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Morrison AG, Sarkar S, Umar S, Lee STM, Thomas SM. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms 2023; 11:318. [PMID: 36838283 PMCID: PMC9962706 DOI: 10.3390/microorganisms11020318] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.
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Affiliation(s)
- Austin Gregory Morrison
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Shahid Umar
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
- 1717 Claflin Road, 136 Ackert Hall, Manhattan, KS 66506, USA
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Otolaryngology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- 3901 Rainbow Blvd., 4031 Wahl Hall East, MS 3040, Kansas City, KS 66160, USA
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2
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Kontro MH, Kirsi M, Laitinen SK. Exposure to bacterial and fungal bioaerosols in facilities processing biodegradable waste. Front Public Health 2022; 10:789861. [PMID: 36466510 PMCID: PMC9708704 DOI: 10.3389/fpubh.2022.789861] [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: 10/05/2021] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The aim of the study was to determine the exposure of workers within biodegradable waste processing facilities to bacteria and fungi to identify any exposures of potential concern to health. Occupational measurements were performed in six composting and three bioenergy (bioethanol or methane/biogas) producing facilities. Bioaerosols were measured from breathing zones with Button aerosol or open face cassette filter samplers, and swab specimens were taken from the nasal mucous membranes of the workers. Aspergillus fumigatus, Bacillus cereus group, Campylobacter spp., Salmonella spp., Streptomyces spp., and Yersinia spp. were determined by real-time polymerase chain reaction (qPCR). A. fumigatus, and mesophilic and thermophilic actinobacteria were also cultivated from filters. Bacterial airborne endotoxins collected by IOM samplers were analyzed using a Limulus assay. Bioaerosol levels were high, especially in composting compared to bioenergy producing facilities. Endotoxin concentrations in composting often exceeded the occupational exposure value of 90 EU/m3, which may be harmful to the health. In addition to endotoxins, the concentrations of A. fumigatus (up to 2.4 × 105 copies/m3) and actinobacteria/Streptomyces spp. (up to 1.6 × 106 copies/m3) in the air of composting facilities were often high. Microbial and endotoxin concentrations were typically highest in waste reception and pre-treatment, equal or decreased during processing and handling of treated waste, and lowest in wheel loader cabins and control rooms/outdoors. Still, the parameters measured in wheel loader cabins were often higher than in the control sites, which suggests that the use of preventive measures could be improved. B. cereus group, Salmonella spp., and Yersinia spp. were rarely detected in bioaerosols or nasal swabs. Although Campylobacter spp. DNA was rarely detected in air, as a new finding, Campylobacter ureolyticus DNA was frequently detected in the nasal mucous membranes of workers, based on partial 16S rDNA sequencing. Moreover, especially A. fumigatus and C. ureolyticus spp. DNA concentrations in swabs after the work shift were significantly higher than before the shift, which indicates their inhalation or growth during the work shift. Microbial qPCR analysis of bioaerosols and swab samples of nasal mucosa allowed measuring exposure in various work operations and during the work shift, identifying problems for health risk assessment to improve working conditions, and evaluating the effectiveness of preventive measures and personal protection of workers.
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Affiliation(s)
- Merja H. Kontro
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - Maija Kirsi
- Work Environment Laboratories, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Sirpa K. Laitinen
- Department of Occupational Safety, Finnish Institute of Occupational Health, Helsinki, Finland,*Correspondence: Sirpa K. Laitinen
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3
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Rusch DB, Huang J, Hemmerich C, Hahn MW. High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS. ISME COMMUNICATIONS 2022; 2:99. [PMID: 37938727 PMCID: PMC9723582 DOI: 10.1038/s43705-022-00183-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2023]
Abstract
Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities at the subspecies designation. Using rolling-circle amplification, this methodology produces long-read sequences from a circular construct containing the complete 16S ribosomal gene and the neighboring internally transcribed spacer (ITS). These long reads can be used to generate a high-fidelity circular consensus sequence. Generally, the ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism and the assessment of their relative stoichiometry, as well as the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to an artificial microbial community that was also sequenced using the Illumina platform, to assess its accuracy in quantifying the relative abundance and identity of each species.
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Affiliation(s)
- Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA.
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Matthew W Hahn
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
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4
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A first report on the identification of a novel archaea, Methanospirillum lacunae from spoilt paints in Lagos, Nigeria using a metagenomic approach. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2021.e01029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Murugkar PP, Collins AJ, Chen T, Dewhirst FE. Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts. J Oral Microbiol 2020; 12:1814666. [PMID: 33209205 PMCID: PMC7651992 DOI: 10.1080/20002297.2020.1814666] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The vast majority of bacteria on earth have not yet been cultivated. There are many bacterial phyla with no cultivated examples including most members of the Candidate Phylum Radiation with the exception of human oral isolates from the phylum Saccharibacteria. Aims The aims of this research were to develop reproducible methods and validate approaches for the cultivation of human oral Saccharibacteria and to identify the conceptual pitfalls that delayed isolation of these bacteria for 20 years after their discovery. Methods Oral samples were dispersed and passed through 0.2 µm membrane filters. The ultrasmall saccharibacterial cells in the filtrate were pelleted, inoculated into broth cultures of potential bacterial host cells and passaged into fresh medium every 2–3 days. Results Thirty-two isolates representing four species of Saccharibacteria were isolated in stable coculture with three species of host bacteria from the phylum Actinobacteria. Complete genome sequences were obtained for 16 isolates. Conclusions Human oral Saccharibacteria are obligate bacterial parasites that can be stably passaged in coculture with specific species of host bacteria. Isolating these important members of the human oral microbiome, and many natural environments, requires abandoning many of Koch’s concepts and methods and embracing novel microbiological approaches.
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Affiliation(s)
- Pallavi P Murugkar
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Andrew J Collins
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Floyd E Dewhirst
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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Li X, Lau SKP, Woo PCY. Molecular characterisation of emerging pathogens of unexplained infectious disease syndromes. Expert Rev Mol Diagn 2019; 19:839-848. [PMID: 31385539 DOI: 10.1080/14737159.2019.1651200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: The discoveries of HIV and Helicobacter pylori in the 1980s were landmarks in identification of novel pathogens causing unexplained infectious syndromes using conventional microbiological technologies. In the last few decades, advancement of molecular technologies has provided us with more robust tools to expand our armamentarium in this microbial hunting process. Areas covered: In this article, we give a brief overview of the most important molecular technologies we use for identification of emerging microbes associated with unexplained infectious syndromes, including 16S rRNA and other conserved targets sequencing for bacteria, internal transcribed spacer (ITS) and other target gene sequencing for fungi, polymerase and other gene sequencing for viruses, as well as deep sequencing. Then, we use several representative examples to illustrate how these techniques have been used for the discoveries of a few notable bacterial, fungal and viral pathogens associated with unexplained infectious syndromes in the last 20-30 years. Expert opinion: In the past and present, characterization of emerging pathogens of unexplained infectious disease syndromes has relied on a combination of conventional culture- and phenotype-based technologies and nucleic acid amplification and sequencing. In the next era, we envisage more widespread adoption of next generation technologies that can detect both known and previously undescribed pathogens.
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Affiliation(s)
- Xin Li
- Department of Microbiology, The University of Hong Kong , Hong Kong , China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong , Hong Kong , China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong , China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong , China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University , Hangzhou , China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong , Hong Kong , China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong , China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong , China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University , Hangzhou , China
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Van TTH, Lacey JA, Vezina B, Phung C, Anwar A, Scott PC, Moore RJ. Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria. Front Microbiol 2019; 10:107. [PMID: 30804905 PMCID: PMC6371046 DOI: 10.3389/fmicb.2019.00107] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
Chickens infected with Campylobacter jejuni or Campylobacter coli are largely asymptomatic, however, infection with the closely related species, Campylobacter hepaticus, can result in Spotty Liver Disease (SLD). C. hepaticus has been detected in the liver, bile, small intestine and caecum of SLD affected chickens. The survival and colonization mechanisms that C. hepaticus uses to colonize chickens remain unknown. In this study, we compared the genome sequences of 14 newly sequenced Australian isolates of C. hepaticus, isolates from outbreaks in the United Kingdom, and reference strains of C. jejuni and C. coli, with the aim of identifying virulence genes associated with SLD. We also carried out global comparative transcriptomic analysis between C. hepaticus recovered from the bile of SLD infected chickens and C. hepaticus grown in vitro. This revealed how the bacteria adapt to proliferate in the challenging host environment in which they are found. Additionally, biochemical experiments confirmed some in silico metabolic predictions. We found that, unlike other Campylobacter sp., C. hepaticus encodes glucose and polyhydroxybutyrate metabolism pathways. This study demonstrated the metabolic plasticity of C. hepaticus, which may contribute to survival in the competitive, nutrient and energy-limited environment of the chicken. Transcriptomic analysis indicated that gene clusters associated with glucose utilization, stress response, hydrogen metabolism, and sialic acid modification may play an important role in the pathogenicity of C. hepaticus. An understanding of the survival and virulence mechanisms that C. hepaticus uses will help to direct the development of effective intervention methods to protect birds from the debilitating effects of SLD.
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Affiliation(s)
- Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, VIC, Australia
| | - Jake A Lacey
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ben Vezina
- School of Science, RMIT University, Bundoora, VIC, Australia
| | - Canh Phung
- School of Science, RMIT University, Bundoora, VIC, Australia
| | - Arif Anwar
- Scolexia Pty Ltd., Moonee Ponds, VIC, Australia
| | | | - Robert J Moore
- School of Science, RMIT University, Bundoora, VIC, Australia
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Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential. Emerg Microbes Infect 2018; 7:116. [PMID: 29946138 PMCID: PMC6018663 DOI: 10.1038/s41426-018-0118-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/20/2018] [Accepted: 05/24/2018] [Indexed: 01/10/2023]
Abstract
In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn’s disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.
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Magana M, Chatzipanagiotou S, Burriel AR, Ioannidis A. Inquiring into the Gaps of Campylobacter Surveillance Methods. Vet Sci 2017; 4:E36. [PMID: 29056694 PMCID: PMC5644652 DOI: 10.3390/vetsci4030036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/07/2017] [Accepted: 07/17/2017] [Indexed: 01/20/2023] Open
Abstract
Campylobacter is one of the most common pathogen-related causes of diarrheal illnesses globally and has been recognized as a significant factor of human disease for more than three decades. Molecular typing techniques and their combinations have allowed for species identification among members of the Campylobacter genus with good resolution, but the same tools usually fail to proceed to subtyping of closely related species due to high sequence similarity. This problem is exacerbated by the demanding conditions for isolation and detection from the human, animal or water samples as well as due to the difficulties during laboratory maintenance and long-term storage of the isolates. In an effort to define the ideal typing tool, we underline the strengths and limitations of the typing methodologies currently used to map the broad epidemiologic profile of campylobacteriosis in public health and outbreak investigations. The application of both the old and the new molecular typing tools is discussed and an indirect comparison is presented among the preferred techniques used in current research methodology.
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Affiliation(s)
- Maria Magana
- Department of Biopathology and Clinical Microbiology, Aeginition Hospital, Athens Medical School, Athens 15772, Greece.
| | - Stylianos Chatzipanagiotou
- Department of Biopathology and Clinical Microbiology, Aeginition Hospital, Athens Medical School, Athens 15772, Greece.
| | - Angeliki R Burriel
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta 23100, Greece.
| | - Anastasios Ioannidis
- Department of Biopathology and Clinical Microbiology, Aeginition Hospital, Athens Medical School, Athens 15772, Greece.
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta 23100, Greece.
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10
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The ribosomal RNA operon ( rrn ) of Campylobacter concisus supports molecular typing to genomospecies level. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Bishoyi AK, Kavane A, Sharma A, Geetha KA. A report on identification of sequence polymorphism in barcode region of six commercially important Cymbopogon species. Mol Biol Rep 2017; 44:19-24. [PMID: 28110431 DOI: 10.1007/s11033-017-4097-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 01/02/2017] [Indexed: 11/26/2022]
Abstract
CYMBOPOGON: is an important member of grass family Poaceae, cultivated for essential oils which have greater medicinal and industrial value. Taxonomic identification of Cymbopogon species is determined mainly by morphological markers, odour of essential oils and concentration of bioactive compounds present in the oil matrices which are highly influenced by environment. Authenticated molecular marker based taxonomical identification is also lacking in the genus; hence effort was made to evaluate potential DNA barcode loci in six commercially important Cymbopogon species for their individual discrimination and authentication at the species level. Four widely used DNA barcoding regions viz., ITS 1 & ITS 2 spacers, matK, psbA-trnH and rbcL were taken for the study. Gene sequences of the same or related genera of the concerned loci were mined from NCBI domain and primers were designed and validated for barcode loci amplification. Out of the four loci studied, sequences from matK and ITS spacer loci revealed 0.46% and 5.64% nucleotide sequence diversity, respectively whereas the other two loci i.e., psbA-trnH and rbcL showed 100% sequence homology. The newly developed primers can be used for barcode loci amplification in the genus Cymbopogon. The identified Single Nucleotide Polymorphisms from the studied sequences may be used as barcodes for the six Cymbopogon species. The information generated can also be utilized for barcode development of the genus by including more number of Cymbopgon species in future.
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Affiliation(s)
- Ashok Kumar Bishoyi
- PDPIAS, Charotar University of Science and Technology, Changa, Anand, Gujarat, India
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India
| | - Aarti Kavane
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India
| | - Anjali Sharma
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India
| | - K A Geetha
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India.
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Calleros L, Betancor L, Iraola G, Méndez A, Morsella C, Paolicchi F, Silveyra S, Velilla A, Pérez R. Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers. J Microbiol Methods 2016; 132:86-94. [PMID: 27867047 DOI: 10.1016/j.mimet.2016.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022]
Abstract
Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans. Genotypic differentiation of Cff and Cfv is difficult, and epidemiological information is scarce because there are few methods to study the genetic diversity of the strains. We analyze the efficacy of MLST, ribosomal sequences (23S gene and internal spacer region), and CRISPRs to assess the genetic variability of C. fetus in bovine and human isolates. Sequences retrieved from complete genomes were included in the analysis for comparative purposes. MLST and ribosomal sequences had scarce or null variability, while the CRISPR-cas system structure and the sequence of CRISPR1 locus showed remarkable diversity. None of the sequences here analyzed provided evidence of a genetic differentiation of Cff and Cfv in bovine isolates. Comparison of bovine and human isolates with Cft strains showed a striking divergence. Inter-host differences raise the possibility of determining the original host of human infections using CRISPR sequences. CRISPRs are the most variable sequences analyzed in C. fetus so far, and constitute excellent representatives of a dynamic fraction of the genome. CRISPR typing is a promising tool to characterize isolates and to track the source and transmission route of C. fetus infections.
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Affiliation(s)
- Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Laura Betancor
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Dr. Alfredo Navarro 3051, 11600 Montevideo, Uruguay.
| | - Gregorio Iraola
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Unidad de Bioinformática, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay.
| | - Alejandra Méndez
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Claudia Morsella
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Silvia Silveyra
- División de Laboratorios Veterinarios, Ministerio de Ganadería Agricultura y Pesca, Ruta 8 Brig. Gral. J. A. Lavalleja Km. 17.500, Montevideo, 12000, Uruguay.
| | - Alejandra Velilla
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Tokajian S, Issa N, Salloum T, Ibrahim J, Farah M. 16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads. Front Microbiol 2016; 7:149. [PMID: 26904019 PMCID: PMC4749711 DOI: 10.3389/fmicb.2016.00149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/26/2016] [Indexed: 11/13/2022] Open
Abstract
Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S–23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S–23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2–57.9 mol%. Five distinct ITS types were identified: ITSnone (without tRNA genes), ITSAla(TGC), ITSAla(TGC)+Ile(GAT), ITSIle(GAT)+Ala(TGC), and ITS Ile(GAT)+Pseudo. All of the identified tRNAAla(TGC) molecules consisted of 73 bases, and all of the tRNAIle(GAT) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S–23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.
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Affiliation(s)
- Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Nahla Issa
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Joe Ibrahim
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Maya Farah
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
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Kaakoush NO, Castaño-Rodríguez N, Mitchell HM, Man SM. Global Epidemiology of Campylobacter Infection. Clin Microbiol Rev 2015; 28:687-720. [PMID: 26062576 PMCID: PMC4462680 DOI: 10.1128/cmr.00006-15] [Citation(s) in RCA: 874] [Impact Index Per Article: 97.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Campylobacter jejuni infection is one of the most widespread infectious diseases of the last century. The incidence and prevalence of campylobacteriosis have increased in both developed and developing countries over the last 10 years. The dramatic increase in North America, Europe, and Australia is alarming, and data from parts of Africa, Asia, and the Middle East indicate that campylobacteriosis is endemic in these areas, especially in children. In addition to C. jejuni, there is increasing recognition of the clinical importance of emerging Campylobacter species, including Campylobacter concisus and Campylobacter ureolyticus. Poultry is a major reservoir and source of transmission of campylobacteriosis to humans. Other risk factors include consumption of animal products and water, contact with animals, and international travel. Strategic implementation of multifaceted biocontrol measures to reduce the transmission of this group of pathogens is paramount for public health. Overall, campylobacteriosis is still one of the most important infectious diseases that is likely to challenge global health in the years to come. This review provides a comprehensive overview of the global epidemiology, transmission, and clinical relevance of Campylobacter infection.
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Affiliation(s)
- Nadeem O Kaakoush
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Si Ming Man
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Ng BLN, Omarzuki M, Lau GSK, Pannell CM, Yeo TC. A nucleotide signature for identification of Aglaia stellatopilosa Pannell. Mol Biotechnol 2015; 56:671-9. [PMID: 24623047 DOI: 10.1007/s12033-014-9746-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Members of the genus Aglaia have been reported to contain bioactive phytochemicals. The genus, belonging to the Meliaceae family, is represented by at least 120 known species of woody trees or shrubs in the tropical rain forest. As some of these species are very similar in their morphology, taxonomic identification can be difficult. A reliable and definitive molecular method which can identify Aglaia to the level of the species will hence be useful in comparing the content of specific bioactive compounds between the species of this genus. Here, we report the analysis of DNA sequences in the internal transcribed spacer (ITS) of the nuclear ribosomal DNA and the observation of a unique nucleotide signature in the ITS that can be used for the identification of Aglaia stellatopilosa. The nucleotide signature consists of nine bases over the length of the ITS sequence (654 bp). This uniqueness was validated in 37 samples identified as Aglaia stellatopilosa by an expert taxonomist, whereas the nucleotide signature was lacking in a selection of other Aglaia species and non-Aglaia genera. This finding suggests that molecular typing could be utilized in the identification of Aglaia stellatopilosa.
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Affiliation(s)
- Belinda Ling Nah Ng
- Sarawak Biodiversity Centre, KM20, Jalan Borneo Heights, Semengoh, Locked Bag No. 3032, 93990, Kuching, Sarawak, Malaysia
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16
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Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80-100. [PMID: 24886836 DOI: 10.1016/j.mimet.2014.05.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
| | - Hirak R Dash
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
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17
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Fontanot M, Iacumin L, Cecchini F, Comi G, Manzano M. Rapid detection and differentiation of important Campylobacter spp. in poultry samples by dot blot and PCR. Food Microbiol 2014; 43:28-34. [PMID: 24929879 DOI: 10.1016/j.fm.2014.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 04/29/2014] [Accepted: 05/01/2014] [Indexed: 10/25/2022]
Abstract
The detection of Campylobacter, the most commonly reported cause of foodborne gastroenteritis in the European Union, is very important for human health. The most commonly recognised risk factor for infection is the handling and/or consumption of undercooked poultry meat. The methods typically applied to evaluate the presence/absence of Campylobacter in food samples are direct plating and/or enrichment culture based on the Horizontal Method for Detection and Enumeration of Campylobacter spp. (ISO 10272-1B: 2006) and PCR. Molecular methods also allow for the detection of cells that are viable but cannot be cultivated on agar media and that decrease the time required for species identification. The current study proposes the use of two molecular methods for species identification: dot blot and PCR. The dot blot method had a sensitivity of 25 ng for detection of DNA extracted from a pure culture using a digoxigenin-labelled probe for hybridisation; the target DNA was extracted from the enrichment broth at 24 h. PCR was performed using a pair of sensitive and specific primers for the detection of Campylobacter jejuni and Campylobacter coli after 24 h of enrichment in Preston broth. The initial samples were contaminated by 5 × 10 C. jejuni cells/g and 1.5 × 10(2)C. coli cells/g, thus the number of cells present in the enrichment broth at 0 h was 1 or 3 cell/g, respectively.
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Affiliation(s)
- Marco Fontanot
- Department of Food Science, University of Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Lucilla Iacumin
- Department of Food Science, University of Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Francesca Cecchini
- Department of Food Science, University of Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Giuseppe Comi
- Department of Food Science, University of Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Marisa Manzano
- Department of Food Science, University of Udine, Via Sondrio 2/A, 33100 Udine, Italy.
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Zhang H, Feng J, Xue R, Du XJ, Lu X, Wang S. Loop-mediated isothermal amplification assays for detecting Yersinia pseudotuberculosis in milk powders. J Food Sci 2014; 79:M967-71. [PMID: 24697660 DOI: 10.1111/1750-3841.12436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/26/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Yersinia pseudotuberculosis is a Gram-negative foodborne pathogen that causes several diseases, such as enteritis, septicemia, and reactive arthritis. Loop-mediated isothermal amplification (LAMP) assay targeting the 16S-23S rDNA internal transcribed spacer (ITS) region was developed to detect Y. pseudotuberculosis in milk powder. The DNA amplification could be completed in 1 h, and detected by produced white precipitate visible to naked eyes. The detection limit of LAMP assay was 10(0) fg/reaction for genomic DNA, and 10(0) CFU/100 g milk powder coupled with 12 h enrichment. LAMP assay is 100 times more sensitive than conventional polymerase chain reaction method for detecting Y. pseudotuberculosis, and correctly identified 18 cases of Y. pseudotuberculosis contaminations from 236 commercial milk powder products. In conclusion, the developed LAMP assay may facilitate rapid detection of Y. pseudotuberculosis contaminations in agricultural and food products. PRACTICAL APPLICATION Rapid and accurate detection of Yersinia pseudotuberculosis in milk products.
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Affiliation(s)
- Hongwei Zhang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin Univ. of Science and Technology, Tianjin, 300457, China; Food, Nutrition, and Health Program, Faculty of Land and Food Systems, Univ. of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Giessler S, Wolinska J. Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach. Mol Ecol Resour 2014; 13:918-28. [PMID: 23937576 DOI: 10.1111/1755-0998.12144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 05/23/2013] [Accepted: 06/18/2013] [Indexed: 11/28/2022]
Abstract
The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a common marker not only for the molecular identification of different taxa and strains, but also for the analysis of population structure of wild microparasite communities. Importantly, the multicopy nature of this region allows the amplification of low-quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS-types [as identified by statistical parsimony network analysis (SPN)] is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency in detecting different sequence types was even higher after sample pooling. As shown by simulations, an easily manageable number of sequences from pooled DNA samples are sufficient to resolve the spatial population structure in this system. In summary, the ITS region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, the application of SPN analysis is a good alternative to the well-established neighbour-joining method (NJ) for the identification of representative ITS-types. SPN can even outperform NJ by joining most of the singleton sequences to representative sequence clusters.
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Affiliation(s)
- Sabine Giessler
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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20
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Yadegar A, Alebouyeh M, Lawson AJ, Mirzaei T, Nazemalhosseini Mojarad E, Zali MR. Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene. World J Microbiol Biotechnol 2014; 30:1909-17. [PMID: 24493015 DOI: 10.1007/s11274-014-1615-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/27/2014] [Indexed: 01/21/2023]
Abstract
Phenotypic identification of non-pylori Helicobacter species has always been problematic and time-consuming in comparison with many other bacteria. We developed a rapid two-step identification assay based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 23S rRNA gene for differentiating between non-pylori Helicobacter species. A new genus-specific primer pair based on all available complete and partial 23S rRNA sequences of Helicobacter species was designed. In silico restriction analysis of variable regions of the 23S rRNA gene suggested SmaI and HindIII endonucleases would provide a good level of differentiation. Analysis of the obtained 23S rRNA RFLP patterns divided all Helicobacter study strains into three species groups (groups A-C) and 12 unique restriction patterns. Wolinella succinogenes also gave a unique pattern. Our proposed PCR-RFLP method was found to be as a valuable tool for routine identification of non-pylori Helicobacter species from human or animal samples.
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Affiliation(s)
- Abbas Yadegar
- Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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21
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Molecular analysis of the 16S-23S rDNA internal spacer region (ISR) and truncated tRNAAla gene segments in Campylobacter lari. World J Microbiol Biotechnol 2012; 28:2403-10. [DOI: 10.1007/s11274-012-1049-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/22/2012] [Indexed: 10/28/2022]
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Abstract
A growing number of Campylobacter species other than C. jejuni and C. coli have been recognized as emerging human and animal pathogens. Although C. jejuni continues to be the leading cause of bacterial gastroenteritis in humans worldwide, advances in molecular biology and development of innovative culture methodologies have led to the detection and isolation of a range of under-recognized and nutritionally fastidious Campylobacter spp., including C. concisus, C. upsaliensis and C. ureolyticus. These emerging Campylobacter spp. have been associated with a range of gastrointestinal diseases, particularly gastroenteritis, IBD and periodontitis. In some instances, infection of the gastrointestinal tract by these bacteria can progress to life-threatening extragastrointestinal diseases. Studies have shown that several emerging Campylobacter spp. have the ability to attach to and invade human intestinal epithelial cells and macrophages, damage intestinal barrier integrity, secrete toxins and strategically evade host immune responses. Members of the Campylobacter genus naturally colonize a wide range of hosts (including pets, farm animals and wild animals) and are frequently found in contaminated food products, which indicates that these bacteria are at risk of zoonotic transmission to humans. This Review presents the latest information on the role and clinical importance of emerging Campylobacter spp. in gastrointestinal health and disease.
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Affiliation(s)
- Si Ming Man
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
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Kaakoush NO, Deshpande NP, Wilkins MR, Raftery MJ, Janitz K, Mitchell H. Comparative analyses of Campylobacter concisus strains reveal the genome of the reference strain BAA-1457 is not representative of the species. Gut Pathog 2011; 3:15. [PMID: 21992484 PMCID: PMC3219677 DOI: 10.1186/1757-4749-3-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 10/13/2011] [Indexed: 12/25/2022] Open
Abstract
Background Several studies have shown that significant genotypic heterogeneity exists among Campylobacter concisus strains. Recently, the genome of C. concisus UNSWCD, isolated from a patient with Crohn's disease, was sequenced. Results In this study, comparative analyses were performed between strain UNSWCD and BAA-1457, isolated from a patient with acute gastroenteritis. Searches between C. concisus UNSWCD and BAA-1457 showed that 76% of genes were homologues, whereas those between C. jejuni strains showed 90-91% to be homologues, indicating substantial variation exists within these two C. concisus genomes. More specific bidirectional homology searches identified 1593 genes that are shared between these strains, and 115 and 281 genes unique to UNSWCD and BAA-1457, respectively. Significantly, differences in the type of flagellin glycosylation pathways between the two strains were identified and confirmed by PCR. The protein profiles of UNSWCD, BAA-1457 and a further six strains of C. concisus were compared and analyzed bioinformatically, and this differentiated the strains into four clades. BAA-1457 was found to be highly divergent (average similarity: 56.8%) from the other seven strains (mean average similarity ± standard deviation: 64.7 ± 1.7%). Furthermore, searches for homologues of the 1593 proteins found to be common between UNSWCD and BAA-1457 were conducted against all available bacterial genomes, and 18 proteins were found to be unique to C. concisus, of which 6 were predicted to be secreted, and may represent good markers for detection of this species. Conclusions This study has elucidated several features that may be responsible for the heterogeneity that exists among C. concisus strains, and has determined that the strain BAA-1457 is genetically atypical to other C. concisus strains and is not a good candidate reference strain.
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Affiliation(s)
- Nadeem O Kaakoush
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
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Kovach Z, Kaakoush NO, Lamb S, Zhang L, Raftery MJ, Mitchell H. Immunoreactive proteins of Campylobacter concisus, an emergent intestinal pathogen. ACTA ACUST UNITED AC 2011; 63:387-96. [PMID: 22092566 DOI: 10.1111/j.1574-695x.2011.00864.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/09/2011] [Accepted: 08/23/2011] [Indexed: 12/13/2022]
Abstract
Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Recently, a significantly higher prevalence of C. concisus DNA and higher levels of antibodies specific to C. concisus was detected in children with Crohn's disease when compared with controls. The aim of this study was to identify C. concisus immunoreactive antigens. Proteins from C. concisus were separated using two-dimensional gel electrophoresis, and sera from 10 C. concisus-positive children with Crohn's disease were employed for immunoprobing. The patients' sera reacted with 69 spots, which corresponded to 31 proteins identified by mass spectrometry. The proteins were functionally classified as involved in chemotaxis, signal transduction, flagellar motility, surface binding and membrane protein assembly. Although the individual patients' sera reacted to different sets of proteins, common antigens that were recognized by all patients were flagellin B, ATP synthase F1 alpha subunit, and outer membrane protein 18. Cross-reactivity between proteins of the Campylobacter genus was tested using patients' sera absorbed with Campylobacter showae, Campylobacter jejuni and Campylobacter ureolyticus. Most of the C. concisus immunoreactive proteins identified in this study showed cross-reactivity with other species except for three antigens. In conclusion, this study has identified C. concisus proteins that are immunoreactive within patients with Crohn's disease.
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Affiliation(s)
- Zsuzsanna Kovach
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity. PLoS One 2011; 6:e22170. [PMID: 21829448 PMCID: PMC3146479 DOI: 10.1371/journal.pone.0022170] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Accepted: 06/16/2011] [Indexed: 01/31/2023] Open
Abstract
Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as 'hypothetical' in Campylobacter. Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.
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Meinersmann RJ, Ladely SR, Lindsey RL. Ribosomal operon intergenic sequence region (ISR) heterogeneity in Campylobacter coli and Campylobacter jejuni. Lett Appl Microbiol 2010; 51:539-45. [PMID: 20849393 DOI: 10.1111/j.1472-765x.2010.02930.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The intergenic sequence regions (ISR) between the 16S and 23S genes of Campylobacter jejuni and Campylobacter coli are markedly different for each species. However, in the genomic sequence for Camp. coli RM2228, two rRNA operons have an ISR that is characteristic of Camp. coli, and the third operon is characteristic of Camp. jejuni. The aim of this study was to determine the prevalence of ISR heterogeneity in these organisms. METHODS AND RESULTS PCR primers were designed to yield a 327-base pair (bp) product for Camp. coli and 166-bp product for Camp. jejuni. A strain like Camp. coli RM2228 should yield products of both sizes. DNA from a panel of Camp. coli (n=133) and Camp. jejuni (n=134) isolates were tested. All of the isolates yielded products of the predicted size for the species. To verify the data for Camp. coli RM2228, each ribosomal operon from the isolate was individually amplified by PCR and tested with the ISR primer pair. Products of both sizes were produced as predicted. CONCLUSIONS The cross-species heterogeneity of the ISR seen in Camp. coli RM2228 is uncommon. SIGNIFICANCE AND IMPACT OF THE STUDY The heterogeneity must have been caused by horizontal gene transfer at a frequency lower than predicted from housekeeping gene data. Thus, it can be expected that species identification based on the ISR can be confused in rare isolates.
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