Strain identifier

BacDive ID: 11570

Type strain: Yes

Species: Paenibacillus agaridevorans

Strain Designation: 65

Strain history: CIP <- 2002, DSMZ <- 1978, W. Hunger

NCBI tax ID(s): 171404 (species)

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General

@ref: 640

BacDive-ID: 11570

DSM-Number: 1355

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

description: Paenibacillus agaridevorans 65 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from volcanic soil.

NCBI tax id

  • NCBI tax id: 171404
  • Matching level: species

strain history

@refhistory
640<- W. Hunger, 65
116150CIP <- 2002, DSMZ <- 1978, W. Hunger

doi: 10.13145/bacdive11570.20230509.8.1

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 agaridevorans
  • full scientific name: Paenibacillus agaridevorans Uetanabaro et al. 2003

@ref: 640

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus agaridevorans

full scientific name: Paenibacillus agaridevorans Uetanabaro et al. 2003

strain designation: 65

type strain: yes

Morphology

cell morphology

  • @ref: 116150
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 116150

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
640NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Urea 1.0 g/l Distilled water
116150CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
640positivegrowth30mesophilic
116150positivegrowth22-37
116150nogrowth10psychrophilic
116150nogrowth45thermophilic
116150nogrowth55thermophilic

culture pH

  • @ref: 116150
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 116150
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 116150
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
116150NaClnogrowth0 %
116150NaClnogrowth2 %
116150NaClnogrowth4 %
116150NaClnogrowth6 %
116150NaClnogrowth8 %
116150NaClnogrowth10 %

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
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116150citrate-carbon source16947
116150esculin+hydrolysis4853
116150hippurate+hydrolysis606565
116150nitrate-reduction17632
116150nitrite-reduction16301
116150nitrate-respiration17632

metabolite production

  • @ref: 116150
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11615015688acetoin-
11615017234glucose-

enzymes

@refvalueactivityec
116150oxidase-
116150beta-galactosidase+3.2.1.23
116150alcohol dehydrogenase-1.1.1.1
116150gelatinase-
116150amylase+
116150DNase-
116150caseinase-3.4.21.50
116150catalase+1.11.1.6
116150tween esterase-
116150gamma-glutamyltransferase-2.3.2.2
116150lecithinase+
116150lipase-
116150lysine decarboxylase-4.1.1.18
116150ornithine decarboxylase-4.1.1.17
116150protease-
116150urease-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
116150--+----------+-----+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116150---+/-----+++---------+-+++/-+++++++-+/-+---++---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116150-+++--+++++++++++-+-+-+--+-----+--++-----+------------++-------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
640volcanic soilVolcano ParicutinMexicoMEXNorth America
116150Environment, Volcanic soilMexicoMEXNorth America1975

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Volcanic
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_21879.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_7772;97_9742;98_16498;99_21879&stattab=map
  • Last taxonomy: Paenibacillus agaridevorans
  • 16S sequence: AJ345023
  • Sequence Identity:
  • Total samples: 271
  • soil counts: 157
  • aquatic counts: 33
  • animal counts: 53
  • plant counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
6401Risk group (German classification)
1161501Risk group (French classification)

Sequence information

16S sequences

  • @ref: 640
  • description: Paenibacillus agaridevorans partial 16S rRNA gene, strain DSM 1355
  • accession: AJ345023
  • length: 1509
  • database: ena
  • NCBI tax ID: 171404

GC content

  • @ref: 640
  • GC-content: 51.3

External links

@ref: 640

culture collection no.: DSM 1355, CIP 107436, KCTC 3849

straininfo link

  • @ref: 80798
  • straininfo: 265468

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892125Paenibacillus agarexedens sp. nov., nom. rev., and Paenibacillus agaridevorans sp. nov.Uetanabaro AP, Wahrenburg C, Hunger W, Pukall R, Sproer C, Stackebrandt E, de Canhos VP, Claus D, Fritze DInt J Syst Evol Microbiol10.1099/ijs.0.02420-02003Bacillus/*classification/genetics/metabolism, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phenotype, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny19126736Paenibacillus siamensis sp. nov., Paenibacillus septentrionalis sp. nov. and Paenibacillus montaniterrae sp. nov., xylanase-producing bacteria from Thai soils.Khianngam S, Tanasupawat S, Lee JS, Lee KC, Akaracharanya AInt J Syst Evol Microbiol10.1099/ijs.0.65851-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/*classification/*enzymology/genetics/isolation & purification, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Thailand, Xylosidases/*biosynthesisEnzymology
Phylogeny19244442Paenibacillus thailandensis sp. nov. and Paenibacillus nanensis sp. nov., xylanase-producing bacteria isolated from soil.Khianngam S, Akaracharanya A, Tanasupawat S, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.000406-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/*classification/*enzymology/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/physiology, Thailand, Xylosidases/*biosynthesisEnzymology
Phylogeny19946060Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease.Kim KK, Lee KC, Yu H, Ryoo S, Park Y, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.017137-02009Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Gram-Positive Bacterial Infections/*microbiology, Humans, Lung Diseases/*microbiology, Molecular Sequence Data, Paenibacillus/*classification/*isolation & purification, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology, Sputum/*microbiologyPathogenicity
Phylogeny20228214Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment.Park MH, Traiwan J, Jung MY, Nam YS, Jeong JH, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.021832-02010Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Geologic Sediments/microbiology, Lipids/analysis, Molecular Sequence Data, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, *Water MicrobiologyGenetics
Phylogeny26133115Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba.Han TY, Tong XM, Wang YW, Wang HM, Chen XR, Kong DL, Guo X, Ruan ZYAntonie Van Leeuwenhoek10.1007/s10482-015-0521-42015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, *Populus, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny31702533Paenibacillus protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis.Heo J, Kim SJ, Kim JS, Hong SB, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0038602020Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Coleoptera/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Larva/microbiology, Paenibacillus/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
640Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1355)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1355
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
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
80798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265468.1StrainInfo: A central database for resolving microbial strain identifiers
116150Curators of the CIPCollection of Institut Pasteur (CIP 107436)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107436