Brachybacterium squillarum (KACC 14221, JCM 16464, M-6-3)

Name: Brachybacterium squillarum (KACC 14221, JCM 16464, M-6-3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133630

Type strain

Strain Designation M-6-3

Culture col. no. KACC 14221 JCM 16464 M-6-3

NCBI tax ID(s) 1074488 661979

Special Collections JCM Literature strains

History JCM <-- J.-W. Bae M-6-3.

Links

Brachybacterium squillarum M-6-3 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from food product.

Gram-positive coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 133650

JCM 16464

@ref 20215

Last LPSN update 2026-05-29 08:38:08

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermabacteraceae

Genus Brachybacterium

Species Brachybacterium squillarum

Full scientific name Brachybacterium squillarum Park et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29850	positive	coccus-shaped
125438			92.5
125438	positive		90.24

Pigmentation

29850

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29850	positive	growth	25-37
29850	positive	optimum	31
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29850	positive	optimum	7
29850	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29850	aerobe
125439	facultative anaerobe	93.454

Spore formation

29850

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29850	NaCl	positive	growth	0-10 %
29850	NaCl	positive	optimum	5 %

Observation

@ref	Observation
29850	aggregates in clumps
67770	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29850	23652 ChEBI	dextrin	+	carbon source
29850	33984 ChEBI	fucose	+	carbon source
29850	28260 ChEBI	galactose	+	carbon source
29850	5291 ChEBI	gelatin	+	carbon source
29850	24265 ChEBI	gluconate	+	carbon source
29850	17234 ChEBI	glucose	+	carbon source
29850	28087 ChEBI	glycogen	+	carbon source
29850	17596 ChEBI	inosine	+	carbon source
29850	18403 ChEBI	L-arabitol	+	carbon source
29850	17306 ChEBI	maltose	+	carbon source
29850	29864 ChEBI	mannitol	+	carbon source
29850	37684 ChEBI	mannose	+	carbon source
29850	28053 ChEBI	melibiose	+	carbon source
29850	15361 ChEBI	pyruvate	+	carbon source
29850	16634 ChEBI	raffinose	+	carbon source
29850	26546 ChEBI	rhamnose	+	carbon source
29850	30911 ChEBI	sorbitol	+	carbon source
29850	17992 ChEBI	sucrose	+	carbon source
29850	53425 ChEBI	tween 60	+	carbon source
29850	16704 ChEBI	uridine	+	carbon source

Enzymes

@ref	Value	Activity
29850	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
29850	food product
67770	Salt-fermented food made of tiny shrimp	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ339911 (>99% sequence identity) for Brachybacterium squillarum from Microbeatlas

Aquatic Samples	413
Soil Samples	115
Animal Samples	1599
Plant Samples	64
Total Samples	2191

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM22582v2 assembly for Brachybacterium squillarum M-6-3	contig	GCA_000225825	1074488.3	2548876527	1074488	71.67

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29850	Brachybacterium squillarum strain M-6-3 16S ribosomal RNA gene, partial sequence	GQ339911	1444		1074488

GC content

@ref	GC-content (mol%)	Method
29850	71.5
67770	72.8	genome sequence analysis
67770	71.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM22582v2 assembly for Brachybacterium squillarum M-6-3
NCBI: GCA_000225825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	87.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.45	no
125439	motility	BacteriaNetⓘ	no	68.96	no
125439	spore_formation	BacteriaNetⓘ	no	87.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Brachybacterium squillarum M-6-3
PATRIC: 1074488.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.24	yes
125438	anaerobic	anaerobicⓘ	no	93.99	yes
125438	spore-forming	spore-formingⓘ	no	73.61	no
125438	aerobic	aerobicⓘ	yes	70.20	no
125438	thermophilic	thermophileⓘ	no	93.50	no
125438	flagellated	motile2+ⓘ	no	92.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	First case of a bloodstream infection caused by the genus Brachybacterium.	Tamai K, Akashi Y, Yoshimoto Y, Yaguchi Y, Takeuchi Y, Shiigai M, Igarashi J, Hirose Y, Suzuki H, Ohkusu K	J Infect Chemother	10.1016/j.jiac.2018.06.005	2018
Genetics	Genome sequence of Brachybacterium squillarum M-6-3(T), isolated from salt-fermented seafood.	Park SK, Roh SW, Whon TW, Bae JW	J Bacteriol	10.1128/JB.06183-11	2011
Phylogeny	Brachybacterium subflavum sp. nov., a novel actinobacterium isolated from the foregut of grass carp.	Ming H, Cheng LJ, Yi BF, Xia TT, Niu MM, Zhao ZY, Liu BB, Nie GX, Cui CX	Int J Syst Evol Microbiol	10.1099/ijsem.0.004839	2021
Phylogeny	Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch.	Liu Y, Zhai L, Yao S, Cao Y, Cao Y, Zhang X, Su J, Ge Y, Zhao R, Cheng C	Int J Syst Evol Microbiol	10.1099/ijsem.0.000559	2015
Phylogeny	Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood.	Park SK, Kim MS, Jung MJ, Nam YD, Park EJ, Roh SW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.022517-0	2010

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 )
#26224	IJSEM 1118 2011 ( DOI 10.1099/ijs.0.022517-0 , PubMed 20543157 )
#29850	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 #26224
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )
#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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About us

Brachybacterium squillarum (KACC 14221, JCM 16464, M-6-3)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000225825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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