Name: Salimicrobium flavidum ISL-25
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1551

Type strain:

Species: Salimicrobium flavidum

Strain Designation: ISL-25

Culture col. no.: DSM 23127, CCUG 56755, KCTC 13260, ISL -25

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 570947 (species)

SI-ID 403569

DSM 23127, CCUG 56755

Special Collections

Section

When using BacDive for research please cite our paper

Salimicrobium flavidum ISL-25 is an aerobe, mesophilic, Gram-variable bacterium that was isolated from marine solar saltern sediment.

Gram-variable
motile
aerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Salimicrobium*
	Species	**Salimicrobium flavidum**
	Full Scientific Name (LPSN)	Salimicrobium flavidum Yoon et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29285]	Gram stain	variable
[Ref.: #67771]	Gram stain	positive

[Ref.: #29285]	Cell length	4.9 µm

[Ref.: #29285]	Cell width	0.85 µm

[Ref.: #29285]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	ovoid-shaped

[Ref.: #67771]	Flagellum arrangement	peritrichous

[Ref.: #61077]

Incubation period

5 days

[Ref.: #29285]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16720]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #16720]

Culture medium growth

[Ref.: #16720]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16720]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16720]	growth	35 °C
[Ref.: #29285]	growth	04-40 °C
[Ref.: #29285]	optimum	33.5 °C
[Ref.: #61077]	growth	37 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #29285]			optimum	7.5
[Ref.: #29285]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #61077]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29285]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29285]		NaCl		growth	01-26	%
[Ref.: #29285]		NaCl		optimum	10	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29285]	fructose ChEBI	+	carbon source
[Ref.: #29285]	glucose ChEBI	+	carbon source
[Ref.: #29285]	mannitol ChEBI	+	carbon source
[Ref.: #29285]	mannose ChEBI	+	carbon source
[Ref.: #29285]	melibiose ChEBI	+	carbon source
[Ref.: #29285]	ribose ChEBI	+	carbon source
[Ref.: #29285]	sucrose ChEBI	+	carbon source
[Ref.: #29285]	trehalose ChEBI	+	carbon source
[Ref.: #29285]	tween 20 ChEBI	+	carbon source
[Ref.: #29285]	tween 40 ChEBI	+	carbon source
[Ref.: #29285]	tween 60 ChEBI	+	carbon source
[Ref.: #29285]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29285]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29285]	catalase	+	1.11.1.6
[Ref.: #29285]	cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16720]	Sample type/isolated from	marine solar saltern sediment
[Ref.: #16720]	Geographic location (country and/or sea, region)	Yellow Sea
[Ref.: #16720]	Country	Republic of Korea
[Ref.: #16720]	Country ISO 3 Code	KOR
[Ref.: #16720]	Continent	Asia

[Ref.: #61077]	Sample type/isolated from	Marine solar saltern sediment
[Ref.: #61077]	Sampling date	2006
[Ref.: #61077]	Geographic location (country and/or sea, region)	Yellow Sea
[Ref.: #61077]	Country	Republic of Korea
[Ref.: #61077]	Country ISO 3 Code	KOR
[Ref.: #61077]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From marine solar saltern of the Yellow Sea
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ357160 (>99% sequence identity) for Salimicrobium flavidum from Microbeatlas

Aquatic Samples	49
Soil Samples	9
Animal Samples	191
Plant Samples	1
Total Samples	250

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

[Ref.: #16720]

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.: #16720]	Salimicrobium sp. ISL-25 16S ribosomal RNA gene, partial sequence	FJ357160	1524	GenBank ENA	570947 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Salimicrobium flavidum DSM 23127	GCA_900156645	scaffold	GenBank ENA	570947 tax ID	*
[Ref.: #66792]	Salimicrobium flavidum strain DSM 23127	570947.3	wgs	PATRIC	570947 tax ID	*
[Ref.: #66792]	Salimicrobium flavidum DSM 23127	2681813511	draft	JGI IMG/M	570947 tax ID	*

[Ref.: #16720]	GC-content	49.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29285]	GC-content	49.3 mol%

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: Salimicrobium flavidum DSM 23127 NCBI: GCA_900156645.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	80.779	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.192	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	81.911	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	52.521	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	90.84	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	80.768	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Salimicrobium flavidum DSM 23127 NCBI: GCA_900156645
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	86.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	84.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	88.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative anaerobe	73.1

Availability in culture collections External links

[Ref.: #16720]

Culture collection no.

DSM 23127, CCUG 56755, KCTC 13260, ISL -25

[Ref.: #71196]

SI-ID 403569

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Salimicrobium jeotgali sp. nov., isolated from salted, fermented seafood.	Choi EJ, Jin HM, Kim KH, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.062042-0	2014	*
Phylogeny	Salimicrobium salexigens sp. nov., a moderately halophilic bacterium from salted hides.	de la Haba RR, Yilmaz P, Sanchez-Porro C, Birbir M, Ventosa A	Syst Appl Microbiol	10.1016/j.syapm.2011.04.002	2011	*
Phylogeny	Salimicrobium flavidum sp. nov., isolated from a marine solar saltern.	Yoon JH, Kang SJ, Oh KH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.010215-0	2009	*

References

#16720

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23127

#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 )

#29285

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25701 (see below)

#61077 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56755

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#71196

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-ID403569.1 )

#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 .

#25701

IJSEM 2839 2009 ( DOI 10.1099/ijs.0.010215-0 , PubMed 19628596 )

* These data were automatically processed and therefore are not curated

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Salimicrobium flavidum DSM 23127

Salimicrobium flavidum DSM 23127

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