Strain identifier

BacDive ID: 23348

Type strain: Yes

Species: Patulibacter medicamentivorans

Strain Designation: I11

Strain history: CECT 8141 <-- M. T. Barreto Crespo; Inst. Biol. Exp. Technol. (iBET), Portugal; I11.

NCBI tax ID(s): 1097667 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 19369

BacDive-ID: 23348

DSM-Number: 25962

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

description: Patulibacter medicamentivorans I11 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge, enriched for ibuprofen degradation.

NCBI tax id

  • NCBI tax id: 1097667
  • Matching level: species

strain history

@refhistory
19369<- M.T. Barreto Crespo, IBET <- B. Almeida, IBET, Oeiras, Portugal; strain I11
67770CECT 8141 <-- M. T. Barreto Crespo; Inst. Biol. Exp. Technol. (iBET), Portugal; I11.

doi: 10.13145/bacdive23348.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Patulibacteraceae
  • genus: Patulibacter
  • species: Patulibacter medicamentivorans
  • full scientific name: Patulibacter medicamentivorans Almeida et al. 2013

@ref: 19369

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Patulibacteraceae

genus: Patulibacter

species: Patulibacter medicamentivorans

full scientific name: Patulibacter medicamentivorans Almeida et al. 2013

strain designation: I11

type strain: yes

Morphology

cell morphology

  • @ref: 30919
  • gram stain: positive
  • cell length: 1.05 µm
  • cell width: 0.35 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 19369
  • incubation period: 2-3 days

pigmentation

  • @ref: 30919
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19369
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19369positivegrowth28mesophilic
30919positivegrowth20-39
30919positiveoptimum32mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
30919positivegrowth5.5-8.0
30919positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30919
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30919
  • spore formation: no

halophily

  • @ref: 30919
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1.5 %

observation

  • @ref: 67770
  • observation: quinones: DMK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3091930089acetate+carbon source
3091916449alanine+carbon source
30919286442-oxopentanoate+carbon source
3091918403L-arabitol+carbon source
3091917057cellobiose+carbon source
3091923652dextrin+carbon source
3091928757fructose+carbon source
3091917234glucose+carbon source
3091929987glutamate+carbon source
3091924996lactate+carbon source
3091917272propionate+carbon source
3091915361pyruvate+carbon source
3091926546rhamnose+carbon source
3091933942ribose+carbon source
3091917814salicin+carbon source
3091930031succinate+carbon source
3091953423tween 40+carbon source
3091953426tween 80+carbon source
3091918222xylose+carbon source
3091917632nitrate+reduction

enzymes

@refvalueactivityec
30919acid phosphatase+3.1.3.2
30919alkaline phosphatase+3.1.3.1
30919catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19369activated sludge, enriched for ibuprofen degradationLisbonPortugalPRTEurope
67770Activated sludge of a wastewater treatment plantLisbonPortugalPRTEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_8050.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_373;96_3721;97_4573;98_5868;99_8050&stattab=map
  • Last taxonomy: Patulibacter medicamentivorans subclade
  • 16S sequence: NR_121691
  • Sequence Identity:
  • Total samples: 1662
  • soil counts: 1218
  • aquatic counts: 177
  • animal counts: 188
  • plant counts: 79

Safety information

risk assessment

  • @ref: 19369
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
19369Patulibacter medicamentivorans strain I11 contig68, whole genome shotgun sequenceAGUD01000068.112509ena1097667
67770Patulibacter medicamentivorans strain I11 contig68, whole genome shotgun sequenceAGUD0100006812509ena1097667
67770Patulibacter medicamentivorans strain I11 16S ribosomal RNA, partial sequenceNR_1216911541nuccore1097667

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Patulibacter medicamentivorans I112537561813draftimg1097667
67770Patulibacter medicamentivorans I11GCA_000240225contigncbi1097667

GC content

@refGC-contentmethod
1936974.1sequence analysis
3091974.1
6777074.1genome sequence analysis

External links

@ref: 19369

culture collection no.: DSM 25962, CECT 8141, JCM 31708

straininfo link

  • @ref: 87564
  • straininfo: 390202

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23264500Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant.Almeida B, Vaz-Moreira I, Schumann P, Nunes OC, Carvalho G, Crespo MTBInt J Syst Evol Microbiol10.1099/ijs.0.047522-02012Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Phosphatidylglycerols/analysis, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/analysis, Waste WaterTranscriptome
Phylogeny27620694Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).Jin D, Kong X, Li H, Luo L, Zhuang X, Zhuang G, Deng Y, Bai ZInt J Syst Evol Microbiol10.1099/ijsem.0.0014692016Bacterial Typing Techniques, Base Composition, Brassica/*microbiology, Cardiolipins/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19369Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25962)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25962
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
30919Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2724928776041
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/
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
87564Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID390202.1StrainInfo: A central database for resolving microbial strain identifiers