Strain identifier
BacDive ID: 6354
Type strain:
Species: Dorea formicigenerans
Strain history: <- DSM <- ATCC <- LV Holdeman, VPI C8-13
NCBI tax ID(s): 411461 (strain), 39486 (species)
General
@ref: 1562
BacDive-ID: 6354
DSM-Number: 3992
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped
description: Dorea formicigenerans DSM 3992 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from human faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
39486 | species |
411461 | strain |
strain history
@ref | history |
---|---|
1562 | <- ATCC <- L.V. Holdeman, VPI C8-13 |
67771 | <- DSM <- ATCC <- LV Holdeman, VPI C8-13 |
doi: 10.13145/bacdive6354.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Dorea
- species: Dorea formicigenerans
- full scientific name: Dorea formicigenerans (Holdeman and Moore 1974) Taras et al. 2002
synonyms
- @ref: 20215
- synonym: Eubacterium formicigenerans
@ref: 1562
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Dorea
species: Dorea formicigenerans
full scientific name: Dorea formicigenerans (Holdeman and Moore 1974) Taras et al. 2002
type strain: yes
Morphology
cell morphology
@ref | cell shape | motility | gram stain | confidence |
---|---|---|---|---|
67771 | rod-shaped | no | ||
67771 | positive | |||
69480 | no | 91.049 | ||
69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 1562
- 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 Glucose 10.0 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 (optional) NaOH (optional) Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1562 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
1562 | anaerobe | |
67771 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
67771 | no | |
69480 | no | 99.964 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 |
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 |
---|---|---|---|
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 | leucyl glycin arylamidase | - | 3.4.11.1 |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1562 | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
1562 | human faeces |
67771 | From human faeces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
Safety information
risk assessment
- @ref: 1562
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Dorea formicigenerans strain ATCC 27755 16S ribosomal RNA gene, partial sequence
- accession: L34619
- length: 1479
- database: ena
- NCBI tax ID: 39486
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dorea formicigenerans ATCC 27755 | GCA_000169235 | contig | ncbi | 411461 |
66792 | Dorea formicigenerans ATCC 27755 | 411461.4 | wgs | patric | 411461 |
66792 | Dorea formicigenerans ATCC 27755 | 411461.20 | wgs | patric | 411461 |
66792 | Dorea formicigenerans ATCC 27755 | 641736133 | draft | img | 411461 |
66792 | Dorea formicigenerans ATCC 27755 | GCA_025150245 | complete | ncbi | 39486 |
66792 | Dorea formicigenerans strain ATCC 27755 | 39486.544 | complete | patric | 39486 |
GC content
- @ref: 67771
- GC-content: 40-44
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 51 | no |
motile | no | 89.912 | no |
flagellated | no | 96.441 | yes |
gram-positive | yes | 91.743 | yes |
anaerobic | yes | 99.999 | yes |
aerobic | no | 98.691 | yes |
halophile | no | 77.584 | no |
spore-forming | no | 70.244 | no |
glucose-ferment | yes | 71.474 | no |
thermophile | no | 98.068 | yes |
glucose-util | yes | 82.336 | no |
External links
@ref: 1562
culture collection no.: DSM 3992, ATCC 27755, JCM 10342, KCTC 15690, VPI C8-13
straininfo link
- @ref: 75827
- straininfo: 39158
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 33512312 | Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse. | Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, Vogensen FK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004673 | 2021 | ||
Transcriptome | 34252073 | Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects. | Verma S, Dutta SK, Firnberg E, Phillips L, Vinayek R, Nair PP | PLoS One | 10.1371/journal.pone.0251590 | 2021 | Adult, Clostridioides/*physiology, *Fecal Microbiota Transplantation, Gastrointestinal Microbiome/genetics, *Healthy Volunteers, Humans, Male, *Metagenome, Middle Aged, Sequence Analysis | Pathogenicity |
Pathogenicity | 35578355 | Golden bifid might improve diarrhea-predominant irritable bowel syndrome via microbiota modulation. | Luo M, Liu Q, Xiao L, Xiong LS | J Health Popul Nutr | 10.1186/s41043-022-00302-0 | 2022 | *Bacterial Infections, Diarrhea/etiology/therapy, Feces/microbiology, *Gastrointestinal Microbiome, Humans, *Irritable Bowel Syndrome/complications/diagnosis/therapy |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1562 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3992) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3992 | |||
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 | |
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) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68380 | Automatically annotated from API rID32A | |||||
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) | |||
75827 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39158.1 | StrainInfo: A central database for resolving microbial strain identifiers |