Strain identifier

BacDive ID: 158812

Type strain: Yes

Species: Pseudomonas profundi

Strain Designation: M5

NCBI tax ID(s): 1981513 (species)

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General

@ref: 65576

BacDive-ID: 158812

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

description: Pseudomonas profundi M5 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from deep-sea water sample.

NCBI tax id

  • NCBI tax id: 1981513
  • Matching level: species

doi: 10.13145/bacdive158812.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas profundi
  • full scientific name: Pseudomonas profundi Sun et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Neopseudomonas profundi

@ref: 65576

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas profundi

strain designation: M5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65576negative1.8-2 µm0.6-0.7 µmrod-shapedyespolar
69480yes97.612
69480negative99.993

colony morphology

  • @ref: 65576
  • colony size: 0.5-1 mm
  • colony color: creamy
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowth
65576Marine agar (MA)yes
65576MByes

culture temp

@refgrowthtypetemperaturerange
65576positivegrowth4-40
65576positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
65576positivegrowth7-10alkaliphile
65576positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 65576
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69480no99.992
69481no100

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65576NaClpositivegrowth0-10 %
65576NaClpositiveoptimum1-2 %slightly halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6557616651(S)-lactate+carbon source
6557615589L-malate+carbon source
6557630089acetate+carbon source
6557617128adipate-assimilation
655768295beta-hydroxybutyrate+carbon source
6557673706bromosuccinate+carbon source
6557627689decanoate-assimilation
6557617634D-glucose-assimilation
6557616899D-mannitol-assimilation
6557616024D-mannose-assimilation
655764853esculin-hydrolysis
655765291gelatin-hydrolysis
6557624265gluconate-assimilation
6557617234glucose-fermentation
6557630849L-arabinose-assimilation
6557629985L-glutamate+carbon source
6557625115malate-assimilation
6557617306maltose-assimilation
65576506227N-acetylglucosamine-assimilation
6557617632nitrate+reduction
6557618401phenylacetate-assimilation
6557617272propionate+carbon source
6557653258sodium citrate-assimilation
6557628017starch-hydrolysis
6557653424tween 20+hydrolysis
6557653423tween 40+carbon source
6557653425tween 60+hydrolysis
6557653426tween 80+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
655763745clindamycinyesyes2 µg (disc)
655767731ofloxacinyesyes5 µg (disc)
65576100241ciprofloxacinyesyes5 µg (disc)
6557663598levofloxacinyesyes5 µg (disc)
6557628971ampicillinyesyes10 µg (disc)
6557628864tobramycinyesyes10 µg (disc)
6557617833gentamicinyesyes10 µg (disc)
6557617076streptomycinyesyes10 µg (disc)
6557618208penicillin gyesyes10 µg (disc)
65576100246norfloxacinyesyes10 µg (disc)
6557648923erythromycinyesyes15 µg (disc)
655763732clarithromycinyesyes15 µg (disc)
655762637amikacinyesyes30 µg (disc)
65576161680aztreonamyesyes30 µg (disc)
65576474053cefazolinyesyes30 µg (disc)
65576124991cefalotinyesyes30 µg (disc)
655763515cefuroximeyesyes30 µg (disc)
65576204928cefotaximeyesyes30 µg (disc)
6557629007ceftriaxoneyesyes30 µg (disc)
65576478164cefepimeyesyes30 µg (disc)
655763508ceftazidimeyesyes30 µg (disc)
65576209807cefoxitinyesyes30 µg (disc)
655766104kanamycinyesyes30 µg (disc)
655768309polymyxin byesyes30 µg (disc)
6557628001vancomycinyesyes30 µg (disc)
6557617698chloramphenicolyesyes30 µg (disc)
6557627902tetracyclineyesyes30 µg (disc)
6557650694minocyclineyesyes30 µg (disc)
655763493cefoperazoneyesyes75 µg (disc)
655768232piperacillinyesyes100 µg (disc)
655769215spectinomycinyesyes100 µg (disc)
6557671415nitrofurantoinyesyes300 µg (disc)
655767809oxacillinyesyes1 µg (disc)
655763745clindamycinyesyes2 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6557616136hydrogen sulfideyes
6557635581indoleno

enzymes

@refvalueactivityec
65576cytochrome oxidase+1.9.3.1
65576catalase+1.11.1.6
65576alkaline phosphatase+3.1.3.1
65576esterase (C 4)+
65576esterase Lipase (C 8)+
65576leucine arylamidase+3.4.11.1
65576naphthol-AS-BI-phosphohydrolase+
65576lipase (C 14)-
65576valine arylamidase-
65576cystine arylamidase-3.4.11.3
65576trypsin-3.4.21.4
65576alpha-chymotrypsin-3.4.21.1
65576acid phosphatase-3.1.3.2
65576alpha-galactosidase-3.2.1.22
65576beta-galactosidase-3.2.1.23
65576beta-glucuronidase-3.2.1.31
65576alpha-glucosidase-3.2.1.20
65576beta-glucosidase-3.2.1.21
65576N-acetyl-beta-glucosaminidase-3.2.1.52
65576alpha-mannosidase-3.2.1.24
65576alpha-fucosidase-3.2.1.51
65576arginine dihydrolase-3.5.3.6
65576urease-3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 65576
  • sample type: deep-sea water sample
  • sampling date: 2016-09
  • geographic location: Mariana Trench
  • country: Pacific Ocean
  • latitude: 11.3859
  • longitude: 142.484
  • enrichment culture: MA
  • enrichment culture duration: 14 days
  • enrichment culture temperature: 4
  • isolation procedure: standard dilution-plating method, purification repeated three times

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Sequence information

16S sequences

  • @ref: 65576
  • description: 16S rRNA gene sequence
  • accession: KY988340
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Pseudomonas profundi M5
  • accession: GCA_008638305
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1981513

GC content

  • @ref: 65576
  • GC-content: 62.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.557no
flagellatedyes88.743yes
gram-positiveno98.552no
anaerobicno97.501yes
aerobicyes88.031no
halophileyes52.118no
spore-formingno94.856no
thermophileno99.583yes
glucose-utilno52.303no
glucose-fermentno91.044no

External links

@ref: 65576

culture collection no.: CCTCC AB 2017186, KCTC 62119, CICC 24308

literature

  • topic: Phylogeny
  • Pubmed-ID: 29620498
  • title: Pseudomonas profundi sp. nov., isolated from deep-sea water.
  • authors: Sun J, Wang W, Ying Y, Zhu X, Liu J, Hao J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002748
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65576Jingjing Sun, Wei Wang, Yu Ying, Xiangjie Zhu, Junzhong Liu and Jianhua HaoPseudomonas profundi sp. nov., isolated from deep-sea water10.1099/ijsem.0.002748IJSEM 68: 1776-1780 201829620498
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
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1