Strain identifier

BacDive ID: 158690

Type strain: Yes

Species: Flavobacterium sediminilitoris

Strain Designation: YSM-43

Strain history: <- Jung-Hoon Yoon, Sungkyunkwan Univ.

NCBI tax ID(s): 2024526 (species)

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 8.1 (current version)

General

@ref: 65427

BacDive-ID: 158690

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

description: Flavobacterium sediminilitoris YSM-43 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from a tidal flat.

NCBI tax id

  • NCBI tax id: 2024526
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Hoon Yoon, Sungkyunkwan Univ.

doi: 10.13145/bacdive158690.20230509.8.1

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 sediminilitoris
  • full scientific name: Flavobacterium sediminilitoris Park et al. 2018

@ref: 65427

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium sediminilitoris

strain designation: YSM-43

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
65427negative0.8-4.0 µm0.2-0.5 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative

colony morphology

  • @ref: 65427
  • colony size: 0.5-1.0 mm
  • colony color: moderate yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: marine agar

pigmentation

  • @ref: 65427
  • production: no
  • name: Flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 65427
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65427positiveoptimum30mesophilic
65427positivegrowth10psychrophilic
65427positivegrowth37mesophilic
65427nogrowth4psychrophilic
65427nogrowth40thermophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
65427positiveoptimum7-8
65427positivegrowth5.5
65427nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65427aerobe
67771facultative anaerobe

spore formation

  • @ref: 65427
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65427NaClpositivegrowth0-6 %(w/v)
65427NaClpositiveoptimum1-2 %(w/v)

observation

@refobservation
65427Mg2+ Ions are not required for growth
65427the predominant menaquinone is MK-6
65427the major polar lipids are phosphatidylethanolamine and one unidentified lipid
67771quinones: MK-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
65427casein+hydrolysis
65427cellobiose-builds acid from17057
65427D-fructose-builds acid from15824
65427D-galactose-builds acid from12936
65427D-glucose+builds acid from17634
65427D-mannitol-builds acid from16899
65427D-mannose+builds acid from16024
65427D-ribose-builds acid from16988
65427D-sorbitol-builds acid from17924
65427D-xylose-builds acid from65327
65427esculin-hydrolysis4853
65427gelatin+hydrolysis5291
65427hypoxanthine-hydrolysis17368
65427L-arabinose-builds acid from30849
65427L-rhamnose-builds acid from62345
65427L-tyrosine+hydrolysis17895
65427lactose-builds acid from17716
65427maltose+builds acid from17306
65427melezitose-builds acid from6731
65427melibiose-builds acid from28053
65427myo-inositol-builds acid from17268
65427nitrate+reduction17632
65427raffinose-builds acid from16634
65427starch+hydrolysis28017
65427sucrose-builds acid from17992
65427trehalose-builds acid from27082
65427tween 80+hydrolysis53426
65427urea-hydrolysis16199
65427xanthine-hydrolysis15318

metabolite production

  • @ref: 65427
  • Chebi-ID: 15138
  • metabolite: sulfide
  • production: no

enzymes

@refvalueactivityec
65427catalase+1.11.1.6
65427cytochrome oxidase+1.9.3.1
65427alkaline phosphatase+3.1.3.1
65427esterase Lipase (C 8)+
65427leucine arylamidase+3.4.11.1
65427valine arylamidase+
65427cystine arylamidase+3.4.11.3
65427trypsin+3.4.21.4
65427acid phosphatase+3.1.3.2
65427naphthol-AS-BI-phosphohydrolase+
65427N-acetyl-beta-glucosaminidase+3.2.1.52
65427lipase (C 14)-
65427alpha-chymotrypsin-3.4.21.1
65427alpha-galactosidase-3.2.1.22
65427beta-galactosidase-3.2.1.23
65427beta-glucuronidase-3.2.1.31
65427alpha-glucosidase-3.2.1.20
65427beta-glucosidase-3.2.1.21
65427alpha-mannosidase-3.2.1.24
65427alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperature
65427a tidal flatSouth SeaRepublic of KoreaKORAsiamarine agar 2216 (MA; BD Difco)30
67771From tidal flatYeosu on the South SeaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_5065.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2469;97_3013;98_3780;99_5065&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: MF595513
  • Sequence Identity:
  • Total samples: 1349
  • soil counts: 81
  • aquatic counts: 989
  • animal counts: 266
  • plant counts: 13

Sequence information

16S sequences

  • @ref: 65427
  • description: 16S rRNA gene sequence
  • accession: MF595513
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Flavobacterium sediminilitoris YSM-43
  • accession: GCA_023008245
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2024526

GC content

  • @ref: 67771
  • GC-content: 29.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.035yes
gram-positiveno98.613yes
anaerobicno99.459yes
aerobicyes87.468no
halophileno89.218no
spore-formingno93.354yes
motileno86.848no
glucose-fermentno90.616no
thermophileno99.591no
glucose-utilyes76.608no

External links

@ref: 65427

culture collection no.: KACC 19435, KCTC 62142, NBRC 113020

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29303697Flavobacterium sediminilitoris sp. nov., isolated from a tidal flat.Park S, Choi J, Choi SJ, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0025552018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics35993777Complete Genome Sequence of Flavobacterium sediminilitoris YSM-43(T), Isolated from Tidal Sediment in Yeosu.Lee PA, Cha IT, Lee KE, Son YK, Yu J, Kim JN, Seol DMicrobiol Resour Announc10.1128/mra.00054-222022Phylogeny

Reference

@idauthorstitledoi/urljournalpubmed
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
65427Sooyeon Park, Jeehyun Choi, Su Jung Choi, Jung-Hoon YoonFlavobacterium sediminilitoris sp. nov., isolated from a tidal flat10.1099/ijsem.0.002555IJSEM 68: 630-635 201829303697
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/