Strain identifier

BacDive ID: 10570

Type strain: Yes

Species: Gordonia sputi

Strain Designation: 3884

Strain history: CIP <- 1984, ATCC <- M. Tsukamara: strain 3884, Rhodococcus sputi

NCBI tax ID(s): 1089453 (strain), 36823 (species)

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General

@ref: 11372

BacDive-ID: 10570

DSM-Number: 43896

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic

description: Gordonia sputi 3884 is a microaerophile, mesophilic bacterium that was isolated from sputum of patient with pulmonary disease.

NCBI tax id

NCBI tax idMatching level
36823species
1089453strain

strain history

@refhistory
11372<- JCM <- KCC <- M. Tsukamura, 3884, Nagura 8539
67770KCC A-0228 <-- M. Tsukamura 3884 (strain Nagura 8539).
123278CIP <- 1984, ATCC <- M. Tsukamara: strain 3884, Rhodococcus sputi

doi: 10.13145/bacdive10570.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia sputi
  • full scientific name: Gordonia sputi corrig. (Tsukamura and Yano 1985 ex Tsukamura 1978) Stackebrandt et al. 1989

  • synonyms

    @refsynonym
    20215Rhodococcus sputi
    20215Gordona sputi

@ref: 11372

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia sputi

full scientific name: Gordonia sputi (Tsukamura and Yano 1985) Stackebrandt et al. 1989 emend. Tsukamura 1991 emend. Riegel et al. 1994

strain designation: 3884

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.59
69480100positive
123278nopositiverod-shaped

colony morphology

  • @ref: 123278

multimedia

  • @ref: 11372
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43896.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11372GYM 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
11372TRYPTICASE 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
40246MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123278CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
11372positivegrowth28mesophilic
40246positivegrowth30mesophilic
57531positivegrowth37mesophilic
67770positivegrowth28mesophilic
123278positivegrowth25-37mesophilic
123278nogrowth10psychrophilic
123278nogrowth41thermophilic
123278nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57531microaerophile
123278obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.417

halophily

  • @ref: 123278
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

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
123278citrate-carbon source16947
123278esculin+hydrolysis4853
123278hippurate-hydrolysis606565
123278nitrate+reduction17632
123278nitrite-reduction16301
123278nitrate-respiration17632

antibiotic resistance

  • @ref: 123278
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123278
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12327815688acetoin-
12327817234glucose-

enzymes

@refvalueactivityec
123278oxidase-
123278beta-galactosidase+3.2.1.23
123278alcohol dehydrogenase-1.1.1.1
123278gelatinase+/-
123278amylase-
123278DNase-
123278caseinase-3.4.21.50
123278catalase+1.11.1.6
123278tween esterase+/-
123278gamma-glutamyltransferase+2.3.2.2
123278lecithinase-
123278lipase-
123278lysine decarboxylase-4.1.1.18
123278ornithine decarboxylase-4.1.1.17
123278phenylalanine ammonia-lyase-4.3.1.24
123278protease-
123278tryptophan deaminase-
123278urease+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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57531C10:00.610
    57531C14:02.714
    57531C15:00.915
    57531C16:048.716
    57531C17:00.717
    57531C18:02.818
    57531C16:0 anteiso115.717
    57531C16:1 ω9c0.515.774
    57531C17:0 anteiso0.316.722
    57531C17:1 ω9c0.616.773
    57531C18:1 ω9c17.217.769
    57531C18:2 ω6,9c/C18:0 ANTE6.417.724
    57531C20:2 ω6,9c0.419.735
    57531TBSA 10Me18:016.618.392
    57531Unidentified0.519.458
  • 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
123278--++-+----++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123278-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123278-+-++--+----------+-------+----+-+-++----------------+---------++---------+---------+---+-------+--

Isolation, sampling and environmental information

isolation

@refsample type
11372sputum of patient with pulmonary disease
57531Human sputum
67770Sputa of patients with pulmonary disease
123278Human, Sputum

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Airways
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_3430.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_2147;98_2632;99_3430&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: X80634
  • Sequence Identity:
  • Total samples: 5392
  • soil counts: 169
  • aquatic counts: 1283
  • animal counts: 3862
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113722Risk group (German classification)
1232781Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia sputi strain ATCC 29627 16S ribosomal RNA gene, partial sequenceGQ871823611ena36823
20218G.sputi 16S rRNA gene (ATCC 29627T)X819231320ena36823
20218Gordonia sputi 16S rRNA gene, strain DSM43896TX806341486ena36823

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia sputi NBRC 1004141089453.3wgspatric1089453
66792Gordonia sputi strain ATCC 2962736823.3wgspatric36823
66792Gordonia sputi NBRC 1004142513237321draftimg1089453
67770Gordonia sputi NBRC 100414GCA_000248055contigncbi1089453
67770Gordonia sputi ATCC 29627GCA_012396255contigncbi36823

GC content

  • @ref: 67770
  • GC-content: 66.7
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
motileno94.559no
flagellatedno98.277no
gram-positiveyes91.998no
anaerobicno99.374yes
aerobicyes86.809yes
halophileno87.468no
spore-formingno76.669no
glucose-utilyes90.314no
thermophileno99.333yes
glucose-fermentno87.511no

External links

@ref: 11372

culture collection no.: DSM 43896, ATCC 29627, IMET 7569, JCM 3228, KCC A-0228, CCUG 47138, CIP 100849, BCRC 13698, CCM 3354, IFO 16049, KCTC 3436, NBRC 100414, NBRC 16049, PCM 2576

straininfo link

  • @ref: 79845
  • straininfo: 39624

literature

  • topic: Enzymology
  • Pubmed-ID: 25213797
  • title: Purification, characterization and in-silico analysis of nitrilase from Gordonia terrae.
  • authors: Kumar V, Seth A, Kumari V, Kumar V, Bhalla TC
  • journal: Protein Pept Lett
  • DOI: 10.2174/0929866521666140909154537
  • year: 2015
  • mesh: *Amino Acid Sequence, Aminohydrolases/*chemistry/*genetics/isolation & purification, Catalytic Domain, Cloning, Molecular, Computer Simulation, Kinetics, Sequence Alignment, Sequence Homology, Amino Acid, Substrate Specificity, Theaceae/*enzymology/genetics
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11372Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43896)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43896
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
40246Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12359
57531Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47138)https://www.ccug.se/strain?id=47138
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
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)
79845Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39624.1StrainInfo: A central database for resolving microbial strain identifiers
123278Curators of the CIPCollection of Institut Pasteur (CIP 100849)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100849