A phylogenetic comparison of urease‐positive thermophilic <i>Campylobacter</i> (UPTC) and urease‐negative (UN) <i>C. lari</i>

Hirayama, Junichi; Tazumi, Akihiro; Hayashi, Kyohei; Tasaki, Erina; Kuribayashi, Takashi; Moore, John E.; Millar, B. Cherie; Matsuda, Motoo

doi:10.1002/jobm.201000367

Cited by 2 publications

(4 citation statements)

References 23 publications

(37 reference statements)

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“…At each step, the two nearest clusters are combined into a higher-level cluster, based on the average distance between elements of each cluster. UPGMA was reported to produce adequate results for genome-based clustering of bacteria on the subspecies level ( 46 ). The main disadvantage of UPGMA is the ‘molecular clock’ assumption, which pre-supposes a constant rate of changes in all lineages.…”

Section: Resultsmentioning

confidence: 99%

“…Its improved version, BIONJ, chooses the reduction, which minimizes the variance of a new distance matrix at each step of matrix reduction, allowing better estimations for selection of the pair of taxa to be agglomerated during the next steps ( 42 ). The ability of both UPGMA and NJ methods to differentiate various taxa depends on the underlying structure of the data used to construct the dissimilarity matrix ( 46 , 51 ).…”

Section: Resultsmentioning

confidence: 99%

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Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes

2015

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Carbohydrates are biological blocks participating in diverse and crucial processes both at cellular and organism levels. They protect individual cells, establish intracellular interactions, take part in the immune reaction and participate in many other processes. Glycosylation is considered as one of the most important modifications of proteins and other biologically active molecules. Still, the data on the enzymatic machinery involved in the carbohydrate synthesis and processing are scattered, and the advance on its study is hindered by the vast bulk of accumulated genetic information not supported by any experimental evidences for functions of proteins that are encoded by these genes. In this article, we present novel instruments for statistical analysis of glycomes in taxa. These tools may be helpful for investigating carbohydrate-related enzymatic activities in various groups of organisms and for comparison of their carbohydrate content. The instruments are developed on the Carbohydrate Structure Database (CSDB) platform and are available freely on the CSDB web-site at http://csdb.glycoscience.ru.Database URL: http://csdb.glycoscience.ru

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes

2015

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“…Three composite full-length gene sequences of ciaB, flaC, and vacJ were shown to be reliable for discrimination between UN C. lari and UPTC organisms, using the UPGMA method, as well as for the differentiation among the four thermophilic Campylobacter species (Hirayama et al 2011).…”

Section: Discussionmentioning

confidence: 99%

“…Previously, our research group demonstrated that fulllength Campylobacter invasion antigen B (ciaB), dnaK, flagellin C (flaC), and virulence-associated chromosome J (vacJ) gene sequence information were reliable for the discrimination between UN C. lari and UPTC taxa, separating from more than other 10 thermophilic Campylobacter isolates, including C. jejuni, C. coli, and C. upsaliensis, using the UPGMA dendrogram (Hirayama et al 2011). Three composite full-length gene sequences of ciaB, flaC, and vacJ were shown to be reliable for discrimination between UN C. lari and UPTC organisms, using the UPGMA method, as well as for the differentiation among the four thermophilic Campylobacter species (Hirayama et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Molecular analysis of the tlyA gene in Campylobacter lari

et al. 2015

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Full-length tlyA gene and its adjacent genetic loci from the urease-positive thermophilic Campylobacter (UPTC) CF89-12 [approximately 15,000 base pairs (bp) in length], as well as a reference strain Campylobacter lari RM2100 (approximately 9,000 bp), were analyzed. The possible open-reading frame of tlyA from UPTC CF89-12 was shown to have 720 bp with a calculated molecular mass of approximately 26.7 kDa. Using a primer pair designed in silico, a total of approximately 1.1 kbp consisting of putative promoter region, structural gene for tlyA, and its adjacent genetic loci were identified in all 17 C. lari isolates [n = 13 for UPTC; n = 4 for urease-negative (UN) C. lari]. Although sequence differences were demonstrated at approximately 20 loci within the 90 bp non-coding (NC) region, including the putative promoter structure candidates immediately upstream of the tlyA gene among the 18 isolates including C. lari RM2100, no sequence differences were identified within the NC region among the five UN C. lari isolates examined. A start codon ATG and a probable ribosome-binding site, AGGC(T)GG(A), for the tlyA gene were identified in all 18 isolates, including C. lari RM2100. The putative intrinsic ρ-independent transcriptional terminator structure candidate was also identified for the tlyA gene in both UPTC CF89-12 and C. lari RM2100. Additionally, the hemolysis assay was performed with some of the C. lari isolates. The tlyA gene nucleotide sequence data may possibly be useful for discrimination between UN C. lari and UPTC organisms, as well as for the differentiation among the four thermophilic Campylobacter species.

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A phylogenetic comparison of urease‐positive thermophilic Campylobacter (UPTC) and urease‐negative (UN) C. lari

Abstract: Campylobacter lari is frequently isolated from shore birds and can cause illness in humans. Here, we report the draft whole-genome sequence of a urease-positive strain of C. lari that was isolated in estuarial water on the coast of Delaware, USA.

Cited by 2 publications

References 23 publications

Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes

Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes

Molecular analysis of the tlyA gene in Campylobacter lari

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