Strain identifier

BacDive ID: 98

Type strain: Yes

Species: Acidaminococcus fermentans

Strain Designation: VR4

Strain history: CIP <- 2000, CCUG <- 1985, ATCC <- M. Rogosa: strain VR4 <- R. Fuller

NCBI tax ID(s): 591001 (strain), 905 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 9041

BacDive-ID: 98

DSM-Number: 20731

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

description: Acidaminococcus fermentans VR4 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from pig gut.

NCBI tax id

NCBI tax idMatching level
905species
591001strain

strain history

@refhistory
9041<- ATCC <- M. Rogosa, VR4 <- R. Fuller
119306CIP <- 2000, CCUG <- 1985, ATCC <- M. Rogosa: strain VR4 <- R. Fuller

doi: 10.13145/bacdive98.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Acidaminococcales
  • family: Acidaminococcaceae
  • genus: Acidaminococcus
  • species: Acidaminococcus fermentans
  • full scientific name: Acidaminococcus fermentans Rogosa 1969 (Approved Lists 1980)

@ref: 9041

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Acidaminococcaceae

genus: Acidaminococcus

species: Acidaminococcus fermentans

full scientific name: Acidaminococcus fermentans Rogosa 1969 emend. Cook et al. 1994

strain designation: VR4

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.743
119306negativecoccus-shapedno

colony morphology

  • @ref: 119306

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20731_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42016MEDIUM 348 - for AcidaminococcusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (5.000g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (2.000 g);Tween 80 (0.500 ml);Tryptone (5.000 g);Sodium glutamate (4.000 g);Casamino acids (10.000 g);Cysteine hydrochloride
9041COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
9041ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414)yesName: ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414) Composition: Casamino acids 10.0 g/l Yeast extract 5.0 g/l Trypticase peptone 5.0 g/l Glucose 5.0 g/l Na glutamate 4.0 g/l KH2PO4 2.0 g/l Arginine 1.0 g/l Glycine 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l DL-Tryptophan 0.1 g/l Tween 80 Distilled waterhttps://mediadive.dsmz.de/medium/414
9041CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yesName: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled waterhttps://mediadive.dsmz.de/medium/110
119306CIP Medium 348yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=348

culture temp

@refgrowthtypetemperaturerange
42016positivegrowth37mesophilic
9041positivegrowth37mesophilic
45249positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
9041anaerobe
45249anaerobe
69480anaerobe100

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.946

murein

  • @ref: 9041
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11930617108D-arabinose-degradation
11930615824D-fructose-degradation
11930617634D-glucose-degradation
11930665327D-xylose-degradation
11930617057cellobiose-degradation
11930617716lactose-degradation
11930617306maltose-degradation
11930617814salicin-degradation
11930617992sucrose-degradation
1193064853esculin-hydrolysis
119306606565hippurate-hydrolysis
11930617632nitrate-reduction
11930616301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 119306
  • ChEBI: 86455
  • metabolite: optochin
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
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
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-
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
119306oxidase-
119306beta-galactosidase-3.2.1.23
119306alcohol dehydrogenase-1.1.1.1
119306gelatinase-
119306amylase-
119306DNase-
119306caseinase-3.4.21.50
119306catalase-1.11.1.6
119306tween esterase-
119306gamma-glutamyltransferase+2.3.2.2
119306lecithinase-
119306lipase-
119306lysine decarboxylase-4.1.1.18
119306ornithine decarboxylase-4.1.1.17
119306protease-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119306-----+----+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
9041-----------------+---+---++--
9041-----------------+-+-+---++--

Isolation, sampling and environmental information

isolation

@refsample type
9041pig gut
45249Pig gut
119306Animal, Pig, gut

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_1907.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_220;96_800;97_934;98_1498;99_1907&stattab=map
  • Last taxonomy: Acidaminococcus fermentans subclade
  • 16S sequence: X78017
  • Sequence Identity:
  • Total samples: 27317
  • soil counts: 391
  • aquatic counts: 1130
  • animal counts: 25473
  • plant counts: 323

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
9041yesyes2Risk group (German classification)
1193061Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218A.fermentans 16S rRNAX659351488ena591001
20218A.fermentans (DSM 20731) 16S rRNA geneX780171516ena591001

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidaminococcus fermentans DSM 20731GCA_000025305completencbi591001
66792Acidaminococcus fermentans DSM 20731 FDAARGOS_1571GCA_020735645completencbi591001
66792Acidaminococcus fermentans DSM 20731591001.3completepatric591001
66792Acidaminococcus fermentans VR4, DSM 20731646311901completeimg591001
66792Acidaminococcus fermentans DSM 20731 strain FDAARGOS_1571591001.18completepatric591001
66792Acidaminococcus fermentans DSM 20731 strain FDAARGOS_1571591001.17completepatric591001

GC content

  • @ref: 9041
  • GC-content: 56.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
motileno93.585no
flagellatedno96.065no
gram-positiveno92.99no
anaerobicyes99.701yes
aerobicno98.103yes
halophileno68.28no
spore-formingno91.521no
thermophileno97.027no
glucose-utilyes70.606no
glucose-fermentyes55.273no

External links

@ref: 9041

culture collection no.: CCUG 9996, CIP 106432, DSM 20731, ATCC 25085

straininfo link

  • @ref: 69781
  • straininfo: 44705

literature

  • topic: Metabolism
  • Pubmed-ID: 8929281
  • title: Fermentation of trans-aconitate via citrate, oxaloacetate, and pyruvate by Acidaminococcus fermentans.
  • authors: Hartel U, Buckel W
  • journal: Arch Microbiol
  • DOI: 10.1007/s002030050393
  • year: 1996
  • mesh: Aconitic Acid/*metabolism, Cell Extracts, Chromatography, Gas, Citric Acid/*metabolism, *Fermentation, Glutamic Acid/metabolism, Gram-Negative Anaerobic Bacteria/*metabolism, Isomerism, Oxaloacetates/*metabolism, Pyruvic Acid/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9041Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20731
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
42016Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18562
45249Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 9996)https://www.ccug.se/strain?id=9996
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
69781Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44705.1StrainInfo: A central database for resolving microbial strain identifiers
119306Curators of the CIPCollection of Institut Pasteur (CIP 106432)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106432