Name: Deefgea rivuli DSM 18356
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10515

Type strain:

Species: Deefgea rivuli

Culture col. no.: DSM 18356, WB 3.4-79, CIP 109326

Strain history: CIP <- 2006, DSMZ

NCBI tax ID(s): 1121375 (strain), 400948 (species)

SI-ID 297185

CIP 109326, DSM 18356

Other strains from Deefgea rivuli

D. rivuli DSM 18355, WB 3.3-25

Section

Deefgea rivuli DSM 18356 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from hardwater creek.

Gram-negative
motile
rod-shaped
facultative 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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Neisseriales*
	Family	*Chromobacteriaceae*
	Genus	*Deefgea*
	Species	**Deefgea rivuli**
	Full Scientific Name (LPSN)	Deefgea rivuli Stackebrandt et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31990]	Gram stain	negative
[Ref.: #122242]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.992

[Ref.: #31990]	Cell length	3.5 µm

[Ref.: #31990]	Cell width	0.75 µm

[Ref.: #31990]	Cell shape	rod-shaped
[Ref.: #122242]	Cell shape	rod-shaped

[Ref.: #31990]	Motility	yes
[Ref.: #122242]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.591

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7435]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7435]

Culture medium growth

[Ref.: #7435]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7435]

Culture medium composition

expand / minimize

[Ref.: #37512]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #37512]

Culture medium growth

[Ref.: #37512]

Culture medium composition

expand / minimize

[Ref.: #122242]

Culture medium

CIP Medium 566

[Ref.: #122242]

Culture medium growth

[Ref.: #122242]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7435]	growth	28 °C
[Ref.: #31990]	growth	04-32 °C
[Ref.: #31990]	optimum	25.5 °C
[Ref.: #37512]	growth	25 °C

[Ref.: #7435]	Temperature range	mesophilic
[Ref.: #31990]	Temperature range	mesophilic
[Ref.: #37512]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31990]			optimum	7.45
[Ref.: #31990]			growth	5.8-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31990]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31990]		NaCl		growth	<2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	dextrin ChEBI	+	carbon source
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31990]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31990]	nitrate ChEBI	+	reduction
[Ref.: #122242]	nitrate ChEBI	+	reduction
[Ref.: #122242]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	ribose ChEBI	+	carbon source
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31990]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122242]		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.: #31990]	catalase	+	1.11.1.6
[Ref.: #122242]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31990]	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.: #122242]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122242]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #122242]	11522	not determinedn.d.	-	-	-	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	+/-	+/-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+/-

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.: #122242]	11792	-	+	+	-	-	+	-	-	-	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #7435]	Sample type/isolated from	hardwater creek
[Ref.: #7435]	Geographic location (country and/or sea, region)	Harz mountains, Westerhöfer Bach
[Ref.: #7435]	Country	Germany
[Ref.: #7435]	Country ISO 3 Code	DEU
[Ref.: #7435]	Continent	Europe

[Ref.: #122242]	Sample type/isolated from	Environment, Hardwater creek
[Ref.: #122242]	Geographic location (country and/or sea, region)	Harz Mountains
[Ref.: #122242]	Country	Germany
[Ref.: #122242]	Country ISO 3 Code	DEU
[Ref.: #122242]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM397080 (>99% sequence identity) for Deefgea rivuli subclade from Microbeatlas

Aquatic Samples	760
Soil Samples	50
Animal Samples	226
Plant Samples	16
Total Samples	1052

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

[Ref.: #7435]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122242]	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.: #7435]	Deefgea rivuli partial 16S rRNA gene, type strain WB 3.4-79T	AM397080	1508	ENA	400948 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Deefgea rivuli DSM 18356	GCA_000620145	scaffold	GenBank	1121375 tax ID	*
[Ref.: #66792]	Deefgea rivuli DSM 18356	1121375.3	wgs	PATRIC	1121375 tax ID	*
[Ref.: #66792]	Deefgea rivuli DSM 18356	2556921014	draft	JGI IMG/M	1121375 tax ID	*

[Ref.: #31990]

GC-content

48.5 mol%

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: Deefgea rivuli DSM 18356 DSM 18356 NCBI: GCA_000620145.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Deefgea rivuli DSM 18356 DSM 18356 NCBI: GCA_000620145.1
[Ref.: #69480]	motile	yes	92.261	no
[Ref.: #69480]	flagellated	yes	89.196	no
[Ref.: #69480]	gram-positive	no	98.069	yes
[Ref.: #69480]	anaerobic	no	97.71	yes
[Ref.: #69480]	halophile	no	93.607	no
[Ref.: #69480]	spore-forming	no	91.263	no
[Ref.: #69480]	thermophile	no	99.56	no
[Ref.: #69480]	glucose-util	yes	86.966	yes
[Ref.: #69480]	aerobic	yes	64.548	no
[Ref.: #69480]	glucose-ferment	no	80.574	no

Availability in culture collections External links

[Ref.: #7435]

Culture collection no.

DSM 18356, WB 3.4-79, CIP 109326

[Ref.: #79792]

SI-ID 297185

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deefgea salmonis sp. nov., isolated from gills of rainbow trout (Oncorhynchus mykiss).	Chen MQ, Tian Y, Zhang C, Zhou JS, Tashi L, Wang WL, Pan H	Arch Microbiol	10.1007/s00203-022-02980-0	2022	*
Phylogeny	Deefgea chitinilytica sp. nov., isolated from a wetland.	Chen WM, Chung YN, Chiu TF, Cheng CY, Arun AB, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.015263-0	2009	*
Phylogeny	Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture.	Chang SC, Chen WM, Wang JT, Wu MC	Int J Syst Evol Microbiol	10.1099/ijs.0.65168-0	2007	*
Phylogeny	Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria.	Stackebrandt E, Lang E, Cousin S, Pauker O, Brambilla E, Kroppenstedt R, Lunsdorf H	Int J Syst Evol Microbiol	10.1099/ijs.0.64771-0	2007	*
Phylogeny	Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish.	Gim DH, Lee SY, Han JE, Lee JY, Kang SM, Bae JW	J Microbiol	10.1007/s12275-022-2250-5	2022	*

References

#7435

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18356

#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 )

#31990

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 #28244 (see below)

#37512 ; Curators of the CIP;

#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) .

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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) .

#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 )

#79792

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-ID297185.1 )

#122242 Collection of Institut Pasteur ; Curators of the CIP; CIP 109326

#28244

IJSEM 639 2007 ( DOI 10.1099/ijs.0.64771-0 , PubMed 17329799 )

* These data were automatically processed and therefore are not curated

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Deefgea rivuli DSM 18356 DSM 18356

Deefgea rivuli DSM 18356 DSM 18356

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