Strain identifier

BacDive ID: 598

Type strain: Yes

Species: Bacillus amyloliquefaciens

Strain Designation: F

Strain history: CIP <- 1988, DSMZ <- ATCC <- L.L. Campbell: strain F <- J. Fukumoto, Bacillus subtilis

NCBI tax ID(s): 692420 (strain), 1390 (species)

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General

@ref: 2015

BacDive-ID: 598

DSM-Number: 7

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, psychrophilic, Gram-positive, motile, rod-shaped, antibiotic compound production

description: Bacillus amyloliquefaciens F is an obligate aerobe, spore-forming, psychrophilic bacterium that produces antibiotic compounds and was isolated from soil and industrial amylase fermentations.

NCBI tax id

NCBI tax idMatching level
1390species
692420strain

strain history

@refhistory
2015<- ATCC <- L.L. Campbell, F (Bacillus subtilis)
116352CIP <- 1988, DSMZ <- ATCC <- L.L. Campbell: strain F <- J. Fukumoto, Bacillus subtilis

doi: 10.13145/bacdive598.20230509.8.1

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 amyloliquefaciens
  • full scientific name: Bacillus amyloliquefaciens (ex Fukomoto 1943) Priest et al. 1987

@ref: 2015

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus amyloliquefaciens

full scientific name: Bacillus amyloliquefaciens (ex Fukumoto 1943) Priest et al. 1987 emend. Wang et al. 2008

strain designation: F

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
24474positive1.8-3.0 µm0.7-0.9 µmrod-shapedyesperitrichous
69480yes91.406
69480positive100
116352positiverod-shapedno

colony morphology

  • @ref: 24474
  • medium used: medium of Gordon et al.

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
24474medium of Gordon et al.yes
35323MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2015NUTRIENT 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
116352CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116352CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
24474nogrowth<15psychrophilic
24474nogrowth>50thermophilic
24474positiveoptimum30-40
2015positivegrowth30mesophilic
35323positivegrowth30mesophilic
116352positivegrowth30-45
116352nogrowth10psychrophilic
116352nogrowth55thermophilic

culture pH

  • @ref: 116352
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 116352
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
24474central or paracentralsporeyes
69481yes100
69480yes100

compound production

@refcompound
2015alpha amylase
20151-deoxynojirimycin
2015inhibitors for glycoside hydrolases
2015restriction endonuclease BamFI (BamHI)
24474Acetoin

halophily

@refsaltgrowthtested relationconcentration
24474NaClpositivegrowth5 %(w/v)
24474NaClpositivegrowth10 %
116352NaClpositivegrowth0-6 %
116352NaClnogrowth8 %
116352NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2447416708adenine-other
24474casein+other
2447462968cellulose-other
2447416947citrate+growth
244744767elastin+other
244745291gelatin+other
2447416235guanine-other
2447417368hypoxanthine-other
2447428017starch+other
2447417347testosterone-other
2447435020tributyrin+other
2447453424tween 20+other
2447453423tween 40+other
2447453425tween 60+other
2447418186tyrosine-other
2447416199urea-other
2447415318xanthine-other
2447417925alpha-D-glucose+builds acid from
2447436219alpha-lactose+builds acid from
2447416708adenine-degradation
2447485146carboxymethylcellulose-degradation
2447416235guanine-degradation
2447417368hypoxanthine-degradation
2447417309pectin-degradation
2447417347testosterone-degradation
2447418186tyrosine-degradation
2447415318xanthine-degradation
2447415676allantoin-hydrolysis
2447416199urea-hydrolysis
2447417057cellobiose+builds acid from
2447428757fructose+builds acid from
2447417234glucose+builds acid from
2447417754glycerol+builds acid from
2447417716lactose+builds acid from
2447417306maltose+builds acid from
2447429864mannitol+builds acid from
2447437684mannose+builds acid from
2447416634raffinose+builds acid from
2447417814salicin+builds acid from
2447430911sorbitol+builds acid from
2447417992sucrose+builds acid from
2447427082trehalose+builds acid from
2447416947citrate+carbon source
24474casein+degradation
244744767elastin+degradation
2447428017starch+degradation
2447435020tributyrin+degradation
2447453424tween 20+degradation
2447453423tween 40+degradation
2447453425tween 60+degradation
2447418305arbutin+hydrolysis
244744853esculin+hydrolysis
2447415688acetoin+other
2447417632nitrate+reduction
2447416991dna+/-degradation
11635216947citrate-carbon source
11635217632nitrate-reduction
11635216301nitrite-reduction
11635217632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2447415688acetoinyes
11635235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
2447415688acetoin+
11635215688acetoin+

enzymes

@refvalueactivityec
24474arginine dihydrolase-3.5.3.6
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
116352oxidase-
116352beta-galactosidase-3.2.1.23
116352alcohol dehydrogenase-1.1.1.1
116352gelatinase-
116352amylase-
116352caseinase-3.4.21.50
116352catalase+1.11.1.6
116352lecithinase+
116352lysine decarboxylase-4.1.1.18
116352ornithine decarboxylase-4.1.1.17
116352urease-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
116352-+++------++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116352+++++-++++++--++++++--+--------+-++++----+-------+++-------++------------+-+--+++-----+--++++++----

Isolation, sampling and environmental information

isolation

@refsample type
24474soil and industrial amylase fermentations
49266Soil
2015soil
116352Environment, Soil

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Industrial production
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_21.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_17;97_17;98_20;99_21&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: HQ231913
  • Sequence Identity:
  • Total samples: 18201
  • soil counts: 3768
  • aquatic counts: 2854
  • animal counts: 9674
  • plant counts: 1905

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20151Risk group (German classification)
1163521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus amyloliquefaciens clone BamyloDH3R 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478077408ena692420
20218Bacillus amyloliquefaciens clone DH-19 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478078466ena692420
20218Bacillus amyloliquefaciens clone DH-11-1 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478079584ena692420
20218Bacillus amyloliquefaciens strain DSM7 (F) 16S ribosomal RNA gene, partial sequenceAY055225500ena692420
20218Bacillus amyloliquefaciens strain MPA 1034 16S ribosomal RNA gene, partial sequenceHQ2319131448ena1390
20218Zhouia sp. DSM7 16S ribosomal RNA gene, partial sequenceKC439236910ena1343290
20218B.amyloliquefaciens 16S ribosomal RNAX606051427ena692420
2015Bacillus amyloliquefaciens gene for 16S rRNA, partial sequenceAB006920274ena692420

Genome sequences

  • @ref: 66792
  • description: Bacillus amyloliquefaciens DSM 7 = ATCC 23350
  • accession: GCA_000196735
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 692420

GC content

@refGC-contentmethod
2447444.6
201546.2thermal denaturation, midpoint method (Tm)
201544.5Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.292yes
flagellatedyes87.663yes
gram-positiveyes88.832yes
anaerobicno99.324no
aerobicyes88.946no
halophileyes91.142yes
spore-formingyes96.737no
thermophileno97.921no
glucose-utilyes88.126no
glucose-fermentno92.25no

External links

@ref: 2015

culture collection no.: DSM 7, ATCC 23350, CCUG 28519, NRRL B-14393, Fukumoto strain F, CIP 103265, LMG 9814, NRRL : B-14393

straininfo link

  • @ref: 70275
  • straininfo: 1093

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2999078Bacteriophage SPO2-mediated plasmid transduction in transpositional mutagenesis within the genus Bacillus.Kopec LK, Yasbin RE, Marrero RJ Bacteriol10.1128/jb.164.3.1283-1287.19851985Acetyltransferases/genetics, Bacillus/*genetics, Bacteriophages/*genetics, Chimera, Chloramphenicol O-Acetyltransferase, DNA Restriction Enzymes/metabolism, DNA Transposable Elements, Deoxyribonuclease EcoRI, Drug Resistance, Microbial, Enterococcus faecalis/genetics, Erythromycin/pharmacology, *Mutation, Nucleic Acid Hybridization, *Plasmids, *Transduction, GeneticEnzymology
Metabolism18374441Phytate utilization by genetically engineered lysine-producing Corynebacterium glutamicum.Tzvetkov MV, Liebl WJ Biotechnol10.1016/j.jbiotec.2008.02.00520086-Phytase/*genetics/*metabolism, Bacillus/enzymology/genetics, Corynebacterium glutamicum/cytology/*enzymology/genetics, Culture Media/metabolism, Genetic Engineering, Genetic Vectors, Lysine/analysis/biosynthesis, Phosphates/metabolism, Phosphorus/analysis/metabolism, Phytic Acid/*metabolism, Transformation, Bacterial, Transgenes/physiologyEnzymology
Biotechnology18587901Cell growth and alpha-amylase production characteristics of Bacillus amyloliquefaciens.Roychoudhury S, Parulekar SJ, Weigand WABiotechnol Bioeng10.1002/bit.2603302091989
Phylogeny20817842Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons.Borriss R, Chen XH, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Sproer C, Junge H, Vater J, Puhler A, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.023267-02010Bacillus/*classification/genetics/*isolation & purification, Bacterial Proteins/genetics, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Genome, Bacterial, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil MicrobiologyGenetics
Genetics21262282Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42.Ruckert C, Blom J, Chen X, Reva O, Borriss RJ Biotechnol10.1016/j.jbiotec.2011.01.0062011Bacillus/classification/*genetics, *Chromosome Mapping, *Genes, Bacterial, *Genome, Bacterial, Plants/microbiology, Sequence Alignment, Sequence Analysis, DNA, Soil Microbiology, Species SpecificityPhylogeny
Genetics21515778Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin.Zhang G, Deng A, Xu Q, Liang Y, Chen N, Wen TJ Bacteriol10.1128/JB.00440-112011Bacillus/*classification/*genetics, *Genome, Bacterial, Guanosine/*metabolism, Molecular Sequence Data, Ribavirin/*metabolismMetabolism
Enzymology26171785Characterization of a Mannose-6-Phosphate Isomerase from Bacillus amyloliquefaciens and Its Application in Fructose-6-Phosphate Production.Sigdel S, Singh R, Kim TS, Li J, Kim SY, Kim IW, Jung WS, Pan CH, Kang YC, Lee JKPLoS One10.1371/journal.pone.01315852015Amino Acid Sequence, Bacillus/*enzymology/genetics, Cloning, Molecular, Crystallography, X-Ray, Enzyme Stability, Escherichia coli/genetics, Fructosephosphates/*biosynthesis, Hydrogen-Ion Concentration, Kinetics, Mannose-6-Phosphate Isomerase/chemistry/*genetics/*metabolism, Metals/pharmacology, Molecular Docking Simulation, Molecular Dynamics Simulation, Molecular Sequence Data, Molecular Weight, Protein Structure, Quaternary, Sequence Homology, Amino Acid, Substrate Specificity, TemperatureGenetics
Genetics28112210Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45.Zhi Y, Wu Q, Xu YSci Rep10.1038/srep409762017Bacillus amyloliquefaciens/*genetics/*metabolism, *Gene Expression Profiling, Gene Regulatory Networks, *Genomics, Lipopeptides/*biosynthesis/*genetics, Peptides, Cyclic/*biosynthesis/*geneticsTranscriptome
28163698Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an "Operational Group B. amyloliquefaciens" within the B. subtilis Species Complex.Fan B, Blom J, Klenk HP, Borriss RFront Microbiol10.3389/fmicb.2017.000222017
Genetics31098827Complete Genome of Bacillus velezensis CMT-6 and Comparative Genome Analysis Reveals Lipopeptide Diversity.Deng Q, Wang R, Sun D, Sun L, Wang Y, Pu Y, Fang Z, Xu D, Liu Y, Ye R, Yin S, Xie S, Gooneratne RBiochem Genet10.1007/s10528-019-09927-z2019Bacillus/*genetics, Bacterial Proteins/*genetics, Genetic Variation, Genome, Bacterial/*genetics, Lipopeptides/*genetics, Peptide Synthases/genetics, Whole Genome Sequencing
Cultivation33573182Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria.Schwarz J, Hubmann G, Rosenthal K, Lutz SBiomolecules10.3390/biom110201932021Bacillus amyloliquefaciens/genetics, Culture Media, Data Mining, Deferoxamine/chemistry, Genome, Lysine/analogs & derivatives/chemistry, *Microbial Sensitivity Tests, *Multigene Family, Myxococcales/genetics, Oligopeptides/chemistry, Rhodococcus/genetics, Secondary Metabolism/genetics, Streptomyces/geneticsGenetics
Cultivation34897250Control Efficacy of Bacillus velezensis AFB2-2 against Potato Late Blight Caused by Phytophthora infestans in Organic Potato Cultivation.Kim MJ, Shim CK, Park JHPlant Pathol J10.5423/PPJ.FT.09.2021.01382021
Metabolism35107331Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects.Zaid DS, Cai S, Hu C, Li Z, Li YMicrobiol Spectr10.1128/spectrum.02169-212022Antifungal Agents/metabolism, Bacillus/classification/*genetics/metabolism, Bacterial Proteins/genetics/metabolism, Biological Control Agents/*metabolism, Genome, Bacterial, Genomics, Multigene Family, *Phylogeny, Plant Growth Regulators/biosynthesis, Secondary MetabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2015Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7
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
24474F. G. Priest, M. Goodfellow, L. A. Shute, R. C. W. Berkeley10.1099/00207713-37-1-69Bacillus amyloliquefaciens sp. nov., nom. rev.IJSEM 37: 69-71 1987
35323Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15043
49266Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28519)https://www.ccug.se/strain?id=28519
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)
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
70275Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1093.1StrainInfo: A central database for resolving microbial strain identifiers
116352Curators of the CIPCollection of Institut Pasteur (CIP 103265)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103265