Strain identifier
BacDive ID: 130827
Type strain:
Species: Tractidigestivibacter scatoligenes
Strain Designation: SK9K4
Strain history: B. B. Jensen SK9K4.
NCBI tax ID(s): 1299998 (species)
General
@ref: 21710
BacDive-ID: 130827
DSM-Number: 28304
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Tractidigestivibacter scatoligenes SK9K4 is an anaerobe, mesophilic bacterium that was isolated from pig faeces.
NCBI tax id
- NCBI tax id: 1299998
- Matching level: species
strain history
@ref | history |
---|---|
21710 | <- B. B. Jensen, Dept. Animal Sci., Aarhus Univ., Denmark; SK9K4 |
67770 | B. B. Jensen SK9K4. |
doi: 10.13145/bacdive130827.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Coriobacteriia
- order: Coriobacteriales
- family: Atopobiaceae
- genus: Tractidigestivibacter
- species: Tractidigestivibacter scatoligenes
- full scientific name: Tractidigestivibacter scatoligenes (Li et al. 2015) Zgheib et al. 2021
synonyms
- @ref: 20215
- synonym: Olsenella scatoligenes
@ref: 21710
domain: Bacteria
phylum: Actinobacteria
class: Coriobacteriia
order: Coriobacteriales
family: Atopobiaceae
genus: Tractidigestivibacter
species: Tractidigestivibacter scatoligenes
full scientific name: Tractidigestivibacter scatoligenes (Li et al. 2015) Zgheib et al. 2021
strain designation: SK9K4
type strain: yes
Culture and growth conditions
culture medium
- @ref: 21710
- name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104
- composition: 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21710 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 21710
- oxygen tolerance: anaerobe
compound production
@ref | compound |
---|---|
21710 | methyl (chroman-4-on-2-yl)-acetate |
21710 | p cresol |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | + | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
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 | glutamyl-glutamate arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
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 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
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 | beta-galactosidase | + | 3.2.1.23 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21710 | - | - | - | + | - | + | + | - | - | - | + | - | - | - | - | - | - | +/- | + | - | +/- | + | - | +/- | +/- | +/- | +/- | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
21710 | pig faeces | Aarhus University | Denmark | DNK | Europe |
67770 | Pig feces at Aarhus University | Denmark | DNK | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Suidae (Pig,Swine) |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_2861.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_150;96_1518;97_1810;98_2215;99_2861&stattab=map
- Last taxonomy: Olsenella scatoligenes subclade
- 16S sequence: JX905358
- Sequence Identity:
- Total samples: 26540
- soil counts: 660
- aquatic counts: 2207
- animal counts: 23279
- plant counts: 394
Safety information
risk assessment
- @ref: 21710
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21710
- description: Olsenella scatoligenes strain SK9K4 16S ribosomal RNA gene, partial sequence
- accession: JX905358
- length: 1469
- database: ena
- NCBI tax ID: 1299998
Genome sequences
- @ref: 67770
- description: Tractidigestivibacter scatoligenes SK9K4
- accession: GCA_001494635
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1299998
GC content
- @ref: 21710
- GC-content: 62.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 97.68 | no |
gram-positive | yes | 96.705 | no |
anaerobic | yes | 98.811 | no |
halophile | no | 79.83 | no |
spore-forming | no | 96.266 | no |
glucose-util | yes | 86.378 | no |
motile | no | 91.068 | no |
aerobic | no | 97.196 | no |
thermophile | no | 82.358 | yes |
glucose-ferment | yes | 78.672 | no |
External links
@ref: 21710
culture collection no.: DSM 28304, JCM 19907, KCTC 15503
straininfo link
- @ref: 89314
- straininfo: 405547
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25634945 | Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces. | Li X, Jensen RL, Hojberg O, Canibe N, Jensen BB | Int J Syst Evol Microbiol | 10.1099/ijs.0.000083 | 2015 | Actinobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Cresols/*metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Fermentation, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Skatole/*metabolism, Sus scrofa/*microbiology | Metabolism |
Genetics | 26950328 | Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces. | Li X, Hojberg O, Noel SJ, Canibe N, Jensen BB | Genome Announc | 10.1128/genomeA.00042-16 | 2016 | Phylogeny | |
Phylogeny | 29458507 | Parolsenella catena gen. nov., sp. nov., isolated from human faeces. | Sakamoto M, Iino T, Hamada M, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002645 | 2018 | Actinobacteria/*classification/genetics/isolation & purification, Adult, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, Japan, Male, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
Phylogeny | 31135332 | Olsenella faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces. | Han KI, Lee KC, Eom MK, Kim JS, Suh MK, Park SH, Lee JH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003469 | 2019 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Glycolipids/chemistry, Humans, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA | Pathogenicity |
Phylogeny | 34914571 | Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu. | Lu LF, Yang Y, Zheng L, Zhang R, Liu GQ, Tu TY, Xu T, Luo X, Ran MF, Zhang LQ, Wang ST, Shen CH, Zhang YG | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005192 | 2021 | Actinobacteria/*classification/isolation & purification, Alcoholic Beverages, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Fermentation, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
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 | |
21710 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28304 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28304) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68380 | Automatically annotated from API rID32A | |||
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/ | |
89314 | 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-ID405547.1 |