Name: Larkinella knui 15J6-3T6
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158687

Type strain:

Species: Larkinella knui

Strain Designation: 15J6-3T6

Culture col. no.: KCTC 42998, JCM 31989

Strain history: <- Myung Kyum, Kim, Seoul Womens Univ.

NCBI tax ID(s): 2025310 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Larkinella knui 15J6-3T6 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from a soil sample.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Spirosomataceae*
	Genus	*Larkinella*
	Species	**Larkinella knui**
	Full Scientific Name (LPSN)	Larkinella knui Jeon et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65423]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.109
[Ref.: #125439]	Gram stain	negative Confidence in %98.4

[Ref.: #65423]	Cell length	1.9-4.2 µm

[Ref.: #65423]	Cell width	0.7-0.9 µm

[Ref.: #65423]	Cell shape	rod-shaped

[Ref.: #65423]	Motility	yes

[Ref.: #65423]	Flagellum arrangement	gliding

[Ref.: #65423]	Colony size	0.5-1.5 mm
[Ref.: #65423]	Colony color	pink
[Ref.: #65423]	Colony shape	circular
[Ref.: #65423]	Incubation period	3 days
[Ref.: #65423]	Cultivation medium used	R2A plates

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65423]

Culture medium

R2A plates

[Ref.: #65423]

Culture medium growth

		Temperature
[Ref.: #65423]	growth	4-30 °C
[Ref.: #65423]	optimum	25 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #65423]			optimum	7
[Ref.: #65423]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	aerobe Confidence in %96

[Ref.: #125439]

Ability of spore formation

no Confidence in %94

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65423]		NaCl		growth	0-1	%(w/v)
[Ref.: #65423]		NaCl		optimum	0	%(w/v)

[Ref.: #65423]	Observation	grows on NA and R2A, but not on LB or TSA agar
[Ref.: #65423]	Observation	the predominant isoprenoid quinone is MK-7
[Ref.: #65423]	Observation	the major polar lipids are phosphatidylethanolamine and an unidentified polar lipid

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65423]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #65423]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #65423]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65423]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #65423]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #65423]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #65423]	adipate ChEBI	-	assimilation
[Ref.: #65423]	amygdalin ChEBI	-	builds acid from
[Ref.: #65423]	arbutin ChEBI	+	builds acid from
[Ref.: #65423]	cellobiose ChEBI	+	builds acid from
[Ref.: #65423]	D-arabinose ChEBI	+	builds acid from
[Ref.: #65423]	D-arabitol ChEBI	-	builds acid from
[Ref.: #65423]	D-fructose ChEBI	+	builds acid from
[Ref.: #65423]	D-fucose ChEBI	-	builds acid from
[Ref.: #65423]	D-galactose ChEBI	-	builds acid from
[Ref.: #65423]	D-glucose ChEBI	-	assimilation
[Ref.: #65423]	D-glucose ChEBI	+	builds acid from
[Ref.: #65423]	D-lyxose ChEBI	-	builds acid from
[Ref.: #65423]	D-mannitol ChEBI	-	assimilation
[Ref.: #65423]	D-mannitol ChEBI	-	builds acid from
[Ref.: #65423]	D-mannose ChEBI	+	assimilation
[Ref.: #65423]	D-mannose ChEBI	+	builds acid from
[Ref.: #65423]	D-ribose ChEBI	-	assimilation
[Ref.: #65423]	D-ribose ChEBI	+	builds acid from
[Ref.: #65423]	D-sorbitol ChEBI	-	assimilation
[Ref.: #65423]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #65423]	D-tagatose ChEBI	-	builds acid from
[Ref.: #65423]	D-xylose ChEBI	+	builds acid from
[Ref.: #65423]	decanoate ChEBI	-	assimilation
[Ref.: #65423]	erythritol ChEBI	-	builds acid from
[Ref.: #65423]	esculin ChEBI	+	hydrolysis
[Ref.: #65423]	esculin ferric citrate	+	builds acid from
[Ref.: #65423]	galactitol ChEBI	-	builds acid from
[Ref.: #65423]	gelatin ChEBI	+	hydrolysis
[Ref.: #65423]	gentiobiose ChEBI	+	builds acid from
[Ref.: #65423]	gluconate ChEBI	-	assimilation
[Ref.: #65423]	gluconate ChEBI	-	builds acid from
[Ref.: #65423]	glucose ChEBI	+	fermentation
[Ref.: #65423]	glycerol ChEBI	-	builds acid from
[Ref.: #65423]	glycogen ChEBI	-	assimilation
[Ref.: #65423]	glycogen ChEBI	-	builds acid from
[Ref.: #65423]	inulin ChEBI	+	builds acid from
[Ref.: #65423]	isocitrate ChEBI	-	assimilation
[Ref.: #65423]	isovalerate ChEBI	-	assimilation
[Ref.: #65423]	itaconate ChEBI	-	assimilation
[Ref.: #65423]	L-alanine 4-nitroanilide	-	assimilation
[Ref.: #65423]	L-arabinose ChEBI	-	assimilation
[Ref.: #65423]	L-arabinose ChEBI	+	builds acid from
[Ref.: #65423]	L-arabitol ChEBI	-	builds acid from
[Ref.: #65423]	L-fucose ChEBI	-	assimilation
[Ref.: #65423]	L-fucose ChEBI	-	builds acid from
[Ref.: #65423]	L-histidine ChEBI	-	assimilation
[Ref.: #65423]	L-malate ChEBI	-	assimilation
[Ref.: #65423]	L-proline ChEBI	-	assimilation
[Ref.: #65423]	L-rhamnose ChEBI	-	assimilation
[Ref.: #65423]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #65423]	L-serine ChEBI	-	assimilation
[Ref.: #65423]	L-sorbose ChEBI	-	builds acid from
[Ref.: #65423]	L-xylose ChEBI	+	builds acid from
[Ref.: #65423]	lactate ChEBI	-	assimilation
[Ref.: #65423]	lactose ChEBI	+	builds acid from
[Ref.: #65423]	maltose ChEBI	+	assimilation
[Ref.: #65423]	maltose ChEBI	+	builds acid from
[Ref.: #65423]	melezitose ChEBI	-	builds acid from
[Ref.: #65423]	melibiose ChEBI	+	assimilation
[Ref.: #65423]	melibiose ChEBI	+	builds acid from
[Ref.: #65423]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #65423]	methyl alpha-D-mannoside ChEBI	+	builds acid from
[Ref.: #65423]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #65423]	myo-inositol ChEBI	-	assimilation
[Ref.: #65423]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65423]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #65423]	nitrate ChEBI	+	reduction
[Ref.: #65423]	phenylacetate ChEBI	-	assimilation
[Ref.: #65423]	raffinose ChEBI	+	builds acid from
[Ref.: #65423]	ribitol ChEBI	-	builds acid from
[Ref.: #65423]	salicin ChEBI	+	assimilation
[Ref.: #65423]	salicin ChEBI	+	builds acid from
[Ref.: #65423]	sodium acetate ChEBI	-	assimilation
[Ref.: #65423]	sodium malonate ChEBI	-	assimilation
[Ref.: #65423]	sodium propionate ChEBI	-	assimilation
[Ref.: #65423]	starch ChEBI	-	builds acid from
[Ref.: #65423]	suberic acid ChEBI	-	assimilation
[Ref.: #65423]	sucrose ChEBI	-	assimilation
[Ref.: #65423]	sucrose ChEBI	+	builds acid from
[Ref.: #65423]	trehalose ChEBI	+	builds acid from
[Ref.: #65423]	turanose ChEBI	+	builds acid from
[Ref.: #65423]	urea ChEBI	-	hydrolysis
[Ref.: #65423]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65423]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65423]	6-phospho-beta-galactosidase	+	3.2.1.85
[Ref.: #65423]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65423]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65423]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65423]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65423]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65423]	alpha-mannosidase	+	3.2.1.24
[Ref.: #65423]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65423]	beta-galactosidase	+	3.2.1.23
[Ref.: #65423]	beta-glucosidase	+	3.2.1.21
[Ref.: #65423]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65423]	cystine arylamidase	+	3.4.11.3
[Ref.: #65423]	esterase	+
[Ref.: #65423]	esterase Lipase (C 8)	+
[Ref.: #65423]	leucine arylamidase	+	3.4.11.1
[Ref.: #65423]	lipase (C 14)	-
[Ref.: #65423]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65423]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65423]	phosphatase	+
[Ref.: #65423]	trypsin	+	3.4.21.4
[Ref.: #65423]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65423]

Fatty acid	Percentage
C16:1ω5c	40.4
C15:0 iso	21.4
C17:0 iso 3OH	9.5
C16:0 N alcohol	7.5
C15:0 iso 3OH	4.2
C16:1ω7c and/or C16:1ω6c	3.9
C16:0	3
isoC17:1I and/or anteisoC17:1B	1.9
C17:0 iso	1.5
C20:0	1.4
anteiso-C 15:0	1.2
C18:0	1.1

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

[Ref.: #65423]	Sample type/isolated from	a soil sample
[Ref.: #65423]	Sampling date	2015-12
[Ref.: #65423]	Geographic location (country and/or sea, region)	Jeju Island
[Ref.: #65423]	Country	Republic of Korea
[Ref.: #65423]	Country ISO 3 Code	KOR
[Ref.: #65423]	Continent	Asia
[Ref.: #65423]	Geographic location	33.3069°/126.2900°
[Ref.: #65423]	Enrichment culture	Reasoner's 2A agar plates (Difco)
[Ref.: #65423]	Enrichment culture duration	1 week
[Ref.: #65423]	Enrichment culture temperature	25 ̊C

[Ref.: #67770]	Sample type/isolated from	Soil from Jeju Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil(O'sulloc tea fields
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jeju Island)
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

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.: #65423]	Larkinella knui gene for 16S ribosomal RNA, partial sequence	LC315194		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Larkinella knui KCTC42998	GCA_003858645	contig	GenBank ENA	2025310 tax ID	*
[Ref.: #66792]	Larkinella knui strain KCTC42998	2025310.3	wgs	PATRIC	2025310 tax ID	*
[Ref.: #66792]	Larkinella knui KCTC42998	2882134870	draft	JGI IMG/M	2025310 tax ID	*

[Ref.: #65423]

GC-content

50.6 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: Larkinella knui strain KCTC42998 PATRIC: 2025310.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.109	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.802	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.377	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.723	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.703	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	88.75	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Larkinella knui KCTC42998 NCBI: GCA_003858645
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	59.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	96

Availability in culture collections External links

[Ref.: #65423]

Culture collection no.

KCTC 42998, JCM 31989

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Larkinella knui sp. nov., isolated from soil.	Jeon J, Ten LN, Lee JJ, Lee SY, Park S, Cho YJ, Kim MK, Jung HY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002550	2018	*
Phylogeny	Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil.	Park Y, Ten LN, Lee YK, Jung HY, Kim MK	Arch Microbiol	10.1007/s00203-022-02790-4	2022	*
Phylogeny	Larkinella punicea sp. nov., isolated from manganese mine soil.	Zhou Z, Zhu L, Dong Y, Xia X, Wu S, Wang G	Arch Microbiol	10.1007/s00203-020-01863-6	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 )

#65423

Jongguen Jeon, Leonid N. Ten, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Young-Je Cho, Myung Kyum Kim, Hee-Young Jung: Larkinella knui sp. nov., isolated from soil. IJSEM 68: 582 - 588 2018 ( DOI 10.1099/ijsem.0.002550 , PubMed 29300161 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

#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 .

* These data were automatically processed and therefore are not curated

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Larkinella knui strain KCTC42998

Larkinella knui KCTC42998

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