Strain identifier

BacDive ID: 11466

Type strain: Yes

Species: Paenibacillus amylolyticus

Strain history: CIP <- 1988, L.K. Nakamura, NRRL: strain B-377 <- N.R. Smith: strain NRS-290, Bacillus circulans <- Kellerman, USDA, Bacillus amylolyticus

NCBI tax ID(s): 1451 (species)

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General

@ref: 5758

BacDive-ID: 11466

DSM-Number: 15211

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-negative, motile, rod-shaped

description: Paenibacillus amylolyticus DSM 15211 is a facultative anaerobe, spore-forming, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1451
  • Matching level: species

strain history

@refhistory
5758<- NRRL <- K. F. Kellerman
67770HSCC 434 <-- NRRL NRS-290 <-- N. R. Smith NRS-290 <-- K. F. Kellerman.
116359CIP <- 1988, L.K. Nakamura, NRRL: strain B-377 <- N.R. Smith: strain NRS-290, Bacillus circulans <- Kellerman, USDA, Bacillus amylolyticus

doi: 10.13145/bacdive11466.20240916.9.1

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 amylolyticus
  • full scientific name: Paenibacillus amylolyticus (Nakamura 1984 ex Choukévitch 1911) Ash et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Bacillus amylolyticus

@ref: 5758

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus amylolyticus

full scientific name: Paenibacillus amylolyticus (Nakamura 1984) Ash et al. 1994 emend. Shida et al. 1997

type strain: yes

Morphology

cell morphology

  • @ref: 116359
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5758NUTRIENT 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
116359CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116359CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
5758positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 116359
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69480yes92.466
69481yes99

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
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
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
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
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
116359nitrate+reduction17632
116359nitrite-reduction16301

metabolite production

  • @ref: 116359
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116359oxidase+
116359catalase+1.11.1.6
116359urease-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
116359-+++-+----++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116359+-+/-+++--+++++-+/---+-+/-+++++++++++++++++-++---+/---+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5758soilUSAUSANorth America
67770Soil
116359Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57581Risk group (German classification)
1163591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Paenibacillus amylolyticus gene for 16S rRNA, partial sequenceAB0731901503nuccore1451
67770Paenibacillus amylolyticus gene for 16S rRNA, partial sequence, strain: NBRC 15957AB3637431478nuccore1451
67770Paenibacillus amylolyticus DNA for 16S rRNAD853961508nuccore1451

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus amylolyticus strain NBRC 159571451.36wgspatric1451
67770Paenibacillus amylolyticus NBRC 15957GCA_004001025contigncbi1451

GC content

@refGC-contentmethod
575846.3-46.6
6777046.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes99no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes65.763no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.568yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes92.466no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no53.924yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.179yes
69480flagellatedmotile2+Ability to perform flagellated movementyes86.373no

External links

@ref: 5758

culture collection no.: DSM 15211, KACC 11263, LMG 21767, VTT E-02256, NRRL NRS-290, JCM 9906, ATCC 9995, CCUG 28514, CIP 103117, DSM 11730, DSM 11747, DSM 3034, IFO 13625, IFO 15957, KCTC 3455, LMG 11153, NBRC 13625, NBRC 15957, NRRL B-14940, NRRL B-377

straininfo link

  • @ref: 80700
  • straininfo: 297024

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18319478Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine.Roux V, Fenner L, Raoult DInt J Syst Evol Microbiol10.1099/ijs.0.65228-02008Adult, Bacterial Typing Techniques, Cerebrospinal Fluid/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Female, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/*isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Urine/*microbiologyGenetics
Phylogeny19542122Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra.Nelson DM, Glawe AJ, Labeda DP, Cann IK, Mackie RIInt J Syst Evol Microbiol10.1099/ijs.0.004572-02009Alaska, Bacterial Typing Techniques, Base Composition, *Cold Temperature, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xylans/*metabolismGenetics
24031795Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut.de Castro AL, Vollu RE, Peixoto RS, Grigorevski-Lima AL, Coelho RR, Bon EP, Rosado AS, Seldin LBraz J Microbiol10.1590/S1517-8382201100040000482011
Phylogeny28671536Paenibacillus polysaccharolyticus sp. nov., a xylanolytic and cellulolytic bacteria isolated from leaves of Bamboo Phyllostachys aureosulcata.Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA, Kwon SW, Whitman WBInt J Syst Evol Microbiol10.1099/ijsem.0.0019012017Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29679163Paenibacillus panacihumi sp. nov., a potential plant growth-promoting bacterium isolated from ginseng-cultivated soil.Kim CG, Kang JP, Huo Y, Chokkalingam M, Kim YJ, Kim DH, Yang DCArch Microbiol10.1007/s00203-018-1517-z2018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Paenibacillus/classification/genetics/*isolation & purification/metabolism, Panax/*growth & development/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism
Phylogeny30361975Paenibacillus seodonensis sp. nov., isolated from a plant of the genus Campanula.Kang MS, Lee KE, Lee EY, Park SJJ Microbiol10.1007/s12275-018-8455-y2018Bacterial Typing Techniques, Base Composition, Campanulaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Genotype, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, TemperatureGenetics
Metabolism31991163Potential synergistic antimicrobial efficiency of binary combinations of essential oils against Bacillus cereus and Paenibacillus amylolyticus-Part A.Ayari S, Shankar S, Follett P, Hossain F, Lacroix MMicrob Pathog10.1016/j.micpath.2020.1040082020Anti-Bacterial Agents/pharmacology, Anti-Infective Agents/pharmacology, Bacillus cereus/*drug effects, Cinnamomum zeylanicum/metabolism, Drug Synergism, Food Microbiology, Food Preservation/methods, Microbial Sensitivity Tests, Origanum/metabolism, Paenibacillus/*drug effects, Plant Oils/*pharmacology, Thymus Plant/metabolismPathogenicity

Reference

@idauthorscataloguedoi/urltitle
5758Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15211)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15211
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
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
68382Automatically annotated from API zym
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
80700Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297024.1StrainInfo: A central database for resolving microbial strain identifiers
116359Curators of the CIPCollection of Institut Pasteur (CIP 103117)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103117