Strain identifier

BacDive ID: 11564

Type strain: Yes

Species: Paenibacillus agarexedens

Strain Designation: 10

Strain history: CIP <- 2002, DSMZ <- 1978, I. Miehlmann: strain Bacillus agarexedens

NCBI tax ID(s): 171401 (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: 524

BacDive-ID: 11564

DSM-Number: 1327

keywords: 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Paenibacillus agarexedens 10 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from meadow soil.

NCBI tax id

  • NCBI tax id: 171401
  • Matching level: species

strain history

@refhistory
524<- I. Miehlmann, 10 (Bacillus agarexedens)
116146CIP <- 2002, DSMZ <- 1978, I. Miehlmann: strain Bacillus agarexedens

doi: 10.13145/bacdive11564.20230509.8.1

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 agarexedens
  • full scientific name: Paenibacillus agarexedens (ex Wieringa 1941) Uetanabaro et al. 2003

@ref: 524

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus agarexedens

full scientific name: Paenibacillus agarexedens (ex Wieringa 1941) Uetanabaro et al. 2003

strain designation: 10

type strain: yes

Morphology

cell morphology

  • @ref: 116146
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 116146

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
524NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Urea 1.0 g/l Distilled water
40471MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116146CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
524positivegrowth30mesophilic
40471positivegrowth30mesophilic
116146positivegrowth22-45
116146nogrowth10psychrophilic
116146nogrowth55thermophilic

culture pH

  • @ref: 116146
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
116146NaClnogrowth0 %
116146NaClnogrowth2 %
116146NaClnogrowth4 %
116146NaClnogrowth6 %
116146NaClnogrowth8 %
116146NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116146citrate-carbon source16947
116146esculin+hydrolysis4853
116146hippurate+hydrolysis606565
116146nitrate-reduction17632
116146nitrite-reduction16301
116146nitrate-respiration17632

metabolite production

  • @ref: 116146
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11614615688acetoin-
11614617234glucose-

enzymes

@refvalueactivityec
116146oxidase-
116146beta-galactosidase+3.2.1.23
116146alcohol dehydrogenase-1.1.1.1
116146gelatinase-
116146amylase+
116146DNase-
116146caseinase-3.4.21.50
116146catalase+1.11.1.6
116146tween esterase-
116146gamma-glutamyltransferase-2.3.2.2
116146lecithinase-
116146lipase-
116146lysine decarboxylase-4.1.1.18
116146ornithine decarboxylase-4.1.1.17
116146urease-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
116146--++-------+++------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116146---------------------++++-----------+-----------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116146+---------+++-----+-------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
524meadow soilGöttingenGermanyDEUEurope
116146Environment, Meadow soilGermanyDEUEurope1972

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Meadow
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_27513.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_3991;97_16590;98_20584;99_27513&stattab=map
  • Last taxonomy: Paenibacillus agarexedens
  • 16S sequence: AJ345020
  • Sequence Identity:
  • Total samples: 186
  • soil counts: 46
  • aquatic counts: 15
  • animal counts: 9
  • plant counts: 116

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
5241Risk group (German classification)
1161461Risk group (French classification)

Sequence information

16S sequences

  • @ref: 524
  • description: Paenibacillus agarexedens partial 16S rRNA gene, strain DSM 1327
  • accession: AJ345020
  • length: 1513
  • database: ena
  • NCBI tax ID: 171401

GC content

  • @ref: 524
  • GC-content: 47.3

External links

@ref: 524

culture collection no.: DSM 1327, CIP 107437, KCTC 3848

straininfo link

  • @ref: 80792
  • straininfo: 47365

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892125Paenibacillus agarexedens sp. nov., nom. rev., and Paenibacillus agaridevorans sp. nov.Uetanabaro AP, Wahrenburg C, Hunger W, Pukall R, Sproer C, Stackebrandt E, de Canhos VP, Claus D, Fritze DInt J Syst Evol Microbiol10.1099/ijs.0.02420-02003Bacillus/*classification/genetics/metabolism, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phenotype, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny26419406Paenibacillus ripae sp. nov., isolated from bank side soil.Sun Y, Guo Z, Zhao Q, Gao Q, Xie Q, Yang R, Liu R, Wu Z, Chen P, Li Y, Wang X, Li HInt J Syst Evol Microbiol10.1099/ijsem.0.0006452015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
524Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1327)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1327
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
40471Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4873
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
80792Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47365.1StrainInfo: A central database for resolving microbial strain identifiers
116146Curators of the CIPCollection of Institut Pasteur (CIP 107437)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107437