Strain identifier

BacDive ID: 14151

Type strain: Yes

Species: Caenibius tardaugens

Strain Designation: ARi-1

Strain history: CIP <- 2003, JCM <- K. Fujii: strain ARI-1

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

@ref: 6574

BacDive-ID: 14151

DSM-Number: 16702

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

description: Caenibius tardaugens ARi-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of sewage treatment plant.

NCBI tax id

NCBI tax idMatching level
1219035strain
169176species

strain history

@refhistory
6574<- K. Fujii, Muroran; ARi-1
67770K. Fujii ARI-1.
123430CIP <- 2003, JCM <- K. Fujii: strain ARI-1

doi: 10.13145/bacdive14151.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Caenibius
  • species: Caenibius tardaugens
  • full scientific name: Caenibius tardaugens (Fujii et al. 2003) Hördt et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Novosphingobium tardaugens

@ref: 6574

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Hyphomicrobiaceae

genus: Caenibius

species: Caenibius tardaugens

full scientific name: Caenibius tardaugens (Fujii et al. 2003) Hördt et al. 2020

strain designation: ARi-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
123430negativerod-shapedno

colony morphology

@refincubation period
65743-7 days
609103 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6574REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39969MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123430CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123430CIP Medium 35yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=35

culture temp

@refgrowthtypetemperaturerange
6574positivegrowth28mesophilic
39969positivegrowth25mesophilic
60910positivegrowth30mesophilic
67770positivegrowth25mesophilic
123430positivegrowth25-37mesophilic
123430nogrowth5psychrophilic
123430nogrowth10psychrophilic
123430nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60910aerobe
123430obligate aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.972

halophily

@refsaltgrowthtested relationconcentration
123430NaClpositivegrowth0 %
123430NaClnogrowth2 %
123430NaClnogrowth4 %
123430NaClnogrowth6 %
123430NaClnogrowth8 %
123430NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

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
123430citrate-carbon source16947
123430esculin-hydrolysis4853
123430nitrate+reduction17632
123430nitrite-reduction16301
123430nitrate-respiration17632

metabolite production

  • @ref: 123430
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123430oxidase+
123430beta-galactosidase-3.2.1.23
123430alcohol dehydrogenase-1.1.1.1
123430gelatinase-
123430amylase-
123430DNase-
123430caseinase-3.4.21.50
123430catalase+1.11.1.6
123430tween esterase-
123430lecithinase-
123430lipase-
123430lysine decarboxylase-4.1.1.18
123430ornithine decarboxylase-4.1.1.17
123430protease-
123430tryptophan deaminase-
123430urease-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
123430-+++-+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123430---------++++--------+---------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6574activated sludge of sewage treatment plantTokyoJapanJPNAsia
60910Activated sludge of sewage treatment plantJapanJPNAsia
67770Activated sludge of sewage treatment plant in Tokyo
123430Environment, Activated sludge of a sewage treatment plantTokyoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_1545.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_883;97_1031;98_1220;99_1545&stattab=map
  • Last taxonomy: Novosphingobium tardaugens subclade
  • 16S sequence: AB681118
  • Sequence Identity:
  • Total samples: 2030
  • soil counts: 462
  • aquatic counts: 1092
  • animal counts: 373
  • plant counts: 103

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65741Risk group (German classification)
1234301Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Novosphingobium tardaugens gene for 16S rRNA, partial sequence, strain: NBRC 16725AB6811181410ena169176
6574Novosphingomonas sp. ARI-1 gene for 16S rRNAAB0702371418ena169176

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caenibius tardaugens NBRC 16725GCA_003860345completencbi1219035
66792Novosphingobium tardaugens NBRC 167251219035.3wgspatric1219035
66792Novosphingobium tardaugens NBRC 167251219035.9completepatric1219035
66792Novosphingobium tardaugens NBRC 167252600255065draftimg1219035
67770Caenibius tardaugens NBRC 16725GCA_000466945contigncbi1219035

GC content

  • @ref: 6574
  • GC-content: 61
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno79.778no
flagellatedno96.67no
gram-positiveno96.986no
anaerobicno98.944no
aerobicyes91.302yes
halophileno95.632no
spore-formingno93.013no
thermophileno97.886no
glucose-utilyes67.92no
glucose-fermentno93.129no

External links

@ref: 6574

culture collection no.: DSM 16702, ATCC BAA 531, IFO 16725, JCM 11434, NBRC 16725, CCUG 56307, CIP 107959, KCTC 12110

straininfo link

  • @ref: 83317
  • straininfo: 100829

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656151Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo.Fujii K, Satomi M, Morita N, Motomura T, Tanaka T, Kikuchi SInt J Syst Evol Microbiol10.1099/ijs.0.02301-02003Alphaproteobacteria/classification/genetics/*isolation & purification/*metabolism, Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Estradiol/*metabolism, Fatty Acids/analysis, Lipids/analysis, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, TokyoMetabolism
Phylogeny24737793Novosphingobium kunmingense sp. nov., isolated from a phosphate mine.Xie F, Quan S, Liu D, He W, Wang Y, Ma H, Chen G, Chao Y, Qian SInt J Syst Evol Microbiol10.1099/ijs.0.057273-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphates/*chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
29997609A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses.Zheng Q, Chen Q, Xu Y, Suttle CA, Jiao NFront Microbiol10.3389/fmicb.2018.014182018
Genetics30938330High-Quality Whole-Genome Sequence of an Estradiol-Degrading Strain, Novosphingobium tardaugens NBRC 16725.Ibero J, Sanz D, Galan B, Diaz E, Garcia JLMicrobiol Resour Announc10.1128/MRA.01715-182019
Metabolism31683600Testosterone Degradative Pathway of Novosphingobium tardaugens.Ibero J, Galan B, Diaz E, Garcia JLGenes (Basel)10.3390/genes101108712019Androgens/*metabolism, Bacterial Proteins/genetics/*metabolism, Biotransformation, Hydroxysteroid Dehydrogenases/genetics/*metabolism, Sphingomonadaceae/*enzymology/genetics, Testosterone/*metabolismEnzymology
Metabolism33424788Unraveling the 17beta-Estradiol Degradation Pathway in Novosphingobium tardaugens NBRC 16725.Ibero J, Galan B, Rivero-Buceta V, Garcia JLFront Microbiol10.3389/fmicb.2020.5883002020
Genetics34946795Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor.Ibero J, Galan B, Garcia JLGenes (Basel)10.3390/genes121218462021Bacterial Proteins/*genetics, Biosensing Techniques/methods, Estradiol/*genetics, Estrogens/*genetics, Estrone/*genetics, Promoter Regions, Genetic/genetics, Sphingomonadaceae/*genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6574Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16702)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16702
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
39969Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5527
60910Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56307)https://www.ccug.se/strain?id=56307
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/
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
83317Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100829.1StrainInfo: A central database for resolving microbial strain identifiers
123430Curators of the CIPCollection of Institut Pasteur (CIP 107959)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107959