Strain identifier

BacDive ID: 11612

Type strain: Yes

Species: Paenibacillus barengoltzii

Strain Designation: SAFN-016

Strain history: CIP <- 2006, NBRC <- M. Satomi, Nat. Res. Inst. Fish. Sci., Yokohama, Japan: strain SAFN-016 <- K. Venkateswaran

NCBI tax ID(s): 1220556 (strain), 343517 (species)

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General

@ref: 16237

BacDive-ID: 11612

DSM-Number: 22255

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

description: Paenibacillus barengoltzii SAFN-016 is an aerobe, spore-forming, mesophilic bacterium that was isolated from clean room floors of the Jet Propulsion Laboratory Spacecraft Assembly Facility .

NCBI tax id

NCBI tax idMatching level
343517species
1220556strain

strain history

@refhistory
16237<- M. Miyashita, Natl. Inst. of Technol. and Evaluation (NITE), Japan <- K. Venkateswaran; SAFN-016
116734CIP <- 2006, NBRC <- M. Satomi, Nat. Res. Inst. Fish. Sci., Yokohama, Japan: strain SAFN-016 <- K. Venkateswaran

doi: 10.13145/bacdive11612.20230509.8.1

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 barengoltzii
  • full scientific name: Paenibacillus barengoltzii Osman et al. 2006

@ref: 16237

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus barengoltzii

full scientific name: Paenibacillus barengoltzii Osman et al. 2006

strain designation: SAFN-016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31703positive03-05 µm0.5-0.8 µmrod-shapedyes
69480yes96.973
69480positive100
116734positiverod-shapedyes

pigmentation

  • @ref: 31703
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16237CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
37525MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116734CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16237positivegrowth30mesophilic
31703positivegrowth10-50
31703positiveoptimum37mesophilic
37525positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31703positivegrowth4.5-9alkaliphile
31703positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31703aerobe
116734facultative anaerobe

spore formation

@refspore formationconfidence
31703yes
69481yes100
69480yes100
116734no

halophily

@refsaltgrowthtested relationconcentration
31703NaClpositivegrowth2 %
31703NaClpositiveoptimum2 %

observation

  • @ref: 31703
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170324265gluconate+carbon source
317034853esculin+hydrolysis
3170317632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-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
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+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
11673417632nitrate+reduction
11673416301nitrite-reduction

metabolite production

  • @ref: 116734
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31703catalase+1.11.1.6
31703cytochrome oxidase+1.9.3.1
116734oxidase+
116734amylase+
116734catalase+1.11.1.6
116734tween esterase-
116734urease-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
116734--++------++++-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116734---+-+--+++++-+--+-+/-+++++++++++++-+++-++---+--+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16237clean room floors of the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF)California, PasadenaUSAUSANorth America
116734Clean room floor, spacecraft assembly facilityPasadena, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment
  • Cat3: #Clean room

taxonmaps

  • @ref: 69479
  • File name: preview.99_6104.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2906;97_3575;98_4527;99_6104&stattab=map
  • Last taxonomy: Paenibacillus barengoltzii subclade
  • 16S sequence: AB681405
  • Sequence Identity:
  • Total samples: 498
  • soil counts: 164
  • aquatic counts: 39
  • animal counts: 185
  • plant counts: 110

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162371Risk group (German classification)
1167341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus barengoltzii gene for 16S rRNA, partial sequence, strain: NBRC 101215AB6814051478ena343517
16237Paenibacillus barengoltzii strain SAFN-016 16S ribosomal RNA gene, partial sequenceAY1678141339ena343517

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus barengoltzii NBRC 101215GCA_004000745contigncbi1220556
66792Paenibacillus barengoltzii NBRC 1012151220556.3wgspatric1220556

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.865yes
gram-positiveyes90.476yes
anaerobicno97.569yes
aerobicyes86.545yes
halophileno92.565no
spore-formingyes95.385yes
glucose-utilyes88.763no
flagellatedyes72.653no
thermophileno94.047yes
glucose-fermentno88.95no

External links

@ref: 16237

culture collection no.: DSM 22255, ATCC BAA 1209, CIP 109354, NBRC 101215

straininfo link

  • @ref: 80838
  • straininfo: 297279

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825621Paenibacillus pasadenensis sp. nov. and Paenibacillus barengoltzii sp. nov., isolated from a spacecraft assembly facility.Osman S, Satomi M, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijs.0.64085-02006Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environment, Controlled, Environmental Microbiology, Genes, rRNA, Gram-Positive Bacteria/*classification/cytology/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Spacecraft, Spores, Bacterial, United StatesGenetics
Phylogeny17551056Paenibacillus fonticola sp. nov., isolated from a warm spring.Chou JH, Chou YJ, Lin KY, Sheu SY, Sheu DS, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.64872-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Gram-Positive Endospore-Forming Rods/chemistry/*classification/*isolation & purification/physiology, Hot Springs/*microbiology, Lipids/analysis, Locomotion, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, TaiwanGenetics
Phylogeny21831630Characterization of a microbial consortium capable of degrading lignocellulose.Wang W, Yan L, Cui Z, Gao Y, Wang Y, Jing RBioresour Technol10.1016/j.biortech.2011.07.0652011Bacteria/genetics/*metabolism, Base Sequence, Biodegradation, Environmental, *Bioreactors, Cluster Analysis, Computational Biology, DNA Primers/genetics, Denaturing Gradient Gel Electrophoresis, Lignin/*metabolism, Molecular Sequence Data, Oryza/*chemistry, Phylogeny, Plant Stems/*chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny26394885Paenibacillus faecis sp. nov., isolated from human faeces.Clermont D, Gomard M, Hamon S, Bonne I, Fernandez JC, Wheeler R, Malosse C, Chamot-Rooke J, Gribaldo S, Boneca IG, Bizet CInt J Syst Evol Microbiol10.1099/ijsem.0.0006222015Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, France, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Phylogeny26675308Paenibacillus cathormii sp. nov., isolated from tree bark.Sitdhipol J, Paek J, Sin Y, Park IS, Thamacharoensuk T, Wannissorn B, Tanasupawat S, Chang YHInt J Syst Evol Microbiol10.1099/ijsem.0.0008542015
Phylogeny27188601Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser.Yokota A, Ningsih F, Nurlaili DG, Sakai Y, Yabe S, Oetari A, Santoso I, Sjamsuridzal WInt J Syst Evol Microbiol10.1099/ijsem.0.0011512016Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Indonesia, Nucleic Acid Hybridization, Paenibacillus/classification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30167766Biological Synthesis of Ginsenoside Rd Using Paenibacillus horti sp. nov. Isolated from Vegetable Garden.Akter S, Huq MACurr Microbiol10.1007/s00284-018-1561-62018Bacterial Typing Techniques/methods, Base Composition/genetics, DNA, Bacterial/genetics, Fatty Acids/genetics, Gardens, Ginsenosides/*biosynthesis/*genetics, Nucleic Acid Hybridization/genetics, Paenibacillus/*genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA/methods, Soil Microbiology, Vegetables/*microbiologyTranscriptome
Phylogeny35974114Paenibacillus mellifer sp. nov., isolated from gut of the honey bee Apis mellifera.Cho ES, Hwang CY, Kwon HW, Seo MJArch Microbiol10.1007/s00203-022-03178-02022Animals, Bacterial Typing Techniques, Bees, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Paenibacillus, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics/metabolism, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16237Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22255)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22255
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
31703Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127980
37525Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7086
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
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
80838Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297279.1StrainInfo: A central database for resolving microbial strain identifiers
116734Curators of the CIPCollection of Institut Pasteur (CIP 109354)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109354