Ilumatobacter coccineus (NBRC 103263, KCTC 29153, YM16-304)

Name: Ilumatobacter coccineus (NBRC 103263, KCTC 29153, YM16-304)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133934

Type strain

Strain Designation YM16-304

Culture col. no. NBRC 103263 KCTC 29153 YM16-304

NCBI tax ID(s) 467094

Special Collections KCTC Literature strains

Links

Ilumatobacter coccineus YM16-304 is an aerobe, Gram-positive, rod-shaped prokaryote that was isolated from soil.

Gram-positive rod-shaped aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 28359

KCTC 29153,NBRC 103263

@ref 20215

Last LPSN update 2025-12-16 10:01:55

Domain Bacillati

Phylum Actinomycetota

Class Acidimicrobiia

Order Acidimicrobiales

Family Ilumatobacteraceae

Genus Ilumatobacter

Species Ilumatobacter coccineus

Full scientific name Ilumatobacter coccineus corrig. Matsumoto et al. 2013

Synonyms (1)

Ilumatobacter coccineum

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30911	positive	1.4 µm	0.5 µm	rod-shaped

Pigmentation

30911

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
30911	positive	growth	12-36
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
30911	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30911	aerobe
67771	aerobe

Observation

67771

Observationquinones: MK-9(H8)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30911	4853 ChEBI	esculin	+	hydrolysis

Enzymes

@ref	Value	Activity	Ec
30911	acid phosphatase	+	3.1.3.2
30911	alkaline phosphatase	+	3.1.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
30911	soil
67771	From marine sand	Hinomisaki, Shimane Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB360346 (>99% sequence identity) for Ilumatobacter coccineus subclade from Microbeatlas

Aquatic Samples	1810
Soil Samples	852
Animal Samples	127
Plant Samples	63
Total Samples	2852

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM34878v1 assembly for Ilumatobacter coccineus YM16-304	complete	GCA_000348785	467094.3	2545824624	1313172	98.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30911	Ilumatobacter coccineus YM16-304 gene for 16S rRNA, partial sequence	AB360346	1443		1313172

GC content

@ref	GC-content (mol%)
30911	67
67771	67.0

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ilumatobacter coccineus YM16-304 YM16-304
NCBI: GCA_000348785.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.97	yes
125438	anaerobic	anaerobicⓘ	no	90.50	no
125438	aerobic	aerobicⓘ	yes	80.42	yes
125438	spore-forming	spore-formingⓘ	no	57.56	no
125438	thermophilic	thermophileⓘ	no	91.05	yes
125438	flagellated	motile2+ⓘ	no	81.54	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Ilumatobacter coccineum YM16-304(T.).	Fujinami S, Takarada H, Kasai H, Sekine M, Omata S, Harada T, Fukai R, Hosoyama A, Horikawa H, Kato Y, Nakazawa H, Fujita N	Stand Genomic Sci	10.4056/sigs.4007734	2013
Phylogeny	Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand.	Matsumoto A, Kasai H, Matsuo Y, Shizuri Y, Ichikawa N, Fujita N, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.047316-0	2013

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 )
#30911	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27241 (see below)
#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;
#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 .
#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 )
#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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Ilumatobacter coccineus (NBRC 103263, KCTC 29153, YM16-304)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000348785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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