Strain identifier

BacDive ID: 134231

Type strain: Yes

Species: Persicitalea jodogahamensis

Strain Designation: Shu-9-SY12-35C

Strain history: IAM 15412 <-- J. Yoon et al. Shu-9-SY12-35C.

NCBI tax ID(s): 402147 (species)

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General

@ref: 32004

BacDive-ID: 134231

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

description: Persicitalea jodogahamensis Shu-9-SY12-35C is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 402147
  • Matching level: species

strain history

  • @ref: 67770
  • history: IAM 15412 <-- J. Yoon et al. Shu-9-SY12-35C.

doi: 10.13145/bacdive134231.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Persicitalea
  • species: Persicitalea jodogahamensis
  • full scientific name: Persicitalea jodogahamensis Yoon et al. 2007

@ref: 32004

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Persicitalea

species: Persicitalea jodogahamensis

strain designation: Shu-9-SY12-35C

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32004negative4.5 µm0.4 µmrod-shapedno
125439negative99.8
125438negative98.354

pigmentation

  • @ref: 32004
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
32004positiveoptimum27.5
67770positivegrowth30

culture pH

@refabilitytypepHPH range
32004positivegrowth05-10alkaliphile
32004positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32004aerobe
125438aerobe90.809

spore formation

@refspore formationconfidence
32004no
125439no99.1

halophily

@refsaltgrowthtested relationconcentration
32004NaClpositivegrowth0-7 %
32004NaClpositiveoptimum3.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3200422599arabinose+carbon source
3200417057cellobiose+carbon source
3200428757fructose+carbon source
3200433984fucose+carbon source
3200428260galactose+carbon source
3200417234glucose+carbon source
3200417716lactose+carbon source
3200417306maltose+carbon source
3200437684mannose+carbon source
3200428053melibiose+carbon source
32004506227N-acetylglucosamine+carbon source
3200416634raffinose+carbon source
3200426546rhamnose+carbon source
3200417814salicin+carbon source
3200417992sucrose+carbon source
3200427082trehalose+carbon source
3200418222xylose+carbon source

enzymes

@refvalueactivityec
32004catalase+1.11.1.6
32004cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
32004seawater
67770Seawater in JodogahamaIwateJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_92263.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1930;96_38033;97_48395;98_63505;99_92263&stattab=map
  • Last taxonomy: Persicitalea jodogahamensis subclade
  • 16S sequence: AB272165
  • Sequence Identity:
  • Total samples: 1769
  • soil counts: 354
  • aquatic counts: 1245
  • animal counts: 153
  • plant counts: 17

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32004Persicitalea jodogahamensis gene for 16S rRNA, partial sequenceAB2721651464nuccore402147
124043Persicitalea jodogahamensis gene for 16S rRNA, partial sequence, strain: NBRC 103568.AB6821321437nuccore402147

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Persicitalea jodogahamensis KCTC 12866GCA_014651615scaffoldncbi402147
66792Persicitalea jodogahamensis strain KCTC 12866402147.3wgspatric402147

GC content

@refGC-contentmethod
3200456.3
6777056.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.354yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.248no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.809no
125438spore-formingspore-formingAbility to form endo- or exosporesno83.94yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.851yes
125438motile2+flagellatedAbility to perform flagellated movementno89.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.1
125439BacteriaNetmotilityAbility to perform movementno66.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe82.3

External links

@ref: 32004

culture collection no.: MBIC 07417, IAM 15412, KCTC 12866, JCM 23195, CIP 109672, NBRC 103568

straininfo link

  • @ref: 91825
  • straininfo: 308624

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473250
  • title: Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family 'Flexibacteraceae', isolated from seawater in Japan.
  • authors: Yoon J, Ishikawa S, Kasai H, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64792-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Japan, Microscopy, Phase-Contrast, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/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
32004Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172825828776041
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/
91825Reimer, 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-ID308624.1
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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