Exiguobacterium marinum (DSM 16307, KCTC 19036, TF-80)

Name: Exiguobacterium marinum (DSM 16307, KCTC 19036, TF-80)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18111

Type strain

Strain Designation TF-80

Culture col. no. DSM 16307 KCTC 19036 TF-80 CIP 108731

NCBI tax ID(s) 1397696 273528

Special Collections DSMZ KCTC CIP

History <- J.-H. Yoon; TF-80 <- IG Kim, KRIBB CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain TF-80

Links

Exiguobacterium marinum TF-80 is a facultative anaerobe, mesophilic, motile prokaryote that was isolated from tidal flat.

motile rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 81160

DSM 16307,KCTC 19036,CIP 108731,VTT E-072702

@ref 20215

Last LPSN update 2026-02-09 11:22:23

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Exiguobacterium

Species Exiguobacterium marinum

Full scientific name Exiguobacterium marinum Kim et al. 2005

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement	Gram stain
67771	rod-shaped	monotrichous, polar
67771	coccus-shaped
67771			variable
120811	oval-shaped		negative

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6355	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
37447	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120811	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6355	positive	growth	28	mesophilic
37447	positive	growth	30	mesophilic
67771	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	facultative anaerobe
120811	facultative anaerobe
125439	facultative anaerobe	97.3

Murein

@ref	Murein short key	Type
6355	A11.01	A3alpha L-Lys-Gly

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
120811	17632 ChEBI	nitrate	-	reduction
120811	17632 ChEBI	nitrate	+	respiration
120811	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120811	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120811	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120811	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120811	ornithine decarboxylase	-	4.1.1.17
120811	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120811	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120811	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
120811	not determinedn.d.	+	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	-	+	-	-	+	+	+/-	+/-	+/-	+	+	+	-	-	+	+	-	-	-	+	+	-	+	-	-	-	-	-	-	-	+	-	-

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
6355	tidal flat	Yellow Sea, Daepo Beach	Republic of Korea	KOR	Asia
67771	From tidal flat; Daepo Beach	Yellow Sea, near Mokpo City	Republic of Korea	KOR	Asia
120811	Environment, Tidal flat	Yellow Sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY594266 (>99% sequence identity) for Exiguobacterium from Microbeatlas

Aquatic Samples	453
Soil Samples	61
Animal Samples	1235
Plant Samples	41
Total Samples	1790

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6355	1	Risk group (German classification) According to TRBA 466
120811	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM62084v1 assembly for Exiguobacterium marinum DSM 16307	scaffold	GCA_000620845	1397696.3	2558860114	1397696	76.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6355	Exiguobacterium marinum strain TF-80 16S ribosomal RNA, partial sequence	AY594266	1519		273528

GC content

6355

GC-content (mol%)48.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Exiguobacterium marinum DSM 16307
NCBI: GCA_000620845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	68.50	no
125439	motility	BacteriaNetⓘ	yes	64.30	no
125439	gram_stain	BacteriaNetⓘ	variable	82.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Exiguobacterium marinum DSM 16307 DSM 16307
NCBI: GCA_000620845.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	75.72	no
125438	anaerobic	anaerobicⓘ	no	96.15	yes
125438	aerobic	aerobicⓘ	yes	50.46	yes
125438	spore-forming	spore-formingⓘ	yes	50.27	no
125438	thermophilic	thermophileⓘ	no	92.14	yes
125438	flagellated	motile2+ⓘ	yes	79.27	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft genome sequence of Exiguobacterium sp. strain MMG028 isolated from a salt marsh.	Farrell MV, Airkin MY, Ali TN, Altoblani ZS, Bowman CR, Diaz AAB, Faurot PF, Frausto JE, Haji SF, Hamad BA, Lively JB, Luistro DCC, Macias Y, Mathew S, McKinley KM, Nasirimoseloo S, Tran BP, Trinh AN, Shikuma NJ.	Microbiol Resour Announc	10.1128/mra.00116-23	2024
	A Mesophilic Argonaute from Cohnella algarum Mediates Programmable DNA/RNA Cleavage with Distinctive Guide Specificity.	Peng Y, Pan W, Wang Y, Liu Y, Ma L.	Biomolecules	10.3390/biom15101459	2025
	Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo.	Lisitskaya L, Kropocheva E, Agapov A, Prostova M, Panteleev V, Yudin D, Ryazansky S, Kuzmenko A, Aravin AA, Esyunina D, Kulbachinskiy A.	Nucleic Acids Res	10.1093/nar/gkad290	2023
	Characterization and Salt Response in Recurrent Halotolerant Exiguobacterium sp. SH31 Isolated From Sediments of Salar de Huasco, Chilean Altiplano.	Remonsellez F, Castro-Severyn J, Pardo-Este C, Aguilar P, Fortt J, Salinas C, Barahona S, Leon J, Fuentes B, Areche C, Hernandez KL, Aguayo D, Saavedra CP.	Front Microbiol	10.3389/fmicb.2018.02228	2018
Phylogeny	Exiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas.	Singh NK, Raichand R, Kaur I, Kaur C, Pareek S, Mayilraj S.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9861-5	2013
Phylogeny	Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent.	Crapart S, Fardeau ML, Cayol JL, Thomas P, Sery C, Ollivier B, Combet-Blanc Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64639-0	2007
Phylogeny	Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.	Kim IG, Lee MH, Jung SY, Song JJ, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.63308-0	2005

References

#6355	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16307
#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 )
#37447	; 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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#120811	Collection of Institut Pasteur ; Curators of the CIP; CIP 108731
#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 )

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Exiguobacterium marinum (DSM 16307, KCTC 19036, TF-80)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Observation

Metabolite utilization

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000620845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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