Name: Lutimaribacter pacificus W11-2B
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130637

Type strain:

Species: Lutimaribacter pacificus

Strain Designation: W11-2B

Culture col. no.: DSM 29620, CCTCC AB 208224, LMG 24619, MCCC 1A01034

Strain history: <- LMG <- Q. Lai, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China

NCBI tax ID(s): 391948 (species)

SI-ID 351949

LMG 24619, KCTC 22755, CECT 7832

Section

Lutimaribacter pacificus W11-2B is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from pyrene-degrading consortium enriched from sediment.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Lutimaribacter*
	Species	**Lutimaribacter pacificus**
	Full Scientific Name (LPSN)	Lutimaribacter pacificus (Yuan et al. 2009) Iwaki et al. 2013

Synonym

Oceanicola pacificus

Information on morphological and physiological properties Morphology

[Ref.: #28997]	Gram stain	negative

[Ref.: #28997]	Cell length	1.1 µm

[Ref.: #28997]	Cell width	0.65 µm

[Ref.: #28997]	Cell shape	rod-shaped

[Ref.: #28997]	Motility	no

[Ref.: #21705]

Incubation period

2-3 days

[Ref.: #28997]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21705]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #21705]

Culture medium growth

[Ref.: #21705]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21705]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21705]	growth	30 °C
[Ref.: #28997]	growth	10-41 °C
[Ref.: #28997]	optimum	27.5 °C

[Ref.: #21705]	Temperature range	mesophilic
[Ref.: #28997]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28997]			growth	6.5-11

Information on physiology and metabolism Physiology and metabolism

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28997]		NaCl		optimum	2.5	%

[Ref.: #28997]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28997]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #28997]	alanine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #28997]	asparagine ChEBI	+	carbon source
[Ref.: #28997]	aspartate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #28997]	formate ChEBI	+	carbon source
[Ref.: #28997]	galacturonate ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #28997]	glutamate ChEBI	+	carbon source
[Ref.: #28997]	glycogen ChEBI	+	carbon source
[Ref.: #28997]	histidine ChEBI	+	carbon source
[Ref.: #28997]	itaconate ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #28997]	lactate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #28997]	ornithine ChEBI	+	carbon source
[Ref.: #28997]	proline ChEBI	+	carbon source
[Ref.: #28997]	propionate ChEBI	+	carbon source
[Ref.: #28997]	serine ChEBI	+	carbon source
[Ref.: #28997]	succinate ChEBI	+	carbon source
[Ref.: #28997]	thymidine ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #28997]	acid phosphatase	+	3.1.3.2
[Ref.: #28997]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #21705]	catalase	+	1.11.1.6
[Ref.: #28997]	catalase	+	1.11.1.6
[Ref.: #28997]	cytochrome oxidase	+	1.9.3.1
[Ref.: #21705]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #21705]	24069	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	+/-	not determinedn.d.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21705]	Sample type/isolated from	pyrene-degrading consortium enriched from sediment
[Ref.: #21705]	Geographic location (country and/or sea, region)	Pacific Ocean
[Ref.: #21705]	Country	China
[Ref.: #21705]	Country ISO 3 Code	CHN
[Ref.: #21705]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	-
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ659449 (>99% sequence identity) for Lutimaribacter pacificus subclade from Microbeatlas

Aquatic Samples	51
Soil Samples
Animal Samples	8
Plant Samples	1
Total Samples	60

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21705]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21705]	Oceanicola pacificus strain W11-2B 16S ribosomal RNA gene, partial sequence	DQ659449	1427	ENA	391948 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lutimaribacter pacificus DSM 29620	GCA_900142185	contig	GenBank	391948 tax ID	*
[Ref.: #66792]	Lutimaribacter pacificus strain DSM 29620	391948.4	wgs	PATRIC	391948 tax ID	*
[Ref.: #66792]	Lutimaribacter pacificus DSM 29620	2695420927	draft	JGI IMG/M	391948 tax ID	*

[Ref.: #28997]

GC-content

64.6 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lutimaribacter pacificus strain DSM 29620 PATRIC: 391948.4
[Ref.: #69480]	gram-positive	no	98.098	yes
[Ref.: #69480]	anaerobic	no	98.585	no
[Ref.: #69480]	halophile	yes	82.492	no
[Ref.: #69480]	spore-forming	no	97.299	no
[Ref.: #69480]	glucose-util	no	53.015	yes
[Ref.: #69480]	aerobic	yes	87.134	no
[Ref.: #69480]	flagellated	no	86.212	no
[Ref.: #69480]	thermophile	no	94.857	yes
[Ref.: #69480]	motile	no	54.621	no
[Ref.: #69480]	glucose-ferment	no	91.959	yes

Availability in culture collections External links

[Ref.: #21705]

Culture collection no.

DSM 29620, CCTCC AB 208224, LMG 24619, MCCC 1A01034

[Ref.: #89148]

SI-ID 351949

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment.	Chen S, Zheng S, Zhang D, Hetharua B, Gui J, An X, Xu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004801	2021	*
Phylogeny	Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium.	Yuan J, Lai Q, Wang B, Sun F, Liu X, Du Y, Li G, Gu L, Zheng T, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.003400-0	2009	*
Phylogeny	Lutimaribacter marinistellae sp. nov., isolated from a starfish.	Zhang Y, Tang P, Xu Y, Fang W, Wang X, Fang Z, Xiao Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001251	2016	*
Phylogeny	Isolation and characterization of a marine cyclohexylacetate-degrading bacterium Lutimaribacter litoralis sp. nov., and reclassification of Oceanicola pacificus as Lutimaribacter pacificus comb. nov.	Iwaki H, Yasukawa N, Fujioka M, Takada K, Hasegawa Y	Curr Microbiol	10.1007/s00284-013-0321-x	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 )

#21705

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29620

#28997

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 #25430 (see below)

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#89148

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID351949.1 )

#25430

IJSEM 1158 2009 ( DOI 10.1099/ijs.0.003400-0 , PubMed 19406811 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Lutimaribacter pacificus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Lutimaribacter pacificus strain DSM 29620

Change proposal

Change proposal