Strain identifier

BacDive ID: 10623

Type strain: Yes

Species: Gordonia neofelifaecis

Strain Designation: AD-6

Strain history: DSM 45646 <-- NRRL B-59395 <-- J. Dai; AD-6.

NCBI tax ID(s): 644548 (strain), 945692 (species)

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General

@ref: 17966

BacDive-ID: 10623

DSM-Number: 45646

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

description: Gordonia neofelifaecis AD-6 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from faeces of a clouded leopard .

NCBI tax id

NCBI tax idMatching level
644548strain
945692species

strain history

@refhistory
17966<- NRRL; NRRL B-59395 <- J. Dai
67770DSM 45646 <-- NRRL B-59395 <-- J. Dai; AD-6.

doi: 10.13145/bacdive10623.20230509.8.1

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 neofelifaecis
  • full scientific name: Gordonia neofelifaecis Liu et al. 2011

@ref: 17966

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia neofelifaecis

full scientific name: Gordonia neofelifaecis Liu et al. 2011 emend. Nouioui et al. 2018

strain designation: AD-6

type strain: yes

Morphology

cell morphology

  • @ref: 29762
  • gram stain: positive
  • cell length: 1.3 µm
  • cell width: 0.45 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
21403sand yellow (1002)10-14 daysISP 2
2140310-14 daysISP 3
2140310-14 daysISP 4
2140310-14 daysISP 5
21403Light ivory (1015)10-14 daysISP 7
21403Sand yellow (1002) – Brown beige (1011)10-14 daysSuter with tyrosine
21403Ivory (1015)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21403noISP 2
21403noISP 3
21403noISP 4
21403noISP 5
21403noISP 7
21403noSuter with tyrosine
21403noSuter without tyrosine

multimedia

  • @ref: 17966
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45646.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17966GYM 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
21403ISP 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
21403ISP 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:
21403ISP 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
21403ISP 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
21403ISP 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
21403Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21403Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
17966positivegrowth28mesophilic
29762positiveoptimum30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 29762
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29762
  • spore formation: no

halophily

  • @ref: 21403
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2140317234glucose+
2140322599arabinose-
2140317992sucrose+
2140318222xylose+
2140317268myo-inositol-
2140337684mannose-
2140328757fructose+
2140326546rhamnose-
2140316634raffinose-
2140362968cellulose+
2976228260galactose+carbon source
2976225017leucine+carbon source
2976226546rhamnose+carbon source
2976217822serine+carbon source
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

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
68379pyrrolidonyl arylamidase-3.4.19.3
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21403-+/--+--+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21403+++++++--++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
17966faeces of a clouded leopard (Neofelis nebulosa)Sichuan ProvinceChinaCHNAsia
67770Fresh faeces of a specimen of a clouded leopard Neofelis nebulosa at Chengdu ZooChinaCHNAsiaNeofelis nebulosa

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Felidae (Cat)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2948.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_1820;98_2276;99_2948&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: FJ938167
  • Sequence Identity:
  • Total samples: 1008
  • soil counts: 85
  • aquatic counts: 620
  • animal counts: 263
  • plant counts: 40

Safety information

risk assessment

  • @ref: 17966
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17966
  • description: Gordonia neofelifaecis NRRL B-59395 strain AD-6 16S ribosomal RNA gene, partial sequence
  • accession: FJ938167
  • length: 1417
  • database: ena
  • NCBI tax ID: 644548

Genome sequences

  • @ref: 67770
  • description: Gordonia neofelifaecis NRRL B-59395
  • accession: GCA_000192435
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 644548

GC content

@refGC-contentmethod
6777068.62genome sequence analysis
6777068.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.138no
flagellatedno98.687no
gram-positiveyes90.056yes
anaerobicno99.391yes
aerobicyes88.938yes
halophileno89.485no
spore-formingno84.673yes
glucose-utilyes88.076yes
thermophileno99.298no
glucose-fermentno85.808yes

External links

@ref: 17966

culture collection no.: DSM 45646, CCTCC AB 209144, JCM 31031, NRRL B-59395

straininfo link

  • @ref: 79895
  • straininfo: 401192

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20190025Gordonia neofelifaecis sp. nov., a cholesterol side-chain-cleaving actinomycete isolated from the faeces of Neofelis nebulosa.Liu Y, Ge F, Chen G, Li W, Ma P, Zhang G, Zeng LInt J Syst Evol Microbiol10.1099/ijs.0.020321-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Bacterial Proteins/genetics, Cholesterol/*metabolism, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, Felidae/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Genetics21742880Draft genome sequence of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete.Ge F, Li W, Chen G, Liu Y, Zhang G, Yong B, Wang Q, Wang N, Huang Z, Li W, Wang J, Wu C, Xie Q, Liu GJ Bacteriol10.1128/JB.05531-112011Actinomycetales/*genetics/isolation & purification/metabolism, Animals, Cholesterol/metabolism, DNA, Bacterial/*chemistry/*genetics, Feces/microbiology, Felidae/microbiology, *Genome, Bacterial, Molecular Sequence Data, *Sequence Analysis, DNAMetabolism
Metabolism25264805Identification of gene expression profiles in the actinomycete Gordonia neofelifaecis grown with different steroids.Li W, Ge F, Zhang Q, Ren Y, Yuan J, He J, Li W, Chen G, Zhang G, Zhuang Y, Xu LGenome10.1139/gen-2014-00302014Androstenedione/metabolism/pharmacology, Bacterial Proteins/genetics/metabolism, Carrier Proteins/genetics/metabolism, Cholesterol/metabolism/pharmacology, Gene Expression Regulation, Bacterial/drug effects, Gordonia Bacterium/*genetics/growth & development/*metabolism, Operon, Pyruvic Acid/metabolism/pharmacology, Steroids/*metabolism/pharmacology, TranscriptomeTranscriptome
Metabolism26380409[Accumulation of 9alpha-hydroxy-4-androstene-3,17-dione by co-expressing kshA and kshB encoding component of 3-ketosteroid-9alpha-hydroxylase in Mycobacterium sp. NRRL B-3805].Yuan J, Chen G, Cheng S, Ge F, Qiong W, Li W, Li JSheng Wu Gong Cheng Xue Bao2015Androstenedione/*analogs & derivatives/biosynthesis, Bacterial Proteins/genetics/*metabolism, Biotransformation, Ketosteroids, Mixed Function Oxygenases/genetics/*metabolism, Mycobacterium/*metabolism, Mycobacterium smegmatis/enzymology, PlasmidsEnzymology
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
17966Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45646)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45646
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
21403Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45646.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29762Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2614328776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
79895Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401192.1StrainInfo: A central database for resolving microbial strain identifiers