scholarly journals Domestication of Campylobacter jejuni NCTC 11168

2019 ◽  
Vol 5 (7) ◽  
Author(s):  
Ben Pascoe ◽  
Lisa K. Williams ◽  
Jessica K. Calland ◽  
Guillaume Meric ◽  
Matthew D. Hitchings ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Campylobacter Jejuni ◽  
Type Species ◽  
Reference Strain ◽  
Careful Consideration ◽  
Trait Variation ◽  
Content Type ◽  
Link Type ◽  
The Uk ◽  
Reference Strains

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C . jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

scholarly journals Domestication ofCampylobacter jejuniNCTC 11168

2019 ◽  
Author(s):  
Ben Pascoe ◽  
Lisa K. Williams ◽  
Jessica K. Calland ◽  
Guillaume Méric ◽  
Matthew D. Hitchings ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Reference Strain ◽  
Model Organism ◽  
Careful Consideration ◽  
Short Read ◽  
Link Type ◽  
Laboratory Reference ◽  
Data Files ◽  
The Uk ◽  
Reference Strains

AbstractReference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics.Campylobacter jejunistrain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the firstCampylobacterfor which the complete genome was published (in 2000). In this study, we collected 23C. jejuniNCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37°C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change amongC. jejuniisolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.Impact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 referenceCampylobactergenomes and compare them with observable differences in common laboratory phenotypes.Data summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).All assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact:https://microreact.org/project/NCTC11168.RepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467;Table S1).The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Xue Zhang ◽  
Lida Zhang ◽  
XiaoYan Yu ◽  
Jing Zhang ◽  
Yanjie Jiao ◽  
...  
Keyword(s):  
Type Species ◽  
Cow Dung ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Pr China ◽  
Taxonomic Characterization ◽  
Reference Strains

A novel actinobacterium, designated strain NEAU-351T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351T belonged to the genus Nocardia , with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801T and less than 98.0 % identity with other type strains of the genus Nocardia . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H4, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C16 : 0, C18 : 1  ω9c and 10-methyl C18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351T and its reference strains, Nocardia takedensis DSM 44801T and Nocardia arizonensis NBRC 108935T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA–DNA hybridization between them were 24.8 % (22.5–27.3 %) and 26.3 % (24–28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351T represents a new species of the genus Nocardia , for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351T (=CCTCC AA 2019090T=DSM 110681T).

scholarly journals Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Janine T. Bossé ◽  
Yanwen Li ◽  
Liza Miriam Cohen ◽  
Marc Stegger ◽  
Øystein Angen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Comparative Analysis ◽  
Illumina Sequencing ◽  
Complete Genome ◽  
Type Species ◽  
Reference Strain ◽  
Actinobacillus Pleuropneumoniae ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
The Pacific

We report here the complete genome sequence of the widely studied Actinobacillus pleuropneumoniae serovar 8 reference strain 405, generated using the Pacific Biosciences (PacBio) RS II platform. Furthermore, we compared draft sequences generated by Illumina sequencing of six stocks of this strain, including the same original stock used to generate the PacBio sequence, held in different countries and found little genetic variation, with only three SNPs identified, all within the degS gene. However, sequences of two small plasmids, pARD3079 and p405tetH, detected by Illumina sequencing of the draft genomes were not identified in the PacBio sequence of the reference strain.

scholarly journals Streptomyces barkulensis sp. nov., isolated from an estuarine lake

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1365-1372 ◽  
Author(s):  
Lopamudra Ray ◽  
Samir Ranjan Mishra ◽  
Ananta Narayan Panda ◽  
Gurdeep Rastogi ◽  
Ajit Kumar Pattanaik ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Threshold Value ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Phyletic Line ◽  
Actinomycete Strain ◽  
Reference Strains

The taxonomic position of a novel actinomycete, strain RC 1831T, isolated from the sediment of a fish dumping yard at Barkul village near Chilika Lake, Odisha, India, was determined by a polyphasic approach. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Streptomyces . The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1428 nt) with representative strains showed that the strain consistently falls into a distinct phyletic line together with Streptomyces glaucosporus DSM 41689T (98.22 % similarity) and a subclade consisting of Streptomyces atacamensis DSM 42065T (98.40 %), Streptomyces radiopugnans R97 DSM 41901T (98.27 %), Streptomyces fenghuangensis GIMN4.003T (98.33 %), Streptomyces nanhaiensis DSM 41926T (98.13 %), Streptomyces megasporus NBRC 14749T (97.37 %) and Streptomyces macrosporus NBRC 14748T (98.22 %). However, the levels of DNA–DNA relatedness between strain RC 1831T and phylogenetically related strains Streptomyces atacamensis DSM 42065T (28.75±3.25 %) and Streptomyces glaucosporus DSM 41689T (15±2.40 %) were significantly lower than the 70 % threshold value for delineation of genomic species. Furthermore, the isolate could be distinguished phenotypically on the basis of physiological, morphological and biochemical differences from its closest phylogenetic neighbours and other related reference strains. Strain RC 1831T is therefore considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces barkulensis sp. nov. is proposed. The type strain is RC 1831T ( = JCM 18754T = DSM 42082T).

scholarly journals Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand

2020 ◽  
Vol 70 (10) ◽  
pp. 5296-5303 ◽  
Author(s):  
Kenika Lipun ◽  
Wee Fei Aaron Teo ◽  
Paweena Suksaard ◽  
Wasu Pathom-aree ◽  
Kannika Duangmal
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Whole Cell ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid ◽  
Reference Strains

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Nonomuraea . Strain NN258T showed the highest 16S rRNA gene sequence similarity values to Nonomuraea candida HMC10T, Nonomuraea mesophila 6K102T, Nonomuraea rubra DSM 43768T, Nonomuraea diastatica KC712T and Nonomuraea helvata IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).

scholarly journals gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Thea G. Fennell ◽  
Grace A. Blackwell ◽  
Nicholas R. Thomson ◽  
Matthew J. Dorman
Keyword(s):  
Vibrio Cholerae ◽  
Metabolic Pathway ◽  
Type Species ◽  
Gene Encoding ◽  
Natural Competence ◽  
Content Type ◽  
Metabolic Substrate ◽  
Link Type ◽  
Reference Strains ◽  
Present Experimental Evidence

Members of the bacterial genus Vibrio utilize chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae . We show that the gene encoding GbpA, known to be an important colonization and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae . We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within V. cholerae is more complex than previously thought, and emphasize the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains.

scholarly journals Emergence of ciprofloxacin-resistant Neisseria meningitidis B from asymptomatic carriers during an outbreak in Peru, 2017

2020 ◽  
Author(s):  
Eduardo Juscamayta-López ◽  
Faviola Valdivia ◽  
Sara Morales ◽  
Luis Fernando Donaires ◽  
Victor Fiestas-Solórzano ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Type Species ◽  
Acquired Resistance ◽  
Whole Genome Sequence ◽  
Fluoroquinolone Resistance ◽  
Content Type ◽  
Asymptomatic Carriers ◽  
Link Type ◽  
Ciprofloxacin Resistance ◽  
The Uk

Asymptomatic carriers are a likely source of transmission of Neisseria meningitidis to close contacts who are placed at a higher risk for invasive meningococcal disease (IMD). Although N. meningitidis ciprofloxacin-resistance is rare, there have been an increase in the reports of resistant isolates mainly in patients diagnosed with IMD, and little is known about the N. meningitidis ciprofloxacin-resistance in the carrier populations. We performed a pharyngeal carriage study during a 2017 military setting outbreak in Peru, caused by a ciprofloxacin-resistant N. meningitidis B. The isolates analysed came from two hospitalized cases and six asymptomatic carriers. Whole-genome sequence-based analysis was performed and showed that strains carrying the Thr91Ile mutation, in the gene encoding for subunit A of DNA gyrase (gyrA), were responsible for the fluoroquinolone resistance (MICs ≥0.256 µg ml−1) and were closely related to highly virulent strains from France, Norway and the UK. Phylogenetic analysis of the gyrA gene revealed that likely these Peruvian isolates acquired resistance through horizontal gene transfer from Neisseria lactamica . Our study provides evidence for the emergence and propagation of ciprofloxacin-resistant N. meningitidis B from asymptomatic carriers, and recommends the introduction of serogroup B vaccines for high-risk populations.

Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2598-2601 ◽  
Author(s):  
Georges Wauters ◽  
Michèle Janssens ◽  
Thierry De Baere ◽  
Mario Vaneechoutte ◽  
Pieter Deschaght
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Reference Strain ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Group Ii ◽  
Indole Production ◽  
The 16S Rrna Gene

Two clinical strains, NF 296 and NF 931, present in our collection, were identified biochemically as members of CDC group II-i. Determination of the 16S rRNA gene sequence revealed highest similarity with strains of Sphingobacterium mizutaii . Because these strains produced indole, whereas S. mizutaii has been described as indole-negative, we also investigated the type strain and a reference strain of S. mizutaii , LMG 8340T ( = CCUG 15907T) and LMG 8341 ( = CCUG 15908), and found both strains also to be positive for indole production. These data warrant inclusion of some of the CDC group II-i strains into S. mizutaii and emended descriptions of Sphingobacterium mizutaii as indole-production-positive and of the genus Sphingobacterium as variable for indole production.

scholarly journals Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1193-1198 ◽  
Author(s):  
Yanwei Wang ◽  
Jinlong Song ◽  
Yi Zhai ◽  
Chi Zhang ◽  
Jacoline Gerritsen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Saline Lake ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Method Analysis ◽  
Reference Strains ◽  
The 16S Rrna Gene

A Gram-stain-positive, spore-forming, obligately anaerobic bacterium, designated LAM201T, was isolated from sediment samples from an alkaline-saline lake located in Daqing oilfield, Daqing City, PR China. Cells of strain LAM201T were non-motile and straight or spiral rod-shapes. Strain LAM201T was able to utilize glucose, fructose, maltose, trehalose and sorbitol as the sole carbon source. Acetic acid, ethanol, iso-butanoic acid and iso-valeric acid were the main products of glucose fermentation. The major fatty acids of LAM201T were C16 : 0 (26.7 %) and C18 : 0 (11.2 %). The main polar lipids were four unknown glycolipids and five unknown phospholipids. The predominant cell-wall sugars were ribose and galactose. The cell-wall peptidoglycan of strain LAM201T contained alanine, glycine, glutamic acid and aspartic acid. Sodium sulfite was used as the electron acceptor. The G+C content of the genomic DNA was 32±0.8 mol%, as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Romboutsia and was most closely related to Romboutsia lituseburensis DSM 797T and Romboutsia ilealis CRIBT with 97.3 % and 97.2 % similarities, respectively. The DNA–DNA hybridization values between strain LAM201T and the two reference strains were 37 % and 31 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM201T is suggested to represent a novel species within the genus Romboutsia , for which the name Romboutsia sedimentorum sp. nov. is proposed. The type strain is LAM201T ( = ACCC 00717T = JCM 19607T).

scholarly journals Novel genotypes of Leptospira interrogans serogroup Sejroe isolated from human patients in Okinawa Prefecture, Japan

2020 ◽  
Vol 69 (4) ◽  
pp. 587-590
Author(s):  
Tetsuya Kakita ◽  
Hisako Kyan ◽  
Masato Miyahira ◽  
Taketoshi Takara ◽  
Eri Nakama ◽  
...  
Keyword(s):  
Type Species ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Public Health Issue ◽  
Content Type ◽  
Link Type ◽  
The Tropics ◽  
Sequence Types ◽  
Reference Strains

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of Leptospira species. It is a public health issue in the tropics, including Okinawa, the southernmost prefecture of Japan. This study reports the first isolation of L. interrogans serogroup Sejroe from two human patients in Japan, and describes its molecular characterization using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). MLST on the two isolates, 168036 and 178129, showed that pfkB in 178129 is a novel allele, and that both isolates constitute novel sequence types (STs); ST286 for 168036 and ST287 for 178129. A minimum spanning tree based on seven alleles of L. interrogans indicates that both isolates are genetically close, but are distinct from known L. interrogans serogroup Sejroe strains. MLVA using 11 loci demonstrated that seven of the 11 loci were identical between the two isolates, whereas the identity between the isolates and the seven reference strains of L. interrogans serogroup Sejroe was zero to three loci. These results indicate that the isolates investigated in this study have novel genotypes, and are genetically closest to each other among the known L. interrogans serogroup Sejroe strains.

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