Strain identifier

BacDive ID: 2927

Type strain: Yes

Species: Comamonas terrigena

Strain history: CIP <- 1963, NCTC, Vibrio percolans <- 1925, S. Mudd, Harvard, UK

NCBI tax ID(s): 1219032 (strain), 32013 (species)

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General

@ref: 2985

BacDive-ID: 2927

DSM-Number: 7099

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

description: Comamonas terrigena DSM 7099 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hay-infusion filtrate.

NCBI tax id

NCBI tax idMatching level
1219032strain
32013species

strain history

@refhistory
2985<- ATCC <- NCTC <- S. Mudd and S. Warren (Vibrio percolans)
67770J. Tamaoka KS 0020 <-- AJ 2083 <-- R. Hugh 247.
123475CIP <- 1963, NCTC, Vibrio percolans <- 1925, S. Mudd, Harvard, UK

doi: 10.13145/bacdive2927.20230509.8.1

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 terrigena
  • full scientific name: Comamonas terrigena (ex Hugh 1962) De Vos et al. 1985

  • synonyms

    @refsynonym
    20215Comamonas terrigena
    20215Comamonas percolans

@ref: 2985

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Comamonas

species: Comamonas terrigena

full scientific name: Comamonas terrigena (ex Hugh 1962) De Vos et al. 1985 emend. Willems et al. 1991 emend. Wauters et al. 2003

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityflagellum arrangementconfidence
23079negativerod-shapedyeslophotrichous
69480yes92.679
69480negative99.998

colony morphology

  • @ref: 23079
  • colony size: 1.0 mm
  • incubation period: 1 day
  • medium used: blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2985CASO 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
37574MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123475CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2985positivegrowth30mesophilic
23079positivegrowth30.0mesophilic
23079positivegrowth35.0mesophilic
23079nogrowth40.0thermophilic
23079nogrowth42.0thermophilic
23079nogrowth44.0thermophilic
37574positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 23079
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2307930742ethylene glycol-builds acid from
23079161933-hydroxybenzoate-growth
23079178794-hydroxybenzoate-growth
230794853esculin-hydrolysis
230795291gelatin-hydrolysis
2307916301nitrite-reduction
2307916947citrate+carbon source
23079370543-hydroxybutyrate+growth
2307930089acetate+growth
2307916977L-alanine+growth
2307917203L-proline+growth
2307924996lactate+growth
2307917272propionate+growth
230799300suberic acid+growth
2307931011valerate+growth
2307918186tyrosine+hydrolysis
2307928938ammonium+nitrogen source
2307917632nitrate+reduction
2307927689decanoate+/-growth
2307917240itaconate+/-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

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
2307937943colistinyesyes
2307950453desferrioxamineyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2307935581indoleno
2307916136hydrogen sulfideno
6836935581indoleno

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
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
2985+-------------+-+---+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
2985hay-infusion filtrate
123475Environment, Hay-infusion filtrateUnited KingdomGBREurope1921

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5975.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_704;97_822;98_4438;99_5975&stattab=map
  • Last taxonomy: Comamonas terrigena subclade
  • 16S sequence: AJ430342
  • Sequence Identity:
  • Total samples: 697
  • soil counts: 34
  • aquatic counts: 451
  • animal counts: 190
  • plant counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29852Risk group (German classification)
1234751Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Comamonas terrigena 16S rRNA gene, strain DSM 7099AJ4203261498ena32013
20218Comamonas terrigena gene for 16S rRNA, strain: IAM 12052AB0214181520ena32013
20218Comamonas terrigena gene for 16S rRNA, partial sequence, strain: NBRC 12685AB6803151456ena32013
20218Comamonas terrigena gene for 16S rRNA, partial sequence, strain: NBRC 13299AB6804001456ena32013
23079Comamonas terrigena partial 16S rRNA gene, type strain LMG 1253TAJ4303421377nuccore32013

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Comamonas terrigena NBRC 132991219032.4wgspatric1219032
66792Comamonas terrigena strain NCTC193732013.6wgspatric32013
66792Comamonas terrigena NBRC 132992731957557draftimg1219032
66792Comamonas terrigena NCTC 19372808606720draftimg32013
67770Comamonas terrigena NBRC 13299GCA_006740045completencbi1219032
67770Comamonas terrigena NCTC1937GCA_900461435contigncbi32013

GC content

@refGC-contentmethod
2307964.0
6777064thermal denaturation, midpoint method (Tm)
6777065.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.782no
gram-positiveno98.634yes
anaerobicno98.657yes
aerobicyes94.303yes
halophileno94.01no
spore-formingno97.06no
glucose-utilno82.153no
flagellatedyes82.647yes
thermophileno99.53no
glucose-fermentno88.773no

External links

@ref: 2985

culture collection no.: DSM 7099, ATCC 8461, CCUG 15327, CIP 63.44, LMG 5929, NCIB 8193, NCTC 1937, NRRL B-1055, JCM 6230, BCRC 10911, CCM 2409, CCUG 2185, IAM 12052, IAM 12421, IFO 12685, IFO 13299, IMET 10768, LMG 1253, NBRC 12685, NBRC 13299, NCIMB 8193, NRRL B-781

straininfo link

  • @ref: 72450
  • straininfo: 2018

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology16110914Production of catalases by Comamonas spp. and resistance to oxidative stress.Godocikova J, Bohacova V, Zamocky M, Polek BFolia Microbiol (Praha)10.1007/BF029314582005Catalase/*biosynthesis, Comamonas/drug effects/enzymology/*growth & development/isolation & purification, *Drug Resistance, Bacterial, Hydrogen Peroxide/*pharmacology, Oxidative Stress/*physiology, Petroleum, Sewage/microbiology, Soil Microbiology, Soil Pollutants, Waste Disposal, FluidBiotechnology
Phylogeny17392226Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus.Chou JH, Sheu SY, Lin KY, Chen WM, Arun AB, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.64551-02007Animals, Comamonas/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Digestive System/microbiology, Isoptera/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18175717Comamonas composti sp. nov., isolated from food waste compost.Young CC, Chou JH, Arun AB, Yen WS, Sheu SY, Shen FT, Lai WA, Rekha PD, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65277-02008Bacterial Typing Techniques, Comamonas/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, Fatty Acids/analysis, *Food Microbiology, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, Species Specificity, TaiwanGenetics
Phylogeny23125317Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil.Sun LN, Zhang J, Chen Q, He J, Li QF, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.045716-02012Agriculture, 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, UbiquinoneGenetics
Phylogeny25212224Comamonas humi sp. nov., isolated from soil.Hatayama KInt J Syst Evol Microbiol10.1099/ijs.0.067439-02014Bacterial Typing Techniques, Base Composition, Comamonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2985Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7099)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7099
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
37574Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10053
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
72450Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2018.1StrainInfo: A central database for resolving microbial strain identifiers
123475Curators of the CIPCollection of Institut Pasteur (CIP 63.44)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2063.44