Strain identifier
BacDive ID: 158153
Type strain: 
Species: Phascolarctobacterium succinatutens
Strain Designation: A177
Strain history: Y. Watane A177 (=YIT 12067).
NCBI tax ID(s): 626939 (strain), 626940 (species)
version 8.1 (current version)
General
@ref: 64739
BacDive-ID: 158153
DSM-Number: 22533
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Phascolarctobacterium succinatutens A177 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 626939 | strain |
| 626940 | species |
strain history
| @ref | history |
|---|---|
| 64739 | <- Y. Watanabe, Yakult Central Institute for Microbiological Research; YIT 12067 <- M. Morotomi and F. Nagai; A177 |
| 67770 | Y. Watane A177 (=YIT 12067). |
doi: 10.13145/bacdive158153.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Negativicutes
- order: Acidaminococcales
- family: Acidaminococcaceae
- genus: Phascolarctobacterium
- species: Phascolarctobacterium succinatutens
- full scientific name: Phascolarctobacterium succinatutens Watanabe et al. 2012
@ref: 64739
domain: Bacteria
phylum: Firmicutes
class: Negativicutes
order: Selenomonadales
family: Acidaminococcaceae
genus: Phascolarctobacterium
species: Phascolarctobacterium succinatutens
full scientific name: Phascolarctobacterium succinatutens Watanabe et al. 2012
strain designation: A177
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.722
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 64739 | PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) | yes | https://mediadive.dsmz.de/medium/104c | Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Disodium succinate 8.0 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 |
| 64739 | 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 |
| 64739 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 64739 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 99.358
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.539 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 64739 | human faeces (healthy Japanese adult) | Tokyo | Japan | JPN | Asia |
| 67770 | Human feces |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Human |
taxonmaps
- @ref: 69479
- File name: preview.99_5130.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_220;96_2496;97_3047;98_3825;99_5130&stattab=map
- Last taxonomy: Phascolarctobacterium succinatutens subclade
- 16S sequence: AB490811
- Sequence Identity:
- Total samples: 75901
- soil counts: 672
- aquatic counts: 3216
- animal counts: 71670
- plant counts: 343
Safety information
risk assessment
- @ref: 64739
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64739
- description: Phascolarctobacterium succinatutens YIT 12067 gene for 16S rRNA, partial sequence
- accession: AB490811
- length: 1610
- database: ena
- NCBI tax ID: 626939
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Phascolarctobacterium succinatutens YIT 12067 | 626939.3 | wgs | patric | 626939 |
| 66792 | Phascolarctobacterium succinatutens YIT 12067 strain Phascolarctobacterium succinatutens 82G5 | 626939.32 | complete | patric | 626939 |
| 66792 | Phascolarctobacterium succinatutens YIT 12067 ERS2913222 | 2836699358 | complete | img | 626939 |
| 66792 | Phascolarctobacterium succinatutens YIT 12067 | 649989983 | draft | img | 626939 |
| 67770 | Phascolarctobacterium succinatutens YIT 12067 | GCA_000188175 | scaffold | ncbi | 626939 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 64739 | 47 | sequence analysis |
| 64739 | 46.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 95.663 | no |
| anaerobic | yes | 99.999 | no |
| halophile | no | 93.871 | no |
| spore-forming | no | 78.295 | no |
| glucose-util | no | 53.429 | no |
| thermophile | no | 97.99 | no |
| flagellated | no | 95.452 | no |
| aerobic | no | 98.267 | no |
| motile | no | 85.836 | no |
| glucose-ferment | no | 66.404 | no |
External links
@ref: 64739
culture collection no.: DSM 22533, JCM 16074, YIT 12067
straininfo link
- @ref: 110986
- straininfo: 406749
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22081579 | Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. | Watanabe Y, Nagai F, Morotomi M | Appl Environ Microbiol | 10.1128/AEM.06035-11 | 2011 | Bacterial Typing Techniques, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Succinic Acid/*metabolism, Veillonellaceae/*classification/genetics/*isolation & purification/metabolism | Pathogenicity |
| Phylogeny | 31038451 | Phascolarctobacterium wakonense sp. nov., isolated from common marmoset (Callithrix jacchus) faeces. | Shigeno Y, Kitahara M, Shime M, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003407 | 2019 | Animals, Bacterial Typing Techniques, Base Composition, Callithrix/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Veillonellaceae/*classification/isolation & purification | Transcriptome |
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 | |||
| 64739 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22533 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22533) | |||
| 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/ | ||||
| 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/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 110986 | 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-ID406749.1 |