Strain identifier

BacDive ID: 1151

Type strain: Yes

Species: Bacillus pseudomycoides

Strain history: CIP <- 1998, L.K. Nakamura, NCAUR, Peoria, Illinois, USA: strain NRRL B-617

NCBI tax ID(s): 527000 (strain), 64104 (species)

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General

@ref: 4718

BacDive-ID: 1151

DSM-Number: 12442

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

description: Bacillus pseudomycoides DSM 12442 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms rhizoid colonies and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
527000strain
64104species

strain history

@refhistory
4718<- L. K. Nakamura, NRRL
67770NRRL B-617 <-- L. J. Wickerham.
121998CIP <- 1998, L.K. Nakamura, NCAUR, Peoria, Illinois, USA: strain NRRL B-617

doi: 10.13145/bacdive1151.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus pseudomycoides
  • full scientific name: Bacillus pseudomycoides Nakamura 1998

@ref: 4718

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus pseudomycoides

full scientific name: Bacillus pseudomycoides Nakamura 1998

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23303positive3.0-5.0 µm1.0 µmrod-shapedno
69480positive100
121998positiverod-shapedno

colony morphology

@refcolony colorcolony shape
23303white to cream, opaquerhizoid
121998

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4718NUTRIENT 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
41877MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121998CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121998CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4718positivegrowth30mesophilic
23303positivemaximum40thermophilic
23303positiveminimum15psychrophilic
23303positiveoptimum28mesophilic
41877positivegrowth30mesophilic
67770positivegrowth30mesophilic
121998positivegrowth22-45
121998nogrowth10psychrophilic
121998nogrowth55thermophilic

culture pH

@refabilitytypepH
23303positivegrowth5.7
121998positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23303facultative anaerobe
121998facultative anaerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23303ellipsoidal spores in sporangia, not distendedendosporeyes
69481yes100
69480yes100
121998yes

halophily

@refsaltgrowthtested relationconcentration
23303NaClpositivegrowth7 %
121998NaClpositivegrowth0-2 %
121998NaClnogrowth4 %
121998NaClnogrowth6 %
121998NaClnogrowth8 %
121998NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2330317272propionate-assimilation
2330317634D-glucose+builds acid from
2330317634D-glucose+builds gas from
23303casein+degradation
23303egg yolk+degradation
2330361995lecithin+degradation
2330328017starch+degradation
2330318186tyrosine+degradation
2330316899D-mannitol+fermentation
2330365327D-xylose+fermentation
2330330849L-arabinose+fermentation
2330317632nitrate+reduction
2330316947citrate+/-assimilation
1219984853esculin-hydrolysis
121998606565hippurate-hydrolysis
12199817632nitrate+reduction
12199816301nitrite-reduction
12199817632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
2330335581indoleno
2330316136hydrogen sulfideno
2330316016dihydroxyacetoneno
2330315688acetoinyes
12199835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2330315688acetoin+
12199815688acetoin+
12199817234glucose+

enzymes

@refvalueactivityec
23303catalase+1.11.1.6
23303cytochrome oxidase-1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121998oxidase-
121998beta-galactosidase-3.2.1.23
121998alcohol dehydrogenase-1.1.1.1
121998gelatinase+
121998amylase+
121998DNase-
121998caseinase-3.4.21.50
121998catalase+1.11.1.6
121998tween esterase-
121998gamma-glutamyltransferase-2.3.2.2
121998lecithinase+
121998lipase-
121998lysine decarboxylase-4.1.1.18
121998ornithine decarboxylase-4.1.1.17
121998phenylalanine ammonia-lyase-4.3.1.24
121998protease-
121998tryptophan deaminase-
121998urease-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
121998-+++-+---+++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121998++-+-----++----+---+-----------+-----------------+---+-----+------------+--+--+++------------++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
4718soilGhanaGHAAfrica
67770Soil
121998Environment, SoilSwedenSWEEurope1945

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_26.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_21;97_22;98_25;99_26&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: LC107614
  • Sequence Identity:
  • Total samples: 4969
  • soil counts: 1920
  • aquatic counts: 446
  • animal counts: 1524
  • plant counts: 1079

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47181Risk group (German classification)
1219981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus pseudomycoides gene for 16S rRNA, partial sequence, strain: GTC 02831AB5925421455ena64104
20218Bacillus pseudomycoides partial 16S rRNA gene and ITS1, strain DSM 12442AJ841871543ena64104
20218Bacillus pseudomycoides partial 16S rRNA gene and ITS1, strain DSM 12442AM7472261663ena64104
23303Bacillus pseudomycoides 16S ribosomal RNA gene, complete sequenceAF0131211532nuccore64104
67770Bacillus pseudomycoides gene for 16S rRNA, partial sequence, strain: NBRC 101232AB6814141477ena64104
67770Bacillus pseudomycoides gene for 16S ribosomal RNA, partial sequence, strain: JCM 12231LC1076141474ena64104

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus pseudomycoides DSM 12442GCA_000161455chromosomencbi527000
66792Bacillus pseudomycoides DSM 12442527000.3wgspatric527000
66792Bacillus pseudomycoides DSM 12442643886172draftimg527000

GC content

  • @ref: 23303
  • GC-content: 34-36
  • method: fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno89.893yes
flagellatedno82.516yes
gram-positiveyes91.236yes
anaerobicno98.434yes
aerobicyes75.483yes
halophileno86.342yes
spore-formingyes90.03no
thermophileno98.71no
glucose-utilyes90.374no
glucose-fermentno90.985no

External links

@ref: 4718

culture collection no.: DSM 12442, NRRL B-617, JCM 12231, CIP 105700, LMG 18993, KCTC 3862, NBRC 101232, BCRC 17606, BCRC 17107

straininfo link

  • @ref: 70822
  • straininfo: 12955

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734060Bacillus pseudomycoides sp. nov.Nakamura LKInt J Syst Bacteriol10.1099/00207713-48-3-10311998Bacillus/*classification/genetics, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/chemistry, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny24370979Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China.Liu B, Liu GH, Hu GP, Sengonca C, Lin NQ, Tang JY, Tang WQ, Lin YZAntonie Van Leeuwenhoek10.1007/s10482-013-0102-32013Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Fatty Acids/chemistry, Genes, Bacterial, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyPhenotype
Metabolism25769830Pseudomycoicidin, a Class II Lantibiotic from Bacillus pseudomycoides.Basi-Chipalu S, Dischinger J, Josten M, Szekat C, Zweynert A, Sahl HG, Bierbaum GAppl Environ Microbiol10.1128/AEM.00299-152015Amino Acid Sequence, Anti-Bacterial Agents/chemistry/*metabolism/pharmacology, Bacillus/chemistry/genetics/*metabolism, Bacterial Proteins/genetics/metabolism, Bacteriocins/chemistry/genetics/*metabolism/pharmacology, Gram-Positive Bacteria/drug effects, Molecular Sequence Data, Sequence AlignmentGenetics
32055339Efficient in vivo synthesis of lasso peptide pseudomycoidin proceeds in the absence of both the leader and the leader peptidase.Zyubko T, Serebryakova M, Andreeva J, Metelev M, Lippens G, Dubiley S, Severinov KChem Sci10.1039/c9sc02370d2019
Phylogeny35767195Bacillus arachidis sp. nov., Isolated from Peanut Rhizosphere Soil.Chen Y, Li Y, Shen J, Liu Q, Liu Y, Chu Y, Xiao ZCurr Microbiol10.1007/s00284-022-02925-22022Arachis, *Bacillus, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fabaceae/genetics, Fatty Acids, Phosphatidylglycerols, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome
36399337Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin.Janssen K, Krasenbrink J, Strangfeld S, Kroheck S, Josten M, Engeser M, Bierbaum GChembiochem10.1002/cbic.2022005402022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4718Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12442)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12442
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
23303L. K. Nakamura10.1099/00207713-48-3-1031Bacillus pseudomycoides sp. nov.IJSEM 48: 1031-1035 19989734060
41877Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17748
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/
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
70822Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12955.1StrainInfo: A central database for resolving microbial strain identifiers
121998Curators of the CIPCollection of Institut Pasteur (CIP 105700)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105700