Strain identifier

BacDive ID: 11503

Type strain: Yes

Species: Paenibacillus durus

Strain history: CIP <- 1997, L. Seldin, Univ. Fed. Rio de Janeiro, Brasil <- DSM <- ATCC <- L.D.S. Smith: strain VPI 6563-1

NCBI tax ID(s): 44251 (species)

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General

@ref: 890

BacDive-ID: 11503

DSM-Number: 1735

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

description: Paenibacillus durus DSM 1735 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 44251
  • Matching level: species

strain history

@refhistory
890<- ATCC <- L.DS. Smith, VPI 6563-1 (Clostridium durum)
116692CIP <- 1997, L. Seldin, Univ. Fed. Rio de Janeiro, Brasil <- DSM <- ATCC <- L.D.S. Smith: strain VPI 6563-1

doi: 10.13145/bacdive11503.20250331.9.3

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 durus
  • full scientific name: Paenibacillus durus corrig. (Smith and Cato 1974) Collins et al. 1994

  • synonyms

    @refsynonym
    20215Paenibacillus durum
    20215Clostridium durum

@ref: 890

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus durus

full scientific name: Paenibacillus durus (Smith and Cato 1974) Collins et al. 1994

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116692positiverod-shapedno
125439yes91.3

colony morphology

  • @ref: 116692

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35804MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
890NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
116692CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
890positivegrowth30
35804positivegrowth30
116692positivegrowth22-37
116692nogrowth10
116692nogrowth45
116692nogrowth55

culture pH

  • @ref: 116692
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
890anaerobe
116692facultative anaerobe

spore formation

@refspore formationconfidence
125439yes96.9
125438yes93.4

halophily

@refsaltgrowthtested relationconcentration
116692NaClpositivegrowth0-4 %
116692NaClnogrowth6 %
116692NaClnogrowth8 %
116692NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11669216947citrate-carbon source
1166924853esculin-hydrolysis
116692606565hippurate-hydrolysis
11669217632nitrate-reduction
11669216301nitrite-reduction
11669217632nitrate+respiration
6837127613amygdalin+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837116899D-mannitol+builds acid from
68371Potassium 5-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
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+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
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
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite production

  • @ref: 116692
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11669215688acetoin+
11669217234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
116692oxidase-
116692beta-galactosidase+3.2.1.23
116692alcohol dehydrogenase-1.1.1.1
116692gelatinase-
116692amylase-
116692DNase-
116692caseinase-3.4.21.50
116692catalase+1.11.1.6
116692tween esterase-
116692gamma-glutamyltransferase-2.3.2.2
116692lecithinase-
116692lipase-
116692lysine decarboxylase-4.1.1.18
116692ornithine decarboxylase-4.1.1.17
116692urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116692--++------+++--+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116692---------++++----++/--+-++/-+++++++++++++-++------++/-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116692+++++-+++++++++++-+-++++-+-------+-+-----+-------+---++++--++-++---+-------+---++-----+-+++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
890marine sedimentBlack Sea
116692Environment, Sediment coreBlack Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
8901Risk group (German classification)
1166921Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Paenibacillus durus 16S rRNA gene, strain DSM 1735
  • accession: X77846
  • length: 1455
  • database: nuccore
  • NCBI tax ID: 44251

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus durus DSM 1735GCA_000756615completencbi44251
66792Paenibacillus durus DSM 173544251.7completepatric44251
66792Paenibacillus durus strain DSM 173544251.11plasmidpatric44251

GC content

  • @ref: 890
  • GC-content: 50.0

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes65.186no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.47no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no69.202yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes93.4no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.759yes
125438motile2+flagellatedAbility to perform flagellated movementyes86.128no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes96.9
125439BacteriaNetmotilityAbility to perform movementyes91.3
125439BacteriaNetgram_stainReaction to gram-stainingvariable86.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe81.5

External links

@ref: 890

culture collection no.: DSM 1735, ATCC 27763, LMG 15707, VPI 6563-1, CIP 105291

straininfo link

  • @ref: 80735
  • straininfo: 9005

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807223Paenibacillus durus (Collins et al. 1994, formerly Clostridium durum Smith and Cato 1974) has priority over Paenibacillus azotofixans (Seldin et al. 1984). Opinion 73.Judicial Commission Of The International Committee On Systematics Of ProkaryotesInt J Syst Evol Microbiol10.1099/ijs.0.02496-02003Bacillus/*classification, Clostridium/*classification, *Terminology as Topic
Phylogeny20435753Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica.Jin HJ, Lv J, Chen SFInt J Syst Evol Microbiol10.1099/ijs.0.021709-02010Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/genetics, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sophora/*microbiologyGenetics
Phylogeny22707528Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L.Kong BH, Liu QF, Liu M, Liu Y, Liu L, Li CL, Yu R, Li YHInt J Syst Evol Microbiol10.1099/ijs.0.042747-02012Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/analysis, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Typhaceae/*microbiology, Vitamin K 2/analogs & derivatives/analysis, WetlandsGenetics
Phylogeny22791017Paenibacillus taohuashanense sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of the root of Caragana kansuensis Pojark.Xie JB, Zhang LH, Zhou YG, Liu HC, Chen SFAntonie Van Leeuwenhoek10.1007/s10482-012-9773-42012Bacterial Typing Techniques, Base Composition, Caragana/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/genetics, Paenibacillus/classification/genetics/*isolation & purification/*metabolism, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny31259683Genomic metrics analyses indicate that Paenibacillus azotofixans is not a later synonym of Paenibacillus durus.Guella F, Porto RZ, Sant'Anna FH, Ambrosini A, Passaglia LMPInt J Syst Evol Microbiol10.1099/ijsem.0.0035722019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genes, Bacterial, Genomics, Multilocus Sequence Typing, Nucleic Acid Hybridization, Paenibacillus/*classification, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
890Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1735)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1735
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
35804Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17294
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
80735Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9005.1StrainInfo: A central database for resolving microbial strain identifiers
116692Curators of the CIPCollection of Institut Pasteur (CIP 105291)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105291
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1