Strain identifier

BacDive ID: 5558

Type strain: Yes

Species: Flavobacterium saliperosum

Strain Designation: S13

Strain history: CIP <- 2006, JCM <- 2005, S.J. Liu, Chinese Academy Sciences, Beijing, China: strain S13

NCBI tax ID(s): 329186 (species)

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General

@ref: 15874

BacDive-ID: 5558

DSM-Number: 21664

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

description: Flavobacterium saliperosum S13 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater lake sediment.

NCBI tax id

  • NCBI tax id: 329186
  • Matching level: species

strain history

@refhistory
15874<- JCM <- S.-J. Liu; S13
67770S.-J. Liu S13.
122386CIP <- 2006, JCM <- 2005, S.J. Liu, Chinese Academy Sciences, Beijing, China: strain S13

doi: 10.13145/bacdive5558.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium saliperosum
  • full scientific name: Flavobacterium saliperosum Wang et al. 2006

@ref: 15874

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium saliperosum

full scientific name: Flavobacterium saliperosum Wang et al. 2006 emend. Dong et al. 2013 emend. Hahnke et al. 2016

strain designation: S13

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31692negative1.5-2.5 µm0.35-0.55 µmrod-shapedno
69480negative99.997
122386negativerod-shapedno

colony morphology

@refincubation period
624622 days
122386

pigmentation

  • @ref: 31692
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15874R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
33996MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
122386CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
122386CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368
122386CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15874positivegrowth25mesophilic
31692positivegrowth20-34
31692positiveoptimum28mesophilic
33996positivegrowth30mesophilic
62462positivegrowth30mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31692positivegrowth6.5-8.5alkaliphile
31692positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31692aerobe
62462aerobe

spore formation

@refspore formationconfidence
31692no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31692NaClpositivegrowth0-1 %
31692NaClpositiveoptimum0-1 %

observation

@refobservation
31692aggregates in chains
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12238617632nitrate-reduction
12238616301nitrite-reduction

metabolite production

  • @ref: 122386
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31692catalase+1.11.1.6
31692gelatinase+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122386oxidase-
122386alcohol dehydrogenase-1.1.1.1
122386catalase+1.11.1.6
122386lysine decarboxylase-4.1.1.18
122386ornithine decarboxylase-4.1.1.17
122386urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122386-+++-++++-++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
15874freshwater lake sedimentTaihu Lake (also known as Lake Tai; 120° 02' 16.8'' E, 31° 27' 10.7'' N), Jiangsu ProvinceChinaCHNAsia31.453120.038
62462Fresh water sedimentJiangsu Province,Taihu LakeChinaCHNAsia2005
67770Freshwater sediment of Taihu Lake in central China
122386Environment, Fresh water, sedimentTaihu lake, JiangsuChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_5070.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2149;97_3016;98_3784;99_5070&stattab=map
  • Last taxonomy: Flavobacterium saliperosum subclade
  • 16S sequence: DQ021903
  • Sequence Identity:
  • Total samples: 377
  • soil counts: 101
  • aquatic counts: 246
  • animal counts: 27
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158741Risk group (German classification)
1223861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15874
  • description: Flavobacterium saliperosum strain AS 1.3801 16S ribosomal RNA gene, partial sequence
  • accession: DQ021903
  • length: 1408
  • database: ena
  • NCBI tax ID: 329186

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium saliperosum CGMCC 1.3801GCA_900100625scaffoldncbi329186
66792Flavobacterium saliperosum S131341155.3wgspatric1341155
66792Flavobacterium saliperosum strain CGMCC 1.3801329186.7wgspatric329186
66792Flavobacterium saliperosum S132576861653draftimg1341155
66792Flavobacterium saliperosum CGMCC 1.38012596583547draftimg329186
67770Flavobacterium saliperosum S13GCA_000498515contigncbi1341155

GC content

@refGC-contentmethod
1587441.0
3169241
1587439.6sequence analysis
6777041thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.067yes
flagellatedno95.406yes
gram-positiveno98.995yes
anaerobicno99.34yes
aerobicyes93.289yes
halophileno95.478yes
spore-formingno95.725yes
glucose-fermentno94.01no
thermophileno98.307yes
glucose-utilyes78.185no

External links

@ref: 15874

culture collection no.: DSM 21664, CGMCC 1.3801, JCM 13331, CCUG 60843, CIP 109164

straininfo link

  • @ref: 75040
  • straininfo: 286038

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449454Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment.Wang ZW, Liu YH, Dai X, Wang BJ, Jiang CY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64065-02006Bacterial Typing Techniques, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny17625200Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil.Weon HY, Song MH, Son JA, Kim BY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64935-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny19625416Flavobacterium cauense sp. nov., isolated from sediment of a eutrophic lake.Qu JH, Yuan HL, Li HF, Deng CPInt J Syst Evol Microbiol10.1099/ijs.0.009688-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Eutrophication, Fatty Acids/chemistry/metabolism, Flavobacterium/classification/genetics/*isolation & purification/metabolism, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15874Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21664
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
31692Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2796928776041
33996Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6875
62462Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60843)https://www.ccug.se/strain?id=60843
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75040Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID286038.1StrainInfo: A central database for resolving microbial strain identifiers
122386Curators of the CIPCollection of Institut Pasteur (CIP 109164)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109164