Strain identifier
BacDive ID: 5428
Type strain: 
Species: Anaerobutyricum hallii
Strain history: <- E.P. Cato, VPI B4-27
NCBI tax ID(s): 411469 (strain), 39488 (species)
version 9.3 (current version)
General
@ref: 1360
BacDive-ID: 5428
DSM-Number: 3353
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Anaerobutyricum hallii DSM 3353 is an anaerobe, mesophilic bacterium that was isolated from human faeces.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 39488 | species |
| 411469 | strain |
strain history
- @ref: 1360
- history: <- E.P. Cato, VPI B4-27
doi: 10.13145/bacdive5428.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Anaerobutyricum
- species: Anaerobutyricum hallii
- full scientific name: Anaerobutyricum hallii (Holdeman and Moore 1974) Shetty et al. 2018
synonyms
- @ref: 20215
- synonym: Eubacterium hallii
@ref: 1360
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Anaerobutyricum
species: Anaerobutyricum hallii
full scientific name: Anaerobutyricum hallii (Holdeman and Moore 1974) Shetty et al. 2018
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 1360 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water |
| 1360 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | 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 |
culture temp
- @ref: 1360
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1360 | anaerobe | |
| 125438 | anaerobe | 90.89 |
| 125439 | anaerobe | 90 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68380 | 17632 | nitrate | - | reduction |
| 68380 | 29985 | L-glutamate | - | degradation |
| 68380 | 16024 | D-mannose | - | fermentation |
| 68380 | 16634 | raffinose | - | fermentation |
| 68380 | 27897 | tryptophan | - | energy source |
| 68380 | 29016 | arginine | - | hydrolysis |
| 68380 | 16199 | urea | - | hydrolysis |
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 | leucyl glycin arylamidase | - | 3.4.11.1 |
| 68380 | proline-arylamidase | - | 3.4.11.5 |
| 68380 | alkaline phosphatase | - | 3.1.3.1 |
| 68380 | tryptophan deaminase | - | 4.1.99.1 |
| 68380 | glutamate decarboxylase | - | 4.1.1.15 |
| 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 | L-arginine arylamidase | - | |
| 68380 | alpha-fucosidase | - | 3.2.1.51 |
| 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1360 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 1360 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 1360 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 1360 | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 1360
- sample type: human faeces
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
Safety information
risk assessment
- @ref: 1360
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Eubacterium hallii strain ATCC 27751 16S ribosomal RNA gene, partial sequence
- accession: L34621
- length: 1479
- database: nuccore
- NCBI tax ID: 39488
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Anaerobutyricum hallii DSM 3353 | GCA_000173975 | contig | ncbi | 411469 |
| 66792 | [Eubacterium] hallii DSM 3353 | 411469.11 | wgs | patric | 411469 |
| 66792 | Eubacterium hallii DSM 3353 | 411469.3 | wgs | patric | 411469 |
| 66792 | Anaerobutyricum hallii DSM 3353 | 643886203 | draft | img | 411469 |
GC content
- @ref: 1360
- GC-content: 38.0
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 80.482 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 90.89 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 52.706 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 97.116 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.477 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 76.909 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 87 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 81.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 78.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 90 |
External links
@ref: 1360
culture collection no.: DSM 3353, ATCC 27751, JCM 7789, VPI B4-27
straininfo link
- @ref: 74916
- straininfo: 39157
literature
- topic: Phylogeny
- Pubmed-ID: 30351260
- title: Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces.
- authors: Shetty SA, Zuffa S, Bui TPN, Aalvink S, Smidt H, De Vos WM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.003041
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, Butyrates/metabolism, DNA, Bacterial/genetics, Eubacterium/*classification/metabolism, Fatty Acids/chemistry, Feces/*microbiology, Humans, Infant, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, Propionates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1360 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3353) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3353 | |||
| 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) | |||
| 68380 | Automatically annotated from API rID32A | |||||
| 74916 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39157.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |