Strain identifier

BacDive ID: 10579

Type strain: Yes

Species: Gordonia hydrophobica

Strain Designation: 1610/1b

Strain history: CIP <- 1995, DSMZ <- 1991, B. Bendinger, Osnabrück Univ., Osnabrück, Germany <- Biofilter

NCBI tax ID(s): 1223541 (strain), 40516 (species)

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General

@ref: 11457

BacDive-ID: 10579

DSM-Number: 44015

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Gordonia hydrophobica 1610/1b is an aerobe, mesophilic bacterium that was isolated from compost biofilter for waste gas purification of animal rendering plant emissions.

NCBI tax id

NCBI tax idMatching level
40516species
1223541strain

strain history

@refhistory
11457<- B. Bendinger, 1610/1b
67770CIP 104672 <-- DSM 44015 <-- B. Bendinger 1610/1b.
120010CIP <- 1995, DSMZ <- 1991, B. Bendinger, Osnabrück Univ., Osnabrück, Germany <- Biofilter

doi: 10.13145/bacdive10579.20230509.8.1

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 hydrophobica
  • full scientific name: Gordonia hydrophobica corrig. Bendinger et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Gordona hydrophobica

@ref: 11457

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia hydrophobica

full scientific name: Gordonia hydrophobica Bendinger et al. 1995 emend. Nouioui et al. 2018

strain designation: 1610/1b

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.262
69480100positive
120010nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19992Pastel yellow (1034)10-14 daysISP 2
19992Colorless10-14 daysISP 3
19992Pastel yellow (1034)10-14 daysISP 4
19992Colorless10-14 daysISP 5
19992Pastel yellow (1034)10-14 daysISP 6
19992Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19992noISP 2
19992noISP 3
19992noISP 4
19992noISP 5
19992noISP 6
19992noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11457TRYPTICASE 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
19992ISP 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
19992ISP 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:
19992ISP 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
19992ISP 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
19992ISP 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
19992ISP 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
41265MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120010CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
11457positivegrowth28mesophilic
41265positivegrowth30mesophilic
54292positivegrowth22-37
67770positivegrowth28mesophilic
120010positivegrowth30-41
120010nogrowth10psychrophilic
120010nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54292aerobe
120010obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.994

halophily

  • @ref: 19992
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12001016947citrate+carbon source
1200104853esculin-hydrolysis
12001017632nitrate+reduction
12001016301nitrite-reduction
12001017632nitrate-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
12001035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12001015688acetoin-
12001017234glucose-

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
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
120010oxidase-
120010beta-galactosidase-3.2.1.23
120010alcohol dehydrogenase-1.1.1.1
120010gelatinase-
120010amylase-
120010DNase-
120010caseinase-3.4.21.50
120010catalase+1.11.1.6
120010tween esterase-
120010gamma-glutamyltransferase-2.3.2.2
120010lecithinase-
120010lipase-
120010lysine decarboxylase-4.1.1.18
120010ornithine decarboxylase-4.1.1.17
120010protease-
120010tryptophan deaminase-
120010urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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
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
19992-----------------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19992+++++++--++---++---
120010+++-+-+--++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19992-++++----+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120010++-++--+---------------------------+-------------+---+-----+-------+-+---------++-------+-------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11457compost biofilter for waste gas purification of animal rendering plant emissionsLingenGermanyDEUEurope
54292Compost biofilter,waste gas purification
67770Tree bark compost of biofilter for waste gas purification of animal rendering plant emissions
120010Environment, Compost biofilter for waste gas treatmentLingenGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Livestock (Husbandry)
#Engineered#Biodegradation#Composting
#Engineered#Bioremediation#Biofilter
#Engineered#Waste#Waste gas

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114571Risk group (German classification)
199921German classification
1200101Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia hydrophobica strain DSM 44015 16S ribosomal RNA gene, partial sequenceKF4103371385ena40516
20218G.hydrophobica DNA for 16S ribosomal RNAX873401470ena40516

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia hydrophobica NBRC 160571223541.3wgspatric1223541
66792Gordonia hydrophobica NBRC 160572675903489draftimg1223541
67770Gordonia hydrophobica NBRC 16057GCA_001592365contigncbi1223541

GC content

@refGC-contentmethod
1145769
6777069high performance liquid chromatography (HPLC)
6777067.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno95.579no
gram-positiveyes91.333no
anaerobicno99.566yes
aerobicyes89.107no
halophileno90.608no
spore-formingno82.631no
glucose-utilyes89.382no
flagellatedno98.863no
thermophileno97.718yes
glucose-fermentno86.242yes

External links

@ref: 11457

culture collection no.: DSM 44015, ATCC 700089, CIP 104672, IFO 16057, NBRC 16057, CCUG 38497, CECT 7021, JCM 10086, BCRC 16394, KCTC 9814, PCM 2575

straininfo link

  • @ref: 79854
  • straininfo: 43766

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130028Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor.Kim KK, Lee CS, Kroppenstedt RM, Stackebrandt E, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.02224-02003Bioreactors, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gordonia Bacterium/classification/genetics/*isolation & purification/*metabolism, Korea, Molecular Sequence Data, Mycolic Acids/analysis, Nitrates/metabolism, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Waste Disposal, FluidMetabolism
Phylogeny17329793Gordonia shandongensis sp. nov., isolated from soil in China.Luo H, Gu Q, Xie J, Hu C, Liu Z, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.64536-02007China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gordonia Bacterium/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny22228669Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant.Srinivasan S, Park G, Yang H, Hwang S, Bae Y, Jung YA, Kim MK, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.029736-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gordonia Bacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny22389287Gordonia phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal.Kampfer P, Martin K, Dott WInt J Syst Evol Microbiol10.1099/ijs.0.037093-02012Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gordonia Bacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phosphorus/*metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Waste Water/microbiologyGenetics
Phylogeny22427452Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment.Cha JH, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.039289-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Gordonia Bacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny29068282Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge.Jin D, Kong X, Jia M, Yu X, Wang X, Zhuang X, Deng Y, Bai ZInt J Syst Evol Microbiol10.1099/ijsem.0.0024302017Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Dibutyl Phthalate/*metabolism, Fatty Acids/chemistry, Gordonia Bacterium/*classification/genetics/isolation & purification, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11457Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44015)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44015
19992Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44015.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
41265Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16606
54292Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38497)https://www.ccug.se/strain?id=38497
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/
68368Automatically annotated from API 20E
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
79854Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43766.1StrainInfo: A central database for resolving microbial strain identifiers
120010Curators of the CIPCollection of Institut Pasteur (CIP 104672)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104672