Brachybacterium fresconis (DSM 14564, LMG 20336, R-5509)

Name: Brachybacterium fresconis (DSM 14564, LMG 20336, R-5509)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3911

Type strain

Strain Designation R-5509

Culture col. no. DSM 14564 LMG 20336 R-5509 CCUG 50350 CIP 108248 1 more

NCBI tax ID(s) 173363

Special Collections DSMZ CCUG JCM CIP

Links

Brachybacterium fresconis R-5509 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from mural painting.

Gram-positive ovoid-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 19648

LMG 20336,DSM 14564,JCM 12138,CCUG 50350,CIP 108248

@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 fresconis

Full scientific name Brachybacterium fresconis Heyrman et al. 2002

BacDive ID	Other strains from **Brachybacterium fresconis** (1)	Type strain
3912	B. fresconis R-5387, DSM 14565, LMG 20333

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119454	positive	ovoid-shaped
125438			92
125438	positive		91.284
125439	positive		97.8

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5386	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
33216	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119454	CIP Medium 29	Medium recipe at CIP
119454	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5386	positive	growth	28	mesophilic
33216	positive	growth	30	mesophilic
58850	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic
119454	positive	growth	10-37
119454	negative	growth	41
119454	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
58850	aerobe
119454	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119454	NaCl	positive	growth	0-10 %

Murein

@ref	Murein short key	Type
5386	A31.02	A4gamma m-Dpm-D-Glu₂; alpha-carboxyl group of D-Glu substituted by glycine

Observation

67770

Observationquinones: MK-7, MK-8, MK-7(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
119454	16947 ChEBI	citrate	-	carbon source
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
119454	4853 ChEBI	esculin	+	hydrolysis
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
119454	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
119454	17632 ChEBI	nitrate	+	reduction
119454	17632 ChEBI	nitrate	-	respiration
119454	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119454	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119454	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119454	15688 ChEBI	acetoin	-
119454	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119454	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119454	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
119454	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119454	caseinase	+	3.4.21.50
119454	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119454	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
119454	gamma-glutamyltransferase	-	2.3.2.2
119454	gelatinase	+/-
119454	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119454	lipase	-
68382	lipase (C 14)	-		from API zym
119454	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119454	ornithine decarboxylase	-	4.1.1.17
119454	oxidase	-
119454	phenylalanine ammonia-lyase	-	4.3.1.24
119454	protease	+
68382	trypsin	-	3.4.21.4	from API zym
119454	tryptophan deaminase	-
119454	tween esterase	-
119454	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119454	-	-	-	+	-	+	-	-	-	-	-	+	+	+	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119454	not determinedn.d.	+/-	+/-	+/-	+/-	+/-	+/-	-	+/-	+/-	+/-	+/-	+/-	+/-	-	+/-	-	+/-	+/-	-	-	-	-	-	-	+/-	-	+/-	-	-	+/-	+/-	-	-	+/-	+/-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	-
#Engineered	#Other	#Painting

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5386	mural painting	Herberstein, St. Katharinen Kapelle	Austria	AUT	Europe
58850	Mural painting	Castle Herberstein	Austria	AUT	Europe
67770	Microbial biofilm damaging the mural painting at the Saint-Catherine chapel of Castle Herberstein		Austria	AUT	Europe
119454	Microbial biofilm damaging the mural painting	Herberstein castle, Himsdorf	Austria	AUT	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ415378 (>99% sequence identity) for Brachybacterium from Microbeatlas

Aquatic Samples	270
Soil Samples	75
Animal Samples	767
Plant Samples	30
Total Samples	1142

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5386	1	Risk group (German classification) According to TRBA 466
119454	1	Risk group (French 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	ASM1787651v1 assembly for Brachybacterium fresconis DSM 14564	contig	GCA_017876515	173363.3	2918358370	173363	68.47
124043	ASM4265520v1 assembly for Brachybacterium fresconis CCUG 50350	contig	GCA_042655205			173363	37.05
124043	ASM3952734v1 assembly for Brachybacterium fresconis JCM 12138	scaffold	GCA_039527345			173363	34.85

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5386	Brachybacterium fresconis partial 16S rRNA gene, type strain LMG 20336T	AJ415378	1471		173363

GC content

@ref	GC-content (mol%)	Method
5386	70.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Brachybacterium fresconis DSM 14564
NCBI: GCA_017876515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	74.20	no
125439	motility	BacteriaNetⓘ	no	69.80	no
125439	gram_stain	BacteriaNetⓘ	positive	97.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Brachybacterium fresconis strain DSM 14564
PATRIC: 173363.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.28	no
125438	anaerobic	anaerobicⓘ	no	96.25	yes
125438	spore-forming	spore-formingⓘ	no	65.66	no
125438	aerobic	aerobicⓘ	yes	79.95	yes
125438	thermophilic	thermophileⓘ	no	95.67	yes
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Selective isolation and genomic characterization of biopolymer producer-a novel feature of halophile Brachybacterium paraconglomeratum MTCC 13074.	Mandragutti T, Sudhakar G.	J Genet Eng Biotechnol	10.1186/s43141-023-00484-y	2023
Phylogeny	Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain.	Buczolits S, Schumann P, Weidler G, Radax C, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.02728-0	2003
Phylogeny	Brachybacterium fresconis sp. nov. and Brachybacterium sacelli sp. nov., isolated from deteriorated parts of a medieval wall painting of the chapel of Castle Herberstein (Austria).	Heyrman J, Balcaen A, De Vos P, Schumann P, Swings J	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1641	2002

References

#5386	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14564
#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 )
#33216	; Curators of the CIP;
#58850	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50350
#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;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#119454	Collection of Institut Pasteur ; Curators of the CIP; CIP 108248
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 fresconis (DSM 14564, LMG 20336, R-5509)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017876515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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