Strain identifier

BacDive ID: 2388

Type strain: Yes

Species: Sediminihabitans luteus

Strain Designation: H97-3

Strain history: <- M. Hamada, NBRC, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; H97-3

NCBI tax ID(s): 1138585 (species)

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General

@ref: 18043

BacDive-ID: 2388

DSM-Number: 25478

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

description: Sediminihabitans luteus H97-3 is a mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1138585
  • Matching level: species

strain history

  • @ref: 18043
  • history: <- M. Hamada, NBRC, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; H97-3

doi: 10.13145/bacdive2388.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Sediminihabitans
  • species: Sediminihabitans luteus
  • full scientific name: Sediminihabitans luteus Hamada et al. 2012

@ref: 18043

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Sediminihabitans

species: Sediminihabitans luteus

full scientific name: Sediminihabitans luteus Hamada et al. 2012

strain designation: H97-3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.037
69480100positive

Culture and growth conditions

culture medium

  • @ref: 18043
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

  • @ref: 18043
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.945

murein

  • @ref: 18043
  • murein short key: A11.48
  • type: A4alpha L-Lys-L-Ser-D-Glu

Isolation, sampling and environmental information

isolation

  • @ref: 18043
  • sample type: marine sediment
  • geographic location: Kyonan beach, coast of Tokyo Bay
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

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

Safety information

risk assessment

  • @ref: 18043
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18043
  • description: Sediminihabitans luteus gene for 16S rRNA, partial sequence, strain: H97-3
  • accession: AB695376
  • length: 1475
  • database: ena
  • NCBI tax ID: 1138585

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sediminihabitans luteus NBRC 108568GCA_016863455contigncbi1138585
66792Sediminihabitans luteus DSM 25478GCA_002797595contigncbi1138585
66792Sediminihabitans luteus strain DSM 254781138585.3wgspatric1138585
66792Sediminihabitans luteus strain NBRC 1085681138585.4wgspatric1138585
66792Sediminihabitans luteus DSM 254782734482071draftimg1138585

GC content

  • @ref: 18043
  • GC-content: 74.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
motileno89.805no
flagellatedno97.566no
gram-positiveyes89.115no
anaerobicno99.203no
aerobicyes86.224no
halophileno78.247no
spore-formingno85.341no
glucose-utilyes89.853no
thermophileno98.443yes
glucose-fermentno79.349no

External links

@ref: 18043

culture collection no.: DSM 25478, NBRC 108568

straininfo link

  • @ref: 71943
  • straininfo: 397338

literature

  • topic: Phylogeny
  • Pubmed-ID: 22543749
  • title: Sediminihabitans luteus gen. nov., sp. nov., a new member of the family Cellulomonadaceae isolated from sea sediment.
  • authors: Hamada M, Tamura T, Shibata C, Yamamura H, Hayakawa M, Suzuki K
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-012-9742-y
  • year: 2012
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18043Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25478)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25478
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
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
71943Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397338.1StrainInfo: A central database for resolving microbial strain identifiers