Strain identifier

BacDive ID: 133541

Type strain: Yes

Species: Algoriphagus lutimaris

Strain Designation: S1-3

Strain history: <- Jung-Hoon Yoon, KRIBB

NCBI tax ID(s): 613197 (species)

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General

@ref: 29415

BacDive-ID: 133541

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

description: Algoriphagus lutimaris S1-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 613197
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Hoon Yoon, KRIBB

doi: 10.13145/bacdive133541.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Algoriphagus
  • species: Algoriphagus lutimaris
  • full scientific name: Algoriphagus lutimaris Park et al. 2010

@ref: 29415

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus lutimaris

strain designation: S1-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29415negative2.7 µm0.55 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.99

pigmentation

  • @ref: 29415
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29415positivegrowth04-40
29415positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
29415positivegrowth05-08
29415positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29415aerobe
67771aerobe

spore formation

@refspore formationconfidence
29415no
69480no99.986

halophily

@refsaltgrowthtested relationconcentration
29415NaClpositivegrowth0-8 %
29415NaClpositiveoptimum2 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2941528260galactose+carbon source
2941527082trehalose+carbon source

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    61387C15:01.415
    61387C16:00.816
    61387C11:0 ANTEISO1.710.693
    61387C11:0 iso0.510.605
    61387C14:0 ISO0.513.618
    61387C15:0 ANTEISO4.114.711
    61387C15:0 ISO27.414.621
    61387C15:0 ISO 3OH1.416.135
    61387C15:1 ω6c0.714.856
    61387C16:0 iso5.215.626
    61387C16:0 iso 3OH1.317.145
    61387C16:1 ISO H2.315.461
    61387C16:1 ω5c4.815.908
    61387C16:1 ω7c12.815.819
    61387C16:1 ω7c/C15:0 ISO 2OH9.915.85
    61387C17:0 iso0.616.629
    61387C17:0 iso 3OH6.618.161
    61387C17:1 ISO I/C16:0 DMA2.516.481
    61387C17:1 ω6c2.616.862
    61387C17:1 ω8c0.616.792
    61387C17:1 ω9c ISO11.316.416
    61387unknown 14.9660.814.966
    61387unknown 16.5800.616.58
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
29415marine sediment
61387Tidal flat sediment2007-01-01SaemankumRepublic of KoreaKORAsia
67771From sediment of a tidal flatSaemankum on the west coastRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8271.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2463;97_3006;98_6024;99_8271&stattab=map
  • Last taxonomy: Algoriphagus
  • 16S sequence: FJ669216
  • Sequence Identity:
  • Total samples: 420
  • soil counts: 82
  • aquatic counts: 282
  • animal counts: 32
  • plant counts: 24

Sequence information

16S sequences

  • @ref: 29415
  • description: Algoriphagus lutimaris strain S1-3 16S ribosomal RNA gene, partial sequence
  • accession: FJ669216
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 613197

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus lutimaris KCTC 22630GCA_017051705scaffoldncbi613197
66792Algoriphagus lutimaris strain KCTC 22630613197.3wgspatric613197

GC content

@refGC-contentmethod
2941541.4
6777141.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno69no
flagellatedno96.274yes
gram-positiveno98.357no
anaerobicno98.486yes
aerobicyes89.841yes
halophileno70.716no
spore-formingno95.631no
thermophileno97.712yes
glucose-utilyes92.671no
motileno92.067no
glucose-fermentno89.388no

External links

@ref: 29415

culture collection no.: KCTC 22630, CCUG 57608

straininfo link

  • @ref: 91494
  • straininfo: 411629

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648320Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment.Park S, Kang SJ, Oh KH, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.012682-02009Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny21515706Algoriphagus namhaensis sp. nov., isolated from seawater.Oh KH, Kang SJ, Lee SY, Park S, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.030791-02011Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Phylogeny22368173Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate.Alegado RA, Grabenstatter JD, Zuzow R, Morris A, Huang SY, Summons RE, King NInt J Syst Evol Microbiol10.1099/ijs.0.038646-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Choanoflagellata, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, VirginiaGenetics
Phylogeny22544791Algoriphagus chungangensis sp. nov., isolated from a tidal flat sediment.Kang H, Weerawongwiwat V, Jung MY, Myung SC, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.039214-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
29415Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172582228776041
61387Curators of the CCUGhttps://www.ccug.se/strain?id=57608Culture Collection University of Gothenburg (CCUG) (CCUG 57608)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/
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
91494Reimer, 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-ID411629.1