Name: Tenacibaculum todarodis LPB0136
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158792

Type strain:

Species: Tenacibaculum todarodis

Strain Designation: LPB0136

Culture col. no.: KACC 18887, JCM 31564

Strain history: H. Yi; Korea Univ., South Korea; LPB0136.

NCBI tax ID(s): 1850252 (species)

Section

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

colony-forming
Gram-negative
motile
rod-shaped
aerobe
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Tenacibaculum*
	Species	**Tenacibaculum todarodis**
	Full Scientific Name (LPSN)	Tenacibaculum todarodis Shin et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65551]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.972

[Ref.: #65551]	Cell length	1.5-2.3 µm

[Ref.: #65551]	Cell width	0.5-0.6 µm

[Ref.: #65551]	Cell shape	rod-shaped

[Ref.: #65551]	Motility	yes

[Ref.: #65551]	Flagellum arrangement	gliding

[Ref.: #65551]	Colony size	0.5-1.5 mm
[Ref.: #65551]	Colony color	yellow
[Ref.: #65551]	Colony shape	circular
[Ref.: #65551]	Incubation period	3 days
[Ref.: #65551]	Cultivation medium used	MA

[Ref.: #65551]	Pigment production	no
[Ref.: #65551]	Pigment name	Flexirubin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65551]

Culture medium

Marine agar (MA)

[Ref.: #65551]

Culture medium growth

		Temperature
[Ref.: #65551]	growth	4-25 °C
[Ref.: #65551]	optimum	25 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #65551]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65551]			optimum	7.0
[Ref.: #65551]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65551]

Oxygen tolerance

aerobe

[Ref.: #65551]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.983
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65551]		NaCl		growth	2-4	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65551]	adipate ChEBI	-	carbon source
[Ref.: #65551]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #65551]	casein	+	hydrolysis
[Ref.: #65551]	chitin ChEBI	-	hydrolysis
[Ref.: #65551]	citrate ChEBI	-	carbon source
[Ref.: #65551]	D-glucose ChEBI	-	carbon source
[Ref.: #65551]	D-mannitol ChEBI	-	carbon source
[Ref.: #65551]	D-mannose ChEBI	-	carbon source
[Ref.: #65551]	decanoate ChEBI	-	carbon source
[Ref.: #65551]	dna ChEBI	+	hydrolysis
[Ref.: #65551]	gelatin ChEBI	+	hydrolysis
[Ref.: #65551]	gluconate ChEBI	-	carbon source
[Ref.: #65551]	glucose ChEBI	-	fermentation
[Ref.: #65551]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #65551]	L-arabinose ChEBI	-	carbon source
[Ref.: #65551]	L-tyrosine ChEBI	+	hydrolysis
[Ref.: #65551]	malate ChEBI	-	carbon source
[Ref.: #65551]	maltose ChEBI	-	carbon source
[Ref.: #65551]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #65551]	nitrate ChEBI	-	reduction
[Ref.: #65551]	phenylacetate ChEBI	-	carbon source
[Ref.: #65551]	sodium alginate ChEBI	-	hydrolysis
[Ref.: #65551]	starch ChEBI	-	hydrolysis
[Ref.: #65551]	tween 20 ChEBI	-	hydrolysis
[Ref.: #65551]	tween 40 ChEBI	-	hydrolysis
[Ref.: #65551]	tween 60 ChEBI	-	hydrolysis
[Ref.: #65551]	tween 80 ChEBI	+	hydrolysis
[Ref.: #65551]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65551]		hydrogen sulfide ChEBI	no
[Ref.: #65551]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65551]	acid phosphatase	+	3.1.3.2
[Ref.: #65551]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65551]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65551]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65551]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65551]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65551]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65551]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65551]	beta-galactosidase	-	3.2.1.23
[Ref.: #65551]	beta-glucosidase	-	3.2.1.21
[Ref.: #65551]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65551]	catalase	+	1.11.1.6
[Ref.: #65551]	cystine arylamidase	+	3.4.11.3
[Ref.: #65551]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65551]	esterase (C 4)	-
[Ref.: #65551]	esterase Lipase (C 8)	-
[Ref.: #65551]	leucine arylamidase	+	3.4.11.1
[Ref.: #65551]	lipase (C 14)	-
[Ref.: #65551]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65551]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65551]	trypsin	+	3.4.21.4
[Ref.: #65551]	urease	-	3.5.1.5
[Ref.: #65551]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	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]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #65551]	Sample type/isolated from	isolated from a squid, Todarodes pacificus
[Ref.: #65551]	Geographic location (country and/or sea, region)	East Sea
[Ref.: #65551]	Country	Republic of Korea
[Ref.: #65551]	Country ISO 3 Code	KOR
[Ref.: #65551]	Continent	Asia
[Ref.: #65551]	Geographic location	37.8908°/128.8290°
[Ref.: #65551]	Enrichment culture	MA

[Ref.: #67770]	Sample type/isolated from	Squid Todarodes pacificus
[Ref.: #67770]	Host species	Todarodes pacificus
* marker position based on {}

Isolation sources categories

#Host

#Reptilia

What are isolation sources categories?

[Ref.: #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

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.: #65551]	16S rRNA gene sequence	KX066858		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tenacibaculum todarodis LPB0136	GCA_001889045	complete	GenBank	1850252 tax ID	*
[Ref.: #66792]	Tenacibaculum todarodis LPB0136	2728369366	complete	JGI IMG/M	1850252 tax ID	*

[Ref.: #65551]

GC-content

30.7 mol%

genome sequence analysis

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: Tenacibaculum todarodis LPB0136 NCBI: GCA_001889045.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tenacibaculum todarodis LPB0136 NCBI: GCA_001889045.1
[Ref.: #69480]	flagellated	no	95.225	yes
[Ref.: #69480]	gram-positive	no	97.681	yes
[Ref.: #69480]	anaerobic	no	99.575	yes
[Ref.: #69480]	halophile	no	70.17	no
[Ref.: #69480]	spore-forming	no	96.776	yes
[Ref.: #69480]	glucose-util	yes	74.179	yes
[Ref.: #69480]	aerobic	yes	92.596	yes
[Ref.: #69480]	thermophile	no	99.572	no
[Ref.: #69480]	motile	no	88.565	no
[Ref.: #69480]	glucose-ferment	no	91.784	no

Availability in culture collections External links

[Ref.: #65551]

Culture collection no.

KACC 18887, JCM 31564

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 .

#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 )

* These data were automatically processed and therefore are not curated

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