Strain identifier

BacDive ID: 2931

Type strain: Yes

Species: Comamonas badia

Strain Designation: No.12

Strain history: CIP <- 2005, IAM <- Y. Tago

NCBI tax ID(s): 1121348 (strain), 265291 (species)

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General

@ref: 6968

BacDive-ID: 2931

DSM-Number: 17552

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Comamonas badia No.12 is an aerobe, mesophilic, motile bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
1121348strain
265291species

strain history

@refhistory
6968<- A. Yokota <- Y. Tago; No.12
67770IAM 14839 <-- Y. Tago and A. Yokota.
116700CIP <- 2005, IAM <- Y. Tago

doi: 10.13145/bacdive2931.20230509.8.1

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 badia
  • full scientific name: Comamonas badia Tago and Yokota 2005

@ref: 6968

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Comamonas

species: Comamonas badia

full scientific name: Comamonas badia Tago and Yokota 2005

strain designation: No.12

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.07
69480100negative
116700yesnegativerod-shaped

pigmentation

  • @ref: 116700
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6968TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6968LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
38320MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116700CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368
116700CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
6968positivegrowth28mesophilic
38320positivegrowth30mesophilic
59190positivegrowth30mesophilic
67770positivegrowth27mesophilic
116700positivegrowth25-30mesophilic
116700nogrowth5psychrophilic
116700nogrowth10psychrophilic
116700nogrowth37mesophilic
116700nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59190aerobe
116700obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
116700NaClpositivegrowth0-2 %
116700NaClnogrowth4 %
116700NaClnogrowth6 %
116700NaClnogrowth8 %
116700NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
11670016947citrate-carbon source
1167004853esculin-hydrolysis
11670017632nitrate-reduction
11670016301nitrite-reduction
11670017632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11670035581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
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
116700oxidase+
116700beta-galactosidase-3.2.1.23
116700alcohol dehydrogenase-1.1.1.1
116700gelatinase-
116700amylase-
116700DNase-
116700caseinase-3.4.21.50
116700catalase+1.11.1.6
116700tween esterase+
116700lecithinase-
116700lipase-
116700lysine decarboxylase-4.1.1.18
116700ornithine decarboxylase-4.1.1.17
116700protease+
116700tryptophan deaminase-
116700urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116700--++-+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6968-------------------++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6968activated sludgeKawasaki, Kanagawa Pre.JapanJPNAsia
67770Activated sludgeNoborito, Kawasaki, Kanagawa Pref.JapanJPNAsia
116700Environment, Activated sludgeKawasaki, KanagawaJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_4171.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_2113;97_2545;98_3150;99_4171&stattab=map
  • Last taxonomy: Comamonas badia subclade
  • 16S sequence: AB164432
  • Sequence Identity:
  • Total samples: 3774
  • soil counts: 996
  • aquatic counts: 2420
  • animal counts: 200
  • plant counts: 158

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69681Risk group (German classification)
1167001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6968
  • description: Comamonas badia gene for 16S rRNA, partial sequence
  • accession: AB164432
  • length: 1496
  • database: ena
  • NCBI tax ID: 265291

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Comamonas badia DSM 175521121348.4wgspatric1121348
66792Comamonas badia DSM 175522528768012draftimg1121348
67770Comamonas badia DSM 17552 DSM 17552GCA_000484635contigncbi1121348

GC content

  • @ref: 67770
  • GC-content: 66.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.431no
flagellatedyes56.394no
gram-positiveno98.438no
anaerobicno98.613yes
aerobicyes90.391yes
halophileno89.695no
spore-formingno93.857no
thermophileno91.627yes
glucose-utilno89.272no
glucose-fermentno91.293no

External links

@ref: 6968

culture collection no.: DSM 17552, IAM 14839, KCTC 12244, CCUG 51443, JCM 21345, CIP 108817

straininfo link

  • @ref: 72454
  • straininfo: 131035

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15747228Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge.Tago Y, Yokota AJ Gen Appl Microbiol10.2323/jgam.50.2432004Base Composition, Comamonas/chemistry/classification/*isolation & purification, Fatty Acids/analysis, Phylogeny, Sewage/*microbiologyEnzymology
Phylogeny32170406Comamonas flocculans sp. nov., a Floc-Forming Bacterium Isolated from Livestock Wastewater.Kim DH, Han KI, Kwon HJ, Kim MG, Kim YG, Choi DH, Lee KC, Suh MK, Kim HS, Lee JS, Kim JGCurr Microbiol10.1007/s00284-020-01940-52020Animals, Bacterial Typing Techniques, Base Composition, Comamonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial, Livestock/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, Waste Water/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitle
6968Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17552)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17552
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
38320Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6488
59190Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51443)https://www.ccug.se/strain?id=51443
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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
72454Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131035.1StrainInfo: A central database for resolving microbial strain identifiers
116700Curators of the CIPCollection of Institut Pasteur (CIP 108817)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108817