Strain identifier

BacDive ID: 134087

Type strain: Yes

Species: Paenibacillus antarcticus

Strain Designation: 20CM

Strain history: CIP <- 2004, CECT <- Jesus Guinea, Barcelona, Spain: strain 20CM

NCBI tax ID(s): 253703 (species)

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General

@ref: 31222

BacDive-ID: 134087

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-variable, motile, rod-shaped

description: Paenibacillus antarcticus 20CM is a facultative anaerobe, spore-forming, Gram-variable bacterium that was isolated from Environment, Soil.

NCBI tax id

  • NCBI tax id: 253703
  • Matching level: species

strain history

  • @ref: 116408
  • history: CIP <- 2004, CECT <- Jesus Guinea, Barcelona, Spain: strain 20CM

doi: 10.13145/bacdive134087.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus antarcticus
  • full scientific name: Paenibacillus antarcticus Montes et al. 2004

@ref: 31222

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus antarcticus

strain designation: 20CM

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31222variable2.5 µm0.7 µmrod-shapedyes
116408positiverod-shapedyes

colony morphology

  • @ref: 116408

pigmentation

  • @ref: 31222
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33995MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116408CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
31222positivegrowth04-31
31222positiveoptimum12.5psychrophilic
33995positivegrowth15psychrophilic
116408positivegrowth10-30
116408nogrowth37mesophilic
116408nogrowth45thermophilic
116408nogrowth55thermophilic

culture pH

  • @ref: 116408
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31222facultative anaerobe
116408facultative anaerobe

spore formation

@refspore formation
31222yes
116408no

halophily

@refsaltgrowthtested relationconcentration
31222NaClpositivegrowth0-4 %
31222NaClpositiveoptimum2 %
116408NaClpositivegrowth0-2 %
116408NaClnogrowth4 %
116408NaClnogrowth6 %
116408NaClnogrowth8 %
116408NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3122222599arabinose+carbon source
3122217057cellobiose+carbon source
3122228757fructose+carbon source
3122228260galactose+carbon source
3122217234glucose+carbon source
3122217716lactose+carbon source
3122217306maltose+carbon source
3122237684mannose+carbon source
3122228053melibiose+carbon source
3122237657methyl D-glucoside+carbon source
31222506227N-acetylglucosamine+carbon source
3122216634raffinose+carbon source
3122233942ribose+carbon source
3122217814salicin+carbon source
3122217992sucrose+carbon source
3122227082trehalose+carbon source
3122253426tween 80+carbon source
3122218222xylose+carbon source
312224853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose+builds acid from
6837127082trehalose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11640816947citrate-carbon source
116408606565hippurate-hydrolysis
11640817632nitrate-reduction
11640816301nitrite-reduction

metabolite production

  • @ref: 116408
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11640815688acetoin-
11640817234glucose-

enzymes

@refvalueactivityec
31222catalase+1.11.1.6
31222cytochrome oxidase+1.9.3.1
31222urease+3.5.1.5
116408oxidase+
116408beta-galactosidase+3.2.1.23
116408alcohol dehydrogenase-1.1.1.1
116408gelatinase-
116408amylase+
116408DNase-
116408caseinase-3.4.21.50
116408catalase+1.11.1.6
116408tween esterase-
116408gamma-glutamyltransferase-2.3.2.2
116408lecithinase-
116408lipase-
116408lysine decarboxylase-4.1.1.18
116408ornithine decarboxylase-4.1.1.17
116408protease-
116408urease+3.5.1.5
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116408--++-------++++-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116408---+/-++/---+/-+/-+++-------+/-+++/-++/-+++++/-++/-+/-++/---++--------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116408------------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 116408
  • sample type: Environment, Soil
  • country: Antarctica
  • origin.country: ATA
  • continent: Antarctica
  • isolation date: 1999

taxonmaps

  • @ref: 69479
  • File name: preview.99_4494.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_113;97_120;98_3378;99_4494&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: AJ605292
  • Sequence Identity:
  • Total samples: 1731
  • soil counts: 1259
  • aquatic counts: 100
  • animal counts: 152
  • plant counts: 220

Safety information

risk assessment

  • @ref: 116408
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31222
  • description: Paenibacillus antarcticus 16S rRNA gene, strain LMG 22078
  • accession: AJ605292
  • length: 1510
  • database: nuccore
  • NCBI tax ID: 253703

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus antarcticus CECT 5836GCA_001637225contigncbi253703
66792Paenibacillus antarcticus strain CECT 5836253703.3wgspatric253703
66792Paenibacillus antarcticus CECT 58362744054795draftimg253703

GC content

  • @ref: 31222
  • GC-content: 40.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.748yes
gram-positiveyes70.47yes
anaerobicno98.094yes
aerobicyes80.49yes
halophileno92.482no
spore-formingyes96.187yes
glucose-utilyes89.551no
flagellatedyes87.714no
thermophileno99.943no
glucose-fermentno82.758no

External links

@ref: 31222

culture collection no.: LMG 22078, CECT 5836, CIP 108571

straininfo link

  • @ref: 91696
  • straininfo: 94010

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388704Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment.Montes MJ, Mercade E, Bozal N, Guinea JInt J Syst Evol Microbiol10.1099/ijs.0.63078-02004Anaerobiosis, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Gram-Positive Bacteria/*classification/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureEnzymology
Phylogeny19605719Paenibacillus macquariensis subsp. defensor subsp. nov., isolated from boreal soil.Hoshino T, Nakabayashi T, Hirota K, Matsuno T, Koiwa R, Fujiu S, Saito I, Tkachenko OB, Matsuyama H, Yumoto IInt J Syst Evol Microbiol10.1099/ijs.0.006304-02009Aerobiosis, Antibiosis, Bacterial Typing Techniques, Base Composition, Basidiomycota/growth & development, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Far East, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytologyGenetics
Phylogeny19783613Paenibacillus glacialis sp. nov., isolated from the Kafni glacier of the Himalayas, India.Kishore KH, Begum Z, Pathan AAK, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.015271-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ice Cover/*microbiology, India, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny29068277Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas.Shin SK, Kim E, Yi HInt J Syst Evol Microbiol10.1099/ijsem.0.0024442017Animals, Bacterial Typing Techniques, Base Composition, Crassostrea/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournalcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
31222Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172754828776041
33995Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6208
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
68371Automatically annotated from API 50CH acid
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91696Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID94010.1
116408Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108571Collection of Institut Pasteur (CIP 108571)