Strain identifier

BacDive ID: 14282

Type strain: Yes

Species: Parasphingorhabdus litoris

Strain Designation: FR1093

Strain history: <- J Chun, Seoul Nat. Univ.

NCBI tax ID(s): 394733 (species)

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General

@ref: 16314

BacDive-ID: 14282

DSM-Number: 22379

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

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

NCBI tax id

  • NCBI tax id: 394733
  • Matching level: species

strain history

@refhistory
16314<- KCTC <- J. Chun, Seoul Natl. Univ., Republic of Korea
67770J. Chun FR1093.
67771<- J Chun, Seoul Nat. Univ.

doi: 10.13145/bacdive14282.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • 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

    @refsynonym
    20215Sphingopyxis litoris
    20215Sphingorhabdus litoris

@ref: 16314

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingorhabdus

species: Sphingorhabdus litoris

full scientific name: Sphingorhabdus litoris (Kim et al. 2008) Jogler et al. 2013

strain designation: FR1093

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32518negativerod-shapedyes
67771negative
125438negative97.469
125439negative99.1

pigmentation

  • @ref: 32518
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16314
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: 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

@refgrowthtypetemperature
16314positivegrowth30
32518positivegrowth15-34.4
32518positiveoptimum23.7-31.8
67770positivegrowth30
67771positivegrowth30

culture pH

@refabilitytypepH
32518positivegrowth7
32518positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32518aerobe
67771aerobe
125439obligate aerobe97.7

spore formation

@refspore formationconfidence
32518no
125439no96

halophily

@refsaltgrowthtested relationconcentration
32518NaClpositivegrowth02-07 %
32518NaClpositiveoptimum3.5 %

observation

  • @ref: 32518
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3251816947citrate+carbon source
3251825115malate+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32518alkaline phosphatase+3.1.3.1
32518catalase+1.11.1.6
32518cytochrome oxidase+1.9.3.1
32518urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16314------++------------+
16314-------+------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16314surface seawaterJeju IslandRepublic of KoreaKORAsia
67770Surface seawater collected off Jeju IslandRepublic of KoreaKORAsia
67771From seawaterJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_32883.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1750;97_2092;98_2569;99_32883&stattab=map
  • Last taxonomy: Parasphingorhabdus
  • 16S sequence: DQ781321
  • Sequence Identity:
  • Total samples: 440
  • soil counts: 48
  • aquatic counts: 208
  • animal counts: 23
  • plant counts: 161

Safety information

risk assessment

  • @ref: 16314
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16314
  • description: Sphingopyxis litoris strain FR1093 16S ribosomal RNA gene, partial sequence
  • accession: DQ781321
  • length: 1409
  • database: nuccore
  • NCBI tax ID: 394733

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parasphingorhabdus litoris DSM 223792574179751draftimg1123271
66792Parasphingorhabdus litoris DSM 22379GCA_020906275completencbi1123271
66792Parasphingorhabdus litoris DSM 223791123271.4completepatric1123271

GC content

  • @ref: 16314
  • GC-content: 52.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.1
125439BacteriaNetmotilityAbility to perform movementyes63.9
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.469yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.284no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.933yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.424yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.248no
125438motile2+flagellatedAbility to perform flagellated movementyes54.399no

External links

@ref: 16314

culture collection no.: DSM 22379, IMSNU 14133, JCM 14162, KCTC 12764

straininfo link

  • @ref: 83437
  • straininfo: 359533

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny33993373Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.Kim SJ, Kim M, Lee KE, Cha IT, Park SJArch Microbiol10.1007/s00203-021-02366-82021Adenoma, Islet Cell, Fatty Acids/analysis, *Geologic Sediments/microbiology, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Species Specificity, *Sphingomonadaceae/classification/genetics
Phylogeny35929988Parasphingorhabdus 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 JWInt J Syst Evol Microbiol10.1099/ijsem.0.0054702022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Gastropoda, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16314Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22379)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22379
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32518Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2873828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83437Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359533.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1