Name: Tractidigestivibacter scatoligenes SK9K4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130827

Type strain:

Species: Tractidigestivibacter scatoligenes

Strain Designation: SK9K4

Culture col. no.: DSM 28304, JCM 19907, KCTC 15503

Strain history: B. B. Jensen SK9K4.

NCBI tax ID(s): 1299998 (species)

SI-ID 405547

DSM 28304

Section

Tractidigestivibacter scatoligenes SK9K4 is an anaerobe, mesophilic bacterium that was isolated from pig faeces.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Coriobacteriia*
	Order	*Coriobacteriales*
	Family	*Atopobiaceae*
	Genus	*Tractidigestivibacter*
	Species	**Tractidigestivibacter scatoligenes**
	Full Scientific Name (LPSN)	Tractidigestivibacter scatoligenes (Li et al. 2015) Zgheib et al. 2021

Synonym

Olsenella scatoligenes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21710]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #21710]

Culture medium growth

[Ref.: #21710]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21710]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21710]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #21710]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21710]

Oxygen tolerance

anaerobe

[Ref.: #21710]	Name of produced compound	methyl (chroman-4-on-2-yl)-acetate
[Ref.: #21710]	Name of produced compound	p cresol

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	+	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	proline-arylamidase	+	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #21710]	12831	-	-	-	+	-	+	+	-	-	-	+	-	-	-	-	-	-	+/-	+	-	+/-	+	-	+/-	+/-	+/-	+/-	-	+/-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21710]	Sample type/isolated from	pig faeces
[Ref.: #21710]	Geographic location (country and/or sea, region)	Aarhus University
[Ref.: #21710]	Country	Denmark
[Ref.: #21710]	Country ISO 3 Code	DNK
[Ref.: #21710]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Pig feces at Aarhus University
[Ref.: #67770]	Country	Denmark
[Ref.: #67770]	Country ISO 3 Code	DNK
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JX905358 (>99% sequence identity) for Olsenella scatoligenes subclade from Microbeatlas

Aquatic Samples	2207
Soil Samples	660
Animal Samples	23279
Plant Samples	394
Total Samples	26540

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21710]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21710]	Olsenella scatoligenes strain SK9K4 16S ribosomal RNA gene, partial sequence	JX905358	1469	ENA	1299998 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Tractidigestivibacter scatoligenes SK9K4	GCA_001494635	contig	GenBank	1299998 tax ID

[Ref.: #21710]

GC-content

62.1 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tractidigestivibacter scatoligenes SK9K4 NCBI: GCA_001494635.1
[Ref.: #69480]	flagellated	no	97.68	no
[Ref.: #69480]	gram-positive	yes	96.705	no
[Ref.: #69480]	anaerobic	yes	98.811	no
[Ref.: #69480]	halophile	no	79.83	no
[Ref.: #69480]	spore-forming	no	96.266	no
[Ref.: #69480]	glucose-util	yes	86.378	no
[Ref.: #69480]	motile	no	91.068	no
[Ref.: #69480]	aerobic	no	97.196	no
[Ref.: #69480]	thermophile	no	82.358	yes
[Ref.: #69480]	glucose-ferment	yes	78.672	no

Availability in culture collections External links

[Ref.: #21710]

Culture collection no.

DSM 28304, JCM 19907, KCTC 15503

[Ref.: #89314]

SI-ID 405547

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*
Genetics	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	*

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#21710

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28304

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#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) .

#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 . ( DOI 10.60712/SI-ID405547.1 )

* These data were automatically processed and therefore are not curated

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