Strain identifier

BacDive ID: 3776

Type strain: Yes

Species: Dyadobacter fermentans

Strain Designation: NS 114, NS114

Strain history: CIP <- 2001, M. K. Chelius, Univ. Wisconsin-Madison, USA: strain NS114

NCBI tax ID(s): 471854 (strain), 94254 (species)

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General

@ref: 7272

BacDive-ID: 3776

DSM-Number: 18053

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, mesophilic, Gram-negative, coccus-shaped

description: Dyadobacter fermentans NS 114 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from surface sterilized stems of Zea mays.

NCBI tax id

NCBI tax idMatching level
94254species
471854strain

strain history

@refhistory
7272<- CIP <- M. K. Chelius, Univ. Wisconsin, USA; NS 114
119308CIP <- 2001, M. K. Chelius, Univ. Wisconsin-Madison, USA: strain NS114

doi: 10.13145/bacdive3776.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Dyadobacter
  • species: Dyadobacter fermentans
  • full scientific name: Dyadobacter fermentans Chelius and Triplett 2000

@ref: 7272

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter fermentans

full scientific name: Dyadobacter fermentans Chelius and Triplett 2000 emend. Hahnke et al. 2016

strain designation: NS 114, NS114

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43374negative0.75-2 µmcoccus-shapedno
69480no91.348
69480negative99.992
119308negativerod-shapedno

colony morphology

  • @ref: 43374
  • colony color: yellow

pigmentation

  • @ref: 119308
  • production: no
  • name: Flexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_18053_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7272REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
39632MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
43374Reasoner's 2A agar (R2A)yes
43374YM brothyes
43374AcD (nitrogen-limited agar)yescontaining 10 p.p.m nitrogen and Litmus milk
43374Ayers mediumyes
119308CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
7272positivegrowth28mesophilic
39632positivegrowth30mesophilic
43374nogrowth4psychrophilic
43374positivegrowth15-37
43374positivemaximum37mesophilic
119308positivegrowth30mesophilic
119308nogrowth5psychrophilic
119308nogrowth15psychrophilic
119308nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43374aerobe
119308obligate aerobe

nutrition type

  • @ref: 43374
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
43374NaClpositivegrowth1.5 %
119308NaClpositivegrowth0-6 %
119308NaClnogrowth8 %
119308NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43374168082-dehydro-D-gluconate-carbon source
43374581435-dehydro-D-gluconate+growth
43374581435-dehydro-D-gluconate+carbon source
4337430089acetate+growth
4337430089acetate+carbon source
4337415963ribitol-carbon source
433742509agar-degradation
4337427613amygdalin+carbon source
4337418305arbutin+carbon source
4337417057cellobiose+carbon source
4337462968cellulose-degradation
4337417108D-arabinose+carbon source
4337418333D-arabitol+growth
4337418333D-arabitol+carbon source
4337415824D-fructose+carbon source
4337428847D-fucose+carbon source
4337417634D-glucose+carbon source
4337462318D-lyxose+growth
4337462318D-lyxose+carbon source
4337416634raffinose+carbon source
4337416443D-tagatose+carbon source
4337432528turanose+carbon source
4337465327D-xylose+carbon source
4337425115malate+growth
4337425115malate+carbon source
4337416813galactitol+/-growth
4337416813galactitol+/-carbon source
4337417113erythritol+carbon source
433744853esculin+carbon source
4337429806fumarate+growth
4337429806fumarate+carbon source
4337428260galactose+carbon source
433745291gelatin-degradation
4337428066gentiobiose+carbon source
4337424265gluconate-carbon source
4337417234glucose+builds acid from
4337417234glucose+fermentation
4337417754glycerol+/-growth
4337417754glycerol+/-carbon source
4337428087glycogen-growth
4337428087glycogen-carbon source
4337417268myo-inositol+growth
4337417268myo-inositol+carbon source
4337415443inulin+carbon source
4337430849L-arabinose+carbon source
4337418403L-arabitol+/-growth
4337418403L-arabitol+/-carbon source
4337418287L-fucose+carbon source
4337465328L-xylose+carbon source
4337417716lactose+carbon source
4337415792malonate+growth
4337415792malonate+carbon source
4337417306maltose+carbon source
4337429864mannitol+growth
4337429864mannitol+carbon source
4337437684mannose+carbon source
433746731melezitose+carbon source
4337428053melibiose+carbon source
4337417790methanol-growth
4337417790methanol-carbon source
4337443943methyl alpha-D-mannoside+carbon source
4337474863methyl beta-D-xylopyranoside+carbon source
4337437657methyl D-glucoside+carbon source
43374506227N-acetylglucosamine+carbon source
4337417632nitrate-electron acceptor
43374peptone+growth
4337426546rhamnose+carbon source
4337433942ribose+builds acid from
4337417992sucrose+carbon source
4337417814salicin+carbon source
4337430911sorbitol+/-growth
4337430911sorbitol+/-carbon source
4337427922sorbose+growth
4337427922sorbose+carbon source
4337428017starch-degradation
4337428017starch+growth
4337428017starch+carbon source
4337417992sucrose+builds acid from
4337417992sucrose+fermentation
4337430929tartrate+growth
4337430929tartrate+carbon source
4337427082trehalose+carbon source
4337417151xylitol+carbon source
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin+builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11930816947citrate-carbon source
1193084853esculin+hydrolysis
11930817234glucose-fermentation
11930817632nitrate-reduction
11930816301nitrite-reduction
119308132112sodium thiosulfate-builds gas from
11930817234glucose+/-degradation
11930817632nitrate-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
433746104kanamycinyesyes50 µg/mL
4337428971ampicillinyesyes25 µg/mL
4337417698chloramphenicolyesyes25 µg/mL
4337445924trimethoprimyesyes25 µg/mL
433749215spectinomycinyesyes10 µg/mL
4337417076streptomycinyesyes10 µg/mL
4337428077rifampicinyesno25 µg/mL
4337427902tetracyclineyesno10 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11930835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11930815688acetoin-
11930817234glucose-

enzymes

@refvalueactivityec
43374catalase+1.11.1.6
43374cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119308oxidase+
119308beta-galactosidase+3.2.1.23
119308alcohol dehydrogenase-1.1.1.1
119308gelatinase-
119308amylase-
119308DNase-
119308caseinase-3.4.21.50
119308catalase+1.11.1.6
119308tween esterase-
119308gamma-glutamyltransferase+2.3.2.2
119308lecithinase-
119308lipase-
119308lysine decarboxylase-4.1.1.18
119308ornithine decarboxylase-4.1.1.17
119308phenylalanine ammonia-lyase-4.3.1.24
119308tryptophan deaminase-
119308urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119308-+++-++++-++-+-++++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7272-----+-++++-++------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119308--++-----++++-+----++++++++++++++++---+++--+----+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119308------------+----++--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
7272surface sterilized stems of Zea maysZea maysUSAUSANorth America
43374surface-sterilized Zea mays stems
119308Surface sterilized Zea mays stemsUnited States of AmericaUSANorth America1998

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_5763.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_2412;97_2936;98_3670;99_5763&stattab=map
  • Last taxonomy: Dyadobacter
  • 16S sequence: AF137029
  • Sequence Identity:
  • Total samples: 3843
  • soil counts: 517
  • aquatic counts: 233
  • animal counts: 2781
  • plant counts: 312

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72721Risk group (German classification)
1193081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7272
  • description: Dyadobacter fermentans 16S ribosomal RNA gene, partial sequence
  • accession: AF137029
  • length: 1393
  • database: ena
  • NCBI tax ID: 471854

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter fermentans DSM 18053GCA_000023125completencbi471854
66792Dyadobacter fermentans DSM 18053471854.5completepatric471854
66792Dyadobacter fermentans NS114, DSM 18053644736356completeimg471854

GC content

@refGC-contentmethod
727248
727251.5sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.871no
flagellatedno97.199no
gram-positiveno97.771yes
anaerobicno99.348yes
aerobicyes90.993yes
halophileno94.29yes
spore-formingno93.342no
thermophileno98.966yes
glucose-utilyes87.554yes
glucose-fermentno87.743no

External links

@ref: 7272

culture collection no.: DSM 18053, ATCC 700827, CIP 107007, KCTC 52180

straininfo link

  • @ref: 73288
  • straininfo: 44159

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392220Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China.Dong Z, Guo X, Zhang X, Qiu F, Sun L, Gong H, Zhang FInt J Syst Evol Microbiol10.1099/ijs.0.64754-02007China, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny20008109Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil.Lee M, Woo SG, Park J, Yoo SAInt J Syst Evol Microbiol10.1099/ijs.0.019653-02009Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Starch/*metabolismMetabolism
Phylogeny23291764Identification and characterization of cellobiose 2-epimerases from various aerobes.Ojima T, Saburi W, Yamamoto T, Mori H, Matsui HBiosci Biotechnol Biochem10.1271/bbb.1207422013Aerobiosis, Bacteria, Aerobic/chemistry/*enzymology, Bacterial Proteins/classification/*isolation & purification/*metabolism, Carbohydrate Epimerases/classification/*isolation & purification/*metabolism, Cellobiose/*metabolism, Enzyme Assays, Enzyme Stability, Escherichia coli/genetics, Glucose/metabolism, Hydrogen-Ion Concentration, Isoenzymes/classification/isolation & purification/metabolism, Kinetics, Lactose/metabolism, Mannose/metabolism, Phylogeny, Recombinant Proteins/classification/isolation & purification/metabolism, Species Specificity, Stereoisomerism, Substrate Specificity, TemperatureEnzymology
Phylogeny25604339Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory.Wang L, Chen L, Ling Q, Li CC, Tao Y, Wang MInt J Syst Evol Microbiol10.1099/ijs.0.0000692015Azo Compounds/*metabolism, Bacterial Typing Techniques, Base Composition, China, Coloring Agents/metabolism, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism
Phylogeny27412002Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root.Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JGInt J Syst Evol Microbiol10.1099/ijsem.0.0013042016Bacterial Typing Techniques, Base Composition, Beijing, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7272Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18053)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18053
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
39632Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19201
43374Marisa K. Chelius, Eric W. Triplett10.1099/00207713-50-2-751Dyadobacter fermentans gen. nov., sp. nov., a novel Gram-negative bacterium isolated from surface-sterilized Zea mays stemsIJSEM 50: 751-758 200010758885
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73288Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44159.1StrainInfo: A central database for resolving microbial strain identifiers
119308Curators of the CIPCollection of Institut Pasteur (CIP 107007)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107007