Strain identifier

BacDive ID: 10615

Type strain: Yes

Species: Gordonia malaquae

Strain history: CIP <- 2007, CCUG <- 2006, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB WWC-22

NCBI tax ID(s): 1223542 (strain), 410332 (species)

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General

@ref: 12309

BacDive-ID: 10615

DSM-Number: 45064

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

description: Gordonia malaquae DSM 45064 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sludge of wastewater treatment plant.

NCBI tax id

NCBI tax idMatching level
1223542strain
410332species

strain history

@refhistory
12309<- A. F. Yassin; IMMIB WWCC-22 <- A. B. Arun
67770IFM 10866 <-- DSM 45064 <-- A. F. Yassin IMMIB WWCC-22 <-- A. B. Arun.
120753CIP <- 2007, CCUG <- 2006, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB WWC-22

doi: 10.13145/bacdive10615.20230509.8.1

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 malaquae
  • full scientific name: Gordonia malaquae Yassin et al. 2007

@ref: 12309

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia malaquae

full scientific name: Gordonia malaquae Yassin et al. 2007 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32058positiverod-shaped
69480no92.489
69480positive100
120753positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
19907Sand yellow10-14 daysISP 2
19907Cream10-14 daysISP 3
19907Cream10-14 daysISP 4
19907Cream10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
19907noISP 2
19907noISP 3
19907noISP 4
19907noISP 6

pigmentation

  • @ref: 32058
  • production: no

multimedia

  • @ref: 12309
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45064.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12309GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
12309TRYPTICASE 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
19907ISP 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
19907ISP 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:
19907ISP 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
19907ISP 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
33313MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120753CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12309positivegrowth28mesophilic
19907positiveoptimum28mesophilic
32058positivegrowth22-37
32058positiveoptimum29.5mesophilic
33313positivegrowth25mesophilic
59929positivegrowth22-37
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32058aerobe
59929aerobe
120753obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.961

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1990717234glucose+
1990722599arabinose-
1990717992sucrose+
1990718222xylose-
1990717268myo-inositol-
1990729864mannitol-
1990728757fructose+
1990726546rhamnose-
1990716634raffinose-
1990762968cellulose-
32058620642,3-butanediol+carbon source
3205830089acetate+carbon source
3205816449alanine+carbon source
3205816947citrate+carbon source
3205817234glucose+carbon source
3205829864mannitol+carbon source
3205826271proline+carbon source
3205817822serine+carbon source
3205817992sucrose+carbon source
3205827082trehalose+carbon source
3205816199urea+carbon source
3205818222xylose+carbon source
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
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
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
6837116024D-mannose-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
12075317632nitrate+reduction
12075316301nitrite-reduction
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

  • @ref: 120753
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32058urease+3.5.1.5
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
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
120753oxidase-
120753catalase+1.11.1.6
120753urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19907---+--+--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19907+++++----++-+-++---
120753+++-+----++-+-++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120753-------------------------------+-----------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12309sludge of wastewater treatment plantTaichung city, Taichung Industrial ParkTaiwanTWNAsia
59929Sludge,wastewater treatment plantTaichung cityTaiwanTWNAsia
67770Sludge of a wastewater treatment plant in Taichung Industrial ParkTaichung CityTaiwanTWNAsia
120753Environment, Sludge, wastewater treatment plantTaichungTaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Water treatment plant
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2883.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_1820;98_2231;99_2883&stattab=map
  • Last taxonomy: Gordonia malaquae subclade
  • 16S sequence: AM406674
  • Sequence Identity:
  • Total samples: 2858
  • soil counts: 282
  • aquatic counts: 1583
  • animal counts: 959
  • plant counts: 34

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123091Risk group (German classification)
199071Risk group (German classification)
1207531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12309
  • description: Gordonia malaquae partial 16S rRNA gene, type strain IMMIB WWCC-22
  • accession: AM406674
  • length: 1489
  • database: ena
  • NCBI tax ID: 410332

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia malaquae NBRC 1082501223542.3wgspatric1223542
66792Gordonia malaquae strain DSM 45064410332.5wgspatric410332
66792Gordonia malaquae DSM 450642639762576draftimg410332
66792Gordonia malaquae NBRC 1082502523231040draftimg1223542
67770Gordonia malaquae NBRC 108250GCA_000344135contigncbi1223542
67770Gordonia malaquae DSM 45064GCA_900105435contigncbi410332

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
motileno95.487no
gram-positiveyes90.738yes
anaerobicno99.506yes
aerobicyes89.883yes
halophileno92.377no
spore-formingno78.392no
glucose-utilyes90.087yes
flagellatedno98.16no
thermophileno99.18no
glucose-fermentno87.451no

External links

@ref: 12309

culture collection no.: DSM 45064, CCUG 53555, CIP 109612, IMMIB WWCC-22, JCM 14874, IFM 10866, NBRC 108250, IMMIB WWC-22

straininfo link

  • @ref: 79888
  • straininfo: 297516

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473260Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant.Yassin AF, Shen FT, Hupfer H, Arun AB, Lai WA, Rekha PD, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.64893-02007Actinomycetales/chemistry/*classification/*isolation & purification, Bacterial Typing Techniques, Carbon/metabolism, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nitrogen/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Vitamin K 2/analysis, *Water MicrobiologyMetabolism
Phylogeny25052399Gordonia iterans sp. nov., isolated from a patient with pneumonia.Kang YQ, Ming H, Gonoi T, Chen Y, Cao Y, Wang YY, Cheng J, Koga T, Mikami Y, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.063438-02014Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Gordonia Bacterium/*classification/genetics/isolation & purification, Humans, Japan, Male, Middle Aged, Molecular Sequence Data, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Pneumonia, Bacterial/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/*microbiology, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Phylogeny32427091Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant.Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y, Gonoi T, Mikami Y, Yaguchi TInt J Syst Evol Microbiol10.1099/ijsem.0.0042252020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12309Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45064)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45064
19907Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45064.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
32058Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2830728776041
33313Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7375
59929Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53555)https://www.ccug.se/strain?id=53555
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
68379Automatically annotated from API Coryne
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)
79888Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297516.1StrainInfo: A central database for resolving microbial strain identifiers
120753Curators of the CIPCollection of Institut Pasteur (CIP 109612)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109612