Strain identifier

BacDive ID: 13540

Type strain: Yes

Species: Aminobacter carboxidus

Strain Designation: Z-1171

Strain history: CIP <- 1998, ATCC <- DSM <- G.A. Zavarzin: strain Z-1171, "Achromobacter carboxydus"

NCBI tax ID(s): 376165 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 540

BacDive-ID: 13540

DSM-Number: 1086

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

description: Aminobacter carboxidus Z-1171 is a mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 376165
  • Matching level: species

strain history

@refhistory
540<- G.A. Zavarzin, Z-1171 (Achromobacter carboxydus)
117179CIP <- 1998, ATCC <- DSM <- G.A. Zavarzin: strain Z-1171, "Achromobacter carboxydus"

doi: 10.13145/bacdive13540.20230509.8.1

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: 540

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aminobacter

species: Aminobacter carboxidus

full scientific name: Aminobacter carboxidus (Meyer et al. 1994) Hördt et al. 2020

strain designation: Z-1171

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.895
117179negativerod-shapedyes

colony morphology

  • @ref: 117179
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
540CARBON MONOXIDE OXIDIZER MEDIUM (DSMZ Medium 133)yeshttps://mediadive.dsmz.de/medium/133Name: CARBON MONOXIDE OXIDIZER MEDIUM (DSMZ Medium 133) Composition: Agar 12.0 g/l Na2HPO4 x 12 H2O 4.5 g/l NH4Cl 1.5 g/l KH2PO4 0.75 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.03 g/l Ferric ammonium citrate 0.018 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
32818MEDIUM 288 - for Carbophilus carboxidusyesSodium hydrogen carbonate (1.000 g);Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (30.000 mg);Agar (12.000 g);Ammonium chloride (1.500 g);Sodium acetate (3.000 g);Di Potassium monohydrogenoph
117179CIP Medium 288yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=288

culture temp

@refgrowthtypetemperaturerange
540positivegrowth30mesophilic
32818positivegrowth30mesophilic
117179positivegrowth15-30
117179nogrowth5psychrophilic
117179nogrowth37mesophilic
117179nogrowth41thermophilic
117179nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.954

halophily

@refsaltgrowthtested relationconcentration
117179NaClpositivegrowth0 %
117179NaClnogrowth2 %
117179NaClnogrowth4 %
117179NaClnogrowth6 %
117179NaClnogrowth8 %
117179NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
117179esculin-hydrolysis4853
117179hippurate+hydrolysis606565
117179nitrate-builds gas from17632
117179nitrate-reduction17632
117179nitrite-builds gas from16301
117179nitrite-reduction16301
117179malonate-assimilation15792
117179nitrate-respiration17632

antibiotic resistance

  • @ref: 117179
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 117179
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11717915688acetoin-
11717917234glucose-

enzymes

@refvalueactivityec
117179oxidase+
117179beta-galactosidase-3.2.1.23
117179alcohol dehydrogenase-1.1.1.1
117179gelatinase-
117179amylase-
117179DNase-
117179caseinase-3.4.21.50
117179catalase+1.11.1.6
117179tween esterase-
117179gamma-glutamyltransferase+2.3.2.2
117179lecithinase-
117179lipase-
117179lysine decarboxylase-4.1.1.18
117179ornithine decarboxylase-4.1.1.17
117179phenylalanine ammonia-lyase+4.3.1.24
117179protease-
117179tryptophan deaminase-
117179urease-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
117179--++-----------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117179-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117179+++++--+--+-----+----+-++-+----+++-++----------------------+--+---------------+--------------+---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
540soilMoscow, near stream in Neskuchny GardenRussiaRUSEurope
117179Environment, SoilMoscowRussian FederationRUSEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #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: JN175336
  • 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
5401Risk group (German classification)
1171791Risk group (French classification)

Sequence information

16S sequences

  • @ref: 540
  • description: Carbophilus carboxidus strain CIP 105722 16S ribosomal RNA gene, complete sequence
  • accession: JN175336
  • length: 1477
  • database: ena
  • NCBI tax ID: 376165

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aminobacter carboxidus DSM 1086GCA_014863355contigncbi376165
66792Aminobacter carboxidus strain DSM 1086376165.4wgspatric376165

GC content

  • @ref: 540
  • GC-content: 48.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.779no
anaerobicno98.551no
halophileno87.564no
spore-formingno94.436no
glucose-utilyes93.197no
aerobicyes93.557no
motileyes91.375no
flagellatedno61.729no
thermophileno99.107yes
glucose-fermentno89.651no

External links

@ref: 540

culture collection no.: DSM 1086, ATCC 51424, CIP 105722

straininfo link

  • @ref: 82729
  • straininfo: 46151

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics33154019Draft Genome Sequence of the Carboxydotrophic Alphaproteobacterium Aminobacter carboxidus Type Strain DSM 1086.Turrini P, Artuso I, Tescari M, Lugli GA, Frangipani E, Ventura M, Visca PMicrobiol Resour Announc10.1128/MRA.01170-202020
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/urltitle
540Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1086)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1086
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
32818Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17773
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)
68371Automatically annotated from API 50CH acid
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
82729Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46151.1StrainInfo: A central database for resolving microbial strain identifiers
117179Curators of the CIPCollection of Institut Pasteur (CIP 105722)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105722