Strain identifier

BacDive ID: 133848

Type strain: Yes

Species: Profundibacterium mesophilum

Strain Designation: KAUST100406-0324

Strain history: P. Y. Lai KAUST100406-0324.

NCBI tax ID(s): 1258573 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 9.3 (current version)

General

@ref: 30668

BacDive-ID: 133848

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

description: Profundibacterium mesophilum KAUST100406-0324 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1258573
  • Matching level: species

strain history

  • @ref: 67770
  • history: P. Y. Lai KAUST100406-0324.

doi: 10.13145/bacdive133848.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Profundibacterium
  • species: Profundibacterium mesophilum
  • full scientific name: Profundibacterium mesophilum corrig. Lai 2012

  • synonyms

    @refsynonym
    20215Profundibacterium mesophila
    20215Profundibacterium mesophilum

@ref: 30668

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Profundibacterium

species: Profundibacterium mesophilum

strain designation: KAUST100406-0324

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
30668negative0.2 µm0.2 µmcoccus-shapedyesgliding
125439negative97.5
125438negative97.5

pigmentation

  • @ref: 30668
  • production: no

Culture and growth conditions

culture temp

@refgrowthtypetemperature
30668positivegrowth15-25
30668positiveoptimum22.5
67770positivegrowth25

culture pH

@refabilitytypepHPH range
30668positivegrowth6-8.5alkaliphile
30668positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30668aerobe
125439aerobe90.6

spore formation

@refspore formationconfidence
30668no
125439no94.7

halophily

  • @ref: 30668
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 4 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3066829016arginine+carbon source
3066816947citrate+carbon source
3066828260galactose+carbon source
3066817234glucose+carbon source
3066829987glutamate+carbon source
3066817754glycerol+carbon source
3066817272propionate+carbon source
3066815361pyruvate+carbon source
3066830031succinate+carbon source
3066818222xylose+carbon source

enzymes

@refvalueactivityec
30668acid phosphatase+3.1.3.2
30668alkaline phosphatase+3.1.3.1
30668catalase+1.11.1.6
30668cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
30668marine sediment
67770Sea-floor sediment collected from the Red SeaSaudi ArabiaSAUAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_115395.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_45790;97_58757;98_78019;99_115395&stattab=map
  • Last taxonomy: Profundibacterium mesophilum subclade
  • 16S sequence: JF776971
  • Sequence Identity:
  • Total samples: 351
  • soil counts: 56
  • aquatic counts: 284
  • animal counts: 10
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 30668
  • description: Profundibacterium mesophilum KAUST100406-0324 16S ribosomal RNA gene, partial sequence
  • accession: JF776971
  • length: 1436
  • database: nuccore
  • NCBI tax ID: 1037889

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Profundibacterium mesophilum KAUST100406-0324GCA_009835145contigncbi1037889
66792Profundibacterium mesophilum KAUST100406-03241037889.3wgspatric1037889

GC content

@refGC-contentmethod
3066864
6777064high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.508yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.837no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.64yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.358yes
125438motile2+flagellatedAbility to perform flagellated movementyes54.237no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.7
125439BacteriaNetmotilityAbility to perform movementyes53.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe90.6

External links

@ref: 30668

culture collection no.: JCM 17872, NRRL B-59665

literature

  • topic: Phylogeny
  • Pubmed-ID: 22685108
  • title: Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia.
  • authors: Lai PY, Miao L, Lee OO, Liu LL, Zhou XJ, Xu Y, Al-Suwailem A, Qian PY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.041525-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Saudi Arabia, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
30668Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172699928776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG