Strain identifier

BacDive ID: 11559

Type strain: Yes

Species: Paenibacillus graminis

Strain Designation: RSA 19, RSA19

Strain history: CIP <- 2002, O. Berge, CNRS-CEA, Saint Paul Lez Durance, France: strain RSA19

NCBI tax ID(s): 189425 (species)

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General

@ref: 5764

BacDive-ID: 11559

DSM-Number: 15220

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Paenibacillus graminis RSA 19 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from maize rhizosphere.

NCBI tax id

  • NCBI tax id: 189425
  • Matching level: species

strain history

@refhistory
5764<- O. Berge, CEA/Cadarache; RSA 19
405702002, O. Berge, St Paul Lez Durance, France: strain RSA19
119724CIP <- 2002, O. Berge, CNRS-CEA, Saint Paul Lez Durance, France: strain RSA19

doi: 10.13145/bacdive11559.20230509.8.1

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 graminis
  • full scientific name: Paenibacillus graminis Berge et al. 2002

@ref: 5764

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus graminis

full scientific name: Paenibacillus graminis Berge et al. 2002

strain designation: RSA 19, RSA19

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.543
69480100positive
119724yespositiverod-shaped

colony morphology

  • @ref: 119724

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5764CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40570MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119724CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5764positivegrowth30mesophilic
40570positivegrowth30mesophilic
119724positivegrowth10-37
119724nogrowth45thermophilic
119724nogrowth55thermophilic

culture pH

  • @ref: 119724
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119724
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
119724yes

halophily

@refsaltgrowthtested relationconcentration
119724NaClpositivegrowth0-2 %
119724NaClnogrowth4 %
119724NaClnogrowth6 %
119724NaClnogrowth8 %
119724NaClnogrowth10 %

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
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-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
119724citrate-carbon source16947
119724esculin+hydrolysis4853
119724hippurate+hydrolysis606565
119724nitrate+reduction17632
119724nitrite-reduction16301
119724nitrate+respiration17632

metabolite production

  • @ref: 119724
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11972415688acetoin+
11972417234glucose+

enzymes

@refvalueactivityec
119724oxidase-
119724beta-galactosidase+3.2.1.23
119724alcohol dehydrogenase-1.1.1.1
119724gelatinase-
119724amylase+
119724DNase-
119724caseinase+3.4.21.50
119724catalase+1.11.1.6
119724tween esterase+
119724gamma-glutamyltransferase-2.3.2.2
119724lecithinase-
119724lipase-
119724lysine decarboxylase-4.1.1.18
119724ornithine decarboxylase-4.1.1.17
119724protease-
119724urease-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
119724--++-+----++++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119724+/---+-+--+++++----+--+/-+++++++++++-+/-+++-++------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119724--++--++-+--++-++++---+----------++------------------------++-------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
5764maize rhizosphereFranceFRAEurope
119724Environment, Rhizosphere, Zea maysFranceFRAEurope1985

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_3149.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_335;97_1860;98_2285;99_3149&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: AJ223987
  • Sequence Identity:
  • Total samples: 202
  • soil counts: 152
  • aquatic counts: 22
  • animal counts: 13
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57641Risk group (German classification)
1197241Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5764
  • description: Paenibacillus graminis 16S rRNA gene, strain RSA19
  • accession: AJ223987
  • length: 1437
  • database: ena
  • NCBI tax ID: 189425

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus graminis DSM 15220GCA_000758705completencbi189425
66792Paenibacillus graminis DSM 15220189425.5completepatric189425
66792Paenibacillus graminis DSM 152202630968473completeimg189425

GC content

  • @ref: 5764
  • GC-content: 52.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes86.618no
flagellatedyes84.316no
gram-positiveyes88.964no
anaerobicno94.857no
aerobicyes85.411no
halophileno96.382no
spore-formingyes96.317no
glucose-utilyes90.191no
thermophileno99.917yes
glucose-fermentno77.81no

External links

@ref: 5764

culture collection no.: DSM 15220, ATCC BAA 95, LMG 19080, CIP 107688

straininfo link

  • @ref: 80787
  • straininfo: 13204

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931174Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food.Berge O, Guinebretiere MH, Achouak W, Normand P, Heulin TInt J Syst Evol Microbiol10.1099/00207713-52-2-6072002*Food Microbiology, Genes, rRNA, Genome, Bacterial, Gram-Positive Endospore-Forming Rods/*classification/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/microbiology, Plants/*microbiology, RNA, Ribosomal, 16S/chemistry, *Soil Microbiology, Species SpecificityGenetics
Phylogeny26979511Paenibacillus salinicaeni sp. nov., isolated from saline silt sample.Guo X, Zhou S, Wang YW, Wang HM, Kong DL, Zhu J, Dong WW, He MX, Zhao BQ, Hu GQ, Ruan ZYAntonie Van Leeuwenhoek10.1007/s10482-016-0674-92016Anaerobiosis, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Salinity, Seawater/*microbiology, Spores, Bacterial/cytologyEnzymology
Phylogeny34435945Paenibacillus agri sp. nov., isolated from soil.KIm KH, Seo YL, Baek JH, Jin HM, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0049812021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Paenibacillus/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5764Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15220)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15220
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
40570Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5151
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)
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80787Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13204.1StrainInfo: A central database for resolving microbial strain identifiers
119724Curators of the CIPCollection of Institut Pasteur (CIP 107688)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107688