Strain identifier

BacDive ID: 1075

Type strain: No

Species: Bacillus atrophaeus

Strain history: CIP <- 1990, DSM <- NCTC <- J.C. Kelsey <- C.R. Phillips, Bacillus globigii

NCBI tax ID(s): 1452 (species)

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General

@ref: 730

BacDive-ID: 1075

DSM-Number: 2277

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

description: Bacillus atrophaeus DSM 2277 is an obligate aerobe, spore-forming, mesophilic bacterium of the family Bacillaceae.

NCBI tax id

  • NCBI tax id: 1452
  • Matching level: species

strain history

@refhistory
730<- NCTC <- J.C. Kelsey <- C.R. Phillips (Bacillus globigii, Bacillus subtilis var. niger)
67770IAM 1633 <-- NCIB 8649 ("Bacillus subtilis var. niger") <-- NRC B467 ("Bacillus globigii").
67772NCTC <- J.C. Kelsey <- C.R. Phillips (Bacillus globigii, Bacillus subtilis var. niger)
123357CIP <- 1990, DSM <- NCTC <- J.C. Kelsey <- C.R. Phillips, Bacillus globigii

doi: 10.13145/bacdive1075.20250331.9.3

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: 730

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus atrophaeus

full scientific name: Bacillus atrophaeus Nakamura 1989

type strain: no

Morphology

cell morphology

  • @ref: 123357
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
730NUTRIENT 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
37027MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123357CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123357CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
730positivegrowth30
37027positivegrowth30
67770positivegrowth30
67772positiveminimum5-10
67772positiveoptimum28-30
67772positivemaximum50-55
123357positivegrowth30-45
123357nogrowth10
123357nogrowth55

culture pH

@refabilitytypepH
67772positivemaximum5.7
67772positiveminimum5.6
123357positivegrowth6

Physiology and metabolism

oxygen tolerance

  • @ref: 123357
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 123357
  • spore formation: yes

halophily

  • @ref: 123357
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12335716947citrate-carbon source
12335717632nitrate+reduction
12335716301nitrite-reduction
12335717632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin-builds acid from
6837112936D-galactose-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
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
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-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
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
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
12335735581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
12335715688acetoin+
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
123357oxidase-
123357beta-galactosidase-3.2.1.23
123357alcohol dehydrogenase-1.1.1.1
123357gelatinase+
123357amylase+
123357DNase+
123357caseinase+3.4.21.50
123357catalase+1.11.1.6
123357tween esterase-
123357gamma-glutamyltransferase+2.3.2.2
123357lecithinase+
123357lysine decarboxylase-4.1.1.18
123357ornithine decarboxylase-4.1.1.17
123357urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382trypsin-3.4.21.4
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

fatty acid profile

  • @reffatty acidpercentageECL
    45604C15:01.215
    45604C16:03.616
    45604C14:0 ISO1.413.618
    45604C15:0 ANTEISO50.414.711
    45604C15:0 ISO20.114.621
    45604C15:0 ISO 3OH0.716.135
    45604C16:0 iso2.615.626
    45604C17:0 anteiso9.816.722
    45604C17:0 iso5.416.629
    45604C17:1 ω5c ISO0.616.461
    45604Unidentified0.414.918
    45604Unidentified0.515.739
    45604Unidentified1.716.287
    45604Unidentified0.716.367
    45604Unidentified1.117.701
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    45604C15:01.615
    45604C16:02.116
    45604C14:0 ISO1.313.618
    45604C15:0 ANTEISO42.214.711
    45604C15:0 ISO35.214.621
    45604C16:0 iso1.715.626
    45604C16:1 ω11c1.115.757
    45604C17:0 anteiso5.116.722
    45604C17:0 iso5.616.629
    45604C17:1 ISO I/C16:0 DMA116.481
    45604C17:1 ω10c ISO1.916.387
    45604C18:2 ω6,9c/C18:0 ANTE1.417.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123357--------------------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
45604----------+---------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
45604-----------+++----+---+-+++----++-----------------
123357+---------+++----+/----+/--+++-+/---++---++------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123357---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 67772
  • sampling date: 1982

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: EF188847
  • Sequence Identity:
  • Total samples: 133
  • soil counts: 16
  • aquatic counts: 40
  • animal counts: 61
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
7301Risk group (German classification)
677721
1233571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus atrophaeus ATCC 51189 16S ribosomal RNA gene, partial sequenceAY379772495nuccore1529886
20218Bacillus atrophaeus strain ATCC 51189 16S ribosomal RNA gene, partial sequenceEF1888471481nuccore1529886
124043Bacillus atrophaeus gene for 16S rRNA, partial sequence, strain: NBRC 14117.AB6805601475nuccore1452

External links

@ref: 730

culture collection no.: DSM 2277, ATCC 51189, CIP 103406, IAM 1633, NCIB 8649, NCTC 10073, CCUG 11738, JCM 20230, NBRC 14117, NCIMB 8649, NRC B467, UCCCB119

straininfo link

  • @ref: 70747
  • straininfo: 64068

literature

  • topic: Phylogeny
  • Pubmed-ID: 11211269
  • title: Reclassification of bioindicator strains Bacillus subtilis DSM 675 and Bacillus subtilis DSM 2277 as Bacillus atrophaeus.
  • authors: Fritze D, Pukall R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-1-35
  • year: 2001
  • mesh: Bacillus/*classification/genetics/physiology, Bacillus subtilis/*classification/genetics/physiology, Ethylene Oxide, Nucleic Acid Hybridization, Pigmentation, Reference Standards, Spores, Bacterial/physiology, Sterilization/methods

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
730Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2277)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2277
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
37027Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15199
45604Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 11738)https://www.ccug.se/strain?id=11738
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68368Automatically annotated from API 20E
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
70747Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID64068.1StrainInfo: A central database for resolving microbial strain identifiers
123357Curators of the CIPCollection of Institut Pasteur (CIP 103406)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103406
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy