Strain identifier

BacDive ID: 11459

Type strain: Yes

Species: Paenibacillus alginolyticus

Strain Designation: 1347

Strain history: CIP <- 1988, L.K. Nakamura, NRRL <- N.R. Smith: strain NRS-1347, Bacillus circulans <- F.E. Clark

NCBI tax ID(s): 1122915 (strain), 59839 (species)

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General

@ref: 1914

BacDive-ID: 11459

DSM-Number: 5050

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

description: Paenibacillus alginolyticus 1347 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1122915strain
59839species

strain history

@refhistory
1914<- NRRL <- N.R. Smith, 1347 (Bacillus circulans) <- F.E. Clark
67770NRRL NRS-1347 <-- N. R. Smith NRS-1347.
116229CIP <- 1988, L.K. Nakamura, NRRL <- N.R. Smith: strain NRS-1347, Bacillus circulans <- F.E. Clark

doi: 10.13145/bacdive11459.20230509.8.1

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 alginolyticus
  • full scientific name: Paenibacillus alginolyticus (Nakamura 1987) Shida et al. 1997

  • synonyms

    • @ref: 20215
    • synonym: Bacillus alginolyticus

@ref: 1914

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus alginolyticus

full scientific name: Paenibacillus alginolyticus (Nakamura 1987) Shida et al. 1997

strain designation: 1347

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.75
69480100positive
116229yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34117MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
1914NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
116229CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1914positivegrowth30mesophilic
34117positivegrowth30mesophilic
67770positivegrowth30mesophilic
116229positivegrowth30-41
116229nogrowth10psychrophilic
116229nogrowth22psychrophilic
116229nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116229
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes96
69480yes100

halophily

@refsaltgrowthtested relationconcentration
116229NaClpositivegrowth0 %
116229NaClnogrowth2 %
116229NaClnogrowth4 %
116229NaClnogrowth6 %
116229NaClnogrowth8 %
116229NaClnogrowth10 %

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
116229esculin+hydrolysis4853
116229nitrate-reduction17632
116229nitrite-reduction16301
116229nitrate+respiration17632

enzymes

@refvalueactivityec
116229oxidase+
116229beta-galactosidase+3.2.1.23
116229alcohol dehydrogenase-1.1.1.1
116229amylase-
116229caseinase-3.4.21.50
116229catalase+1.11.1.6
116229lecithinase-
116229lysine decarboxylase-4.1.1.18
116229ornithine decarboxylase-4.1.1.17

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116229-----+--+++++----+-----++--+-+++--+-+-++---------

Isolation, sampling and environmental information

isolation

@refsample type
1914soil
67770Soil
116229Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_162122.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2674;97_4826;98_6184;99_162122&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: D78465
  • Sequence Identity:
  • Total samples: 13
  • soil counts: 11
  • aquatic counts: 1
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
19141Risk group (German classification)
1162291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus alginolyticus clone JV-1F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478104429ena59839
20218Paenibacillus alginolyticus gene for 16S rRNA, partial sequenceAB0733621497ena59839
20218Paenibacillus aliginolyticus DNA for 16S rRNAD784651424ena59839
20218Paenibacillus alginolyticus gene for 16S rRNA, partial sequence, strain: NBRC 15375AB6808481467ena59839

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus alginolyticus DSM 50501122915.3wgspatric1122915
66792Paenibacillus alginolyticus DSM 5050 = NBRC 153751122915.5wgspatric1122915
66792Paenibacillus alginolyticus DSM 50502524614879draftimg1122915
67770Paenibacillus alginolyticus DSM 5050 = NBRC 15375GCA_000422905scaffoldncbi1122915
67770Paenibacillus alginolyticus DSM 5050 = NBRC 15375GCA_004000725contigncbi1122915

GC content

@refGC-contentmethod
191447.1-48.0
6777047-49Buoyant density centrifugation (BD)
6777048Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
motileyes85.215no
flagellatedyes82.441no
gram-positiveyes68.616no
anaerobicno98.761no
aerobicyes87.579no
halophileno97.67no
spore-formingyes91.054no
glucose-utilyes87.529no
thermophileno99.614yes
glucose-fermentno92.054no

External links

@ref: 1914

culture collection no.: DSM 5050, NRRL NRS-1347, JCM 9068, ATCC 51185, CIP 103122, IFO 15375, NBRC 15375, NCIMB 12517

straininfo link

  • @ref: 80696
  • straininfo: 10613

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22535437Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China.Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJAntonie Van Leeuwenhoek10.1007/s10482-012-9738-72012China, Molecular Sequence Data, Paenibacillus/classification/genetics/*isolation & purification, Soil/analysis, *Soil Microbiology, WetlandsGenetics
Phylogeny25794481Paenibacillus alba nov., isolated from peat soil.Kim HS, Srinivasan S, Lee SSCurr Microbiol10.1007/s00284-015-0795-92015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny27734255Paenibacillus oryzisoli sp. nov., isolated from the rhizosphere of rice.Zhang J, Ma XT, Gao JS, Zhang CW, Zhao JJ, Zhang RJ, Ma LA, Zhang XXAntonie Van Leeuwenhoek10.1007/s10482-016-0777-32016Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Oryza/growth & development, Paenibacillus/classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, *Soil MicrobiologyMetabolism
Phylogeny27902261Paenibacillus qinlingensis sp. nov., an indole-3-acetic acid-producing bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying.Xin K, Li M, Chen C, Yang X, Li Q, Cheng J, Zhang L, Shen XInt J Syst Evol Microbiol10.1099/ijsem.0.0016662017Bacterial Typing Techniques, Base Composition, Berberidaceae/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Indoleacetic Acids/*metabolism, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27995861Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea.Hwang YJ, Ghim SYInt J Syst Evol Microbiol10.1099/ijsem.0.0017482017Acer/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Islands, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny32556479Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil.Huq MACurr Microbiol10.1007/s00284-020-02086-02020Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Metal Nanoparticles, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silver, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1914Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5050)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5050
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
34117Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14885
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
80696Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10613.1StrainInfo: A central database for resolving microbial strain identifiers
116229Curators of the CIPCollection of Institut Pasteur (CIP 103122)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103122