Strain identifier
BacDive ID: 5424
Type strain:
Species: Amedibacillus dolichus
Strain history: DSM 3991 <-- ATCC 29143 <-- L. Holdeman VPI C9-20.
NCBI tax ID(s): 428127 (strain), 31971 (species)
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 id | Matching level |
---|---|
428127 | strain |
31971 | species |
strain history
@ref | history |
---|---|
1561 | <- ATCC <- L.V. Holdeman, VPI C9-20 |
67770 | DSM 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
@ref synonym 20215 Absiella dolichum 20215 Eubacterium 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
1561 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 1561
- oxygen tolerance: anaerobe
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1561 | - | + | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
1561 | human faeces |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | [Eubacterium] dolichum strain ATCC 29143 16S ribosomal RNA gene, partial sequence | L34682 | 1486 | ena | 428127 |
20218 | Eubacterium dolichum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10413 | AB649277 | 1490 | ena | 31971 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Eubacterium dolichum DSM 3991 | 428127.7 | wgs | patric | 428127 |
66792 | Amedibacillus dolichus DSM 3991 | 641380446 | draft | img | 428127 |
67770 | Amedibacillus dolichus DSM 3991 | GCA_000154285 | scaffold | ncbi | 428127 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | yes | 95.11 | no |
anaerobic | yes | 97.939 | yes |
halophile | no | 66.226 | no |
spore-forming | no | 84.733 | no |
glucose-util | yes | 87.765 | no |
aerobic | no | 98.685 | no |
flagellated | no | 97.908 | no |
thermophile | no | 97.926 | no |
motile | no | 92.7 | no |
glucose-ferment | yes | 73.972 | no |
External links
@ref: 1561
culture collection no.: DSM 3991, ATCC 29143, VPI C9-20, JCM 10413
straininfo link
- @ref: 74912
- straininfo: 39376
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 32416738 | Amedibacterium 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 M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004215 | 2020 | Bacterial 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, DNA | Pathogenicity |
Phylogeny | 33083133 | Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces. | Ghimire S, Wongkuna S, Scaria J | PeerJ | 10.7717/peerj.10071 | 2020 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1561 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3991) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3991 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
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 | |||
74912 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39376.1 | StrainInfo: A central database for resolving microbial strain identifiers |