Cite this strain

Gaetbulibacter saemankumensis (DSM 17032, KCTC 12379, SMK-12)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5590

Type strain

Strain Designation SMK-12

Culture col. no. DSM 17032 KCTC 12379 SMK-12 IAM 15373 JCM 12931 1 more

NCBI tax ID(s) 1121909 311208

Special Collections DSMZ JCM KCTC CIP Literature strains

Links

Name and taxonomic classification

Gaetbulibacter saemankumensis SMK-12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat.

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 265598

DSM 17032, KCTC 12379, JCM 12931, IAM 15373, CIP 108967

Last LPSN update 2024-12-09 10:43:44

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Gaetbulibacter

Species Gaetbulibacter saemankumensis

Full scientific name Gaetbulibacter saemankumensis Jung et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
31523	negative	3.75 µm	0.45 µm	rod-shaped	gliding
67771				rod-shaped	gliding
67771	negative
125438
125438	negative
125439	negative

Multimedia

@ref:	66793
manual_annotation:	1
multimedia content:	EM_DSM_17032_1.jpg
multimedia.multimedia content:	EM_DSM_17032_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde

@ref:	66793
manual_annotation:	1
multimedia content:	EM_DSM_17032_2.jpg
multimedia.multimedia content:	EM_DSM_17032_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde

@ref:	66793
manual_annotation:	1
multimedia content:	EM_DSM_17032_3.jpg
multimedia.multimedia content:	EM_DSM_17032_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde

@ref:	66793
manual_annotation:	1
multimedia content:	EM_DSM_17032_4.jpg
multimedia.multimedia content:	EM_DSM_17032_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde

@ref:	66793
manual_annotation:	1
multimedia content:	EM_DSM_17032_5.jpg
multimedia.multimedia content:	EM_DSM_17032_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde

Pigmentation

31523

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6696	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
37404	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
122344	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6696	positive	growth	28	mesophilic
31523	positive	growth	13-40
31523	positive	optimum	27	mesophilic
37404	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31523	positive	optimum	7.5
31523	positive	growth	5.5-8.0

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31523	NaCl	positive	growth	02-07 %
31523	NaCl	positive	optimum	3.5 %

Observation

@ref	Observation
67770	quinones: MK-6
67771	quinones: MK-6

Spore formation

@ref	Spore formation
31523
125438
125439

Enzymes

@ref	Value	Activity	Ec
31523	acid phosphatase	+	3.1.3.2
31523	alkaline phosphatase	+	3.1.3.1
31523	catalase	+	1.11.1.6
31523	cytochrome oxidase	+	1.9.3.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31523	17057 ChEBI	cellobiose	+	carbon source
31523	4853 ChEBI	esculin	+	hydrolysis
31523	28757 ChEBI	fructose	+	carbon source
31523	28260 ChEBI	galactose	+	carbon source
31523	17234 ChEBI	glucose	+	carbon source
31523	17716 ChEBI	lactose	+	carbon source
31523	17306 ChEBI	maltose	+	carbon source
31523	17632 ChEBI	nitrate	+	reduction
31523	26271 ChEBI	proline	+	carbon source
31523	26546 ChEBI	rhamnose	+	carbon source
31523	17992 ChEBI	sucrose	+	carbon source
31523	18222 ChEBI	xylose	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
6696	aerobe
31523	aerobe
67771	aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6696	tidal flat	Republic of Korea	KOR	Asia
67770	Tidal flat sediment at Saemankum	Republic of Korea	KOR	Asia
67771	From tidal flat sediment	Republic of Korea	KOR	Asia
122344	Environment, Tidal flat sediment of the Yellow Sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY883937 (>99% sequence identity) for Gaetbulibacter saemankumensis subclade from Microbeatlas

Aquatic Samples	84
Soil Samples	6
Animal Samples
Plant Samples
Total Samples	90

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
6696	1	Risk group (German classification) According to TRBA 466
122344	1	Risk group (French classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
67770	34.8	high performance liquid chromatography (HPLC)
67771	34.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6696	Gaetbulibacter saemankumensis strain SMK-12 16S ribosomal RNA gene, partial sequence	AY883937	1474		311208

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Gaetbulibacter saemankumensis DSM 17032	1121909.4	wgs	PATRIC	1121909
66792	Gaetbulibacter saemankumensis DSM 17032	2524614665	draft	JGI IMG/M	1121909
67770	Gaetbulibacter saemankumensis DSM 17032	GCA_000425645	scaffold		1121909

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Gaetbulibacter saemankumensis DSM 17032
NCBI: GCA_000425645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	no	63.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	86.80	no

Predictions from Diaspora project based on:
Gaetbulibacter saemankumensis DSM 17032
PATRIC: 1121909.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.34	yes
125438	anaerobic	anaerobicⓘ	no	95.54	yes
125438	spore-forming	spore-formingⓘ	no	92.83	yes
125438	aerobic	aerobicⓘ	yes	81.26	no
125438	thermophilic	thermophileⓘ	no	98.72	yes
125438	flagellated	motile2+ⓘ	no	95.17	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater.	Jung YT, Lee JS, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000845	2015
Phylogeny	Gaetbulibacter lutimaris sp. nov., isolated from a tidal flat sediment.	Yoon JH, Lee SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.040352-0	2012
Phylogeny	Gaetbulibacter aestuarii sp. nov., isolated from shallow coastal seawater, and emended description of the genus Gaetbulibacter.	Park SC, Choe HN, Baik KS, Lee KH, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.028944-0	2011
Phylogeny	Gaetbulibacter marinus sp. nov., isolated from coastal seawater, and emended description of the genus Gaetbulibacter.	Yang SJ, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.65382-0	2008
Phylogeny	Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea.	Jung SY, Kang SJ, Lee MH, Lee SY, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.63738-0	2005

Straininfo Link

@ref	Straininfo	Culture collections
75072	265598	DSM 17032, KCTC 12379, JCM 12931, IAM 15373, CIP 108967

Culture collection no.

Culture collection no.
DSM 17032
KCTC 12379
SMK-12
IAM 15373
JCM 12931
CIP 108967

References

#6696	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17032
#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 )
#31523	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 #27817 (see below)
#37404	; Curators of the CIP;
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#75072	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-ID265598.1 )
#122344	Collection of Institut Pasteur ; Curators of the CIP; CIP 108967
#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 .

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