Strain identifier

BacDive ID: 17629

Type strain: Yes

Species: Patulibacter americanus

Strain Designation: CP177-2

Strain history: DSM 16676 <-- F. Garcia-Pichel <-- G. S. N. Reddy CP177-2.

NCBI tax ID(s): 1122939 (strain), 588672 (species)

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General

@ref: 6559

BacDive-ID: 17629

DSM-Number: 16676

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

description: Patulibacter americanus CP177-2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Biological soil crusts.

NCBI tax id

NCBI tax idMatching level
1122939strain
588672species

strain history

@refhistory
6559<- F. Garcia-Pichel <- G. S. N. Reddy, School of Life Sciences, Arizona State University; CP177-2
67770DSM 16676 <-- F. Garcia-Pichel <-- G. S. N. Reddy CP177-2.

doi: 10.13145/bacdive17629.20230509.8.1

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 americanus
  • full scientific name: Patulibacter americanus Reddy and Garcia-Pichel 2009

@ref: 6559

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Patulibacteraceae

genus: Patulibacter

species: Patulibacter americanus

full scientific name: Patulibacter americanus Reddy and Garcia-Pichel 2009 emend. Nouioui et al. 2018

strain designation: CP177-2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31752positiverod-shapedyes
69480positive99.565

pigmentation

  • @ref: 31752
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6559
  • 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
6559positivegrowth25mesophilic
31752positivegrowth10-30
31752positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31752positivegrowth05-09alkaliphile
31752positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31752
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31752no
69480no98.988

halophily

  • @ref: 31752
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3175229016arginine+carbon source
3175217234glucose+carbon source
3175217306maltose+carbon source
3175228053melibiose+carbon source
3175230911sorbitol+carbon source
3175217992sucrose+carbon source
3175218222xylose+carbon source

enzymes

  • @ref: 31752
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6559Biological soil crustsColorado PlateauUSAUSANorth America
67770Biological soil crust from the Colorado PlateauUSAUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3132.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_373;96_1632;97_1954;98_2403;99_3132&stattab=map
  • Last taxonomy: Patulibacter americanus subclade
  • 16S sequence: AJ871306
  • Sequence Identity:
  • Total samples: 1980
  • soil counts: 849
  • aquatic counts: 275
  • animal counts: 471
  • plant counts: 385

Safety information

risk assessment

  • @ref: 6559
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 31752
  • description: Patulibacter americanus 16S rRNA gene, strain CP177-2
  • accession: AJ871306
  • length: 1459
  • database: nuccore
  • NCBI tax ID: 588672

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Patulibacter americanus DSM 166761122939.3wgspatric1122939
66792Patulibacter americanus DSM 166762524614558draftimg1122939
67770Patulibacter americanus DSM 16676GCA_000420025contigncbi1122939

GC content

@refGC-contentmethod
3175272
6777072thermal denaturation, midpoint method (Tm)
6777074.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno66no
motileyes80.008yes
flagellatedno90.178no
gram-positiveyes89.999yes
anaerobicno98.555no
aerobicyes92.448yes
halophileno94.471no
spore-formingno85.047yes
glucose-utilyes87.681yes
thermophileno98.962yes
glucose-fermentno85.805no

External links

@ref: 6559

culture collection no.: DSM 16676, ATCC BAA 1038, JCM 16550, KCTC 19770

straininfo link

  • @ref: 86621
  • straininfo: 407105

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126730Description of Patulibacter americanus sp. nov., isolated from biological soil crusts, emended description of the genus Patulibacter Takahashi et al. 2006 and proposal of Solirubrobacterales ord. nov. and Thermoleophilales ord. nov.Reddy GS, Garcia-Pichel FInt J Syst Evol Microbiol10.1099/ijs.0.64185-02009Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Vitamin K 2/analysisPhenotype
Phylogeny21515709Patulibacter ginsengiterrae sp. nov., isolated from soil of a ginseng field, and an emended description of the genus Patulibacter.Kim KK, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.032052-02011Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
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
6559Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16676)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16676
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
31752Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2802628776041
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
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)
86621Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407105.1StrainInfo: A central database for resolving microbial strain identifiers