Strain identifier
BacDive ID: 132618
Type strain:
Species: Agathobaculum butyriciproducens
Strain Designation: SR79
Strain history: <- BC Kim, KRIBB
NCBI tax ID(s): 1628085 (species)
General
@ref: 24407
BacDive-ID: 132618
DSM-Number: 100391
keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, Gram-positive, rod-shaped
description: Agathobaculum butyriciproducens SR79 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces of a 23-years-old healthy Korean woman.
NCBI tax id
- NCBI tax id: 1628085
- Matching level: species
strain history
@ref | history |
---|---|
24407 | <- S. Ahn, KCTC, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; SR79 <- S. Ahn {2014} |
67770 | B.-C. Kim; KCTC, South Korea; SR79. |
67771 | <- BC Kim, KRIBB |
doi: 10.13145/bacdive132618.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Agathobaculum
- species: Agathobaculum butyriciproducens
- full scientific name: Agathobaculum butyriciproducens Ahn et al. 2016
@ref: 24407
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Agathobaculum
species: Agathobaculum butyriciproducens
full scientific name: Agathobaculum butyriciproducens Ahn et al. 2016
strain designation: SR79
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
43140 | positive | 0.9-1.1 µm | 0.6-0.7 µm | rod-shaped | no |
67771 | rod-shaped | no | |||
67771 | positive |
Culture and growth conditions
culture medium
- @ref: 24407
- name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104c
- composition: Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43140 | positive | optimum | 37 | mesophilic |
43140 | positive | growth | 30-40 | |
24407 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43140 | positive | growth | 6-8 |
43140 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43140 | obligate anaerobe |
67771 | anaerobe |
spore formation
@ref | type of spore | spore formation |
---|---|---|
43140 | spore | no |
67771 | no |
compound production
- @ref: 24407
- compound: butyrate
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43140 | NaCl | positive | maximum | 1 %(w/v) |
43140 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
43140 | esculin ferric citrate | + | hydrolysis | |
43140 | D-glucose | + | builds acid from | 17634 |
43140 | D-mannitol | + | builds acid from | 16899 |
43140 | lactose | + | builds acid from | 17716 |
43140 | sucrose | + | builds acid from | 17992 |
43140 | maltose | + | builds acid from | 17306 |
43140 | salicin | + | builds acid from | 17814 |
43140 | D-xylose | + | builds acid from | 65327 |
43140 | D-arabinose | + | builds acid from | 17108 |
43140 | cellobiose | + | builds acid from | 17057 |
43140 | D-mannose | + | builds acid from | 16024 |
43140 | melezitose | + | builds acid from | 6731 |
43140 | L-rhamnose | + | builds acid from | 62345 |
43140 | D-trehalose | + | builds acid from | 16551 |
43140 | L-tryptophan | - | assimilation | 16828 |
43140 | urea | - | hydrolysis | 16199 |
43140 | gelatin | - | hydrolysis | 5291 |
43140 | glycerol | - | builds acid from | 17754 |
43140 | raffinose | - | builds acid from | 16634 |
43140 | D-sorbitol | - | builds acid from | 17924 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43140 | 17968 | butyrate | yes |
43140 | 16236 | ethanol | yes |
43140 | 28885 | butanol | yes |
43140 | 30089 | acetate | yes |
fatty acid profile
fatty acids
@ref fatty acid percentage 43140 C16:0 21.6 43140 cis9-C18:1 14.1 43140 cyc9,10-C19:1 14 43140 C14:0 11.8 - type of FA analysis: whole cell analysis
- incubation medium: DSM 104
- agar/liquid: agar
- incubation temperature: 37
- incubation time: 2
- system: MIS MIDI
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
24407 | human faeces of a 23-years-old healthy Korean woman | Republic of Korea | KOR | Asia |
43140 | human faeces samples of a 23-years-old healthy Korean woman | |||
67770 | Faeces of a healthy 23-year-old Korean female | |||
67771 | From human faeces of a 23-years-old healthy Korean woman | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | #Female |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_10866.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_341;96_5189;97_6263;98_8088;99_10866&stattab=map
- Last taxonomy: Eubacteriales
- 16S sequence: KP889099
- Sequence Identity:
- Total samples: 57580
- soil counts: 133
- aquatic counts: 757
- animal counts: 56625
- plant counts: 65
Safety information
risk assessment
- @ref: 24407
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24407
- description: Agathobaculum butyriciproducens strain SR79 16S ribosomal RNA gene, partial sequence
- accession: KP889099
- length: 1383
- database: ena
- NCBI tax ID: 1628085
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Agathobaculum butyriciproducens strain DSM 100391 | 1628085.3 | wgs | patric | 1628085 |
66792 | Agathobaculum butyriciproducens DSM 100391 | 2756170243 | draft | img | 1628085 |
GC content
@ref | GC-content | method |
---|---|---|
24407 | 52.9 | high performance liquid chromatography (HPLC) |
67771 | 52.9 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 89.998 | yes |
gram-positive | yes | 92.955 | no |
anaerobic | yes | 99.567 | no |
aerobic | no | 97.47 | yes |
halophile | no | 93.629 | yes |
spore-forming | no | 80.938 | yes |
thermophile | no | 98.278 | yes |
glucose-util | yes | 80.943 | no |
flagellated | no | 95.728 | yes |
glucose-ferment | yes | 64.704 | no |
External links
@ref: 24407
culture collection no.: DSM 100391, KCTC 15532, JCM 30795
straininfo link
- @ref: 90932
- straininfo: 397368
literature
- topic: Phylogeny
- Pubmed-ID: 27334534
- title: Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.
- authors: Ahn S, Jin TE, Chang DH, Rhee MS, Kim HJ, Lee SJ, Park DS, Kim BC
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001195
- year: 2016
- mesh: Bacterial Typing Techniques, Base Composition, Butyrates/metabolism, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Eubacterium/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Feces/*microbiology, Humans, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA
- topic2: Pathogenicity
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
24407 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100391 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100391) | |||
43140 | Sharon Ahn, Tae-Eun Jin, Dong-Ho Chang, Moon-Soo Rhee, Hyun Ju Kim, Sang Jun Lee, Doo-Sang Park and Byoung-Chan Kim | Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov. | 10.1099/ijsem.0.001195 | IJSEM 66: 3656-3661 2016 | 27334534 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
90932 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID397368.1 |