Strain identifier

BacDive ID: 10542

Type strain: Yes

Species: Gordonia bronchialis

Strain Designation: 3410

Strain history: CIP <- 1984, ATCC <- M. Tsukamara : strain 3410 <- Kondo

NCBI tax ID(s): 526226 (strain), 2054 (species)

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

@ref: 10903

BacDive-ID: 10542

DSM-Number: 43247

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

description: Gordonia bronchialis 3410 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from sputum of woman with cavitary disease of both upper lungs.

NCBI tax id

NCBI tax idMatching level
2054species
526226strain

strain history

@refhistory
10903<- NCTC
67770KCC A-0198 <-- M. Tsukamura 3410.
117049CIP <- 1984, ATCC <- M. Tsukamara : strain 3410 <- Kondo

doi: 10.13145/bacdive10542.20230509.8.1

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 bronchialis
  • full scientific name: Gordonia bronchialis corrig. (Tsukamura 1971) Stackebrandt et al. 1989
  • synonyms

    @refsynonym
    20215Gordona bronchialis
    20215Rhodococcus bronchialis

@ref: 10903

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia bronchialis

full scientific name: Gordonia bronchialis (Tsukamura 1971) Stackebrandt et al. 1989 emend. Nouioui et al. 2018

strain designation: 3410

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
117049positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19562Pastel orange10-14 daysISP 2
19562Pastel orange10-14 daysISP 3
19562Pastel orange10-14 daysISP 4
19562Pastel orange10-14 daysISP 5
19562Pastel orange10-14 daysISP 6
19562Pastel orange10-14 daysISP 7
117049

multicellular morphology

@refmedium nameforms multicellular complex
19562ISP 2
19562ISP 3no
19562ISP 4no
19562ISP 5no
19562ISP 6no
19562ISP 7no

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_43247_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10903TRYPTICASE 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
10903GLYCEROL-SOIL MEDIUM (DSMZ Medium 80)yeshttps://mediadive.dsmz.de/medium/80Name: GLYCEROL-SOIL MEDIUM (DSMZ Medium 80) Composition: Glycerol 20.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Beef extract 3.0 g/l Soil extract Distilled water
19562ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19562ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19562ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19562ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19562ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19562ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40091MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
117049CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
10903positivegrowth28mesophilic
40091positivegrowth30mesophilic
67770positivegrowth28mesophilic
117049positivegrowth10-37
117049nogrowth41thermophilic
117049nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117049
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
19562no
69480no99.743

halophily

@refsaltgrowthtested relationconcentration
19562NaClpositivemaximum2.5 %
117049NaClpositivegrowth0-6 %
117049NaClnogrowth8 %
117049NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1956217234glucose+
1956222599arabinose-
1956217992sucrose+
1956218222xylose-
1956217268myo-inositol+
1956229864mannitol-
1956228757fructose+
1956226546rhamnose-
1956216634raffinose-
1956262968cellulose-
68371Potassium 5-ketogluconate-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
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-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
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
11704916947citrate-carbon source
1170494853esculin-hydrolysis
11704917632nitrate+reduction
11704916301nitrite-reduction
117049132112sodium thiosulfate+builds gas from
11704917632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11704935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11704915688acetoin-
11704917234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
117049oxidase-
117049beta-galactosidase-3.2.1.23
117049alcohol dehydrogenase-1.1.1.1
117049gelatinase-
117049amylase-
117049DNase-
117049caseinase-3.4.21.50
117049catalase+1.11.1.6
117049tween esterase+
117049gamma-glutamyltransferase-2.3.2.2
117049lecithinase-
117049lysine decarboxylase-4.1.1.18
117049ornithine decarboxylase-4.1.1.17
117049phenylalanine ammonia-lyase+4.3.1.24
117049tryptophan deaminase-
117049urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19562--+/-+--+--+-+-----+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19562+---+++--++---++---
117049+++-+----++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19562-++-+-+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117049----------+++/------------------+/-+/------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117049++-++--+------------------------+----------------+-----------------+-------+---++-------+-------+--

Isolation, sampling and environmental information

isolation

@refsample type
10903sputum of woman with cavitary disease of both upper lungs
67770Sputa of patients with pulmonary disease
117049Human, Sputum

isolation source categories

Cat1Cat2Cat3
#Infection
#Host#Human#Female
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
109032Risk group (German classification)
195622Risk group (German classification)
1170491Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia bronchialis clone C2 16S ribosomal RNA gene, partial sequenceAY262331504ena526226
20218Gordona bronchialis partial 16S rRNAX53201798ena526226
20218G.bronchialis 16S rRNA geneX759031331ena526226
20218G.bronchialis (DSM 43247) 16S rRNA geneX792871472ena526226
67770G.bronchialis 16S rRNA gene (CIP 1780.88T)X819191393ena2054

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia bronchialis DSM 43247GCA_000024785completencbi526226
66792Gordonia bronchialis DSM 43247526226.8completepatric526226
66792Gordonia bronchialis DSM 43247526226.15plasmidpatric526226
66792Gordonia bronchialis strain NCTC106672054.5wgspatric2054
66792Gordonia bronchialis 3410, DSM 43247646311932completeimg526226
66792Gordonia bronchialis NCTC 106672854968586draftimg2054
67770Gordonia bronchialis NCTC10667GCA_900450805contigncbi2054

GC content

@refGC-contentmethod
6777067.1genome sequence analysis
6777065thermal denaturation, midpoint method (Tm)
6777065.5thermal denaturation, midpoint method (Tm)
6777067.04genome sequence analysis
6777065.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
motileno94.349no
flagellatedno98.283no
gram-positiveyes88.107no
anaerobicno99.431no
aerobicyes88.48no
halophileno92.015no
spore-formingno84.65yes
thermophileno98.446no
glucose-utilyes89.801yes
glucose-fermentno84.334yes

External links

@ref: 10903

culture collection no.: DSM 43247, ATCC 25592, JCM 3198, KCC A-0198, NCTC 10667, BCRC 13721, CCM 2631, CCUG 20989, CCUG 34317, CCUG 34956, CIP 100847, IFM 0150, IFO 16047, IMET 7370, IMSNU 22088, JCM 3231, KCTC 3076, LMG 5355, NBRC 16047, PCM 2167, VKM Ac-956

straininfo link

  • @ref: 79818
  • straininfo: 2980

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny16400987[Isolation and comparative analysis of glycolipid fractions in bifidobacteria].Novik GI, Astapovich NI, Grzegorzewicz A, Gamian AMikrobiologiia2005Bifidobacterium/*chemistry, Chromatography, Thin Layer, Glycolipids/*analysis/isolation & purificationEnzymology
Phylogeny17012545Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam.Soddell JA, Stainsby FM, Eales KL, Seviour RJ, Goodfellow MInt J Syst Evol Microbiol2006Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Gordonia Bacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyGenetics10.1099/ijs.0.64034-0
Phylogeny30994431Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment.Sangkanu S, Suriyachadkun C, Phongpaichit SInt J Syst Evol Microbiol2019Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Gordonia Bacterium/*classification/isolation & purification, Mycolic Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome10.1099/ijsem.0.003399
Phylogeny32667871Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan.Xie Y, Zhou S, Xu Y, Wu W, Xia W, Zhang R, Huang D, Huang XInt J Syst Evol Microbiol2020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome10.1099/ijsem.0.004310

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10903Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43247)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43247
19562Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43247.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
40091Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12357
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
79818Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2980.1StrainInfo: A central database for resolving microbial strain identifiers
117049Curators of the CIPCollection of Institut Pasteur (CIP 100847)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100847