Strain identifier

BacDive ID: 5731

Type strain: Yes

Species: Zunongwangia profunda

Strain Designation: SM-A87

Strain history: Zhang Y, Marine Biotechnology Research Center, Shandong University, SM-A87 < Dang H.-Y., Institute Oceanology, Chinese Academy of Science [Synonyms: Wangia profunda Qin et al. 2007]

NCBI tax ID(s): 398743 (species)

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General

@ref: 7685

BacDive-ID: 5731

DSM-Number: 18752

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

description: Zunongwangia profunda SM-A87 is an obligate aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and has a Non-diffusable yellow pigmentation.

NCBI tax id

  • NCBI tax id: 398743
  • Matching level: species

strain history

@refhistory
7685<- Y. Zhang, State Key Lab. Microbial Technol., Marine Biotechnol. Res. Center, Shandong Univ., Jinan, China; SM-A87 <- H.-Y. Dang, Key Lab. Marine Geology and Environment, Inst. Oceanology, Chinese Academy of Sci., Qingdao, China
67772Zhang Y, Marine Biotechnology Research Center, Shandong University, SM-A87 < Dang H.-Y., Institute Oceanology, Chinese Academy of Science [Synonyms: Wangia profunda Qin et al. 2007]

doi: 10.13145/bacdive5731.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Zunongwangia
  • species: Zunongwangia profunda
  • full scientific name: Zunongwangia profunda corrig. Qin et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Wangia profunda

@ref: 7685

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Zunongwangia

species: Zunongwangia profunda

full scientific name: Zunongwangia profunda Qin et al. 2007

strain designation: SM-A87

type strain: yes

Morphology

cell morphology

  • @ref: 43398
  • gram stain: negative
  • cell length: 1.5-3.3 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43398
  • colony size: 1-3 mm
  • colony color: yellow to orange
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Marine agar

pigmentation

  • @ref: 43398
  • production: yes
  • name: Non-diffusable yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7685BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
43398MacConkey agarno
43398Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
7685positivegrowth28mesophilic
43398positiveoptimum25-30mesophilic
43398positivegrowth4-38
67772positiveoptimum25-30mesophilic
67772positiveminimum4psychrophilic
67772positivemaximum38mesophilic

culture pH

@refabilitytypepHPH range
43398positivegrowth5-8.5alkaliphile
67772positivemaximum8.5
67772positiveminimum5.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43398
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 43398
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43398NaClpositivegrowth0-12 %
43398NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43398309162-oxoglutarate-oxidation
43398286442-oxopentanoate-oxidation
43398620642,3-butanediol+oxidation
43398181014-hydroxyphenylacetic acid-oxidation
4339830089acetate+oxidation
4339815963ribitol-oxidation
433982509agar-hydrolysis
4339840585alpha-cyclodextrin+oxidation
4339817925alpha-D-glucose+oxidation
4339836219alpha-lactose+oxidation
43398645522-hydroxybutyrate-oxidation
4339827613amygdalin-builds acid from
4339822599arabinose+builds acid from
433988295beta-hydroxybutyrate-oxidation
4339873706bromosuccinate-oxidation
43398casein+hydrolysis
4339862968cellulose-hydrolysis
4339817029chitin-hydrolysis
4339816383cis-aconitate-oxidation
4339816947citrate+oxidation
4339815570D-alanine-oxidation
4339818333D-arabitol-oxidation
4339817057cellobiose+oxidation
4339815824D-fructose+oxidation
4339815895D-galactonic acid lactone-oxidation
4339812936D-galactose+oxidation
4339818024D-galacturonic acid+oxidation
433988391D-gluconate-oxidation
4339817784D-glucosaminic acid-oxidation
4339814314D-glucose 6-phosphate+oxidation
4339815748D-glucuronate-oxidation
4339816899D-mannitol-oxidation
4339816024D-mannose+oxidation
4339828053melibiose+oxidation
4339827605D-psicose-oxidation
4339816634raffinose+oxidation
4339833801D-saccharate-oxidation
4339816523D-serine-oxidation
4339817924D-sorbitol+oxidation
4339816551D-trehalose+oxidation
4339823652dextrin+oxidation
4339817126DL-carnitine+oxidation
4339817113erythritol-oxidation
4339816000ethanolamine+oxidation
4339815740formate-oxidation
4339816865gamma-aminobutyric acid-oxidation
43398167244-hydroxybutyrate-oxidation
433985291gelatin+hydrolysis
4339828066gentiobiose+oxidation
4339817234glucose+builds acid from
4339829042glucose 1-phosphate+oxidation
4339832323glucuronamide-oxidation
4339817754glycerol+oxidation
4339814336glycerol 1-phosphate+oxidation
4339873804glycyl L-aspartic acid+oxidation
4339824741hydroxyproline-oxidation
4339817596inosine-oxidation
4339817268myo-inositol-builds acid from
4339817268myo-inositol-oxidation
4339817240itaconate-oxidation
4339821217L-alaninamide-oxidation
4339816977L-alanine-oxidation
4339873786L-alanylglycine-oxidation
4339830849L-arabinose+oxidation
4339817196L-asparagine-oxidation
4339829991L-aspartate-oxidation
4339818287L-fucose-oxidation
4339829985L-glutamate-oxidation
4339815971L-histidine-oxidation
4339815603L-leucine-oxidation
4339815729L-ornithine-oxidation
4339817295L-phenylalanine-oxidation
4339817203L-proline-oxidation
4339818183L-pyroglutamic acid-oxidation
4339862345L-rhamnose-oxidation
4339817115L-serine-oxidation
4339816857L-threonine+oxidation
4339824996lactate-oxidation
433986359lactulose+oxidation
4339815792malonate-oxidation
4339817306maltose+oxidation
4339837684mannose-builds acid from
4339828053melibiose-builds acid from
4339837657methyl D-glucoside-oxidation
4339851850methyl pyruvate+oxidation
4339875146monomethyl succinate-oxidation
4339828037N-acetylgalactosamine-oxidation
43398506227N-acetylglucosamine-oxidation
4339873784glycyl-l-glutamate-oxidation
4339817632nitrate+reduction
4339850048phenylethylamine-oxidation
4339817272propionate-oxidation
4339817148putrescine-oxidation
4339826490quinate-oxidation
4339826546rhamnose-builds acid from
4339841865sebacic acid-oxidation
4339830911sorbitol-builds acid from
4339828017starch-hydrolysis
43398143136succinamate-oxidation
4339830031succinate-oxidation
4339817992sucrose+builds acid from
4339817992sucrose+oxidation
4339827897tryptophan-energy source
4339832528turanose+oxidation
4339853424tween 20+hydrolysis
4339853423tween 40-oxidation
4339853423tween 40+hydrolysis
4339853426tween 80-oxidation
4339853426tween 80+hydrolysis
4339816704uridine-oxidation
4339827248urocanic acid-oxidation
4339817151xylitol-oxidation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4339823066cephalosporinyesyes
4339848923erythromycinyesyes
4339827902tetracyclineyesyes
4339828971ampicillinyesyes
4339817833gentamicinyesyes
433986104kanamycinyesyes
433987507neomycinyesyes
4339817076streptomycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
4339815688acetoinno
4339835581indoleno
4339816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
4339815688acetoin-
4339835581indole-

enzymes

@refvalueactivityec
43398catalase+1.11.1.6
43398cytochrome oxidase+1.9.3.1
43398gelatinase+
43398alkaline phosphatase+3.1.3.1
43398acid phosphatase+3.1.3.2
43398trypsin+3.4.21.4
43398leucine arylamidase+3.4.11.1
43398valine arylamidase+
43398naphthol-AS-BI-phosphohydrolase+
43398beta-galactosidase+3.2.1.23
43398alpha-glucosidase+3.2.1.20
43398beta-glucosidase+3.2.1.21
43398N-acetyl-beta-glucosaminidase+3.2.1.52
43398arginine dihydrolase-3.5.3.6
43398lysine decarboxylase-4.1.1.18
43398ornithine decarboxylase-4.1.1.17
43398esterase (C 4)-
43398esterase Lipase (C 8)-
43398lipase (C 14)-
43398cystine arylamidase-3.4.11.3
43398alpha-chymotrypsin-3.4.21.1
43398alpha-galactosidase-3.2.1.22
43398beta-glucuronidase-3.2.1.31
43398alpha-mannosidase-3.2.1.24
43398alpha-fucosidase-3.2.1.51
43398tryptophan deaminase-4.1.99.1
433982-nitrophenyl beta-D-galactopyranoside+3.2.1.52

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7685deep-sea sedimentEast China Sea, southern Okinawa Trough areaChinaCHNAsia
67772Deep-sea sedimentSouthern Okinawa Trough (East China Sea)ChinaCHNAsia2005

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3515.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_1827;97_2195;98_2694;99_3515&stattab=map
  • Last taxonomy: Flavobacteriaceae
  • 16S sequence: DQ855467
  • Sequence Identity:
  • Total samples: 6647
  • soil counts: 259
  • aquatic counts: 5051
  • animal counts: 1255
  • plant counts: 82

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76851Risk group (German classification)
677721

Sequence information

16S sequences

  • @ref: 7685
  • description: Zunongwangia profunda strain SMA-87 16S ribosomal RNA gene, partial sequence
  • accession: DQ855467
  • length: 1493
  • database: ena
  • NCBI tax ID: 655815

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zunongwangia profunda SM-A87655815.4completepatric655815
66792Zunongwangia profunda SM-A87646564591completeimg655815
67772Zunongwangia profunda SM-A87 SMA-87GCA_000023465completencbi655815

GC content

@refGC-contentmethod
768535.8
4339835.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.19no
anaerobicno99.589yes
halophileno58.448no
spore-formingno94.891yes
glucose-utilyes88.841no
thermophileno99.749yes
flagellatedno93.537yes
aerobicyes89.369yes
motileno87.786yes
glucose-fermentno90.022no

External links

@ref: 7685

culture collection no.: DSM 18752, CCTCC AB 206139, UCCCB18

straininfo link

  • @ref: 75211
  • straininfo: 400121

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17391365Wangia profunda gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from southern Okinawa Trough deep-sea sediment.Qin QL, Zhao DL, Wang J, Chen XL, Dang HY, Li TG, Zhang YZ, Gao PJFEMS Microbiol Lett10.1111/j.1574-6968.2007.00694.x2007Aerobiosis, Catalase/biosynthesis, China, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/chemistry/*classification/*isolation & purification/physiology, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Oxidoreductases/biosynthesis, Phenotype, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidEnzymology
19477106Biosorption of copper(II) and cadmium(II) by a novel exopolysaccharide secreted from deep-sea mesophilic bacterium.Zhou W, Wang J, Shen B, Hou W, Zhang YColloids Surf B Biointerfaces10.1016/j.colsurfb.2009.04.0182009Biodegradation, Environmental, Cadmium/*chemistry, Copper/*chemistry, Flavobacterium/*chemistry, Polysaccharides, Bacterial/*chemistry, Spectroscopy, Fourier Transform Infrared
Metabolism20398413The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J, Zhang YZBMC Genomics10.1186/1471-2164-11-2472010Cold Temperature, Flavobacteriaceae/classification/*genetics/metabolism, *Genome, Bacterial, Geologic Sediments/*microbiology, Hydrolysis, Nitrogen/*metabolism, Polysaccharides/metabolism, Salinity, Seawater/*microbiology, Sulfur/metabolismGenetics
Metabolism22096500Optimization of fermentation conditions and rheological properties of exopolysaccharide produced by deep-sea bacterium Zunongwangia profunda SM-A87.Liu SB, Qiao LP, He HL, Zhang Q, Chen XL, Zhou WZ, Zhou BC, Zhang YZPLoS One10.1371/journal.pone.00268252011Fermentation/*physiology, Flavobacteriaceae/*metabolism, Hydrogen-Ion Concentration, Polysaccharides, Bacterial/*metabolism, Viscosity
22344657Characterization of bacterial polysaccharide capsules and detection in the presence of deliquescent water by atomic force microscopy.Su HN, Chen ZH, Liu SB, Qiao LP, Chen XL, He HL, Zhao X, Zhou BC, Zhang YZAppl Environ Microbiol10.1128/AEM.00207-122012Flavobacteriaceae/*chemistry, Microscopy, Atomic Force/*methods, Polysaccharides, Bacterial/*analysis, *Water Microbiology
Phylogeny24002475Zunongwangia atlantica sp. nov., isolated from deep-sea water.Shao R, Lai Q, Liu X, Sun F, Du Y, Li G, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.054007-02013Atlantic Ocean, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
Phylogeny24126636Zunongwangia mangrovi sp. nov., isolated from mangrove (Avicennia marina) rhizosphere, and emended description of the genus Zunongwangia.Rameshkumar N, Krishnan R, Lang E, Matsumura Y, Sawabe T, Sawabe TInt J Syst Evol Microbiol10.1099/ijs.0.053512-02013Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Metabolism24872221A novel exopolysaccharide from deep-sea bacterium Zunongwangia profunda SM-A87: low-cost fermentation, moisture retention, and antioxidant activities.Sun ML, Liu SB, Qiao LP, Chen XL, Pang X, Shi M, Zhang XY, Qin QL, Zhou BC, Zhang YZ, Xie BBAppl Microbiol Biotechnol10.1007/s00253-014-5839-82014Antioxidants/isolation & purification/*metabolism, Aquatic Organisms/metabolism, Culture Media/chemistry, Fermentation, Flavobacteriaceae/*metabolism, Hygroscopic Agents/isolation & purification/*metabolism, Polysaccharides, Bacterial/isolation & purification/*metabolismEnzymology
Metabolism25679965Comparative transcriptome analysis reveals that lactose acts as an inducer and provides proper carbon sources for enhancing exopolysaccharide yield in the deep-sea bacterium Zunongwangia profunda SM-A87.Qin QL, Li Y, Sun ML, Rong JC, Liu SB, Chen XL, Su HN, Zhou BC, Xie BB, Zhang YZ, Zhang XYPLoS One10.1371/journal.pone.01159982015Culture Media/chemistry, Flavobacteriaceae/drug effects/*genetics/*metabolism, *Gene Expression Profiling, Lactose/metabolism/*pharmacology, Multigene Family/genetics, Polysaccharides, Bacterial/*metabolism, Up-Regulation/drug effectsPathogenicity
26852104Hyperbranched exopolysaccharide-enhanced foam properties of sodium fatty alcohol polyoxyethylene ether sulfate.Deng Q, Li H, Sun H, Sun Y, Li YColloids Surf B Biointerfaces10.1016/j.colsurfb.2016.01.0502016Ethers/*chemistry, Fatty Alcohols/*chemistry, Hydrogen Bonding, Models, Molecular, Molecular Structure, Polyethylene Glycols/*chemistry, Polysaccharides, Bacterial/*chemistry, Rheology, Solutions/chemistry, Surface Tension, Surface-Active Agents/*chemistry, Viscosity, Water/chemistry
Phylogeny28853694Zunongwangia endophytica sp. nov., an endophyte isolated from the salt marsh plant, Halimione portulacoides, and emended description of the genus Zunongwangia.Fidalgo C, Martins R, Proenca DN, Morais PV, Alves A, Henriques IInt J Syst Evol Microbiol10.1099/ijsem.0.0020692017Amaranthaceae/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsEnzymology
Biotechnology34808314Engineering Cupriavidus necator DSM 545 for the one-step conversion of starchy waste into polyhydroxyalkanoates.Brojanigo S, Gronchi N, Cazzorla T, Wong TS, Basaglia M, Favaro L, Casella SBioresour Technol10.1016/j.biortech.2021.1263832021Biomass, *Cupriavidus necator/genetics, *Polyhydroxyalkanoates, Starch
35930130Structural determination of the lipid A from the deep-sea bacterium Zunongwangia profunda SM-A87: a small-scale approach.Pither MD, Sun ML, Speciale I, Silipo A, Zhang YZ, Molinaro A, Di Lorenzo FGlycoconj J10.1007/s10719-022-10076-62022*Flavobacteriaceae/chemistry, *Lipid A, Lipopolysaccharides, Polysaccharides

Reference

@idauthorscataloguedoi/urltitlejournal
7685Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18752)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18752
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
43398Qi-Long Qin, Dian-Li Zhao, Jing Wang, Xiu-Lan Chen, Hong-Yue Dang, Tie-Gang Li, Yu-Zhong Zhang, Pei-Ji Gao10.1111/j.1574-6968.2007.00694Wangia profunda gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from southern Okinawa Trough deep-sea sedimentFEMS 271: 53-58 2007
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)
67772Curators of the UCCCBhttps://ucccb.uc.pt/
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
75211Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400121.1StrainInfo: A central database for resolving microbial strain identifiers