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 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 Complete Genome Sequence of Mycoplasma pneumoniae Type 2 Reference Strain FH Using Single-Molecule Real-Time Sequencing Technology

2017 ◽  
Vol 5 (8) ◽  
Author(s):  
Heta P. Desai ◽  
Shatavia S. Morrison ◽  
Maureen H. Diaz ◽  
Alvaro J. Benitez ◽  
Bernard J. Wolff ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Reference Strain ◽  
Sequencing Technology ◽  
Content Type ◽  
The Pacific

ABSTRACT Mycoplasma pneumoniae type 2 strain FH was previously sequenced with Illumina (FH-Illumina) and 454 (FH-454) technologies according to Xiao et al. (2015) and Krishnakumar et al. (2010). Comparative analyses revealed differences in genomic content between these sequences, including a 6-kb region absent from the FH-454 submission. Here, we present a complete genome sequence of FH sequenced with the Pacific Biosciences RSII platform.

Adaptation of gltA and ssrA assays for diversity profiling by Illumina sequencing to identify Bartonella henselae, B. clarridgeiae and B. koehlerae

2021 ◽  
Vol 70 (7) ◽  
Author(s):  
Rosemonde Isabella Power ◽  
Nichola Elisa Davies Calvani ◽  
Yaarit Nachum-Biala ◽  
Harold Salant ◽  
Shimon Harrus ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Type Species ◽  
Bacterial Infections ◽  
Sanger Sequencing ◽  
Bartonella Henselae ◽  
Diagnostic Methods ◽  
Mixed Infections ◽  
Accurate Identification ◽  
Content Type ◽  
Link Type

Introduction. Bartonellosis is an emerging zoonotic disease caused by bacteria of the genus Bartonella . Mixed Bartonella infections are a well-documented phenomenon in mammals and their ectoparasites. The accurate identification of Bartonella species in single and mixed infections is valuable, as different Bartonella species have varying impacts on infected hosts. Gap Statement. Current diagnostic methods are inadequate at identifying the Bartonella species present in mixed infections. Aim. The aim of this study was to adopt a Next Generation Sequencing (NGS) approach using Illumina sequencing technology to identify Bartonella species and demonstrate that this approach can resolve mixed Bartonella infections. Methodology. We used Illumina PCR amplicon NGS to target the ssrA and gltA genes of Bartonella in fleas collected from cats, dogs and a hedgehog in Israel. We included artificially mixed Bartonella samples to demonstrate the ability for NGS to resolve mixed infections and we compared NGS to traditional Sanger sequencing. Results. In total, we identified 74 Ctenocephalides felis, two Ctenocephalides canis, two Pulex irritans and three Archaeopsylla e. erinacei fleas. Real-time PCR of a subset of 48 fleas revealed that twelve were positive for Bartonella , all of which were cat fleas. Sanger sequencing of the ssrA and gltA genes confirmed the presence of Bartonella henselae , Bartonella clarridgeiae and Bartonella koehlerae . Illumina NGS of ssrA and gltA amplicons further confirmed the Bartonella species identity in all 12 flea samples and unambiguously resolved the artificially mixed Bartonella samples. Conclusion. The adaptation and multiplexing of existing PCR assays for diversity profiling via NGS is a feasible approach that is superior to traditional Sanger sequencing for Bartonella speciation and resolving mixed Bartonella infections. The adaptation of other PCR primers for Illumina NGS will be useful in future studies where mixed bacterial infections may be present.

scholarly journals Complete Genome Sequences of Two Plant Growth-Inhibiting Bacteria, Acinetobacter ursingii M3 and Asticcacaulis excentricus M6, Isolated from Duckweed (Lemna minor)

2018 ◽  
Vol 7 (12) ◽  
Author(s):  
Hidehiro Ishizawa ◽  
Masashi Kuroda ◽  
Daisuke Inoue ◽  
Michihiko Ike
Keyword(s):  
Plant Growth ◽  
Complete Genome ◽  
Lemna Minor ◽  
Genome Sequences ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Growth Inhibiting

Acinetobacter ursingii M3 and Asticcacaulis excentricus M6 are plant growth-inhibiting bacteria that reduce the yield of the duckweed Lemna minor. We report here the complete genome sequences of A. ursingii M3 and A. excentricus M6, sequenced using the PacBio RS II platform.

scholarly journals Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates

2021 ◽  
Vol 7 (2) ◽  
Author(s):  
Ahmad-Kamal Ghazali ◽  
Su-Anne Eng ◽  
Jia-Shiun Khoo ◽  
Seddon Teoh ◽  
Chee-Choong Hoh ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Virulence Factors ◽  
Type Species ◽  
Burkholderia Pseudomallei ◽  
Clinical Manifestations ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Link Type ◽  
Multiple Organs ◽  
The Difference

Burkholderia pseudomallei , a soil-dwelling Gram-negative bacterium, is the causative agent of the endemic tropical disease melioidosis. Clinical manifestations of B. pseudomallei infection range from acute or chronic localized infection in a single organ to fulminant septicaemia in multiple organs. The diverse clinical manifestations are attributed to various factors, including the genome plasticity across B. pseudomallei strains. We previously characterized B. pseudomallei strains isolated in Malaysia and noted different levels of virulence in model hosts. We hypothesized that the difference in virulence might be a result of variance at the genome level. In this study, we sequenced and assembled four Malaysian clinical B. pseudomallei isolates, UKMR15, UKMPMC2000, UKMD286 and UKMH10. Phylogenomic analysis showed that Malaysian subclades emerged from the Asian subclade, suggesting that the Malaysian strains originated from the Asian region. Interestingly, the low-virulence strain, UKMH10, was the most distantly related compared to the other Malaysian isolates. Genomic island (GI) prediction analysis identified a new island of 23 kb, GI9c, which is present in B. pseudomallei and Burkholderia mallei , but not Burkholderia thailandensis . Genes encoding known B. pseudomallei virulence factors were present across all four genomes, but comparative analysis of the total gene content across the Malaysian strains identified 104 genes that are absent in UKMH10. We propose that these genes may encode novel virulence factors, which may explain the reduced virulence of this strain. Further investigation on the identity and role of these 104 proteins may aid in understanding B. pseudomallei pathogenicity to guide the design of new therapeutics for treating melioidosis.

scholarly journals Solimonas marina sp. nov., isolated from deep seawater of the Pacific Ocean

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Xiupian Liu ◽  
Qiliang Lai ◽  
Fengqin Sun ◽  
Yaping Du ◽  
Yingbao Gai ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Deep Seawater ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

A taxonomic study was carried out on strain C16B3T, which was isolated from deep seawater of the Pacific Ocean. The bacterium was Gram-stain-negative, oxidase- and catalase- positive and rod-shaped. Growth was observed at salinities of 0–8.0 % and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C16B3T belonged to the genus Solimonas , with the highest sequence similarity to Solimonas terrae KIS83-12T (97.2 %), followed by Solimonas variicoloris MN28T (97.0 %) and the other four species of the genus Solimonas (94.5 –96.8 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain C16B3T and the type strains of the genus Solimonas were 74.05−79.48 % and 19.5–22.5 %, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c; 20.9 %), iso-C16 : 0 (14.6 %), C16 : 1  ω5c (9.4 %), iso-C12 : 0 (8.4 %), summed feature 2 (C14 : 0 3-OH/iso I-C16 : 1 and C12 : 0 aldehyde; 6.8 %) and C16 : 0 (5.5 %). The G+C content of the chromosomal DNA was 65.37 mol%. The respiratory quinone was determined to be Q-8 (100 %). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified aminolipids, six unidentified phospholipids and one unidentified polar lipid. The combined genotypic and phenotypic data show that strain C16B3T represents a novel species within the genus Solimonas , for which the name Solimonas marina sp. nov. is proposed, with the type strain C16B3T (=MCCC 1A04678T=KCTC 52314T).

scholarly journals Complete Genome Sequence of Fish Pathogen Flavobacterium columnare Strain B185, Originating from Finland

2019 ◽  
Vol 8 (49) ◽  
Author(s):  
Janne J. Ravantti ◽  
Elina Laanto ◽  
Petri Papponen ◽  
Lotta-Riina Sundberg
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Flavobacterium Columnare ◽  
Fish Pathogen ◽  
Sequencing Technology ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Circular Genome

We report a complete genome sequence of a Finnish isolate of the fish pathogen Flavobacterium columnare. Using PacBio RS II sequencing technology, the complete circular genome of F. columnare strain B185 with 3,261,404 bp was obtained.

scholarly journals Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1

2012 ◽  
Vol 194 (23) ◽  
pp. 6677-6677 ◽  
Author(s):  
Qiliang Lai ◽  
Weiwei Li ◽  
Baojiang Wang ◽  
Zhiwei Yu ◽  
Zongze Shao
Keyword(s):  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Complete Genome Sequence ◽  
Deep Sea ◽  
Complete Genome ◽  
Content Type ◽  
Degrading Bacterium ◽  
The Pacific ◽  
Polycyclic Aromatic ◽  
The Pacific Ocean

ABSTRACTCycloclasticussp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation.

scholarly journals Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92T Using Nanopore and Illumina Sequencing Data

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Michael M. Karl ◽  
Anja Poehlein ◽  
Frank R. Bengelsdorf ◽  
Rolf Daniel ◽  
Peter Dürre
Keyword(s):  
Carbon Monoxide ◽  
Genome Sequence ◽  
Illumina Sequencing ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequencing Data ◽  
Circular Chromosome ◽  
Content Type ◽  
Illumina Sequencing Data

ABSTRACT Here, we report the closed genome sequence of Clostridium formicaceticum, an Rnf- and cytochrome-containing autotrophic acetogen that is able to convert carbon monoxide to acetate using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (4.59 Mb).

scholarly journals Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Luis F. Espinosa-Camacho ◽  
Gabriela Delgado ◽  
Guadalupe Miranda-Novales ◽  
Gloria Soberón-Chávez ◽  
Luis D. Alcaraz ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Real Time ◽  
Mexico City ◽  
Single Molecule ◽  
Complete Genome ◽  
Genome Sequences ◽  
Class 1 Integron ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Class 1

ABSTRACT Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high content of mobile elements, and variation in the genetic content of class 1 integron In1409.

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