Name: Glycomyces paridis DSM 102295
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158367

Type strain:

Species: Glycomyces paridis

Culture col. no.: DSM 102295, KCTC 39745, CPCC 204357

Strain history: <- Yu-Qin Zhang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

NCBI tax ID(s): 2126555 (species)

SI-ID 402434

DSM 102295

Other strains from Glycomyces paridis

G. paridis DSM 102293, KCTC 39747, CPCC 204354
G. paridis DSM 102294, KCTC 39744, CPCC 204355

Section

Glycomyces paridis DSM 102295 is an aerobe, spore-forming, mesophilic bacterium that was isolated from From medicinal plant.

spore-forming
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Glycomycetales*
	Family	*Glycomycetaceae*
	Genus	*Glycomyces*
	Species	**Glycomyces paridis**
	Full Scientific Name (LPSN)	Glycomyces paridis Fang et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	no Confidence in %90.018

[Ref.: #65466]	Pigment production	no
[Ref.: #65466]	Pigment name	soluble pigment

Multimedia content

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Caption:

Medium 83 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

Gauze's synthetic medium No. 1

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Culture medium growth

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Culture medium

Czapek-Dox agar

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Culture medium growth

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Culture medium

ISP 2 medium

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Culture medium growth

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Culture medium

ISP 4 medium

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #65043]		growth	28 °C
[Ref.: #65466]	no	growth	15-30 °C
[Ref.: #65466]		optimum	28-30 °C
[Ref.: #67771]		growth	28 °C

[Ref.: #65043]	Temperature range	mesophilic
[Ref.: #65466]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65466]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65466]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]	Ability of spore formation	yes Confidence in %91.895
[Ref.: #69481]	Ability of spore formation	yes Confidence in %98

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65466]		NaCl		growth	0-4	%

[Ref.: #65466]	Observation	forms yellowish-white substrate mycelium and white aerial mycelium that fragments into square-ended conidia on Gauze's synthetic medium No. 1
[Ref.: #65466]	Observation	whole-cell hydrolysates contain meso-diaminopimelic acid as the diamino acid and the whole-cell sugars are galactose, glucose, ribose and xylose
[Ref.: #65466]	Observation	polar lipid profile consists of DPG, PG, UPL and UL. MK-10 (H 4 ) is the predominant menaquinone

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65466]	(S)-lactate ChEBI	-	carbon source
[Ref.: #65466]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #65466]	3-O-methyl-D-glucose ChEBI	-	carbon source
[Ref.: #65466]	acetate ChEBI	+	carbon source
[Ref.: #65466]	acetoacetate ChEBI	+	carbon source
[Ref.: #65466]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #65466]	bromosuccinate ChEBI	-	carbon source
[Ref.: #65466]	cellobiose ChEBI	+	carbon source
[Ref.: #65466]	citrate ChEBI	-	carbon source
[Ref.: #65466]	D-arabitol ChEBI	-	carbon source
[Ref.: #65466]	D-aspartate ChEBI	-	carbon source
[Ref.: #65466]	D-fructose ChEBI	+	carbon source
[Ref.: #65466]	D-fructose 6-phosphate ChEBI	+	carbon source
[Ref.: #65466]	D-fucose ChEBI	-	carbon source
[Ref.: #65466]	D-galactose ChEBI	+	carbon source
[Ref.: #65466]	D-malate ChEBI	-	carbon source
[Ref.: #65466]	D-mannitol ChEBI	-	carbon source
[Ref.: #65466]	D-mannose ChEBI	+	carbon source
[Ref.: #65466]	D-serine ChEBI	-	carbon source
[Ref.: #65466]	D-sorbitol ChEBI	-	carbon source
[Ref.: #65466]	dextrin ChEBI	+	carbon source
[Ref.: #65466]	galactarate ChEBI	-	carbon source
[Ref.: #65466]	gelatin ChEBI	+	hydrolysis
[Ref.: #65466]	gentiobiose ChEBI	+	carbon source
[Ref.: #65466]	glucuronamide ChEBI	+	carbon source
[Ref.: #65466]	glycerol ChEBI	-	carbon source
[Ref.: #65466]	glycine-proline ChEBI	+	carbon source
[Ref.: #65466]	inosine ChEBI	+	carbon source
[Ref.: #65466]	L-alanine ChEBI	-	carbon source
[Ref.: #65466]	L-arginine ChEBI	-	carbon source
[Ref.: #65466]	L-fucose ChEBI	+	carbon source
[Ref.: #65466]	L-glutamate ChEBI	+	carbon source
[Ref.: #65466]	L-histidine ChEBI	+	carbon source
[Ref.: #65466]	L-malate ChEBI	-	carbon source
[Ref.: #65466]	L-pyroglutamic acid ChEBI	-	carbon source
[Ref.: #65466]	L-rhamnose ChEBI	+	carbon source
[Ref.: #65466]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #65466]	lactose ChEBI	+	carbon source
[Ref.: #65466]	maltose ChEBI	+	carbon source
[Ref.: #65466]	methyl D-glucoside ChEBI	-	carbon source
[Ref.: #65466]	milk	+	assimilation
[Ref.: #65466]	myo-inositol ChEBI	-	carbon source
[Ref.: #65466]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #65466]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #65466]	nitrate ChEBI	+	reduction
[Ref.: #65466]	propionate ChEBI	+	carbon source
[Ref.: #65466]	raffinose ChEBI	-	carbon source
[Ref.: #65466]	salicin ChEBI	+	carbon source
[Ref.: #65466]	stachyose ChEBI	-	carbon source
[Ref.: #65466]	starch ChEBI	+	hydrolysis
[Ref.: #65466]	sucrose ChEBI	+	carbon source
[Ref.: #65466]	trehalose ChEBI	+	carbon source
[Ref.: #65466]	turanose ChEBI	+	carbon source
[Ref.: #65466]	tween 40 ChEBI	+	carbon source
[Ref.: #65466]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #65466]	acid phosphatase	+	3.1.3.2
[Ref.: #65466]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65466]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65466]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65466]	beta-glucosidase	+	3.2.1.21
[Ref.: #65466]	beta-glucuronidase	+	3.2.1.31
[Ref.: #65466]	catalase	+	1.11.1.6
[Ref.: #65466]	cystine arylamidase	+	3.4.11.3
[Ref.: #65466]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65466]	esterase	+
[Ref.: #65466]	esterase Lipase (C 8)	+
[Ref.: #65466]	lipase	+
[Ref.: #65466]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65466]	trypsin	+	3.4.21.4
[Ref.: #65466]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67771]	Sample type/isolated from	From medicinal plant
[Ref.: #67771]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #65043]	Sample type/isolated from	root of medicinal plant Paris polyphylla Sm. var. yunnanensis (Franch)
[Ref.: #65043]	Geographic location (country and/or sea, region)	Yunnan province, Xishuangbanna (24° 56' N, 99° 55' E)
[Ref.: #65043]	Country	China
[Ref.: #65043]	Country ISO 3 Code	CHN
[Ref.: #65043]	Continent	Asia
[Ref.: #65043]	Geographic location	24.9333°/99.9167°

[Ref.: #65466]	Sample type/isolated from	the surfacesterilized root of Paris polyphylla Sm. var. yunnanensis (Franch)
[Ref.: #65466]	Geographic location (country and/or sea, region)	Xishuangbanna in Yunnan province
[Ref.: #65466]	Country	China
[Ref.: #65466]	Country ISO 3 Code	CHN
[Ref.: #65466]	Continent	Asia
[Ref.: #65466]	Enrichment culture duration	7 days
[Ref.: #65466]	Enrichment culture temperature	28 ̊C
[Ref.: #65466]	Isolation/enrichment procedure	plant roots were surface-sterilized using the method of Coombs and Franco, Strains were isolated on isolation medium plates containing 2g starch, 0.5g K2HPO4 , 0.5g MgSO4 , 1g KNO3 , 0.4g NaCl, 0.01g FeSO4 7H2O and 15g agar per litre (pH 7.2). The purified isolates were cultured on Gauze's synthetic medium No. 1 (20g soluble starch, 1g KNO3 , 0.5g NaCl, 0.5g MgSO4 7H2O, 0.5g K2HPO4 , 0.01g FeSO4 7H2O, 15g agar per litre; https://www.dsmz.de)
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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.: #65043]	Glycomyces sp. strain CPCC204357 16S ribosomal RNA gene, partial sequence	MG589943	1524	ENA	2126555 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Glycomyces paridis CPCC 204357	GCA_004912155	scaffold	GenBank	2126555 tax ID	*
[Ref.: #66792]	Glycomyces paridis strain CPCC 204357	2126555.3	wgs	PATRIC	2126555 tax ID	*
[Ref.: #66792]	Glycomyces paridis CPCC 204357	2891549231	draft	JGI IMG/M	2126555 tax ID	*

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GC-content

72.2 mol%

thermal denaturation, midpoint method (Tm)

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: Glycomyces paridis CPCC 204357 NCBI: GCA_004912155.1
[Ref.: #69481]	spore-forming	yes	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Glycomyces paridis CPCC 204357 NCBI: GCA_004912155.1
[Ref.: #69480]	motile	no	93.587	no
[Ref.: #69480]	flagellated	no	97.714	no
[Ref.: #69480]	gram-positive	yes	91.752	no
[Ref.: #69480]	anaerobic	no	99.026	yes
[Ref.: #69480]	aerobic	yes	92.343	yes
[Ref.: #69480]	halophile	no	75.196	no
[Ref.: #69480]	spore-forming	yes	93.029	no
[Ref.: #69480]	glucose-util	yes	85.428	no
[Ref.: #69480]	thermophile	no	97.893	no
[Ref.: #69480]	glucose-ferment	no	87.506	no

Availability in culture collections External links

[Ref.: #65043]

Culture collection no.

DSM 102295, KCTC 39745, CPCC 204357

[Ref.: #111172]

SI-ID 402434

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Glycomyces albidus sp. nov., a novel actinobacterium isolated from rhizosphere soil of wheat (Triticum aestivum L.).	Qian L, Duan L, Lin J, Yang Y, Song J, Wang X, Zhao J, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004131	2020	*
Phylogeny	Glycomyces buryatensis sp. nov., an actinobacterium isolated from steppe soil.	Nikitina E, Liu SW, Li FN, Buyantueva L, Abidueva E, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003923	2020	*

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 )

#65043

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102295

#65466

Xiao-Mei Fang, Jing-Lin Bai, Jing Su, Li-Li Zhao, Hong-Yu Liu, Bai-Ping Ma, Yu-Qin Zhang and Li-Yan Yu: Glycomyces paridis sp. nov., isolated from the medicinal plant Paris polyphylla. IJSEM 68: 1578 - 1583 2018 ( DOI 10.1099/ijsem.0.002713 , PubMed 29547096 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#111172

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-ID402434.1 )

* These data were automatically processed and therefore are not curated

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Glycomyces paridis CPCC 204357

Glycomyces paridis CPCC 204357

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