Strain identifier

BacDive ID: 11608

Type strain: Yes

Species: Paenibacillus hodogayensis

Strain Designation: SG

Strain history: CIP <- 2004, M. Takeda, Yokohama National Univ., Hodogaya, Yokohama, Japan: strain SG

NCBI tax ID(s): 279208 (species)

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General

@ref: 16235

BacDive-ID: 11608

DSM-Number: 22253

keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped

description: Paenibacillus hodogayensis SG is an aerobe, spore-forming, mesophilic bacterium that was isolated from damp humus sample from the campus of Yokohama National University.

NCBI tax id

  • NCBI tax id: 279208
  • Matching level: species

strain history

@refhistory
16235<- JCM/RIKEN <- M. Takeda; SG
343232004, M. Takeda, Yokohama, Japan: strain SG
67770M. Takeda strain SG.
67771<- M Takeda, Yokohama Natl. Univ.
119928CIP <- 2004, M. Takeda, Yokohama National Univ., Hodogaya, Yokohama, Japan: strain SG

doi: 10.13145/bacdive11608.20230509.8.1

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 hodogayensis
  • full scientific name: Paenibacillus hodogayensis Takeda et al. 2005

@ref: 16235

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus hodogayensis

full scientific name: Paenibacillus hodogayensis Takeda et al. 2005

strain designation: SG

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31377variable2.55 µm1.5 µmrod-shapedyes
67771rod-shapedyes
67771variable
119928positiverod-shapedyes

colony morphology

  • @ref: 119928

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16235CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
34323MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119928CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16235positivegrowth30mesophilic
31377positivegrowth20-40
31377positiveoptimum30mesophilic
34323positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
119928positivegrowth22-37
119928nogrowth10psychrophilic
119928nogrowth45thermophilic
119928nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
31377positivegrowth6.2-9.2alkaliphile
31377positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31377aerobe
67771aerobe
119928obligate aerobe

spore formation

  • @ref: 31377
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
119928NaClpositivegrowth0-2 %
119928NaClnogrowth4 %
119928NaClnogrowth6 %
119928NaClnogrowth8 %
119928NaClnogrowth10 %

observation

@refobservation
67770quinones: MK-7(H2)
67771quinones: MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31377581435-dehydro-D-gluconate+carbon source
3137717057cellobiose+carbon source
3137717234glucose+carbon source
3137717754glycerol+carbon source
3137717716lactose+carbon source
3137717306maltose+carbon source
3137729864mannitol+carbon source
3137728053melibiose+carbon source
31377506227N-acetylglucosamine+carbon source
3137733942ribose+carbon source
3137717814salicin+carbon source
3137717992sucrose+carbon source
3137727082trehalose+carbon source
313774853esculin+hydrolysis
68371Potassium 5-ketogluconate+builds acid from
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
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837118305arbutin-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
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
11992816947citrate-carbon source
1199284853esculin+hydrolysis
119928606565hippurate+hydrolysis
11992817632nitrate-reduction
11992816301nitrite-reduction
11992817632nitrate-respiration

metabolite production

  • @ref: 119928
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11992815688acetoin-
11992817234glucose-

enzymes

@refvalueactivityec
31377catalase+1.11.1.6
31377cytochrome oxidase+1.9.3.1
119928oxidase+
119928beta-galactosidase+3.2.1.23
119928alcohol dehydrogenase-1.1.1.1
119928gelatinase-
119928amylase-
119928DNase-
119928caseinase-3.4.21.50
119928catalase+1.11.1.6
119928tween esterase-
119928gamma-glutamyltransferase-2.3.2.2
119928lecithinase-
119928lipase-
119928lysine decarboxylase-4.1.1.18
119928ornithine decarboxylase-4.1.1.17
119928protease-
119928urease-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
119928-+++-+----++-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119928+---+/----+-+/----+/---+--+/--+/--++/-++++++------++------+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119928---+--+---++---++----------------+--------------------+-----+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16235damp humus sample from the campus of Yokohama National UniversityHodogayaJapanJPNAsia
67770Damp humus sample from the campus of Yokohama National UniversityHodogaya, YokohamaJapanJPNAsia
67771From a damp humus sample from the campus of Yokohama National Univ.Hodogaya, YokohamaJapanJPNAsia
119928Environment, Leaf soilYokohamaJapanJPNAsia2000

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162351Risk group (German classification)
1199281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16235
  • description: Paenibacillus hodogayensis gene for 16S rRNA, partial sequence
  • accession: AB179866
  • length: 1488
  • database: ena
  • NCBI tax ID: 279208

GC content

@refGC-contentmethod
1623555.0high performance liquid chromatography (HPLC)
3137755
6777055high performance liquid chromatography (HPLC)

External links

@ref: 16235

culture collection no.: DSM 22253, JCM 12520, KCTC 3919, CIP 108497

straininfo link

  • @ref: 80834
  • straininfo: 138021

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774654
  • title: Paenibacillus hodogayensis sp. nov., capable of degrading the polysaccharide produced by Sphaerotilus natans.
  • authors: Takeda M, Suzuki I, Koizumi JI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63429-0
  • year: 2005
  • mesh: Aerobiosis, Bacillus/*classification/genetics/growth & development/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Endospore-Forming Bacteria/*classification/genetics/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Polysaccharides, Bacterial/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Sphaerotilus/*metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16235Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22253)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22253
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
31377Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2769028776041
34323Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6125
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
80834Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138021.1StrainInfo: A central database for resolving microbial strain identifiers
119928Curators of the CIPCollection of Institut Pasteur (CIP 108497)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108497