Strain identifier

BacDive ID: 11862

Type strain: Yes

Species: Aminobacter carboxidus

Strain history: CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New-Zealand: strain CC495

NCBI tax ID(s): 305698 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6994

BacDive-ID: 11862

DSM-Number: 17454

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

description: Aminobacter carboxidus DSM 17454 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of beech woodland.

NCBI tax id

  • NCBI tax id: 305698
  • Matching level: species

strain history

@refhistory
6994<- P. Kämpfer <- I. R. McDonald; CC495
120627CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New-Zealand: strain CC495

doi: 10.13145/bacdive11862.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Aminobacter
  • species: Aminobacter carboxidus
  • full scientific name: Aminobacter carboxidus (Meyer et al. 1994 ex Nozhevnikova and Zavarzin 1974) Hördt et al. 2020
  • synonyms

    @refsynonym
    20215Aminobacter lissarensis
    20215Carbophilus carboxidus

@ref: 6994

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aminobacter

species: Aminobacter lissarensis

full scientific name: Aminobacter lissarensis McDonald et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31512negative1.4 µm0.55 µmrod-shapedyes
69480negative99.972
120627negativerod-shapedyes

pigmentation

@refproductionname
31512yes
120627noPyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6994R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
34007MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120627CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120627CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
6994positivegrowth28mesophilic
31512positivegrowth25mesophilic
31512positiveoptimum25mesophilic
34007positivegrowth25mesophilic
58909positivegrowth26-37mesophilic
120627positivegrowth25-30mesophilic
120627nogrowth5psychrophilic
120627nogrowth10psychrophilic
120627nogrowth37mesophilic
120627nogrowth41thermophilic

culture pH

@refabilitytypepH
31512positivegrowth6.7-7.2
31512positiveoptimum6.95

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6994aerobe
31512aerobe
58909aerobe
120627obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.982

halophily

@refsaltgrowthtested relationconcentration
120627NaClpositivegrowth0-2 %
120627NaClnogrowth4 %
120627NaClnogrowth6 %
120627NaClnogrowth8 %
120627NaClnogrowth10 %

observation

  • @ref: 31512
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31512370543-hydroxybutyrate+carbon source
3151230089acetate+carbon source
3151216449alanine+carbon source
3151222599arabinose+carbon source
3151235391aspartate+carbon source
3151217057cellobiose+carbon source
3151228757fructose+carbon source
3151228260galactose+carbon source
3151217234glucose+carbon source
3151227570histidine+carbon source
3151224996lactate+carbon source
3151225017leucine+carbon source
3151217306maltose+carbon source
3151229864mannitol+carbon source
3151237684mannose+carbon source
31512506227N-acetylglucosamine+carbon source
3151218257ornithine+carbon source
3151226271proline+carbon source
3151217272propionate+carbon source
3151215361pyruvate+carbon source
3151226546rhamnose+carbon source
3151233942ribose+carbon source
3151217822serine+carbon source
3151230911sorbitol+carbon source
3151217992sucrose+carbon source
3151227082trehalose+carbon source
3151216296D-tryptophan+carbon source
3151218222xylose+carbon source
12062716947citrate-carbon source
1206274853esculin-hydrolysis
12062717632nitrate+reduction
12062716301nitrite+reduction
12062717632nitrate-respiration

antibiotic resistance

  • @ref: 120627
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120627
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120627oxidase+
120627beta-galactosidase-3.2.1.23
120627alcohol dehydrogenase-1.1.1.1
120627gelatinase-
120627amylase-
120627DNase-
120627caseinase-3.4.21.50
120627catalase+1.11.1.6
120627tween esterase-
120627lecithinase-
120627lipase-
120627lysine decarboxylase-4.1.1.18
120627ornithine decarboxylase-4.1.1.17
120627protease-
120627tryptophan deaminase-
120627urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120627--+--+--+-+----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120627+++++--+--+--++++-++-+-++-+----+++-++--+---------------++--+--+-+------+-+-+-------+--+-++++-++--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
6994soil of beech woodlandCounty DownEurope
58909Soil,unpolluted beech woodland soilNorthern Ireland,County DownEuropeUnited KingdomGBR
120627Environment, Soil, Beech woodlandLissara House, county DownEuropeUnited KingdomGBR

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1038.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_697;98_812;99_1038&stattab=map
  • Last taxonomy: Mesorhizobium
  • 16S sequence: AF107722
  • Sequence Identity:
  • Total samples: 1264
  • soil counts: 780
  • aquatic counts: 308
  • animal counts: 145
  • plant counts: 31

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69941Risk group (German classification)
1206271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6994
  • description: Aminobacter lissarensis strain CC495 16S ribosomal RNA gene, complete sequence
  • accession: AF107722
  • length: 1435
  • database: ena
  • NCBI tax ID: 305698

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aminobacter lissarensis DSM 17454GCA_014207495scaffoldncbi305698
66792Aminobacter lissarensis strain DSM 17454305698.3wgspatric305698
66792Aminobacter lissarensis DSM 174542861412741draftimg305698

GC content

  • @ref: 31512
  • GC-content: 62.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno70.554no
gram-positiveno97.676yes
anaerobicno98.917no
aerobicyes94.708yes
halophileno89.358no
spore-formingno94.666no
glucose-utilyes93.72yes
thermophileno99.003no
motileyes89.953yes
glucose-fermentno89.97no

External links

@ref: 6994

culture collection no.: DSM 17454, CCUG 50579, CIP 108661, NCIMB 13798, CC 495

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16102909Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495.Warner KL, Larkin MJ, Harper DB, Murrell JC, McDonald IRFEMS Microbiol Lett10.1016/j.femsle.2005.07.0212005Alphaproteobacteria/enzymology/*genetics/*metabolism, Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics, Biodegradation, Environmental, Cloning, Molecular, Conserved Sequence, DNA, Bacterial/chemistry/genetics, Gene Order, *Genes, Bacterial, Hydrocarbons, Brominated/*metabolism, Hyphomicrobium/genetics, Methyl Chloride/*metabolism, Molecular Sequence Data, Multigene Family, Sequence Analysis, DNA, Sequence Homology, Amino Acid, SyntenyEnzymology
Phylogeny16166673Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments.McDonald IR, Kampfer P, Topp E, Warner KL, Cox MJ, Hancock TLC, Miller LG, Larkin MJ, Ducrocq V, Coulter C, Harper DB, Murrell JC, Oremland RSInt J Syst Evol Microbiol10.1099/ijs.0.63716-02005*Agriculture, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, California, Canada, Carbamates/metabolism, Culture Media, DNA, Bacterial/analysis, Fagus, Genes, rRNA, Herbicides/metabolism, Hydrocarbons, Brominated/metabolism, Methyl Chloride/metabolism, Molecular Sequence Data, Northern Ireland, Pesticides/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, *Trees, Triazines/metabolismMetabolism
Phylogeny33848814Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hordt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005).Artuso I, Turrini P, Pirolo M, Lucidi M, Tescari M, Visaggio D, Mansi A, Lugli GA, Ventura M, Visca PSyst Appl Microbiol10.1016/j.syapm.2021.1261992021Bacterial Typing Techniques, *Carbon Monoxide, DNA, Bacterial, Multilocus Sequence Typing, Phyllobacteriaceae/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6994Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17454)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17454
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31512Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780828776041
34007Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6314
58909Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50579)https://www.ccug.se/strain?id=50579
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
120627Curators of the CIPCollection of Institut Pasteur (CIP 108661)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108661