Name: Aequorivita todarodis MYP2-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158706

Type strain:

Species: Aequorivita todarodis

Strain Designation: MYP2-2

Culture col. no.: KCTC 62141, NBRC 113025

Strain history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

NCBI tax ID(s): 2036821 (species)

Special Collections

Section

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Aequorivita todarodis MYP2-2 is an aerobe, psychrophilic, Gram-negative bacterium that forms circular colonies and was isolated from the intestinal tract of a squid .

colony-forming
Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Aequorivita*
	Species	**Aequorivita todarodis**
	Full Scientific Name (LPSN)	Aequorivita todarodis (Kim et al. 2018) Zhang et al. 2020

	Synonym	Aequorivita todarodis
	Synonym	Vitellibacter todarodis

Information on morphological and physiological properties Morphology

[Ref.: #65448]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.231

[Ref.: #65448]	Cell width	0.2-0.4 µm

[Ref.: #65448]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	ovoid-shaped

[Ref.: #65448]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %94

[Ref.: #65448]	Colony size	1-1.5 mm
[Ref.: #65448]	Colony color	vivid orange yellow
[Ref.: #65448]	Colony shape	circular
[Ref.: #65448]	Incubation period	5 days
[Ref.: #65448]	Cultivation medium used	marine agar

[Ref.: #65448]	Pigment production	yes
[Ref.: #65448]	Pigment name	Flexirubin-type pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65448]

Culture medium

Marine agar (MA)

[Ref.: #65448]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #65448]		growth	4 °C
[Ref.: #65448]		growth	40 °C
[Ref.: #65448]		optimum	30-35 °C
[Ref.: #65448]	negative	growth	45 °C
[Ref.: #67771]		growth	30-35 °C

	Kind of pH		pH
[Ref.: #65448]		optimum	7-8
[Ref.: #65448]		growth	5.5
[Ref.: #65448]	no	growth	5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65448]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125438]

Ability of spore formation

no Confidence in %90.718

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65448]		NaCl		growth	1-8	%(w/v)
[Ref.: #65448]		NaCl		optimum	2.0	%(w/v)

[Ref.: #65448]	Observation	Mg 2+ ions are not required for growth
[Ref.: #65448]	Observation	the predominant menaquinone is MK-6
[Ref.: #65448]	Observation	the major polar lipids are phosphatidylethanolamine and one unidentified lipid
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65448]	casein	+	hydrolysis
[Ref.: #65448]	cellobiose ChEBI	-	builds acid from
[Ref.: #65448]	D-fructose ChEBI	-	builds acid from
[Ref.: #65448]	D-galactose ChEBI	-	builds acid from
[Ref.: #65448]	D-glucose ChEBI	-	builds acid from
[Ref.: #65448]	D-mannitol ChEBI	-	builds acid from
[Ref.: #65448]	D-mannose ChEBI	-	builds acid from
[Ref.: #65448]	D-ribose ChEBI	-	builds acid from
[Ref.: #65448]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #65448]	D-xylose ChEBI	-	builds acid from
[Ref.: #65448]	esculin ChEBI	-	hydrolysis
[Ref.: #65448]	gelatin ChEBI	+	hydrolysis
[Ref.: #65448]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #65448]	L-arabinose ChEBI	-	builds acid from
[Ref.: #65448]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #65448]	L-tyrosine ChEBI	+	hydrolysis
[Ref.: #65448]	lactose ChEBI	-	builds acid from
[Ref.: #65448]	maltose ChEBI	-	builds acid from
[Ref.: #65448]	melezitose ChEBI	-	builds acid from
[Ref.: #65448]	melibiose ChEBI	-	builds acid from
[Ref.: #65448]	myo-inositol ChEBI	-	builds acid from
[Ref.: #65448]	nitrate ChEBI	-	reduction
[Ref.: #65448]	raffinose ChEBI	-	builds acid from
[Ref.: #65448]	starch ChEBI	-	hydrolysis
[Ref.: #65448]	sucrose ChEBI	-	builds acid from
[Ref.: #65448]	trehalose ChEBI	-	builds acid from
[Ref.: #65448]	tween 80 ChEBI	+	hydrolysis
[Ref.: #65448]	urea ChEBI	-	hydrolysis
[Ref.: #65448]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #65448]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #65448]	carbenicillin ChEBI	yes	100	µg (disc)
[Ref.: #65448]	cephalothin ChEBI	yes	30	µg (disc)
[Ref.: #65448]	chloramphenicol ChEBI	yes	100	µg (disc)
[Ref.: #65448]	gentamicin ChEBI	yes	30	µg (disc)
[Ref.: #65448]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65448]	lincomycin ChEBI	yes	15	µg (disc)
[Ref.: #65448]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #65448]	novobiocin ChEBI	yes	5	µg (disc)
[Ref.: #65448]	oleandomycin ChEBI	yes	15	µg (disc)
[Ref.: #65448]	penicillin g ChEBI	yes	20	Unit (disc)
[Ref.: #65448]	polymyxin b ChEBI	yes	100	Unit (disc)
[Ref.: #65448]	streptomycin ChEBI	yes	50	µg (disc)
[Ref.: #65448]	tetracycline ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #65448]	acid phosphatase	+	3.1.3.2
[Ref.: #65448]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65448]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65448]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65448]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65448]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65448]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65448]	beta-galactosidase	-	3.2.1.23
[Ref.: #65448]	beta-glucosidase	-	3.2.1.21
[Ref.: #65448]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65448]	catalase	+	1.11.1.6
[Ref.: #65448]	cystine arylamidase	-	3.4.11.3
[Ref.: #65448]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65448]	esterase (C 4)	+
[Ref.: #65448]	esterase Lipase (C 8)	+
[Ref.: #65448]	leucine arylamidase	+	3.4.11.1
[Ref.: #65448]	lipase (C 14)	-
[Ref.: #65448]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65448]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65448]	trypsin	-	3.4.21.4
[Ref.: #65448]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65448]

Fatty acid	Percentage
C15:0 iso	34.1
C17:0 iso 3OH	22.2
C17:1 iso ω9c	11.7
C16:1ω7c and/or C16:1ω6c	8.1
iso-C15:1G*	5.1
C15:0 iso 3OH	3.9
C15:0 anteiso	3.4
C16:0	1.8
C16:0 iso	1.8
C16:0 iso 3OH	1.1
C17:0 iso	1
C17:0 2OH	0.8
C17:0 3OH	0.7
C15:0 2OH	0.7

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

[Ref.: #65448]	Sample type/isolated from	the intestinal tract of a squid (Todarodes pacificus)
[Ref.: #65448]	Geographic location (country and/or sea, region)	East Sea near Donghae
[Ref.: #65448]	Country	Republic of Korea
[Ref.: #65448]	Country ISO 3 Code	KOR
[Ref.: #65448]	Continent	Asia
[Ref.: #65448]	Geographic location	37.5511°/129.1140°
[Ref.: #65448]	Enrichment culture	marine agar 2216
[Ref.: #65448]	Enrichment culture duration	10 days
[Ref.: #65448]	Enrichment culture temperature	20 ̊C
[Ref.: #65448]	Isolation/enrichment procedure	the content from its intestinal tract was scraped and used as a source for the isolation of bacterial strains, about 1 g of the intestinal content was serially diluted using 0.85 % (w/v) NaCl solution

[Ref.: #67771]	Sample type/isolated from	From stomach of squid, `Todarodes pacificus`
[Ref.: #67771]	Geographic location (country and/or sea, region)	the East Sea near Donghae
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

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.: #65448]	Aequorivita todarodis strain MYP2-2 16S ribosomal RNA gene, partial sequence	MF962575		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Aequorivita todarodis KCTC 62141	GCA_028561335	contig	GenBank ENA	2036821 tax ID	*

[Ref.: #67771]

GC-content

41.6 mol%

high performance liquid chromatography (HPLC)

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: Aequorivita todarodis KCTC 62141 NCBI: GCA_028561335.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.231	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.742	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	83.893	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.718	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.479	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	94	yes

Availability in culture collections External links

[Ref.: #65448]

Culture collection no.

KCTC 62141, NBRC 113025

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov.	Wang Q, Cai SD, Liu J, Zhang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.004174	2020	*

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 )

#65448

Hyun Chul Kim, Young-Ok Kim, Sooyeon Park, Bo-Hye Nam, Dong-Gyun Kim, Ji-Min Park ,Jung-Hoon Yoon: Vitellibacter todarodis sp. nov., isolated from intestinal tract of a squid (Todarodes pacificus). IJSEM 68: 1233 - 1237 2018 ( DOI 10.1099/ijsem.0.002655 , PubMed 29480794 )

#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;

#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 )

* These data were automatically processed and therefore are not curated

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Aequorivita todarodis KCTC 62141

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