Strain identifier

BacDive ID: 11117

Type strain: Yes

Species: Nocardioides aromaticivorans

Strain Designation: H-1

Strain history: CIP <- 2005, JCM <- 2002 K. Kawahara: strain H-1

NCBI tax ID(s): 1305622 (strain), 200618 (species)

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General

@ref: 5724

BacDive-ID: 11117

DSM-Number: 15131

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped

description: Nocardioides aromaticivorans H-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from polluted river water.

NCBI tax id

NCBI tax idMatching level
200618species
1305622strain

strain history

@refhistory
5724<- K. Kawahara, <- M. Kubota; H-1
67770K. Kawahara H-1.
116501CIP <- 2005, JCM <- 2002 K. Kawahara: strain H-1

doi: 10.13145/bacdive11117.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides aromaticivorans
  • full scientific name: Nocardioides aromaticivorans Kubota et al. 2005

@ref: 5724

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides aromaticivorans

full scientific name: Nocardioides aromaticivorans Kubota et al. 2005

strain designation: H-1

type strain: yes

Morphology

cell morphology

  • @ref: 116501
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5724GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
5724TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
38309MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
116501CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
5724positivegrowth28mesophilic
38309positivegrowth30mesophilic
67770positivegrowth28mesophilic
116501positivegrowth25-45
116501nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116501
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 116501
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371salicin-builds acid from17814
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
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116501citrate-carbon source16947
116501esculin-hydrolysis4853
116501hippurate+hydrolysis606565
116501nitrate-reduction17632
116501nitrite-reduction16301
116501nitrate-respiration17632

metabolite production

  • @ref: 116501
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11650115688acetoin+
11650117234glucose-

enzymes

@refvalueactivityec
116501oxidase-
116501beta-galactosidase+3.2.1.23
116501alcohol dehydrogenase-1.1.1.1
116501gelatinase+
116501amylase+
116501DNase+
116501caseinase+3.4.21.50
116501catalase+1.11.1.6
116501tween esterase+
116501gamma-glutamyltransferase+2.3.2.2
116501lecithinase-
116501lipase+
116501lysine decarboxylase-4.1.1.18
116501ornithine decarboxylase-4.1.1.17
116501phenylalanine ammonia-lyase-4.3.1.24
116501protease+
116501tryptophan deaminase-
116501urease+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
116501-+++-++-+-++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116501---+/-------+/-+/-+/-----+/-------+/--+/-+/---+/---------+/---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116501++-+---+-++--------+++-+---------+--------------++------+++-+-++++------++++--+++-------+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5724polluted river waterKanagawaJapanJPNAsia
67770The Hikichi RiverKanagawa Pref.JapanJPNAsia
116501Environment, Dioxin-polluted environments

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_59944.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_4911;99_59944&stattab=map
  • Last taxonomy: Nocardioides aromaticivorans
  • 16S sequence: AB087721
  • Sequence Identity:
  • Total samples: 401
  • soil counts: 220
  • aquatic counts: 59
  • animal counts: 98
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57241Risk group (German classification)
1165011Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Nocardioides sp. H-1 gene for 16S rRNA, partial sequence
  • accession: AB087721
  • length: 1498
  • database: ena
  • NCBI tax ID: 200618

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides aromaticivorans JCM 11674GCA_001313745contigncbi1305622
66792Nocardioides aromaticivorans JCM 116741305622.3wgspatric1305622
66792Nocardioides aromaticivorans strain DSM 15131200618.4wgspatric200618
66792Nocardioides aromaticivorans DSM 151312833977688draftimg200618
66792Nocardioides aromaticivorans JCM 116742734481961draftimg1305622
67770Nocardioides aromaticivorans DSM 15131GCA_013408525contigncbi200618

GC content

@refGC-contentmethod
572472
6777072.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno73.336no
gram-positiveyes76.237no
anaerobicno98.882no
halophileno92.927no
spore-formingno91.639no
thermophileno98.61yes
glucose-utilyes83.402no
flagellatedno93.377no
aerobicyes95.953no
glucose-fermentno81.504no

External links

@ref: 5724

culture collection no.: DSM 15131, IAM 14992, JCM 11674, CIP 108782

straininfo link

  • @ref: 80366
  • straininfo: 139009

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15830809Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments.Kubota M, Kawahara K, Sekiya K, Uchida T, Hattori Y, Futamata H, Hiraishi ASyst Appl Microbiol10.1016/j.syapm.2004.10.0022005Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Benzofurans/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Dioxins/*metabolism, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Water Pollutants, Chemical/*metabolismMetabolism
Phylogeny19625430Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.008821-02009Actinomycetales/classification/enzymology/genetics/*isolation & purification, Bacterial Proteins/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, beta-Glucosidase/*metabolismMetabolism
Metabolism26065513Metabolic fate of the (14)C-labeled herbicide clodinafop-propargyl in a sediment-water system.Yuan Y, Weitzel P, Schaffer A, Schmidt BJ Environ Sci Health B10.1080/03601234.2015.10288252015Benzopyrans/chemistry, Carbon Radioisotopes/analysis, Chemical Fractionation, Chromatography, Gel, Geologic Sediments/*analysis/microbiology, Germany, Herbicides/analysis/*metabolism, Humic Substances, Propionates/analysis/chemistry/*metabolism, Pyridines/analysis/chemistry/*metabolism, Soil Pollutants/analysis/chemistry/metabolism, Water/chemistry, Water Pollutants, Chemical/analysis/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5724Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15131)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15131
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
38309Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6448
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/
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
80366Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139009.1StrainInfo: A central database for resolving microbial strain identifiers
116501Curators of the CIPCollection of Institut Pasteur (CIP 108782)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108782