Strain identifier

BacDive ID: 132970

Type strain: Yes

Species: Mucilaginibacter yixingensis

Strain Designation: yx-36

Strain history: <- H. Cao, Nanjing Agric. Univ., China; yx-36 <- Yiting-Jing <- P. Wang

NCBI tax ID(s): 1295612 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24758

BacDive-ID: 132970

DSM-Number: 26809

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

description: Mucilaginibacter yixingensis yx-36 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil from a vegetable plot.

NCBI tax id

  • NCBI tax id: 1295612
  • Matching level: species

strain history

  • @ref: 24758
  • history: <- H. Cao, Nanjing Agric. Univ., China; yx-36 <- Yiting-Jing <- P. Wang

doi: 10.13145/bacdive132970.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Mucilaginibacter
  • species: Mucilaginibacter yixingensis
  • full scientific name: Mucilaginibacter yixingensis Jing et al. 2016

@ref: 24758

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Mucilaginibacter

species: Mucilaginibacter yixingensis

full scientific name: Mucilaginibacter yixingensis Jing et al. 2016

strain designation: yx-36

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43682negative1.25-2.3 µm0.65-0.75 µmrod-shapedno
69480negative99.998

colony morphology

  • @ref: 43682
  • colony color: Light yellow
  • colony shape: circular
  • medium used: R2A agar

pigmentation

  • @ref: 43682
  • production: yes
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43682Dnase test agarno
43682Low-nutrient mediayes
43682MacConkey agarno
43682Reasoner's 2A agar (R2A)yes
24758R2A 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

culture temp

@refgrowthtypetemperaturerange
43682positivegrowth15-37
43682positiveoptimum37mesophilic
24758positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43682positivegrowth6-9.5alkaliphile
43682positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43682
  • oxygen tolerance: aerobe

spore formation

@reftype of sporespore formationconfidence
43682endosporeno
69481no100
69480no99.949

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43682NaClpositivegrowth0-1 %(w/v)
43682NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4368217128adipate-assimilation
4368227689decanoate-assimilation
4368225115malate-assimilation
4368229864mannitol-assimilation
4368218401phenylacetate-assimilation
4368253258sodium citrate-assimilation
43682168082-dehydro-D-gluconate-builds acid from
43682581435-dehydro-D-gluconate-builds acid from
4368215963ribitol-builds acid from
4368227613amygdalin-builds acid from
4368218305arbutin-builds acid from
4368217057cellobiose-builds acid from
4368218333D-arabitol-builds acid from
4368228847D-fucose-builds acid from
4368262318D-lyxose-builds acid from
4368216813galactitol-builds acid from
4368217113erythritol-builds acid from
4368228757fructose-builds acid from
4368228260galactose-builds acid from
4368228066gentiobiose-builds acid from
4368224265gluconate-builds acid from
4368217234glucose-builds acid from
4368217754glycerol-builds acid from
4368228087glycogen-builds acid from
4368217268myo-inositol-builds acid from
4368215443inulin-builds acid from
4368230849L-arabinose-builds acid from
4368218403L-arabitol-builds acid from
4368265328L-xylose-builds acid from
4368217716lactose-builds acid from
4368229864mannitol-builds acid from
4368237684mannose-builds acid from
436826731melezitose-builds acid from
4368228053melibiose-builds acid from
4368243943methyl alpha-D-mannoside-builds acid from
4368274863methyl beta-D-xylopyranoside-builds acid from
4368237657methyl D-glucoside-builds acid from
43682506227N-acetylglucosamine-builds acid from
4368216634raffinose-builds acid from
4368226546rhamnose-builds acid from
4368217814salicin-builds acid from
4368230911sorbitol-builds acid from
4368227922sorbose-builds acid from
4368228017starch-builds acid from
4368217992sucrose-builds acid from
4368227082trehalose-builds acid from
4368232528turanose-builds acid from
4368217151xylitol-builds acid from
4368258187alginate-hydrolysis
4368285146carboxymethylcellulose-hydrolysis
436825291gelatin-hydrolysis
4368217309pectin-hydrolysis
4368228017starch-hydrolysis
4368253424tween 20-hydrolysis
4368253423tween 40-hydrolysis
4368253425tween 60-hydrolysis
4368253426tween 80-hydrolysis
4368237166xylan-hydrolysis
4368217632nitrate-reduction
43682309162-oxoglutarate-respiration
43682620642,3-butanediol-respiration
43682181014-hydroxyphenylacetic acid-respiration
4368230089acetate-respiration
4368215963ribitol-respiration
4368217925alpha-D-glucose-respiration
4368217665alpha-D-glucose 6-phosphate-respiration
43682645522-hydroxybutyrate-respiration
436828295beta-hydroxybutyrate-respiration
4368273706bromosuccinate-respiration
4368216383cis-aconitate-respiration
4368216947citrate-respiration
4368215570D-alanine-respiration
4368218333D-arabitol-respiration
4368212931D-galactonate-respiration
4368218024D-galacturonic acid-respiration
436828391D-gluconate-respiration
4368217784D-glucosaminic acid-respiration
4368216899D-mannitol-respiration
4368227605D-psicose-respiration
4368233801D-saccharate-respiration
4368216523D-serine-respiration
4368217924D-sorbitol-respiration
4368217126DL-carnitine-respiration
4368217113erythritol-respiration
4368216000ethanolamine-respiration
4368215740formate-respiration
4368216865gamma-aminobutyric acid-respiration
43682167244-hydroxybutyrate-respiration
4368229042glucose 1-phosphate-respiration
4368232323glucuronamide-respiration
4368217754glycerol-respiration
4368214336glycerol 1-phosphate-respiration
4368228087glycogen-respiration
4368273804glycyl L-aspartic acid-respiration
4368224741hydroxyproline-respiration
4368217596inosine-respiration
4368217240itaconate-respiration
4368221217L-alaninamide-respiration
4368216977L-alanine-respiration
4368273786L-alanylglycine-respiration
4368217196L-asparagine-respiration
4368229991L-aspartate-respiration
4368215971L-histidine-respiration
4368215603L-leucine-respiration
4368215729L-ornithine-respiration
4368217295L-phenylalanine-respiration
4368218183L-pyroglutamic acid-respiration
4368262345L-rhamnose-respiration
4368215792malonate-respiration
43682320055methyl beta-D-glucopyranoside-respiration
4368275146monomethyl succinate-respiration
4368228037N-acetylgalactosamine-respiration
4368273784glycyl-l-glutamate-respiration
4368250048phenylethylamine-respiration
4368217272propionate-respiration
4368217148putrescine-respiration
4368226490quinate-respiration
4368216634raffinose-respiration
4368241865sebacic acid-respiration
43682143136succinamate-respiration
4368230031succinate-respiration
4368217992sucrose-respiration
4368217748thymidine-respiration
4368253423tween 40-respiration
4368253426tween 80-respiration
4368227248urocanic acid-respiration
4368217151xylitol-respiration
4368222599arabinose+assimilation
4368217234glucose+assimilation
4368217306maltose+assimilation
4368237684mannose+assimilation
43682506227N-acetylglucosamine+assimilation
4368217108D-arabinose+builds acid from
4368216443D-tagatose+builds acid from
4368265327D-xylose+builds acid from
436824853esculin+builds acid from
4368218287L-fucose+builds acid from
4368217306maltose+builds acid from
4368233942ribose+builds acid from
436824853esculin+hydrolysis
43682167632-oxobutanoate+respiration
43682286442-oxopentanoate+respiration
4368240585alpha-cyclodextrin+respiration
4368217925alpha-D-glucose+respiration
4368236219alpha-lactose+respiration
4368217057cellobiose+respiration
4368215824D-fructose+respiration
4368212936D-galactose+respiration
4368215748D-glucuronate+respiration
4368216024D-mannose+respiration
4368223652dextrin+respiration
4368224996lactate+respiration
4368228066gentiobiose+respiration
4368230849L-arabinose+respiration
4368218287L-fucose+respiration
4368229985L-glutamate+respiration
4368217203L-proline+respiration
4368217115L-serine+respiration
4368216857L-threonine+respiration
436826359lactulose+respiration
4368217306maltose+respiration
4368228053melibiose+respiration
4368251850methyl pyruvate+respiration
43682506227N-acetylglucosamine+respiration
4368227082trehalose+respiration
4368232528turanose+respiration
4368216704uridine+respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4368217334penicillinyesyes10 µg (disc)
436828309polymyxin byesyes300 µg (disc)
4368228077rifampicinyesyes5 µg (disc)
4368248923erythromycinyesyes15 µg (disc)
4368250845doxycyclineyesyes30 µg (disc)
4368227902tetracyclineyesyes30 µg (disc)
43682100147nalidixic acidyesyes30 µg (disc)
4368228368novobiocinyesyes30 µg (disc)
4368217076streptomycinyesyes10 µg (disc)
436827507neomycinyesyes30 µg (disc)
4368228971ampicillinyesyes10 µg (disc)
436823393carbenicillinyesyes100 µg (disc)
436826104kanamycinyesyes30 µg (disc)
4368228001vancomycinyesyes30 µg (disc)
4368217833gentamicinyesyes10 µg (disc)
4368217698chloramphenicolyesyes5 µg (disc)
43682472657cefiximeyesyes5 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4368215688acetoinyes
4368235581indoleyes

enzymes

@refvalueactivityec
43682catalase+1.11.1.6
43682cytochrome oxidase+1.9.3.1
43682alkaline phosphatase+3.1.3.1
43682leucine arylamidase+3.4.11.1
43682valine arylamidase+
43682cystine arylamidase+3.4.11.3
43682acid phosphatase+3.1.3.2
43682naphthol-AS-BI-phosphohydrolase+
43682alpha-galactosidase+3.2.1.22
43682beta-galactosidase+3.2.1.23
43682beta-glucuronidase+3.2.1.31
43682alpha-glucosidase+3.2.1.20
43682beta-glucosidase+3.2.1.21
43682N-acetyl-beta-glucosaminidase+3.2.1.52
43682beta-D-fucosidase+3.2.1.38
43682esterase (C 4)-
43682esterase Lipase (C 8)-
43682lipase (C 14)-
43682trypsin-3.4.21.4
43682chymotrypsin-3.4.4.5
43682alpha-mannosidase-3.2.1.24
43682arginine dihydrolase+3.5.3.6
43682urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43682C15:0 anteiso7.2
    43682C15:1 anteiso A2.1
    43682C15:03
    43682C15:0 2OH3.1
    43682C16:02.2
    43682C16:0 2OH1
    43682C16:0 3OH1.3
    43682C16:1ω7c / C15:0 iso 2OH3.6
    43682C17:0 2OH1.4
    43682C17:0 3OH1.3
    43682C17:1ω6c2.4
    43682C14:0 iso2.6
    43682C15:0 iso19.5
    43682C15:0 iso 3OH1
    43682C15:1 iso G15.8
    43682C16:0 iso5.9
    43682C16:0 iso 3OH3.2
    43682iso-C16:0G4.9
    43682C17:0 iso 3OH9.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 4.0
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • instrument: HP 6890N; Agilent
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24758soil from a vegetable plotJiangsu province, Yixing (31° 21' 36'' N 119° 49' 12''E)ChinaCHNAsia31.36119.82
43682A vegetable plotYixing, Jiangsu ProvinceChinaCHNAsia31.36119.82

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Host#Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_119204.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_14359;97_33756;98_80383;99_119204&stattab=map
  • Last taxonomy: Mucilaginibacter yixingensis subclade
  • 16S sequence: KC480578
  • Sequence Identity:
  • Total samples: 365
  • soil counts: 198
  • aquatic counts: 31
  • animal counts: 71
  • plant counts: 65

Safety information

risk assessment

  • @ref: 24758
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24758
  • description: Mucilaginibacter yixingensis strain YX-36 16S ribosomal RNA gene, partial sequence
  • accession: KC480578
  • length: 1444
  • database: ena
  • NCBI tax ID: 1295612

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mucilaginibacter yixingensis DSM 26809GCA_003050755contigncbi1295612
66792Mucilaginibacter yixingensis strain DSM 268091295612.3wgspatric1295612
66792Mucilaginibacter yixingensis DSM 268092734482263draftimg1295612

GC content

  • @ref: 24758
  • GC-content: 47.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.056no
gram-positiveno97.413yes
anaerobicno99.476yes
aerobicyes92.528yes
halophileno97.094no
spore-formingno94.069yes
thermophileno97.398no
glucose-utilyes89.606no
flagellatedno97.48yes
glucose-fermentno89.382no

External links

@ref: 24758

culture collection no.: DSM 26809, CCTCC AB 2012880

straininfo link

  • @ref: 91247
  • straininfo: 399561

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26827674Mucilaginibacter yixingensis sp. nov., isolated from vegetable soil.Jing YT, Wang P, Zhang H, Dong WL, Jing YJ, Xiao YL, Cao HInt J Syst Evol Microbiol10.1099/ijsem.0.0009412016*Agriculture, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31334699Mucilaginibacter terrenus sp. nov., isolated from manganese mine soil.Zhou Z, Dong Y, Xia X, Wu S, Huang Y, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0035922019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Manganese, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24758Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26809Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26809)
43682Yi-Ting Jing, Ping Wang, Hao Zhang, Wei-Liang Dong, Yin-Juan Jing, Yong-Liang Xiao, Hui CaoMucilaginibacter yixingensis sp. nov., isolated from vegetable soil10.1099/ijsem.0.000941IJSEM 66: 1779-1784 201626827674
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/
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
91247Reimer, 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-ID399561.1