Strain identifier
BacDive ID: 98
Type strain:
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)
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 id | Matching level |
---|---|
905 | species |
591001 | strain |
strain history
@ref | history |
---|---|
9041 | <- ATCC <- M. Rogosa, VR4 <- R. Fuller |
119306 | CIP <- 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
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.743 | ||
119306 | negative | coccus-shaped | no |
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
@ref | name | growth | composition | link |
---|---|---|---|---|
42016 | MEDIUM 348 - for Acidaminococcus | yes | Distilled 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 | |
9041 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base | https://mediadive.dsmz.de/medium/693 |
9041 | ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414) | yes | Name: 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 water | https://mediadive.dsmz.de/medium/414 |
9041 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | Name: 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 water | https://mediadive.dsmz.de/medium/110 |
119306 | CIP Medium 348 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=348 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
42016 | positive | growth | 37 | mesophilic |
9041 | positive | growth | 37 | mesophilic |
45249 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
9041 | anaerobe | |
45249 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.946
murein
- @ref: 9041
- murein short key: A31
- type: A1gamma m-Dpm-direct
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
119306 | 17108 | D-arabinose | - | degradation |
119306 | 15824 | D-fructose | - | degradation |
119306 | 17634 | D-glucose | - | degradation |
119306 | 65327 | D-xylose | - | degradation |
119306 | 17057 | cellobiose | - | degradation |
119306 | 17716 | lactose | - | degradation |
119306 | 17306 | maltose | - | degradation |
119306 | 17814 | salicin | - | degradation |
119306 | 17992 | sucrose | - | degradation |
119306 | 4853 | esculin | - | hydrolysis |
119306 | 606565 | hippurate | - | hydrolysis |
119306 | 17632 | nitrate | - | reduction |
119306 | 16301 | nitrite | - | reduction |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | 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
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | + | |
68380 | glycin arylamidase | + | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
119306 | oxidase | - | |
119306 | beta-galactosidase | - | 3.2.1.23 |
119306 | alcohol dehydrogenase | - | 1.1.1.1 |
119306 | gelatinase | - | |
119306 | amylase | - | |
119306 | DNase | - | |
119306 | caseinase | - | 3.4.21.50 |
119306 | catalase | - | 1.11.1.6 |
119306 | tween esterase | - | |
119306 | gamma-glutamyltransferase | + | 2.3.2.2 |
119306 | lecithinase | - | |
119306 | lipase | - | |
119306 | lysine decarboxylase | - | 4.1.1.18 |
119306 | ornithine decarboxylase | - | 4.1.1.17 |
119306 | protease | - |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119306 | - | - | - | - | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9041 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | + | + | - | - |
9041 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | + | - | - | - | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
9041 | pig gut |
45249 | Pig gut |
119306 | Animal, Pig, gut |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
9041 | yes | yes | 2 | Risk group (German classification) |
119306 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | A.fermentans 16S rRNA | X65935 | 1488 | ena | 591001 |
20218 | A.fermentans (DSM 20731) 16S rRNA gene | X78017 | 1516 | ena | 591001 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Acidaminococcus fermentans DSM 20731 | GCA_000025305 | complete | ncbi | 591001 |
66792 | Acidaminococcus fermentans DSM 20731 FDAARGOS_1571 | GCA_020735645 | complete | ncbi | 591001 |
66792 | Acidaminococcus fermentans DSM 20731 | 591001.3 | complete | patric | 591001 |
66792 | Acidaminococcus fermentans VR4, DSM 20731 | 646311901 | complete | img | 591001 |
66792 | Acidaminococcus fermentans DSM 20731 strain FDAARGOS_1571 | 591001.18 | complete | patric | 591001 |
66792 | Acidaminococcus fermentans DSM 20731 strain FDAARGOS_1571 | 591001.17 | complete | patric | 591001 |
GC content
- @ref: 9041
- GC-content: 56.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 84 | no |
motile | no | 93.585 | no |
flagellated | no | 96.065 | no |
gram-positive | no | 92.99 | no |
anaerobic | yes | 99.701 | yes |
aerobic | no | 98.103 | yes |
halophile | no | 68.28 | no |
spore-forming | no | 91.521 | no |
thermophile | no | 97.027 | no |
glucose-util | yes | 70.606 | no |
glucose-ferment | yes | 55.273 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9041 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20731) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20731 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
42016 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18562 | ||||
45249 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 9996) | https://www.ccug.se/strain?id=9996 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69781 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44705.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119306 | Curators of the CIP | Collection of Institut Pasteur (CIP 106432) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106432 |