Journal of Microbiology

Research Support, Non-U.S. Gov'ts

Soil fungal communities of montane natural secondary forest types in China: Fei Cheng , Xin Wei , Lin Hou , Zhengchun Shang , Xiaobang Peng , Peng Zhao , Zhaoxue Fei , Shuoxin Zhang; J. Microbiol. 2015;53(6):379-389. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-4722-3

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Distinctive plant communities may provide specific physical and chemical properties with soils by specific litters and root exudates to exert effects on soil microorganisms. Past logging activities in the Qinling Mountains induced diverse natural secondary forest types (NSFTs). How these recovered NSFTs regulate patterns of soil microbial communities remain limited. In the study, we used terminal-restriction fragment length polymorphism (T-RFLP) to precisely determine forest type-specific soil fungal diversity and composition in five NSFTs. Our results indicated that NSFTs had significant impacts on the soil fungal communities. The most diverse fungal species were found in the Armand pine (Pinus armandi) and Chinese pine (Pinus tabulaeformis) forest soils, followed by sharptooth oak (Quercus aliena var. acuteserrata) and Chinese pine-sharptooth oak forest soils, the wilson spruce (Picea wilsonii) forests had the lowest soil fungal diversity. The analyses of community composition suggested that the fungal communities of Armand pine forest soils were similar to those of Chinese pine forest soils, while other communities prominently differed from each other. Stepwise multiple regression analysis revealed that soil silt, clay, pH, and ammonium nitrogen had intimate linkages with soil fungal diversity. Furthermore, the patterns of soil fungal communites were strongly governed by the specific soil environments of the tested NSFTs, as described by canonical correspondence analysis (CCA). Finally, our study showed that soil fungal communities may be mediated by NSFTs via specific soil edaphic status. Hence, such a comparable study may provide fundamental information for fungal diversity and community structure of natural forests and assist with better prediction and understanding how soil fungal composition and function alter with forest type transformation.

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Soil Fungal Community Characteristics at Timberlines of Sejila Mountain in Southeast Tibet, China
Fei Cheng, Mingman Li, Yihua Ren, Lei Hou, Tan Gao, Peng He, Xiangsheng Deng, Jie Lu
Journal of Fungi.2023; 9(5): 596. CrossRef
Soil characteristics and microbial community structure on along elevation gradient in a Pinus armandii forest of the Qinling Mountains, China
Yonghua Zhao, Yujie Zhou, Xia Jia, Lei Han, Li Liu, Kun Ren, Xuan Ye, Zhi Qu, Yuanjie Pei
Forest Ecology and Management.2022; 503: 119793. CrossRef
Spatial characteristics of the dominant fungi and their driving factors in forest soils in the Qinling Mountains, China
Yujie Zhou, Xia Jia, Lei Han, Ge Tian, Shuaizhi Kang, Yonghua Zhao
CATENA.2021; 206: 105504. CrossRef
Short-Term Effects of Different Forest Management Methods on Soil Microbial Communities of a Natural Quercus aliena var. acuteserrata Forest in Xiaolongshan, China
Pan Wan, Gongqiao Zhang, Zhonghua Zhao, Yanbo Hu, Wenzhen Liu, Gangying Hui
Forests.2019; 10(2): 161. CrossRef
Influence of seasonality and management practices on diversity and composition of fungal communities in vineyard soils
Maria M. Hernandez, Cristina M. Menéndez
Applied Soil Ecology.2019; 135: 113. CrossRef
Seasonal dynamics of bacterial communities in aBetula albosinensisforest
C. Du, C.‐Y. Xu, J.‐S. Jian, W.‐X. He, L. Hou, Z.‐C. Geng
European Journal of Soil Science.2018; 69(4): 666. CrossRef
Rhododendron aureum Georgi formed a special soil microbial community and competed with above‐ground plants on the tundra of the Changbai Mountain, China
Xiaolong Wang, Lin Li, Wei Zhao, Jiaxin Zhao, Xia Chen
Ecology and Evolution.2017; 7(18): 7503. CrossRef
Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest
Can Du, Zengchao Geng, Qiang Wang, Tongtong Zhang, Wenxiang He, Lin Hou, Yueling Wang
Journal of Microbiology.2017; 55(9): 684. CrossRef
A comparison of species composition and community assemblage of secondary forests between the birch and pine-oak belts in the mid-altitude zone of the Qinling Mountains, China
Zongzheng Chai, Dexiang Wang
PeerJ.2016; 4: e1900. CrossRef

Molecular Detection and Genotyping of Fusarium oxysporum f. sp. psidii Isolates from Different Agro-Ecological Regions of India: Rupesh Kumar Mishra , Brajesh Kumar Pandey , Vijai Singh , Amita John Mathew , Neelam Pathak , Mohammad Zeeshan; J. Microbiol. 2013;51(4):405-412. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2638-3

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Abstract: Twenty one isolates of Fusarium oxysporum f. sp. psidii (Fop), causing a vascular wilt in guava (Psidium guajava L.), were collected from different agro-ecological regions of India. The pathogenicity test was performed in guava seedlings, where the Fop isolates were found to be highly pathogenic. All 21 isolates were confirmed as F. oxysporum f. sp. psidii by a newly developed, species-specific primer against the conserved regions of 28S rDNA and the intergenic spacer region. RAPD and PCR-RFLP were used for genotyping the isolates to determine their genetic relationships. Fifteen RAPD primers were tested, of which five primers produced prominent, polymorphic, and reproducible bands. RAPD yielded an average of 6.5 polymorphic bands per primer, with the amplified DNA fragments ranging from 200–2,000 bp in size. A dendrogram constructed from these data indicated a 22–74% level of homology. In RFLP analysis, two major bands (350 and 220 bp) were commonly present in all isolates of F. oxysporum. These findings provide new insight for rapid, specific, and sensitive disease diagnosis. However, genotyping could be useful in strain-level discrimination of isolates from different agro-ecological regions of India.

The Role of a Dark Septate Endophytic Fungus, Veronaeopsis simplex Y34, in Fusarium Disease Suppression in Chinese Cabbage: Rida O. Khastini , Hiroyuki Ohta , Kazuhiko Narisawa; J. Microbiol. 2012;50(4):618-624. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2105-6

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Abstract: The soil-inhabiting fungal pathogen Fusarium oxysporum has been an increasing threat to Chinese cabbage (Brassica campestris L.). A dark septate endophytic fungus, Veronaeopsis simplex Y34, isolated from Yaku Island, Japan, was evaluated in vitro for the ability to suppress Fusarium disease. Seedlings grown in the presence of the endophyte showed a 71% reduction in Fusarium wilt disease and still had good growth. The disease control was achieved through a synergetic effect involving a mechanical resistance created by a dense network of V. simplex Y34 hyphae, which colonized the host root, and siderophore production acting indirectly to induce a resistance mechanism in the plant. Changes in the relative abundance of the fungal communities in the soil as determined by fluorescently labelled T-RFs (terminal restriction fragments), appeared 3 weeks after application of the fungus. Results showed the dominance of V. simplex Y34, which became established in the rhizosphere and out-competed F. oxysporum.

Microbial Fingerprinting Detects Unique Bacterial Communities in the Faecal Microbiota of Rats with Experimentally-Induced Colitis: Ashis K. Samanta , Valeria A. Torok , Nigel J. Percy , Suzanne M. Abimosleh , Gordon S. Howarth; J. Microbiol. 2012;50(2):218-225. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1362-8

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Abstract: An abnormal composition of the gut microbiota is believed to be associated with the pathogenesis of inflammatory bowel disease (IBD). We utilized terminal restriction fragment length polymorphism (T-RFLP) analysis to quantify faecal bacterial communities from rats with experimental colitis. Male Sprague Dawley rats (n=10/group) ingested 2% dextran sulfate sodium (DSS) or water for up to 7 days. Rats were killed and colonic tissues collected for histological analysis. Damage severity score in the distal colon was significantly greater (P<0.001) following DSS consumption compared to controls. T-RFLP faecal bacterial profiles generated with either MspI or CfoI revealed a significant difference (P<0.001) in community composition between healthy and colitic rats, with bacterial composition in healthy rats more variable than in rats with colitis. Operational taxonomic units (OTU: taxonomically related groups of bacteria) associated with either the healthy or colitic state were identified. OTU (116, 226, 360, and 948; CfoI) and (118 and 188; MspI) were strongly associated with untreated healthy rats, while OTU (94, 98, 174, and 384; CfoI) and (94 and 914; MspI) were predominantly associated with DSS-treated colitic rats. Phylogenetic OTU assignment suggested that Bacteroidales and Lactobacillus sp. were predominantly associated with the colitic and healthy rats, respectively. These
results
show that faecal bacterial profiling is a rapid, sensitive and non-invasive tool for detecting and identifying changes in gut microbiota associated with colitis. Restoring microbial homeostasis by targeting colitis-associated OTU through specific microbiological interventions could form the basis of novel therapeutic strategies for IBD.

Journal Articles

Sequence Analysis of the Gene Encoding H Antigen in Escherichia coli Isolated from Food in Morocco: Samira Badri , Aziz Fassouane , Ingrid Filliol , Mohammed Hassar , Nozha Cohen; J. Microbiol. 2010;48(2):184-187. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9182-1

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Abstract

In order to develop other molecular method useful for typing of motile and non motile Escherichia coli strains, a total of 207 strains of E. coli (133 reference strains, 74 food strains) were characterized by analysis of sequences of their amplified flagellin-encoding (fliC) gene products. The collection of reference strains was used for database building of fliC gene sequences. Application of this identification system to 74 E. coli food isolates revealed a reproducible and clear cut classification with very good correlation to results obtained by HhaI restriction of the amplified flagellin gene. The proposed determination of fliC sequences variations should be helpful for epidemiological studies.

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Molecular Serotyping and Antibiotic Resistance Patterns of Escherichia coli Isolated in Hospital Catering Service in Morocco
Benjelloun Touimi Ghita, Laila Bennani, Sanae Berrada, Moussa Benboubker, Bahia Bennani
International Journal of Microbiology.2020; 2020: 1. CrossRef
Identification of new flagellin-encoding fliC genes in Escherichia coli isolated from domestic animals using RFLP-PCR and sequencing methods
Cláudia de Moura, Monique Ribeiro Tiba, Marcio José da Silva, Domingos da Silva Leite
Pesquisa Veterinária Brasileira.2013; 33(4): 417. CrossRef

Molecular Identification of Fecal Pollution Sources in Water Supplies by Host-Specific Fecal DNA Markers and Terminal Restriction Fragment Length Polymorphism Profiles of 16S rRNA Gene: Ju-Yong Jeong , Kyung-Ik Gil , Kyong-Hee Lee , Jong-Ok Ka; J. Microbiol. 2008;46(6):599-607. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0174-3

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Abstract: Specific fecal DNA markers were investigated for major pollution sources, cow, human, and pig, and occurrence of the identified markers was analyzed in river waters using Terminal Restriction Fragment Length Polymorphism (T-RFLP) techniques and sequencing of 16S rDNA of Bacteroides-Prevotella. The unique and specific DNA markers for cow and human were identified as a 222 bp and 60 bp peak in HaeIII T-RFLP profiles, respectively, and the pig-specific marker was not identified but the unique T-RFLP profile of pig could be used as a substitution. Human-specific marker was detected in most of the river waters tested (92.1%) and T-RFLP profiles of river waters were shown to be similar to those of human feces. Cluster analysis of T-RFLP data showed that the fecal sources were multiple (human plus cow and human plus dairy cow) in most of the river waters. The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources. The other clones from human, pig, and river water formed two groups all together. The results of this study could be used to identify and control the fecal pollution source in the bodies of water in Korea.

Targeting the rpoB Gene Using Nested PCR-Restriction Fragment Length Polymorphism for Identification of Nontuberculous Mycobacteria in Hospital Tap Water: Ji-Hyun Shin , Hae-Kyung Lee , Eun-Jin Cho , Jae-Yon Yu , Yeon-Ho Kang; J. Microbiol. 2008;46(6):608-614. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0102-6

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Abstract: Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and can cause nosocomial infections in immunocompromised patients. Recently the presence of NTM in public drinking water and hospital water distribution systems has been reported. Their ability to form biofilms and their resistance to chlorine both contribute to their survival and colonization in water distribution systems. Here we analyzed thirty-two hospital tap water samples that were collected from different locations in three hospitals so as to evaluate the prevalence of NTM species. The water samples were concentrated by membrane filtration and then eluted with sterilized water following sonication. Two-step direct PCR targeting the rpoB gene, restriction fragment length polymorphism (RFLP) using the MspI restriction enzyme, and sequence analysis were performed for identification of NTM to the species level. The sequences of each PCR product were analyzed using BLASTN. Seven samples (7/32, 21.9%) were positive for NTM as determined by nested-PCR. The PCR-RFLP results indicated five different patterns among the seven positive PCR samples. The waterborn NTM were identified, including M. peregrinum, M. chelonae (2 cases), M. abscessus, M. gordonae (2 cases), and Mycobacterium sp. JLS. The direct two-step PCR-RFLP method targeting the rpoB gene was effective for the detection and the differentiation of NTM species from hospital tap water.

Research Support, Non-U.S. Gov'ts

Bacterial Communities in the Initial Stage of Marine Biofilm Formation on Artificial Surfaces: Jin-Woo Lee , Ji-Hyun Nam , Yang-Hoon Kim , Kyu-Ho Lee , Dong-Hun Lee; J. Microbiol. 2008;46(2):174-182. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0032-3

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Abstract

Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3~15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that γ-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured γ-Proteobacteria) were predominant in the community during 0~9 h, while the ratio of α-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured α-Proteobacteria) increased 2.6~4.8 folds during 24~36 h of the biofilm formation, emerging as the most predominant group. Previously, α-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of γ-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.

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Rapid Detection of Virulence Factors of Aeromonas Isolated from a Trout Farm by Hexaplex-PCR: In-Young Nam , Kiseong Joh; J. Microbiol. 2007;45(4):297-304.; DOI: https://doi.org/2569 [pii]

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Abstract: The detection of virulence factors of Aeromonas is a key component in determining potential pathogenicity because these factors act multifunctionally and multifactorially. In this study water samples were collected from a trout farm on a seasonal basis, and diseased fish and Aeromonas species were isolated and identified. For rapid detection of six virulence factors of isolated Aeromonas, a hexaplex-polymerase chain reaction (hexaplex-PCR) assay was used. The detected virulence factors include aerolysin (aer), GCAT (gcat), serine protease (ser), nuclease (nuc) lipase (lip) and lateral flagella (laf). The dominant strain found in our isolates was Aeromonas sobria, and the dominant virulence factors were aer and nuc for all seasons. We confirmed that A. sobria and two of the virulence genes (aer and nuc) are related. We proposed a method by which one can identify the major strains of Aeromonas: A. hydrophila, A. sobria, A. caviae, and A. veronii, using hexaplex-PCR.

Evaluation of the Diversity of Cyclodextrin-Producing Paenibacillus graminis Strains Isolated from Roots and Rhizospheres of Different Plants by Molecular Methods: Renata Estebanez Vollu , Rafael Fogel , Silvia Cristina Cunha dos Santos , Fabio Faria da Mota , Lucy Seldin; J. Microbiol. 2006;44(6):591-599.; DOI: https://doi.org/2469 [pii]

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Abstract: To address the diversity of cyclodextrin-producing P. graminis strains isolated from wheat roots and rhizospheres of maize and sorghum sown in Australia, Brazil, and France, restriction fragment length polymorphism analysis of part of genes encoding RNA polymerase (rpoB-RFLP) and DNA gyrase subunit B (gyrB-RFLP) was used to produce genetic fingerprints. A phylogenetic tree based on rpoB gene sequences was also constructed. The isolates originated from Brazil could be separated from those from Australia and France, when data from the rpoB-based phylogenetic tree or gyrB-RFLP were considered. These analyses also allowed the separation of all P. graminis strains studied here into four clusters; one group formed by the strains GJK201 and RSA19T, second group formed by the strains MC22.02 and MC04.21, third group formed by the strains TOD61, TOD 221, TOD302, and TOD111, and forth group formed by all strains isolated from plants sown in Cerrado soil, Brazil. As this last group was formed by strains isolated from sorghum and maize sown in the same soil (Cerrado) in Brazil, our results suggest that the diversity of these P. graminis strains is more affected by the soil type than the plant from where they <br>have been isolated.

Phylogenetic relationship of ganoderma species with the polyporaceae base don RFLP analysis of the nuclear ITS region: Park, Hong Je , Shin, Kee Sun , Yoon, Cheol Sik , Lee, Dong Hun , Bae, Kyung Sook; J. Microbiol. 1996;34(2):117-123.

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Abstract: Restriction-polymorphic patterns of nuclear-ITS were examined for the genetic relationships among 12 bisidiomycetous mushrooms to Aphyllophorales and Agaricales. The taxonomic affinity of Ganoderma species with the family Polyporaceae also was examined. With 13 restriction endonucleases, 159 restriction characters were generated form the 12 species examined. UPGMA and neighbor-joining analyses separated the 12 species into two genetically distinct groups that correspond to orders (Agaricales and Aphyllophorales) where each species is included. This result indicates that there is clear genetic demarcation between Agaricales and Aphyllophorales. Dendrograms constructed by several data analyses showed that even though Ganoderma species are somewhat in intermediate taxonomic position between the Polyporaceae and families of the Agaricales, they are genetically more related to the Polyporaceae. These results are consistent with morphological characters observed in those mushrooms. However, it is premature to conclude taxonomic status Ganoderma species in the present study employing small sample size.

Phylogenetic study of trichaptum species based on the RFLP analysis of mitochondrial DNA: Kim, Mi Sun , jung, Hack Sung; J. Microbiol. 1996;34(3):215-219.

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Abstract: Eight strains of Trichaptunm (Polyporaceae), two strains from each species of T. abietinum, T. biforme, T. fusco-violaceum, and T. laricinum were examined to see their phylogenetic relationship by digesting mitochondrial DNAs with EcoRV, Hind III, XbaI, and PstI, and then analyzing fragmentation patterns with the methods of Nei and Li. T. abietinum, T. biforme, and T. laricinum developed an independent phylogenetic lineage, respectively, but T. fusco-violaceum FP-133997-sp showed a close relationship with two strains of T. bioforme, and T. fusco-violaceum HHB-4016-sp barely grouped with those of T. laricinum. Based on the results of the RFLP analysis of mtDNA, it is concluded that T. fusco-violaceum is under way to differentiation into two different subgroups.

Phylogenetic analysis of trichaptum based on the RFLP of PCR amplified DNAs: Ko, Kwan Soo , Jung, Hack Sung; J. Microbiol. 1996;34(4):295-299.

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Abstract: To infer phylogenetic relationships between species of Trichaptum (Polyporaceae), RFLP analyses of PCR-amplified DNAs were accomplished. Regions coding for ITSs of nuclear SSU rRNA genes and for mitochondrial SSU rRNA genes from thirteen strains of four Trichaptum species (T. abietinum, T. biforme, T. fusco-violaceum, and T. laricinum) were amplified and digested with eight restriction enzymes. All the fragmentation patterns were characterized and coded as 0/1 for the absence/presence of fragments. A phylogenetic tree based on the combined data sets was constructed using the Dollo parsimony method. While every two strains of T. abietinum, T. biforme, T. fusco-violaceum, and T. laricinum formed an independent group, the other strains of T. abietimum and T. fusco-violaceum made mixed groupings among compared strains. It is inferred that T. abietinum and T. fusco-violaceum have more variations, possibly geographic or physiological ones, than other species in the genus.

Variation of the Intergenic Spacer (IGS) Region of Ribosomal DNA among Fusarium oxysporum formae speciales: Hyun-Jung Kim , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2001;39(4):265-272.

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Abstract: Variation within the intergenic spacer (IGS) of the ribosomal DNA gene for twenty-two strains of F. oxysporum and its formae speciales was examined by PCR, coupled with RFLP analysis. The length of the amplified IGS region was about 2.6 kb in all strains except F. oxysporum f. sp. cucumerinum from Korea and F. oxysporum f. sp. niveum. Those two strains were 2.5 kb long. Restriction digestion of IGS-RFLP regions by EcoRI, NruI, HincII, SalI, SmaI, BglII, HindIII, XhoI, and KpnI gave rise to nine IGS haplotypes among all strains. Cluster analysis based on the presence or absence of comigrating restriction fragments show the two groups based on 44% genetic similarity. These results demonstrated that analysis of IGS showed some difference within and between F. oxysporum formae speciales.

PCR-Based RFLP Analysis of ureC Gene for Typing of Indian Helicobacter pylori Strains from Gastric Biopsy Specimens and Culture: Kanchan Kumar Mishra , Shashikant Srivastava , Prabhat P. Dwivedi , Kashi Nath Prasad , Archana Ayyagari; J. Microbiol. 2002;40(4):282-288.

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Abstract: Since culture of Helicobacter pylori is relatively insensitive and cumbersome, molecular detection and typing of H. pylori isolates are gaining importance for strain differentiation. In the present study genomic DNA of 42 gastric biopsies and H. pylori isolates from corresponding patients were analyzed and compared by PCR-based RFLP assay. The 1,132-bp product representing an internal portion of ureC gene of H. pylori was amplified by PCR and digested with restriction enzymes HindIII, AluI and PvuI. The HindIII, AluI and PvuI digestion produced 4, 7, and 2 distinguishable RFLP patterns respectively from 42-H. pylori isolates. By combining all three restriction enzyme digestions, 15 RFLP patterns were observed. However, when PCR products from 42 gastric biopsy specimens were digested by restriction enzymes HindIII, AluI and PvuI, we observed 5, 8 and 2 RFLP patterns, respectively. Patterns from 34 of 42 gastric biopsy specimens matched those of corresponding H. pylori isolates from respective patients. Patterns from the remaining eight biopsy specimens differed and appeared to represent infection with two H. pylori strains. The patterns of one strain from each of these biopsies was identical to that of the isolate from corresponding patients and the second pattern presumably represented the co-infecting strain. From the study, it appears that PCR-based RFLP analysis is a useful primary tool to detect and is distinguish H. pylori strains from gastric biopsy specimens and is superior to culture techniques in the diagnosis of infection with multiple strains of H. pylori.

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