Strain identifier

BacDive ID: 166285

Type strain: Yes

Species: Pleomorphovibrio marinus

Strain Designation: SW125

NCBI tax ID(s): 2164132 (species)

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General

@ref: 68029

BacDive-ID: 166285

DSM-Number: 107180

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Pleomorphovibrio marinus SW125 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from deep-sea sediment .

NCBI tax id

  • NCBI tax id: 2164132
  • Matching level: species

doi: 10.13145/bacdive166285.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Pleomorphovibrio
  • species: Pleomorphovibrio marinus
  • full scientific name: Pleomorphovibrio marinus Song et al. 2019

@ref: 68029

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Pleomorphovibrio

species: Pleomorphovibrio marinus

strain designation: SW125

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68029negative3.0-4.0 µm0.5-0.7 µmrod-shapedno
69480negative94.25

colony morphology

  • @ref: 68029
  • colony color: light brown
  • colony shape: circular
  • medium used: Marine agar (MA)

Culture and growth conditions

culture temp

@refgrowthtypetemperature
68029positivegrowth4-42
68029positiveoptimum30

culture pH

@refabilitytypepHPH range
68029positivegrowth5.0-9.0alkaliphile
68029positiveoptimum7.0-7.6

Physiology and metabolism

oxygen tolerance

  • @ref: 68029
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
68029NaClpositivegrowth0.5-10.0 %(w/v)
68029NaClpositiveoptimum2.0-3.0 %(w/v)

observation

@refobservation
68029slightly curved to comma-shaped rods
68029The major quinone system is MK-7
68029The major polar lipid is phosphatidylethanolamine
68029Cells occur singly or in pairs
68029The polar lipid profile is composed of phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, three unidentified glycolipids,two unidentified polar lipids and two unidentified phospholipids

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6802917632nitrate-reduction
680294853esculin+hydrolysis
6802928017starch+hydrolysis
68029casein-hydrolysis
680295291gelatin-hydrolysis
6802916199urea-hydrolysis
6802953423tween 40-hydrolysis
6802953425tween 60-hydrolysis
6802953426tween 80-hydrolysis
68029167632-oxobutanoate-carbon source
6802913705acetoacetate-carbon source
6802932323glucuronamide+carbon source
6802953423tween 40-carbon source
6802917306maltose+carbon source
6802916551D-trehalose+carbon source
6802917057cellobiose+carbon source
6802928066gentiobiose+carbon source
6802917992sucrose+carbon source
6802932528turanose+carbon source
6802917164stachyose-carbon source
6802916634raffinose-carbon source
6802936219alpha-lactose+carbon source
6802928053melibiose+carbon source
68029320055methyl beta-D-glucopyranoside-carbon source
6802917814salicin+carbon source
6802959640N-acetylglucosamine-carbon source
6802963153N-acetyl-D-mannosamine-carbon source
6802928800N-acetylgalactosamine-carbon source
6802935418n-acetylneuraminate-carbon source
6802917925alpha-D-glucose+carbon source
6802916024D-mannose+carbon source
6802915824D-fructose-carbon source
6802912936D-galactose+carbon source
68029739183-O-methyl-D-glucose+carbon source
6802928847D-fucose-carbon source
6802918287L-fucose-carbon source
6802962345L-rhamnose-carbon source
6802917596inosine-carbon source
6802917924D-sorbitol-carbon source
6802916899D-mannitol-carbon source
6802918333D-arabitol-carbon source
6802917268myo-inositol-carbon source
6802917754glycerol-carbon source
6802914314D-glucose 6-phosphate-carbon source
6802978697D-fructose 6-phosphate-carbon source
6802929990D-aspartate-carbon source
6802916523D-serine-carbon source
680295291gelatin-carbon source
6802970744glycine-proline-carbon source
6802916977L-alanine-carbon source
6802916467L-arginine-carbon source
6802929991L-aspartate-carbon source
6802929988L-glutamate-carbon source
6802915971L-histidine-carbon source
6802957606L-pyroglutamate-carbon source
6802917115L-serine-carbon source
6802917309pectin+carbon source
6802918024D-galacturonic acid-carbon source
6802917464L-galactonic acid gamma-lactone-carbon source
680298391D-gluconate-carbon source
6802915748D-glucuronate+carbon source
6802916537galactarate-carbon source
6802926490quinate-carbon source
6802930612D-glucarate-carbon source
68029181014-hydroxyphenylacetic acid-carbon source
6802951850methyl pyruvate-carbon source
6802974611methyl (R)-lactate+carbon source
6802916651(S)-lactate-carbon source
6802916947citrate-carbon source
68029168102-oxoglutarate-carbon source
6802930796(R)-malic acid-carbon source
6802930797(S)-malic acid-carbon source
6802973706bromosuccinate-carbon source
6802916865gamma-aminobutyric acid-carbon source
68029645522-hydroxybutyrate-carbon source
68029370543-hydroxybutyrate-carbon source
6802917272propionate-carbon source
6802916411acetic acid-carbon source
6802915740formate-carbon source

metabolite production

@refChebi-IDmetaboliteproduction
6802935581indoleno
6802916136hydrogen sulfideno

metabolite tests

  • @ref: 68029
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
68029cytochrome oxidase+1.9.3.1
68029catalase+1.11.1.6
68029arginine dihydrolase+3.5.3.6
68029urease-3.5.1.5
68029lysine decarboxylase-4.1.1.18
68029ornithine decarboxylase-4.1.1.17
68029alkaline phosphatase+3.1.3.1
68029esterase (C 4)+
68029esterase Lipase (C 8)+
68029leucine arylamidase+3.4.11.1
68029valine arylamidase+
68029cystine arylamidase+3.4.11.3
68029trypsin+3.4.21.4
68029acid phosphatase+3.1.3.2
68029naphthol-AS-BI-phosphohydrolase+
68029beta-galactosidase+3.2.1.23
68029alpha-glucosidase-3.2.1.20
68029beta-glucosidase-3.2.1.21
68029N-acetyl-beta-glucosaminidase-3.2.1.52
68029alpha-mannosidase-3.2.1.24

Isolation, sampling and environmental information

isolation

  • @ref: 68029
  • sample type: deep-sea sediment (depth of 3690 m)
  • geographic location: Northwest Indian Ocean
  • latitude: 37.9475
  • longitude: 127.819

Sequence information

16S sequences

  • @ref: 68029
  • description: Pleomorphovibrio marinus strain SW125 16S ribosomal RNA gene, partial sequence
  • accession: MH197303
  • length: 1479
  • database: nuccore
  • NCBI tax ID: 1979949

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Negadavirga sp. SW1252164132.3wgspatric2164132
66792Pleomorphovibrio marinus SW1252831830614draftimg2164132
68029Pleomorphovibrio marinus SW125GCA_003347495contigncbi2164132

GC content

  • @ref: 68029
  • GC-content: 43.2
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno94.25yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.573yes
69480spore-formingspore-formingAbility to form endo- or exosporesno83.018no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.702yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.676yes
69480flagellatedmotile2+Ability to perform flagellated movementno84.5no

External links

@ref: 68029

culture collection no.: CGMCC 1.16172, DSM 107180, KCTC 62636

straininfo link

  • @ref: 114767
  • straininfo: 400436

literature

  • topic: Phylogeny
  • Pubmed-ID: 31693474
  • title: Pleomorphovibrio marinus gen. nov., sp. nov., isolated from deep-sea sediment.
  • authors: Song L, Liu H, Huang Y, Dai X, Zhou Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003633
  • year: 2019
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68029Lei Song, Hongcan Liu, Ying Huang, Xin Dai, Yuguang ZhouPleomorphovibrio marinus gen. nov., sp. nov., isolated from deep-sea sediment10.1099/ijsem.0.003633IJSEM 69: 3723-3727 2019
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
114767Reimer, 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 identifiers10.60712/SI-ID400436.1