Name: Dyadobacter beijingensis A54
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23879

Type strain:

Species: Dyadobacter beijingensis

Strain Designation: A54

Culture col. no.: DSM 21582, CGMCC 1.6375, JCM 14200, CIP 109570

Strain history: CIP <- 2007, JCM <- 2006, Z. Dong, Capital Normal Univ., Beijing, China: strain A54

NCBI tax ID(s): 1121482 (strain), 365489 (species)

SI-ID 302754

CGMCC 1.6375, JCM 14200, CIP 109570, DSM 21582

Section

Dyadobacter beijingensis A54 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of turf grasses irrigated with reclaimed water.

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	*Cytophagia*
	Order	*Cytophagales*
	Family	*Spirosomataceae*
	Genus	*Dyadobacter*
	Species	**Dyadobacter beijingensis**
	Full Scientific Name (LPSN)	Dyadobacter beijingensis Dong et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31981]	Gram stain	negative
[Ref.: #116780]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #31981]	Cell shape	rod-shaped
[Ref.: #116780]	Cell shape	rod-shaped

[Ref.: #31981]	Motility	no
[Ref.: #116780]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.285

[Ref.: #31981]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20531]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #20531]

Culture medium growth

[Ref.: #20531]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20531]

Culture medium composition

expand / minimize

[Ref.: #37768]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37768]

Culture medium growth

[Ref.: #37768]

Culture medium composition

expand / minimize

[Ref.: #116780]

Culture medium

CIP Medium 72

[Ref.: #116780]

Culture medium growth

[Ref.: #116780]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #20531]	growth	28 °C
[Ref.: #31981]	growth	04-35 °C
[Ref.: #31981]	optimum	28 °C
[Ref.: #37768]	growth	30 °C

[Ref.: #20531]	Temperature range	mesophilic
[Ref.: #31981]	Temperature range	mesophilic
[Ref.: #37768]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31981]			optimum	7
[Ref.: #31981]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31981]	Oxygen tolerance	aerobe
[Ref.: #116780]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.965

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31981]		NaCl		growth	0-1.5	%
[Ref.: #31981]		NaCl		optimum	0.75	%

[Ref.: #31981]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	citrate ChEBI	+	carbon source
[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.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	fructose ChEBI	+	carbon source
[Ref.: #31981]	fucose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31981]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31981]	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.: #31981]	lactose ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	mannitol ChEBI	+	carbon source
[Ref.: #31981]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	melibiose ChEBI	+	carbon source
[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.: #31981]	myo-inositol ChEBI	+	carbon source
[Ref.: #68371]	myo-inositol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #116780]	nitrate ChEBI	-	reduction
[Ref.: #116780]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31981]	raffinose ChEBI	+	carbon source
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31981]	salicin ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31981]	trehalose ChEBI	+	carbon source
[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
[Ref.: #31981]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116780]		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.: #31981]	catalase	+	1.11.1.6
[Ref.: #116780]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31981]	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.: #116780]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #116780]	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.: #116780]	11600	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.: #116780]	11964	-	+	+	+	-	+	+	+	+	-	+	+	+	+	-	+	+	+	+	-

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

[Ref.: #20531]	Sample type/isolated from	rhizosphere of turf grasses irrigated with reclaimed water
[Ref.: #20531]	Geographic location (country and/or sea, region)	Taoranting Park, Beijing
[Ref.: #20531]	Country	China
[Ref.: #20531]	Country ISO 3 Code	CHN
[Ref.: #20531]	Continent	Asia

[Ref.: #116780]	Sample type/isolated from	Rhizosphere, turf grasses
[Ref.: #116780]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #116780]	Country	China
[Ref.: #116780]	Country ISO 3 Code	CHN
[Ref.: #116780]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ335125 (>99% sequence identity) for Dyadobacter beijingensis from Microbeatlas

Aquatic Samples	68
Soil Samples	102
Animal Samples	766
Plant Samples	54
Total Samples	990

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

[Ref.: #20531]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116780]	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.: #31981]	Dyadobacter beijingensis strain A54 16S ribosomal RNA gene, partial sequence	DQ335125	1411	GenBank	365489 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dyadobacter beijingensis DSM 21582	GCA_000382205	scaffold	GenBank	1121482 tax ID	*
[Ref.: #66792]	Dyadobacter beijingensis CGMCC 1.6375	GCA_014645155	scaffold	GenBank	365489 tax ID	*
[Ref.: #66792]	Dyadobacter beijingensis DSM 21582	1121482.3	wgs	PATRIC	1121482 tax ID	*
[Ref.: #66792]	Dyadobacter beijingensis strain CGMCC 1.6375	365489.3	wgs	PATRIC	365489 tax ID	*
[Ref.: #66792]	Dyadobacter beijingensis DSM 21582	2522125168	draft	JGI IMG/M	1121482 tax ID	*

[Ref.: #31981]	GC-content	49.2 mol%
[Ref.: #20531]	GC-content	52.1 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: Dyadobacter beijingensis DSM 21582 DSM 21582 NCBI: GCA_000382205.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dyadobacter beijingensis DSM 21582 DSM 21582 NCBI: GCA_000382205.1
[Ref.: #69480]	motile	no	91.513	yes
[Ref.: #69480]	flagellated	no	97.557	yes
[Ref.: #69480]	gram-positive	no	97.883	yes
[Ref.: #69480]	anaerobic	no	99.413	yes
[Ref.: #69480]	aerobic	yes	91.712	no
[Ref.: #69480]	halophile	no	95.559	no
[Ref.: #69480]	spore-forming	no	93.91	no
[Ref.: #69480]	thermophile	no	99.206	no
[Ref.: #69480]	glucose-util	yes	89.371	no
[Ref.: #69480]	glucose-ferment	no	86.046	no

Availability in culture collections External links

[Ref.: #20531]

Culture collection no.

DSM 21582, CGMCC 1.6375, JCM 14200, CIP 109570

[Ref.: #87890]

SI-ID 302754

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001304	2016	*
Phylogeny	Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory.	Wang L, Chen L, Ling Q, Li CC, Tao Y, Wang M	Int J Syst Evol Microbiol	10.1099/ijs.0.000069	2015	*
Phylogeny	Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil.	Lee M, Woo SG, Park J, Yoo SA	Int J Syst Evol Microbiol	10.1099/ijs.0.019653-0	2009	*
Phylogeny	Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China.	Dong Z, Guo X, Zhang X, Qiu F, Sun L, Gong H, Zhang F	Int J Syst Evol Microbiol	10.1099/ijs.0.64754-0	2007	*

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 )

#20531

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21582

#31981

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 #28235 (see below)

#37768 ; 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 )

#87890

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-ID302754.1 )

#116780 Collection of Institut Pasteur ; Curators of the CIP; CIP 109570

#28235

IJSEM 862 2007 ( DOI 10.1099/ijs.0.64754-0 , PubMed 17392220 )

* These data were automatically processed and therefore are not curated

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Dyadobacter beijingensis DSM 21582 DSM 21582

Dyadobacter beijingensis DSM 21582 DSM 21582

Change proposal

Change proposal