Strain identifier

BacDive ID: 11591

Type strain: No

Species: Paenibacillus larvae

Strain Designation: 670, NRS-1508

Strain history: CIP <- 1996, ATCC <- NRRL: strain B-3685, Bacillus pulvifaciens <- N.R. Smith: strain NRS 1508 <- J.W. Rouatt <- H. Katznelson: strain 670

NCBI tax ID(s): 1477 (subspecies)

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General

@ref: 1425

BacDive-ID: 11591

DSM-Number: 3615

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, animal pathogen

description: Paenibacillus larvae 670 is a facultative anaerobe, spore-forming, mesophilic animal pathogen that was isolated from powdery scale of honeybee larvae.

NCBI tax id

  • NCBI tax id: 1477
  • Matching level: subspecies

strain history

@refhistory
1425<- NRRL (Bacillus pulvifaciens) <- R.E. Gordon, NRS-1508 <- J.W. Rouatt <- H. Katznelson, 670
120563CIP <- 1996, ATCC <- NRRL: strain B-3685, Bacillus pulvifaciens <- N.R. Smith: strain NRS 1508 <- J.W. Rouatt <- H. Katznelson: strain 670

doi: 10.13145/bacdive11591.20230509.8.1

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 larvae
  • full scientific name: Paenibacillus larvae (White 1906) Ash et al. 1994

  • synonyms

    @refsynonym
    20215Bacillus larvae
    20215Paenibacillus pulvifaciens
    20215Bacillus pulvifaciens
    20215Paenibacillus larvae subsp. pulvifaciens

@ref: 1425

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus larvae

full scientific name: Paenibacillus larvae (White 1906) Ash et al. 1994 emend. Heyndrickx et al. 1996 emend. Genersch et al. 2006

strain designation: 670, NRS-1508

type strain: no

Morphology

cell morphology

  • @ref: 120563
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 120563

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1425NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41169MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
41294MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120563CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1425positivegrowth30mesophilic
41169positivegrowth30mesophilic
41294positivegrowth30mesophilic
120563positivegrowth22-45
120563nogrowth10psychrophilic
120563nogrowth55thermophilic

culture pH

  • @ref: 120563
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 120563
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 120563
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
120563NaClpositivegrowth0-4 %
120563NaClnogrowth6 %
120563NaClnogrowth8 %
120563NaClnogrowth10 %

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-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
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
120563citrate-carbon source16947
120563esculin-hydrolysis4853
120563nitrate+reduction17632
120563nitrite-reduction16301
120563nitrate+respiration17632

metabolite production

  • @ref: 120563
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12056315688acetoin+
12056317234glucose+

enzymes

@refvalueactivityec
120563oxidase-
120563beta-galactosidase+3.2.1.23
120563alcohol dehydrogenase-1.1.1.1
120563gelatinase-
120563amylase-
120563DNase-
120563caseinase-3.4.21.50
120563catalase-1.11.1.6
120563tween esterase-
120563gamma-glutamyltransferase-2.3.2.2
120563lecithinase-
120563lipase+
120563lysine decarboxylase-4.1.1.18
120563ornithine decarboxylase-4.1.1.17
120563urease-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
120563-+-+------+----+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120563+---+----+/-+++----++-+/-+-----+---+-------+-+-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120563+--++----------------------------+-------------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
1425powdery scale of honeybee larvae
120563Animal, Honeybee larva, powdery scale

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Insecta

taxonmaps

  • @ref: 69479
  • File name: preview.99_2500.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_1347;97_1599;98_1944;99_2500&stattab=map
  • Last taxonomy: Paenibacillus larvae subclade
  • 16S sequence: AB073204
  • Sequence Identity:
  • Total samples: 9372
  • soil counts: 4373
  • aquatic counts: 749
  • animal counts: 3706
  • plant counts: 544

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
1425yes1Risk group (German classification)
1205631Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus larvae gene for 16S rRNA, partial sequenceAB0732041541ena1464
20218Paenibacillus larvae subsp. pulvifaciens 16S ribosomal RNA gene, partial sequenceAY0300801388ena1477
20218Paenibacillus larvae subsp. pulvifaciens strain DSM 3615 16S ribosomal RNA gene, partial sequenceAY5302951515ena1477

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus larvae subsp. pulvifaciens ATCC 13537GCA_002007765completencbi1477
66792Paenibacillus larvae subsp. pulvifaciens strain ATCC 135371477.16plasmidpatric1477
66792Paenibacillus larvae subsp. pulvifaciens strain ATCC 135371477.17plasmidpatric1477
66792Paenibacillus larvae subsp. pulvifaciens strain ATCC 135371477.13completepatric1477
66792Paenibacillus larvae pulvifaciens ATCC 135372814123212completeimg1477

GC content

  • @ref: 1425
  • GC-content: 44.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes53.237no
gram-positiveyes83.897no
anaerobicno97.218no
aerobicyes89.579no
halophileno91.965no
spore-formingyes96.905no
glucose-utilyes87.699no
thermophileno93.352yes
motileyes75.961no
glucose-fermentno86.106no

External links

@ref: 1425

culture collection no.: DSM 3615, ATCC 49843, LMG 6911, NCIMB 11201, NRRL B-3685, CCUG 52235, ATCC 13537, LMG 15974, NRRL B-3670, CIP 104990, NRS 1508

straininfo link

  • @ref: 80819
  • straininfo: 92156

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8573507Reclassification of Paenibacillus (formerly Bacillus) pulvifaciens (Nakamura 1984) Ash et al. 1994, a later subjective synonym of Paenibacillus (formerly Bacillus) larvae (White 1906) Ash et al. 1994, as a subspecies of P. larvae, with emended descriptions of P. larvae as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens.Heyndrickx M, Vandemeulebroecke K, Hoste B, Janssen P, Kersters K, De Vos P, Logan NA, Ali N, Berkeley RCInt J Syst Bacteriol10.1099/00207713-46-1-2701996Bacillus/chemistry/*classification/physiology/ultrastructure, Base Sequence, DNA Fingerprinting, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis, Mass Spectrometry, Molecular Sequence Data, Numerical Analysis, Computer-Assisted, Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA TechniqueEnzymology
Phylogeny15530737Proposal to reclassify Paenibacillus larvae subsp. pulvifaciens DSM 3615 (ATCC 49843) as Paenibacillus larvae subsp. larvae. Results of a comparative biochemical and genetic study.Kilwinski J, Peters M, Ashiralieva A, Genersch EVet Microbiol10.1016/j.vetmic.2004.08.0012004Animals, Bacillus/*classification/genetics/metabolism, Base Sequence, Bees/*microbiology, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, Gram-Positive Bacterial Infections/*microbiology, Molecular Sequence Data, Polymerase Chain Reaction/veterinary, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Alignment, Sequence Analysis, DNAMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1425Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3615)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3615
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41169Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16959
41294Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16708
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
80819Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92156.1StrainInfo: A central database for resolving microbial strain identifiers
120563Curators of the CIPCollection of Institut Pasteur (CIP 104990)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104990