Strain identifier

BacDive ID: 2930

Type strain: Yes

Species: Comamonas kerstersii

Strain Designation: AFG1

Strain history: CIP <- 2003, CCUG, <- 1984, K. Kersters, LMG, Gent, Belgium <- J. Shewan

NCBI tax ID(s): 225992 (species)

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General

@ref: 6164

BacDive-ID: 2930

DSM-Number: 16026

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

description: Comamonas kerstersii AFG1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human sample.

NCBI tax id

  • NCBI tax id: 225992
  • Matching level: species

strain history

@refhistory
6164<- M. Vaneechoutte; AFG1 <- Torry Research Station (including NCBI), United Kingdom (Alcaligenes sp.) <- Caselitz
120408CIP <- 2003, CCUG, <- 1984, K. Kersters, LMG, Gent, Belgium <- J. Shewan

doi: 10.13145/bacdive2930.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Comamonas
  • species: Comamonas kerstersii
  • full scientific name: Comamonas kerstersii Wauters et al. 2003

@ref: 6164

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Comamonas

species: Comamonas kerstersii

full scientific name: Comamonas kerstersii Wauters et al. 2003

strain designation: AFG1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityflagellum arrangement
23079negativerod-shapedyeslophotrichous
120408negativerod-shapedyes

colony morphology

  • @ref: 23079
  • colony size: 1.5-2.0 mm
  • incubation period: 1 day
  • medium used: blood agar

pigmentation

  • @ref: 120408
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6164CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23079blood agaryes
23079tryptic soy agar and brothyes
36672MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120408CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6164positivegrowth37mesophilic
23079positivegrowth30.0mesophilic
23079positivegrowth35.0mesophilic
23079positivegrowth42.0thermophilic
23079positivegrowth44.0thermophilic
23079positiveoptimum35.0-40.0
36672positivegrowth30mesophilic
46224positivegrowth30-37mesophilic
120408positivegrowth10-41
120408nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23079aerobe
46224aerobe
120408obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120408NaClpositivegrowth0-4 %
120408NaClnogrowth6 %
120408NaClnogrowth8 %
120408NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2307930742ethylene glycol-builds acid from
23079161933-hydroxybenzoate-growth
2307916977L-alanine-growth
230794853esculin-hydrolysis
230795291gelatin-hydrolysis
2307916301nitrite-reduction
23079370543-hydroxybutyrate+growth
2307930089acetate+growth
23079167244-hydroxybutyrate+growth
2307917240itaconate+growth
2307917203L-proline+growth
2307924996lactate+growth
230799300suberic acid+growth
2307931011valerate+growth
2307918186tyrosine+hydrolysis
2307917632nitrate+reduction
2307916947citrate+/-carbon source
2307927689decanoate+/-growth
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-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
12040816947citrate-carbon source
1204084853esculin-hydrolysis
12040817632nitrate+reduction
12040816301nitrite-reduction
12040817632nitrate-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
2307937943colistinyesyes
2307950453desferrioxamineyesyes
1204080129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesnoyes

metabolite production

@refChebi-IDmetaboliteproduction
2307935581indoleno
2307916136hydrogen sulfideno
6836935581indoleno
12040835581indoleno

metabolite tests

@refChebi-IDmetabolitecitrate testindole test
2307916947citrate+/-
6836935581indole-

enzymes

@refvalueactivityec
23079alkaline phosphatase-3.1.3.1
23079arginine dihydrolase-3.5.3.6
23079benzoyl-D-arginine arylamidase-3.5.1.72
23079catalase+1.11.1.6
23079cytochrome oxidase+1.9.3.1
23079lysine decarboxylase-4.1.1.18
23079ornithine decarboxylase-4.1.1.17
23079pyrrolidonyl arylamidase-3.4.19.3
23079urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120408oxidase-
120408beta-galactosidase-3.2.1.23
120408alcohol dehydrogenase-1.1.1.1
120408gelatinase-
120408amylase-
120408DNase-
120408caseinase-3.4.21.50
120408catalase-1.11.1.6
120408tween esterase+
120408lecithinase+
120408lipase-
120408lysine decarboxylase-4.1.1.18
120408ornithine decarboxylase-4.1.1.17
120408protease-
120408tryptophan deaminase-
120408urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46224C12:03.212
    46224C13:00.313
    46224C14:03.514
    46224C15:0215
    46224C16:02516
    46224C17:00.917
    46224C18:00.318
    46224C10:0 3OH5.311.423
    46224C16:1 ω7c27.415.819
    46224C17:0 CYCLO2.116.888
    46224C18:1 ω7c /12t/9t29.917.824
    46224C18:2 ω6,9c/C18:0 ANTE0.217.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120408--++-+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6164+---------------++--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120408++-+---+-++----+++++-----------+----------------++---+-----++-++---------+-+---+++-----+++++--+-+++

Isolation, sampling and environmental information

isolation

@refsample type
6164human sample
46224Human material
120408Human, Material

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_2701.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_704;97_822;98_2095;99_2701&stattab=map
  • Last taxonomy: Comamonas
  • 16S sequence: AJ430347
  • Sequence Identity:
  • Total samples: 933
  • soil counts: 72
  • aquatic counts: 471
  • animal counts: 363
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61642Risk group (German classification)
1204081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Comamonas kerstersii strain CIP 107987 16S ribosomal RNA gene, partial sequenceEU0241441316ena225992
23079Comamonas kersterii partial 16S rRNA gene, type strain LMG 3475TAJ4303471345nuccore225992

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Comamonas kerstersii CCUG 15333GCA_008801935contigncbi225992
66792Comamonas kerstersii strain CCUG 15333225992.15wgspatric225992

GC content

  • @ref: 23079
  • GC-content: 61.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.702no
gram-positiveno98.495yes
anaerobicno98.926yes
aerobicyes90.785yes
halophileno88.422no
spore-formingno95.772no
glucose-utilno83.173yes
flagellatedyes86.629yes
thermophileno92.264no
glucose-fermentno89.917yes

External links

@ref: 6164

culture collection no.: CIP 107987, DSM 16026, CCUG 15333, LMG 3475

straininfo link

  • @ref: 72453
  • straininfo: 2020

literature

  • topic: Phylogeny
  • Pubmed-ID: 23125317
  • title: Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil.
  • authors: Sun LN, Zhang J, Chen Q, He J, Li QF, Li SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.045716-0
  • year: 2012
  • mesh: Agriculture, Bacterial Typing Techniques, Base Composition, China, Comamonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/microbiology, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Surface-Active Agents/metabolism, Ubiquinone
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6164Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16026)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16026
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23079Georges Wauters,Thierry De Baere,Anne Willems,Enevold Falsen,Mario Vaneechoutte10.1099/ijs.0.02450-0Description of Comamonas aquatica comb. nov. and Comamonas kerstersii sp. nov. for two subgroups of Comamonas terrigena and emended description of Comamonas terrigenaIJSEM 53: 859-862 200312807213
36672Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5558
46224Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15333)https://www.ccug.se/strain?id=15333
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
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
72453Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2020.1StrainInfo: A central database for resolving microbial strain identifiers
120408Curators of the CIPCollection of Institut Pasteur (CIP 107987)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107987