Strain identifier

BacDive ID: 599

Type strain: Yes

Species: Schinkia azotoformans

Strain Designation: 1, BAI

Strain history: CIP <- 1977, Lab. Ident. Inst. Pasteur, Paris, France <- F. Pichinoty, CNRS, Marseille: strain 1 <- 1972, B. Delaporte

NCBI tax ID(s): 1131731 (strain), 1454 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 488

BacDive-ID: 599

DSM-Number: 1046

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

description: Schinkia azotoformans 1 is an aerobe, chemoorganotroph, spore-forming bacterium that was isolated from garden soil.

NCBI tax id

NCBI tax idMatching level
1131731strain
1454species

strain history

@refhistory
488<- F. Pichinoty
67770CIP 77.28 <-- Lab. Ident. Inst. Pasteur, Paris, France <-- F. Pichinoty strain 1 <-- B. Delaporte.
116694CIP <- 1977, Lab. Ident. Inst. Pasteur, Paris, France <- F. Pichinoty, CNRS, Marseille: strain 1 <- 1972, B. Delaporte

doi: 10.13145/bacdive599.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Schinkia
  • species: Schinkia azotoformans
  • full scientific name: Schinkia azotoformans (Pichinoty et al. 1983 ex Pichinoty et al. 1976) Gupta et al. 2020
  • synonyms

    @refsynonym
    20215Calidifontibacillus azotoformans
    20215Bacillus azotoformans

@ref: 488

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Schinkia

species: Schinkia azotoformans

full scientific name: Schinkia azotoformans (Pichinoty et al. 1983) Gupta et al. 2020

strain designation: 1, BAI

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23140positive3-10 µm0.9-1.0 µmrod-shapedyesperitrichous
69480yes96.805
69480positive100
116694positiverod-shapedyes

colony morphology

  • @ref: 23140
  • colony size: 5.0 mm
  • medium used: yeast extract-salts agar

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
23140yeast extract-salts agaryes
37709MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
488YEAST EXTRACT MINERAL MEDIUM (DSMZ Medium 259)yesName: YEAST EXTRACT MINERAL MEDIUM (DSMZ Medium 259) Composition: Agar 15.0 g/l Yeast extract 4.0 g/l Na2HPO4 x 12 H2O 3.5 g/l K2HPO4 1.0 g/l NH4Cl 0.5 g/l MgSO4 x 7 H2O 0.03 g/l Distilled waterhttps://mediadive.dsmz.de/medium/259
116694CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116694CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
23140nogrowth4psychrophilic
23140positivemaximum42-46thermophilic
488positivegrowth30mesophilic
37709positivegrowth30mesophilic
49265positivegrowth37mesophilic
67770positivegrowth30mesophilic
116694positivegrowth22-45
116694nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
49265aerobe
116694obligate aerobe

nutrition type

  • @ref: 23140
  • type: chemoorganotroph

spore formation

@refspore descriptiontype of sporespore formationconfidence
23140oval, sporangium bulge, located terminally or sub-terminallyendosporeyes
69481yes100
69480yes100
116694yes

halophily

@refsaltgrowthtested relationconcentration
116694NaClpositivegrowth0-2 %
116694NaClnogrowth4 %
116694NaClnogrowth6 %
116694NaClnogrowth8 %
116694NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2314017859glutaric acid-degradation
2314015428glycine-degradation
2314029805glycolate-degradation
2314015792malonate-degradation
2314017272propionate-degradation
23140132950tartrate-degradation
2314027897tryptophan-energy source
2314017234glucose-fermentation
231405291gelatin-hydrolysis
2314028017starch-hydrolysis
2314053426tween 80-hydrolysis
2314017234glucose-oxidation
2314030089acetate+degradation
2314016947citrate+degradation
2314024996lactate+degradation
2314029991L-aspartate+degradation
2314029985L-glutamate+degradation
2314025115malate+degradation
2314015361pyruvate+degradation
2314030031succinate+degradation
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
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
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
11669417632nitrate+builds gas from
11669417632nitrate+reduction
11669416301nitrite+reduction
11669417632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
2314035581indoleno
2314015688acetoinno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2314015688acetoin-
2314035581indole-
6836815688acetoin-
6836835581indole-
11669415688acetoin-

enzymes

@refvalueactivityec
231406-phospho-beta-galactosidase-3.2.1.85
23140arginine dihydrolase-3.5.3.6
23140catalase-1.11.1.6
23140cytochrome oxidase+1.9.3.1
23140phenylalanine deaminase-4.3.1.5
23140thiosulfate reductase-2.8.1.5
23140tryptophan deaminase-4.1.99.1
23140urease-3.5.1.5
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
116694oxidase+
116694beta-galactosidase-3.2.1.23
116694alcohol dehydrogenase-1.1.1.1
116694gelatinase+
116694amylase+
116694DNase+
116694caseinase-3.4.21.50
116694catalase+1.11.1.6
116694tween esterase-
116694gamma-glutamyltransferase-2.3.2.2
116694lecithinase-
116694lipase-
116694lysine decarboxylase-4.1.1.18
116694ornithine decarboxylase-4.1.1.17
116694protease-
116694urease-3.5.1.5

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
49265--------------------+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
49265----------------------------+---+-----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116694-------------------+-----------+-----------------++++--------++------------+---++----+--++++-------

Isolation, sampling and environmental information

isolation

@refsample type
488garden soil
49265Garden soil
116694Environment, Soil, garden

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_6004.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2864;97_3521;98_4456;99_6004&stattab=map
  • Last taxonomy: Calidifontibacillus azotoformans subclade
  • 16S sequence: AB363732
  • Sequence Identity:
  • Total samples: 936
  • soil counts: 431
  • aquatic counts: 125
  • animal counts: 341
  • plant counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
4881Risk group (German classification)
1166941Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus azotoformans clone BAZOT-1R 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478065535ena1131731
20218B.azotoformans 16S ribosomal RNAX606091426ena1131731
20218Bacillus azotoformans strain DSM1046 DNA for 16S ribosomal RNA, partial sequenceD783091432ena1131731
20218Bacillus azotoformans gene for 16S rRNA, partial sequence, strain: NBRC 15712AB3637321475ena1131731

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus azotoformans LMG 95811131731.3wgspatric1131731
66792Bacillus azotoformans LMG 95812524023181draftimg1131731
67770Schinkia azotoformans LMG 9581GCA_000307855contigncbi1131731

GC content

@refGC-contentmethod
48839.8
48839.0
6777038.6-41Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.05yes
flagellatedyes76.727no
gram-positiveyes68.614no
anaerobicno92.65no
aerobicyes59.286no
halophileno92.96no
spore-formingyes93.894yes
glucose-utilyes85.152no
thermophileno85.491no
glucose-fermentno91.671yes

External links

@ref: 488

culture collection no.: CCUG 28517, NRRL B-14310, DSM 1046, ATCC 29788, CCM 2849, CIP R925, JCM 12210, BCRC 15923, BCRC 16018, CIP 77.28, HAMBI 1884, IFO 15712, KCTC 3447, LMG 9581, NBRC 15712, NCCB 93150, NCIMB 11859, NRRL B-14522

straininfo link

  • @ref: 70276
  • straininfo: 812

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26076748Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China.Zhang WY, Hu J, Zhang XQ, Zhu XF, Wu MAntonie Van Leeuwenhoek10.1007/s10482-015-0497-02015Aerobiosis, Bacillus/*classification/genetics/*isolation & purification/physiology, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Metabolism28726125Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581(T).Sun Y, De Vos P, Willems AAntonie Van Leeuwenhoek10.1007/s10482-017-0911-x2017Ammonium Compounds/metabolism, Bacillus/*classification/genetics/*metabolism, Energy Metabolism, Genes, Bacterial, Genomics/methods, Metabolic Networks and Pathways/genetics, Nitrates/metabolism, Nitrites/metabolism, Nitrogen/*metabolism, Nitrous Oxide/metabolismPhylogeny
Phylogeny33164726Genome-based classification of Calidifontibacillus erzurumensis gen. nov., sp. nov., isolated from a hot spring in Turkey, with reclassification of Bacillus azotoformans as Calidifontibacillus azotoformans comb. nov. and Bacillus oryziterrae as Calidifontibacillus oryziterrae comb. nov.Adiguzel A, Ay H, Baltaci MO, Akbulut S, Albayrak S, Omeroglu MAInt J Syst Evol Microbiol10.1099/ijsem.0.0045492020Bacillaceae/*classification/isolation & purification, Bacillus/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Turkey, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
488Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1046)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1046
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
23140F. PICHINOTY, H. DE BARJAC, M. MANDEL, J. ASSELINEAU10.1099/00207713-33-3-660Description of Bacillus azotoformans sp. nov.IJSEM 33: 660-662 1983
37709Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10941
49265Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28517)https://www.ccug.se/strain?id=28517
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
70276Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID812.1StrainInfo: A central database for resolving microbial strain identifiers
116694Curators of the CIPCollection of Institut Pasteur (CIP 77.28)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2077.28