Strain identifier

BacDive ID: 5424

Type strain: Yes

Species: Amedibacillus dolichus

Strain history: DSM 3991 <-- ATCC 29143 <-- L. Holdeman VPI C9-20.

NCBI tax ID(s): 428127 (strain), 31971 (species)

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General

@ref: 1561

BacDive-ID: 5424

DSM-Number: 3991

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

description: Amedibacillus dolichus DSM 3991 is an anaerobe, mesophilic bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
428127strain
31971species

strain history

@refhistory
1561<- ATCC <- L.V. Holdeman, VPI C9-20
67770DSM 3991 <-- ATCC 29143 <-- L. Holdeman VPI C9-20.

doi: 10.13145/bacdive5424.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Erysipelotrichaceae
  • genus: Amedibacillus
  • species: Amedibacillus dolichus
  • full scientific name: Amedibacillus dolichus (Moore et al. 1976) Ikeyama et al. 2020
  • synonyms

    @refsynonym
    20215Absiella dolichum
    20215Eubacterium dolichum

@ref: 1561

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Clostridiales

family: Erysipelotrichaceae

genus: Amedibacillus

species: Amedibacillus dolichus

full scientific name: Amedibacillus dolichus (Moore et al. 1976) Ikeyama et al. 2020

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 1561
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 0.0001 g/l NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
1561positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 1561
  • oxygen tolerance: anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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 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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1561-+-------+--+----------------

Isolation, sampling and environmental information

isolation

@refsample type
1561human faeces
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6349.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_135;96_3016;97_3705;98_4694;99_6349&stattab=map
  • Last taxonomy: Amedibacillus dolichus subclade
  • 16S sequence: L34682
  • Sequence Identity:
  • Total samples: 42904
  • soil counts: 239
  • aquatic counts: 861
  • animal counts: 41686
  • plant counts: 118

Safety information

risk assessment

  • @ref: 1561
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218[Eubacterium] dolichum strain ATCC 29143 16S ribosomal RNA gene, partial sequenceL346821486ena428127
20218Eubacterium dolichum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10413AB6492771490ena31971

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Eubacterium dolichum DSM 3991428127.7wgspatric428127
66792Amedibacillus dolichus DSM 3991641380446draftimg428127
67770Amedibacillus dolichus DSM 3991GCA_000154285scaffoldncbi428127

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes95.11no
anaerobicyes97.939yes
halophileno66.226no
spore-formingno84.733no
glucose-utilyes87.765no
aerobicno98.685no
flagellatedno97.908no
thermophileno97.926no
motileno92.7no
glucose-fermentyes73.972no

External links

@ref: 1561

culture collection no.: DSM 3991, ATCC 29143, VPI C9-20, JCM 10413

straininfo link

  • @ref: 74912
  • straininfo: 39376

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny32416738Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov.Ikeyama N, Toyoda A, Morohoshi S, Kunihiro T, Murakami T, Mori H, Iino T, Ohkuma M, Sakamoto MInt J Syst Evol Microbiol10.1099/ijsem.0.0042152020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Eubacterium/classification, Fatty Acids/chemistry, Feces/*microbiology, Firmicutes/*classification/isolation & purification, Humans, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny33083133Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces.Ghimire S, Wongkuna S, Scaria JPeerJ10.7717/peerj.100712020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1561Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3991)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3991
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
74912Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39376.1StrainInfo: A central database for resolving microbial strain identifiers