Strain identifier

BacDive ID: 1077

Type strain: Yes

Species: Bacillus atrophaeus

Strain history: CIP <- 2001, DSMZ <- NRRL <- NRS, Bacillus subtilis var. niger

NCBI tax ID(s): 1220587 (strain), 1452 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3083

BacDive-ID: 1077

DSM-Number: 7264

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

description: Bacillus atrophaeus DSM 7264 is an aerobe, spore-forming, mesophilic human pathogen that forms circular colonies and has a dark brown pigmentation.

NCBI tax id

NCBI tax idMatching level
1452species
1220587strain

strain history

@refhistory
3083<- NRRL <- NRS, 213 ("B. subtilis var. niger")
67770NRRL NRS-213 <-- N. R. Smith NRS-213.
116542CIP <- 2001, DSMZ <- NRRL <- NRS, Bacillus subtilis var. niger

doi: 10.13145/bacdive1077.20230509.8.1

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 atrophaeus
  • full scientific name: Bacillus atrophaeus Nakamura 1989

@ref: 3083

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus atrophaeus

full scientific name: Bacillus atrophaeus Nakamura 1989

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23299positive2.0-4.0 µm0.5-1.0 µmrod-shapedyes
116542positiverod-shapedyes

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodhemolysis ability
232991-2 mmopaquecircular2 days
1165421

pigmentation

  • @ref: 23299
  • production: yes
  • color: dark brown

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3083NUTRIENT 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
36886MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116542CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3083positivegrowth30mesophilic
23299positivemaximum50-55thermophilic
23299positiveminimum5-10psychrophilic
23299positiveoptimum28-30mesophilic
36886positivegrowth30mesophilic
67770positivegrowth30mesophilic
116542positivegrowth22-37
116542nogrowth10psychrophilic
116542nogrowth45thermophilic
116542nogrowth55thermophilic

culture pH

@refabilitytypepH
23299positivegrowth5.6-5.7
116542positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23299aerobe
116542obligate aerobe

spore formation

  • @ref: 23299
  • spore description: ellipsoidal
  • type of spore: endospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
23299NaClpositivegrowth7 %
116542NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2329917272propionate-assimilation
2329915824D-fructose-builds gas from
2329917634D-glucose-builds gas from
2329965327D-xylose-builds gas from
2329930849L-arabinose-builds gas from
2329929864mannitol-builds gas from
2329917814salicin-builds gas from
2329917992sucrose-builds gas from
2329927082trehalose-builds gas from
2329929016arginine-degradation
23299egg yolk-degradation
2329961995lecithin-degradation
2329925094lysine-degradation
2329918257ornithine-degradation
2329928044phenylalanine-degradation
2329953426tween 80-degradation
2329918186tyrosine-degradation
2329916199urea-degradation
2329917716lactose-fermentation
2329928053melibiose-fermentation
2329916947citrate+assimilation
2329915824D-fructose+builds acid from
2329917634D-glucose+builds acid from
2329965327D-xylose+builds acid from
2329930849L-arabinose+builds acid from
2329929864mannitol+builds acid from
2329917814salicin+builds acid from
2329917992sucrose+builds acid from
2329927082trehalose+builds acid from
23299casein+degradation
23299casein+hydrolysis
2329928017starch+hydrolysis
2329917632nitrate+reduction
2329917057cellobiose+/-builds acid from
2329912936D-galactose+/-builds acid from
2329916024D-mannose+/-builds acid from
2329916988D-ribose+/-builds acid from
2329962345L-rhamnose+/-builds acid from
2329917306maltose+/-builds acid from
2329930911sorbitol+/-builds acid from
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
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
6837117057cellobiose-builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-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
1165424853esculin+hydrolysis
116542606565hippurate-hydrolysis
11654217632nitrate+reduction
11654216301nitrite-reduction
11654217632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2329935581indoleno
2329916136hydrogen sulfideno
2329916016dihydroxyacetoneno
2329915688acetoinyes
11654235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2329915688acetoin+
11654215688acetoin+
11654217234glucose-

enzymes

@refvalueactivityec
23299catalase+1.11.1.6
23299cytochrome 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
116542oxidase+
116542beta-galactosidase+3.2.1.23
116542alcohol dehydrogenase-1.1.1.1
116542gelatinase+/-
116542amylase+
116542DNase-
116542caseinase+3.4.21.50
116542catalase+1.11.1.6
116542tween esterase-
116542gamma-glutamyltransferase+2.3.2.2
116542lecithinase+
116542lipase-
116542lysine decarboxylase-4.1.1.18
116542ornithine decarboxylase-4.1.1.17
116542urease-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
116542-+++-+----+----++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116542+---++----+++----+---+/--+++-+/---++----+/-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116542++-++--+-++----++++++-+--------++++++----+-++----++--+-----++-+-++---------+---++-----+---++++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3083soilColorado
49270SoilColoradoUSAUSANorth America
67770SoilCOUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_454.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_17;97_17;98_20;99_454&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: AB021181
  • Sequence Identity:
  • Total samples: 133
  • soil counts: 16
  • aquatic counts: 40
  • animal counts: 61
  • plant counts: 16

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
3083yes, in single cases1Risk group (German classification)
1165421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus atrophaeus clone EP-1_F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478080415ena1452
20218Bacillus atrophaeus strain BCRC 17123 16S ribosomal RNA gene, partial sequenceEF4334091468ena1452
20218Bacillus atrophaeus gene for 16S ribosomal RNAAB0211811515ena1452
20218Bacillus atrophaeus gene for 16S rRNA, partial sequence, strain: NBRC 15539AB3637311475ena1452
20218B.atrophaeus 16S ribosomal RNAX606071427ena1452
20218Bacillus atrophaeus strain NRRL NRS-213 16S ribosomal RNA gene, partial sequenceEU1385161168ena1452

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus atrophaeus NBRC 155391220587.3wgspatric1220587
66792Bacillus atrophaeus NBRC 155392731957673draftimg1220587
67770Bacillus atrophaeus NBRC 15539GCA_001591925contigncbi1220587
67770Bacillus atrophaeus NRRL NRS 213GCA_001584335scaffoldncbi1452

GC content

  • @ref: 23299
  • GC-content: 41-43
  • method: Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.832no
gram-positiveyes91.648yes
anaerobicno99.235yes
aerobicyes91.005no
halophileyes88.502yes
spore-formingyes97.196no
glucose-utilyes86.583no
flagellatedyes87.759no
thermophileno99.063no
glucose-fermentno91.673no

External links

@ref: 3083

culture collection no.: DSM 7264, ATCC 49337, NRRL NRS-213, CCUG 28524, JCM 9070, CIP 107159, IFO 15539, KCTC 3701, LMG 16797, NBRC 15539, NCIMB 12899

straininfo link

  • @ref: 70749
  • straininfo: 8286

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10740862An algorithm for automated bacterial identification using matrix-assisted laser desorption/ionization mass spectrometry.Jarman KH, Cebula ST, Saenz AJ, Petersen CE, Valentine NB, Kingsley MT, Wahl KLAnal Chem10.1021/ac990832j2000*Algorithms, Automation, Bacteria/*classification, *Bacterial Typing Techniques, Species Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods
Biotechnology14503733Effect of microorganism characteristics on leak size critical to predicting package sterility.Keller S, Marcy J, Blakistone B, Hackney C, Carter WH, Lacy GJ Food Prot10.4315/0362-028x-66.9.17162003Bacillus/cytology/physiology, Bacteria/*cytology, Chemical Phenomena, Chemistry, Physical, Colony Count, Microbial, Enterobacter aerogenes/cytology/physiology, Food Contamination/analysis, Food Industry/methods/standards, *Food Microbiology, Food Packaging/methods/*standards, Particle Size, Pressure, Pseudomonas/cytology/physiology, Quality Control, Random Allocation, Sterilization
Phylogeny14661830Identification of bacterial spores using statistical analysis of Fourier transform infrared photoacoustic spectroscopy data.Thompson SE, Foster NS, Johnson TJ, Valentine NB, Amonette JEAppl Spectrosc10.1366/0003702033222588322003Acoustics, Algorithms, Bacillus/classification/*isolation & purification, *Data Interpretation, Statistical, Principal Component Analysis, Spectroscopy, Fourier Transform Infrared/*methods, Spores, Bacterial/classification/*isolation & purificationEnzymology
Phylogeny15128533Detection of molecular diversity in Bacillus atrophaeus by amplified fragment length polymorphism analysis.Burke SA, Wright JD, Robinson MK, Bronk BV, Warren RLAppl Environ Microbiol10.1128/AEM.70.5.2786-2790.20042004Bacillus/*classification/*genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Genetic Variation, Molecular Sequence Data, *Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Pathogenicity16329871Role of pigmentation in protecting Bacillus sp. endospores against environmental UV radiation.Moeller R, Horneck G, Facius R, Stackebrandt EFEMS Microbiol Ecol10.1016/j.femsec.2004.08.0082005Bacillus/chemistry/physiology/*radiation effects, Pigmentation/drug effects/*physiology, Spores, Bacterial/chemistry/*physiology/*radiation effects, *Ultraviolet Rays

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3083Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7264)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7264
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
23299L. K. NAKAMURA10.1099/00207713-39-3-295Taxonomic Relationship of Black-Pigmented Bacillus subtilis Strains and a Proposal for Bacillus atrophaeus sp. nov.IJSEM 39: 295-300 1989
36886Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4564
49270Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28524)https://www.ccug.se/strain?id=28524
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
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
70749Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8286.1StrainInfo: A central database for resolving microbial strain identifiers
116542Curators of the CIPCollection of Institut Pasteur (CIP 107159)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107159