Ornithinimicrobium cavernae (DSM 105806, CGMCC 1.16393, KCTC 49018)

Name: Ornithinimicrobium cavernae (DSM 105806, CGMCC 1.16393, KCTC 49018)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159683

Type strain

Culture col. no. DSM 105806 CGMCC 1.16393 KCTC 49018 CFH 30183

NCBI tax ID(s) 2666047

Special Collections DSMZ KCTC

History DSMZ <- W.-J. Li, Sun Yat-Sen University, Guangzhou, China <- L. Zhang, College of Fisheries, Henan Normal University, Xinxiang; CFH30183 KCTC <- Wenjun Li, Sun Sat-Sen Univ.

Links

Ornithinimicrobium cavernae DSM 105806 is an aerobe bacterium that was isolated from sediment of cave.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398553

KCTC 49018,DSM 105806

@ref 20215

Last LPSN update 2026-05-29 08:44:15

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Ornithinimicrobiaceae

Genus Ornithinimicrobium

Species Ornithinimicrobium cavernae

Full scientific name Ornithinimicrobium cavernae Zhang et al. 2019

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	91
125438	90.024	positive
125439	98.287	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66534	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
66534	positive	growth	28
67771	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	96.65

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
66534	sediment of cave	Henan Province, Luoyang county (33° 46' N, 111° 34' E)	China	CHN	Asia	33.7667	111.567 33.7667/111.567
67771	From the sediment of cave	Henan province	China	CHN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM312162v1 assembly for Ornithinimicrobium cavernae KCTC 49018	contig	GCA_003121625	2144182.3	2833498065	2666047	65.42

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66534	Ornithinimicrobium cavernae 16S ribosomal RNA gene, partial sequence	MH177974	1498		2666047

GC content

@ref	GC-content (mol%)	Method
66534	70.9	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM312162v1 assembly for Ornithinimicrobium cavernae KCTC 49018
NCBI: GCA_003121625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.65	no
125439	gram_stain	BacteriaNetⓘ	positive	98.29	no
125439	motility	BacteriaNetⓘ	no	89.10	no
125439	spore_formation	BacteriaNetⓘ	yes	45.59	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ornithinimicrobium sp. KCTC 49018
PATRIC: 2144182.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.02	no
125438	anaerobic	anaerobicⓘ	no	95.94	no
125438	spore-forming	spore-formingⓘ	no	67.38	no
125438	aerobic	aerobicⓘ	yes	87.95	yes
125438	thermophilic	thermophileⓘ	no	93.21	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Description of Ornithinimicrobium cryptoxanthini sp. nov., a Novel Actinomycete Producing beta-cryptoxanthin Isolated from the Tongtian River Sediments.	Huang Y, Jiao Y, Zhang S, Tao Y, Zhang S, Jin D, Pu J, Liu L, Yang J, Lu S.	J Microbiol	10.1007/s12275-023-00029-5	2023
Phylogeny	Ornithinimicrobium sediminis sp. nov., a novel actinobacterium isolated from a saline lake sediment.	Gao L, Fang BZ, Liu YH, Huang Y, Jiao JY, Li L, Antunes A, Li WJ	Arch Microbiol	10.1007/s00203-022-02898-7	2022
Phylogeny	Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave.	Zhang LY, Ming H, Meng XL, Fang BZ, Jiao JY, Salam N, Zhang XT, Li WJ, Nie GX	Antonie Van Leeuwenhoek	10.1007/s10482-018-1141-6	2018
Phylogeny	Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds.	Lee SY, Sung H, Kim PS, Kim HS, Lee JY, Lee JY, Jeong YS, Tak EJ, Han JE, Hyun DW, Bae JW	J Microbiol	10.1007/s12275-021-1323-1	2021

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 )
#66534	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105806
#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 )
#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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Ornithinimicrobium cavernae (DSM 105806, CGMCC 1.16393, KCTC 49018)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003121625

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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