Glycomyces paridis (DSM 102295, KCTC 39745, CPCC 204357)

Name: Glycomyces paridis (DSM 102295, KCTC 39745, CPCC 204357)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158367

Type strain

Culture col. no. DSM 102295 KCTC 39745 CPCC 204357

NCBI tax ID(s) 2126555

Special Collections DSMZ KCTC Literature strains

History <- Y. Q. Zhang, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; CPCC 204357 <- X. M. Fang; CPCC 204357 <- Yu-Qin Zhang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

Links

Glycomyces paridis DSM 102295 is an aerobe bacterium that was isolated from From medicinal plant.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402434

KCTC 39745,DSM 102295

@ref 20215

Last LPSN update 2026-02-09 11:38:18

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Glycomycetales

Family Glycomycetaceae

Genus Glycomyces

Species Glycomyces paridis

Full scientific name Glycomyces paridis Fang et al. 2018

BacDive ID	Other strains from **Glycomyces paridis** (2)	Type strain
158365	G. paridis DSM 102293, KCTC 39747, CPCC 204354
158366	G. paridis DSM 102294, KCTC 39744, CPCC 204355

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.7
125439		94.8
125438		95
125438	positive	92.843

Pigmentation

@ref	Production	Name
65466		soluble pigment

Multimedia

@ref:	65043
multimedia content:	DSM_102295.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_102295.jpg
caption:	Medium 83 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
65043	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
65043	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
65466	Gauze's synthetic medium No. 1
65466	Czapek-Dox agar
65466	ISP 2 medium
65466	ISP 4 medium
65043	CZAPEK PEPTONE AGAR (DSMZ Medium 83)	Medium recipe at MediaDive	Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
65043	positive	growth	28
65466	negative	growth	15-30
65466	positive	optimum	28-30
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH
65466	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65466	aerobe
67771	aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
125439		94.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65466	NaCl	positive	growth	0-4 %

Observation

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65466	16651 ChEBI	(S)-lactate	-	carbon source
65466	64552 ChEBI	2-hydroxybutyrate	+	carbon source
65466	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
65466	30089 ChEBI	acetate	+	carbon source
65466	13705 ChEBI	acetoacetate	+	carbon source
65466	17925 ChEBI	alpha-D-glucose	+	carbon source
65466	73706 ChEBI	bromosuccinate	-	carbon source
65466	17057 ChEBI	cellobiose	+	carbon source
65466	16947 ChEBI	citrate	-	carbon source
65466	18333 ChEBI	D-arabitol	-	carbon source
65466	29990 ChEBI	D-aspartate	-	carbon source
65466	15824 ChEBI	D-fructose	+	carbon source
65466	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
65466	28847 ChEBI	D-fucose	-	carbon source
65466	12936 ChEBI	D-galactose	+	carbon source
65466	15588 ChEBI	D-malate	-	carbon source
65466	16899 ChEBI	D-mannitol	-	carbon source
65466	16024 ChEBI	D-mannose	+	carbon source
65466	16523 ChEBI	D-serine	-	carbon source
65466	17924 ChEBI	D-sorbitol	-	carbon source
65466	23652 ChEBI	dextrin	+	carbon source
65466	16537 ChEBI	galactarate	-	carbon source
65466	5291 ChEBI	gelatin	+	hydrolysis
65466	28066 ChEBI	gentiobiose	+	carbon source
65466	32323 ChEBI	glucuronamide	+	carbon source
65466	17754 ChEBI	glycerol	-	carbon source
65466	70744 ChEBI	glycine-proline	+	carbon source
65466	17596 ChEBI	inosine	+	carbon source
65466	16977 ChEBI	L-alanine	-	carbon source
65466	16467 ChEBI	L-arginine	-	carbon source
65466	18287 ChEBI	L-fucose	+	carbon source
65466	29985 ChEBI	L-glutamate	+	carbon source
65466	15971 ChEBI	L-histidine	+	carbon source
65466	15589 ChEBI	L-malate	-	carbon source
65466	18183 ChEBI	L-pyroglutamic acid	-	carbon source
65466	62345 ChEBI	L-rhamnose	+	carbon source
65466	17895 ChEBI	L-tyrosine	-	hydrolysis
65466	17716 ChEBI	lactose	+	carbon source
65466	17306 ChEBI	maltose	+	carbon source
65466	37657 ChEBI	methyl D-glucoside	-	carbon source
65466		milk	+	assimilation
65466	17268 ChEBI	myo-inositol	-	carbon source
65466	28037 ChEBI	N-acetylgalactosamine	-	carbon source
65466	35418 ChEBI	n-acetylneuraminate	-	carbon source
65466	17632 ChEBI	nitrate	+	reduction
65466	17272 ChEBI	propionate	+	carbon source
65466	16634 ChEBI	raffinose	-	carbon source
65466	17814 ChEBI	salicin	+	carbon source
65466	17164 ChEBI	stachyose	-	carbon source
65466	28017 ChEBI	starch	+	hydrolysis
65466	17992 ChEBI	sucrose	+	carbon source
65466	27082 ChEBI	trehalose	+	carbon source
65466	32528 ChEBI	turanose	+	carbon source
65466	53423 ChEBI	tween 40	+	carbon source
65466	16199 ChEBI	urea	-	hydrolysis

Enzymes

@ref	Value	Activity	Ec
65466	acid phosphatase	+	3.1.3.2
65466	alkaline phosphatase	+	3.1.3.1
65466	alpha-galactosidase	+	3.2.1.22
65466	alpha-glucosidase	+	3.2.1.20
65466	beta-glucosidase	+	3.2.1.21
65466	beta-glucuronidase	+	3.2.1.31
65466	catalase	+	1.11.1.6
65466	cystine arylamidase	+	3.4.11.3
65466	cytochrome oxidase	+	1.9.3.1
65466	esterase	+
65466	esterase Lipase (C 8)	+
65466	lipase	+
65466	naphthol-AS-BI-phosphohydrolase	+
65466	trypsin	+	3.4.21.4
65466	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture duration	Enrichment culture temperature	Isolation procedure	Latitude	Longitude
67771	From medicinal plant	Yunnan Province	China	CHN	Asia
65043	root of medicinal plant Paris polyphylla Sm. var. yunnanensis (Franch)	Yunnan province, Xishuangbanna (24° 56' N, 99° 55' E)	China	CHN	Asia				24.9333	99.9167 24.9333/99.9167
65466	the surfacesterilized root of Paris polyphylla Sm. var. yunnanensis (Franch)	Xishuangbanna in Yunnan province	China	CHN	Asia	7 days	28	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)

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM491215v1 assembly for Glycomyces paridis CPCC 204357	scaffold	GCA_004912155	2126555.3	2891549231	2126555	52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65043	Glycomyces paridis strain CPCC204357 16S ribosomal RNA gene, partial sequence	MG589943	1524		2126555

GC content

@ref	GC-content (mol%)	Method
65466	72.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Glycomyces paridis CPCC 204357
NCBI: GCA_004912155

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.60	no
125439	motility	BacteriaNetⓘ	no	94.80	no
125439	gram_stain	BacteriaNetⓘ	positive	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Glycomyces paridis CPCC 204357
NCBI: GCA_004912155.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.84	no
125438	anaerobic	anaerobicⓘ	no	95.73	yes
125438	aerobic	aerobicⓘ	yes	87.90	no
125438	spore-forming	spore-formingⓘ	yes	81.24	no
125438	thermophilic	thermophileⓘ	no	93.93	no
125438	flagellated	motile2+ⓘ	no	95.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Glycomyces paridis sp. nov., isolated from the medicinal plant Paris polyphylla.	Fang XM, Bai JL, Su J, Zhao LL, Liu HY, Ma BP, Zhang YQ, Yu LY.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002713	2018
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;
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Glycomyces paridis (DSM 102295, KCTC 39745, CPCC 204357)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_004912155

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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