Strain identifier

BacDive ID: 134918

Type strain: Yes

Species: Achromobacter dolens

Strain Designation: Vandamme R-47430, LiPuma AU4012, AU4012, R-47430

Strain history: <- CCUG; CCUG 62421 <- P. A. R. Vandamme, LMG; LMG 26840

NCBI tax ID(s): 1287738 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 9.3 (current version)

General

@ref: 33592

BacDive-ID: 134918

DSM-Number: 115983

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Achromobacter dolens Vandamme R-47430 is an aerobe, mesophilic, Gram-negative bacterium of the family Alcaligenaceae.

NCBI tax id

  • NCBI tax id: 1287738
  • Matching level: species

strain history

@refhistory
33592CIP <- 2014, LMG <- 2012, P. Vandamme, Gent Univ., Gent, Belgium: strain Vandamme R-47430 <- 2002, J. Lipuma, Michigan Univ., Michigan, USA strain: LiPuma AU4012
125150<- CCUG; CCUG 62421 <- P. A. R. Vandamme, LMG; LMG 26840

doi: 10.13145/bacdive134918.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Achromobacter
  • species: Achromobacter dolens
  • full scientific name: Achromobacter dolens Vandamme et al. 2014

@ref: 33592

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Achromobacter

species: Achromobacter dolens

full scientific name: Achromobacter dolens Vandamme et al. 2014

strain designation: Vandamme R-47430, LiPuma AU4012, AU4012, R-47430

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative97.828
33592negativerod-shapedyes

colony morphology

  • @ref: 62833
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33592MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
33592CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
125150TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
125150COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf

culture temp

@refgrowthtypetemperature
62833positivegrowth37
125150positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
62833aerobe
125438aerobe91.236
125439obligate aerobe93.7

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 96.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836917306maltose-assimilation
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
33592+-------+-+---+-+++++

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typeisolation date
33592USAUSANorth America
62833USAUSANorth Americahuman sputum, non-CF patient
33592United States of AmericaUSANorth AmericaHuman, Sputum2002
125150USAUSANorth Americahuman sputum, non-CF patient

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Sputum
#Host#Human
#Infection#Patient

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
335921Risk group (French classification)
1251502Risk group (German classification)

Sequence information

16S sequences

  • @ref: 124043
  • description: Achromobacter dolens partial 16S rRNA gene, type strain LMG 26840T
  • accession: HF586509
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 1287738

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Achromobacter dolens LMG 26840GCA_902859745contigncbi1287738
66792Achromobacter dolens strain LMG 268401287738.5wgspatric1287738
66792Achromobacter dolens LMG 268402900088174draftimg1287738

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.828no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.163no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.984no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.236no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes85.883no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.1
125439BacteriaNetmotilityAbility to perform movementyes83
125439BacteriaNetgram_stainReaction to gram-stainingnegative89
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.7

External links

@ref: 33592

culture collection no.: CIP 110711, LMG 26840, CCUG 62421, DSM 115983

straininfo link

  • @ref: 92352
  • straininfo: 376265

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23891345Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov., Achromobacter aegrifaciens sp. nov., Achromobacter anxifer sp. nov. and Achromobacter dolens sp. nov., respectively.Vandamme P, Moore ER, Cnockaert M, Peeters C, Svensson-Stadler L, Houf K, Spilker T, LiPuma JJSyst Appl Microbiol10.1016/j.syapm.2013.06.0052013Achromobacter/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Genotype, Molecular Sequence Data, Multilocus Sequence Typing, PhylogenyGenetics
Phylogeny33033853Achromobacter aestuarii sp. nov., Isolated from an Estuary.Kim SC, Chung SO, Lee HJCurr Microbiol10.1007/s00284-020-02231-92020*Achromobacter, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
33592Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110711Collection of Institut Pasteur (CIP 110711)
62833Curators of the CCUGhttps://www.ccug.se/strain?id=62421Culture Collection University of Gothenburg (CCUG) (CCUG 62421)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
92352Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID376265.1
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125150Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-115983Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 115983)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG