Acidicapsa dinghuensis (CGMCC 1.15449, LMG 29213, 4GSKX)

Name: Acidicapsa dinghuensis (CGMCC 1.15449, LMG 29213, 4GSKX)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159709

Type strain

Strain Designation 4GSKX

Culture col. no. CGMCC 1.15449 LMG 29213 4GSKX

NCBI tax ID(s) 2218256

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Acidicapsa dinghuensis 4GSKX is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from upper layer of forest soil .

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 366401

LMG 29213

@ref 20215

Last LPSN update 2025-12-16 10:08:19

Domain Pseudomonadati

Phylum Acidobacteriota

Class Terriglobia

Order Terriglobales

Family Acidobacteriaceae

Genus Acidicapsa

Species Acidicapsa dinghuensis

Full scientific name Acidicapsa dinghuensis Ou Yang et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
66598	negative	0.5-1.5 µm	0.4-0.8 µm	rod-shaped
125439	negative
125438	negative

Colony morphology

@ref	Colony color	Colony shape	Medium used
66598	semitransparent beige	circular	MM1F agar medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition
66598	MM1F agar medium		(0.04 g MgSO4 x 7H2O, 0.02 g CaCl2 x 2H2O, 0.05 g yeast extract, 0.5 g fructose in 1 litre of distilled water, pH 5.0)

Culture temp

@ref	Growth	Type	Temperature (°C)
66598	positive	growth	12-37
66598	positive	optimum	25-30

Culture pH

@ref	Ability	Type	PH
66598	positive	optimum	4.5-5
66598	positive	growth	4-6.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66598	aerobe
125439	obligate aerobe

Spore formation

66598

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66598	NaCl	positive	growth	0-1 %(w/v)

Observation

@ref	Observation
66598	non-capsule-forming
66598	reproduce by binary fusion

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66598	27613 ChEBI	amygdalin	-	carbon source
66598	18305 ChEBI	arbutin	-	carbon source
66598	17057 ChEBI	cellobiose	-	carbon source
66598	17108 ChEBI	D-arabinose	-	carbon source
66598	18333 ChEBI	D-arabitol	-	carbon source
66598	15824 ChEBI	D-fructose	+	carbon source
66598	28847 ChEBI	D-fucose	-	carbon source
66598	12936 ChEBI	D-galactose	+	carbon source
66598	17634 ChEBI	D-glucose	+	carbon source
66598	62318 ChEBI	D-lyxose	-	carbon source
66598	16899 ChEBI	D-mannitol	-	carbon source
66598	16024 ChEBI	D-mannose	+	carbon source
66598	16988 ChEBI	D-ribose	-	carbon source
66598	17924 ChEBI	D-sorbitol	-	carbon source
66598	16443 ChEBI	D-tagatose	-	carbon source
66598	65327 ChEBI	D-xylose	+	carbon source
66598	17113 ChEBI	erythritol	-	carbon source
66598	4853 ChEBI	esculin	+	hydrolysis
66598		esculin ferric citrate	+	carbon source
66598	16813 ChEBI	galactitol	-	carbon source
66598	5291 ChEBI	gelatin	+	hydrolysis
66598	28066 ChEBI	gentiobiose	+	carbon source
66598	17234 ChEBI	glucose	-	fermentation
66598	17754 ChEBI	glycerol	+	carbon source
66598	28087 ChEBI	glycogen	-	carbon source
66598	15443 ChEBI	inulin	+	carbon source
66598	30849 ChEBI	L-arabinose	-	carbon source
66598	18403 ChEBI	L-arabitol	-	carbon source
66598	18287 ChEBI	L-fucose	-	carbon source
66598	62345 ChEBI	L-rhamnose	+	carbon source
66598	17266 ChEBI	L-sorbose	-	carbon source
66598	65328 ChEBI	L-xylose	-	carbon source
66598	17716 ChEBI	lactose	-	carbon source
66598	17306 ChEBI	maltose	-	carbon source
66598	6731 ChEBI	melezitose	+	carbon source
66598	28053 ChEBI	melibiose	+	carbon source
66598	320061 ChEBI	methyl alpha-D-glucopyranoside	-	carbon source
66598	43943 ChEBI	methyl alpha-D-mannoside	+	carbon source
66598	74863 ChEBI	methyl beta-D-xylopyranoside	+	carbon source
66598	17268 ChEBI	myo-inositol	-	carbon source
66598	59640 ChEBI	N-acetylglucosamine	-	carbon source
66598	17632 ChEBI	nitrate	-	reduction
66598		potassium 2-dehydro-D-gluconate	+	carbon source
66598		potassium 5-dehydro-D-gluconate	-	carbon source
66598	32032 ChEBI	potassium gluconate	-	carbon source
66598	16634 ChEBI	raffinose	-	carbon source
66598	15963 ChEBI	ribitol	-	carbon source
66598	17814 ChEBI	salicin	-	carbon source
66598	28017 ChEBI	starch	-	carbon source
66598	17992 ChEBI	sucrose	+	carbon source
66598	27082 ChEBI	trehalose	-	carbon source
66598	32528 ChEBI	turanose	+	carbon source
66598	17151 ChEBI	xylitol	-	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.
66598	2637	Amikacin	30 µg (disc)
66598	17698	chloramphenicol
66598	100241	ciprofloxacin
66598	48923	erythromycin
66598	17833	gentamicin	10 µg (disc)
66598	6104	kanamycin	30 µg (disc)
66598	7507	neomycin
66598	7528	netilmycin	30 µg (disc)
66598	17334	penicillin
66598	59062	polymyxin
66598	17076	streptomycin
66598	27902	tetracycline
66598	28864	tobramycin
66598	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66598	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
66598	acid phosphatase	+	3.1.3.2
66598	alkaline phosphatase	+	3.1.3.1
66598	alpha-chymotrypsin	-	3.4.21.1
66598	alpha-fucosidase	+	3.2.1.51
66598	alpha-galactosidase	+	3.2.1.22
66598	alpha-glucosidase	+	3.2.1.20
66598	alpha-mannosidase	+	3.2.1.24
66598	beta-galactosidase	+	3.2.1.23
66598	beta-glucosidase	+	3.2.1.21
66598	beta-glucuronidase	+	3.2.1.31
66598	catalase	-	1.11.1.6
66598	cystine arylamidase	+	3.4.11.3
66598	cytochrome oxidase	-	1.9.3.1
66598	esterase (C 4)	+
66598	esterase Lipase (C 8)	-
66598	leucine arylamidase	+	3.4.11.1
66598	lipase (C 14)	-
66598	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66598	naphthol-AS-BI-phosphohydrolase	+
66598	trypsin	-	3.4.21.4
66598	urease	-	3.5.1.5
66598	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66598	upper layer of forest soil (0-25 cm)	Dinghushan Biosphere Reserve, located at Guangdong Province	China	CHN	Asia	MM1F agar medium	(0.04 g MgSO4 x 7H2O, 0.02 g CaCl2 x 2H2O, 0.05 g yeast extract, 0.5 g fructose in 1 litre of distilled water, pH 5.0)	2 weeks	28	sample was suspended in 100 mM phosphate buffered saline, 1/10 diluted three times, and then innoculated on MM1F agar medium and incubated at 28°C for 2 weeks.

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2568568v1 assembly for Acidicapsa dinghuensis 4GSKX	contig	GCA_025685685	2218256.3	8047326792	2218256	71.4
124043	ASM4265662v1 assembly for Acidicapsa dinghuensis CGMCC 1.15449	contig	GCA_042656625			2218256	70.85

Genome browser: GCA_025685685

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66598	Acidicapsa dinghuensis strain 4GSKX 16S ribosomal RNA gene, partial sequence	MF150300	1464		2218256

GC content

@ref	GC-content (mol%)	Method
66598	52.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidicapsa dinghuensis 4GSKX
NCBI: GCA_025685685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	73.00	no
125439	motility	BacteriaNetⓘ	no	78.50	no
125439	gram_stain	BacteriaNetⓘ	negative	92.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidicapsa dinghuensis 4GSKX
NCBI: GCA_025685685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.21	yes
125438	anaerobic	anaerobicⓘ	no	88.33	yes
125438	aerobic	aerobicⓘ	yes	78.99	no
125438	spore-forming	spore-formingⓘ	no	82.36	no
125438	thermophilic	thermophileⓘ	no	95.38	no
125438	flagellated	motile2+ⓘ	no	77.55	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Acidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil.	Ou-Yang TN, Xia F, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002846	2018

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 )
#66598	Tian-na Ou-yang, Fan Xia, Li-hong Qiu: Acidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil. IJSEM 68: 2364 - 2369 2018 ( DOI 10.1099/ijsem.0.002846 , PubMed 29873630 )
#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) .
#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 .
#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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Acidicapsa dinghuensis (CGMCC 1.15449, LMG 29213, 4GSKX)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_025685685

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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