Cite this strain

Parasphingorhabdus litoris (DSM 22379, IMSNU 14133, JCM 14162)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14282

Type strain

Strain Designation FR1093

Culture col. no. DSM 22379 IMSNU 14133 JCM 14162 KCTC 12764 FR1093

NCBI tax ID(s) 394733

Special Collections DSMZ JCM KCTC Literature strains

Links

Name and taxonomic classification

Parasphingorhabdus litoris FR1093 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface seawater.

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

SI-ID 359533

JCM 14162, KCTC 12764, DSM 22379

Last LPSN update 2024-12-09 10:44:41

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Parasphingorhabdus

Species Parasphingorhabdus litoris

Full scientific name Parasphingorhabdus litoris (Kim et al. 2008) Feng et al. 2020

Synonyms (2)

Sphingopyxis litoris
Sphingorhabdus litoris

Morphology

Cell morphology

@ref	Gram stain	Cell shape
32518	negative	rod-shaped
67771	negative
125438	negative
125439	negative

Pigmentation

32518

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16314	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)	Range
16314	positive	growth	30	mesophilic
32518	positive	growth	15-34.4
32518	positive	optimum	23.7-31.8
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
32518	positive	optimum	7
32518	positive	growth	7

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32518	NaCl	positive	growth	02-07 %
32518	NaCl	positive	optimum	3.5 %

Observation

32518

Observationaggregates in chains

Spore formation

@ref	Spore formation
32518
125439

Enzymes

@ref	Value	Activity	Ec
32518	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
32518	catalase	+	1.11.1.6
32518	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
32518	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	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

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
32518	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
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
32518	25115 ChEBI	malate	+	carbon source
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

Oxygen tolerance

@ref	Oxygen tolerance
32518	aerobe
67771	aerobe
125439	obligate aerobe

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
16314	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+
16314	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16314	surface seawater	Jeju Island	Republic of Korea	KOR	Asia
67770	Surface seawater collected off Jeju Island		Republic of Korea	KOR	Asia
67771	From seawater	Jeju	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ781321 (>99% sequence identity) for Parasphingorhabdus from Microbeatlas

Aquatic Samples	208
Soil Samples	48
Animal Samples	23
Plant Samples	161
Total Samples	440

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
16314	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
16314	52.6	high performance liquid chromatography (HPLC)

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16314	Sphingopyxis litoris strain FR1093 16S ribosomal RNA gene, partial sequence	DQ781321	1409		394733

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Parasphingorhabdus litoris DSM 22379	2574179751	draft	JGI IMG/M	1123271
66792	Parasphingorhabdus litoris DSM 22379	GCA_020906275	complete		1123271
66792	Parasphingorhabdus litoris DSM 22379	1123271.4	complete	PATRIC	1123271

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Parasphingorhabdus litoris DSM 22379
PATRIC: 1123271.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	motility	BacteriaNetⓘ	yes	63.90	no
125439	spore_formation	BacteriaNetⓘ	no	96.00	no

Predictions from Diaspora project based on:
Parasphingorhabdus litoris DSM 22379 DSM 22379
NCBI: GCA_020906275.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.47	yes
125438	anaerobic	anaerobicⓘ	no	93.28	no
125438	aerobic	aerobicⓘ	yes	87.93	yes
125438	spore-forming	spore-formingⓘ	no	88.42	yes
125438	thermophilic	thermophileⓘ	no	98.25	no
125438	flagellated	motile2+ⓘ	yes	54.40	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.	Kim SJ, Kim M, Lee KE, Cha IT, Park SJ	Arch Microbiol	10.1007/s00203-021-02366-8	2021
Phylogeny	Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma.	Yoo JH, Han JE, Lee JY, Jeong SW, Jeong YS, Lee JY, Lee SY, Sung H, Tak EJ, Kim HS, Kim PS, Choi JW, Kim DY, Jeong IC, Gim DH, Kang SM, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.005470	2022

Straininfo Link

@ref	Straininfo	Culture collections
83437	359533	JCM 14162, KCTC 12764, DSM 22379

Culture collection no.

Culture collection no.
DSM 22379
IMSNU 14133
JCM 14162
KCTC 12764
FR1093

References

#16314	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22379
#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 )
#32518	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 #28738 (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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#83437	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-ID359533.1 )
#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 .

Rate our new design

Content

About us