Larkinella arboricola (DSM 21851, VKM B-2528, Z-0532)

Name: Larkinella arboricola (DSM 21851, VKM B-2528, Z-0532)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3828

Type strain

Strain Designation Z-0532, Z0532

Culture col. no. DSM 21851 VKM B-2528 Z-0532 Z0532

NCBI tax ID(s) 643671

Special Collections DSMZ

History DSMZ <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow; Z0532 <- I. S. Kulichevskaya

Links

Larkinella arboricola Z-0532 is a bacterium that was isolated from decaying wood.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398361

DSM 21851

@ref 20215

Last LPSN update 2026-05-29 08:25:48

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Larkinella

Species Larkinella arboricola

Full scientific name Larkinella arboricola Kulichevskaya et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.336
125439	negative	96.207

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15990	LARKINELLA ARBORICOLA MEDIUM (DSMZ Medium 1327)		Medium recipe at MediaDive	Name: LARKINELLA ARBORICOLA MEDIUM (DSMZ Medium 1327) Composition: Agar 15.0 g/l N-Acetylglucosamine 1.0 g/l MgSO4 x 7 H2O 0.594 g/l Glucose 0.5 g/l Nitrilotriacetic acid 0.2 g/l Peptone 0.1 g/l KH2PO4 0.1 g/l Yeast extract 0.1 g/l Casamino acids 0.1 g/l CaCl2 x 2 H2O 0.0667 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15990	positive	growth	22-28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	90.234

Spore formation

@ref	Spore formation	Confidence
125439		99.291

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Decomposing plant
#Host Body Product	#Plant	#Timber
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15990	decaying wood	Moscow region	Russia	RUS	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15990	1	Risk group (German 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	ASM325974v1 assembly for Larkinella arboricola DSM 21851	scaffold	GCA_003259745	643671.4	2593339304	643671	70.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15990	Larkinella arboricola partial 16S rRNA gene, type strain Z0532T	FN391025	1437		643671

GC content

15990

GC-content (mol%)52.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM325974v1 assembly for Larkinella arboricola DSM 21851
BV-BRC: 643671.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.23	no
125439	gram_stain	BacteriaNetⓘ	negative	96.21	no
125439	motility	BacteriaNetⓘ	no	65.41	no
125439	spore_formation	BacteriaNetⓘ	no	99.29	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Larkinella arboricola DSM 21851
NCBI: GCA_003259745.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.34	no
125438	anaerobic	anaerobicⓘ	no	96.97	no
125438	aerobic	aerobicⓘ	yes	88.59	no
125438	spore-forming	spore-formingⓘ	no	85.64	no
125438	thermophilic	thermophileⓘ	no	96.38	no
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING.	Hou MH, Wang YC, Yang CS, Liao KF, Chang JW, Shih O, Yeh YQ, Sriramoju MK, Weng TW, Jeng US, Hsu SD, Chen Y.	Nat Commun	10.1038/s41467-023-44052-x	2023
	Effect of intra- and inter-specific plant interactions on the rhizosphere microbiome of a single target plant at different densities.	Newberger DR, Deel HL, Manter DK, Vivanco JM.	PLoS One	10.1371/journal.pone.0316676	2025
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 roseus sp. nov., a species of the family Cytophagaceae isolated from beach soil.	Lee JB, Hong S, Lee SY, Park SJ, Park KI, Choi SG, Kim MK, Ten LN, Jung HY	J Microbiol	10.1007/s12275-018-7476-x	2018
Phylogeny	Larkinella terrae sp. nov., isolated from soil on Jeju Island, South Korea.	Ten LN, Jeon J, Park SJ, Park S, Lee SY, Kim MK, Jung HY	Antonie Van Leeuwenhoek	10.1007/s10482-017-0955-y	2017
Phylogeny	Larkinella ripae sp. nov., isolated from seashore soil.	Lee YH, Lee JJ, Lee SY, Lee DS, Kim MK, Ten LN, Jung HY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002188	2017
Phylogeny	Larkinella harenae sp. nov., Isolated from Korean Beach Soil.	Park SJ, Lee JJ, Lee SY, Lee DS, Kim MK, Ten LN, Jung HY	Curr Microbiol	10.1007/s00284-017-1246-6	2017

References

#15990	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21851
#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 )
#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) .
#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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Larkinella arboricola (DSM 21851, VKM B-2528, Z-0532)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003259745

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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