Strain identifier

BacDive ID: 132260

Type strain: Yes

Species: Dysgonomonas alginatilytica

Strain Designation: HUA-2

Strain history: <- A. Kita, Hiroshima Univ., Grad. School of Adv. Sciences of Matter; HUA-2

NCBI tax ID(s): 1605892 (species)

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General

@ref: 24049

BacDive-ID: 132260

DSM-Number: 100214

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Dysgonomonas alginatilytica HUA-2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from alginate-degrading microbial consortium acclimated from sea sand.

NCBI tax id

  • NCBI tax id: 1605892
  • Matching level: species

strain history

  • @ref: 24049
  • history: <- A. Kita, Hiroshima Univ., Grad. School of Adv. Sciences of Matter; HUA-2

doi: 10.13145/bacdive132260.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Dysgonomonadaceae
  • genus: Dysgonomonas
  • species: Dysgonomonas alginatilytica
  • full scientific name: Dysgonomonas alginatilytica Kita et al. 2015

@ref: 24049

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Dysgonomonadaceae

genus: Dysgonomonas

species: Dysgonomonas alginatilytica

full scientific name: Dysgonomonas alginatilytica Kita et al. 2015

strain designation: HUA-2

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.988

Culture and growth conditions

culture medium

  • @ref: 24049
  • name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/693
  • composition: Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

  • @ref: 24049
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 99.319

spore formation

@refspore formationconfidence
69481no100
69480no99.985

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose+builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea+hydrolysis
6838016199urea+hydrolysis
6838029016arginine+hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase+3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase+3.5.3.6
68380urease+3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease+3.5.1.5

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
24049++-++++/-+--+-++-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24049+++++/-+++-+++-+--+--+----+--+-

Isolation, sampling and environmental information

isolation

  • @ref: 24049
  • sample type: alginate-degrading microbial consortium acclimated from sea sand
  • geographic location: Hiroshima
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Plants#Decomposing plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_170292.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_77;96_2454;97_2995;98_15704;99_170292&stattab=map
  • Last taxonomy: Dysgonomonas alginatilytica subclade
  • 16S sequence: LC021528
  • Sequence Identity:
  • Total samples: 32
  • aquatic counts: 14
  • animal counts: 16
  • plant counts: 2

Safety information

risk assessment

  • @ref: 24049
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24049
  • description: Dysgonomonas alginatilytica gene for 16S ribosomal RNA, partial sequence, strain: HUA-2
  • accession: LC021528
  • length: 1450
  • database: ena
  • NCBI tax ID: 1605892

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dysgonomonas alginatilytica DSM 100214GCA_003201355scaffoldncbi1605892
66792Dysgonomonas alginatilytica strain DSM 1002141605892.4wgspatric1605892
66792Dysgonomonas alginatilytica DSM 1002142731639221draftimg1605892

GC content

  • @ref: 24049
  • GC-content: 37.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.671no
gram-positiveno96.266no
anaerobicyes89.221no
halophileno95.103no
spore-formingno92.818no
glucose-utilyes87.244no
aerobicno91.392no
thermophileno99.854yes
motileno91.037no
glucose-fermentyes64.948no

External links

@ref: 24049

culture collection no.: DSM 100214, HUT 8134

straininfo link

  • @ref: 90609
  • straininfo: 406906

literature

  • topic: Phylogeny
  • Pubmed-ID: 26297040
  • title: Dysgonomonas alginatilytica sp. nov., an alginate-degrading bacterium isolated from a microbial consortium.
  • authors: Kita A, Miura T, Okamura Y, Aki T, Matsumura Y, Tajima T, Kato J, Nakashimada Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000459
  • year: 2015
  • mesh: Alginates/*metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Japan, *Microbial Consortia, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Metabolism

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
24049Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100214Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100214)
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
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
90609Reimer, 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-ID406906.1