Strain identifier

BacDive ID: 748

Type strain: Yes

Species: Peribacillus psychrosaccharolyticus

Strain Designation: T25B, B-3394

Strain history: CIP <- 2001, CCUG <- 1991, L.K. Nakamura, NRRL, Peoria, USA: strain B-3394

NCBI tax ID(s): 1174504 (strain), 1407 (species)

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General

@ref: 2014

BacDive-ID: 748

DSM-Number: 6

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

description: Peribacillus psychrosaccharolyticus T25B is an obligate aerobe, psychrophilic, Gram-positive bacterium that was isolated from soil or lowland marsh.

NCBI tax id

NCBI tax idMatching level
1407species
1174504strain

strain history

@refhistory
2014<- J.L. Stokes, T25B
122032CIP <- 2001, CCUG <- 1991, L.K. Nakamura, NRRL, Peoria, USA: strain B-3394

doi: 10.13145/bacdive748.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Peribacillus
  • species: Peribacillus psychrosaccharolyticus
  • full scientific name: Peribacillus psychrosaccharolyticus (Priest et al. 1989 ex Larkin and Stokes 1967) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus psychrosaccharolyticus

@ref: 2014

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Peribacillus

species: Peribacillus psychrosaccharolyticus

full scientific name: Peribacillus psychrosaccharolyticus (Priest et al. 1989) Patel and Gupta 2020

strain designation: T25B, B-3394

type strain: yes

Morphology

cell morphology

  • @ref: 122032
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 122032

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2014BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
2014NUTRIENT 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
41557MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122032CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
2014positivegrowth20psychrophilic
41557positivegrowth20psychrophilic
122032positivegrowth22-45
122032nogrowth10psychrophilic
122032nogrowth55thermophilic

culture pH

  • @ref: 122032
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 122032
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122032NaClpositivegrowth0-2 %
122032NaClnogrowth4 %
122032NaClnogrowth6 %
122032NaClnogrowth8 %
122032NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371starch-builds acid from28017
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
122032esculin+hydrolysis4853
122032hippurate+hydrolysis606565
122032nitrate+reduction17632
122032nitrite-reduction16301
122032nitrate-respiration17632

metabolite production

  • @ref: 122032
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12203215688acetoin-
12203217234glucose-

enzymes

@refvalueactivityec
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
122032oxidase+
122032beta-galactosidase+3.2.1.23
122032alcohol dehydrogenase-1.1.1.1
122032gelatinase-
122032amylase-
122032DNase+
122032caseinase-3.4.21.50
122032catalase+1.11.1.6
122032tween esterase-
122032gamma-glutamyltransferase-2.3.2.2
122032lysine decarboxylase-4.1.1.18
122032ornithine decarboxylase-4.1.1.17
122032tryptophan deaminase-
122032urease-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
122032-+-+-----------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122032+--+++----+-+---+/-+---+++++++++/-+/-+-+/-+/--+/--+-------+-+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122032+--+-----++-+--++-+------------+-+------+----------------------------------------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 2014
  • sample type: soil or lowland marsh

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_143366.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_370;97_418;98_75930;99_143366&stattab=map
  • Last taxonomy: Peribacillus psychrosaccharolyticus subclade
  • 16S sequence: AB681415
  • Sequence Identity:
  • Total samples: 163
  • soil counts: 50
  • aquatic counts: 78
  • animal counts: 32
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20141Risk group (German classification)
1220321Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus psychrosaccharolyticus gene for 16S ribosomal RNAAB0211951507ena1174504
20218Bacillus psychrosaccharolyticus clone LE-5F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478069512ena1174504
20218B.psychrosaccharolyticus 16S ribosomal RNAX606351426ena1174504
20218Aestuariibacter sp. DSM6 16S ribosomal RNA gene, partial sequenceKC439224851ena1343202
20218Bacillus psychrosaccharolyticus gene for 16S rRNA, partial sequence, strain: NBRC 101233AB6814151471ena1174504

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peribacillus psychrosaccharolyticus ATCC 23296GCA_000305495contigncbi1174504
66792Bacillus psychrosaccharolyticus ATCC 232961174504.3wgspatric1174504
66792Bacillus psychrosaccharolyticus ATCC 232962547132175draftimg1174504

GC content

  • @ref: 2014
  • GC-content: 38.5
  • method: Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.353no
gram-positiveyes89.306no
anaerobicno98.35no
halophileno81.865no
spore-formingyes95.569no
flagellatedyes77.231no
thermophileno97.411yes
glucose-utilyes86.133no
aerobicyes82.956no
glucose-fermentno87.792no

External links

@ref: 2014

culture collection no.: DSM 6, ATCC 23296, DSM 13778, LMG 9580, NCIMB 11729, CIP 106932, CCUG 28882

straininfo link

  • @ref: 70422
  • straininfo: 1166

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology2334516Structure and function of L-lactate dehydrogenases from thermophilic, mesophilic and psychrophilic bacteria, IX. Identification, isolation and nucleotide sequence of two L-lactate dehydrogenase genes of the psychrophilic bacterium Bacillus psychrosaccharolyticus.Vckovski V, Schlatter D, Zuber HBiol Chem Hoppe Seyler10.1515/bchm3.1990.371.1.1031990Amino Acid Sequence, Bacillus/enzymology/*genetics, Base Sequence, Cloning, Molecular, DNA, Bacterial/*analysis, Gene Expression, Isoenzymes, L-Lactate Dehydrogenase/*genetics, Molecular Sequence Data, Restriction Mapping, Sequence Homology, Nucleic AcidGenetics
Phylogeny24903955Bacillus huizhouensis sp. nov., isolated from a paddy field soil.Li J, Yang G, Wu M, Zhao Y, Zhou SAntonie Van Leeuwenhoek10.1007/s10482-014-0208-22014Aerobiosis, Anaerobiosis, Bacillus/*classification/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Oryza, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny26303844Bacillus gossypii sp. nov., isolated from the stem of Gossypium hirsutum.Kampfer P, Busse HJ, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0005552015Alabama, Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Stems/*microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2014Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6
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
41557Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19117
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)
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
70422Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1166.1StrainInfo: A central database for resolving microbial strain identifiers
122032Curators of the CIPCollection of Institut Pasteur (CIP 106932)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106932