Name: Olivibacter domesticus DC-186
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14138

Type strain:

Species: Olivibacter domesticus

Strain Designation: DC-186

Culture col. no.: DSM 18733, CCUG 54353, LMG 23837, CIP 109620

Strain history: CIP <- 2007, CCUG

NCBI tax ID(s): 1123028 (strain), 407022 (species)

SI-ID 292883

LMG 23837, DSM 18733, CCUG 54353, CIP 109620

Section

Olivibacter domesticus DC-186 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from home-made compost.

Gram-negative
rod-shaped
aerobe
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Olivibacter*
	Species	**Olivibacter domesticus**
	Full Scientific Name (LPSN)	Olivibacter domesticus (Vaz-Moreira et al. 2007) Siddiqi et al. 2018

Synonym

Pseudosphingobacterium domesticum

Information on morphological and physiological properties Morphology

[Ref.: #32090]	Gram stain	negative
[Ref.: #118962]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #32090]	Cell length	1.35 µm

[Ref.: #32090]	Cell width	0.55 µm

[Ref.: #32090]	Cell shape	rod-shaped
[Ref.: #118962]	Cell shape	oval-shaped

[Ref.: #32090]	Motility	no
[Ref.: #118962]	Motility	no

[Ref.: #32090]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7678]

Culture medium

PLATE COUNT AGAR (DSMZ Medium 464)

[Ref.: #7678]

Culture medium growth

[Ref.: #7678]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7678]

Culture medium composition

expand / minimize

[Ref.: #34469]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #34469]

Culture medium growth

[Ref.: #34469]

Culture medium composition

expand / minimize

[Ref.: #118962]

Culture medium

CIP Medium 72

[Ref.: #118962]

Culture medium growth

[Ref.: #118962]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7678]	growth	37 °C
[Ref.: #32090]	growth	15-36 °C
[Ref.: #32090]	optimum	25.5 °C
[Ref.: #34469]	growth	30 °C
[Ref.: #60144]	growth	30-37 °C

[Ref.: #7678]	Temperature range	mesophilic
[Ref.: #32090]	Temperature range	mesophilic
[Ref.: #34469]	Temperature range	mesophilic
[Ref.: #60144]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32090]			optimum	6.75
[Ref.: #32090]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32090]	Oxygen tolerance	aerobe
[Ref.: #60144]	Oxygen tolerance	aerobe
[Ref.: #118962]	Oxygen tolerance	obligate aerobe

[Ref.: #32090]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.94

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32090]		NaCl		growth	0-5	%
[Ref.: #32090]		NaCl		optimum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32090]	arabinose ChEBI	+	carbon source
[Ref.: #32090]	cellobiose ChEBI	+	carbon source
[Ref.: #32090]	esculin ChEBI	+	hydrolysis
[Ref.: #32090]	fructose ChEBI	+	carbon source
[Ref.: #32090]	galactose ChEBI	+	carbon source
[Ref.: #32090]	glucose ChEBI	+	carbon source
[Ref.: #32090]	lactose ChEBI	+	carbon source
[Ref.: #32090]	maltose ChEBI	+	carbon source
[Ref.: #32090]	mannose ChEBI	+	carbon source
[Ref.: #32090]	melibiose ChEBI	+	carbon source
[Ref.: #32090]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32090]	nitrate ChEBI	+	reduction
[Ref.: #118962]	nitrate ChEBI	+	reduction
[Ref.: #118962]	nitrite ChEBI	-	reduction
[Ref.: #32090]	raffinose ChEBI	+	carbon source
[Ref.: #32090]	sucrose ChEBI	+	carbon source
[Ref.: #32090]	trehalose ChEBI	+	carbon source
[Ref.: #32090]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118962]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	+	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32090]	catalase	+	1.11.1.6
[Ref.: #118962]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32090]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118962]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118962]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118962]	12006	-	+	+	-	-	+	+	-	+	-	+	+	+	+	-	+	+	+	+	+

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

[Ref.: #7678]	Sample type/isolated from	home-made compost
[Ref.: #7678]	Geographic location (country and/or sea, region)	Porto
[Ref.: #7678]	Country	Portugal
[Ref.: #7678]	Country ISO 3 Code	PRT
[Ref.: #7678]	Continent	Europe

[Ref.: #60144]	Sample type/isolated from	Compost,home-made
[Ref.: #60144]	Sampling date	2005
[Ref.: #60144]	Geographic location (country and/or sea, region)	Porto ?
[Ref.: #60144]	Country	Portugal
[Ref.: #60144]	Country ISO 3 Code	PRT
[Ref.: #60144]	Continent	Europe

[Ref.: #118962]	Sample type/isolated from	Environment, Home-made compost
* marker position based on {}

Isolation sources categories

#Engineered

#Biodegradation

#Composting

What are isolation sources categories?

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

[Ref.: #7678]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118962]	Biosafety level	1	Risk group (French classification)

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.: #7678]	Pseudosphingobacterium domesticum 16S rRNA gene, type strain DC-186	AM407725	1481	ENA	407022 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Olivibacter domesticus DSM 18733	GCA_900109575	scaffold	GenBank	407022 tax ID	*
[Ref.: #66792]	Pseudosphingobacterium domesticum strain DSM 18733	407022.6	wgs	PATRIC	407022 tax ID	*
[Ref.: #66792]	Pseudosphingobacterium domesticum DSM 18733	2599185177	draft	JGI IMG/M	407022 tax ID	*

[Ref.: #7678]	GC-content	42.0 mol%
[Ref.: #32090]	GC-content	42 mol%
[Ref.: #7678]	GC-content	38.9 mol%	sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Olivibacter domesticus DSM 18733 NCBI: GCA_900109575.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Olivibacter domesticus DSM 18733 NCBI: GCA_900109575.1
[Ref.: #69480]	glucose-ferment	no	89.21	no
[Ref.: #69480]	motile	no	90.397	no
[Ref.: #69480]	flagellated	no	97.093	yes
[Ref.: #69480]	gram-positive	no	97.58	yes
[Ref.: #69480]	anaerobic	no	99.153	yes
[Ref.: #69480]	aerobic	yes	84.665	yes
[Ref.: #69480]	halophile	no	92.7	no
[Ref.: #69480]	spore-forming	no	94.547	yes
[Ref.: #69480]	thermophile	no	99.14	no
[Ref.: #69480]	glucose-util	yes	91.334	yes

Availability in culture collections External links

[Ref.: #7678]

Culture collection no.

DSM 18733, CCUG 54353, LMG 23837, CIP 109620

[Ref.: #83303]

SI-ID 292883

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Olivibacter ginsenosidimutans sp nov., with ginsenoside converting activity isolated from compost, and reclassification of Pseudosphingobacterium domesticum as Olivibacter domesticus comb. nov.	Siddiqi MZ, Liu Q, Lee SY, Choi KD, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.002819	2018	*
Phylogeny	Olivibacter jilunii sp. nov., isolated from DDT-contaminated soil.	Chen K, Tang SK, Wang GL, Nie GX, Li QF, Zhang JD, Li WJ, Li SP	Int J Syst Evol Microbiol	10.1099/ijs.0.042416-0	2012	*
Phylogeny	Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost.	Vaz-Moreira I, Nobre MF, Nunes OC, Manaia CM	Int J Syst Evol Microbiol	10.1099/ijs.0.64950-0	2007	*

References

#7678

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18733

#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 )

#32090

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28336 (see below)

#34469 ; Curators of the CIP;
#60144 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54353

#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) .

#68382

Automatically annotated from API zym .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83303

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-ID292883.1 )

#118962 Collection of Institut Pasteur ; Curators of the CIP; CIP 109620

#28336

IJSEM 1535 2007 ( DOI 10.1099/ijs.0.64950-0 , PubMed 17625189 )

* These data were automatically processed and therefore are not curated

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Olivibacter domesticus DSM 18733

Olivibacter domesticus DSM 18733

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