Strain identifier

BacDive ID: 132198

Type strain: Yes

Species: Acinetobacter variabilis

Strain Designation: strain Tjernberg & Ursing 151a

Strain history: CIP <- 2012, A. Nemec, Inst. Pasteur, Paris, France: strain NIPH 2171, Genomic sp. 15TU <- CCUG <- Tjernberg 151a

NCBI tax ID(s): 70346 (species)

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General

@ref: 23987

BacDive-ID: 132198

DSM-Number: 102977

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

description: Acinetobacter variabilis strain Tjernberg & Ursing 151a is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human urine.

NCBI tax id

  • NCBI tax id: 70346
  • Matching level: species

strain history

@refhistory
23987<- CCM <- A. Nemec; NIPH 2171 <- I. Tjernberg; strain Tjernberg & Ursing 151a
123796CIP <- 2012, A. Nemec, Inst. Pasteur, Paris, France: strain NIPH 2171, Genomic sp. 15TU <- CCUG <- Tjernberg 151a

doi: 10.13145/bacdive132198.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Moraxellaceae
  • genus: Acinetobacter
  • species: Acinetobacter variabilis
  • full scientific name: Acinetobacter variabilis Krizova et al. 2015

@ref: 23987

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Acinetobacter

species: Acinetobacter variabilis

full scientific name: Acinetobacter variabilis Krizova et al. 2015

strain designation: strain Tjernberg & Ursing 151a

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative98
125439negative92.3
123796negativeoval-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38466MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
23987TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
123796CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
38466positivegrowth30
23987positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
125438aerobe90.969
125439obligate aerobe98.3

spore formation

@refspore formationconfidence
125438no91.485
125439no91

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837430911sorbitol-builds acid from
6837417057cellobiose-builds acid from
6837430849L-arabinose-builds acid from
6837417634D-glucose-builds acid from
6837417992sucrose-builds acid from
6837418394palatinose-builds acid from
6837415963ribitol-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837418403L-arabitol-builds acid from
6837416199urea-hydrolysis
6837425094lysine-degradation
6836917306maltose-assimilation
6837417268myo-inositol-builds acid from
6837462345L-rhamnose-builds acid from
6837427082trehalose-builds acid from
6837418333D-arabitol-builds acid from
6837427897tryptophan-energy source
6837415792malonate-assimilation
6837417306maltose-builds acid from
6837416899D-mannitol-builds acid from
6837418024D-galacturonic acid-builds acid from
6837429016arginine-hydrolysis
6837418257ornithine-degradation
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

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6837435581indole-
6836935581indole-

enzymes

@refvalueactivityec
68374alpha-maltosidase-
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68369gelatinase-
68374L-aspartate arylamidase+3.4.11.21
68374alpha-galactosidase-3.2.1.22
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase+
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
68369cytochrome oxidase-1.9.3.1
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
23987---------------+-+-+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
48431-------++----------------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
23987human urineMalmöSwedenSWEEurope
48431Human urineMalmöSwedenSWEEurope1987
123796Human, UrineMalmöSwedenSWEEurope1980

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1891.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_8;96_11;97_459;98_1490;99_1891&stattab=map
  • Last taxonomy: Acinetobacter
  • 16S sequence: KP278590
  • Sequence Identity:
  • Total samples: 61907
  • soil counts: 6187
  • aquatic counts: 13775
  • animal counts: 39559
  • plant counts: 2386

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1237961Risk group (French classification)
239872Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
23987Acinetobacter variabilis strain NIPH 2171 16S ribosomal RNA gene, complete sequenceKP2785901527nuccore70346
124043Acinetobacter sp. NIPH 2171 16S ribosomal RNA gene, partial sequence.KC7631781500nuccore70346

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acinetobacter variabilis NIPH 2171GCA_000369625scaffoldncbi70346
66792Acinetobacter sp. NIPH 21711217693.3wgspatric70346
66792Acinetobacter variabilis strain FDAARGOS_148770346.10completepatric70346
66792Acinetobacter variabilis NIPH 21712565956655draftimg70346
66792Acinetobacter variabilis strain FDAARGOS_148770346.13completepatric70346
66792Acinetobacter variabilis strain FDAARGOS_148770346.11completepatric70346
66792Acinetobacter variabilis strain FDAARGOS_148770346.12completepatric70346

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative92.3
125439BacteriaNetmotilityAbility to perform movementyes50.1
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91
125438gram-positivegram-positivePositive reaction to Gram-stainingno98no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.907no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.485no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.969no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.475yes
125438motile2+flagellatedAbility to perform flagellated movementno78.722no

External links

@ref: 23987

culture collection no.: DSM 102977, CCM 8555, CCUG 26390, CIP 110486, NIPH 2171

straininfo link

  • @ref: 90552
  • straininfo: 51044

literature

  • topic: Phylogeny
  • Pubmed-ID: 25510976
  • title: Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals.
  • authors: Krizova L, McGinnis J, Maixnerova M, Nemec M, Poirel L, Mingle L, Sedo O, Wolfgang W, Nemec A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000028
  • year: 2014
  • mesh: Acinetobacter/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • topic2: Pathogenicity

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
23987Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102977Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102977)
38466Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8351
48431Curators of the CCUGhttps://www.ccug.se/strain?id=26390Culture Collection University of Gothenburg (CCUG) (CCUG 26390)
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
68374Automatically annotated from API ID32E
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90552Reimer, 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-ID51044.1
123796Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110486Collection of Institut Pasteur (CIP 110486)
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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