Strain identifier

BacDive ID: 6156

Type strain: Yes

Species: Ancylobacter amanitiformis

Strain history: CIP <- 2005, NCIMB <- I. Frits, MPI, Bremen <- W. R. Abraham and C. Ströpl <- R. Whittenbury and J. M. Nicoll: strain VKM B-1336

NCBI tax ID(s): 217069 (species)

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General

@ref: 6002

BacDive-ID: 6156

DSM-Number: 15561

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Ancylobacter amanitiformis DSM 15561 is an aerobe, mesophilic bacterium that was isolated from fresh water pond.

NCBI tax id

  • NCBI tax id: 217069
  • Matching level: species

strain history

@refhistory
6002<- I. Fritz, MPI, Bremen <- W. R. Abraham and C. Strömpl <- R. Whittenbury and J. M. Nicoll
116320CIP <- 2005, NCIMB <- I. Frits, MPI, Bremen <- W. R. Abraham and C. Ströpl <- R. Whittenbury and J. M. Nicoll: strain VKM B-1336

doi: 10.13145/bacdive6156.20230509.8.1

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 amanitiformis
  • full scientific name: Ancylobacter amanitiformis (Fritz et al. 2004) Doronina et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Angulomicrobium amanitiforme

@ref: 6002

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Angulomicrobium

species: Angulomicrobium amanitiforme

full scientific name: Angulomicrobium amanitiforme Fritz et al. 2004

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthmotilitygram stain
299601.5 µm1 µmno
116320nonegative

pigmentation

  • @ref: 116320
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6002R2A 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
6002NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37646MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116320CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
6002positivegrowth30mesophilic
29960positivegrowth15-40
29960positiveoptimum29mesophilic
37646positivegrowth30mesophilic
116320positivegrowth10-37
116320nogrowth5psychrophilic
116320nogrowth41thermophilic

culture pH

@refabilitytypepH
29960positivegrowth5.2-8.0
29960positiveoptimum6.9

Physiology and metabolism

oxygen tolerance

  • @ref: 29960
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29960
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
116320NaClpositivegrowth0-2 %
116320NaClnogrowth4 %
116320NaClnogrowth6 %
116320NaClnogrowth8 %
116320NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2996030089acetate+carbon source
2996022599arabinose+carbon source
2996016947citrate+carbon source
2996015740formate+carbon source
2996028757fructose+carbon source
2996028260galactose+carbon source
2996017234glucose+carbon source
2996017754glycerol+carbon source
2996024996lactate+carbon source
2996029864mannitol+carbon source
2996017272propionate+carbon source
2996033942ribose+carbon source
2996017822serine+carbon source
2996030031succinate+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-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
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
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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117113erythritol-builds acid from
11632016947citrate-carbon source
1163204853esculin+hydrolysis
11632017632nitrate-reduction
11632016301nitrite-reduction
11632017632nitrate-respiration

metabolite production

  • @ref: 116320
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29960catalase+1.11.1.6
29960cytochrome 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
116320oxidase+
116320beta-galactosidase+3.2.1.23
116320alcohol dehydrogenase-1.1.1.1
116320gelatinase-
116320amylase+
116320DNase-
116320caseinase-3.4.21.50
116320catalase+1.11.1.6
116320tween esterase-
116320lecithinase-
116320lipase-
116320lysine decarboxylase-4.1.1.18
116320ornithine decarboxylase-4.1.1.17
116320tryptophan deaminase-
116320urease+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
116320-++--+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116320+/--+/-+/--+/----+/-+/-------+/-------+/-------------+/-----+/-+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116320+-+-----------------++--+-+-+--+-+--++-----------+----++----+----------+---+--+++-+-----+----+-++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6002fresh water pondScotlandUnited KingdomGBREurope
116320Environment, Fresh water pondUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Pond (small)

taxonmaps

  • @ref: 69479
  • File name: preview.99_141378.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_2984;97_3669;98_93938;99_141378&stattab=map
  • Last taxonomy: Xanthobacteraceae
  • 16S sequence: AJ535709
  • Sequence Identity:
  • Total samples: 258
  • soil counts: 12
  • aquatic counts: 52
  • animal counts: 170
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60021Risk group (German classification)
1163201Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6002
  • description: Angulomicrobium amanitiformis 16S rRNA gene, type strain NCIMB 1785T
  • accession: AJ535709
  • length: 1409
  • database: ena
  • NCBI tax ID: 217069

Genome sequences

  • @ref: 66792
  • description: Angulomicrobium amanitiforme DSM 15561
  • accession: 2928225989
  • assembly level: draft
  • database: img
  • NCBI tax ID: 217069

GC content

  • @ref: 29960
  • GC-content: 67.7

External links

@ref: 6002

culture collection no.: DSM 15561, NCIMB 1785, CIP 108770, VKM B-1336

straininfo link

  • @ref: 75642
  • straininfo: 59129

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143003Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov.Fritz I, Strompl C, Abraham WRInt J Syst Evol Microbiol10.1099/ijs.0.02746-02004Acetobacteraceae/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Hyphomicrobiaceae/*classification/genetics/metabolism, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny17012571Starkeya koreensis sp. nov., isolated from rice straw.Im WT, Aslam Z, Lee M, Ten LN, Yang DC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64093-02006Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6002Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15561)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15561
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
29960Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2632928776041
37646Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6435
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)
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
75642Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID59129.1StrainInfo: A central database for resolving microbial strain identifiers
116320Curators of the CIPCollection of Institut Pasteur (CIP 108770)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108770