Name: Leucothrix pacifica XH122
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158186

Type strain:

Species: Leucothrix pacifica

Strain Designation: XH122

Culture col. no.: DSM 25984, JCM 18388

Strain history: X.-H. Zhang XH122.

NCBI tax ID(s): 1247513 (species)

SI-ID 405777

DSM 25984

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Leucothrix pacifica XH122 is a mesophilic, Gram-negative bacterium that was isolated from surface seawater.

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Beggiatoales*
	Family	*Leucotrichaceae*
	Genus	*Leucothrix*
	Species	**Leucothrix pacifica**
	Full Scientific Name (LPSN)	Leucothrix pacifica Zhang et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %96
[Ref.: #125439]	Gram stain	negative Confidence in %95.1

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %96.3

[Ref.: #125438]	Ability of spore formation	no Confidence in %90.287
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.2

[Ref.: #67770]

Observation

quinones: Q-8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #64782]	Sample type/isolated from	surface seawater
[Ref.: #64782]	Geographic location (country and/or sea, region)	South Pacific Gyre
[Ref.: #64782]	Country	Southwest Pacific Ocean
[Ref.: #64782]	Geographic location	-45.9667°/-163.1830°

[Ref.: #67770]	Sample type/isolated from	Surface seawater from the South Pacific Gyre (163° 11' S 45° 58' E)
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ082190 (>99% sequence identity) for Leucothrix pacifica from Microbeatlas

Aquatic Samples	660
Soil Samples	4
Animal Samples	123
Plant Samples	5
Total Samples	792

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

[Ref.: #64782]

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.: #64782]	Leucothrix pacifica strain XH122 16S ribosomal RNA gene, partial sequence	JX501256	1445	GenBank ENA	1247513 tax ID
[Ref.: #67770]	Leucothrix sp. U1371-101227-XH122 16S ribosomal RNA gene, partial sequence	JQ082190	1447	GenBank ENA	1171542 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Leucothrix pacifica JCM 18388	GCA_003172875	scaffold	GenBank ENA	1247513 tax ID
[Ref.: #66792]	Leucothrix pacifica strain JCM 18388	1247513.4	wgs	PATRIC	1247513 tax ID	*
[Ref.: #66792]	Leucothrix pacifica JCM 18388	2889727904	draft	JGI IMG/M	1247513 tax ID	*

[Ref.: #64782]

GC-content

46.2 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Leucothrix pacifica strain JCM 18388 PATRIC: 1247513.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.349	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.287	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	72.151	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.235	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	64.159	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leucothrix pacifica JCM 18388 NCBI: GCA_003172875
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	51.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	95.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.3

Availability in culture collections External links

[Ref.: #64782]

Culture collection no.

DSM 25984, JCM 18388

[Ref.: #111017]

SI-ID 405777

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Leucothrix sargassi sp. nov., isolated from a marine alga [Sargassum natans (L.) Gaillon].	Liu T, Zhang Y, Zhang X, Zhou L, Meng C, Zhou C, Jing C, Zhu W, Wang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.003694	2019	*
Phylogeny	Leucothrix arctica sp. nov., isolated from Arctic seawater.	Baek K, Choi A, Lee YM, Lee HK, Cho JC	Int J Syst Evol Microbiol	10.1099/ijsem.0.003072	2018	*
Phylogeny	Leucothrix pacifica sp. nov., isolated from seawater, and emended description of the genus Leucothrix.	Zhang Z, Gao X, Wang L, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijs.0.000270	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 )

#64782

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25984

#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;

#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 .

#111017

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-ID405777.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Leucothrix pacifica strain JCM 18388

Leucothrix pacifica JCM 18388

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