Name: Dongshaea marina DM2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164191

Type strain:

Species: Dongshaea marina

Strain Designation: DM2

Culture col. no.: JCM 32096, BCRC 81069

Strain history: W. Y. Shieh; Inst. of Oceanogr., Natl. Taiwan Univ., Taiwan; DM2.

NCBI tax ID(s): 2047966 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Dongshaea marina DM2 is a facultative anaerobe, halophilic, chemoheterotroph bacterium that forms circular colonies and was isolated from Lagoon sediment sample of Dongsha Island.

colony-forming
Gram-negative
rod-shaped
chemoheterotroph
facultative anaerobe
halophilic
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Aeromonadales*
	Family	*Aeromonadaceae*
	Genus	*Dongshaea*
	Species	**Dongshaea marina**
	Full Scientific Name (LPSN)	Dongshaea marina Huang et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67775]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %97.7
[Ref.: #125438]	Gram stain	negative Confidence in %99.994

[Ref.: #67775]	Cell length	1.4-2.2 µm

[Ref.: #67775]	Cell width	1-1.2 µm

[Ref.: #67775]	Cell shape	rod-shaped

[Ref.: #67775]	Motility	no
[Ref.: #67775]	Motility	yes

[Ref.: #67775]	Flagellum arrangement	monotrichous

[Ref.: #67775]	Colony size	2-4 mm
[Ref.: #67775]	Colony color	off-white
[Ref.: #67775]	Colony shape	circular
[Ref.: #67775]	Incubation period	3-5 days
[Ref.: #67775]	Cultivation medium used	Peptone-yeast extract agar

Information on culture and growth conditions Culture and growth conditions

	Kind of temperature		Temperature
[Ref.: #67770]		growth	30 °C
[Ref.: #67775]		growth	15-35 °C
[Ref.: #67775]		optimum	30 °C
[Ref.: #67775]	negative	growth	4-10 °C
[Ref.: #67775]	negative	growth	42 °C

	pH	Kind of pH		pH
[Ref.: #67775]			growth	5-9
[Ref.: #67775]		no	growth	10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67775]

Oxygen tolerance

facultative anaerobe

[Ref.: #67775]

Nutrition type

chemoheterotroph

[Ref.: #67775]	Type of spore	endospore
[Ref.: #67775]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.691

[Ref.: #67775]

Halophily / tolerance level

halophilic

	Salt	Tested relation		Salt conc.
[Ref.: #67775]	NaCl		growth	1-5	%
[Ref.: #67775]	NaCl		optimum	2-3	%
[Ref.: #67775]	NaCl	no	growth	0	%
[Ref.: #67775]	NaCl	no	growth	7-10	%

[Ref.: #67770]	Observation	quinones: Q-8
[Ref.: #67775]	Observation	Nearly all cells are non-motile and non-flagellated, whereas a few of the cells exhibit motility and monotrichous flagella.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67775]	agar ChEBI	-	hydrolysis
[Ref.: #67775]	casein	-	hydrolysis
[Ref.: #67775]	cellobiose ChEBI	+	builds acid from
[Ref.: #67775]	cellobiose ChEBI	+	builds gas from
[Ref.: #67775]	D-galactose ChEBI	+	builds acid from
[Ref.: #67775]	D-galactose ChEBI	+	builds gas from
[Ref.: #67775]	D-glucose ChEBI	+	fermentation
[Ref.: #67775]	D-mannose ChEBI	+	builds acid from
[Ref.: #67775]	D-mannose ChEBI	+	builds gas from
[Ref.: #67775]	D-xylose ChEBI	+	builds acid from
[Ref.: #67775]	D-xylose ChEBI	+	builds gas from
[Ref.: #67775]	dna ChEBI	-	hydrolysis
[Ref.: #67775]	gelatin ChEBI	-	hydrolysis
[Ref.: #67775]	nitrate ChEBI	+	reduction
[Ref.: #67775]	sodium chloride ChEBI	+	required for growth
[Ref.: #67775]	starch ChEBI	+	hydrolysis
[Ref.: #67775]	sucrose ChEBI	+	builds acid from
[Ref.: #67775]	sucrose ChEBI	+	builds gas from
[Ref.: #67775]	trehalose ChEBI	+	builds acid from
[Ref.: #67775]	trehalose ChEBI	+	builds gas from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67775]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #67775]	acid phosphatase	+	3.1.3.2
[Ref.: #67775]	alkaline phosphatase	+	3.1.3.1
[Ref.: #67775]	alpha-glucosidase	-	3.2.1.20
[Ref.: #67775]	arginine dihydrolase	+	3.5.3.6
[Ref.: #67775]	beta-galactosidase	+	3.2.1.23
[Ref.: #67775]	beta-glucuronidase	-	3.2.1.31
[Ref.: #67775]	catalase	-	1.11.1.6
[Ref.: #67775]	cytochrome oxidase	-	1.9.3.1
[Ref.: #67775]	esterase (C 4)	+
[Ref.: #67775]	esterase Lipase (C 8)	-
[Ref.: #67775]	leucine arylamidase	+	3.4.11.1
[Ref.: #67775]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #67775]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #67775]	trypsin	-	3.4.21.4
[Ref.: #67775]	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.: #67770]	Sample type/isolated from	Lagoon sediment sample of Dongsha Island
[Ref.: #67770]	Country	Taiwan, Province of China
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia

[Ref.: #67775]	Sample type/isolated from	lagoon sediment sample
[Ref.: #67775]	Geographic location (country and/or sea, region)	Dongsha Island
[Ref.: #67775]	Country	Taiwan, Province of China
[Ref.: #67775]	Country ISO 3 Code	TWN
[Ref.: #67775]	Continent	Asia
[Ref.: #67775]	Enrichment culture temperature	25 ̊C
[Ref.: #67775]	Isolation/enrichment procedure	Some wet mass (2 g) of each sample was taken and vigorously shaken in 98 ml sterile NaCl-Tris buffer (30 g NaCl and 0.24 g Tris in 1 l deionized water, pH 8.0). The shaken solutions were decimally diluted with the same buffer. Aliquots (1 ml) of the dilutions (10-3 to 10-5) were transferred to rimless tubes containing PYG medium (5 ml) in triplicate. All cultures were set in anaerobic jars (Difco) and incubated at 25°C in the dark for 3-7 days. The air in each anaerobic jar was replaced by N2 before incubation. The gas replacement was performed by flushing the anaerobic jar 30 times with high-purity N2 (99.9 %). Oxygen-free or nearly oxygen-free conditions could be established in the culturesystem throughout such a gas replacement treatment. Cultures that developed visible turbidity were streaked (one loopful) onto the PY plate medium and the plates were incubated at 25°C in the dark for 2-3 days under aerobic conditions. Individual colonies appearing on the plates were picked off and purified by successive streaking on PY plates.
* marker position based on {}

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.: #67775]	Dongshaea marina strain DM2 16S ribosomal RNA gene, partial sequence	MG232375	1471	GenBank ENA	2047966 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dongshaea marina DM2	GCA_003072645	complete	GenBank ENA	2047966 tax ID	*

[Ref.: #67770]	GC-content	51 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	51.8 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dongshaea marina DM2 NCBI: GCA_003072645.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99.994	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.896	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	74.037	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.691	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	82.199	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dongshaea marina DM2 NCBI: GCA_003072645
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	82
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	78.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	62.7

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 32096, BCRC 81069

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production.	Huang SP, Chen TY, Chen JS, Wang LT, Huang L, Lin ST, Wei CL, Lin S, Wang PL, Chen YM, Shieh WY	Int J Syst Evol Microbiol	10.1099/ijsem.0.003080	2019	*

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 )

#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;

#67775

Ssu-Po Huang, Tzu-Yin Chen, Jwo-Sheng Chen, Li-Ting Wang, Lina Huang, Shih-Ting Lin, Chih-Lin Wei, Saulwood Lin, Pei-Ling Wang, Yi-Min Chen, Wung Yang Shieh: Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production. IJSEM 69: 3318 - 3325 2019 ( DOI 10.1099/ijsem.0.003080 )

#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 .

* These data were automatically processed and therefore are not curated

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