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Krieger M, AbdelRahman YM, Choi D, Palmer EA, Yoo A, McGuire S, Kreth J, Merritt J. Stratification of Fusobacterium nucleatum by local health status in the oral cavity defines its subspecies disease association. Cell Host Microbe 2024; 32:479-488.e4. [PMID: 38479393 PMCID: PMC11018276 DOI: 10.1016/j.chom.2024.02.010] [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: 11/14/2023] [Revised: 12/24/2023] [Accepted: 02/16/2024] [Indexed: 03/25/2024]
Abstract
The ubiquitous inflammophilic oral pathobiont Fusobacterium nucleatum (Fn) is widely recognized for its strong association with inflammatory dysbiotic diseases and cancer. Fn is subdivided into four subspecies, which are historically considered functionally interchangeable in the oral cavity. To test this assumption, we analyzed patient-matched dental plaque and odontogenic abscess clinical specimens and examined whether an inflammatory environment selects for/against particular Fn subspecies. Dental plaque harbored a greater diversity of fusobacteria, with Fn. polymorphum dominating, whereas odontogenic abscesses were exceptionally biased for the largely uncharacterized organism Fn. animalis. Comparative genomic analyses revealed significant genotypic distinctions among Fn subspecies that correlate with their preferred ecological niches and support a taxonomic reassignment of each as a distinct Fusobacterium species. Despite originating as a low-abundance organism in dental plaque, Fn. animalis typically outcompetes other oral fusobacteria within the inflammatory abscess environment, which may explain its prevalence in other oral and extraoral diseases.
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Affiliation(s)
- Madeline Krieger
- Division of Biomaterial and Biomedical Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Yasser M AbdelRahman
- Division of Biomaterial and Biomedical Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA; Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Giza, Egypt; Predicine, Hayward, CA, USA
| | - Dongseok Choi
- Department of Community Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA; School of Public Health, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Elizabeth A Palmer
- Division of Pediatric Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Anna Yoo
- Division of Pediatric Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Sean McGuire
- Division of Pediatric Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Jens Kreth
- Division of Biomaterial and Biomedical Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Justin Merritt
- Division of Biomaterial and Biomedical Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR, USA.
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Krieger M, AbdelRahman YM, Choi D, Palmer EA, Yoo A, McGuire S, Kreth J, Merritt J. The prevalence of Fusobacterium nucleatum subspecies in the oral cavity stratifies by local health status. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.563997. [PMID: 37961321 PMCID: PMC10634819 DOI: 10.1101/2023.10.25.563997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The ubiquitous inflammophilic pathobiont Fusobacterium nucleatum is widely recognized for its strong association with a variety of human dysbiotic diseases such as periodontitis and oral/extraoral abscesses, as well as multiple types of cancer. F. nucleatum is currently subdivided into four subspecies: F. nucleatum subspecies nucleatum (Fn. nucleatum), animalis (Fn. animalis), polymorphum (Fn. polymorphum), and vincentii/fusiforme (Fn. vincentii). Although these subspecies have been historically considered as functionally interchangeable in the oral cavity, direct clinical evidence is largely lacking for this assertion. Consequently, we assembled a collection of oral clinical specimens to determine whether F. nucleatum subspecies prevalence in the oral cavity stratifies by local oral health status. Patient-matched clinical specimens of both disease-free dental plaque and odontogenic abscess were analyzed with newly developed culture-dependent and culture-independent approaches using 44 and 60 oral biofilm/tooth abscess paired specimens, respectively. Most oral cavities were found to simultaneously harbor multiple F. nucleatum subspecies, with a greater diversity present within dental plaque compared to abscesses. In dental plaque, Fn. polymorphum is clearly the dominant organism, but this changes dramatically within odontogenic abscesses where Fn. animalis is heavily favored over all other fusobacteria. Surprisingly, the most commonly studied F. nucleatum subspecies, Fn. nucleatum, is only a minor constituent in the oral cavity. To gain further insights into the genetic basis for these phenotypes, we subsequently performed pangenome, phylogenetic, and functional enrichment analyses of oral fusobacterial genomes using the Anvi'o platform, which revealed significant genotypic distinctions among F. nucleatum subspecies. Accordingly, our results strongly support a taxonomic reassignment of each F. nucleatum subspecies into distinct Fusobacterium species. Of these, Fn. animalis should be considered as the most clinically relevant at sites of active inflammation, despite being among the least characterized oral fusobacteria.
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Affiliation(s)
- Madeline Krieger
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Yasser M. AbdelRahman
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Dongseok Choi
- Department of Community Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
- School of Public Health, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Elizabeth A. Palmer
- Division of Pediatric Dentistry, Department of Regenerative and Reconstructive Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Anna Yoo
- Division of Pediatric Dentistry, Department of Regenerative and Reconstructive Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Sean McGuire
- Division of Pediatric Dentistry, Department of Regenerative and Reconstructive Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
- Division of Pediatric Dentistry, Department of Regenerative and Reconstructive Sciences, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR, USA
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Eisenberg T, Fawzy A, Nicklas W, Semmler T, Ewers C. Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis. BMC Genomics 2016; 17:864. [PMID: 27809782 PMCID: PMC5093955 DOI: 10.1186/s12864-016-3206-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/25/2016] [Indexed: 11/30/2022] Open
Abstract
Background The Leptotrichiaceae are a family of fairly unnoticed bacteria containing both microbiota on mucous membranes as well as significant pathogens such as Streptobacillus moniliformis, the causative organism of streptobacillary rat bite fever. Comprehensive genomic studies in members of this family have so far not been carried out. We aimed to analyze 47 genomes from 20 different member species to illuminate phylogenetic aspects, as well as genomic and discriminatory properties. Results Our data provide a novel and reliable basis of support for previously established phylogeny from this group and give a deeper insight into characteristics of genome structure and gene functions. Full genome analyses revealed that most S. moniliformis strains under study form a heterogeneous population without any significant clustering. Analysis of infra-species variability for this highly pathogenic rat bite fever organism led to the detection of three specific variable number tandem analysis loci with high discriminatory power. Conclusions This highly useful and economical tool can be directly employed in clinical samples without laborious prior cultivation. Our and prospective case-specific data can now easily be compared by using a newly established MLVA database in order to gain a better insight into the epidemiology of this presumably under-reported zoonosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3206-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Eisenberg
- Abteilung Veterinärmedizin, Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60/H13, D-35392, Giessen, Germany.
| | - Ahmad Fawzy
- Abteilung Veterinärmedizin, Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60/H13, D-35392, Giessen, Germany.,Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza Square, 12211, Egypt.,Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392, Giessen, Germany
| | - Werner Nicklas
- Deutsches Krebsforschungszentrum, D-69120, Heidelberg, Germany
| | | | - Christa Ewers
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392, Giessen, Germany
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Eisenberg T, Ewers C, Rau J, Akimkin V, Nicklas W. Approved and novel strategies in diagnostics of rat bite fever and other Streptobacillus infections in humans and animals. Virulence 2016; 7:630-48. [PMID: 27088660 DOI: 10.1080/21505594.2016.1177694] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rat bite fever (RBF), a worldwide occurring and most likely under-diagnosed zoonosis caused by Streptobacillus moniliformis, represents the most prominent disease of Streptobacillus infections. Recently, novel members have been described, from which a reservoir in rats and other animal species and a zoonotic potential can be assumed. Despite regularly published case reports, diagnostics of RBF continues to represent a 'diagnostic dilemma', because the mostly applied 16S rRNA sequence analysis may be uncertain for proper pathogen identification. Virtually nothing is known regarding prevalence in humans and animal reservoirs. For a realistic assessment of the pathogen's spread, epidemiology and virulence traits, future studies should focus on the genomic background of Streptobacillus. Full genome sequence analyses of a representative collection of strains might facilitate to unequivocally identify and type isolates. Prevalence studies using selective enrichment mechanisms may also enable the isolation of novel strains and candidate species of this neglected group of microorganisms.
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Affiliation(s)
| | - Christa Ewers
- b Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen , Gießen , Germany
| | - Jörg Rau
- c Chemisches und Veterinäruntersuchungsamt Stuttgart , Fellbach , Germany
| | - Valerij Akimkin
- c Chemisches und Veterinäruntersuchungsamt Stuttgart , Fellbach , Germany
| | - Werner Nicklas
- d Deutsches Krebsforschungszentrum , Heidelberg , Germany
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5
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Richards L, Li M, van Esch B, Garssen J, Folkerts G. The effects of short-chain fatty acids on the cardiovascular system. PHARMANUTRITION 2016. [DOI: 10.1016/j.phanu.2016.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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6
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Zuo G, Zhi X, Xu Z, Hao B. LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:94-102. [PMID: 27018315 PMCID: PMC4880948 DOI: 10.1016/j.gpb.2015.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/04/2015] [Accepted: 12/21/2015] [Indexed: 11/18/2022]
Abstract
We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China
| | - Xiaoyang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
| | - Zhao Xu
- Thermo Fisher Scientific, South San Francisco, CA 94080, USA
| | - Bailin Hao
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
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7
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Eisenberg T, Nicklas W, Mauder N, Rau J, Contzen M, Semmler T, Hofmann N, Aledelbi K, Ewers C. Phenotypic and Genotypic Characteristics of Members of the Genus Streptobacillus. PLoS One 2015; 10:e0134312. [PMID: 26252790 PMCID: PMC4529157 DOI: 10.1371/journal.pone.0134312] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Streptobacillus (S.) remained monotypic for almost 90 years until two new species were recently described. The type species, S. moniliformis, is one of the two etiological agents of rat bite fever, an under-diagnosed, worldwide occurring zoonosis. In a polyphasic approach field isolates and reference strains of S. moniliformis, S. hongkongensis, S. felis as well as divergent isolates were characterized by comparison of molecular data (n = 29) and from the majority also by their physiological as well as proteomic properties (n = 22). Based on growth-independent physiological profiling using VITEK2-compact, API ZYM and the Micronaut system fastidious growth-related difficulties could be overcome and streptobacilli could definitively be typed despite generally few differences. While differing in their isolation sites and dates, S. moniliformis isolates were found to possess almost identical spectra in matrix-assisted laser desorption ionization-time of flight mass spectrometry and Fourier transform infrared spectroscopy. Spectroscopic methods facilitated differentiation of S. moniliformis, S. hongkongensis and S. felis as well as one divergent isolate. Sequencing of 16S rRNA gene as well as functional genes groEL, recA and gyrB revealed only little intraspecific variability, but generally proved suitable for interspecies discrimination between all three taxa and two groups of divergent isolates.
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Affiliation(s)
- Tobias Eisenberg
- Hessian State Laboratory, Department of Veterinary Medicine, Giessen, Germany
- * E-mail:
| | | | - Norman Mauder
- Chemical and Veterinary Investigation Office (CVUA) Stuttgart, Fellbach, Germany
| | - Jörg Rau
- Chemical and Veterinary Investigation Office (CVUA) Stuttgart, Fellbach, Germany
| | - Matthias Contzen
- Chemical and Veterinary Investigation Office (CVUA) Stuttgart, Fellbach, Germany
| | | | - Nicola Hofmann
- Institute for Multiphase Processes, Leibniz University, Hannover, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
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8
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Gonzales-Marin C, Spratt DA, Allaker RP. Maternal oral origin of Fusobacterium nucleatum in adverse pregnancy outcomes as determined using the 16S-23S rRNA gene intergenic transcribed spacer region. J Med Microbiol 2012; 62:133-144. [PMID: 23002071 DOI: 10.1099/jmm.0.049452-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Fusobacterium nucleatum, a common Gram-negative anaerobe prevalent in the oral cavity, possesses the ability to colonize the amniotic cavity and the fetus. However, F. nucleatum may also be part of the vaginal microbiota from where it could reach the amniotic tissues. Due to the heterogeneity of F. nucleatum, consisting of five subspecies, analysis at the subspecies/strain level is desirable to determine its precise origin. The aims of this study were: (i) to evaluate the use of the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region as a tool to differentiate subspecies of F. nucleatum, and (ii) to design a simplified technique based on the ITS to determine the origin of F. nucleatum strains associated with adverse pregnancy outcomes. Amplified fragments of the 16S-23S rRNA gene ITS region corresponding to the five subspecies of F. nucleatum were subjected to cloning and sequencing to characterize the different ribosomal operons of the subspecies. Distinctive length and sequence patterns with potential to be used for identification of the subspecies/strain were identified. These were used to evaluate the origin of F. nucleatum identified in neonatal gastric aspirates (swallowed amniotic fluid) by sequence comparisons with the respective oral and vaginal maternal samples. A simplified technique using a strain-specific primer in a more sensitive nested PCR was subsequently developed to analyse ten paired neonatal-maternal samples. Analysing the variable fragment of the ITS region allowed the identification of F. nucleatum subsp. polymorphum from an oral origin as potentially being involved in neonatal infections. Using a strain-specific primer, the F. nucleatum subsp. polymorphum strain was detected in both neonatal gastric aspirates and maternal oral samples in cases of preterm birth from mothers presenting with localized periodontal pockets. Interestingly, the same strain was not present in the vaginal sample of any case investigated. The 16S-23S rRNA gene ITS can be a useful tool to determine the origin of F. nucleatum. The results of this study strongly indicate that F. nucleatum subsp. polymorphum of oral origin could be involved with pregnancy complications.
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Affiliation(s)
- Cecilia Gonzales-Marin
- Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - David A Spratt
- Division of Microbial Diseases, Eastman Dental Institute, University College London, 256 Gray's Inn Road, London WC1X 8LD, UK
| | - Robert P Allaker
- Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
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Yang HM, Lou K, Sun J, Zhang T, Ma XL. Prokaryotic diversity of an active mud volcano in the Usu City of Xinjiang, China. J Basic Microbiol 2011; 52:79-85. [PMID: 21656823 DOI: 10.1002/jobm.201100074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 03/18/2011] [Indexed: 11/12/2022]
Abstract
The Usu mud volcanoes are the largest group of terrestrial mud volcanoes in China. The volcanoes are located in a typical arid and semi-arid region, and the group consists of 36 erupting active mud volcanoes. In this study, the prokaryotic diversity and community structure in the sediment of an active mud volcano were investigated by constructing bacterial and archaeal clone libraries of the 16S rRNA gene. A total of 100 bacterial and 100 archaeal clones were analysed and found to comprise 11 and 7 distinct phylotypes, respectively. The bacterial phylotypes were classified into three phyla (Proteobacteria, Actinobacteria, and Fusobacteria). Of these, Proteobacteria were the most abundant bacterial group, with Deltaproteobacteria dominating the sediment community, and these were affiliated with the order Desulfuromonadales. The archaeal phylotypes were all closely related to uncultivated species, and the majority of the members were related to the orders Methanosarcinales and Halobacteriales of the Euryarchaeota originating from methane hydrate bearing or alkaline sediments. The rest of the archaeal phylotypes belonged to the phylum Crenarchaeota, with representatives from similar habitats. These results suggested that a large number of novel microbial groups and potential methanogenesis may exist in this unique ecosystem.
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Affiliation(s)
- Hong-Mei Yang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
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10
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Han YW. Laboratory maintenance of fusobacteria. CURRENT PROTOCOLS IN MICROBIOLOGY 2008; Chapter 13:Unit 13A.1. [PMID: 18770577 DOI: 10.1002/9780471729259.mc13a01s00] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit describes routine laboratory handling of fusobacteria. Different media that can be used to grow or enrich Fusobacterium nucleatum and other species of this genus are described. The growth and stock conditions as well as the susceptibility of F. nucleatum to oxygen in a pure culture are also discussed.
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Affiliation(s)
- Yiping W Han
- Case Western Reserve University, Cleveland, Ohio, USA
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11
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Han YW, Ikegami A, Rajanna C, Kawsar HI, Zhou Y, Li M, Sojar HT, Genco RJ, Kuramitsu HK, Deng CX. Identification and characterization of a novel adhesin unique to oral fusobacteria. J Bacteriol 2005; 187:5330-40. [PMID: 16030227 PMCID: PMC1196005 DOI: 10.1128/jb.187.15.5330-5340.2005] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fusobacterium nucleatum is a gram-negative anaerobe that is prevalent in periodontal disease and infections of different parts of the body. The organism has remarkable adherence properties, binding to partners ranging from eukaryotic and prokaryotic cells to extracellular macromolecules. Understanding its adherence is important for understanding the pathogenesis of F. nucleatum. In this study, a novel adhesin, FadA (Fusobacterium adhesin A), was demonstrated to bind to the surface proteins of the oral mucosal KB cells. FadA is composed of 129 amino acid (aa) residues, including an 18-aa signal peptide, with calculated molecular masses of 13.6 kDa for the intact form and 12.6 kDa for the secreted form. It is highly conserved among F. nucleatum, Fusobacterium periodonticum, and Fusobacterium simiae, the three most closely related oral species, but is absent in the nonoral species, including Fusobacterium gonidiaformans, Fusobacterium mortiferum, Fusobacterium naviforme, Fusobacterium russii, and Fusobacterium ulcerans. In addition to FadA, F. nucleatum ATCC 25586 and ATCC 49256 also encode two paralogues, FN1529 and FNV2159, each sharing 31% identity with FadA. A double-crossover fadA deletion mutant, F. nucleatum 12230-US1, was constructed by utilizing a novel sonoporation procedure. The mutant had a slightly slower growth rate, yet its binding to KB and Chinese hamster ovarian cells was reduced by 70 to 80% compared to that of the wild type, indicating that FadA plays an important role in fusobacterial colonization in the host. Furthermore, due to its uniqueness to oral Fusobacterium species, fadA may be used as a marker to detect orally related fusobacteria. F. nucleatum isolated from other parts of the body may originate from the oral cavity.
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Affiliation(s)
- Yiping W Han
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905, USA.
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12
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Narongwanichgarn W, Misawa N, Jin JH, Amoako KK, Kawaguchi E, Shinjo T, Haga T, Goto Y. Specific detection and differentiation of two subspecies of Fusobacterium necrophorum by PCR. Vet Microbiol 2003; 91:183-95. [PMID: 12458167 DOI: 10.1016/s0378-1135(02)00295-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phylogenic relationships of two subspecies of Fusobacterium necrophorum were investigated by randomly amplified polymorphism DNA-polymerase chain reaction (RAPD-PCR). With each of the 12 random primers, the DNA fingerprints generated were subjected to cluster analysis for dendrograms. The analysis indicated that twelve strains were organized into two major clusters, and that all strains of each subspecies were confined to one cluster. Furthermore, two of the random primers examined each generated a unique band in F. n. necrophorum strains. We cloned these specific bands and determined the nucleotide sequences. A search for amino acid sequence homologies revealed that the two specific fragments had significant homology to the rpoB gene of Lactococcus lactis subsp. lactis and the hemagglutinin-related protein gene of Ralstonia solanacearum, respectively. New specific primers designed for the rpoB gene were able to amplify 900bp fragments from both subspecies. However, the specific primers designed for the hemagglutinin-related protein gene amplified only a 250bp fragment of the genome of the F. n. necrophorum strains, suggesting that this gene is unique to F. n. necrophorum. These results were further confirmed by dot blot hybridization. Finally, a one-step duplex PCR technique in a single tube for the rapid detection and differentiation of the F. necrophorum subspecies was developed.
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Affiliation(s)
- Wonganun Narongwanichgarn
- Department of Veterinary Microbiology, Faculty of Agriculture, Miyazaki University, 1-1 Gakuen Kibanadai Nishi, 889-2192, Miyazaki, Japan
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13
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Narayanan SK, Nagaraja TG, Chengappa MM, Stewart GC. Cloning, sequencing, and expression of the leukotoxin gene from Fusobacterium necrophorum. Infect Immun 2001; 69:5447-55. [PMID: 11500416 PMCID: PMC98656 DOI: 10.1128/iai.69.9.5447-5455.2001] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fusobacterium necrophorum is a gram-negative, rod-shaped, anaerobic bacterium that is a primary or secondary etiological agent in a variety of necrotic purulent infections in animals and humans. Included are diseases of cattle such as liver abscesses and foot rot, which have economically important consequences for the cattle industry. The major virulence factor of this bacterium is leukotoxin, a secreted protein of high molecular weight active against leukocytes from ruminants. The screening of a genomic DNA library with polyclonal antisera raised against native affinity-purified leukotoxin and further extension of the sequence using inverse PCR led to the cloning of the entire leukotoxin gene. The leukotoxin gene open reading frame (ORF; lktA) consists of 9,726 bp and encodes a protein of 3,241 amino acids with an overall molecular weight of 335,956. The leukotoxin does not have sequence similarity with any other bacterial leukotoxin. Five truncated overlapping polypeptides covering the whole lktA ORF were used to immunize rabbits. In Western blot assays, polyclonal antisera raised against all five truncated polypeptides recognized affinity-purified leukotoxin from F. necrophorum culture supernatant in a Western blot assay. Antisera directed against two of the five polypeptides had neutralizing activity against the toxin. The entire leukotoxin ORF was expressed in Escherichia coli. Flow-cytometric analysis showed that the recombinant leukotoxin was active against bovine polymorphonuclear leukocytes and was inhibited with antiserum raised against the F. necrophorum leukotoxin. Southern blot hybridization analysis revealed different patterns of lktA hybridizing bands between isolates of the two subspecies of F. necrophorum.
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Affiliation(s)
- S K Narayanan
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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14
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Barcenilla A, Pryde SE, Martin JC, Duncan SH, Stewart CS, Henderson C, Flint HJ. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol 2000; 66:1654-61. [PMID: 10742256 PMCID: PMC92037 DOI: 10.1128/aem.66.4.1654-1661.2000] [Citation(s) in RCA: 691] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/1999] [Accepted: 01/28/2000] [Indexed: 11/20/2022] Open
Abstract
Butyrate is a preferred energy source for colonic epithelial cells and is thought to play an important role in maintaining colonic health in humans. In order to investigate the diversity and stability of butyrate-producing organisms of the colonic flora, anaerobic butyrate-producing bacteria were isolated from freshly voided human fecal samples from three healthy individuals: an infant, an adult omnivore, and an adult vegetarian. A second isolation was performed on the same three individuals 1 year later. Of a total of 313 bacterial isolates, 74 produced more than 2 mM butyrate in vitro. Butyrate-producing isolates were grouped by 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphism analysis. The results indicate very little overlap between the predominant ribotypes of the three subjects; furthermore, the flora of each individual changed significantly between the two isolations. Complete sequences of 16S rDNAs were determined for 24 representative strains and subjected to phylogenetic analysis. Eighty percent of the butyrate-producing isolates fell within the XIVa cluster of gram-positive bacteria as defined by M. D. Collins et al. (Int. J. Syst. Bacteriol. 44:812-826, 1994) and A. Willems et al. (Int. J. Syst. Bacteriol. 46:195-199, 1996), with the most abundant group (10 of 24 or 42%) clustering with Eubacterium rectale, Eubacterium ramulus, and Roseburia cecicola. Fifty percent of the butyrate-producing isolates were net acetate consumers during growth, suggesting that they employ the butyryl coenzyme A-acetyl coenzyme A transferase pathway for butyrate production. In contrast, only 1% of the 239 non-butyrate-producing isolates consumed acetate.
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Affiliation(s)
- A Barcenilla
- Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, United Kingdom
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15
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Ramezani M, MacIntosh SE, White RL. Utilization of D-amino acids by Fusobacterium nucleatum and Fusobacterium varium. Amino Acids 1999; 17:185-93. [PMID: 10524276 DOI: 10.1007/bf01361881] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The utilization of D- and L-amino acids with acidic, basic or polar side chains was demonstrated by HPLC. Two species of the anaerobe Fusobacterium utilized D-lysine and the L isomers of glutamate, glutamine, histidine, lysine and serine. Only F. varium used L-arginine, D-glutamate and D-serine as substrates, whereas F. nucleatum specifically utilized D-histidine and D-glutamine. D-Glutamate accumulated in F. nucleatum cultures supplemented with D-glutamine, and ornithine was detected when either DL- or L-arginine was included in F. varium cultures. Based on literature precedents, D-glutamate and D-histidine are isomerized to their L isomers prior to degradation, but separate catabolic pathways are possible for each enantiomer of lysine and serine.
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Affiliation(s)
- M Ramezani
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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16
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Characteristics of Fusobacterium ulcerans, a New and Unusual Species Compared with Fusobacterium varium and Fusobacterium mortiferum. Anaerobe 1999. [DOI: 10.1006/anae.1999.0201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Olsen I, Shah HN, Gharbia SE. Taxonomy and biochemical characteristics of Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis. Periodontol 2000 1999; 20:14-52. [PMID: 10522221 DOI: 10.1111/j.1600-0757.1999.tb00156.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- I Olsen
- Department of Oral Biology, Dental Faculty, University of Oslo, Norway
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18
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Logan JM, Orange GV, Maggs AF. Identification of the cause of a brain abscess by direct 16S ribosomal DNA sequencing. J Infect 1999; 38:45-7. [PMID: 10090508 DOI: 10.1016/s0163-4453(99)90030-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We report the case of a young man who apparently suffered successive episodes of meningitis and cerebral abscess over a 1-month period, both of which were diagnosed by two different molecular approaches; PCR for Neisseria meningitidis IS1106 from CSF and 16S rRNA gene sequencing on a specimen of brain pus. In each case, cultures were negative due to prior antibiotic therapy.
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Affiliation(s)
- J M Logan
- Department of Medical Microbiology, University of Dundee Medical School, Ninewells Hospital, UK
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19
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Abstract
The pathogenic potential of Fusobacterium nucleatum and its significance in the development of periodontal diseases, as well as in infections in other organs, have gained new interest for several reasons. First, this bacterium has the potential to be pathogenic because of its number and frequency in periodontal lesions, its production of tissue irritants, its synergism with other bacteria in mixed infections, and its ability to form aggregates with other suspected pathogens in periodontal disease and thus act as a bridge between early and late colonizers on the tooth surface. Second, of the microbial species that are statistically associated with periodontal disease, F. nucleatum is the most common in clinical infections of other body sites. Third, during the past few years, new techniques have made it possible to obtain more information about F. nucleatum on the genetic level, thereby also gaining better knowledge of the structure and functions of the outer membrane proteins (OMPs). OMPs are of great interest with respect to coaggregation, cell nutrition, and antibiotic susceptibility. This review covers what is known to date about F. nucleatum in general, such as taxonomy and biology, with special emphasis on its pathogenic potential. Its possible relationship to other periodontal bacteria in the development of periodontal diseases and the possible roles played by OMPs are considered.
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20
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Bolstad AI, Jensen HB, Bakken V. Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum. Clin Microbiol Rev 1996; 9:55-71. [PMID: 8665477 PMCID: PMC172882 DOI: 10.1128/cmr.9.1.55] [Citation(s) in RCA: 266] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The pathogenic potential of Fusobacterium nucleatum and its significance in the development of periodontal diseases, as well as in infections in other organs, have gained new interest for several reasons. First, this bacterium has the potential to be pathogenic because of its number and frequency in periodontal lesions, its production of tissue irritants, its synergism with other bacteria in mixed infections, and its ability to form aggregates with other suspected pathogens in periodontal disease and thus act as a bridge between early and late colonizers on the tooth surface. Second, of the microbial species that are statistically associated with periodontal disease, F. nucleatum is the most common in clinical infections of other body sites. Third, during the past few years, new techniques have made it possible to obtain more information about F. nucleatum on the genetic level, thereby also gaining better knowledge of the structure and functions of the outer membrane proteins (OMPs). OMPs are of great interest with respect to coaggregation, cell nutrition, and antibiotic susceptibility. This review covers what is known to date about F. nucleatum in general, such as taxonomy and biology, with special emphasis on its pathogenic potential. Its possible relationship to other periodontal bacteria in the development of periodontal diseases and the possible roles played by OMPs are considered.
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Affiliation(s)
- A I Bolstad
- Department of Periodontology, University of Bergen, Norway
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21
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Bolstad AI, Høgh BT, Jensen HB. Molecular characterization of a 40-kDa outer membrane protein, FomA, of Fusobacterium periodonticum and comparison with Fusobacterium nucleatum. ORAL MICROBIOLOGY AND IMMUNOLOGY 1995; 10:257-64. [PMID: 8596666 DOI: 10.1111/j.1399-302x.1995.tb00151.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The 40 kDa-outer membrane protein FomA of Fusobacterium periodonticum ATCC 33693 was found to exhibit heat modifiable properties, typical for a porin, and N-terminal sequencing indicated a close relationship to the porin FomA of Fusobacterium nucleatum. A polymerase chain reaction approach was therefore applied for sequencing the fomA gene of F. periodonticum, and nucleotide and deduced amino acid sequences were aligned and compared with the corresponding sequences of different strains of F. nucleatum. In all strains we found a common protein upstream of the fomA gene. The noncoding area upstream of the putative -35 region of the F. periodonticum fomA gene exhibited little sequence similarity with the F. nucleatum gene. The transcriptional unit of FomA, on the other hand, was very similar, with the similarities concentrated in domains that were interspersed with hypervariable regions. A topology model was made and compared with those made for F. nucleatum. This indicated that the great similarities reside in the membrane-spanning segments of the protein, while most cell surface exposed loops were hypervariable. The results strongly support the proposed model for FomA and also indicate that these taxa are related but on a lower level than the subspecies level. The codon usage of F. periodonticum is comparable to that of F. nucleatum, and the triplet AGA is the only codon used for arginine.
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Affiliation(s)
- A I Bolstad
- Department of Biochemistry and Molecular Biology, School of Dentistry, University of Bergen, Norway
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22
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Relationship of a Novel Bacterial Fish Pathogen to Streptobacillus moniliformis and the Fusobacteria Group, based on 16S Ribosomal RNA Analysis. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80452-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Hodgson AL, Nicholson LA, Doran TJ, Corner LA. Restriction fragment length polymorphism analysis of Fusobacterium necrophorum using a novel repeat DNA sequence and a 16S rRNA gene probe. FEMS Microbiol Lett 1993; 107:205-10. [PMID: 8097174 DOI: 10.1111/j.1574-6968.1993.tb06031.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A repeated DNA sequence was isolated from Fusobacterium necrophorum biotype AB, strain FnS1. The repeated sequence shared considerable homology with the transposase gene from the Pseudomonas syringiae insertion sequence IS801. The repeat sequence was used together with a 16S ribosomal RNA gene probe to type F. necrophorum isolates using restriction fragment length polymorphisms. The probes revealed differences between several clinical isolates and will be useful tools to study the epidemiology of ovine foot abscess and other diseases caused by F. necrophorum.
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Affiliation(s)
- A L Hodgson
- CSIRO Division of Animal Health, Animal Health Research Laboratory, Parkville, Vic., Australia
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24
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Klees AG, Linder D, Buckel W. 2-Hydroxyglutaryl-CoA dehydratase from Fusobacterium nucleatum (subsp. nucleatum): an iron-sulfur flavoprotein. Arch Microbiol 1992; 158:294-301. [PMID: 1417419 DOI: 10.1007/bf00245248] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Anaerobically prepared cell-free extracts from Fusobacterium nucleatum contain 2-hydroxyglutaryl-CoA dehydratase with a specific activity of 20 nkat mg-1. The enzyme was purified 24-fold to a specific activity of 480 nkat mg-1 by anion exchange chromatography, gel filtration and chromatography on Blue-Sepharose. The activity of the purified enzyme was strictly dependent on the reductant Ti(III)citrate and stimulated 25-fold by 0.15 mM ATP and 5 mM MgCl2. ATP is hydrolysed to ADP during incubation with 2-hydroxyglutaryl-CoA dehydratase in the presence or absence of the substrate. The enzyme is extremely sensitive towards oxygen and is inhibited by 10 microM chloramphenicol, 10 microM 2,4-dinitrophenol or 0.15 mM hydroxylamine. The pure enzyme consists of three subunits alpha (49 kDa), beta (39 kDa) and gamma (24 kDa) in approximately equal amounts. In this respect the enzyme differs from the related 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans and lactyl-CoA dehydratase from Clostridium propionicum both of which are composed of only two subunits with sizes comparable to those of alpha and beta but require an additional protein for activity. The relative molecular mass of the native enzyme of about 100 kDa suggests a trimeric alpha beta gamma-structure. The homogeneous enzyme contains riboflavin (0.5 mol/112 kDa), iron and sulfur (3.5 mol/112 kDa each). Polyclonal antibodies directed against the 2-hydroxyglutaryl-CoA dehydratase from A. fermentans did not crossreact with cell free extracts or purified dehydratase from F. nucleatum. A comparison of the N-terminal amino acid sequences of the dehydratase subunits from A. fermentans and F. nucleatum, however, showed some similarities in the beta-subunits.
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Affiliation(s)
- A G Klees
- Laboratorium für Mikrobiologie des Fachbereichs Biologie, Philipps-Universität, Marburg, Federal Republic of Germany
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25
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O'Neill SL, Giordano R, Colbert AM, Karr TL, Robertson HM. 16S rRNA phylogenetic analysis of the bacterial endosymbionts associated with cytoplasmic incompatibility in insects. Proc Natl Acad Sci U S A 1992; 89:2699-702. [PMID: 1557375 PMCID: PMC48729 DOI: 10.1073/pnas.89.7.2699] [Citation(s) in RCA: 720] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bacterial endosymbionts of insects have long been implicated in the phenomenon of cytoplasmic incompatibility, in which certain crosses between symbiont-infected individuals lead to embryonic death or sex ratio distortion. The taxonomic position of these bacteria has, however, not been known with any certainty. Similarly, the relatedness of the bacteria infecting various insect hosts has been unclear. The inability to grow these bacteria on defined cell-free medium has been the major factor underlying these uncertainties. We circumvented this problem by selective PCR amplification and subsequent sequencing of the symbiont 16S rRNA genes directly from infected insect tissue. Maximum parsimony analysis of these sequences indicates that the symbionts belong in the alpha-subdivision of the Proteobacteria, where they are most closely related to the Rickettsia and their relatives. They are all closely related to each other and are assigned to the type species Wolbachia pipientis. Lack of congruence between the phylogeny of the symbionts and their insect hosts suggest that horizontal transfer of symbionts between insect species may occur. Comparison of the sequences for W. pipientis and for Wolbachia persica, an endosymbiont of ticks, shows that the genus Wolbachia is polyphyletic. A PCR assay based on 16S primers was designed for the detection of W. pipientis in insect tissue, and initial screening of insects indicates that cytoplasmic incompatibility may be a more general phenomenon in insects than is currently recognized.
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Affiliation(s)
- S L O'Neill
- Department of Entomology, University of Illinois, Urbana 61801
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