Strain identifier

BacDive ID: 23714

Type strain: Yes

Species: Halalkalibacterium ligniniphilum

Strain Designation: L1

Strain history: D. Zhu L1.

NCBI tax ID(s): 1134413 (species)

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General

@ref: 20442

BacDive-ID: 23714

DSM-Number: 26145

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Halalkalibacterium ligniniphilum L1 is a mesophilic bacterium that was isolated from marine benthic sediment.

NCBI tax id

  • NCBI tax id: 1134413
  • Matching level: species

strain history

@refhistory
20442<- D. Zhu, Jiangsu Univ., Zhenjiang, People's Republic of China; L1
67770D. Zhu L1.

doi: 10.13145/bacdive23714.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halalkalibacterium
  • species: Halalkalibacterium ligniniphilum
  • full scientific name: Halalkalibacterium ligniniphilum (Zhu et al. 2014) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Alkalihalobacillus ligniniphilus
    20215Bacillus ligniniphilus

@ref: 20442

domain: Bacteria

phylum: Bacillota

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Halalkalibacterium

species: Halalkalibacterium ligniniphilum

full scientific name: Halalkalibacterium ligniniphilum (Zhu et al. 2014) Joshi et al. 2022

strain designation: L1

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 20442
  • name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/31
  • composition: Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20442positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20442marine benthic sedimentSouth China Sea (18° 44.606' N, 119° 44.263' W at a depth of 3415 m)ChinaCHNAsia18.7434119.738
67770Sediment sample from the South China Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_255.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_178;97_194;98_217;99_255&stattab=map
  • Last taxonomy: Alkalihalobacillus ligniniphilus subclade
  • 16S sequence: JQ044788
  • Sequence Identity:
  • Total samples: 336
  • soil counts: 91
  • aquatic counts: 12
  • animal counts: 229
  • plant counts: 4

Safety information

risk assessment

  • @ref: 20442
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20442
  • description: Bacillus sp. L1(2012) 16S ribosomal RNA gene, partial sequence
  • accession: JQ044788
  • length: 1469
  • database: ena
  • NCBI tax ID: 1134413

Genome sequences

  • @ref: 67770
  • description: Halalkalibacterium ligniniphilum L1
  • accession: GCA_000334155
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1134413

GC content

@refGC-contentmethod
2044240.76sequence analysis
6777040.76genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.998no
flagellatedyes77.976no
gram-positiveyes88.791no
anaerobicno98.314no
aerobicyes90.286no
halophileyes52.412no
spore-formingyes95.635no
thermophileno89.324no
glucose-utilyes88.349no
glucose-fermentno93.008no

External links

@ref: 20442

culture collection no.: DSM 26145, JCM 18543

straininfo link

  • @ref: 87760
  • straininfo: 408188

literature

  • topic: Phylogeny
  • Pubmed-ID: 24554634
  • title: Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.
  • authors: Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.058610-0
  • year: 2014
  • mesh: Bacillus/*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 Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
20442Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26145Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26145)
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/
87760Reimer, 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-ID408188.1