Strain identifier
BacDive ID: 162023
Type strain: 
Species: Agathobacter rectalis
Strain history: KCTC 5835 <-- CIP 105953 <-- ATCC 33656 <-- VPI 0990.
NCBI tax ID(s): 39491 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 162023
DSM-Number: 3377
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive
description: Agathobacter rectalis JCM 17463 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from Human feces.
NCBI tax id
- NCBI tax id: 39491
- Matching level: species
strain history
- @ref: 67770
- history: KCTC 5835 <-- CIP 105953 <-- ATCC 33656 <-- VPI 0990.
doi: 10.13145/bacdive162023.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Agathobacter
- species: Agathobacter rectalis
- full scientific name: Agathobacter rectalis (Hauduroy et al. 1937) Rosero et al. 2016
synonyms
@ref synonym 20215 Bacteroides rectalis 20215 Eubacterium rectale
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Lachnospiraceae
genus: Agathobacter
species: Agathobacter rectalis
full scientific name: Agathobacter rectalis (Hauduroy et al. 1937) Rosero et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 99.713
spore formation
- @ref: 69480
- spore formation: no
- confidence: 98.979
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Human feces
taxonmaps
- @ref: 69479
- File name: preview.99_3750.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_1928;97_2319;98_2862;99_3750&stattab=map
- Last taxonomy: [Eubacterium] rectale subclade
- 16S sequence: AB626630
- Sequence Identity:
- Total samples: 70417
- soil counts: 291
- aquatic counts: 1562
- animal counts: 68496
- plant counts: 68
Sequence information
16S sequences
- @ref: 67770
- description: Eubacterium rectale gene for 16S ribosomal RNA, partial sequence
- accession: AB626630
- length: 1494
- database: ena
- NCBI tax ID: 39491
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Agathobacter rectalis ATCC 33656 | GCA_000020605 | complete | ncbi | 515619 |
| 66792 | [Eubacterium rectale] ATCC 33656 | 515619.32 | complete | patric | 515619 |
| 66792 | Eubacterium rectale ATCC 33656 | 515619.6 | complete | patric | 515619 |
| 66792 | Eubacterium rectale ATCC 33656 | 644736367 | complete | img | 515619 |
| 66792 | Agathobacter rectalis VPI 0990 | GCA_022453685 | complete | ncbi | 39491 |
GC content
- @ref: 67770
- GC-content: 41.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 56 | no |
| motile | yes | 79.89 | no |
| flagellated | yes | 56.409 | no |
| gram-positive | yes | 85.808 | no |
| anaerobic | yes | 99.999 | no |
| aerobic | no | 99.332 | no |
| halophile | no | 80.537 | no |
| spore-forming | yes | 58.536 | no |
| glucose-util | yes | 85.679 | no |
| thermophile | no | 92.768 | no |
| glucose-ferment | yes | 74.64 | no |
External links
@ref: 67770
culture collection no.: JCM 17463, ATCC 33656, CIP 105953, DSM 3377, KCTC 5835, LMG 30912, VPI 0990
straininfo link
- @ref: 113487
- straininfo: 40605
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18599726 | Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an opinion. | Duncan SH, Flint HJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.2008/004580-0 | 2008 | Eubacterium/*classification/growth & development/metabolism, Feces/microbiology, Fermentation, Humans, Species Specificity | Pathogenicity |
| Phylogeny | 19904524 | Characterization of an O-desmethylangolensin-producing bacterium isolated from human feces. | Yokoyama S, Niwa T, Osawa T, Suzuki T | Arch Microbiol | 10.1007/s00203-009-0524-5 | 2009 | Anaerobiosis/genetics, Bacterial Typing Techniques, Bioreactors, Clostridium/classification/genetics/isolation & purification, DNA Gyrase/genetics, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry/genetics, Eubacterium/classification/genetics, Fatty Acids/genetics, Feces/*microbiology, Fermentation/genetics, Genes, rRNA, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification, Humans, Isoflavones/*biosynthesis, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Enzymology |
| Metabolism | 26319874 | Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides. | Riviere A, Gagnon M, Weckx S, Roy D, De Vuyst L | Appl Environ Microbiol | 10.1128/AEM.02089-15 | 2015 | Bacterial Proteins/*genetics/metabolism, Bifidobacterium/*genetics/growth & development/metabolism, Eubacterium/*genetics/growth & development/metabolism, Gene Expression, Oligosaccharides/*metabolism, Reverse Transcriptase Polymerase Chain Reaction, Xylans/metabolism | |
| Phylogeny | 26619944 | Reclassification of Eubacterium rectale (Hauduroy et al. 1937) Prevot 1938 in a new genus Agathobacter gen. nov. as Agathobacter rectalis comb. nov., and description of Agathobacter ruminis sp. nov., isolated from the rumen contents of sheep and cows. | Rosero JA, Killer J, Sechovcova H, Mrazek J, Benada O, Fliegerova K, Havlik J, Kopecny J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000788 | 2015 | ||
| Metabolism | 28548573 | Inulin-type fructan degradation capacity of Clostridium cluster IV and XIVa butyrate-producing colon bacteria and their associated metabolic outcomes. | Moens F, De Vuyst L | Benef Microbes | 10.3920/BM2016.0142 | 2017 | Butyrates/metabolism, Carbon Dioxide/metabolism, Colon/metabolism/microbiology, Eubacterium/*metabolism, Faecalibacterium prausnitzii/*metabolism, Fermentation/physiology, Formates/metabolism, Fructose/*metabolism, Humans, Hydrogen/metabolism, Inulin/*metabolism, Lactic Acid/metabolism, Oligosaccharides/*metabolism | Pathogenicity |
| Phylogeny | 32812861 | Opinions 100, 101 and 102. | Arahal DR | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004390 | 2020 | Eubacterium/*classification, Myxococcales/*classification, Myxococcus/*classification, Phylogeny |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 113487 | 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-ID40605.1 |