Olivibacter sitiensis AW-6 | Type strain | DSM 17696, CECT 7133 | BacDiveID:14091

Strain identifier

BacDive ID: 14091

Type strain:

Species: Olivibacter sitiensis

Strain Designation: AW-6

Culture col. no.: DSM 17696, CECT 7133

Strain history: <- S. Ntougias and G. Zervakis, Natl. Agricultural Research Foundation, Institute of Kalamata; AW-6 <- S. Ntougias

NCBI tax ID(s): 1122621 (strain), 376470 (species)

SI-ID 297275

CECT 7133, DSM 17696, CIP 109529

Special Collections

Section

When using BacDive for research please cite our paper

Olivibacter sitiensis AW-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from alkaline olive-oil mill wastes .

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Olivibacter*
	Species	**Olivibacter sitiensis**
	Full Scientific Name (LPSN)	Olivibacter sitiensis Ntougias et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31867]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.5
[Ref.: #125438]	Gram stain	negative Confidence in %97.019

[Ref.: #31867]	Cell shape	rod-shaped

[Ref.: #31867]	Motility	no

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6980]			growth	25-32 °C
[Ref.: #31867]			growth	05-45 °C
[Ref.: #31867]			optimum	30 °C

	pH	Kind of pH		pH
[Ref.: #31867]			optimum	6.5
[Ref.: #31867]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #31867]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.7
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.798

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31867]		NaCl		growth	<3	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31867]		fructose ChEBI	+	carbon source
[Ref.: #31867]		galactose ChEBI	+	carbon source
[Ref.: #31867]		glucose ChEBI	+	carbon source
[Ref.: #31867]		histidine ChEBI	+	carbon source
[Ref.: #31867]		lactose ChEBI	+	carbon source
[Ref.: #31867]		sorbitol ChEBI	+	carbon source
[Ref.: #31867]		sucrose ChEBI	+	carbon source
[Ref.: #31867]		xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31867]		catalase	+	1.11.1.6
[Ref.: #31867]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #6980]	Sample type/isolated from	alkaline olive-oil mill wastes (alpeorujo)
[Ref.: #6980]	Geographic location (country and/or sea, region)	Crete, Sitia
[Ref.: #6980]	Country	Greece
[Ref.: #6980]	Country ISO 3 Code	GRC
[Ref.: #6980]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Industrial waste
#Condition	#Alkaline	-

What are isolation sources categories?

Global distribution of 16S sequence DQ421387 (>99% sequence identity) for Olivibacter sitiensis subclade from Microbeatlas

Aquatic Samples	31
Soil Samples	10
Animal Samples	3508
Plant Samples	18
Total Samples	3567

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

Biosafety level

1

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.: #6980]	Olivibacter sitiensis strain AW-6 16S ribosomal RNA gene, partial sequence	DQ421387	1477	GenBank ENA	376470 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Olivibacter sitiensis DSM 17696	GCA_000427965	scaffold	GenBank ENA	1122621 tax ID	*
[Ref.: #66792]	Olivibacter sitiensis DSM 17696	1122621.3	wgs	PATRIC	1122621 tax ID	*
[Ref.: #66792]	Olivibacter sitiensis DSM 17696	2515154027	draft	JGI IMG/M	1122621 tax ID	*

GC-content

45.6 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Olivibacter sitiensis DSM 17696 DSM 17696 NCBI: GCA_000427965.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.019	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.731	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.677	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.798	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.479	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	86	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Olivibacter sitiensis DSM 17696 NCBI: GCA_000427965
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	65.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	70.6

Availability in culture collections External links

Culture collection no.

DSM 17696, CECT 7133

SI-ID 297275

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway.	Ntougias S, Lapidus A, Han J, Mavromatis K, Pati A, Chen A, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI	Stand Genomic Sci	10.4056/sigs.5088950	2014	*
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	Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete.	Ntougias S, Fasseas C, Zervakis GI	Int J Syst Evol Microbiol	10.1099/ijs.0.64561-0	2007	*

References

#6980

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17696

#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 )

#31867

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 #28127 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 .

#83259

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-ID297275.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#28127

IJSEM 398 2007 ( DOI 10.1099/ijs.0.64561-0 , PubMed 17267986 )

* These data were automatically processed and therefore are not curated

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