoebae are well known for their role in controlling microbial community composition through grazing, but some groups, namely Acanthamoeba species, also frequently serve as hosts for bacterial symbionts. Here we report the first identification of a bacterial symbiont in the testate amoeba Cochliopodium. The amoeba was isolated from a cooling tower water sample and identified as C. minus. Fluorescence in situ hybridization and transmission electron microscopy revealed intracellular symbionts located in vacuoles. 16S rRNA-based phylogenetic analysis identified the endosymbiont as member of a monophyletic group within the family Coxiellaceae (Gammaprotebacteria; Legionellales), only moderately related to known amoeba symbionts. We propose to tentatively classify these bacteria as 'Candidatus Cochliophilus cryoturris'. Our findings add both, a novel group of amoeba and a novel group of symbionts, to the growing list of bacteria-amoeba relationships.
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Affiliation(s)
- Han-Fei Tsao
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ute Scheikl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Jean-Marie Volland
- Department of Limnology and Oceanography, University of Vienna, Vienna, Austria
| | - Martina Köhsler
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Monika Bright
- Department of Limnology and Oceanography, University of Vienna, Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Matthias Horn
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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12
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Free-Living Amoebae as Hosts for and Vectors of Intracellular Microorganisms with Public Health Significance. Viruses 2017; 9:v9040065. [PMID: 28368313 PMCID: PMC5408671 DOI: 10.3390/v9040065] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 12/14/2022] Open
Abstract
Free-living amoebae (FLA) are parasites within both humans and animals causing a wide range of symptoms and act as hosts of, and vehicles for phylogenetically diverse microorganisms, called endocytobionts. The interaction of the FLA with sympatric microorganisms leads to an exceptional diversity within FLA. Some of these bacteria, viruses, and even eukaryotes, can live and replicate intracellularly within the FLA. This relationship provides protection to the microorganisms from external interventions and a dispersal mechanism across various habitats. Among those intracellularly-replicating or -residing organisms there are obligate and facultative pathogenic microorganisms affecting the health of humans or animals and are therefore of interest to Public Health Authorities. Mimiviruses, Pandoraviruses, and Pithoviruses are examples for interesting viral endocytobionts within FLA. Future research is expected to reveal further endocytobionts within free-living amoebae and other protozoa through co-cultivation studies, genomic, transcriptomic, and proteomic analyses.
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13
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Advances and Obstacles in the Genetic Dissection of Chlamydial Virulence. Curr Top Microbiol Immunol 2017; 412:133-158. [PMID: 29090367 DOI: 10.1007/82_2017_76] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Obligate intracellular pathogens in the family Chlamydiaceae infect taxonomically diverse eukaryotes ranging from amoebae to mammals. However, many fundamental aspects of chlamydial cell biology and pathogenesis remain poorly understood. Genetic dissection of chlamydial biology has historically been hampered by a lack of genetic tools. Exploitation of the ability of chlamydia to recombine genomic material by lateral gene transfer (LGT) ushered in a new era in chlamydia research. With methods to map mutations in place, genetic screens were able to assign functions and phenotypes to specific chlamydial genes. Development of an approach for stable transformation of chlamydia also provided a mechanism for gene delivery and platforms for disrupting chromosomal genes. Here, we explore how these and other tools have been used to test hypotheses concerning the functions of known chlamydial virulence factors and discover the functions of completely uncharacterized genes. Refinement and extension of the existing genetic tools to additional Chlamydia spp. will substantially advance understanding of the biology and pathogenesis of this important group of pathogens.
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14
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Lienard J, Croxatto A, Gervaix A, Lévi Y, Loret JF, Posfay-Barbe KM, Greub G. Prevalence and diversity of Chlamydiales and other amoeba-resisting bacteria in domestic drinking water systems. New Microbes New Infect 2016; 15:107-116. [PMID: 28070335 PMCID: PMC5219624 DOI: 10.1016/j.nmni.2016.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 12/01/2022] Open
Abstract
A growing number of human infections incriminate environmental bacteria that have evolved virulent mechanisms to resist amoebae and use them as a replicative niche. These bacteria are designated amoeba-resisting bacteria (ARB). Despite the isolation of these ARB in various human clinical samples, the possible source of infection remains undetermined in most cases. However, it is known that the ARB Legionella pneumophila, for instance, causes a respiratory infection in susceptible hosts after inhalation of contaminated water aerosols from various sources. The Chlamydiales order contains many ARB, such as Parachlamydia acanthamoebae or Simkania negevensis, previously implicated in human respiratory infections with no identified contamination sources. We thus investigated whether domestic water systems are a potential source of transmission of these Chlamydiales to humans by using amoebal culture and molecular methods. Other important ARB such as mycobacteria and Legionella were also investigated, as were their possible amoebal hosts. This work reports for the first time a very high prevalence and diversity of Chlamydiales in drinking water, being detected in 35 (72.9%) of 48 investigated domestic water systems, with members of the Parachlamydiaceae family being dominantly detected. Furthermore, various Legionella and mycobacteria species were also recovered, some species of which are known to be causal agents of human infections.
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Affiliation(s)
- J Lienard
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - A Croxatto
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - A Gervaix
- Children's Hospital of Geneva, University Hospitals of Geneva and Medical School of the University of Geneva, Geneva, Switzerland
| | - Y Lévi
- University of Paris-Sud XI, Faculty of Pharmacy, Paris, France
| | - J-F Loret
- Suez Environnement CIRSEE, Le Pecq, France
| | - K M Posfay-Barbe
- Children's Hospital of Geneva, University Hospitals of Geneva and Medical School of the University of Geneva, Geneva, Switzerland
| | - G Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Infectious Diseases Service, Lausanne University Hospital, Lausanne, Switzerland
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15
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Scheikl U, Tsao HF, Horn M, Indra A, Walochnik J. Free-living amoebae and their associated bacteria in Austrian cooling towers: a 1-year routine screening. Parasitol Res 2016; 115:3365-74. [PMID: 27177720 PMCID: PMC4980419 DOI: 10.1007/s00436-016-5097-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 12/15/2022]
Abstract
Free-living amoebae (FLA) are widely spread in the environment and known to cause rare but often serious infections. Besides this, FLA may serve as vehicles for bacterial pathogens. In particular, Legionella pneumophila is known to replicate within FLA thereby also gaining enhanced infectivity. Cooling towers have been the source of outbreaks of Legionnaires' disease in the past and are thus usually screened for legionellae on a routine basis, not considering, however, FLA and their vehicle function. The aim of this study was to incorporate a screening system for host amoebae into a Legionella routine screening. A new real-time PCR-based screening system for various groups of FLA was established. Three cooling towers were screened every 2 weeks over the period of 1 year for FLA and Legionella spp., by culture and molecular methods in parallel. Altogether, 83.3 % of the cooling tower samples were positive for FLA, Acanthamoeba being the dominating genus. Interestingly, 69.7 % of the cooling tower samples were not suitable for the standard Legionella screening due to their high organic burden. In the remaining samples, positivity for Legionella spp. was 25 % by culture, but overall positivity was 50 % by molecular methods. Several amoebal isolates revealed intracellular bacteria.
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Affiliation(s)
- Ute Scheikl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Han-Fei Tsao
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Alexander Indra
- Department of Mycobacteriology and Clinical Molecular Biology, AGES, Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria.
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16
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Pizzetti I, Schulz F, Tyml T, Fuchs BM, Amann R, Horn M, Fazi S. Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake. Environ Microbiol 2015; 18:2405-17. [PMID: 26530333 DOI: 10.1111/1462-2920.13111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 12/01/2022]
Abstract
The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.
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Affiliation(s)
- Ilaria Pizzetti
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
| | - Frederik Schulz
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Tomáš Tyml
- University of South Bohemia, Faculty of Science, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Masaryk University, Department of Botany and Zoology, Faculty of Science, Kotlářská 2, 61137, Brno, Czech Republic
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Matthias Horn
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Stefano Fazi
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
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17
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Amoebal endosymbiont Parachlamydia acanthamoebae Bn9 can grow in immortal human epithelial HEp-2 cells at low temperature; an in vitro model system to study chlamydial evolution. PLoS One 2015; 10:e0116486. [PMID: 25643359 PMCID: PMC4314085 DOI: 10.1371/journal.pone.0116486] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/08/2014] [Indexed: 01/07/2023] Open
Abstract
Ancient chlamydiae diverged into pathogenic and environmental chlamydiae 0.7–1.4 billion years ago. However, how pathogenic chlamydiae adapted to mammalian cells that provide a stable niche at approximately 37°C, remains unknown, although environmental chlamydiae have evolved as endosymbionts of lower eukaryotes in harsh niches of relatively low temperatures. Hence, we assessed whether an environmental chlamydia, Parachlamydia Bn9, could grow in human HEp-2 cells at a low culture temperature of 30°C. The assessment of inclusion formation by quantitative RT-PCR revealed that the numbers of bacterial inclusion bodies and the transcription level of 16SrRNA significantly increased after culture at 30°C compared to at 37°C. Confocal microscopy showed that the bacteria were located close to HEp-2 nuclei and were actively replicative. Transmission electron microscopy also revealed replicating bacteria consisting of reticular bodies, but with a few elementary bodies. Cytochalasin D and rifampicin inhibited inclusion formation. Lactacystin slightly inhibited bacterial inclusion formation. KEGG analysis using a draft genome sequence of the bacteria revealed that it possesses metabolic pathways almost identical to those of pathogenic chlamydia. Interestingly, comparative genomic analysis with pathogenic chlamydia revealed that the Parachlamydia similarly possess the genes encoding Type III secretion system, but lacking genes encoding inclusion membrane proteins (IncA to G) required for inclusion maturation. Taken together, we conclude that ancient chlamydiae had the potential to grow in human cells, but overcoming the thermal gap was a critical event for chlamydial adaptation to human cells.
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18
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Hammerschlag MR, Kohlhoff SA, Gaydos CA. Chlamydia pneumoniae. MANDELL, DOUGLAS, AND BENNETT'S PRINCIPLES AND PRACTICE OF INFECTIOUS DISEASES 2015. [PMCID: PMC7173483 DOI: 10.1016/b978-1-4557-4801-3.00184-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Taylor-Brown A, Vaughan L, Greub G, Timms P, Polkinghorne A. Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae. Pathog Dis 2014; 73:1-15. [PMID: 25854000 DOI: 10.1093/femspd/ftu009] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2014] [Indexed: 11/13/2022] Open
Abstract
Chlamydiae are obligate intracellular bacteria that share a unique but remarkably conserved biphasic developmental cycle that relies on a eukaryotic host cell for survival. Although the phylum was originally thought to only contain one family, the Chlamydiaceae, a total of nine families are now recognized. These so-called Chlamydia-like organisms (CLOs) are also referred to as 'environmental chlamydiae', as many were initially isolated from environmental sources. However, these organisms are also emerging pathogens, as many, such as Parachlamydia sp., Simkania sp. and Waddlia sp., have been associated with human disease, and others, such as Piscichlamydia sp. and Parilichlamydia sp., have been documented in association with diseases in animals. Their strict intracellular nature and the requirement for cell culture have been a confounding factor in characterizing the biology and pathogenicity of CLOs. Nevertheless, the genomes of seven CLO species have now been sequenced, providing new information on their potential ability to adapt to a wide range of hosts. As new isolation and diagnostic methods advance, we are able to further explore the richness of this phylum with further research likely to help define the true pathogenic potential of the CLOs while also providing insight into the origins of the 'traditional' chlamydiae.
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Affiliation(s)
- Alyce Taylor-Brown
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
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20
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Aistleitner K, Anrather D, Schott T, Klose J, Bright M, Ammerer G, Horn M. Conserved features and major differences in the outer membrane protein composition of chlamydiae. Environ Microbiol 2014; 17:1397-413. [DOI: 10.1111/1462-2920.12621] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/06/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Karin Aistleitner
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
| | - Dorothea Anrather
- Department of Mass Spectrometry Facility Max F. Perutz Laboratories University of Vienna Vienna Austria
| | - Thomas Schott
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
| | - Julia Klose
- Department of Limnology and Oceanography University of Vienna Vienna Austria
| | - Monika Bright
- Department of Limnology and Oceanography University of Vienna Vienna Austria
| | - Gustav Ammerer
- Department of Biochemistry and Cell Biology Max F. Perutz Laboratories University of Vienna Vienna Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
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21
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Naim MA, Morillo JA, Sørensen SJ, Waleed AAS, Smidt H, Sipkema D. Host-specific microbial communities in three sympatric North Sea sponges. FEMS Microbiol Ecol 2014; 90:390-403. [DOI: 10.1111/1574-6941.12400] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Mohd Azrul Naim
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
- Institute of Oceanography and Maritime Studies; International Islamic University Malaysia; Jalan Istana, Kuantan Pahang Malaysia
| | - Jose A. Morillo
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
- Institute of Water Research, Department of Microbiology; University of Granada; Granada Spain
| | - Søren J. Sørensen
- Molecular Microbial Ecology Group; University of Copenhagen; Copenhagen Denmark
| | - Abu Al-Soud Waleed
- Molecular Microbial Ecology Group; University of Copenhagen; Copenhagen Denmark
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
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22
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Lagkouvardos I, Shen J, Horn M. Improved axenization method reveals complexity of symbiotic associations between bacteria and acanthamoebae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:383-388. [PMID: 24992537 DOI: 10.1111/1758-2229.12162] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
Bacteria associated with free-living amoebae have attracted considerable attention because of their role in human disease and as models for studying endosymbiosis. However, the identification and analysis of such novel associations are hindered by the limitations of methods for isolation and axenization of amoebae. Here, we replaced the heat-inactivated Escherichia coli, which is typically used as food source during axenization, with a live E. coli tolC knockout mutant strain hypersensitive to antibiotics. Together with the addition of otherwise sublethal amounts of ampicillin, this approach tripled the success rate and reduced the time required for axenization by at least 3 days. Using this method for two environmental samples, 10 Acanthamoeba strains were isolated, seven of which contained bacterial symbionts. In three cases, amoebae harbouring two phylogenetically distinct symbionts were recovered, supporting a more widespread occurrence of multi-partner symbiotic associations among free-living amoebae.
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Affiliation(s)
- Ilias Lagkouvardos
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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Scheid P. Relevance of free-living amoebae as hosts for phylogenetically diverse microorganisms. Parasitol Res 2014; 113:2407-14. [PMID: 24828345 DOI: 10.1007/s00436-014-3932-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 04/30/2014] [Indexed: 10/25/2022]
Abstract
In addition to their role as parasites, free-living amoebae (FLA) can act as hosts of and vehicles for phylogentically diverse microorganisms while some of them replicate intracellularly. These microorganisms are adapted to the intracellular conditions in the amoeba, find suitable conditions and protection from negative environmental influences and take advantage of the dispersal in the environment by their amoebic host. It is expedient to call these organisms "endocytobionts", at least during the initial steps of any studies. By doing so, it is not necessary to go into potential characteristics of these relationships such as parasitism, phoresy, zoochory, or mutualism at an early stage of study. Among those organisms resisting the lysis within their amoebic host, there are obligate and facultative pathogenic microorganisms affecting the health of humans or animals. FLA-endocytobiont relationships are not only important for the tenacity of the involved microorganisms. Especially if FLA are present in biofilms and there are close ties with many other microorganisms, the odds are for some of these microorganisms to develop human pathogenic properties. Here, the amoebic passage seems to be a prerequisite for the development of virulence factors and it may have an impact on evolutionary processes.
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Affiliation(s)
- Patrick Scheid
- Central Institute of the Bundeswehr Medical Service Koblenz, Koblenz, Germany,
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Omsland A, Sixt BS, Horn M, Hackstadt T. Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities. FEMS Microbiol Rev 2014; 38:779-801. [PMID: 24484402 DOI: 10.1111/1574-6976.12059] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/08/2014] [Accepted: 01/13/2014] [Indexed: 01/07/2023] Open
Abstract
Chlamydiae are a group of obligate intracellular bacteria comprising important human and animal pathogens as well as symbionts of ubiquitous protists. They are characterized by a developmental cycle including two main morphologically and physiologically distinct stages, the replicating reticulate body and the infectious nondividing elementary body. In this review, we reconstruct the history of studies that have led to our current perception of chlamydial physiology, focusing on their energy and central carbon metabolism. We then compare the metabolic capabilities of pathogenic and environmental chlamydiae highlighting interspecies variability among the metabolically more flexible environmental strains. We discuss recent findings suggesting that chlamydiae may not live as energy parasites throughout the developmental cycle and that elementary bodies are not metabolically inert but exhibit metabolic activity under appropriate axenic conditions. The observed host-free metabolic activity of elementary bodies may reflect adequate recapitulation of the intracellular environment, but there is evidence that this activity is biologically relevant and required for extracellular survival and maintenance of infectivity. The recent discoveries call for a reconsideration of chlamydial metabolism and future in-depth analyses to better understand how species- and stage-specific differences in chlamydial physiology may affect virulence, tissue tropism, and host adaptation.
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Affiliation(s)
- Anders Omsland
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, NIAID, NIH, Hamilton, MT, USA
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Goñi P, Fernández MT, Rubio E. Identifying endosymbiont bacteria associated with free-living amoebae. Environ Microbiol 2014; 16:339-49. [PMID: 24422686 DOI: 10.1111/1462-2920.12363] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 12/17/2013] [Accepted: 12/17/2013] [Indexed: 11/30/2022]
Abstract
The association between free-living amoebae and pathogenic bacteria is an issue that has gained great importance due to the environmental and health consequences that it implies. In this paper, we analyse the techniques to follow an epidemiological study to identify associations between genera, species, genotypes and subgenotypes of amoebae with pathogenic bacteria, analysing their evolution and considering their usefulness. In this sense, we highlight the combination of microscopic and molecular techniques as the most appropriate way to obtain fully reliable results as well as the need to achieve the standardization of these techniques to allow the comparison of both environmental and clinical results.
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Affiliation(s)
- Pilar Goñi
- Area of Parasitology, University of Zaragoza, Zaragoza, Spain
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Jacquier N, Aeby S, Lienard J, Greub G. Discovery of new intracellular pathogens by amoebal coculture and amoebal enrichment approaches. J Vis Exp 2013:e51055. [PMID: 24192667 DOI: 10.3791/51055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Intracellular pathogens such as legionella, mycobacteria and Chlamydia-like organisms are difficult to isolate because they often grow poorly or not at all on selective media that are usually used to cultivate bacteria. For this reason, many of these pathogens were discovered only recently or following important outbreaks. These pathogens are often associated with amoebae, which serve as host-cell and allow the survival and growth of the bacteria. We intend here to provide a demonstration of two techniques that allow isolation and characterization of intracellular pathogens present in clinical or environmental samples: the amoebal coculture and the amoebal enrichment. Amoebal coculture allows recovery of intracellular bacteria by inoculating the investigated sample onto an amoebal lawn that can be infected and lysed by the intracellular bacteria present in the sample. Amoebal enrichment allows recovery of amoebae present in a clinical or environmental sample. This can lead to discovery of new amoebal species but also of new intracellular bacteria growing specifically in these amoebae. Together, these two techniques help to discover new intracellular bacteria able to grow in amoebae. Because of their ability to infect amoebae and resist phagocytosis, these intracellular bacteria might also escape phagocytosis by macrophages and thus, be pathogenic for higher eukaryotes.
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Affiliation(s)
- Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne
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Sixt BS, Kostanjšek R, Mustedanagic A, Toenshoff ER, Horn M. Developmental cycle and host interaction of Rhabdochlamydia porcellionis, an intracellular parasite of terrestrial isopods. Environ Microbiol 2013; 15:2980-93. [PMID: 24024954 DOI: 10.1111/1462-2920.12252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/05/2013] [Accepted: 08/12/2013] [Indexed: 12/01/2022]
Abstract
Environmental chlamydiae are a diverse group of obligate intracellular bacteria related to well-known pathogens of humans. To date, only very little is known about chlamydial species infecting arthropods. In this study, we used cocultivation with insect cells for recovery and maintenance of Rhabdochlamydia porcellionis, a parasite of the crustacean host Porcellio scaber. In vitro, the infection cycle of R. porcellionis was completed within 7 days, resulting in the release of infectious particles by host cell lysis. Lack of apoptosis induction during the entire course of infection, combined with a reduced sensitivity of infected cultures to experimentally induced programmed cell death, indicates that R. porcellionis like its human pathogenic relatives counteracts this host defence mechanism. Interestingly, the rod-shaped variant of R. porcellionis, proposed to represent their mature infective stage, was not detected in cell culture, suggesting that its development may require prolonged maturation or may be triggered by specific conditions encountered only in the animal host. This first cell culture-based system for the cultivation and investigation of an arthropod-associated chlamydial species will help to better understand the biology of a so far neglected group of chlamydiae and its recently suggested potential to cause disease in humans.
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Affiliation(s)
- Barbara S Sixt
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Azra Mustedanagic
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Elena R Toenshoff
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
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Lagkouvardos I, Weinmaier T, Lauro FM, Cavicchioli R, Rattei T, Horn M. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. ISME JOURNAL 2013; 8:115-25. [PMID: 23949660 DOI: 10.1038/ismej.2013.142] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 11/09/2022]
Abstract
In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.
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Affiliation(s)
- Ilias Lagkouvardos
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Weinmaier
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Federico M Lauro
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas Rattei
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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Candidatus Syngnamydia venezia, a novel member of the phylum Chlamydiae from the broad nosed pipefish, Syngnathus typhle. PLoS One 2013; 8:e70853. [PMID: 23951025 PMCID: PMC3741330 DOI: 10.1371/journal.pone.0070853] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 06/27/2013] [Indexed: 11/19/2022] Open
Abstract
Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chlamydia-related bacteria are also major fish pathogens, infecting epithelial cells of the gills and skin to cause the disease epitheliocystis. Given the wide distribution, ancient origins and spectacular diversity of bony fishes, this group offers a rich resource for the identification and isolation of novel Chlamydia. The broad-nosed pipefish (Syngnathus typhle) is a widely distributed and genetically diverse temperate fish species, susceptible to epitheliocystis across much of its range. We describe here a new bacterial species, Candidatus Syngnamydia venezia; epitheliocystis agent of S. typhle and close relative to other chlamydial pathogens which are known to infect diverse hosts ranging from invertebrates to humans.
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Pizzetti I, Fazi S, Fuchs BM, Amann R. High abundance of novel environmental chlamydiae in a Tyrrhenian coastal lake (Lago di Paola, Italy). ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:446-452. [PMID: 23760831 DOI: 10.1111/j.1758-2229.2012.00361.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
For a long time the bacterial phylum of Chlamydiae exclusively consisted of one family of obligate intracellular bacteria, the Chlamydiaceae, which encompassed causative agents of severe diseases. In the 1990s, environmental chlamydiae were discovered as symbionts of free-living amoebae and other eukaryotic hosts. During a sampling campaign in September 2008, while monitoring Planctomycetes, we retrieved 20 almost full-length 16S rRNA gene sequences affiliated with Chlamydiales from a lake at the Tyrrhenian coast of central Italy (Lago di Paola, Latium). Two main clusters were identified. The nine sequences within the tight cluster I shared ∼98% identity, just like the six sequences of cluster II. The 16S rRNA sequence identity between the two novel groups was with 88% higher than with all known families of the order Chlamydiales. Four types of less frequent chlamydial 16S rRNA sequences were also detected. Two oligonucleotide probes were designed, and optimized. Chl282 targets the cluster I and almost all other Chlamydiales, while Chl282bis targets the cluster II and few other sequences. By catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH), we identified in the Lago di Paola picoplankton abundant tiny cells with dot-shaped morphology and, interestingly, rarely also protists with intracellular pleomorphic chlamydiae. Abundances of the novel chlamydial clusters were up to 5 × 10(4) cells per millilitre. The two clusters were also detected in similar numbers during a second sampling in October 2010. This confirmed the relevance of the two newly described clusters of chlamydiae in Lago di Paola, not only enlarging the knowledge on the biodiversity of environmental chlamydiae in aquatic habitats, but also raising sanitary issues that should be addressed in the future.
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Affiliation(s)
- Ilaria Pizzetti
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany Water Research Institute (IRSA-CNR), via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
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Ito A, Matsuo J, Nakamura S, Yoshida A, Okude M, Hayashi Y, Sakai H, Yoshida M, Takahashi K, Yamaguchi H. Amoebal endosymbiont Protochlamydia induces apoptosis to human immortal HEp-2 cells. PLoS One 2012; 7:e30270. [PMID: 22276171 PMCID: PMC3261889 DOI: 10.1371/journal.pone.0030270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 12/16/2011] [Indexed: 01/19/2023] Open
Abstract
Protochlamydia, an environmental chlamydia and obligate amoebal endosymbiotic bacterium, evolved to survive within protist hosts, such as Acanthamobae, 700 million years ago. However, these bacteria do not live in vertebrates, including humans. This raises the possibility that interactions between Protochlamydia and human cells could induce a novel cytopathic effect, leading to new insights into host-parasite relationships. Therefore, we studied the effect of Protochlamydia on the survival of human immortal cell line, HEp-2 cells and primary peripheral blood mononuclear cells (PBMC). Using mainly 4',6-diamidino-2-phenylindole staining, fluorescent in situ hybridization, transmission electron microscopy, and also TUNEL and Transwell assays, we demonstrated that the Protochlamydia induced apoptosis in HEp-2 cells. The attachment of viable bacterial cells, but not an increase of bacterial infectious progenies within the cells, was required for the apoptosis. Other chlamydiae [Parachlamydia acanthamoebae and Chlamydia trachomatis (serovars D and L2)] did not induce the same phenomena, indicating that the observed apoptosis may be specific to the Protochlamydia. Furthermore, the bacteria had no effect on the survival of primary PBMCs collected from five volunteers, regardless of activation. We concluded that Protochlamydia induces apoptosis in human-immortal HEp-2 cells and that this endosymbiont could potentially be used as a biological tool for the elucidation of novel host-parasite relationships.
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Affiliation(s)
- Atsushi Ito
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Asahi Yoshida
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Miho Okude
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yasuhiro Hayashi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Haruna Sakai
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mitsutaka Yoshida
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Takahashi
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
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Sixt BS, Hiess B, König L, Horn M. Lack of effective anti-apoptotic activities restricts growth of Parachlamydiaceae in insect cells. PLoS One 2012; 7:e29565. [PMID: 22253735 PMCID: PMC3253803 DOI: 10.1371/journal.pone.0029565] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/30/2011] [Indexed: 12/02/2022] Open
Abstract
The fundamental role of programmed cell death in host defense is highlighted by the multitude of anti-apoptotic strategies evolved by various microbes, including the well-known obligate intracellular bacterial pathogens Chlamydia trachomatis and Chlamydia (Chlamydophila) pneumoniae. As inhibition of apoptosis is assumed to be essential for a successful infection of humans by these chlamydiae, we analyzed the anti-apoptotic capacity of close relatives that occur as symbionts of amoebae and might represent emerging pathogens. While Simkania negevensis was able to efficiently replicate within insect cells, which served as model for metazoan-derived host cells, the Parachlamydiaceae (Parachlamydia acanthamoebae and Protochlamydia amoebophila) displayed limited intracellular growth, yet these bacteria induced typical features of apoptotic cell death, including formation of apoptotic bodies, nuclear condensation, internucleosomal DNA fragmentation, and effector caspase activity. Induction of apoptosis was dependent on bacterial activity, but not bacterial de novo protein synthesis, and was detectable already at very early stages of infection. Experimental inhibition of host cell death greatly enhanced parachlamydial replication, suggesting that lack of potent anti-apoptotic activities in Parachlamydiaceae may represent an important factor compromising their ability to successfully infect non-protozoan hosts. These findings highlight the importance of the evolution of anti-apoptotic traits for the success of chlamydiae as pathogens of humans and animals.
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Affiliation(s)
- Barbara S. Sixt
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Birgit Hiess
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Lena König
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
- * E-mail:
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Sibitz C, Rudnay EC, Wabnegger L, Spergser J, Apfalter P, Nell B. Detection of Chlamydophila pneumoniae in cats with conjunctivitis. Vet Ophthalmol 2011; 14 Suppl 1:67-74. [PMID: 21923826 DOI: 10.1111/j.1463-5224.2011.00919.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To determine the presence of chlamydial species including recently described chlamydial agents as well as the human pathogen Chlamydophila pneumoniae in feline conjunctivitis. ANIMAL STUDIED Twenty five cats without and 49 cats with conjunctivitis were tested for chlamydia using a Chlamydiaceae real time (RT) PCR (targeting the 23S rRNA gene sequence), a Chlamydiales PCR (targeting the 16S rRNA gene sequence), and cell culture. The PCR products of all positive samples were sequenced and subsequently analyzed using a basic local alignment search tool search. RESULTS Chlamydiaceae RT PCR and subsequent sequence analyses identified C. pneumoniae in five cats in the conjunctivitis group. The presence of Chlamydophila felis was shown in two cats with conjunctivitis. Chlamydiae related to uncultured members of Chlamydiales were detected in three conjunctivitis cases and in one cat without clinical symptoms. CONCLUSION This study detects for the first time, the known human pathogen C. pneumoniae in feline conjunctivitis cases using Chlamydiaceae RT PCR and sequence analyses.
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Affiliation(s)
- Christina Sibitz
- Clinic for Surgery and Ophthalmology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
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Collingro A, Tischler P, Weinmaier T, Penz T, Heinz E, Brunham RC, Read TD, Bavoil PM, Sachse K, Kahane S, Friedman MG, Rattei T, Myers GSA, Horn M. Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol 2011; 28:3253-70. [PMID: 21690563 DOI: 10.1093/molbev/msr161] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
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Heinz E, Pichler P, Heinz C, op den Camp HJM, Toenshoff ER, Ammerer G, Mechtler K, Wagner M, Horn M. Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies. Proteomics 2010; 10:4363-76. [DOI: 10.1002/pmic.201000302] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Leitsch D, Köhsler M, Marchetti-Deschmann M, Deutsch A, Allmaier G, König L, Sixt BS, Duchêne M, Walochnik J. Proteomic aspects of Parachlamydia acanthamoebae infection in Acanthamoeba spp. ISME JOURNAL 2010; 4:1366-74. [DOI: 10.1038/ismej.2010.68] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Thomas V, McDonnell G, Denyer SP, Maillard JY. Free-living amoebae and their intracellular pathogenic microorganisms: risks for water quality. FEMS Microbiol Rev 2010; 34:231-59. [DOI: 10.1111/j.1574-6976.2009.00190.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Corsaro D, Pages GS, Catalan V, Loret JF, Greub G. Biodiversity of amoebae and amoeba-associated bacteria in water treatment plants. Int J Hyg Environ Health 2010; 213:158-66. [PMID: 20403728 DOI: 10.1016/j.ijheh.2010.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 02/18/2010] [Accepted: 03/19/2010] [Indexed: 11/27/2022]
Abstract
In this study, we enlarged our previous investigation focusing on the biodiversity of chlamydiae and amoebae in a drinking water treatment plant, by the inclusion of two additional plants and by searching also for the presence of legionellae and mycobacteria. Autochthonous amoebae were recovered onto non-nutritive agar, identified by 18S rRNA gene sequencing, and screened for the presence of bacterial endosymbionts. Bacteria were also searched for by Acanthamoeba co-culture. From a total of 125 samples, we recovered 38 amoebae, among which six harboured endosymbionts (three chlamydiae and three legionellae). In addition, we recovered by amoebal co-culture 11 chlamydiae, 36 legionellae (no L. pneumophila), and 24 mycobacteria (all rapid-growers). Two plants presented a similar percentage of samples positive for chlamydiae (11%), mycobacteria (20%) and amoebae (27%), whereas in the third plant the number of recovered bacteria was almost twice higher. Each plant exhibited a relatively high specific microbiota. Amoebae were mainly represented by various Naegleria species, Acanthamoeba species and Hartmannella vermiformis. Parachlamydiaceae were the most abundant chlamydiae (8 strains in total), and in this study we recovered a new genus-level strain, along with new chlamydiae previously reported. Similarly, about 66% of the recovered legionellae and 47% of the isolated mycobacteria could represent new species. Our work highlighted a high species diversity among legionellae and mycobacteria, dominated by putative new species, and it confirmed the presence of chlamydiae in these artificial water systems.
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Affiliation(s)
- Daniele Corsaro
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Faculty of Biology and Medecine, University of Lausanne, Bugnon 46, 1011 Lausanne, Switzerland
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Abstract
Parachlamydia acanthamoebae is a Chlamydia-like organism that easily grows within Acanthamoeba spp. Thus, it probably uses these widespread free-living amoebae as a replicative niche, a cosmopolite aquatic reservoir and a vector. A potential role of P. acanthamoebae as an agent of lower respiratory tract infection was initially suggested by its isolation within an Acanthamoeba sp. recovered from the water of a humidifier during the investigation of an outbreak of fever. Additional serological and molecular-based investigations further supported its pathogenic role, mainly in bronchiolitis, bronchitis, aspiration pneumonia and community-acquired pneumonia. P. acanthamoebae was shown to survive and replicate within human macrophages, lung fibroblasts and pneumocytes. Moreover, this strict intracellular bacterium also causes severe pneumonia in experimentally infected mice, thus fulfilling the third and fourth Koch criteria for a pathogenic role. Consequently, new tools have been developed for the diagnosis of parachlamydial infections. It will be important to routinely search for this emerging agent of pneumonia, as P. acanthamoebae is apparently resistant to quinolones, which are antibiotics often used for the empirical treatment of atypical pneumonia. Other Chlamydia-related bacteria, including Protochlamydia naegleriophila, Simkania negevensis and Waddlia chondrophila, might also cause lung infections. Moreover, several additional novel chlamydiae, e.g. Criblamydia sequanensis and Rhabdochlamydia crassificans, have been discovered and are now being investigated for their human pathogenicity.
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Affiliation(s)
- G Greub
- Centre for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Centre and University of Lausanne, Lausanne, Switzerland.
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40
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Corsaro D, Feroldi V, Saucedo G, Ribas F, Loret JF, Greub G. NovelChlamydialesstrains isolated from a water treatment plant. Environ Microbiol 2009; 11:188-200. [DOI: 10.1111/j.1462-2920.2008.01752.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Members of the phylum Chlamydiae are obligate intracellular bacteria that were discovered about a century ago. Although Chlamydiae are major pathogens of humans and animals, they were long recognized only as a phylogenetically well-separated, small group of closely related microorganisms. The diversity of chlamydiae, their host range, and their occurrence in the environment had been largely underestimated. Today, several chlamydia-like bacteria have been described as symbionts of free-living amoebae and other eukaryotic hosts. Some of these environmental chlamydiae might also be of medical relevance for humans. Their analysis has contributed to a broader understanding of chlamydial biology and to novel insights into the evolution of these unique microorganisms.
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Affiliation(s)
- Matthias Horn
- Department of Microbial Ecology, University of Vienna, A-1090 Vienna, Austria.
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42
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Abstract
Chlamydiae are obligate intracellular bacteria, parasites of a variety of eukaryotes ranging from amoebae to humans. Among them, the family Parachlamydiaceae comprises endosymbionts of amoebae, mainly Acanthamoeba, currently investigated as emerging pathogens of humans and other vertebrates. 16S rDNA-based PCR culture-independent studies in environmental samples have demonstrated the presence of Chlamydiales in various types of nonmedical habitats. Here we reviewed the biology of the Parachlamydiaceae, and more particularly those studies reporting molecular evidences for their presence in the environment, with a re-analysis of the 16S rDNA phylotypes.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS Chlamydia Research Association, Vandoeuvre-lès-Nancy, France.
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43
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Schmitz-Esser S, Toenshoff ER, Haider S, Heinz E, Hoenninger VM, Wagner M, Horn M. Diversity of bacterial endosymbionts of environmental acanthamoeba isolates. Appl Environ Microbiol 2008; 74:5822-31. [PMID: 18641160 PMCID: PMC2547052 DOI: 10.1128/aem.01093-08] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 07/11/2008] [Indexed: 11/20/2022] Open
Abstract
Free-living amoebae are frequent hosts for bacterial endosymbionts. In this study, the symbionts of eight novel environmental Acanthamoeba strains isolated from different locations worldwide were characterized. Phylogenetic analysis revealed that they were related to one of four evolutionary lineages of amoeba symbionts recognized previously. This study provides evidence for the existence of only a small number of phylogenetically well-separated groups of obligate intracellular endosymbionts of acanthamoebae with global distribution.
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MESH Headings
- Acanthamoeba/genetics
- Acanthamoeba/microbiology
- Animals
- Bacteria/classification
- Bacteria/genetics
- Biodiversity
- DNA, Bacterial/genetics
- DNA, Protozoan/genetics
- Genes, Bacterial
- Genes, Protozoan
- Genes, rRNA
- Geologic Sediments/microbiology
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Symbiosis
- Water Microbiology
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Affiliation(s)
- Stephan Schmitz-Esser
- Department of Microbial Ecology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
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44
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Haider S, Collingro A, Walochnik J, Wagner M, Horn M. Chlamydia-like bacteria in respiratory samples of community-acquired pneumonia patients. FEMS Microbiol Lett 2008; 281:198-202. [PMID: 18312573 DOI: 10.1111/j.1574-6968.2008.01099.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Chlamydia-like bacteria, obligate intracellular relatives of Chlamydia trachomatis and Chlamydophila pneumoniae, are widely distributed in nature. Using a two-step nested and semi-nested PCR approach targeting the 16S rRNA gene, we found DNA of Chlamydia-like bacteria in respiratory samples from patients with community-acquired pneumonia. Of 387 cases tested, four (1.03%) tested positive if only sequences showing less than 99.9% 16S rRNA gene sequence similarity to known Chlamydiae were considered. These included for the first time Protochlamydia amoebophila, Waddlia chondrophila, and 'Candidatus Rhabdochlamydia porcellionis'-related sequences. This study extends previous findings suggesting an association of Chlamydia-like bacteria with respiratory disease, but a causal link between these microorganisms and respiratory tract infections has yet to be established.
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Affiliation(s)
- Susanne Haider
- Department of Microbial Ecology, University of Vienna, Althanstrasse, Vienna, Austria
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45
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Thomas V, Casson N, Greub G. Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture. Environ Microbiol 2006; 8:2125-35. [PMID: 17107554 DOI: 10.1111/j.1462-2920.2006.01094.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Accumulating evidence supports a role for Chlamydia-related organisms as emerging pathogens for human and animals. Assessment of their pathogenicity requires strain availability, at least for animal models and serological studies. As these obligate intracellular species are able to grow inside amoebae, we used co-culture with Acanthamoeba castellanii in an attempt to recover new Chlamydia-related species from river water. We isolated two strains from eight water samples. The first strain is a new Parachlamydia acanthamoebae strain that differs from previously described isolates by only two bases in the complete 16S rRNA gene sequence. The second isolate is the first representative of a new Chlamydiales family, as demonstrated by genetic and phylogenetic analyses of the 16S rRNA, 23S rRNA, ADP/ATP translocase and RnpB encoding genes. Using fluorescent in situ hybridization and electron microscopy, we demonstrated that it grows in high numbers in amoebae, where it exhibits a Chlamydia-like developmental cycle with reticulate bodies and star-like elementary bodies. Based on these results, we propose to name this new species 'Criblamydia sequanensis'. This work confirmed that amoebal co-culture is a relevant method to isolate new chlamydiae, and that it can be successfully applied to ecosystems colonized with a complex microbial community.
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Affiliation(s)
- Vincent Thomas
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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46
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Haferkamp I, Schmitz-Esser S, Wagner M, Neigel N, Horn M, Neuhaus HE. Tapping the nucleotide pool of the host: novel nucleotide carrier proteins of Protochlamydia amoebophila. Mol Microbiol 2006; 60:1534-45. [PMID: 16796686 PMCID: PMC1513512 DOI: 10.1111/j.1365-2958.2006.05193.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protochlamydia amoebophila UWE25 is related to the Chlamydiaceae comprising major pathogens of humans, but thrives as obligate intracellular symbiont in the protozoan host Acanthamoeba sp. The genome of P. amoebophila encodes five paralogous carrier proteins belonging to the nucleotide transporter (NTT) family. Here we report on three P. amoebophila NTT isoforms, PamNTT2, PamNTT3 and PamNTT5, which possess several conserved amino acid residues known to be critical for nucleotide transport. We demonstrated that these carrier proteins are able to transport nucleotides, although substrate specificities and mode of transport differ in an unexpected manner and are unique among known NTTs. PamNTT2 is a counter exchange transporter exhibiting submillimolar apparent affinities for all four RNA nucleotides, PamNTT3 catalyses an unidirectional proton-coupled transport confined to UTP, whereas PamNTT5 mediates a proton-energized GTP and ATP import. All NTT genes of P. amoebophila are transcribed during intracellular multiplication in acanthamoebae. The biochemical characterization of all five NTT proteins from P. amoebophila in this and previous studies uncovered that these metabolically impaired bacteria are intimately connected with their host cell's metabolism in a surprisingly complex manner.
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Affiliation(s)
- Ilka Haferkamp
- Pflanzenphysiologie, Technische Universität KaiserslauternErwin Schrödinger Str., D-67653 Kaiserslautern, Germany
| | | | - Michael Wagner
- Department für Mikrobielle Ökologie, Universität WienA-1090 Vienna, Austria
| | - Nadjeschka Neigel
- Pflanzenphysiologie, Technische Universität KaiserslauternErwin Schrödinger Str., D-67653 Kaiserslautern, Germany
| | - Matthias Horn
- Department für Mikrobielle Ökologie, Universität WienA-1090 Vienna, Austria
- For correspondence. E-mail ; Tel. (+43) 1 4277 54393; Fax (+43) 1 4277 54389
| | - H Ekkehard Neuhaus
- Pflanzenphysiologie, Technische Universität KaiserslauternErwin Schrödinger Str., D-67653 Kaiserslautern, Germany
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Thomas V, Herrera-Rimann K, Blanc DS, Greub G. Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network. Appl Environ Microbiol 2006; 72:2428-38. [PMID: 16597941 PMCID: PMC1449017 DOI: 10.1128/aem.72.4.2428-2438.2006] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Free-living amoebae (FLA) are ubiquitous organisms that have been isolated from various domestic water systems, such as cooling towers and hospital water networks. In addition to their own pathogenicity, FLA can also act as Trojan horses and be naturally infected with amoeba-resisting bacteria (ARB) that may be involved in human infections, such as pneumonia. We investigated the biodiversity of bacteria and their amoebal hosts in a hospital water network. Using amoebal enrichment on nonnutrient agar, we isolated 15 protist strains from 200 (7.5%) samples. One thermotolerant Hartmannella vermiformis isolate harbored both Legionella pneumophila and Bradyrhizobium japonicum. By using amoebal coculture with axenic Acanthamoeba castellanii as the cellular background, we recovered at least one ARB from 45.5% of the samples. Four new ARB isolates were recovered by culture, and one of these isolates was widely present in the water network. Alphaproteobacteria (such as Rhodoplanes, Methylobacterium, Bradyrhizobium, Afipia, and Bosea) were recovered from 30.5% of the samples, mycobacteria (Mycobacterium gordonae, Mycobacterium kansasii, and Mycobacterium xenopi) were recovered from 20.5% of the samples, and Gammaproteobacteria (Legionella) were recovered from 5.5% of the samples. No Chlamydia or Chlamydia-like organisms were recovered by amoebal coculture or detected by PCR. The observed strong association between the presence of amoebae and the presence of Legionella (P < 0.001) and mycobacteria (P = 0.009) further suggests that FLA are a reservoir for these ARB and underlines the importance of considering amoebae when water control measures are designed.
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Affiliation(s)
- Vincent Thomas
- Center for Research on Intracellular Bacteria, Institute of Microbiology, CHUV Hospital, Bugnon 46, 1011 Lausanne, Switzerland
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48
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Wagner M, Horn M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 2006; 17:241-9. [PMID: 16704931 DOI: 10.1016/j.copbio.2006.05.005] [Citation(s) in RCA: 321] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 05/03/2006] [Accepted: 05/05/2006] [Indexed: 01/20/2023]
Abstract
In the rRNA-based tree of life four bacterial phyla, comprising the Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae, form together with the candidate phyla Poribacteria and OP3 a monophyletic group referred to as the PVC superphylum. This assemblage contains organisms that possess dramatically different lifestyles and which colonize sharply contrasting habitats. Some members of this group are among the most successful human pathogens, others are abundant soil microbes, and others still are of major importance for the marine nitrogen cycle and hold much promise for sustainable wastewater treatment. Recent comparative genomic and metagenomic analyses of a few representatives of this group revealed many unusual features and generated unexpected hypotheses regarding their physiology, some of which have already been confirmed experimentally. Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance.
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Affiliation(s)
- Michael Wagner
- Department of Microbial Ecology, University of Vienna, Austria.
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49
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Corsaro D, Greub G. Pathogenic potential of novel Chlamydiae and diagnostic approaches to infections due to these obligate intracellular bacteria. Clin Microbiol Rev 2006; 19:283-97. [PMID: 16614250 PMCID: PMC1471994 DOI: 10.1128/cmr.19.2.283-297.2006] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel chlamydiae are newly recognized members of the phylum Chlamydiales that are only distantly related to the classic Chlamydiaceae, i.e., Chlamydia and Chlamydophila species. They also exhibit an obligate biphasic intracellular life cycle within eukaryote host cells. Some of these new chlamydiae are currently considered potential emerging human and/or animal pathogens. Parachlamydia acanthamoebae and Simkania negevensis are both emerging respiratory human pathogens, Waddlia chondrophila could be a novel abortigenic bovine agent, and Piscichlamydia salmonis has recently been identified as an agent of the gill epitheliocystis in the Atlantic salmon. Fritschea spp. and Rhabdochlamydia spp. seem to be confined to arthropods, but some evidence for human exposure exists. In this review, we first summarize the data supporting a pathogenic potential of the novel chlamydiae for humans and other vertebrates and the interactions that most of these chlamydiae have with free-living amoebae. We then review the diagnostic approaches to infections potentially due to the novel chlamydiae, especially focusing on the currently available PCR-based protocols, mammalian cell culture, the amoebal coculture system, and serology.
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Affiliation(s)
- Daniele Corsaro
- Chlamydia Research Association, 12, rue du Maconnais, 54500 Vandoeuvres-les-Nancy, France
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50
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Apfalter P. Chlamydia pneumoniae, stroke, and serological associations: anything learned from the atherosclerosis-cardiovascular literature or do we have to start over again? Stroke 2006; 37:756-8. [PMID: 16424375 DOI: 10.1161/01.str.0000201970.88546.5e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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