Strain identifier

BacDive ID: 130827

Type strain: Yes

Species: Tractidigestivibacter scatoligenes

Strain Designation: SK9K4

Strain history: B. B. Jensen SK9K4.

NCBI tax ID(s): 1299998 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
21710<- B. B. Jensen, Dept. Animal Sci., Aarhus Univ., Denmark; SK9K4
67770B. 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

@refgrowthtypetemperaturerange
21710positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 21710
  • oxygen tolerance: anaerobe

compound production

@refcompound
21710methyl (chroman-4-on-2-yl)-acetate
21710p cresol

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-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

@refvalueactivityec
68380glutamyl-glutamate arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
21710---+-++---+------+/-+-+/-+-+/-+/-+/-+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21710pig faecesAarhus UniversityDenmarkDNKEurope
67770Pig feces at Aarhus UniversityDenmarkDNKEurope

isolation source categories

Cat1Cat2Cat3
#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

traitpredictionconfidencetraining_data
flagellatedno97.68no
gram-positiveyes96.705no
anaerobicyes98.811no
halophileno79.83no
spore-formingno96.266no
glucose-utilyes86.378no
motileno91.068no
aerobicno97.196no
thermophileno82.358yes
glucose-fermentyes78.672no

External links

@ref: 21710

culture collection no.: DSM 28304, JCM 19907, KCTC 15503

straininfo link

  • @ref: 89314
  • straininfo: 405547

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25634945Olsenella 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 BBInt J Syst Evol Microbiol10.1099/ijs.0.0000832015Actinobacteria/*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/*microbiologyMetabolism
Genetics26950328Draft 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 BBGenome Announc10.1128/genomeA.00042-162016Phylogeny
Phylogeny29458507Parolsenella catena gen. nov., sp. nov., isolated from human faeces.Sakamoto M, Iino T, Hamada M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0026452018Actinobacteria/*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, DNAEnzymology
Phylogeny31135332Olsenella 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 JSInt J Syst Evol Microbiol10.1099/ijsem.0.0034692019Actinobacteria/*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, DNAPathogenicity
Phylogeny34914571Reclassification 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 YGInt J Syst Evol Microbiol10.1099/ijsem.0.0051922021Actinobacteria/*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 MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
21710Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28304Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28304)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João 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 betahttps://microbeatlas.org/
89314Reimer, 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 identifiers10.60712/SI-ID405547.1