Name: Sediminibacterium goheungense DSM 28323
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24738

Type strain:

Species: Sediminibacterium goheungense

Culture col. no.: DSM 28323, CECT 8100, KCTC 23945, HME 7863

Strain history: <- CECT 8100 <- K. Joh, Dept. Biosci. and Biotechnology, Hankuk Univ. of Foreign Studies, Yongin, Republic of Korea; HME7863 <- K. Joh and Y. C. Joung

NCBI tax ID(s): 1086393 (species)

SI-ID 393353

KCTC 23945, CECT 8100, DSM 28323

Section

Sediminibacterium goheungense DSM 28323 is a mesophilic, Gram-negative bacterium that was isolated from freshwater reservoir water.

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Sediminibacterium*
	Species	**Sediminibacterium goheungense**
	Full Scientific Name (LPSN)	Sediminibacterium goheungense Kang et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #21190]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21190]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21190]

Culture medium growth

[Ref.: #21190]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21190]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21190]			growth	28 °C

[Ref.: #21190]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		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.: #21190]	Sample type/isolated from	freshwater reservoir water
[Ref.: #21190]	Geographic location (country and/or sea, region)	Goheung (34° 35' 31'' N 127° 19' 11'' E)
[Ref.: #21190]	Country	Republic of Korea
[Ref.: #21190]	Country ISO 3 Code	KOR
[Ref.: #21190]	Continent	Asia
[Ref.: #21190]	Geographic location	34.5919°/127.3200°
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	#Water reservoir (Aquarium/pool)
#Environmental	#Aquatic	#Freshwater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN674641 (>99% sequence identity) for Sediminibacterium goheungense subclade from Microbeatlas

Aquatic Samples	27764
Soil Samples	17026
Animal Samples	6002
Plant Samples	4100
Total Samples	54892

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21190]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #21190]	Sediminibacterium goheungense strain HME7863 from South Korea 16S ribosomal RNA gene, partial sequence	JN674641	1390	ENA	1086393 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sediminibacterium goheungense DSM 28323	GCA_004361915	contig	GenBank	1086393 tax ID	*
[Ref.: #66792]	Sediminibacterium goheungense strain DSM 28323	1086393.3	wgs	PATRIC	1086393 tax ID	*
[Ref.: #66792]	Sediminibacterium goheungense DSM 28323	2695421017	draft	JGI IMG/M	1086393 tax ID	*

[Ref.: #21190]

GC-content

40.5 mol%

fluorimetric

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sediminibacterium goheungense strain DSM 28323 PATRIC: 1086393.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sediminibacterium goheungense strain DSM 28323 PATRIC: 1086393.3
[Ref.: #69480]	motile	no	93.913	no
[Ref.: #69480]	flagellated	no	96.997	no
[Ref.: #69480]	gram-positive	no	97.872	no
[Ref.: #69480]	anaerobic	no	99.299	no
[Ref.: #69480]	aerobic	yes	88.655	no
[Ref.: #69480]	halophile	no	98.25	no
[Ref.: #69480]	spore-forming	no	96.365	no
[Ref.: #69480]	thermophile	no	95.751	yes
[Ref.: #69480]	glucose-util	yes	86.13	no
[Ref.: #69480]	glucose-ferment	no	89.018	no

Availability in culture collections External links

[Ref.: #21190]

Culture collection no.

DSM 28323, CECT 8100, KCTC 23945, HME 7863

[Ref.: #88566]

SI-ID 393353

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sediminibacterium soli sp. nov., isolated from soil.	Wu S, Zhong L, Liao S, Li T, Zhou Z, Wang G	Arch Microbiol	10.1007/s00203-020-02089-2	2020	*
Phylogeny	Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas.	Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J, Tewalt N, Cleeve N, Rossello-Mora R, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001305	2016	*
Phylogeny	Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir.	Kang H, Kim H, Lee BI, Joung Y, Joh K	Int J Syst Evol Microbiol	10.1099/ijs.0.055137-0	2014	*

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 )

#21190

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28323

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88566

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID393353.1 )

* These data were automatically processed and therefore are not curated

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Sediminibacterium goheungense strain DSM 28323

Sediminibacterium goheungense strain DSM 28323

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