Strain identifier

BacDive ID: 1120

Type strain: Yes

Species: Salipaludibacillus agaradhaerens

Strain Designation: PN 105, AC 13

Strain history: CIP <- 1997, DSMZ <- H. Outtrup, Novo Disc A/S: strain PN 105

NCBI tax ID(s): 76935 (species)

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General

@ref: 3251

BacDive-ID: 1120

DSM-Number: 8721

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Salipaludibacillus agaradhaerens PN 105 is a facultative anaerobe, spore-forming, mesophilic bacterium of the family Bacillaceae.

NCBI tax id

  • NCBI tax id: 76935
  • Matching level: species

strain history

@refhistory
3251<- H. Outtrup, Novo Nordisk A/S; AC 13
116145CIP <- 1997, DSMZ <- H. Outtrup, Novo Disc A/S: strain PN 105

doi: 10.13145/bacdive1120.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Salipaludibacillus
  • species: Salipaludibacillus agaradhaerens
  • full scientific name: Salipaludibacillus agaradhaerens (Nielsen et al. 1995) Sultanpuram and Mothe 2016

  • synonyms

    • @ref: 20215
    • synonym: Bacillus agaradhaerens

@ref: 3251

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Salipaludibacillus

species: Salipaludibacillus agaradhaerens

full scientific name: Salipaludibacillus agaradhaerens (Nielsen et al. 1995) Sultanpuram and Mothe 2016

strain designation: PN 105, AC 13

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43624positiverod-shapedyes
69480yes94.175
69480positive100
116145positiverod-shapedno

colony morphology

  • @ref: 43624
  • colony color: White

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3251ALKALINE 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
41880MEDIUM 113 - for BacillusyesDistilled water make up to (900.000 ml);Columbia agar (39.000 g);Solution 1 - M00343 (100.000 ml)
116145CIP Medium 113yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=113

culture temp

@refgrowthtypetemperaturerange
3251positivegrowth30mesophilic
41880positivegrowth30mesophilic
43624positivegrowth10-45
43624positiveoptimum37mesophilic
116145positivegrowth10-45
116145nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
43624positivegrowth7.5-9.7alkaliphile
43624positiveoptimum8.5-9
116145nogrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43624facultative anaerobe
116145obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43624oval or ellipsoidal endospores at the sub-terminal positionendosporeyes
69481yes99
69480yes100

halophily

@refsaltgrowthtested relationconcentration
43624NaClpositivegrowth0-15 %(w/v)
43624NaClpositiveoptimum2-3 %(w/v)
116145NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4362416947citrate-assimilation
4362427897tryptophan-energy source
4362417234glucose-fermentation
43624casein-hydrolysis
4362462968cellulose-hydrolysis
4362416991dna-hydrolysis
436244853esculin-hydrolysis
436245291gelatin-hydrolysis
4362428017starch-hydrolysis
4362453424tween 20+hydrolysis
4362417632nitrate+reduction
11614517632nitrate+reduction
11614516301nitrite-reduction
11614517632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
4362415688acetoinno
4362416136hydrogen sulfideno
4362435581indoleno
11614535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
4362417234glucose-
4362415688acetoin-
4362435581indole-
11614515688acetoin+
11614517234glucose+

enzymes

@refvalueactivityec
43624cytochrome oxidase+1.9.3.1
43624catalase+1.11.1.6
43624tryptophan deaminase-4.1.99.1
43624urease-3.5.1.5
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
116145oxidase-
116145beta-galactosidase+3.2.1.23
116145alcohol dehydrogenase-1.1.1.1
116145gelatinase+
116145catalase+1.11.1.6
116145gamma-glutamyltransferase-2.3.2.2
116145lysine decarboxylase-4.1.1.18
116145ornithine decarboxylase-4.1.1.17
116145phenylalanine ammonia-lyase-4.3.1.24
116145urease-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
116145--++-----+-+-+--+---

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_203.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_144;97_155;98_173;99_203&stattab=map
  • Last taxonomy: Salipaludibacillus agaradhaerens subclade
  • 16S sequence: X76445
  • Sequence Identity:
  • Total samples: 105
  • soil counts: 22
  • aquatic counts: 54
  • animal counts: 29

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32511Risk group (German classification)
1161451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia thailandensis strain BD11-00023 16S ribosomal RNA gene, partial sequenceKF4449051465ena57975
3251Bacillus agaradhaerens DSM 8721, 16S rRNA geneX764451521ena76935

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salipaludibacillus agaradhaerens DSM 8721GCA_002019735scaffoldncbi76935
66792[Bacillus] agaradhaerens strain DSM 872176935.4wgspatric76935
66792Salipaludibacillus agaradhaerens DSM 87212890278133draftimg76935

GC content

@refGC-contentmethod
325139.2high performance liquid chromatography (HPLC)
4362439.3-39.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
flagellatedyes68.081no
gram-positiveyes87.498yes
anaerobicno97.985yes
aerobicyes63.348yes
halophileyes84.266no
spore-formingyes92.345no
glucose-utilyes90.768no
thermophileno96.652yes
motileyes87.031yes
glucose-fermentno86.732no

External links

@ref: 3251

culture collection no.: DSM 8721, ATCC 700163, CIP 105302

straininfo link

  • @ref: 70791
  • straininfo: 10538

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology14571982Sequence analysis of cyclodextrin glycosyltransferase from the alkaliphilic Bacillus agaradhaerens.Martins RF, Delgado O, Hatti-Kaul RBiotechnol Lett10.1023/a:10254305323332003Amino Acid Sequence, Bacillus/*classification/*enzymology/genetics, Cloning, Molecular, Conserved Sequence, Escherichia coli/enzymology/genetics, Glucosyltransferases/*biosynthesis/*chemistry/classification/genetics, Molecular Biology, Molecular Sequence Data, Recombinant Proteins/biosynthesis/chemistry, *Sequence Alignment, *Sequence Analysis, Protein, Sequence Homology, Amino Acid, Species SpecificityPhylogeny
Enzymology16710633Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens.Hirasawa K, Uchimura K, Kashiwa M, Grant WD, Ito S, Kobayashi T, Horikoshi KAntonie Van Leeuwenhoek10.1007/s10482-005-9023-02006Amino Acid Sequence, Bacillus/classification/drug effects/enzymology/growth & development, Cellulase/isolation & purification/*metabolism, DNA, Bacterial/analysis, Enzyme Induction, Enzyme Stability, Hydrogen-Ion Concentration, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/*pharmacology, Substrate Specificity, TemperaturePhylogeny
Phylogeny17158996Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea.Lim JM, Jeon CO, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.64036-02006Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sodium Chloride, *SunlightGenetics
Phylogeny21640538Bacillus locisalis sp. nov., a new haloalkaliphilic species from hypersaline and alkaline lakes of China, Kenya and Tanzania.Marquez MC, Carrasco IJ, de la Haba RR, Jones BE, Grant WD, Ventosa ASyst Appl Microbiol10.1016/j.syapm.2011.04.0032011Bacillus/chemistry/*classification/genetics/metabolism, Base Sequence, China, DNA, Bacterial/chemistry/genetics, Ecosystem, Genes, Bacterial, Hydrogen-Ion Concentration, Kenya, Lakes/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Tanzania, Water MicrobiologyMetabolism
Phylogeny22039006Salisediminibacterium halotolerans gen. nov., sp. nov., a halophilic bacterium from soda lake sediment.Jiang F, Cao SJ, Li ZH, Fan H, Li HF, Liu WJ, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.034488-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Phylogeny29790846Salipaludibacillus halalkaliphilus sp. nov., a moderately haloalkaliphilic bacterium from a coastal-marine wetland.Amoozegar MA, Shahinpei A, Makzum S, Rafieyan S, Moshtaghi Nikou M, Sproer C, Ventosa AInt J Syst Evol Microbiol10.1099/ijsem.0.0028142018Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Iran, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/genetics, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3251Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8721)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8721
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
41880Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17306
43624Vishnuvardhan Reddy Sultanpuram, Thirumala Mothe10.1099/ijsem.0.001117Salipaludibacillus aurantiacus gen. nov., sp. nov. a novel alkali tolerant bacterium, reclassification of Bacillus agaradhaerens as Salipaludibacillus agaradhaerens comb. nov. and Bacillus neizhouensis as Salipaludibacillus neizhouensis comb. nov.IJSEM 66: 2747-2753 201627118186
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)
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
70791Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10538.1StrainInfo: A central database for resolving microbial strain identifiers
116145Curators of the CIPCollection of Institut Pasteur (CIP 105302)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105302