Acuticoccus yangtzensis (DSM 28604, CGMCC 1.12795, JL1095)

Name: Acuticoccus yangtzensis (DSM 28604, CGMCC 1.12795, JL1095)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132017

Type strain

Strain Designation JL1095

Culture col. no. DSM 28604 CGMCC 1.12795 JL1095

NCBI tax ID(s) 1443441

Special Collections DSMZ

Links

Acuticoccus yangtzensis JL1095 is a mesophilic prokaryote that was isolated from surface seawater from river estuary.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406376

DSM 28604

@ref 20215

Last LPSN update 2025-12-16 10:01:24

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Acuticoccaceae

Genus Acuticoccus

Species Acuticoccus yangtzensis

Full scientific name Acuticoccus yangtzensis Hou et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23808	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
23808	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93

Spore formation

@ref	Spore formation	Confidence
125438		90.83

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	gelatinase	+		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
23808	-	-	-	-	+	-	+	-	-	+	-	-	-	-	+/-	-	-	+/-	+/-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
23808	surface seawater from river estuary	Yangtze Estuary (31° N, 122° E)	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KF741873 (>99% sequence identity) for Acuticoccus yangtzensis subclade from Microbeatlas

Aquatic Samples	1030
Soil Samples	229
Animal Samples	215
Plant Samples	23
Total Samples	1497

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23808	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM192724v1 assembly for Acuticoccus yangtzensis JL1095	contig	GCA_001927245		1443441	70.77
66792	ASM307314v1 assembly for Acuticoccus yangtzensis JL1095	contig	GCA_003073145	1443441.5	1443441	58.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23808	Acuticoccus yangtzensis strain JL1095 16S ribosomal RNA gene, partial sequence	KF741873	1397		1443441

GC content

@ref	GC-content (mol%)	Method
23808	51.5	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: Acuticoccus yangtzensis JL1095
NCBI: GCA_001927245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.20	no
125439	motility	BacteriaNetⓘ	yes	51.20	no
125439	gram_stain	BacteriaNetⓘ	negative	89.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acuticoccus yangtzensis strain JL1095
PATRIC: 1443441.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	92.99	no
125438	spore-forming	spore-formingⓘ	no	90.83	no
125438	aerobic	aerobicⓘ	yes	83.49	no
125438	thermophilic	thermophileⓘ	no	95.47	no
125438	flagellated	motile2+ⓘ	yes	71.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary.	Hou L, Sun J, Xie X, Jiao N, Zhang Y	Stand Genomic Sci	10.1186/s40793-017-0295-6	2017
Genetics	Complete genome sequencing and analysis revealed the nitrogen utilization strategy of a novel Acuticoccus species isolated from surface water of the Indian Ocean.	Shi J, Zeng Y, Wang H, Niu Y, He P, Chen H	Mar Genomics	10.1016/j.margen.2022.100971	2022
Phylogeny	Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov.	Lai Q, Liu X, Sun F, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003289	2019
Phylogeny	Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis.	Yin Q, Liang J, Zhang L, Ma K, Hu ZL, Zhang Y, Xu Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.002990	2018
Phylogeny	Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary.	Hou L, Zhang Y, Sun J, Xie X	Curr Microbiol	10.1007/s00284-014-0698-1	2014
Phylogeny	Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum.	Tian J, Xu L, Zhang X, Sun JQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005521	2022

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 )
#23808	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28604
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#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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Acuticoccus yangtzensis (DSM 28604, CGMCC 1.12795, JL1095)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001927245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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