Strain identifier

BacDive ID: 17123

Type strain: Yes

Species: Dialister micraerophilus

Strain history: CIP <- 2004, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 25-04 <- H. Marchandin, Montpellier Hosp., Montpellier: strain ADV 04-01

NCBI tax ID(s): 888062 (strain), 309120 (species)

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General

@ref: 8410

BacDive-ID: 17123

DSM-Number: 19965

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

description: Dialister micraerophilus DSM 19965 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human amniotic fluid.

NCBI tax id

NCBI tax idMatching level
888062strain
309120species

strain history

@refhistory
8410<- CCUG; CCUG 48837 <- CIP; CIP 108278 <- J.-P. Carlier; AIP 25.04 <- H. Marchandin; ADV 04.01
67770CCUG 48837 <-- CIP 108278 <-- J. P. Carlier AIP 25.04 <-- H. Marchandin ADV 04.01.
120945CIP <- 2004, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 25-04 <- H. Marchandin, Montpellier Hosp., Montpellier: strain ADV 04-01

doi: 10.13145/bacdive17123.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Veillonellales
  • family: Veillonellaceae
  • genus: Dialister
  • species: Dialister micraerophilus
  • full scientific name: Dialister micraerophilus Jumas-Bilak et al. 2005

@ref: 8410

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Dialister

species: Dialister micraerophilus

full scientific name: Dialister micraerophilus Jumas-Bilak et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31511negative0.45 µm0.3 µmovoid-shapedno
69480no94.399
69480negative99.806
120945negativerod-shapedno

colony morphology

@refincubation period
583522-3 days
120945

pigmentation

  • @ref: 31511
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8410COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8410DIALISTER MEDIUM (DSMZ Medium 1107)yeshttps://mediadive.dsmz.de/medium/1107Name: DIALISTER MEDIUM (DSMZ Medium 1107) Composition: Trypticase 14.1667 g/l KNO3 2.5 g/l NaCl 2.5 g/l Yeast extract 2.5 g/l Ethanol 0.0791667 g/l Na-L-lactate 0.05 g/l Glucose 0.04 g/l Na-fumarate 0.03 g/l Na-formate 0.03 g/l NaHCO3 0.01 g/l Cystein-HCl x 2 H2O 0.0025 g/l DTT 0.000771255 g/l Vitamin K1 Horse blood Haemin Distilled water
8410FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203.pdf
38266MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
120945CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8410positivegrowth37mesophilic
38266positivegrowth37mesophilic
58352positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8410anaerobe
31511anaerobe
58352anaerobe
69480anaerobe96.827

spore formation

@refspore formationconfidence
31511no
69481no100
69480no99.998

observation

  • @ref: 31511
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3151129016arginine+carbon source
3151128044phenylalanine+carbon source
3151117822serine+carbon source
12094517108D-arabinose-degradation
12094515824D-fructose-degradation
12094517634D-glucose-degradation
12094565327D-xylose-degradation
12094517057cellobiose-degradation
12094517716lactose-degradation
12094517306maltose-degradation
12094517814salicin-degradation
12094517992sucrose-degradation
1209454853esculin-hydrolysis
12094517632nitrate-reduction
12094516301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine+hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12094535581indoleno
6838035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucyl glycin arylamidase-3.4.11.1
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 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase+3.5.3.6
68380urease-3.5.1.5
120945oxidase-
120945beta-galactosidase-3.2.1.23
120945gelatinase-
120945catalase-1.11.1.6
120945urease-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
120945--+-------+---+-----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8410-+---------------+--++-+--+-+
8410-+---------------+/-+-+/-+/--+-+/-+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
8410human amniotic fluidFranceFRAEurope
58352Human amniotic fluid,38-yr-old womanFranceFRAEurope2001Montpellier
67770Human clinical sample (amniotic fluid)
120945Amniotic liquidFranceFRAEuropeMontpellier2001

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Urogenital tract#Amniotic fluid
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_4752.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_217;96_2351;97_2862;98_3561;99_4752&stattab=map
  • Last taxonomy: Dialister micraerophilus subclade
  • 16S sequence: AF473837
  • Sequence Identity:
  • Total samples: 25936
  • soil counts: 431
  • aquatic counts: 251
  • animal counts: 25214
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84102Risk group (German classification)
1209451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8410Dialister micraerophilus strain ADV 04.01 16S ribosomal RNA gene, partial sequenceAF4738371440ena888062
67770Dialister micraerophilus gene for 16S ribosomal RNA, partial sequenceAB6266331528ena309120

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dialister micraerophilus DSM 19965888062.3wgspatric888062
66792Dialister micraerophilus DSM 19965651324025draftimg888062
67770Dialister micraerophilus DSM 19965GCA_000194985scaffoldncbi888062

GC content

@refGC-contentmethod
841036.3high performance liquid chromatography (HPLC)
3151136.3
6777035.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.387yes
flagellatedno97.007yes
gram-positiveno93.895yes
anaerobicyes98.629yes
halophileno58.052no
spore-formingno93.908yes
thermophileno97.437yes
glucose-utilyes61.445no
aerobicno97.637no
glucose-fermentno57.861no

External links

@ref: 8410

culture collection no.: DSM 19965, CCUG 48837, CIP 108278, ADV 04.01, AIP 25.04, JCM 17567, ADV 04-01, AIP 25-04

straininfo link

  • @ref: 86123
  • straininfo: 214948

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280512Dialister micraerophilus sp. nov. and Dialister propionicifaciens sp. nov., isolated from human clinical samples.Jumas-Bilak E, Jean-Pierre H, Carlier JP, Teyssier C, Bernard K, Gay B, Campos J, Morio F, Marchandin HInt J Syst Evol Microbiol10.1099/ijs.0.63715-02005Humans, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/genetics, Veillonellaceae/*classification/genetics/isolation & purificationPathogenicity
Phylogeny31661048Dialister hominis sp. nov., isolated from human faeces.Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Iino T, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0037972020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Feces/*microbiology, Female, Humans, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Veillonellaceae/*classification/isolation & purificationPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8410Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19965)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19965
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
31511Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780728776041
38266Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5892
58352Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48837)https://www.ccug.se/strain?id=48837
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/
68380Automatically annotated from API rID32A
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
86123Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID214948.1StrainInfo: A central database for resolving microbial strain identifiers
120945Curators of the CIPCollection of Institut Pasteur (CIP 108278)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108278