Strain identifier

BacDive ID: 140837

Type strain: Yes

Species: Jiulongibacter sediminis

Strain Designation: JN14-9

NCBI tax ID(s): 1605367 (species)

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General

@ref: 43640

BacDive-ID: 140837

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

description: Jiulongibacter sediminis JN14-9 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Surface sediment of the Jiulong River.

NCBI tax id

  • NCBI tax id: 1605367
  • Matching level: species

doi: 10.13145/bacdive140837.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Jiulongibacter
  • species: Jiulongibacter sediminis
  • full scientific name: Jiulongibacter sediminis Liu et al. 2016

@ref: 43640

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Jiulongibacter

species: Jiulongibacter sediminis

strain designation: JN14-9

type strain: yes

Morphology

cell morphology

  • @ref: 43640
  • gram stain: negative
  • cell length: 2.8-3 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43640
  • colony size: 2 mm
  • colony color: Orange
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA agar

pigmentation

  • @ref: 43640
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

  • @ref: 43640
  • name: MA agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43640positivegrowth15-37
43640positiveoptimum25-30mesophilic

culture pH

@refabilitytypepH
43640positivegrowth7-8
43640positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43640
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
43640NaClpositivegrowth2-6 %(w/v)
43640NaClpositiveoptimum3-4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4364015963ribitol-builds acid from
4364017108D-arabinose-builds acid from
4364018333D-arabitol-builds acid from
4364015824D-fructose-builds acid from
4364028847D-fucose-builds acid from
4364062318D-lyxose-builds acid from
4364016899D-mannitol-builds acid from
4364016988D-ribose-builds acid from
4364017924D-sorbitol-builds acid from
4364016443D-tagatose-builds acid from
4364016813galactitol-builds acid from
4364017113erythritol-builds acid from
4364017754glycerol-builds acid from
4364028087glycogen-builds acid from
4364017268myo-inositol-builds acid from
4364015443inulin-builds acid from
4364018403L-arabitol-builds acid from
4364018287L-fucose-builds acid from
4364017266L-sorbose-builds acid from
4364065328L-xylose-builds acid from
43640506227N-acetylglucosamine-builds acid from
43640potassium 2-dehydro-D-gluconate-builds acid from
43640potassium 5-dehydro-D-gluconate-builds acid from
4364032032potassium gluconate-builds acid from
4364028017starch-builds acid from
4364017151xylitol-builds acid from
43640casein-hydrolysis
4364016991dna-hydrolysis
436405291gelatin-hydrolysis
43640skimmed milk-hydrolysis
4364028017starch-hydrolysis
4364016199urea-hydrolysis
43640645522-hydroxybutyrate-respiration
43640167632-oxobutanoate-respiration
43640309162-oxoglutarate-respiration
43640286442-oxopentanoate-respiration
43640620642,3-butanediol-respiration
43640370543-hydroxybutyrate-respiration
43640181014-hydroxyphenylacetic acid-respiration
4364015963ribitol-respiration
4364073706bromosuccinate-respiration
4364016383cis-aconitate-respiration
4364016947citrate-respiration
4364015570D-alanine-respiration
4364018333D-arabitol-respiration
4364015895D-galactonic acid lactone-respiration
4364017784D-glucosaminic acid-respiration
4364016899D-mannitol-respiration
4364033801D-saccharate-respiration
4364016523D-serine-respiration
4364017126DL-carnitine-respiration
4364017113erythritol-respiration
4364016000ethanolamine-respiration
4364015740formate-respiration
4364016865gamma-aminobutyric acid-respiration
43640167244-hydroxybutyrate-respiration
4364073804glycyl L-aspartic acid-respiration
4364024741hydroxyproline-respiration
4364017596inosine-respiration
4364017240itaconate-respiration
4364021217L-alaninamide-respiration
4364016977L-alanine-respiration
4364073786L-alanylglycine-respiration
4364030849L-arabinose-respiration
4364017196L-asparagine-respiration
4364029991L-aspartate-respiration
4364018287L-fucose-respiration
4364015971L-histidine-respiration
4364015603L-leucine-respiration
4364015729L-ornithine-respiration
4364017295L-phenylalanine-respiration
4364018183L-pyroglutamic acid-respiration
4364017115L-serine-respiration
4364016857L-threonine-respiration
4364015792malonate-respiration
4364051850methyl pyruvate-respiration
4364017268myo-inositol-respiration
4364028037N-acetylgalactosamine-respiration
4364050048phenylethylamine-respiration
4364017272propionate-respiration
4364017148putrescine-respiration
4364026490quinate-respiration
4364041865sebacic acid-respiration
43640143136succinamate-respiration
4364030031succinate-respiration
4364017748thymidine-respiration
4364053423tween 40-respiration
4364053426tween 80-respiration
4364016704uridine-respiration
4364027248urocanic acid-respiration
4364017151xylitol-respiration
4364027613amygdalin+builds acid from
4364018305arbutin+builds acid from
4364017057cellobiose+builds acid from
4364012936D-galactose+builds acid from
4364017634D-glucose+builds acid from
4364016024D-mannose+builds acid from
436406731melezitose+builds acid from
4364016634raffinose+builds acid from
4364032528turanose+builds acid from
4364065327D-xylose+builds acid from
43640esculin ferric citrate+builds acid from
4364028066gentiobiose+builds acid from
4364030849L-arabinose+builds acid from
4364062345L-rhamnose+builds acid from
4364017716lactose+builds acid from
4364017306maltose+builds acid from
4364028053melibiose+builds acid from
43640320061methyl alpha-D-glucopyranoside+builds acid from
4364043943methyl alpha-D-mannoside+builds acid from
4364074863methyl beta-D-xylopyranoside+builds acid from
4364017814salicin+builds acid from
4364017992sucrose+builds acid from
4364027082trehalose+builds acid from
4364030089acetate+respiration
4364040585alpha-cyclodextrin+respiration
4364017925alpha-D-glucose+respiration
4364036219alpha-lactose+respiration
4364017057cellobiose+respiration
4364015824D-fructose+respiration
4364012936D-galactose+respiration
436408391D-gluconate+respiration
4364014314D-glucose 6-phosphate+respiration
4364016024D-mannose+respiration
4364016634raffinose+respiration
4364023652dextrin+respiration
4364028066gentiobiose+respiration
4364029042glucose 1-phosphate+respiration
4364024996lactate+respiration
436406359lactulose+respiration
4364017306maltose+respiration
4364028053melibiose+respiration
4364037657methyl D-glucoside+respiration
4364075146monomethyl succinate+respiration
43640506227N-acetylglucosamine+respiration
4364017992sucrose+respiration
4364027082trehalose+respiration
4364032528turanose+respiration
4364018024D-galacturonic acid+/-respiration
4364015748D-glucuronate+/-respiration
4364027605D-psicose+/-respiration
4364017924D-sorbitol+/-respiration
4364032323glucuronamide+/-respiration
4364017754glycerol+/-respiration
4364014336glycerol 1-phosphate+/-respiration
4364028087glycogen+/-respiration
4364029985L-glutamate+/-respiration
4364017203L-proline+/-respiration
4364062345L-rhamnose+/-respiration
4364073784glycyl-l-glutamate+/-respiration

enzymes

@refvalueactivityec
43640alkaline phosphatase+3.1.3.1
43640esterase Lipase (C 8)+
43640esterase (C 4)+
43640leucine aminopeptidase+3.4.1.1
43640valine aminopeptidase+
43640cystine aminopeptidase+3.4.11.3
43640trypsin+3.4.21.4
43640alpha-chymotrypsin+3.4.21.1
43640acid phosphatase+3.1.3.2
43640alpha-galactosidase+3.2.1.22
43640beta-galactosidase+3.2.1.23
43640beta-glucuronidase+3.2.1.31
43640alpha-glucosidase+3.2.1.20
43640beta-glucosidase+3.2.1.21
43640alpha-mannosidase+3.2.1.24
43640lipase (C 14)+
43640N-acetyl-beta-glucosaminidase+3.2.1.52
43640naphthol-AS-BI-phosphohydrolase+/-
43640alpha-fucosidase-3.2.1.51
43640cytochrome oxidase+1.9.3.1
43640catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43640C15:0 anteiso13.2
    43640C17:0 anteiso0.8
    43640C17:1 anteiso ω9c1.1
    43640C13:1 at 12-131
    43640C16:06.7
    43640C16:1ω7c / C16:1ω6c1.3
    43640C18:04.9
    43640C18:1ω7c / C18:1ω6c7.2
    43640C18:1ω9c3.1
    43640C9:01.01
    43640C13:0 iso 3OH3.3
    43640C14:0 iso1.1
    43640C15:0 iso46.9
    43640iso-C15:1F3.5
    43640C16:0 iso3.4
    43640C17:0 iso1.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Agilent Technologies 6850
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43640
  • sample type: Surface sediment (0-5 cm) of the Jiulong River
  • geographic location: Fujian
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 24.34
  • longitude: 117.319
  • isolation date: 2013-06

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6048.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16802;96_2885;97_3544;98_4487;99_6048&stattab=map
  • Last taxonomy: Jiulongibacter sediminis subclade
  • 16S sequence: KT345953
  • Sequence Identity:
  • Total samples: 1765
  • soil counts: 106
  • aquatic counts: 1407
  • animal counts: 218
  • plant counts: 34

Sequence information

16S sequences

  • @ref: 43640
  • description: 16S rRNA gene sequence
  • accession: KT345953
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Jiulongibacter sediminis JN14-9GCA_004329705contigncbi1605367
66792Jiulongibacter sediminis JN14-9GCA_001306455contigncbi1605367

GC content

  • @ref: 43640
  • GC-content: 41.6
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.736yes
gram-positiveno97.39no
anaerobicno99.306no
aerobicyes87.978no
halophileno92.54no
spore-formingno96.565no
glucose-utilyes81.925yes
thermophileno98.337yes
motileno93.933yes
glucose-fermentno89.779no

External links

@ref: 43640

culture collection no.: MCCC 1A00733, KCTC 42153

literature

  • topic: Phylogeny
  • Pubmed-ID: 27031260
  • title: Jiulongibacter sediminis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from the surface sediment of the Jiulong River in China.
  • authors: Liu Y, Du J, Lai Q, Dong C, Xie Y, Shao Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001038
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, 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
43640Yang Liu, Juan Du, Qiliang Lai, Chunming Dong, Yanrong Xie, Zongze ShaoJiulongibacter sediminis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from the surface sediment of the Jiulong River in China10.1099/ijsem.0.001038IJSEM 66: 2347-2353 201627031260
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/