Strain identifier

BacDive ID: 159784

Type strain: Yes

Species: Salegentibacter sediminis

Strain Designation: K5023

Strain history: <- Zongjun Du, Shandong Univ.

NCBI tax ID(s): 1930251 (species)

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General

@ref: 66601

BacDive-ID: 159784

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

description: Salegentibacter sediminis K5023 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from marine sediment, which was collected off the coast of Weihai.

NCBI tax id

  • NCBI tax id: 1930251
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zongjun Du, Shandong Univ.

doi: 10.13145/bacdive159784.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Salegentibacter
  • species: Salegentibacter sediminis
  • full scientific name: Salegentibacter sediminis Liang et al. 2018

@ref: 66601

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Salegentibacter

species: Salegentibacter sediminis

strain designation: K5023

type strain: yes

Morphology

cell morphology

  • @ref: 66601
  • gram stain: negative
  • cell length: 0.8-1.4 µm
  • cell width: 0.2-0.3 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 66601
  • colony size: 0.5-1 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Marine agar (MA)

pigmentation

  • @ref: 66601
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

  • @ref: 66601
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66601positivegrowth33mesophilic
66601positivegrowth16-37
67771positivegrowth25-33mesophilic

culture pH

@refabilitytypepH
66601nogrowth6-8.5
66601positivegrowth6.5-8.0
66601positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66601aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
66601NaClpositivegrowth1-10 %(w/v)
66601NaClpositiveoptimum5 %(w/v)

observation

@refobservation
66601The major respiratory quinone is MK-6.
66601The polar lipids are one phosphatidylethanolamine, three phospholipids and four unidentified lipids.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6660131605ferric citrate+assimilation
666014853esculin+builds acid from
6660112936D-galactose+builds acid from
6660115443inulin+builds acid from
6660115824D-fructose+builds acid from
6660116024D-mannose+builds acid from
6660117306maltose+builds acid from
6660117992sucrose+builds acid from
6660127082trehalose+builds acid from
6660128017starch+builds acid from
6660128053melibiose+builds acid from
6660128066gentiobiose+builds acid from
66601potassium 5-dehydro-D-gluconate+builds acid from
6660117716lactose+carbon source
6660117992sucrose+carbon source
6660122599arabinose+carbon source
6660126546rhamnose+carbon source
6660129864mannitol+carbon source
6660130911sorbitol+carbon source
666012509agar-hydrolysis
6660128017starch-hydrolysis
6660153426tween 80-hydrolysis
6660185146carboxymethylcellulose-hydrolysis
6660153423tween 40+hydrolysis
6660153424tween 20+hydrolysis
6660153425tween 60+hydrolysis
6660117632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6660148923erythromycinyesyes15 µg (disc)
6660128971ampicillinyesyes10 µg (disc)
6660117334penicillinyesyes10 µg (disc)
6660117698chloramphenicolyesyes30 µg (disc)
6660128077rifampicinyesyes5 µg (disc)
66601100246norfloxacinyesyes30 µg (disc)
666016472lincomycinyesyes2 µg (disc)
666013498cefotaxime sodiumyesyes30 µg (disc)
6660131168spiramycin IIyesyes30 µg (disc)
6660128864tobramycinyesyes10 µg (disc)
6660127902tetracyclineyesyes30 µg (disc)
666017507neomycinyesyes30 µg (disc)
6660117833gentamicinyesyes10 µg (disc)
66601100147nalidixic acidyesyes30 µg (disc)
6660145924trimethoprimyesyes10 µg (disc)
6660117076streptomycinyesyes10 µg (disc)
666016104kanamycinyesyes30 µg (disc)
6660128001vancomycinyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6660115138sulfideyes
6660135581indoleyes

enzymes

@refvalueactivityec
66601alpha-galactosidase-3.2.1.22
66601alpha-mannosidase-3.2.1.24
66601arginine dihydrolase-3.5.3.6
66601beta-D-fucosidase-3.2.1.38
66601beta-galactosidase-3.2.1.23
66601beta-glucuronidase-3.2.1.31
66601catalase-1.11.1.6
66601cystine arylamidase-3.4.11.3
66601cytochrome oxidase-1.9.3.1
66601esterase (C 4)-
66601esterase Lipase (C 8)-
66601lipase (C 14)-
66601lysine decarboxylase-4.1.1.18
66601ornithine decarboxylase-4.1.1.17
66601trypsin-3.4.21.4
66601tryptophan deaminase-4.1.99.1
66601urease-3.5.1.5
66601acid phosphatase+3.1.3.2
66601alkaline phosphatase+3.1.3.1
66601alpha-glucosidase+3.2.1.20
66601chymotrypsin+3.4.4.5
66601leucine arylamidase+3.4.11.1
66601N-acetyl-beta-glucosaminidase+3.2.1.52
66601naphthol-AS-BI-phosphohydrolase+
66601valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66601C15:0 iso 3OH2
    66601C13:0 iso0.3
    66601C17:0 iso0.5
    66601C17:1 w6c0.7
    66601C15:1 anteiso A0.9
    66601C16:01.4
    66601C16:0 iso 3OH1.5
    66601C16:1 iso H1.8
    66601C15:0 anteiso15.8
    66601C15:02.7
    66601C15:0 iso21.2
    66601C15:0 2OH3.2
    66601C16:0 iso4.7
    66601C17:1 iso w9c4.8
    66601C17:1 anteiso w9c5.6
    66601C17:0 2OH5.6
    66601C17:0 iso 3OH5.8
    66601C15:1 iso G6.8
    66601C16:1 w7c and/or iso-C15 2OH8.4
  • type of FA analysis: whole cell analysis
  • incubation temperature: 33
  • incubation time: 3
  • incubation pH: 7.5
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • method/protocol: Sasser, 2001

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentlatitudelongitudeisolation proceduregeographic location
66601marine sediment, which was collected off the coast of WeihaiChinaCHNAsia37.518122.03The marine sediment sample was processed using an enrichment culture medium as described by Du. Incubation was performed at 25°C for 30 days in a 500 ml beaker-flask (sealed with degreasing cotton, and filled with 300 ml medium and 6 g sediment sample). The beaker-flask was shaken at 130 r.p.m. and kept sealed during incubation. The enrichment cultures were diluted with 9 ml sterile seawater and spread onto marine agar 2216 (MA; BD). The plates were incubated aerobically at 25°C for 7 days.
67771From marine sedimentChinaCHNAsia37.5181122.03the coastal area of Weihai

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6138.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_2922;97_3597;98_4553;99_6138&stattab=map
  • Last taxonomy: Salegentibacter sediminis subclade
  • 16S sequence: KX424878
  • Sequence Identity:
  • Total samples: 170
  • soil counts: 27
  • aquatic counts: 127
  • animal counts: 12
  • plant counts: 4

Sequence information

16S sequences

  • @ref: 66601
  • description: Salegentibacter sp. K5023 16S ribosomal RNA gene, partial sequence
  • accession: KX424878
  • length: 1450
  • database: ena
  • NCBI tax ID: 1930251

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salegentibacter sediminis K5023GCA_002078605contigncbi1930251
66792Salegentibacter sediminis K50232839535834draftimg1930251

GC content

  • @ref: 66601
  • GC-content: 40.1
  • method: sequence analysis

External links

@ref: 66601

culture collection no.: KCTC 52477, MCCC 1H00173

literature

  • topic: Phylogeny
  • Pubmed-ID: 29856310
  • title: Salegentibacter sediminis sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from coastal sediment.
  • authors: Liang QY, Xu ZX, Zhang J, Chen GJ, Du ZJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002849
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
66601Qi-Yun Liang, Zhen-Xing Xu, Jing Zhang, Guan-Jun Chen, Zong-Jun DuSalegentibacter sediminis sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from coastal sediment10.1099/ijsem.0.002849IJSEM 68: 2375-2380 201829856310
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/