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Xu L, Liu X, Wu Q, Hua ZL, Yang F, Zhang JF. Phylogenetic analysis of pathogenic genes in Helicobacter species. Shijie Huaren Xiaohua Zazhi 2024; 32:58-70. [DOI: 10.11569/wcjd.v32.i1.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/01/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Helicobacter bacteria are associated with gastrointestinal diseases, especially Helicobacter pylori (H. pylori). With the isolation of many non-Helicobacter pylori Helicobacters (NHPH) from the liver, intestines, and gallbladder of natural animal reservoirs, NHPH have been potential zoonotic pathogens, but their infection and pathogenic mechanisms are still unclear.
AIM To explore the phylogenetic relationship of Helicobacter species based on their pathogenic genes.
METHODS The present study collected the genomic sequences of 50 strains in genus Helicobacter, including 12 strains of H. pylori and 38 strains of NHPH. Based on 16S rRNA gene and several pathogenic genes (flagella, urease, and virulence factors), MAGA software (Version 11.0) was used to align their sequences and construct phylogenetic trees.
RESULTS The phylogenetic tree of 16S rRNA gene showed that gastric Helicobacter (GH) and enterohepatic Helicobacter species (EHS) were clustered into two large branches, respectively. All of the GH's hosts were mammals, while the hosts of EHS were many wild poultry and mammals. Based on the flagella motility-related genes (flaA, flaB, fliP, fliQ, fliR, fliG, fliM, and fliN), the phylogenetic trees were divided into two major branches (GH and EHS). Similarly, the phylogenetic trees of lipopolysaccharide (LPS) biosynthesis-related genes (lptA, waaC, and waaF) presented two major branches (GH and EHS), too. The urease genes existed in all of the 12 strains of H. pylori, 13 strains of gastric NHPH, and 4 strains of EHS (H. hepaticus, H. muridarum, H. bilis, and H. anseris). However, no significant phylogenetic patterns of GH and EHS were observed in the seven urease genes (ureA, ureB, ureE, ureF, ureG, ureH, and ureI).
CONCLUSION The phylogenetic relationship of Helicobacter species' pathogenic genes is dominated distinctly by the special colonization areas including gastric and enterohepatic niches.
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Affiliation(s)
- Le Xu
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Xing Liu
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Qi Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhao-Lai Hua
- Institute of Tumor Prevention and Control, People's Hospital of Yangzhong City, Zhenjiang 212299, Jiangsu Province, China
| | - Fei Yang
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Jun-Feng Zhang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
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Ochoa S, Collado L. Enterohepatic Helicobacter species - clinical importance, host range, and zoonotic potential. Crit Rev Microbiol 2021; 47:728-761. [PMID: 34153195 DOI: 10.1080/1040841x.2021.1924117] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The genus Helicobacter defined just over 30 years ago, is a highly diverse and fast-growing group of bacteria that are able to persistently colonize a wide range of animals. The members of this genus are subdivided into two groups with different ecological niches, associated pathologies, and phylogenetic relationships: the gastric Helicobacter (GH) and the enterohepatic Helicobacter (EHH) species. Although GH have been mostly studied, EHH species have become increasingly important as emerging human pathogens and potential zoonotic agents in the last years. This group of bacteria has been associated with the development of several diseases in humans from acute pathologies like gastroenteritis to chronic pathologies that include inflammatory bowel disease, and liver and gallbladder diseases. However, their reservoirs, as well as their routes of transmission, have not been well established yet. Therefore, this review summarizes the current knowledge of taxonomy, epidemiology, and clinical role of the EHH group.
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Affiliation(s)
- Sofia Ochoa
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Luis Collado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
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3
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Differentiation of Gastric Helicobacter Species Using MALDI-TOF Mass Spectrometry. Pathogens 2021; 10:pathogens10030366. [PMID: 33803832 PMCID: PMC8003121 DOI: 10.3390/pathogens10030366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Gastric helicobacters (Helicobacter (H.) pylori and non-H. pylori Helicobacter species (NHPHs)) colonize the stomach of humans and/or animals. Helicobacter species identification is essential since many of them are recognized as human and/or animal pathogens. Currently, Helicobacter species can only be differentiated using molecular methods. Differentiation between NHPHs using MALDI-TOF MS has not been described before, probably because these species are poorly represented in current MALDI-TOF MS databases. Therefore, we identified 93 gastric Helicobacter isolates of 10 different Helicobacter species using MALDI-TOF MS in order to establish a more elaborate Helicobacter reference database. While the MALDI Biotyper database was not able to correctly identify any of the isolates, the in-house database correctly identified all individual mass spectra and resulted in 82% correct species identification based on the two highest log score matches (with log scores ≥2). In addition, a dendrogram was constructed using all newly created main spectrum profiles. Nine main clusters were formed, with some phylogenetically closely related Helicobacter species clustering closely together and well-defined subclusters being observed in specific species. Current results suggest that MALDI-TOF MS allows rapid differentiation between gastric Helicobacter species, provided that an extensive database is at hand and variation due to growth conditions and agar-medium-related peaks are taken into account.
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Population abundance of potentially pathogenic organisms in intestinal microbiome of jungle crow (Corvus macrorhynchos) shown with 16S rRNA gene-based microbial community analysis. BIOMED RESEARCH INTERNATIONAL 2013; 2013:438956. [PMID: 24058905 PMCID: PMC3766557 DOI: 10.1155/2013/438956] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 06/26/2013] [Accepted: 07/23/2013] [Indexed: 11/18/2022]
Abstract
Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.
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Won YS, Vandamme P, Yoon JH, Park YH, Hyun BH, Kim HC, Itoh T, Tanioka Y, Choi YK. Helicobacter callitrichissp. nov., a novelHelicobacterspecies isolated from the feces of the common marmoset (Callithrix jacchus). FEMS Microbiol Lett 2007; 271:239-44. [PMID: 17439542 DOI: 10.1111/j.1574-6968.2007.00721.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
A slowly growing microaerophilic Helicobacter species was isolated from the feces of the common marmoset (Callithrix jacchus). This bacterium possessed a pair of nonsheathed bipolar flagella, was positive for oxidase, catalase and alkaline phosphatase activities, but was negative for gamma-glutamyltranspeptidase and urease activity and for nitrate reduction. The bacterium was susceptible to nalidixic acid and resistant to cephalotine and did not hydrolyze hippurate. On the basis of phenotypic characteristics, 16S rRNA gene sequence analysis and whole-cell protein profiles, the isolate represents a new species of the genus Helicobacter, for which the name Helicobacter callitrichis sp. nov. is proposed; the type strain of the new species is R-204(T) (GenBank accession number AY192526).
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Affiliation(s)
- Young Suk Won
- Department of Microbiology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
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Hynes SO, Teneberg S, Roche N, Wadström T. Glycoconjugate binding of gastric and enterohepatic Helicobacter spp. Infect Immun 2003; 71:2976-80. [PMID: 12704182 PMCID: PMC153247 DOI: 10.1128/iai.71.5.2976-2980.2003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Helicobacter pylori is able to utilize several lectin-like, protein-carbohydrate interactions for binding to mucins, cell surfaces, and extracellular matrix proteins. As determined by hemagglutination assays and binding of radiolabeled bacteria to glycosphingolipids on thin-layer chromatograms, strains of gastric helicobacters and enterohepatic helicobacters, including Helicobacter canis, Helicobacter hepaticus, and Helicobacter bilis, also demonstrated evidence for the presence of lectin-hemagglutinin adhesins. In addition, in H. hepaticus and H. bilis, binding may be sialic acid dependent. The presence or absence and differences in the levels of activity of lectin adhesins may reflect the species' ecological niche.
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Affiliation(s)
- Sean O Hynes
- Department of Medical Microbiology, Dermatology and Infection, Lund University, Lund, Sweden
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Won YS, Yoon JH, Lee CH, Kim BH, Hyun BH, Choi YK. Helicobacter muricola sp. nov., a novel Helicobacter species isolated from the ceca and feces of Korean wild mouse (Mus musculus molossinus). FEMS Microbiol Lett 2002; 209:45-51. [PMID: 12007652 DOI: 10.1111/j.1574-6968.2002.tb11107.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A slowly growing microaerophilic Helicobacter strain was isolated from the ceca and fecal pellets of Korean wild mice (Mus musculus molossinus). This bacterial strain possessed a pair of nonsheathed bipolar flagella, was positive for urease, catalase and oxidase, and reduced nitrate to nitrite. It proved susceptible to nalidixic acid and resistant to cephalodine, and did not hydrolyze hippurate. On the basis of phenotypic characteristics and 16S rRNA gene sequence analysis, the isolate represents a new species of the genus Helicobacter, for which the name Helicobacter muricola sp. nov. is proposed; the type strain of the new species is w-06T.
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Affiliation(s)
- Young Suk Won
- ICLAS Monitoring Subcenter Korea, Genetic Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), P.O. Box 115, Yusong, Taejon 305-600, South Korea
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Gueneau P, Fuenmayor J, Aristimuño OC, Cedeño S, Báez E, Reyes N, Michelangeli F, Domínguez-Bello MG. Are goats naturally resistant to gastric Helicobacter infection? Vet Microbiol 2002; 84:115-21. [PMID: 11731164 DOI: 10.1016/s0378-1135(01)00443-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Gastric Helicobacter species are widespread and have been reported in wild and domestic mammals of different dietary habits such as humans, dogs, cats, macaques, mice, cheetahs, ferrets, swine and cattle. All have been associated with gastric pathologies. Recently, gastric Helicobacter species were shown to be widespread in cattle and swine in Europe, and there is a report of Helicobacter pylori in sheep in Italy. However, there are no reports of Helicobacter infection in the goat, another important domestic animal of human consumption. The aim of our study was to assess whether Helicobacter abomasal infection was common in goats slaughtered for human consumption. Infection was detected through PCR analysis of DNA extracted from gastric biopsies, using genus- and species-specific primers. Bovine and porcine gastric samples were also analyzed as positive controls. None of the 70 goats were positive for Helicobacter spp.; however, Candidatus Helicobacter bovis and Candidatus Helicobacter suis were detected in 85% of the bovine and 45% of the porcine samples, respectively. We discuss the possibility that goats may exhibit natural resistance to abomasal infection by Helicobacter spp.
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Affiliation(s)
- Pulchérie Gueneau
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.
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Buczolits S, Rosengarten R, Hirt R, Busse HJ. Classification of a Brevundimonas strain detectable after PCR with a Helicobacter-specific primer pair. Syst Appl Microbiol 2001; 24:368-76. [PMID: 11822672 DOI: 10.1078/0723-2020-00052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In a study for the isolation of new Helicobacter strains, biopsy samples were taken from the gastric mucosa of dogs and subjected to PCR amplification using a Helicobacter-specific primer pair (H276f and H676r, directed to the 16S rDNA) to identify members of this genus in the specimens. From one Helicobacter positive sample, a bacterial strain was isolated which displayed a characteristic band after PCR amplification with the Helicobacter-specific primer pair. The isolate designated H2/98-FUNDUS was motile, oxidase-, catalase- and aminopeptidase-positive and grew only under microaerophilic conditions at 37 degrees C. The bacterium was classified by a polyphasic approach, including analysis of the isoprenoid quinones, fatty acids, polar lipids and partial 16S rDNA sequence. Analysis of the 16S rDNA sequence (1003 bases) indicated that the strain H2/98-FUNDUS is a member of the genus Brevundimonas and most closely related to Brevundimonas aurantiaca DSM 4731T (99.5% sequence similarity). Isolate H2/98-FUNDUS contained a predominant ubiquinone Q-10 and a fatty acid profile with the major compounds C18:1 and C16:0. In the polar lipid extract, phosphatidylglycerol, six unknown phospholipids, one unknown phosphoglycolipid, two unknown glycolipids and two unknown aminolipids were detected. All these results indicate that H2/98-FUNDUS represents a new member of the genus Brevundimonas which gives a positive signal upon PCR employing the Helicobacter-specific primer pair.
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Affiliation(s)
- S Buczolits
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, Wien, Austria
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10
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Solnick JV, Schauer DB. Emergence of diverse Helicobacter species in the pathogenesis of gastric and enterohepatic diseases. Clin Microbiol Rev 2001; 14:59-97. [PMID: 11148003 PMCID: PMC88962 DOI: 10.1128/cmr.14.1.59-97.2001] [Citation(s) in RCA: 255] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since Helicobacter pylori was first cultivated from human gastric biopsy specimens in 1982, it has become apparent that many related species can often be found colonizing the mucosal surfaces of humans and other animals. These other Helicobacter species can be broadly grouped according to whether they colonize the gastric or enterohepatic niche. Gastric Helicobacter species are widely distributed in mammalian hosts and are often nearly universally prevalent. In many cases they cause an inflammatory response resembling that seen with H. pylori in humans. Although usually not pathogenic in their natural host, these organisms serve as models of human disease. Enterohepatic Helicobacter species are an equally diverse group of organisms that have been identified in the intestinal tract and the liver of humans, other mammals, and birds. In many cases they have been linked with inflammation or malignant transformation in immunocompetent hosts and with more severe clinical disease in immunocompromised humans and animals. The purpose of this review is to describe these other Helicobacter species, characterize their role in the pathogenesis of gastrointestinal and enterohepatic disease, and discuss their implications for our understanding of H. pylori infection in humans.
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Affiliation(s)
- J V Solnick
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, California 95616, USA.
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Vandamme P, Harrington CS, Jalava K, On SL. Misidentifying helicobacters: the Helicobacter cinaedi example. J Clin Microbiol 2000; 38:2261-6. [PMID: 10834986 PMCID: PMC86777 DOI: 10.1128/jcm.38.6.2261-2266.2000] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-cell protein electrophoresis and biochemical examination by means of a panel of 64 tests were used to identify 14 putative helicobacters to the species level. The results were confirmed by means of DNA-DNA hybridization experiments and were used to discuss misidentification of helicobacters based on 16S rRNA gene sequence data. The data indicated that comparison of near-complete 16S ribosomal DNA sequences does not always provide conclusive evidence for species level identification and may prove highly misleading. The data also indicated that "Helicobacter westmeadii" is a junior synonym of Helicobacter cinaedi and that Helicobacter sp. strain Mainz belongs to the same species. H. cinaedi occurs in various animal reservoirs, including hamsters, dogs, cats, rats, and foxes. Appropriate growth conditions and identification strategies will be required to establish the genuine significance of this widely distributed Helicobacter species.
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Affiliation(s)
- P Vandamme
- Laboratorium voor Microbiologie, Faculteit Wetenschappen, Universiteit Gent, Ghent, Belgium.
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