Branchiibius hedensis (DSM 22951, NBRC 106121, Mer 29717)

Name: Branchiibius hedensis (DSM 22951, NBRC 106121, Mer 29717)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3932

Type strain

Strain Designation 29717

Culture col. no. DSM 22951 NBRC 106121 Mer 29717 29717

NCBI tax ID(s) 672460

Special Collections DSMZ Wink compendium

History DSMZ <- A. Arisawa, Mercian Corporation, Iwata, Japan; 29717 <- S. Sugimoto

Links

Branchiibius hedensis 29717 is a bacterium that was isolated from branchia of a Japanese codling, Physiculus japonicus.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405955

NBRC 106121,DSM 22951

@ref 20215

Last LPSN update 2026-05-29 08:25:49

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermacoccaceae

Genus Branchiibius

Species Branchiibius hedensis

Full scientific name Branchiibius hedensis Sugimoto et al. 2011

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	94
125438	91.481	positive
125439	95.568	positive

Colony morphology

@ref	Colony color	Medium used
69232	Light ivory (1015)	ISP 7
69232	Oyster white (1013)	ISP 2
69232	Oyster white (1013)	ISP 3
69232	Oyster white (1013)	ISP 4
69232	Oyster white (1013)	ISP 5
69232	Oyster white (1013)	suter with tyrosine
69232	Oyster white (1013)	suter without tyrosine

Multicellular morphology

@ref	Complex name	Medium name
69232	Aerial mycelium	ISP 2
69232	Aerial mycelium	ISP 3
69232	Aerial mycelium	ISP 4
69232	Aerial mycelium	ISP 5
69232	Aerial mycelium	ISP 7
69232	Aerial mycelium	suter with tyrosine
69232	Aerial mycelium	suter without tyrosine

Pigmentation

@ref	Production	Name
69232		melanin pigment
69232		soluble pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16629	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)
16629	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.485

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69232	NaCl	positive	growth	0-2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69232	22599 ChEBI	arabinose	+	growth
69232	62968 ChEBI	cellulose	+	growth
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
69232	28757 ChEBI	fructose	+	growth
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
69232	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69232	37684 ChEBI	mannose	+/-	growth
69232	17268 ChEBI	myo-inositol	+/-	growth
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
69232	16634 ChEBI	raffinose	+/-	growth
69232	26546 ChEBI	rhamnose	+/-	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69232	17992 ChEBI	sucrose	+	growth
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
69232	18222 ChEBI	xylose	+/-	growth

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	+	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68382	trypsin	+	3.4.21.4	from API zym
68379	urease	+	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69232	-	+	+	+	-	-	+	-	+	+	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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
69232	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+/-	+/-	+	+	+	+	+	+/-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Fishes	-
#Host Body-Site	#Oral cavity and airways	#Airways

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16629	branchia of a Japanese codling, Physiculus japonicus	Physiculus japonicus	Shizuoka prefecture, Suruga Bay, Heda	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB520822 (>99% sequence identity) for Branchiibius from Microbeatlas

Aquatic Samples	355
Soil Samples	151
Animal Samples	1282
Plant Samples	55
Total Samples	1843

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16629	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	Score
66792	ASM314919v1 assembly for Branchiibius hedensis DSM 22951	contig	GCA_003149195	672460.3	2634166369	672460	73.49
66792	IMG-taxon 2634166369 annotated assembly for Branchiibius hedensis DSM 22951	contig	GCA_900108585	672460.4		672460	71.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16629	Branchiibius hedensis gene for 16S ribosomal RNA, partial sequence	AB520822	1524		672460

GC content

@ref	GC-content (mol%)	Method
16629	68	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: ASM314919v1 assembly for Branchiibius hedensis DSM 22951
BV-BRC: 672460.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.49	no
125439	gram_stain	BacteriaNetⓘ	positive	95.57	no
125439	motility	BacteriaNetⓘ	no	87.07	no
125439	spore_formation	BacteriaNetⓘ	no	87.65	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Branchiibius hedensis strain DSM 22951
PATRIC: 672460.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.48	no
125438	anaerobic	anaerobicⓘ	no	97.38	no
125438	spore-forming	spore-formingⓘ	no	66.06	no
125438	aerobic	aerobicⓘ	yes	86.54	no
125438	thermophilic	thermophileⓘ	no	97.92	yes
125438	flagellated	motile2+ⓘ	no	94.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Leekyejoonella antrihumi gen. nov., sp. nov., a new member of the family Dermacoccaceae isolated from a cave soil.	Lee SD, Kim IS, Schumann P, Song G.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004177	2020
Phylogeny	Tamlicoccus marinus gen. nov., sp. nov., isolated from seawater.	Lee SD.	Int J Syst Evol Microbiol	10.1099/ijs.0.043117-0	2013
Phylogeny	Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).	Ai MJ, Sun Y, Sun HM, Liu HY, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002284	2017
Phylogeny	Branchiibius cervicis sp. nov., a novel species isolated from patients with atopic dermatitis.	Tomida J, Sakamoto D, Sugita T, Fujiwara N, Naka T, Hamada M, Morita Y, Kawamura Y	Syst Appl Microbiol	10.1016/j.syapm.2011.08.003	2011
Phylogeny	Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus).	Sugimoto S, Kato T, Ito M, Sakata N, Tsuchida T, Matsumoto A, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.023648-0	2010

References

#16629	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22951
#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 )
#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) .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69232	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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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Branchiibius hedensis (DSM 22951, NBRC 106121, Mer 29717)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003149195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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