Tenacibaculum todarodis (KACC 18887, JCM 31564, LPB0136)

Name: Tenacibaculum todarodis (KACC 18887, JCM 31564, LPB0136)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158792

Type strain

Strain Designation LPB0136

Culture col. no. KACC 18887 JCM 31564 LPB0136

NCBI tax ID(s) 1850252

Special Collections JCM Literature strains

History JCM <-- H. Yi; Korea Univ., South Korea; LPB0136.

Links

Tenacibaculum todarodis LPB0136 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from isolated from a squid, Todarodes pacificus.

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

Name and taxonomic classification

SI-ID 132052

JCM 31564

@ref 20215

Last LPSN update 2026-05-29 08:44:02

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Tenacibaculum

Species Tenacibaculum todarodis

Full scientific name Tenacibaculum todarodis Shin et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
65551	negative	1.5-2.3 µm	0.5-0.6 µm	rod-shaped	gliding
125438						93
125438	negative					98.481
125439	negative					99.739

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65551	0.5-1.5 mm	yellow	circular	3 days	MA

Pigmentation

@ref	Production	Name
65551		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
65551	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
65551	positive	growth	4-25
65551	positive	optimum	25
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
65551	positive	optimum	7.0
65551	positive	growth	5.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65551	aerobe
125439	facultative anaerobe	95.831

Spore formation

@ref	Spore formation	Confidence
65551
125439		99.891

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65551	NaCl	positive	growth	2-4 %(w/v)

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65551	17128 ChEBI	adipate	-	carbon source
65551	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
65551		casein	+	hydrolysis
65551	17029 ChEBI	chitin	-	hydrolysis
65551	16947 ChEBI	citrate	-	carbon source
65551	17634 ChEBI	D-glucose	-	carbon source
65551	16899 ChEBI	D-mannitol	-	carbon source
65551	16024 ChEBI	D-mannose	-	carbon source
65551	27689 ChEBI	decanoate	-	carbon source
65551	16991 ChEBI	dna	+	hydrolysis
65551	5291 ChEBI	gelatin	+	hydrolysis
65551	24265 ChEBI	gluconate	-	carbon source
65551	17234 ChEBI	glucose	-	fermentation
65551	17368 ChEBI	hypoxanthine	-	hydrolysis
65551	30849 ChEBI	L-arabinose	-	carbon source
65551	17895 ChEBI	L-tyrosine	+	hydrolysis
65551	25115 ChEBI	malate	-	carbon source
65551	17306 ChEBI	maltose	-	carbon source
65551	506227 ChEBI	N-acetylglucosamine	-	carbon source
65551	17632 ChEBI	nitrate	-	reduction
65551	18401 ChEBI	phenylacetate	-	carbon source
65551	53311 ChEBI	sodium alginate	-	hydrolysis
65551	28017 ChEBI	starch	-	hydrolysis
65551	53424 ChEBI	tween 20	-	hydrolysis
65551	53423 ChEBI	tween 40	-	hydrolysis
65551	53425 ChEBI	tween 60	-	hydrolysis
65551	53426 ChEBI	tween 80	+	hydrolysis
65551	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65551	16136 ChEBI	hydrogen sulfide
65551	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65551	acid phosphatase	+	3.1.3.2
65551	alkaline phosphatase	+	3.1.3.1
65551	alpha-chymotrypsin	-	3.4.21.1
65551	alpha-fucosidase	-	3.2.1.51
65551	alpha-galactosidase	-	3.2.1.22
65551	alpha-glucosidase	-	3.2.1.20
65551	alpha-mannosidase	-	3.2.1.24
65551	arginine dihydrolase	-	3.5.3.6
65551	beta-galactosidase	-	3.2.1.23
65551	beta-glucosidase	-	3.2.1.21
65551	beta-glucuronidase	-	3.2.1.31
65551	catalase	+	1.11.1.6
65551	cystine arylamidase	+	3.4.11.3
65551	cytochrome oxidase	+	1.9.3.1
65551	esterase (C 4)	-
65551	esterase Lipase (C 8)	-
65551	leucine arylamidase	+	3.4.11.1
65551	lipase (C 14)	-
65551	N-acetyl-beta-glucosaminidase	-	3.2.1.52
65551	naphthol-AS-BI-phosphohydrolase	+
65551	trypsin	+	3.4.21.4
65551	urease	-	3.5.1.5
65551	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	vitamin K metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	denitrification	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	glycine betaine biosynthesis	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	kanosamine biosynthesis II	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	sulfopterin metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pyrimidine metabolism	82.22	37 of 45
66794	threonine metabolism	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	tryptophan metabolism	76.32	29 of 38
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	alanine metabolism	62.07	18 of 29
66794	methionine metabolism	61.54	16 of 26
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	non-pathway related	57.89	22 of 38
66794	degradation of sugar alcohols	56.25	9 of 16
66794	sulfate reduction	53.85	7 of 13
66794	cyclohexanol degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ethanol fermentation	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	glycine metabolism	50	5 of 10
66794	glutathione metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	vitamin B1 metabolism	46.15	6 of 13
66794	carotenoid biosynthesis	45.45	10 of 22
66794	vitamin B6 metabolism	45.45	5 of 11
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	oxidative phosphorylation	40.66	37 of 91
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	urea cycle	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	cyanate degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	methane metabolism	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	degradation of pentoses	32.14	9 of 28
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	biotin biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	degradation of sugar acids	24	6 of 25
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23

Fatty acid profile

Metadata FA analysis

@ref

65551

Fatty acid	Percentage
C15:0 iso 3OH	18.8
C15:0 iso	16.9
C15:1 iso G	14.6
C16:0 iso 3OH	7.5
C16:1ω6c / C16:1ω7c	6.8
C15:0 3OH	6.6
C17:0 iso 3OH	5.9
C15:1ω6c	5.3
C14:0 iso	2.8
C13:0 iso	2.6
C16:1 iso H	1.3
C16:0 3OH	1.1
C16:0 iso	1
C17:1ω6c	0.9
C13:0	0.6
C15:0 2OH	0.6
iso-C17:1ω9c / iso-C16:0 10-methyl	0.5
C15:0 anteiso	0.4
C14:0	0.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Reptilia

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Host species
65551	isolated from a squid, Todarodes pacificus	East Sea	Republic of Korea	KOR	Asia	37.8908	128.829 37.8908/128.829	MA
67770	Squid Todarodes pacificus								Todarodes pacificus

Taxonmaps

69479

Global distribution of 16S sequence KX066858 (>99% sequence identity) for Tenacibaculum todarodis subclade from Microbeatlas

Aquatic Samples	2941
Soil Samples	104
Animal Samples	550
Plant Samples	32
Total Samples	3627

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM188904v1 assembly for Tenacibaculum todarodis LPB0136	complete	GCA_001889045	2728369366	1850252	90.23

16S sequences

@ref	Description	Accession	Database
65551	Tenacibaculum todarodis strain LPB0136 16S ribosomal RNA gene, partial sequence	KX066858

GC content

@ref	GC-content (mol%)	Method
65551	30.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM188904v1 assembly for Tenacibaculum todarodis LPB0136
NCBI: GCA_001889045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.83	no
125439	motility	BacteriaNetⓘ	no	63.24	no
125439	gram_stain	BacteriaNetⓘ	negative	99.74	no
125439	spore_formation	BacteriaNetⓘ	no	99.89	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tenacibaculum todarodis LPB0136
NCBI: GCA_001889045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.48	yes
125438	anaerobic	anaerobicⓘ	no	98.80	yes
125438	aerobic	aerobicⓘ	yes	85.13	yes
125438	spore-forming	spore-formingⓘ	no	89.33	yes
125438	thermophilic	thermophileⓘ	no	96.93	yes
125438	flagellated	motile2+ⓘ	no	93.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tenacibaculum todarodis sp. nov., isolated from a squid.	Shin SK, Kim E, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.002692	2018
Phylogeny	Tenacibaculum aquimarinum sp. nov., isolated from a marine alga and seawater.	Kristyanto S, Kim KR, Jung J, Kim HM, Kim K, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.005477	2022

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 )
#65551	Su-Kyoung Shin, Eunji Kim and Hana Yi: Tenacibaculum todarodis sp. nov., isolated from a squid. IJSEM 68: 1479 - 1483 2018 ( DOI 10.1099/ijsem.0.002692 , PubMed 29521615 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Tenacibaculum todarodis (KACC 18887, JCM 31564, LPB0136)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001889045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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