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BacDive ID 10570
Type strain
Strain Designation 3884
Culture col. no. DSM 43896 ATCC 29627 IMET 7569 JCM 3228 KCC A-0228 CCUG 47138 CIP 100849 3884 PCM 2576 NBRC 16049 NBRC 100414 KCTC 3436 IFO 16049 CCM 3354 BCRC 13698 10 more
NCBI tax ID(s) 1089453 36823
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 11372

BacDive-ID: 10570

DSM-Number: 43896

keywords: genome sequence, 16S sequence, microaerophile, mesophilic, Gram-positive, rod-shaped

description: Gordonia sputi 3884 is a microaerophile, mesophilic, Gram-positive prokaryote 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/bacdive10570.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/actinomycetota
  • 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

@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
123278negativegrowth10
123278negativegrowth41
123278negativegrowth45

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
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
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
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
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
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
68382alpha-mannosidase-3.2.1.24

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

Interaction and safety

risk assessment

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

Sequence information

Genome sequences

@refdescriptionassembly levelINSDC accessionBV-BRC accessionIMG accessionNCBI tax IDscore
67770ASM24805v2 assembly for Gordonia sputi NBRC 100414contigGCA_0002480551089453.32513237321108945347.82
67770ASM1239625v1 assembly for Gordonia sputi ATCC 29627contigGCA_01239625536823.381107473583682368.48

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

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

Literature

@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: 126262
  • straininfo: 39624

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology25213797Purification, characterization and in-silico analysis of nitrilase from Gordonia terrae.Kumar V, Seth A, Kumari V, Kumar V, Bhalla TCProtein Pept Lett10.2174/09298665216661409091545372015*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/geneticsPhylogeny
30715639In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2.Nahurira R, Wang J, Yan Y, Jia Y, Fan S, Khokhar I, Eltoukhy A.AMB Express10.1186/s13568-019-0733-52019Heavy metals, Secondary metabolites, Phthalic acid esters, Gordonia, Aromatic Pollutants
33746349Disease-Suppressive Soils-Beyond Food Production: a Critical Review.Jayaraman S, Naorem AK, Lal R, Dalal RC, Sinha NK, Patra AK, Chaudhari SK.J Soil Sci Plant Nutr10.1007/s42729-021-00451-x2021Parasitism, Predation, Microbiome, Soil-borne Pathogens, Disease-suppressive Soils, Antibiotics And Drugs From The Soil, Metabiostasis, Soil Disease Triangle
35215141The Role of Serratomolide-like Amino Lipids Produced by Bacteria of Genus Serratia in Nematicidal Activity.Marques-Pereira C, Proenca DN, Morais PV.Pathogens10.3390/pathogens110201982022Pine wilt disease, Bursaphelenchus xylophilus, Pinewood nematode, Serratia, Serrawettin W1, Serrawettin W2, Serratomolides
37998770Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny.Pino-Rosa S, Medina-Pascual MJ, Carrasco G, Garrido N, Villalon P, Valiente M, Valdezate S.Antibiotics (Basel)10.3390/antibiotics121115682023Resistance, Pneumonia, bacteremia, Seca1, Gordonia Bronchialis, Gordonia Terrae, Gordonia Otitidis, Gordonia Spp. Gordonia Sputi

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
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
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
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer10.1093/database/baaf059StrainInfo—the central database for linked microbial strain identifiers

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