Alloyangia pacifica (DSM 26894, CGMCC 1.3455, JCM 12573)

Name: Alloyangia pacifica (DSM 26894, CGMCC 1.3455, JCM 12573)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23231

Type strain

Strain Designation DX5-10

Culture col. no. DSM 26894 CGMCC 1.3455 JCM 12573 DX5-10 NCIMB 14310 1 more

NCBI tax ID(s) 311180

Special Collections DSMZ JCM CIP Literature strains

History DSMZ <- JCM <- D. Xin; DX5-10 CIP <- 2006, JCM JCM <-- AS 1.3455 <-- D. Xin DX5-10. CIP <- 2006, JCM

Links

Alloyangia pacifica DX5-10 is an aerobe, Gram-negative, motile bacterium that was isolated from coastal sediment.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 291017

CGMCC 1.3455,JCM 12573,CIP 109187,AS 1.3455,DSM 26894

@ref 20215

Last LPSN update 2026-05-29 08:30:24

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Alloyangia

Species Alloyangia pacifica

Full scientific name Alloyangia pacifica (Dai et al. 2006) Deshmukh and Oren 2023

Synonyms (2)

Yangia pacifica
Salipiger pacificus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31669	negative	1-1.5 µm	0.8 µm	rod-shaped
125439	negative				94.452
125438	negative				98.5
121501	negative			rod-shaped

Colony morphology

19043

Incubation period1-2 days

Pigmentation

31669

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19043	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
40025	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121501	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
19043	positive	growth	30
31669	positive	growth	22-40
31669	positive	optimum	37
40025	positive	growth	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31669	positive	optimum	7.5
31669	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31669	aerobe
121501	obligate aerobe
125439	obligate aerobe	90.173

Spore formation

@ref	Spore formation	Confidence
31669
125438		91.013
125439		99.531

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31669	NaCl	positive	growth	01-10 %
31669	NaCl	positive	optimum	5 %

Observation

@ref	Observation
31669	aggregates in chains
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31669	29016 ChEBI	arginine	+	carbon source
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	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	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
31669	24996 ChEBI	lactate	+	carbon source
31669	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31669	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
121501	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121501	16301 ChEBI	nitrite	-	reduction
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
121501	35581 ChEBI	indole

Metabolite tests

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

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
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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
19043	catalase	+	1.11.1.6
31669	catalase	+	1.11.1.6
121501	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31669	cytochrome oxidase	+	1.9.3.1
19043	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121501	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
31669	urease	+	3.5.1.5
121501	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE
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
121501	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	+	+	-	-

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
19043	-	-	-	-	+	+/-	-	+/-	+	+	+	+	+	+	+	-	-	+	+	+	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19043	coastal sediment	East China Sea
67770	Coastal sediment of the East China Sea
121501	Environment, Coastal sediment	East Sea	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19043	1	Risk group (German classification) According to TRBA 466
121501	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
67770	IMG-taxon 2619618962 annotated assembly for Alloyangia pacifica DSM 26894	scaffold	GCA_900116195	311180.11	2619618962	311180	70.22
67770	IMG-taxon 2617270881 annotated assembly for Alloyangia pacifica CGMCC 1.3455	contig	GCA_900100725	311180.10	2617270881	311180	69.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19043	Yangia pacifica partial 16S rRNA gene, type strain DX5-10T	AJ877265	1351		311180
67770	Yangia pacifica gene for 16S ribosomal RNA, partial sequence, strain: JCM 12573	LC076758	1384		311180

GC content

@ref	GC-content (mol%)	Method
19043	63.3	thermal denaturation, midpoint method (Tm)
31669	63.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2619618962 annotated assembly for Alloyangia pacifica DSM 26894
NCBI: GCA_900116195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.17	no
125439	gram_stain	BacteriaNetⓘ	negative	94.45	no
125439	motility	BacteriaNetⓘ	yes	67.74	no
125439	spore_formation	BacteriaNetⓘ	no	99.53	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yangia pacifica strain CGMCC 1.3455
PATRIC: 311180.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	92.91	yes
125438	spore-forming	spore-formingⓘ	no	91.01	yes
125438	aerobic	aerobicⓘ	yes	85.03	yes
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	73.68	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Yangia mangrovi sp. nov., a novel member of the Roseobacter clade isolated from mangrove soil and emended description of Yangia pacifica Dai et al. 2006.	Verma A, Sundharam SS, Pal Y, Bisht B, Yadav P, Krishnamurthi S	Int J Syst Evol Microbiol	10.1099/ijsem.0.005021	2021
Phylogeny	Yangia pacifica gen. nov., sp. nov., a novel member of the Roseobacter clade from coastal sediment of the East China Sea.	Dai X, Wang BJ, Yang QX, Jiao NZ, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64013-0	2006

References

#19043	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26894
#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 )
#27948	IJSEM 529 2006 ( DOI 10.1099/ijs.0.64013-0 , PubMed 16514022 )
#31669	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 #27948
#40025	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#121501	Collection of Institut Pasteur ; Curators of the CIP; CIP 109187
#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

Alloyangia pacifica (DSM 26894, CGMCC 1.3455, JCM 12573)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900116195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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