Strain identifier

BacDive ID: 1556

Type strain: Yes

Species: Sediminibacillus albus

Strain Designation: NHBX-5, NHBX5

Strain history: CIP <- 2009, DSMZ <- X. Wang, Chinese Acad. Sci., Beijing, China: strain NHBX5

NCBI tax ID(s): 407036 (species)

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General

@ref: 8057

BacDive-ID: 1556

DSM-Number: 19340

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

description: Sediminibacillus albus NHBX-5 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediment of a salt lake.

NCBI tax id

  • NCBI tax id: 407036
  • Matching level: species

strain history

@refhistory
8057<- X. Wang, Chinese Acad. Sci. (CAS), Beijing; NHBX-5
116203CIP <- 2009, DSMZ <- X. Wang, Chinese Acad. Sci., Beijing, China: strain NHBX5

doi: 10.13145/bacdive1556.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Sediminibacillus
  • species: Sediminibacillus albus
  • full scientific name: Sediminibacillus albus Wang et al. 2009

@ref: 8057

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Sediminibacillus

species: Sediminibacillus albus

full scientific name: Sediminibacillus albus Wang et al. 2009

strain designation: NHBX-5, NHBX5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29021positive3 µm0.5 µmrod-shapedyes
69480yes95.104
69480positive100
116203positiverod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8057BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 100.0 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
37912Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116203CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116203CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8057positivegrowth30mesophilic
29021positivegrowth10-45
29021positiveoptimum37mesophilic
37912positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29021positivegrowth5.5-9.0alkaliphile
29021positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29021aerobe
116203obligate aerobe

spore formation

@refspore formationconfidence
29021yes
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
29021NaClpositivegrowth0-22 %
29021NaClpositiveoptimum7 %

observation

  • @ref: 29021
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2902122599arabinose+carbon source
2902117057cellobiose+carbon source
2902116947citrate+carbon source
2902128757fructose+carbon source
2902128260galactose+carbon source
290215291gelatin+carbon source
290215417glucosamine+carbon source
2902117234glucose+carbon source
2902117754glycerol+carbon source
2902117716lactose+carbon source
2902117306maltose+carbon source
2902129864mannitol+carbon source
2902137684mannose+carbon source
2902128053melibiose+carbon source
29021506227N-acetylglucosamine+carbon source
2902126546rhamnose+carbon source
2902117814salicin+carbon source
2902127082trehalose+carbon source
2902153426tween 80+carbon source
290214853esculin+hydrolysis
11620317632nitrate-reduction
11620316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2902116136hydrogen sulfideyes
2902135581indoleyes
11620335581indoleyes

metabolite tests

  • @ref: 29021
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29021catalase+1.11.1.6
29021gelatinase+
29021cytochrome oxidase+1.9.3.1
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
116203oxidase+
116203catalase+1.11.1.6
116203urease-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
116203-++--------+-+------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8057sediment of a salt lakeQinghai province, Lake NanhuobuxunChinaCHNAsia
116203Environment, Salt lake, sedimentBeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_77035.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2171;97_2627;98_3257;99_77035&stattab=map
  • Last taxonomy: Sediminibacillus albus
  • 16S sequence: DQ989634
  • Sequence Identity:
  • Total samples: 60
  • soil counts: 23
  • aquatic counts: 13
  • animal counts: 23
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80571Risk group (German classification)
1162031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8057
  • description: Sediminibacillus albus strain NHBX5 16S ribosomal RNA gene, partial sequence
  • accession: DQ989634
  • length: 1478
  • database: ena
  • NCBI tax ID: 407036

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sediminibacillus albus CGMCC 1.6502GCA_900101125scaffoldncbi407036
66792Sediminibacillus albus strain CGMCC 1.6502407036.4wgspatric407036
66792Sediminibacillus albus CGMCC 1.65022675902963draftimg407036

GC content

@refGC-contentmethod
805744.9thermal denaturation, midpoint method (Tm)
2902144.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes93.265no
flagellatedyes89.528no
gram-positiveyes95.055yes
anaerobicno99.004no
aerobicyes88.359no
halophileyes94.672yes
spore-formingyes92.991yes
glucose-fermentno87.962no
thermophileno98.06yes
glucose-utilyes88.349no

External links

@ref: 8057

culture collection no.: DSM 19340, CGMCC 1.6502, CIP 110033

straininfo link

  • @ref: 71201
  • straininfo: 363432

literature

  • topic: Phylogeny
  • Pubmed-ID: 19542144
  • title: Sediminibacillus albus sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a hypersaline lake, and emended description of the genus Sediminibacillus Carrasco et al. 2008.
  • authors: Wang X, Xue Y, Ma Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.004234-0
  • year: 2009
  • mesh: Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/chemistry/microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity, Spores, Bacterial/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8057Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19340)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19340
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
29021Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2545128776041
37912Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7845
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
71201Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363432.1StrainInfo: A central database for resolving microbial strain identifiers
116203Curators of the CIPCollection of Institut Pasteur (CIP 110033)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110033