Strain identifier

BacDive ID: 8515

Type strain: No

Species: Mycobacterium austroafricanum

Strain Designation: PYR-1

Strain history: CIP <- 2003, C. E. Cerniglia, Nat. Cent. Toxicol., Jefferson, USA: strain PYR-1

NCBI tax ID(s): 110539 (species)

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General

@ref: 3073

BacDive-ID: 8515

DSM-Number: 7251

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

description: Mycobacterium austroafricanum PYR-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from estuarine sediments polluted with petrols.

NCBI tax id

  • NCBI tax id: 110539
  • Matching level: species

strain history

@refhistory
3073<- W. Franklin; PYR-1
67770KCTC 9966 <-- S. B. Kim <-- D. D. Paine PYR-1.
123792CIP <- 2003, C. E. Cerniglia, Nat. Cent. Toxicol., Jefferson, USA: strain PYR-1

doi: 10.13145/bacdive8515.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium austroafricanum
  • full scientific name: Mycobacterium austroafricanum Tsukamura et al. 1983

  • synonyms

    @refsynonym
    20215Mycobacterium vanbaalenii
    20215Mycolicibacterium austroafricanum
    20215Mycolicibacterium vanbaalenii

@ref: 3073

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium austroafricanum

full scientific name: Mycobacterium austroafricanum Tsukamura et al. 1983 emend. Nouioui et al. 2018

strain designation: PYR-1

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
123792rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20199Golden yellow (1004)10-14 days5006
20199Golden yellow (1004)10-14 daysMB7H10
20199Golden yellow (1004)10-14 daysMB7H11

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3073TRYPTICASE 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
3073MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
3073PLATES WITH FLUORANTHENE (DSMZ Medium 462a)yeshttps://mediadive.dsmz.de/medium/462aName: PLATES WITH FLUORANTHENE (DSMZ Medium 462a) Composition: Na2HPO4 2.44 g/l Fluoranthene 2.0 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l Pyridoxamine 0.000125 g/l ZnSO4 x 7 H2O 0.0001 g/l Vitamin B12 5e-05 g/l Nicotinic acid 5e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l Thiamine-HCl x 2 H2O 2.5e-05 g/l p-Aminobenzoate 2.5e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Calcium pantothenate 1.25e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Biotin 5e-06 g/l Distilled water
3073BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
20199MB7H10yesName: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
20199MB7H11yesName: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
201995006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
36373MEDIUM 55 - for Mycobacteriumyes
3073MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf
123792CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
20199positiveoptimum30mesophilic
3073positivegrowth25mesophilic
3073positivegrowth30mesophilic
36373positivegrowth30mesophilic
67770positivegrowth28mesophilic
123792positivegrowth30mesophilic
123792nogrowth10psychrophilic
123792nogrowth22psychrophilic
123792nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123792
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.964

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
123792606565hippurate-hydrolysis
12379217632nitrate+reduction
12379216301nitrite-reduction
12379217632nitrate-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

antibiotic resistance

  • @ref: 123792
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123792
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
123792oxidase-
123792beta-galactosidase-3.2.1.23
123792gelatinase-
123792amylase+
123792DNase-
123792caseinase-3.4.21.50
123792catalase+1.11.1.6
123792tween esterase+
123792gamma-glutamyltransferase-2.3.2.2
123792lecithinase-
123792lipase-
123792protease+
123792urease+3.5.1.5
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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    60758C14:05.414
    60758C16:015.216
    60758C18:00.618
    60758C14:0 N alcohol19.913.524
    60758C16:0 anteiso0.515.717
    60758C16:1 ω7c/C15:0 ISO 2OH9.615.85
    60758C16:1 ω9c1.315.774
    60758C17:1 ω7c18.116.818
    60758C18:1 ω9c12.217.769
    60758C18:2 ω6,9c/C18:0 ANTE1.917.724
    60758C20:0 alcohol (C20:0 2OH alc)8.418.835
    60758TBSA 10Me18:03.718.392
    60758Unidentified1.411.502
    60758Unidentified1.213.208
    60758Unidentified0.514.807
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20199-++/----+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20199-++-++++-+----+----
123792+++-++++-++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123792-+-----+-------------+----------++---------------+----------+------------------++---+---+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3073estuarine sediments polluted with petrolsTexasUSAUSANorth America
60758Estuarine sediments polluted with petrolsUSAUSANorth America
67770Sediment in an oil-contaminated site in Redfish BayTXUSAUSANorth America
123792Environment, Oil contaminated sedimentRedfish bay, TexasUnited States of AmericaUSANorth America1988

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic#Brackish
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30731Risk group (German classification)
201991German classification
1237921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium vanbaalenii 16S ribosomal RNA gene, partial sequenceAY438079542ena350058
3073Mycobacterium vanbaalenii partial 16S rRNA gene and 16S-23S intergenic spacer (IGS), type strain DSM 7251X849771908ena350058

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium vanbaalenii PYR-1350058.8completepatric350058
67770Mycolicibacterium vanbaalenii PYR-1GCA_000015305completencbi350058
66792Mycolicibacterium vanbaalenii PYR-1 DSM 7251GCA_025821565scaffoldncbi350058

GC content

@refGC-contentmethod
307366.6
307367.8sequence analysis
6777067.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
gram-positiveyes89.42no
anaerobicno99.008no
halophileno91.217no
spore-formingno82.408no
glucose-utilyes86.419no
motileno91.798no
flagellatedno97.936no
aerobicyes86.938no
thermophileno99.656yes
glucose-fermentno91.39yes

External links

@ref: 3073

culture collection no.: CCUG 55853, LMG 19257, CIP 107822, JCM 13017, KCTC 9966, DSM 7251, NRRL B-24157, BCRC 16820

straininfo link

  • @ref: 77905
  • straininfo: 13223

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508859Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov.Khan AA, Kim SJ, Paine DD, Cerniglia CEInt J Syst Evol Microbiol10.1099/00207713-52-6-19972002Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Environmental Pollutants/metabolism, Fatty Acids/analysis, Geologic Sediments/microbiology, Mycobacterium/*classification/genetics/isolation & purification/*metabolism, Mycolic Acids/analysis, Petroleum/metabolism, Phenotype, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
Enzymology12829283Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp.Brezna B, Khan AA, Cerniglia CEFEMS Microbiol Lett10.1016/S0378-1097(03)00328-82003Blotting, Southern, Cloning, Molecular, DNA, Bacterial/analysis, Genetic Variation, Mycobacterium/*enzymology/*genetics, Oxygenases/*genetics/metabolism, Polycyclic Aromatic Hydrocarbons/*metabolism, Polymerase Chain ReactionMetabolism
Metabolism12839762Regio- and stereoselective metabolism of 7,12-dimethylbenz[a]anthracene by Mycobacterium vanbaalenii PYR-1.Moody JD, Fu PP, Freeman JP, Cerniglia CEAppl Environ Microbiol10.1128/AEM.69.7.3924-3931.200320039,10-Dimethyl-1,2-benzanthracene/*chemistry/*metabolism, Biodegradation, Environmental, Chromatography, High Pressure Liquid, Culture Media, Magnetic Resonance Spectroscopy, Mass Spectrometry, Mycobacterium/growth & development/*metabolism, StereoisomerismCultivation
Metabolism14711661Degradation of benzo[a]pyrene by Mycobacterium vanbaalenii PYR-1.Moody JD, Freeman JP, Fu PP, Cerniglia CEAppl Environ Microbiol10.1128/AEM.70.1.340-345.20042004Benzopyrenes/*metabolism, Biodegradation, Environmental, Chromatography, High Pressure Liquid, Circular Dichroism, Environmental Pollutants/*metabolism, Magnetic Resonance Spectroscopy, Mass Spectrometry, Mycobacterium/growth & development/*metabolism, Stereoisomerism
Metabolism15313184Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1.Stingley RL, Khan AA, Cerniglia CEBiochem Biophys Res Commun10.1016/j.bbrc.2004.07.0892004Amino Acid Sequence, Biodegradation, Environmental, Gene Expression Regulation, Bacterial/physiology, Gene Expression Regulation, Enzymologic/physiology, Molecular Sequence Data, Multienzyme Complexes/chemistry/metabolism, Mycobacterium/*genetics/*metabolism, Oxidoreductases/chemistry/genetics/metabolism, Oxygenases/*chemistry/genetics/*metabolism, Phenanthrenes/*metabolism, Phthalic Acids/*metabolism, Signal Transduction/*physiology, Transposases/chemistry/genetics/metabolismGenetics
Metabolism15528661Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1.Stingley RL, Brezna B, Khan AA, Cerniglia CEMicrobiology (Reading)10.1099/mic.0.27263-02004Catalytic Domain/genetics, Cloning, Molecular, DNA, Bacterial/chemistry/isolation & purification, Escherichia coli/genetics/metabolism, Gene Order, Genes, Bacterial, Gram-Positive Bacteria/genetics, Molecular Sequence Data, Mycobacterium/*genetics/metabolism, *Operon, Oxygenases/genetics, Phthalic Acids/*metabolism, Phylogeny, Protein Subunits/genetics, Sequence Analysis, DNA, SyntenyEnzymology
Genetics15540208Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods.Kim SJ, Jones RC, Cha CJ, Kweon O, Edmondson RD, Cerniglia CEProteomics10.1002/pmic.2004008722004Amino Acid Sequence, Bacterial Proteins/*chemistry, Electrophoresis, Gel, Two-Dimensional/*methods, Genome, Hydrogen-Ion Concentration, Ions, Isoelectric Focusing, Mass Spectrometry/*methods, Molecular Sequence Data, Mycobacterium/*metabolism, Polycyclic Aromatic Hydrocarbons/*chemistry, Protein Structure, Tertiary, Proteins/analysis/chemistry, Proton-Translocating ATPases/metabolismEnzymology
Metabolism15549609Evidence for the existence of PAH-quinone reductase and catechol-O-methyltransferase in Mycobacterium vanbaalenii PYR-1.Kim YH, Moody JD, Freeman JP, Brezna B, Engesser KH, Cerniglia CEJ Ind Microbiol Biotechnol10.1007/s10295-004-0178-x2004Biotransformation, Catechol O-Methyltransferase/genetics/*metabolism, Mycobacterium/chemistry/classification/*enzymology/metabolism, Polycyclic Aromatic Hydrocarbons/chemistry/*metabolism, Quinone Reductases/biosynthesis/classification/*metabolismEnzymology
Metabolism15592827Effects of pH on the degradation of phenanthrene and pyrene by Mycobacterium vanbaalenii PYR-1.Kim YH, Freeman JP, Moody JD, Engesser KH, Cerniglia CEAppl Microbiol Biotechnol10.1007/s00253-004-1796-y2004Biodegradation, Environmental, Hydrogen-Ion Concentration, Mycobacterium/growth & development/*metabolism, Phenanthrenes/*metabolism, Pyrenes/*metabolism
Metabolism15865344Degradation of benz[a]anthracene by Mycobacterium vanbaalenii strain PYR-1.Moody JD, Freeman JP, Cerniglia CEBiodegradation10.1007/s10532-004-7217-12005Benz(a)Anthracenes/chemistry/*metabolism, Biodegradation, Environmental, Chromatography, High Pressure Liquid, Gas Chromatography-Mass Spectrometry, Geologic Sediments/microbiology, Magnetic Resonance Spectroscopy, Molecular Structure, Mycobacterium/growth & development/isolation & purification/*metabolism, Oxidation-Reduction, Polycyclic Aromatic Hydrocarbons/chemistry/metabolism, Soil Pollutants/metabolismEnzymology
Enzymology16317545Molecular characterization of cytochrome P450 genes in the polycyclic aromatic hydrocarbon degrading Mycobacterium vanbaalenii PYR-1.Brezna B, Kweon O, Stingley RL, Freeman JP, Khan AA, Polek B, Jones RC, Cerniglia CEAppl Microbiol Biotechnol10.1007/s00253-005-0190-82005Amino Acid Sequence, Base Sequence, Blotting, Southern, Cloning, Molecular, Cytochrome P-450 Enzyme System/*genetics/metabolism, DNA, Bacterial/genetics, Gas Chromatography-Mass Spectrometry, Molecular Sequence Data, Mycobacterium/*enzymology/*genetics, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, Polymerase Chain Reaction, Recombinant Proteins/chemistry/*metabolism, Sequence Alignment, Sequence Analysis, DNA, Spectrophotometry, UltravioletMetabolism
Metabolism16461648Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1.Kim SJ, Kweon O, Freeman JP, Jones RC, Adjei MD, Jhoo JW, Edmondson RD, Cerniglia CEAppl Environ Microbiol10.1128/AEM.72.2.1045-1054.20062006Amino Acid Sequence, Base Sequence, Biodegradation, Environmental, Cloning, Molecular, DNA, Bacterial/genetics, Dioxygenases/*genetics/*metabolism, Gas Chromatography-Mass Spectrometry, Gene Expression, *Genes, Bacterial, Molecular Sequence Data, Molecular Weight, Mycobacterium/*genetics/isolation & purification/*metabolism, Phylogeny, Polycyclic Aromatic Hydrocarbons/chemistry/*metabolism, Recombinant Proteins/chemistry/metabolism, Soil Microbiology, Spectrometry, Mass, Electrospray IonizationEnzymology
Metabolism17085566Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology.Kim SJ, Kweon O, Jones RC, Freeman JP, Edmondson RD, Cerniglia CEJ Bacteriol10.1128/JB.01310-062006Bacterial Proteins/genetics/metabolism, Gas Chromatography-Mass Spectrometry, Gene Order, Genes, Bacterial/genetics, Genomics/methods, Metabolic Networks and Pathways, Molecular Structure, Multigene Family, Mycobacterium/genetics/*metabolism, Proteomics/methods, Pyrenes/chemistry/*metabolism, Systems Biology/*methodsGenetics
Metabolism17449607A polyomic approach to elucidate the fluoranthene-degradative pathway in Mycobacterium vanbaalenii PYR-1.Kweon O, Kim SJ, Jones RC, Freeman JP, Adjei MD, Edmondson RD, Cerniglia CEJ Bacteriol10.1128/JB.00128-072007Acetyl Coenzyme A/metabolism, Acyl Coenzyme A/metabolism, Bacterial Proteins/analysis/metabolism, Biodegradation, Environmental, Chromatography, High Pressure Liquid, Fluorenes/chemistry/*metabolism, Gas Chromatography-Mass Spectrometry, Gene Expression Regulation, Bacterial, Gene Order, Genomics/methods, Metabolic Networks and Pathways, Models, Biological, Molecular Structure, Mycobacterium/*genetics/*metabolism, Proteome/analysis/metabolism, Proteomics/methods, Spectrophotometry, UltravioletGenetics
Metabolism18421421Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1.Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CEBiodegradation10.1007/s10532-008-9189-z2008Adipates/metabolism, Biodegradation, Environmental, Citric Acid Cycle/genetics, DNA Transposable Elements/genetics, Environmental Pollutants/*metabolism, Genome, Bacterial, Inactivation, Metabolic/genetics, Models, Biological, Mycobacterium/*genetics/*metabolism, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolismGenetics
Enzymology18717621Biotransformation of acridine by Mycobacterium vanbaalenii.Sutherland JB, Heinze TM, Pearce MG, Deck J, Williams AJ, Freeman JPEnviron Toxicol Chem10.1897/08-206.12009Acridines/*pharmacokinetics, Biotransformation, Chromatography, High Pressure Liquid, Mycobacterium/*metabolism, Spectrometry, Mass, Electrospray Ionization, Spectrophotometry, UltravioletMetabolism
Phylogeny18941994Characterization of a pyrene-degrading Mycobacterium sp. strain CH-2.Churchill PF, Morgan AC, Kitchens EJ Environ Sci Health B10.1080/036012308023888012008Base Sequence, Biodegradation, Environmental, Cloning, Molecular, Cytochrome P-450 CYP4A/*genetics/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gene Amplification, Gene Expression, Molecular Sequence Data, Mycobacterium/classification/enzymology/*isolation & purification/*metabolism, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, Pyrenes/*metabolism, Reverse Transcriptase Polymerase Chain Reaction, Soil Microbiology, Species SpecificityEnzymology
Metabolism19712404Two distinct gene clusters encode pyrene degradation in Mycobacterium sp. strain S65.Sho M, Hamel C, Greer CWFEMS Microbiol Ecol10.1016/j.femsec.2004.01.0112004Alcohol Dehydrogenase/genetics, Bacterial Proteins/genetics, Blotting, Southern/methods, Canada, DNA Transposable Elements, Dioxygenases/genetics, Environmental Microbiology, Evolution, Molecular, Gene Duplication, Gene Expression Profiling, Gene Order, *Genes, Bacterial, Metabolic Networks and Pathways/*genetics, Molecular Sequence Data, *Multigene Family, Mycobacterium/*genetics/isolation & purification/*metabolism, Pyrenes/*metabolism, Quebec, Reverse Transcriptase Polymerase Chain Reaction/methods, Sequence Analysis, DNA, Sequence Homology, Amino AcidEnzymology
Metabolism20714442Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1.Kweon O, Kim SJ, Freeman JP, Song J, Baek S, Cerniglia CEmBio10.1128/mBio.00135-102010Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, Binding Sites, Hydroxylation, Iron/metabolism, Molecular Sequence Data, Molecular Structure, Mycobacterium/chemistry/classification/*enzymology/genetics, Oxygenases/*chemistry/genetics/metabolism, Phylogeny, Polycyclic Aromatic Hydrocarbons/*chemistry/metabolism, Substrate SpecificityPhylogeny
Metabolism20714921Biodegradation of pyrene in sand, silt and clay fractions of sediment.Cui X, Hunter W, Yang Y, Chen Y, Gan JBiodegradation10.1007/s10532-010-9399-z2010Aluminum Silicates/*chemistry, Biodegradation, Environmental, Clay, Geologic Sediments/*chemistry/*microbiology, Mycobacterium/metabolism, Polymers/metabolism, Pyrenes/*metabolism, Silicon Dioxide/*chemistry
Metabolism21255317Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria.Kanaly RA, Harayama SMicrob Biotechnol10.1111/j.1751-7915.2009.00130.x2009Biotransformation, Metabolic Networks and Pathways/genetics, Molecular Weight, Mycobacterium/enzymology/*metabolism, Polycyclic Aromatic Hydrocarbons/chemistry/*metabolismEnzymology
Metabolism21656161Influence of single-walled carbon nanotubes on microbial availability of phenanthrene in sediment.Cui XY, Jia F, Chen YX, Gan JEcotoxicology10.1007/s10646-011-0684-32011Adsorption, Charcoal/chemistry, Environmental Restoration and Remediation/*methods, Geologic Sediments/chemistry/*microbiology, Humic Substances, Nanotubes, Carbon/*chemistry, Peptones/chemistry, Phenanthrenes/chemistry/*metabolism, Tannins/chemistry, *Water Microbiology, Water Pollutants, Chemical/chemistry/*metabolism
Pathogenicity21678910Microbially mediated O-methylation of bisphenol A results in metabolites with increased toxicity to the developing zebrafish (Danio rerio) embryo.McCormick JM, Van Es T, Cooper KR, White LA, Haggblom MMEnviron Sci Technol10.1021/es200588w2011Animals, Benzhydryl Compounds, Biodegradation, Environmental/drug effects, Embryo, Nonmammalian/*drug effects/metabolism/pathology, Environmental Exposure/analysis, Humans, Mass Spectrometry, Methyl Ethers/toxicity, Methylation/drug effects, Mycobacterium/drug effects/*metabolism, Phenols/chemistry/*metabolism/*toxicity, Survival Analysis, Time Factors, Zebrafish/*embryologyMetabolism
Proteome21725022Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1.Kweon O, Kim SJ, Holland RD, Chen H, Kim DW, Gao Y, Yu LR, Baek S, Baek DH, Ahn H, Cerniglia CEJ Bacteriol10.1128/JB.00215-112011Bacterial Proteins/analysis, Biodegradation, Environmental, Chromatography, Liquid, Cluster Analysis, Computational Biology, Electrophoresis, Polyacrylamide Gel, Evolution, Molecular, Gene Expression Regulation, Bacterial, Genome, Bacterial, High-Throughput Nucleotide Sequencing, Metabolic Networks and Pathways/*genetics, Mycobacterium/genetics/*metabolism, Phylogeny, Polycyclic Aromatic Hydrocarbons/chemistry/*metabolism, Proteome/*analysis, Proteomics, Tandem Mass SpectrometryEnzymology
Metabolism22407691Functional robustness of a polycyclic aromatic hydrocarbon metabolic network examined in a nidA aromatic ring-hydroxylating oxygenase mutant of Mycobacterium vanbaalenii PYR-1.Kim SJ, Song J, Kweon O, Holland RD, Kim DW, Kim J, Yu LR, Cerniglia CEAppl Environ Microbiol10.1128/AEM.07798-112012Bacterial Proteins/analysis, Culture Media/chemistry, DNA Transposable Elements, *Gene Deletion, Gene Expression Profiling, *Metabolic Networks and Pathways, Mutagenesis, Insertional, Mycobacterium/enzymology/*genetics/growth & development/*metabolism, Oxygenases/*genetics, Polycyclic Aromatic Hydrocarbons/*metabolism, Proteome/analysisCultivation
Pathogenicity24162371Mid-infrared spectroscopic assessment of nanotoxicity in gram-negative vs. gram-positive bacteria.Heys KA, Riding MJ, Strong RJ, Shore RF, Pereira MG, Jones KC, Semple KT, Martin FLAnalyst10.1039/c3an01649h2013Animals, Cattle, Gram-Negative Bacteria/*chemistry/drug effects, Gram-Positive Bacteria/*chemistry/drug effects, Nanostructures/*analysis/*toxicity, Serum Albumin, Bovine, Spectroscopy, Fourier Transform Infrared/methods/*standards, Synchrotrons/*standards, Toxicity Tests/methods/standards
Metabolism25070740Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1.Kweon O, Kim SJ, Kim DW, Kim JM, Kim HL, Ahn Y, Sutherland JB, Cerniglia CEJ Bacteriol10.1128/JB.01945-142014Bacterial Proteins/*chemistry/genetics/*metabolism, Molecular Weight, Mycobacterium/chemistry/*enzymology/genetics/metabolism, Oxygenases/*chemistry/genetics/*metabolism, Polycyclic Aromatic Hydrocarbons/chemistry/*metabolism, Substrate SpecificityEnzymology
Metabolism25305469Metabolic engineering of Arabidopsis for remediation of different polycyclic aromatic hydrocarbons using a hybrid bacterial dioxygenase complex.Peng R, Fu X, Tian Y, Zhao W, Zhu B, Xu J, Wang B, Wang L, Yao QMetab Eng10.1016/j.ymben.2014.09.0052014Arabidopsis/*physiology, Bacterial Proteins/genetics/*metabolism, Biodegradation, Environmental, Dioxygenases/genetics/*metabolism, Environmental Pollutants/*metabolism, Genetic Enhancement/methods, Metabolic Engineering/*methods, Multienzyme Complexes/genetics/metabolism, Naphthalenes/metabolism, Plants, Genetically Modified/genetics/metabolism, Polycyclic Aromatic Hydrocarbons/isolation & purification/*metabolismBiotechnology
Metabolism25888169Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil.Kim SJ, Kweon O, Sutherland JB, Kim HL, Jones RC, Burback BL, Graves SW, Psurny E, Cerniglia CEAppl Environ Microbiol10.1128/AEM.00730-152015Alkenes/*metabolism, Bacterial Proteins/*biosynthesis, Gas Chromatography-Mass Spectrometry, Gene Expression Profiling, Gene Expression Regulation, Bacterial/*drug effects, Mycobacterium/*drug effects/genetics/*metabolism, Petroleum/*metabolism, Petroleum Pollution, Polycyclic Aromatic Hydrocarbons/*metabolism, Proteome/analysisPathogenicity
26299864[Polymorphism of the bphA genes in bacteria destructing biphenyl/chlorinated biphenils].Shumkova ES, Egorova DO, Boronnikova SV, Plotnikova EGMol Biol (Mosk)10.7868/S00268984150401512015
Metabolism28081361Microbial Transformation of Multiwalled Carbon Nanotubes by Mycobacterium vanbaalenii PYR-1.You Y, Das KK, Guo H, Chang CW, Navas-Moreno M, Chan JW, Verburg P, Poulson SR, Wang X, Xing B, Yang YEnviron Sci Technol10.1021/acs.est.6b045232017Microscopy, Electron, Transmission, Mycobacterium/*metabolism, Nanotechnology, Nanotubes, Carbon/*chemistry, Polycyclic Aromatic Hydrocarbons
Metabolism28148980Simultaneous Biodegradation of Polyaromatic Hydrocarbons by a Stenotrophomonas sp: Characterization of nid Genes and Effect of Surfactants on Degradation.Kumari S, Regar RK, Bajaj A, Ch R, Satyanarayana GNV, Mudiam MKR, Manickam NIndian J Microbiol10.1007/s12088-016-0612-62016
Metabolism28774858A comparative intracellular proteomic profiling of Pseudomonas aeruginosa strain ASP-53 grown on pyrene or glucose as sole source of carbon and identification of some key enzymes of pyrene biodegradation pathway.Mukherjee AK, Bhagowati P, Biswa BB, Chanda A, Kalita BJ Proteomics10.1016/j.jprot.2017.07.0202017Bacterial Proteins/*biosynthesis, *Gene Expression Profiling, Gene Expression Regulation, Bacterial/*physiology, Gene Expression Regulation, Enzymologic/*physiology, Glucose/*metabolism, *Proteomics, Pseudomonas aeruginosa/*enzymology/growth & development, Pyrenes/*metabolismEnzymology
Metabolism30408872Influence of rhamnolipid biosurfactant and Brij-35 synthetic surfactant on (14)C-Pyrene mineralization in soil.Wolf DC, Gan JEnviron Pollut10.1016/j.envpol.2018.10.0312018*Biodegradation, Environmental, Biological Availability, Carbon Radioisotopes/analysis, Environmental Pollutants/metabolism, Glycolipids/*chemistry, Mycobacterium/drug effects/metabolism, Polycyclic Aromatic Hydrocarbons/analysis/chemistry, Polyethylene Glycols/*chemistry, Pyrenes/*chemistry/metabolism, Soil/*chemistry, Soil Microbiology, Soil Pollutants/analysis/*chemistry, Solubility, Surface-Active Agents/chemistryPathogenicity
Metabolism31128356Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils.Wolf DC, Cryder Z, Gan JChemosphere10.1016/j.chemosphere.2019.05.1452019Bacteria/metabolism, Biodegradation, Environmental, Biological Availability, Environmental Monitoring, Environmental Pollutants/metabolism, Environmental Restoration and Remediation/*methods, Glycolipids, Microbiota, Phylogeny, Polycyclic Aromatic Hydrocarbons/analysis, Polyethylene Glycols, Pyrenes/analysis/*metabolism, RNA, Ribosomal, 16S/genetics, Soil, *Soil Microbiology, Soil Pollutants/analysis/*metabolism, Surface-Active Agents/metabolism/*toxicityPhylogeny
Metabolism31445023Preparation of dihydroxy polycyclic aromatic hydrocarbons and activities of two dioxygenases in the phenanthrene degradative pathway.Erwin KL, Johnson WH Jr, Meichan AJ, Whitman CPArch Biochem Biophys10.1016/j.abb.2019.1080812019Biocatalysis, Dioxygenases/*metabolism, Environmental Pollutants/*chemistry/*metabolism, Phenanthrenes/*chemistry/*metabolism
31657903Humic Acid Can Enhance the Mineralization of Phenanthrene Sorbed on Biochars.Zhang M, Shen X, Zhang H, Werner D, Wang B, Yang Y, Tao S, Wang XEnviron Sci Technol10.1021/acs.est.9b051472019Adsorption, Charcoal, *Humic Substances, *Phenanthrenes
32315846Bioremediation of PAH-contaminated shooting range soil using integrated approaches.Wolf DC, Cryder Z, Khoury R, Carlan C, Gan JSci Total Environ10.1016/j.scitotenv.2020.1384402020Biodegradation, Environmental, Polycyclic Aromatic Hydrocarbons/*analysis, Soil, Soil Microbiology, Soil Pollutants/*analysis

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3073Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7251)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7251
20199Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7251.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
36373Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5376
60758Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55853)https://www.ccug.se/strain?id=55853
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/
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)
77905Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13223.1StrainInfo: A central database for resolving microbial strain identifiers
123792Curators of the CIPCollection of Institut Pasteur (CIP 107822)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107822