Allosediminivita pacifica (DSM 29329, CGMCC 1.12410, JCM 18866)

Name: Allosediminivita pacifica (DSM 29329, CGMCC 1.12410, JCM 18866)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24495

Type strain

Strain Designation 22DY03

Culture col. no. DSM 29329 CGMCC 1.12410 JCM 18866 22DY03

NCBI tax ID(s) 1267769

Special Collections DSMZ JCM Literature strains

History <- JCM <- J.-H. Wu; 22DY03 Y.-H. Wu 22DY03.

Links

Allosediminivita pacifica 22DY03 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from deep-sea sediment sample.

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

Name and taxonomic classification

SI-ID 398993

JCM 18866,DSM 29329

@ref 20215

Last LPSN update 2026-02-09 11:23:59

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Allosediminivita

Species Allosediminivita pacifica

Full scientific name Allosediminivita pacifica (Wu et al. 2013) Hördt et al. 2020

Synonyms (1)

Roseivivax pacificus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31107	negative	1.4 µm	0.75 µm	rod-shaped
125439	negative				96.6
125438	negative				96.833

Colony morphology

20778

Incubation period1-2 days

Pigmentation

31107

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20778	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)
20778	positive	growth	30
31107	positive	growth	10-40
31107	positive	optimum	32.5
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31107	positive	optimum	7
31107	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31107	aerobe
125439	obligate aerobe	93.3

Spore formation

@ref	Spore formation	Confidence
125439		93.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31107	NaCl	positive	growth	0.5-15 %

Observation

@ref	Observation
31107	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31107	30089 ChEBI	acetate	+	carbon source
31107	17128 ChEBI	adipate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31107	16449 ChEBI	alanine	+	carbon source
31107	22599 ChEBI	arabinose	+	carbon source
31107	29016 ChEBI	arginine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31107	17057 ChEBI	cellobiose	+	carbon source
31107	16947 ChEBI	citrate	+	carbon source
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
31107	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31107	16236 ChEBI	ethanol	+	carbon source
31107	15740 ChEBI	formate	+	carbon source
31107	28757 ChEBI	fructose	+	carbon source
31107	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
31107	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31107	17234 ChEBI	glucose	+	carbon source
31107	17754 ChEBI	glycerol	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
31107	17716 ChEBI	lactose	+	carbon source
31107	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31107	15792 ChEBI	malonate	+	carbon source
31107	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
31107	29864 ChEBI	mannitol	+	carbon source
31107	37684 ChEBI	mannose	+	carbon source
31107	17268 ChEBI	myo-inositol	+	carbon source
31107	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
31107	18257 ChEBI	ornithine	+	carbon source
31107	17272 ChEBI	propionate	+	carbon source
31107	15361 ChEBI	pyruvate	+	carbon source
31107	16634 ChEBI	raffinose	+	carbon source
31107	26546 ChEBI	rhamnose	+	carbon source
31107	33942 ChEBI	ribose	+	carbon source
31107	17814 ChEBI	salicin	+	carbon source
31107	17822 ChEBI	serine	+	carbon source
31107	30911 ChEBI	sorbitol	+	carbon source
31107	30031 ChEBI	succinate	+	carbon source
31107	17992 ChEBI	sucrose	+	carbon source
31107	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
31107	18222 ChEBI	xylose	+	carbon source

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
31107	acid phosphatase	+	3.1.3.2
31107	alkaline phosphatase	+	3.1.3.1
31107	alpha-galactosidase	+	3.2.1.22
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
20778	catalase	+	1.11.1.6
31107	catalase	+	1.11.1.6
31107	cytochrome oxidase	+	1.9.3.1
20778	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
31107	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cyanate degradation	100	3 of 3
66794	enterobactin biosynthesis	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	denitrification	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	propanol degradation	100	7 of 7
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	quinate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	Entner Doudoroff pathway	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	glycogen biosynthesis	100	4 of 4
66794	vitamin B1 metabolism	92.31	12 of 13
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	ketogluconate metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	methionine metabolism	84.62	22 of 26
66794	pyrimidine metabolism	82.22	37 of 45
66794	purine metabolism	81.91	77 of 94
66794	proline metabolism	81.82	9 of 11
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	creatinine degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	sulfopterin metabolism	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	isoleucine metabolism	75	6 of 8
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	glutamate and glutamine metabolism	75	21 of 28
66794	pentose phosphate pathway	72.73	8 of 11
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	non-pathway related	71.05	27 of 38
66794	oxidative phosphorylation	67.03	61 of 91
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	degradation of hexoses	66.67	12 of 18
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	sulfate reduction	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	metabolism of disaccharids	54.55	6 of 11
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	polyamine pathway	52.17	12 of 23
66794	kanosamine biosynthesis II	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	alginate biosynthesis	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	ascorbate metabolism	50	11 of 22
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	starch degradation	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	ethanol fermentation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	d-xylose degradation	45.45	5 of 11
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	cellulose degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	ginsenoside metabolism	31.25	5 of 16
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4

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
20778	+	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	+	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location
20778	deep-sea sediment sample	East Pacific Rise
67770	Deep-sea sediment from the East Pacific Rise

Taxonmaps

69479

Global distribution of 16S sequence KC018453 (>99% sequence identity) for Allosediminivita pacifica subclade from Microbeatlas

Aquatic Samples	472
Soil Samples	27
Animal Samples	109
Plant Samples	3
Total Samples	611

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20778	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	ASM305417v1 assembly for Allosediminivita pacifica DSM 29329	scaffold	GCA_003054175	1267769.4	2739367657	1267769	59.35
66792	ASM1463749v1 assembly for Allosediminivita pacifica CGMCC 1.12410	contig	GCA_014637495	1267769.6	8062759556	1267769	57.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20778	Roseivivax pacificus strain 22DY03 16S ribosomal RNA gene, partial sequence	KC018453	1424		1267769

GC content

@ref	GC-content (mol%)	Method
31107	64.6
67770	64.6	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: Allosediminivita pacifica DSM 29329
NCBI: GCA_003054175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.30	no
125439	gram_stain	BacteriaNetⓘ	negative	96.60	no
125439	motility	BacteriaNetⓘ	yes	69.90	no
125439	spore_formation	BacteriaNetⓘ	no	93.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Allosediminivita pacifica DSM 29329
NCBI: GCA_003054175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	yes
125438	anaerobic	anaerobicⓘ	no	94.71	yes
125438	aerobic	aerobicⓘ	yes	86.42	yes
125438	spore-forming	spore-formingⓘ	no	87.90	no
125438	thermophilic	thermophileⓘ	no	94.71	yes
125438	flagellated	motile2+ⓘ	no	59.08	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	Roseivivax pacificus sp. nov., isolated from deep-sea sediment.	Wu YH, Meng FX, Xu L, Zhang XQ, Wang CS, Oren A, Wu M, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.052274-0	2013

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 )
#20778	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29329
#27436	IJSEM 4574 2013 ( DOI 10.1099/ijs.0.052274-0 , PubMed 23907228 )
#31107	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 #27436
#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 )

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Allosediminivita pacifica (DSM 29329, CGMCC 1.12410, JCM 18866)

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

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_003054175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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