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, Gram-positive, rod-shaped

description: Gordonia sputi 3884 is a microaerophile, mesophilic, Gram-positive 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/bacdive10570.20250331.9.3

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
    20215Gordona sputi
    20215Rhodococcus 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

@refgram staincell shapemotilityconfidence
123278positiverod-shapedno
125438no92.6
125438positive90.054
125439positive96.5

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

@refgrowthtypetemperature
11372positivegrowth28
40246positivegrowth30
57531positivegrowth37
67770positivegrowth28
123278positivegrowth25-37
123278nogrowth10
123278nogrowth41
123278nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
57531microaerophile
123278aerobe
125438aerobe90.556
125439obligate aerobe96.5

halophily

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

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12327816947citrate-carbon source
1232784853esculin+hydrolysis
123278606565hippurate-hydrolysis
12327817632nitrate+reduction
12327816301nitrite-reduction
12327817632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

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
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
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
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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
68382beta-galactosidase-3.2.1.23
68382esterase lipase (C 8)+

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 sequenceGQ871823611nuccore36823
20218G.sputi 16S rRNA gene (ATCC 29627T)X819231320nuccore36823
20218Gordonia sputi 16S rRNA gene, strain DSM43896TX806341486nuccore36823

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive96.5
125439BacteriaNetmotilityAbility to perform movementno82.4
125439BacteriaNetspore_formationAbility to form endo- or exosporesno76.5
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.054no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.451yes
125438spore-formingspore-formingAbility to form endo- or exosporesno53.648no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.556no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97no
125438motile2+flagellatedAbility to perform flagellated movementno92.6no

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1