Strain identifier

BacDive ID: 24736

Type strain: Yes

Species: Sediminibacterium salmoneum

Strain Designation: NJ-44

Strain history: <- NBRC <- China General Microbiological Culture Collection Center, CGMCC <- J.-H. Qu, China Agric. Univ., College Biol. Sci., Beijing; NJ-44

NCBI tax ID(s): 1400522 (strain), 426421 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21188

BacDive-ID: 24736

DSM-Number: 27476

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Sediminibacterium salmoneum NJ-44 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment from Guanting Reservoir.

NCBI tax id

NCBI tax idMatching level
426421species
1400522strain

strain history

  • @ref: 21188
  • history: <- NBRC <- China General Microbiological Culture Collection Center, CGMCC <- J.-H. Qu, China Agric. Univ., College Biol. Sci., Beijing; NJ-44

doi: 10.13145/bacdive24736.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Sediminibacterium
  • species: Sediminibacterium salmoneum
  • full scientific name: Sediminibacterium salmoneum Qu and Yuan 2008

@ref: 21188

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Sediminibacterium

species: Sediminibacterium salmoneum

full scientific name: Sediminibacterium salmoneum Qu and Yuan 2008 emend. Kim et al. 2013

strain designation: NJ-44

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32449negative1-1.2 µm0.2-0.3 µmrod-shapedyesgliding
69480no90.706
69480negative99.999

colony morphology

  • @ref: 21188
  • incubation period: 8-14 days

pigmentation

  • @ref: 32449
  • production: no

Culture and growth conditions

culture medium

  • @ref: 21188
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21188positivegrowth28mesophilic
32449positivegrowth18-37
32449positiveoptimum22-28

culture pH

@refabilitytypepH
32449positivegrowth6-7.5
32449positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32449
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32449no
69481no99
69480no99.999

halophily

  • @ref: 32449
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

  • @ref: 32449
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3244917234glucose+carbon source
3244917716lactose+carbon source
3244917306maltose+carbon source
3244937684mannose+carbon source
3244928053melibiose+carbon source
3244916634raffinose+carbon source
3244917814salicin+carbon source
3244917992sucrose+carbon source
3244927082trehalose+carbon source
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
32449catalase+1.11.1.6
32449cytochrome oxidase+1.9.3.1
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21188+--------+----------+

Isolation, sampling and environmental information

isolation

  • @ref: 21188
  • sample type: sediment from Guanting Reservoir
  • geographic location: Beijing
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_5693.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_2735;97_3362;98_4241;99_5693&stattab=map
  • Last taxonomy: Sediminibacterium salmoneum subclade
  • 16S sequence: EF407879
  • Sequence Identity:
  • Total samples: 3756
  • soil counts: 190
  • aquatic counts: 2905
  • animal counts: 572
  • plant counts: 89

Safety information

risk assessment

  • @ref: 21188
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21188
  • description: Sediminibacterium salmoneum strain NJ-44 16S ribosomal RNA gene, partial sequence
  • accession: EF407879
  • length: 1458
  • database: ena
  • NCBI tax ID: 1400522

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sediminibacterium salmoneum NBRC 103935GCA_000511175scaffoldncbi1400522
66792Sediminibacterium salmoneum NBRC 1039351400522.3wgspatric1400522
66792Sediminibacterium salmoneum NBRC 1039352585428137draftimg1400522

GC content

  • @ref: 21188
  • GC-content: 40.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.68no
flagellatedno97.834yes
gram-positiveno98.133yes
anaerobicno98.659yes
halophileno97.69yes
spore-formingno96.778no
thermophileno92.592yes
glucose-utilyes84.25yes
aerobicyes88.626yes
glucose-fermentno90.436yes

External links

@ref: 21188

culture collection no.: DSM 27476, CGMCC 1.6845, NBRC 103935

straininfo link

  • @ref: 88564
  • straininfo: 405286

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18768628Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir.Qu JH, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.65514-02008Aerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny20061500Solibius ginsengiterrae gen. nov., sp. nov., isolated from soil of a ginseng field, and emended description of the genus Sediminibacterium and of Sediminibacterium salmoneium.Kim YJ, Kim MK, Bui TP, Kim HB, Srinivasan S, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.011882-02010
Phylogeny20382796Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.Kampfer P, Lodders N, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.023002-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sweden, Water MicrobiologyGenetics
Phylogeny22634704Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum.Kim YJ, Nguyen NL, Weon HY, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.038554-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Panax/*microbiology, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24170777Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water.Albert RA, Zitomer D, Dollhopf M, Schauer-Gimenez AE, Struble C, King M, Son S, Langer S, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.056663-02013Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Lakes/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, WisconsinGenetics
Phylogeny24425738Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir.Kang H, Kim H, Lee BI, Joung Y, Joh KInt J Syst Evol Microbiol10.1099/ijs.0.055137-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics24435857Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge.Ayarza JM, Figuerola EL, Erijman LGenome Announc10.1128/genomeA.01073-132014Phylogeny
Phylogeny25563914Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water.Eder W, Peplies J, Wanner G, Fruhling A, Verbarg SInt J Syst Evol Microbiol10.1099/ijs.0.0000402015Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny33104819Sediminibacterium soli sp. nov., isolated from soil.Wu S, Zhong L, Liao S, Li T, Zhou Z, Wang GArch Microbiol10.1007/s00203-020-02089-22020Bacteroidetes/*classification/genetics, Base Composition, Fatty Acids/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21188Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27476Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27476)
32449Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172867128776041
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
68368Automatically annotated from API 20E
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
88564Reimer, 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-ID405286.1