scholarly journals Genome-based taxonomic reclassification of Acinetobacter species using type and reference strains

2021 ◽  
Author(s):  
Masato Suzuki ◽  
Shotaro Maehana ◽  
Hidero Kitasato
Keyword(s):  
Genome Sequence ◽  
Dna Hybridization ◽  
Type Strain ◽  
Genomic Analysis ◽  
Clinical Settings ◽  
Human Pathogens ◽  
Acinetobacter Species ◽  
Antimicrobial Resistance Genes ◽  
Reference Strains ◽  
Genome Comparisons

Abstract Acinetobacter species are widely distributed in the environment and clinical settings worldwide and serve as natural reservoirs of antimicrobial resistance genes and occasional human pathogens responsible for nosocomial infections. In this study, we performed genomic analysis of Acinetobacter seohaensis DSM 16313, a type strain of the proposed Acinetobacter species. This species was estimated to be evolutionary close to Acinetobacter towneri but the genome sequence of A. seohaensis was not publicly available. Pangenome analysis of the genome sequence of A. seohaensis along with those of genome-available type and reference strains of 82 Acinetobacter species including A. towneri suggested that three groups of Acinetobacter species, A. seohaensis and A. towneri; Acinetobacter pullorum and Acinetobacter portensis; and Acinetobacter idrijaensis, Acinetobacter mesopotamicus, and Acinetobacter lwoffii, were phylogenetically very similar to each other. Genome comparisons based on in silico DNA-DNA hybridization and the average nucleotide identity confirmed that these three groups of Acinetobacter species are conspecific. Based on the rules of priority, A. seohaensis, A. pullorum, and A. idrijaensis/A. mesopotamicus should be reclassified as later heterotypic synonyms of A. towneri, A. portensis, and A. lwoffii, respectively.

scholarly journals Genome Sequence of Acinetobacter towneri Strain DSM 16313, Previously Known as the Proposed Type Strain of Acinetobacter seohaensis

2021 ◽  
Vol 10 (35) ◽  
Author(s):  
Shotaro Maehana ◽  
Hidero Kitasato ◽  
Masato Suzuki
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Type Strain ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Clinical Settings ◽  
Content Type ◽  
Genome Comparisons

Acinetobacter species are widely distributed in the environment and clinical settings worldwide. We report the 2.99-Mbp draft genome sequence of Acinetobacter towneri strain DSM 16313, which was isolated from seawater in South Korea and proposed as a type strain of Acinetobacter seohaensis . Genome comparisons demonstrated that A. seohaensis should be reclassified as A. towneri .

scholarly journals Whole Genome Sequencing Reveals Identification of New Acinetobacter spp. (maqsudiensis) from Local Meat Samples Collected from Dhaka, Bangladesh

2018 ◽  
Author(s):  
Muhammad Maqsud Hossain ◽  
Abdus Sadique ◽  
Aura Rahman ◽  
Abdul Khaleque ◽  
Abdul Mueed Ibne Momen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Acinetobacter Species ◽  
E Coli ◽  
Potential Marker ◽  
Meat Samples ◽  
Generation Technology

In this study we announce the draft genome sequence of a newly identified Acinetobacter species cross-reacting with E. coli serotype 0157:H7. The advent of Next-Generation technology has paved to way to discover new species which could otherwise be misidentified using conventional cultural and serotyping methods. The whole genome sequence of this isolate will help to identify potential marker/s of intervention and further genomic analysis might also shed light onto the virulence properties of this newly identified Acinetobacter species which has been provided the new name of Acinetobacter maqsudiensis.

scholarly journals Complete Genome Sequence of the Arcobacter trophiarum Type Strain LMG 25534

2018 ◽  
Vol 7 (13) ◽  
Author(s):  
William G. Miller ◽  
Emma Yee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Human Pathogens ◽  
Fecal Samples ◽  
Content Type ◽  
Food Animals

Arcobacter species have been recovered from food and/or food animals, and several of these species are potential human pathogens. Arcobacter trophiarum was recovered from fecal samples taken from pigs on two Belgian farms.

scholarly journals Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giuseppe Andolfo ◽  
Christina Schuster ◽  
Haifa Ben Gharsa ◽  
Michelina Ruocco ◽  
Andreas Leclerque
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Type Strain ◽  
Genomic Analysis ◽  
Multi Drug Resistance ◽  
Striking Difference ◽  
Human Pathogens ◽  
Biological Pest Control ◽  
Genetic Elements ◽  
Close Phylogenetic Relationship

Abstract Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

scholarly journals Genomic Analysis of Bacteriophage ΦJL001: Insights into Its Interaction with a Sponge-Associated Alpha-Proteobacterium

2005 ◽  
Vol 71 (3) ◽  
pp. 1598-1609 ◽  
Author(s):  
Jayme E. Lohr ◽  
Feng Chen ◽  
Russell T. Hill
Keyword(s):  
Dna Polymerase ◽  
Genome Sequence ◽  
Dna Hybridization ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Host Bacterium ◽  
Host Chromosome ◽  
Integrase Gene ◽  
Ircinia Strobilina ◽  
Marine Phage

ABSTRACT Bacteriophage ΦJL001 infects a novel marine bacterium in the α subclass of the Proteobacteria isolated from the marine sponge Ircinia strobilina. ΦJL001 is a siphovirus and forms turbid plaques on its host. The genome sequence of ΦJL001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. The complete genome sequence of ΦJL001 comprised 63,469 bp with an overall G+C content of 62%. The genome has 91 predicted open reading frames (ORFs), and 17 ORFs have been assigned putative functions. ΦJL001 appears to be a temperate phage, and the integrase gene was identified in the genome. DNA hybridization analysis showed that the ΦJL001 genome does not integrate into the host chromosome under the conditions tested. DNA hybridization experiments therefore suggested that ΦJL001 has some pseudolysogenic characteristics. The genome of ΦJL001 contains many putative genes involved in phage DNA replication (e.g., helicase, DNA polymerase, and thymidylate synthase genes) and also contains a putative integrase gene associated with the lysogenic cycle. Phylogeny based on DNA polymerase gene sequences indicates that ΦJL001 is related to a group of siphoviruses that infect mycobacteria. Designation of ΦJL001 as a siphovirus is consistent with the morphology of the phage visualized by transmission electron microscopy. The unique marine phage-host system described here provides a model system for studying the role of phages in sponge microbial communities.

scholarly journals Whole Genome Sequencing Reveals Identification of New Acinetobacter spp. (maqsudiensis) from Cow Fecal Sample Collected from Dhaka, Bangladesh

2018 ◽  
Author(s):  
Muhammad Maqsud Hossain ◽  
Abdus Sadique ◽  
Aura Rahman ◽  
Tahmina Tabassum ◽  
Arman Hossain ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Acinetobacter Species ◽  
E Coli ◽  
Potential Marker ◽  
Shed Light ◽  
Generation Technology

In this study we announce the draft genome sequence of a newly identified Acinetobacter species cross-reacting with E. coli serotype 0157:H7. The advent of Next-Generation technology has paved to way to discover new species which could otherwise be misidentified using conventional cultural and serotyping methods. The whole genome sequence of this isolate will help to identify potential marker/s of intervention and further genomic analysis might also shed light onto the virulence properties of this newly identified Acinetobacter species which has been provided the new name of Acinetobacter maqsudiensis.

scholarly journals Phylogenomic analysis of the genus Pseudomonas and reclassification of P. humi, P. zeshuii, P. psychrotolerans, P. nitritireducens, P. pharmacofabricae and P. panacis are later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively

2021 ◽  
Author(s):  
Ritu Rani Kujur ◽  
Sushanta Deb ◽  
Subrata K Das
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Taxonomic Assignment ◽  
Genome Database ◽  
Average Amino Acid Identity ◽  
Genome Comparisons

The present study described the comparative genomic analysis of the validly named species of the genus Pseudomonas to define the taxonomic assignment. Genomic information for 208 type strains was available in the NCBI genome database at the time of conducting this analysis. The ANI, AAI and in silico DNA DNA hybridization (isDDH) data were higher than the threshold values for the twelve strains with their closely related type species. Whole genome comparisons shared 97 - 99 % average nucleotide identity, 97.85 to 99.19 % average amino acid identity and 72.80 to 90.40 % digital DNA DNA hybridization values. Further, the phylogenomic analysis based on the core genome confirmed that P. humi CCA1 and P. citronellolis LMG 18378, P. zeshuii KACC 15471 and P. luteola NBRC 103146, P. oryzihabitans DSM 6835 and P. psychrotolerans DSM 15758, P. nitroreducens DSM 14399 and P. nitritireducens WZBFD3-5A2, P. fluvialis CCM 8778 and P. pharmacofabricae ZYSR67-Z, P. panacis DSM 18529 and P. marginalis DSM 13124 formed a monophyletic clade. Thus, we proposed six type species viz., P. humi CCA1, P. zeshuii KACC 15471, P. psychrotolerans DSM 15758, P. nitritireducens WZBFD3 5A2, P. pharmacofabricae ZYSR67 Z and P. panacis DSM 18529 are the later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively considering the priority date of publication.

scholarly journals Agromyces kandeliae sp. nov., isolated from rhizosphere soil of Kandelia candel in a mangrove

2020 ◽  
Vol 70 (11) ◽  
pp. 5861-5867 ◽  
Author(s):  
Ruijun Wang ◽  
Yanghui Ye ◽  
Yanfen Huang ◽  
Yanfang Nie ◽  
ShuaiBo Han ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Rhizosphere Soil ◽  
Novel Species ◽  
Kandelia Candel ◽  
Gram Stain ◽  
Mangrove Plant ◽  
Content Type ◽  
Reference Strains

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22T was isolated from the rhizosphere soil of mangrove plant, Kandelia candel collected in Zhangzhou, Fujian province, China. Strain Q22T was able to grow at 10–40 °C (optimum 30 °C), pH 5.5–9.0 (optimum 7.0–8.0) and with 0–5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and in silico DNA–DNA hybridization values between strain Q22T and the reference strains were 79.7–88.9% and 22.6–37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The major polar lipids of strain Q22T were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22T contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22T represents a novel species of the genus Agromyces , for which the name Agromyces kandeliae sp. nov. is proposed. The type strain is Q22T (=MCCC 1K03340T= KCTC 39961T).

scholarly journals Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2

2010 ◽  
Vol 60 (8) ◽  
pp. 1725-1728 ◽  
Author(s):  
Geert Huys ◽  
Margo Cnockaert ◽  
Sharon L. Abbott ◽  
J. Michael Janda ◽  
Peter Vandamme
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Reference Strains ◽  
Sequence Similarities

It has been shown previously, based largely on DNA–DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5 %, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1 %. Mean DNA–DNA hybridization values of 74.7–99.9 % were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7–48.7 % DNA–DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and β-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.

scholarly journals Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms

2011 ◽  
Vol 61 (3) ◽  
pp. 561-567 ◽  
Author(s):  
María M. López ◽  
Montserrat Roselló ◽  
Pablo Llop ◽  
Sergi Ferrer ◽  
Richard Christen ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Restriction Analysis ◽  
The Novel ◽  
Closely Related Species ◽  
Phenotypic Group ◽  
The Family ◽  
Pcr Products ◽  
Reference Strains ◽  
Erwinia Piriflorinigrans

Eight Erwinia strains, isolated from necrotic pear blossoms in València, Spain, were compared with reference strains of Erwinia amylovora and Erwinia pyrifoliae, both of which are pathogenic to species of pear tree, and to other species of the family Enterobacteriaceae using a polyphasic approach. Phenotypic analyses clustered the novel isolates into one phenon, distinct from other species of the genus Erwinia, showing that the novel isolates constituted a homogeneous phenotypic group. Rep-PCR profiles, PCR products obtained with different pairs of primers and plasmid contents determined by restriction analysis showed differences between the novel strains and reference strains of E. amylovora and E. pyrifoliae. Phylogenetic analysis of 16S rRNA, gpd and recA gene sequences showed that the eight novel strains could not be assigned to any recognized species. On the basis of DNA–DNA hybridization studies, the novel isolates constituted a single group with relatedness values of 87–100 % to the designated type strain of the group, CFBP 5888T. Depending on the method used, strain CFBP 5888T showed DNA–DNA relatedness values of between 22.7 and 50 % to strains of the closely related species E. amylovora and E. tasmaniensis. The DNA G+C contents of two of the novel strains, CFBP 5888T and CFBP 5883, were 51.1 and 50.5 mol%, respectively. On the basis of these and previous results, the novel isolates represent a novel species of the genus Erwinia, for which the name Erwinia piriflorinigrans sp. nov. is proposed. The type strain is CFBP 5888T (=CECT 7348T).

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