Strain identifier

BacDive ID: 23707

Type strain: Yes

Species: Halalkalibacter nanhaiisediminis

Strain Designation: NH3

Strain history: J. Zhang NH3.

NCBI tax ID(s): 688079 (species)

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

@ref: 20435

BacDive-ID: 23707

DSM-Number: 27953

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

description: Halalkalibacter nanhaiisediminis NH3 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 688079
  • Matching level: species

strain history

@refhistory
20435<- JCM <- J. Zhang; NH3
67770J. Zhang NH3.

doi: 10.13145/bacdive23707.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halalkalibacter
  • species: Halalkalibacter nanhaiisediminis
  • full scientific name: Halalkalibacter nanhaiisediminis (Zhang et al. 2011) Joshi et al. 2022
  • synonyms

    @refsynonym
    20215Alkalihalobacillus nanhaiisediminis
    20215Bacillus nanhaiisediminis

@ref: 20435

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Halalkalibacter

species: Halalkalibacter nanhaiisediminis

full scientific name: Halalkalibacter nanhaiisediminis (Zhang et al. 2011) Joshi et al. 2022

strain designation: NH3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29877positive1.9 µm0.6 µmrod-shapedyes
69480yes96.892
69480positive100

pigmentation

  • @ref: 29877
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20435
  • name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220
  • composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20435positivegrowth30mesophilic
29877positivegrowth10-43
29877positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29877positivegrowth6.5-10alkaliphile
29877positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 29877
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29877yes
69481yes100
69480yes100

halophily

  • @ref: 29877
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-11 %

observation

@refobservation
29877aggregates in clumps
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2987730089acetate+carbon source
2987722599arabinose+carbon source
2987717057cellobiose+carbon source
2987728260galactose+carbon source
298775417glucosamine+carbon source
2987717234glucose+carbon source
2987717754glycerol+carbon source
2987717306maltose+carbon source
2987729864mannitol+carbon source
2987737684mannose+carbon source
2987728053melibiose+carbon source
2987715361pyruvate+carbon source
2987716634raffinose+carbon source
2987726546rhamnose+carbon source
2987730911sorbitol+carbon source
2987730031succinate+carbon source
2987727082trehalose+carbon source
2987716199urea+carbon source
2987717151xylitol+carbon source
2987717632nitrate+reduction

metabolite production

  • @ref: 29877
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29877
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29877catalase+1.11.1.6
29877urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinent
20435sedimentSouth China SeaAsia
67770Sediment sample collected from the South China Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_60426.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2523;97_33372;98_42890;99_60426&stattab=map
  • Last taxonomy: Alkalihalobacillus nanhaiisediminis subclade
  • 16S sequence: GQ292773
  • Sequence Identity:
  • Total samples: 1840
  • soil counts: 517
  • aquatic counts: 594
  • animal counts: 650
  • plant counts: 79

Safety information

risk assessment

  • @ref: 20435
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20435
  • description: Bacillus nanhaiisediminis 16S ribosomal RNA gene, partial sequence
  • accession: GQ292773
  • length: 1419
  • database: ena
  • NCBI tax ID: 688079

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halalkalibacter nanhaiisediminis CGMCC 1.10116GCA_007830185scaffoldncbi688079
66792Bacillus nanhaiisediminis strain CGMCC 1.10116688079.3wgspatric688079
66792Bacillus nanhaiisediminis CGMCC 1.101162596583586draftimg688079

GC content

@refGC-contentmethod
2043540.3thermal denaturation, midpoint method (Tm)
2987740.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes91.491yes
flagellatedyes86.909no
gram-positiveyes89.146yes
anaerobicno98.136no
aerobicyes90.227no
halophileyes67.065no
spore-formingyes94.279yes
thermophileno97.91no
glucose-utilyes89.811yes
glucose-fermentno93.938no

External links

@ref: 20435

culture collection no.: DSM 27953, CGMCC 1.10116, JCM 16507

straininfo link

  • @ref: 87753
  • straininfo: 401112

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20525818Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6.Zhang J, Wang J, Song F, Fang C, Xin Y, Zhang YInt J Syst Evol Microbiol10.1099/ijs.0.023671-02010Alkalies/*metabolism, Bacillus/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/*genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny24554634Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai LInt J Syst Evol Microbiol10.1099/ijs.0.058610-02014Bacillus/*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, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny26604103Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils.Dou G, Liu H, He W, Ma YAntonie Van Leeuwenhoek10.1007/s10482-015-0616-y2015Bacillus/*classification/genetics/*isolation & purification/metabolism, Base Sequence, Cell Wall/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/metabolism, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism/pharmacology, Soil/chemistry, *Soil MicrobiologyMetabolism
Phylogeny26971318Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye.Hirota K, Aino K, Yumoto IInt J Syst Evol Microbiol10.1099/ijsem.0.0010152016Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Indigo Carmine/*chemistry, Nucleic Acid Hybridization, *Phylogeny, Polygonum/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20435Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27953Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27953)
29877Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172625128776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87753Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401112.1