Brevirhabdus pacifica (DSM 27767, CGMCC 1.12416, JCM 19489)

Name: Brevirhabdus pacifica (DSM 27767, CGMCC 1.12416, JCM 19489)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132259

Type strain

Strain Designation 22DY15

Culture col. no. DSM 27767 CGMCC 1.12416 JCM 19489 MCCC 1K00276 22DY15

NCBI tax ID(s) 1267768

Special Collections DSMZ JCM

History DSMZ <- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; 22DY15 JCM <-- Y.-H. Wu 22DY15.

Links

Brevirhabdus pacifica 22DY15 is a bacterium that was isolated from deep-sea sediment from a hydrothermal vent field.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407036

JCM 19489,DSM 27767

@ref 20215

Last LPSN update 2026-05-29 08:37:49

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Brevirhabdus

Species Brevirhabdus pacifica

Full scientific name Brevirhabdus pacifica Wu et al. 2015

Synonyms (1)

Xuhuaishuia manganoxidans

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	91.474
125438	negative	97.833

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24048	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

Culture temp

@ref	Growth	Type	Temperature (°C)
24048	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98.872

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gluconeogenesis	100	8 of 8
66794	CMP-KDO biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	octane oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	photosynthesis	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	glutathione metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	sulfopterin metabolism	75	3 of 4
66794	purine metabolism	73.4	69 of 94
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	methionine metabolism	69.23	18 of 26
66794	IAA biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	non-pathway related	65.79	25 of 38
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	oxidative phosphorylation	62.64	57 of 91
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	factor 420 biosynthesis	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	alanine metabolism	58.62	17 of 29
66794	arginine metabolism	58.33	14 of 24
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	histidine metabolism	51.72	15 of 29
66794	phenylmercury acetate degradation	50	1 of 2
66794	alginate biosynthesis	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	acetate fermentation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	carnitine metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	lysine metabolism	47.62	20 of 42
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	degradation of pentoses	42.86	12 of 28
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	elloramycin biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cholesterol biosynthesis	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of sugar acids	32	8 of 25
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	starch degradation	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	mevalonate metabolism	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	glycogen biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
24048	+	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	+	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude
24048	deep-sea sediment from a hydrothermal vent field	East Pacific Rise (3° 06' 15'' S 102° 33' 16'' W)	-3.1042	-102.554 -3.1042/-102.554
67770	Deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise

Taxonmaps

69479

Global distribution of 16S sequence KC018457 (>99% sequence identity) for Brevirhabdus pacifica subclade from Microbeatlas

Aquatic Samples	2087
Soil Samples	98
Animal Samples	47
Plant Samples	7
Total Samples	2239

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24048	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM279775v1 assembly for Brevirhabdus pacifica DSM 27767	contig	GCA_002797755	1267768.4	2728369741	1267768	75.3
66792	ASM209487v1 assembly for Brevirhabdus pacifica 22DY15	scaffold	GCA_002094875	1267768.3	8117427298	1267768	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24048	Brevirhabdus pacifica strain 22DY15 16S ribosomal RNA gene, partial sequence	KC018457	1384		1267768

GC content

@ref	GC-content (mol%)	Method
24048	64.3	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: ASM279775v1 assembly for Brevirhabdus pacifica DSM 27767
NCBI: GCA_002797755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.26	no
125439	motility	BacteriaNetⓘ	yes	61.65	no
125439	gram_stain	BacteriaNetⓘ	negative	91.47	no
125439	spore_formation	BacteriaNetⓘ	no	98.87	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Brevirhabdus pacifica 22DY15
NCBI: GCA_002094875.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	no
125438	anaerobic	anaerobicⓘ	no	89.31	no
125438	aerobic	aerobicⓘ	yes	73.56	no
125438	spore-forming	spore-formingⓘ	no	89.52	no
125438	thermophilic	thermophileⓘ	no	93.92	no
125438	flagellated	motile2+ⓘ	no	50.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Reclassification of Xuhuaishuia manganoxidans Wang et al. 2015 as a later heterotypic synonym of Brevirhabdus pacifica Wu et al. 2015 and emendation of the species description.	Liu Y, Lai Q, Xu XW, Wu YH, Cheng H, Zhang XH, Wang L, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002097	2017
Phylogeny	Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field.	Wu YH, Xu L, Zhou P, Wang CS, Oren A, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.000469	2015

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 )
#24048	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27767
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 )

Content

About us

Brevirhabdus pacifica (DSM 27767, CGMCC 1.12416, JCM 19489)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002797755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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