Name: Arcobacter defluvii SW28-11
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 22945

Type strain:

Species: Arcobacter defluvii

Strain Designation: SW28-11

Culture col. no.: DSM 25359, CECT 7697, LMG 25694, JCM 33356

Strain history: LMG 25694 <-- M. J. Figueras; Univ. Rovira i Virgili, Spain; SW28-11.

NCBI tax ID(s): 873191 (species)

SI-ID 369524

LMG 25694, CECT 7697, DSM 25359

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Arcobacter defluvii SW28-11 is a microaerophile, mesophilic bacterium that was isolated from raw sewage, waste water plant.

mesophilic
microaerophile
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	*Pseudomonadota*
	Class	*Epsilonproteobacteria*
	Order	*Campylobacterales*
	Family	*Arcobacteraceae*
	Genus	*Arcobacter*
	Species	**Arcobacter defluvii**
	Full Scientific Name (LPSN)	Arcobacter defluvii Collado et al. 2011

	Synonym	Pseudarcobacter defluvii
	Synonym	Pseudoarcobacter defluvii

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %99.2
[Ref.: #125438]	Gram stain	negative Confidence in %96.871

[Ref.: #19121]	Type of hemolysis	gamma
[Ref.: #19121]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19121]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #19121]

Culture medium growth

[Ref.: #19121]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19121]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #19121]			growth	37 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #19121]

Oxygen tolerance

microaerophile

[Ref.: #125439]	Ability of spore formation	no Confidence in %95.6
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.72

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68373]	acetate ChEBI	-	assimilation	* from API CAM
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68373]	citrate ChEBI	-	assimilation	* from API CAM
[Ref.: #68373]	D-glucose ChEBI	-	assimilation	* from API CAM, API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68373]	hippurate ChEBI	-	hydrolysis	* from API CAM
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68373]	malate ChEBI	-	assimilation	* from API CAM, API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68373]	nitrate ChEBI	+	reduction	* from API CAM
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68373]	propionate ChEBI	-	assimilation	* from API CAM
[Ref.: #68373]	succinate ChEBI	-	assimilation	* from API CAM
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68373]	urea ChEBI	-	hydrolysis	* from API CAM, API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #68373]	cefazolin ChEBI	yes	224	µg	* from API CAM
[Ref.: #68373]	erythromycin ChEBI	yes	14	µg	* from API CAM
[Ref.: #68373]	nalidixic acid ChEBI	yes	84	µg	* from API CAM

	Metabolite production	Metabolite	Production
[Ref.: #68373]		hydrogen sulfide ChEBI	no	* from API CAM
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68373]	alkaline phosphatase	-	3.1.3.1	* from API CAM
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #19121]	catalase	-	1.11.1.6
[Ref.: #68373]	catalase	-	1.11.1.6	* from API CAM
[Ref.: #19121]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68373]	esterase	+		* from API CAM
[Ref.: #68373]	gamma-glutamyltransferase	-	2.3.2.2	* from API CAM
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68373]	L-arginine arylamidase	-		* from API CAM
[Ref.: #68373]	L-aspartate arylamidase	-	3.4.11.21	* from API CAM
[Ref.: #68373]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API CAM
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE, API CAM
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #19121]	26577	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

API® CAM:

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

	API ID	Urease/urea hydrolysisURE	Reduction of nitrateNIT	EsteraseEST	Hippuric acidHIP	gamma-Glutamyl transferaseGGT	Reduction of Triphenyl tetrazolium chlorideTTC	Pyrrolidonyl arylamidasePYRA	L-arginine arylamidaseArgA	L-aspartic acid arylamidaseAspA	Alkaline phosphatasePAL	H2S productionH2S	Assimilation of D-glucoseGLU	Assimilation of succinateSUT	Growth inhibitionNAL	Growth inhibitionCFZ	Assimilation of acetateACE	Assimilation of propionic acidPROP	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Erythromycin resistance (+) sensitivity (-)ERO	CatalaseCAT
[Ref.: #19121]	4160	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.
[Ref.: #19121]	4159	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #19121]	Sample type/isolated from	raw sewage, waste water plant
[Ref.: #19121]	Geographic location (country and/or sea, region)	Reus
[Ref.: #19121]	Country	Spain
[Ref.: #19121]	Country ISO 3 Code	ESP
[Ref.: #19121]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Raw sewage from the wastewater treatment plant in the town of Reus
[Ref.: #67770]	Country	Spain
[Ref.: #67770]	Country ISO 3 Code	ESP
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Wastewater
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ115595 (>99% sequence identity) for Arcobacter from Microbeatlas

Aquatic Samples	9375
Soil Samples	408
Animal Samples	847
Plant Samples	137
Total Samples	10767

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

[Ref.: #19121]

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.: #19121]	Arcobacter defluvii strain SW28-11 16S ribosomal RNA gene, partial sequence	HQ115595	1402	GenBank ENA	873191 tax ID
[Ref.: #124043]	Arcobacter defluvii strain SW28-7 16S ribosomal RNA gene, partial sequence.	HQ115596	1402	GenBank ENA	873191 tax ID	*
[Ref.: #124043]	Arcobacter defluvii strain SW28-7 16S ribosomal RNA gene, partial sequence.	HQ115597	1402	GenBank ENA	873191 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Arcobacter defluvii CECT 7697	GCA_004115775	contig	GenBank ENA	873191 tax ID
[Ref.: #66792]	Arcobacter defluvii LMG 25694	GCA_013201725	complete	GenBank ENA	873191 tax ID	*
[Ref.: #66792]	Arcobacter defluvii strain CECT 7697	873191.8	wgs	PATRIC	873191 tax ID	*
[Ref.: #66792]	Arcobacter defluvii strain LMG 25694	873191.9	complete	PATRIC	873191 tax ID	*
[Ref.: #66792]	Arcobacter defluvii CECT 7697	2854854714	draft	JGI IMG/M	873191 tax ID	*

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: Arcobacter defluvii LMG 25694 NCBI: GCA_013201725.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.871	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	64.092	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	61.602	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.72	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	86.477	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	76.253	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arcobacter defluvii strain LMG 25694 PATRIC: 873191.9
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	95.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	52.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	88.1

Availability in culture collections External links

[Ref.: #19121]

Culture collection no.

DSM 25359, CECT 7697, LMG 25694, JCM 33356

[Ref.: #87193]

SI-ID 369524

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish.	Levican A, Collado L, Aguilar C, Yustes C, Dieguez AL, Romalde JL, Figueras MJ	Syst Appl Microbiol	10.1016/j.syapm.2012.01.002	2012	*
Phylogeny	Arcobacter defluvii sp. nov., isolated from sewage samples.	Collado L, Levican A, Perez J, Figueras MJ	Int J Syst Evol Microbiol	10.1099/ijs.0.025668-0	2010	*
Phylogeny	The Effect of Antibiotics on Planktonic Cells and Biofilm Formation Ability of Collected Arcobacter-like Strains and Strains Isolated within the Czech Republic.	Svarcova K, Pejchalova M, Silha D	Antibiotics (Basel)	10.3390/antibiotics11010087	2022	*

References

#19121

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25359

#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 )

#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) .

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

#68369

Automatically annotated from API 20NE .

#68373

Automatically annotated from API CAM .

#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 .

#87193

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-ID369524.1 )

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#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 .

* These data were automatically processed and therefore are not curated

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Arcobacter defluvii LMG 25694

Arcobacter defluvii strain LMG 25694

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