Strain identifier

BacDive ID: 22946

Type strain: Yes

Species: Alkalibacterium gilvum

Strain Designation: 3AD-1

Strain history: M. Ishikawa 3AD-1.

NCBI tax ID(s): 1130080 (species)

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General

@ref: 19281

BacDive-ID: 22946

DSM-Number: 25751

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped

description: Alkalibacterium gilvum 3AD-1 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from mould-ripened, soft cheese .

NCBI tax id

  • NCBI tax id: 1130080
  • Matching level: species

strain history

@refhistory
19281<- M. Ishikawa, Tokyo Univ. Agriculture, Japan; 3AD-1
67770M. Ishikawa 3AD-1.

doi: 10.13145/bacdive22946.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Alkalibacterium
  • species: Alkalibacterium gilvum
  • full scientific name: Alkalibacterium gilvum Ishikawa et al. 2013

@ref: 19281

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Alkalibacterium

species: Alkalibacterium gilvum

full scientific name: Alkalibacterium gilvum Ishikawa et al. 2013

strain designation: 3AD-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30705positive6.7 µm0.7 µmrod-shapedno
69480no94.739
69480positive100

pigmentation

  • @ref: 30705
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19281
  • name: BOGORIELLA MEDIUM (DSMZ Medium 785)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/785
  • composition: Name: BOGORIELLA MEDIUM (DSMZ Medium 785; with strain-specific modifications) Composition: NaCl 40.0 g/l Agar 20.0 g/l Na2CO3 10.0 g/l Glucose 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19281positivegrowth30mesophilic
30705positivegrowth0-37
30705positiveoptimum25mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30705positivegrowth07-10alkaliphile
30705positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
19281microaerophile
30705microaerophile

spore formation

@refspore formationconfidence
30705no
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
30705NaClpositivegrowth0-17.5 %
30705NaClpositiveoptimum3.5 %

murein

  • @ref: 19281
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3070522599arabinose+carbon source
3070517716lactose+carbon source
3070517814salicin+carbon source
3070517992sucrose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
19281mould-ripened, soft cheese (Brie cheese)FranceFRAEurope
67770Mould-ripened, soft cheese (Brie cheese)

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_21949.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_27;96_47;97_49;98_16554;99_21949&stattab=map
  • Last taxonomy: Alkalibacterium gilvum
  • 16S sequence: LC521986
  • Sequence Identity:
  • Total samples: 1029
  • soil counts: 74
  • aquatic counts: 233
  • animal counts: 684
  • plant counts: 38

Safety information

risk assessment

  • @ref: 19281
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
19281Alkalibacterium gilvum gene for 16S rRNA, partial sequence, strain: 3AD-1AB6905661503ena1130080
67770Alkalibacterium gilvum JCM 18271 gene for 16S rRNA, partial sequenceLC5219861489ena1130080

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alkalibacterium gilvum strain DSM 257511130080.4wgspatric1130080
66792Alkalibacterium gilvum DSM 257512616644817draftimg1130080
67770Alkalibacterium gilvum DSM 25751GCA_900109085scaffoldncbi1130080

GC content

@refGC-contentmethod
1928136.8high performance liquid chromatography (HPLC)
3070536.8
6777036.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno89no
motileno91.085yes
flagellatedno97.341no
gram-positiveyes93.64yes
anaerobicno95.92no
aerobicno93.574yes
halophileyes93.664no
spore-formingno93.876no
glucose-utilyes89.21no
thermophileno99.376yes
glucose-fermentyes82.722no

External links

@ref: 19281

culture collection no.: DSM 25751, JCM 18271

straininfo link

  • @ref: 87194
  • straininfo: 403214

literature

  • topic: Phylogeny
  • Pubmed-ID: 22843725
  • title: Alkalibacterium gilvum sp. nov., slightly halophilic and alkaliphilic lactic acid bacterium isolated from soft and semi-hard cheeses.
  • authors: Ishikawa M, Yamasato K, Kodama K, Yasuda H, Matsuyama M, Okamoto-Kainuma A, Koizumi Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.042556-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, Cheese/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Glucose/analysis, Hydrogen-Ion Concentration, Lactic Acid/biosynthesis, Lactobacillaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19281Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25751)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25751
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
30705Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2703628776041
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
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.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)
87194Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403214.1StrainInfo: A central database for resolving microbial strain identifiers