Strain identifier

BacDive ID: 1145

Type strain: Yes

Species: Sutcliffiella halmapala

Strain Designation: PN 118, JP 170

Strain history: CIP <- 1997, DSMZ <- H. Outtrup, Novo Nordisk A/S: strain PN 118

NCBI tax ID(s): 79882 (species)

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General

@ref: 3366

BacDive-ID: 1145

DSM-Number: 8723

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Sutcliffiella halmapala PN 118 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 79882
  • Matching level: species

strain history

@refhistory
3366<- H. Outtrup, Novo Nordisk A/S; JP 170
67770DSM 8723 <-- H. Outtrup JP 170.
119795CIP <- 1997, DSMZ <- H. Outtrup, Novo Nordisk A/S: strain PN 118

doi: 10.13145/bacdive1145.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Sutcliffiella
  • species: Sutcliffiella halmapala
  • full scientific name: Sutcliffiella halmapala (Nielsen et al. 1995) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus halmapalus

@ref: 3366

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Sutcliffiella

species: Sutcliffiella halmapala

full scientific name: Sutcliffiella halmapala (Nielsen et al. 1995) Gupta et al. 2020

strain designation: PN 118, JP 170

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.106
69480100positive
119795yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3366ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31; with strain-specific modifications) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaCl 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
32749MEDIUM 113 - for BacillusyesDistilled water make up to (900.000 ml);Columbia agar (39.000 g);Solution 1 - M00343 (100.000 ml)
119795CIP Medium 113yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=113

culture temp

@refgrowthtypetemperaturerange
3366positivegrowth30mesophilic
32749positivegrowth30mesophilic
67770positivegrowth30mesophilic
119795positivegrowth10-41
119795nogrowth45thermophilic
119795nogrowth55thermophilic

culture pH

  • @ref: 119795
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119795
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
119795NaClpositivegrowth0-4 %
119795NaClnogrowth6 %
119795NaClnogrowth8 %
119795NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
68371myo-inositol-builds acid from17268
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
119795hippurate+hydrolysis606565
119795nitrate-reduction17632
119795nitrite-reduction16301
119795nitrate+respiration17632

metabolite production

  • @ref: 119795
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11979515688acetoin+
11979517234glucose+

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
119795oxidase+
119795beta-galactosidase+3.2.1.23
119795alcohol dehydrogenase-1.1.1.1
119795gelatinase+
119795amylase+
119795caseinase+3.4.21.50
119795catalase+1.11.1.6
119795gamma-glutamyltransferase-2.3.2.2
119795lysine decarboxylase-4.1.1.18
119795ornithine decarboxylase-4.1.1.17
119795phenylalanine ammonia-lyase-4.3.1.24
119795urease-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
119795--++------++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119795----+-----+++--------++/-++++/-+--++---++--+------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119795-+-++--+-++----++----++--------+-+++-----+-------+----+----++--------------+---++-----+-+-+--++----

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
119795Environment, Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1480.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_567;97_659;98_762;99_1480&stattab=map
  • Last taxonomy: Bacillus halmapalus
  • 16S sequence: X76447
  • Sequence Identity:
  • Total samples: 169
  • soil counts: 67
  • aquatic counts: 53
  • animal counts: 43
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33661Risk group (German classification)
1197951Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bacillus halmapalus DSM 8723, 16S rRNA gene
  • accession: X76447
  • length: 1504
  • database: ena
  • NCBI tax ID: 79882

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus halmapalus strain DSM 872379882.3wgspatric79882
67770Sutcliffiella halmapala DSM 8723GCA_002019665scaffoldncbi79882

GC content

  • @ref: 3366
  • GC-content: 38.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.715no
flagellatedyes91.597no
gram-positiveyes88.874no
anaerobicno98.595no
halophileno50no
spore-formingyes96.095no
thermophileno98.574yes
glucose-utilyes87.927no
aerobicyes89.997no
glucose-fermentno91.135no

External links

@ref: 3366

culture collection no.: DSM 8723, ATCC 700165, JCM 12302, CGMCC 1.3595, CIP 105303, LMG 17950, NRRL B-23347

straininfo link

  • @ref: 70816
  • straininfo: 10540

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24614848Bacillus tianshenii sp. nov., isolated from a marine sediment sample.Jiang Z, Zhang DF, Khieu TN, Son CK, Zhang XM, Cheng J, Tian XP, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.062224-02014Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28744555Bacillus catenulatus sp. nov., an alkalitolerant bacterium isolated from a soda lake.Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VRArch Microbiol10.1007/s00203-017-1413-y2017*Bacillus/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, India, Lakes/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylethanolamines/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, Spores, Bacterial/physiologyTranscriptome
Phylogeny35195511Sutcliffiella deserti sp. nov., isolated from desert soil.Bai P, Zhang S, Chen Y, Ping W, Pang H, Du J, Li Y, Zhang JInt J Syst Evol Microbiol10.1099/ijsem.0.0052592022*Bacillaceae/classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Mongolia, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3366Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8723)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8723
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
32749Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17307
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
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
70816Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10540.1StrainInfo: A central database for resolving microbial strain identifiers
119795Curators of the CIPCollection of Institut Pasteur (CIP 105303)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105303