Brachybacterium zhongshanense (DSM 18832, CGMCC 1.6508, LMG 23926)

Name: Brachybacterium zhongshanense (DSM 18832, CGMCC 1.6508, LMG 23926)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3916

Type strain

Strain Designation JB

Culture col. no. DSM 18832 CGMCC 1.6508 LMG 23926 JB JCM 15471

NCBI tax ID(s) 1305859 416230

Special Collections DSMZ JCM Literature strains

Links

Brachybacterium zhongshanense JB is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from sediment, river Qijiang.

Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 293206

LMG 23926,CGMCC 1.6508,DSM 18832,JCM 15471

@ref 20215

Last LPSN update 2025-12-16 09:47:41

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermabacteraceae

Genus Brachybacterium

Species Brachybacterium zhongshanense

Full scientific name Brachybacterium zhongshanense Zhang et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape
32103	positive	rod-shaped
125438
125439	positive

Pigmentation

32103

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7728	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7728	positive	growth	28	mesophilic
32103	positive	growth	25-40
32103	positive	optimum	32.5	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
32103	positive	optimum	7
32103	positive	growth	05-11

Physiology and metabolism

Oxygen tolerance

32103

Oxygen toleranceanaerobe

Spore formation

32103

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32103	NaCl	positive	growth	0-10 %
32103	NaCl	positive	optimum	5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32103	30089 ChEBI	acetate	+	carbon source
32103	22599 ChEBI	arabinose	+	carbon source
32103	17057 ChEBI	cellobiose	+	carbon source
32103	23652 ChEBI	dextrin	+	carbon source
32103	4853 ChEBI	esculin	+	hydrolysis
32103	28757 ChEBI	fructose	+	carbon source
32103	28260 ChEBI	galactose	+	carbon source
32103	24175 ChEBI	galacturonate	+	carbon source
32103	5291 ChEBI	gelatin	+	carbon source
32103	17234 ChEBI	glucose	+	carbon source
32103	17754 ChEBI	glycerol	+	carbon source
32103	28087 ChEBI	glycogen	+	carbon source
32103	17596 ChEBI	inosine	+	carbon source
32103	24996 ChEBI	lactate	+	carbon source
32103	17716 ChEBI	lactose	+	carbon source
32103	17306 ChEBI	maltose	+	carbon source
32103	37684 ChEBI	mannose	+	carbon source
32103	28053 ChEBI	melibiose	+	carbon source
32103	51850 ChEBI	methyl pyruvate	+	carbon source
32103	17632 ChEBI	nitrate	+	reduction
32103	15361 ChEBI	pyruvate	+	carbon source
32103	16634 ChEBI	raffinose	+	carbon source
32103	17992 ChEBI	sucrose	+	carbon source
32103	27082 ChEBI	trehalose	+	carbon source
32103	16199 ChEBI	urea	+	carbon source
32103	17151 ChEBI	xylitol	+	carbon source
32103	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32103	catalase	+	1.11.1.6
32103	gelatinase	+
32103	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7728	sediment, river Qijiang	Zhongshan City	China	CHN	Asia
67770	Sediments along the Qijiang River	Zhongshan City	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7728	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
66792	ASM131408v1 assembly for Brachybacterium zhongshanense JCM 15471	contig	GCA_001314085	1305859.3	2681813033	1305859

Genome browser: GCA_001314085

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7728	Brachybacterium zhongshanense strain JB 16S ribosomal RNA gene, partial sequence	EF125186	1485		416230

GC content

@ref	GC-content (mol%)
7728	71.2
67770	71.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Brachybacterium zhongshanense JCM 15471
NCBI: GCA_001314085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	63.00	no
125439	motility	BacteriaNetⓘ	no	72.90	no
125439	gram_stain	BacteriaNetⓘ	positive	97.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	79.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Brachybacterium zhongshanense JCM 15471
PATRIC: 1305859.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.27	no
125438	anaerobic	anaerobicⓘ	no	69.63	yes
125438	spore-forming	spore-formingⓘ	no	85.42	no
125438	aerobic	aerobicⓘ	no	58.67	no
125438	thermophilic	thermophileⓘ	no	94.30	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Brachybacterium zhongshanense sp. nov., a cellulose-decomposing bacterium from sediment along the Qijiang River, Zhongshan City, China.	Zhang G, Zeng G, Cai X, Deng S, Luo H, Sun G	Int J Syst Evol Microbiol	10.1099/ijs.0.64968-0	2007

References

#7728	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18832
#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 )
#32103	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 #28348 (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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Brachybacterium zhongshanense (DSM 18832, CGMCC 1.6508, LMG 23926)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001314085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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