Strain identifier

BacDive ID: 17402

Type strain: Yes

Species: Ancylobacter rudongensis

Strain Designation: YCM 11671

Strain history: CIP <- 2004, JCM <- 2002, AS <- Y.H. Xin

NCBI tax ID(s): 177413 (species)

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General

@ref: 6778

BacDive-ID: 17402

DSM-Number: 17131

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

description: Ancylobacter rudongensis YCM 11671 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of Spartina anglica.

NCBI tax id

  • NCBI tax id: 177413
  • Matching level: species

strain history

@refhistory
6778<- JCM <- H.L. Zhou, Chin. Academy of Sciences, Beijing; AS 1.1761
67770AS 1.1761 <-- Y. H. Xin.
122301CIP <- 2004, JCM <- 2002, AS <- Y.H. Xin

doi: 10.13145/bacdive17402.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Xanthobacteraceae
  • genus: Ancylobacter
  • species: Ancylobacter rudongensis
  • full scientific name: Ancylobacter rudongensis Xin et al. 2004

@ref: 6778

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Ancylobacter

species: Ancylobacter rudongensis

full scientific name: Ancylobacter rudongensis Xin et al. 2004

strain designation: YCM 11671

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29894negativerod-shapedno
69480negative99.98
122301negativerod-shapedyes

colony morphology

  • @ref: 122301

pigmentation

  • @ref: 29894
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6778R2A 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
39992MEDIUM 593 - for Ancylobacter rudongensisyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (1.000g);Yeast extract (1.000 g);Peptone (1.000 g)
122301CIP Medium 289yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=289

culture temp

@refgrowthtypetemperaturerange
6778positivegrowth30mesophilic
29894positivegrowth05-44
29894positiveoptimum29mesophilic
39992positivegrowth30mesophilic
67770positivegrowth30mesophilic
122301positivegrowth15-37
122301nogrowth10psychrophilic
122301nogrowth41thermophilic
122301nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
29894positivegrowth5.6-9.9alkaliphile
29894positiveoptimum6.9

Physiology and metabolism

oxygen tolerance

  • @ref: 122301
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
29894NaClpositivegrowth0-5 %
29894NaClpositiveoptimum2.5 %
122301NaClpositivegrowth0-4 %
122301NaClnogrowth6 %
122301NaClnogrowth8 %
122301NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2989415963ribitol+carbon source
2989416449alanine+carbon source
2989422599arabinose+carbon source
2989417057cellobiose+carbon source
2989423652dextrin+carbon source
2989428757fructose+carbon source
2989428260galactose+carbon source
2989417234glucose+carbon source
2989417754glycerol+carbon source
2989417716lactose+carbon source
2989417306maltose+carbon source
2989429864mannitol+carbon source
2989428053melibiose+carbon source
2989426271proline+carbon source
2989433942ribose+carbon source
2989430911sorbitol+carbon source
2989417992sucrose+carbon source
2989427082trehalose+carbon source
2989418222xylose+carbon source
298944853esculin+hydrolysis
2989417632nitrate+reduction
12230116947citrate+carbon source
1223014853esculin+hydrolysis
122301606565hippurate-hydrolysis
12230117632nitrate-reduction
12230116301nitrite-reduction
12230117632nitrate-respiration

antibiotic resistance

  • @ref: 122301
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122301
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12230115688acetoin-
12230117234glucose-

enzymes

@refvalueactivityec
122301oxidase+
122301beta-galactosidase+3.2.1.23
122301alcohol dehydrogenase-1.1.1.1
122301gelatinase-
122301amylase-
122301DNase-
122301caseinase-3.4.21.50
122301catalase+1.11.1.6
122301tween esterase+
122301gamma-glutamyltransferase+2.3.2.2
122301lecithinase-
122301lipase-
122301lysine decarboxylase-4.1.1.18
122301ornithine decarboxylase-4.1.1.17
122301phenylalanine ammonia-lyase-4.3.1.24
122301protease-
122301tryptophan deaminase-
122301urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122301-++--++-+-++----+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122301+++---------------+-++----+-+--+-+--++------------+--+------+--------------+---+--+------------++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6778roots of Spartina anglicaSpartina anglicaJiangsu Province, beachChinaCHNAsia
67770Roots of Spartina anglica in Rudong CountrySpartina anglicaJiangsu ProvinceChinaCHNAsia
122301Plant, Root of Spartina anglica

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6269.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_2984;97_3669;98_4644;99_6269&stattab=map
  • Last taxonomy: Ancylobacter
  • 16S sequence: AY056830
  • Sequence Identity:
  • Total samples: 6101
  • soil counts: 1085
  • aquatic counts: 2318
  • animal counts: 1936
  • plant counts: 762

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67781Risk group (German classification)
1223011Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6778
  • description: Ancylobacter sp. AS1.1761 16S ribosomal RNA gene, partial sequence
  • accession: AY056830
  • length: 1457
  • database: ena
  • NCBI tax ID: 177413

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ancylobacter rudongensis strain CGMCC 1.1761177413.3wgspatric177413
66792Ancylobacter rudongensis CGMCC 1.17612596583652draftimg177413
67770Ancylobacter rudongensis CGMCC 1.1761GCA_900100155contigncbi177413

GC content

@refGC-contentmethod
2989468.2
6777068.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes61.966yes
gram-positiveno98.327yes
anaerobicno97.94no
aerobicyes91.045no
halophileno86.984no
spore-formingno95.771no
thermophileno96.744no
glucose-utilyes93.01yes
flagellatedno58.906no
glucose-fermentno90.613no

External links

@ref: 6778

culture collection no.: DSM 17131, AS 1.1761, JCM 11671, BCRC 17434, CGMCC 1.1761, CIP 108316, NCIMB 14355

straininfo link

  • @ref: 86400
  • straininfo: 131414

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023948Ancylobacter rudongensis sp. nov., isolated from roots of Spartina anglica.Xin YH, Zhou YG, Zhou HL, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.02466-02004Base Sequence, China, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Plant Roots/*microbiology, Poaceae/*microbiology, Polymerase Chain Reaction, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny16738088Ancylobacter polymorphus sp. nov. and Ancylobacter vacuolatus sp. nov.Xin YH, Zhou YG, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.64118-02006Alphaproteobacteria/*classification/cytology/*genetics/growth & development, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18768594Description of Ancylobacter oerskovii sp. nov. and two additional strains of Ancylobacter polymorphus.Lang E, Swiderski J, Stackebrandt E, Schumann P, Sproer C, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.65666-02008Alphaproteobacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny28945527Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg.Suarez C, Ratering S, Schafer J, Schnell SInt J Syst Evol Microbiol10.1099/ijsem.0.0023202017Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Phospholipids/chemistry, *Phylogeny, Plantago/growth & development/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salt-Tolerant Plants/growth & development/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6778Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17131)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17131
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
29894Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2626728776041
39992Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5925
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)
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86400Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131414.1StrainInfo: A central database for resolving microbial strain identifiers
122301Curators of the CIPCollection of Institut Pasteur (CIP 108316)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108316