Zhongshania aliphaticivorans (DSM 107354, JCM 30138, SM-2)

Name: Zhongshania aliphaticivorans (DSM 107354, JCM 30138, SM-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158174

Type strain

Strain Designation SM-2

Culture col. no. DSM 107354 JCM 30138 SM-2 KACC 18120

NCBI tax ID(s) 1470434

Special Collections DSMZ JCM

Links

Zhongshania aliphaticivorans SM-2 is a mesophilic prokaryote that was isolated from tidal flat.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 403472

JCM30138,DSM 107354

@ref 20215

Last LPSN update 2025-12-16 10:07:58

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Spongiibacteraceae

Genus Zhongshania

Species Zhongshania aliphaticivorans

Full scientific name Zhongshania aliphaticivorans Lo et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.9
125439		90.2
125438	negative	93

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64767	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
64767	positive	growth	28	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.8

Spore formation

@ref	Spore formation	Confidence
125439		97.9

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	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	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	cytochrome oxidase	+	1.9.3.1	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
64767	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64767	tidal flat	Danjin Bay	Republic of Korea	KOR	Asia
67770	Sea-tidal flat of Danjin bay in South Korea

Taxonmaps

69479

Global distribution of 16S sequence KF982857 (>99% sequence identity) for Zhongshania from Microbeatlas

Aquatic Samples	3986
Soil Samples	107
Animal Samples	283
Plant Samples	21
Total Samples	4397

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64767	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM158625v1 assembly for Zhongshania aliphaticivorans SM-2	complete	GCA_001586255	1470434.5	8064768857	1470434	98.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64767	Zhongshania aliphaticivorans strain SM-2 16S ribosomal RNA gene, partial sequence	KF982857	1403		1470434

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Zhongshania aliphaticivorans SM-2
NCBI: GCA_001586255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	yes	90.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zhongshania aliphaticivorans SM-2
NCBI: GCA_001586255.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.00	no
125438	anaerobic	anaerobicⓘ	no	93.62	no
125438	aerobic	aerobicⓘ	yes	81.26	no
125438	spore-forming	spore-formingⓘ	no	83.80	no
125438	thermophilic	thermophileⓘ	no	95.05	yes
125438	flagellated	motile2+ⓘ	yes	64.03	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome of Zhongshania aliphaticivorans SM-2(T), an aliphatic hydrocarbon-degrading bacterium isolated from tidal flat sediment.	Jia B, Jeong HI, Kim KH, Jeon CO	J Biotechnol	10.1016/j.jbiotec.2016.03.039	2016
Phylogeny	Zhongshania marina sp. nov., isolated from deep-sea water.	On YG, Oh JS, Roh DH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003195	2018
Phylogeny	Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov.	Lo N, Kang HJ, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.068593-0	2014
Phylogeny	Zhongshania aquimaris sp. nov., isolated from seawater.	Weerawongwiwat V, Kim JH, Lee JS, Yoon JH, Sukhoom A, Kim W	Arch Microbiol	10.1007/s00203-022-03184-2	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 )
#64767	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107354
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Rate our new design

Content

About us

Zhongshania aliphaticivorans (DSM 107354, JCM 30138, SM-2)

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_001586255

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media