Strain identifier
BacDive ID: 2798
Type strain: 
Species: Peptacetobacter hiranonis
Strain Designation: TO-931
Strain history: F. Takamine TO-931.
NCBI tax ID(s): 500633 (strain), 89152 (species)
version 8.1 (current version)
General
@ref: 4987
BacDive-ID: 2798
DSM-Number: 13275
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Peptacetobacter hiranonis TO-931 is an anaerobe, mesophilic bacterium that was isolated from human faeces.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 500633 | strain |
| 89152 | species |
strain history
| @ref | history |
|---|---|
| 4987 | <- Y. Benno, JCM <- F. Takamine; TO-931 |
| 67770 | F. Takamine TO-931. |
doi: 10.13145/bacdive2798.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptostreptococcaceae
- genus: Peptacetobacter
- species: Peptacetobacter hiranonis
- full scientific name: Peptacetobacter hiranonis (Kitahara et al. 2001) Chen et al. 2020
synonyms
- @ref: 20215
- synonym: Clostridium hiranonis
@ref: 4987
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptostreptococcaceae
genus: Peptacetobacter
species: Peptacetobacter hiranonis
full scientific name: Peptacetobacter hiranonis (Kitahara et al. 2001) Chen et al. 2020
strain designation: TO-931
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.121 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 4987
- 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 |
|---|---|---|---|---|
| 4987 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4987 | anaerobe | |
| 69480 | anaerobe | 99.226 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 96.223
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 4987 | human faeces | Okinawa | Japan | JPN | Asia |
| 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_16124.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_5447;97_6567;98_8165;99_16124&stattab=map
- Last taxonomy: Peptacetobacter hiranonis subclade
- 16S sequence: AB971817
- Sequence Identity:
- Total samples: 7590
- soil counts: 27
- aquatic counts: 98
- animal counts: 7429
- plant counts: 36
Safety information
risk assessment
- @ref: 4987
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 4987 | Clostridium hiranonis gene for 16S rRNA, partial sequence, strain:TO-931 | AB023970 | 1393 | ena | 500633 |
| 67770 | [Clostridium] hiranonis gene for 16S ribosomal RNA, partial sequence, strain: JCM 10541 | AB971817 | 1410 | ena | 89152 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Peptacetobacter hiranonis DSM 13275 | GCA_008151785 | complete | ncbi | 89152 |
| 66792 | Clostridium hiranonis DSM 13275 | 500633.7 | wgs | patric | 500633 |
| 66792 | [Clostridium] hiranonis strain DSM 13275 | 89152.14 | complete | patric | 89152 |
| 66792 | Clostridium hiranonis TO-931 DSM 13275 | 642979371 | draft | img | 500633 |
| 67770 | Peptacetobacter hiranonis DSM 13275 | GCA_000156055 | scaffold | ncbi | 500633 |
GC content
- @ref: 4987
- GC-content: 31.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 66 | no |
| motile | no | 92.14 | no |
| flagellated | no | 96.889 | no |
| gram-positive | yes | 94.419 | no |
| anaerobic | yes | 99.465 | yes |
| aerobic | no | 98.088 | yes |
| halophile | no | 75.365 | no |
| spore-forming | no | 55.73 | no |
| glucose-util | yes | 86.463 | no |
| thermophile | no | 98.432 | no |
| glucose-ferment | yes | 74.973 | no |
External links
@ref: 4987
culture collection no.: DSM 13275, JCM 10541, KCTC 15199
straininfo link
- @ref: 72324
- straininfo: 49451
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 11211270 | Clostridium hiranonis sp. nov., a human intestinal bacterium with bile acid 7alpha-dehydroxylating activity. | Kitahara M, Takamine F, Imamura T, Benno Y | Int J Syst Evol Microbiol | 10.1099/00207713-51-1-39 | 2001 | Bacterial Typing Techniques, Base Composition, Bile Acids and Salts/*metabolism, Clostridium/*classification/enzymology/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/microbiology, Humans, *Hydroxysteroid Dehydrogenases, Intestines/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Oxidoreductases, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Steroid Hydroxylases/*metabolism | Enzymology |
| Metabolism | 31177942 | The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. | Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR | Gut Microbes | 10.1080/19490976.2019.1618173 | 2019 | Animals, Bacteria, Anaerobic/*genetics/*metabolism, Bacteroides/genetics/metabolism, Bile Acids and Salts/*metabolism, Bilophila/genetics/metabolism, Cecum/*microbiology, Cholic Acids/metabolism, Clostridium/genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Germ-Free Life, Humans, *Metabolome, Mice, Mice, Inbred C57BL, Microbiota, Operon, RNA-Seq, *Transcriptome, Up-Regulation | Genetics |
| Phylogeny | 32369000 | Characterization of Peptacetobacter hominis gen. nov., sp. nov., isolated from human faeces, and proposal for the reclassification of Clostridium hiranonis within the genus Peptacetobacter. | Chen XJ, Wang ZQ, Zhou ZY, Zeng NY, Huang QF, Wang ZW, Tang WL, Zhou HW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003925 | 2020 | Adult, Bacterial Typing Techniques, Base Composition, China, Clostridium/*classification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Glycolipids/chemistry, Gram-Positive Endospore-Forming Rods/*classification/isolation & purification, Humans, Male, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4987 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13275) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13275 | |||
| 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 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 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) | |||
| 72324 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49451.1 | StrainInfo: A central database for resolving microbial strain identifiers |