Strain identifier

BacDive ID: 140412

Type strain: Yes

Species: Oceanispirochaeta sediminicola

Strain Designation: SY2

Strain history: <- Sang-Seob Lee, Kyonggi Univ.

NCBI tax ID(s): 1969108 (species)

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General

@ref: 43019

BacDive-ID: 140412

DSM-Number: 104770

keywords: 16S sequence, Bacteria, obligate anaerobe, chemoorganoheterotroph, Gram-negative, motile, helical-shaped

description: Oceanispirochaeta sediminicola SY2 is an obligate anaerobe, chemoorganoheterotroph, Gram-negative bacterium that was isolated from coastal marine sediments.

NCBI tax id

  • NCBI tax id: 1969108
  • Matching level: species

strain history

@refhistory
43019<- S. Lee; Korean Environmental Microorganisms Bank, Kyonggi University, Suwon-Si, Gyeonggi-Do, South Korea; SY2 <- S. Yadav {2016}
67771<- Sang-Seob Lee, Kyonggi Univ.

doi: 10.13145/bacdive140412.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Spirochaetaceae
  • genus: Oceanispirochaeta
  • species: Oceanispirochaeta sediminicola
  • full scientific name: Oceanispirochaeta sediminicola Subhash and Lee 2017

@ref: 43019

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Spirochaetaceae

genus: Oceanispirochaeta

species: Oceanispirochaeta sediminicola

full scientific name: Oceanispirochaeta sediminicola Subhash and Lee 2017

strain designation: SY2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43495negative15-50 µm0.1-0.2 µmhelical-shapedyes
67771yes
67771negative

Culture and growth conditions

culture medium

  • @ref: 43019
  • name: SEDIMINISPIROCHAETA MEDIUM (DSMZ Medium 1008)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1008
  • composition: Name: SEDIMINISPIROCHAETA MEDIUM (DSMZ Medium 1008) Composition: Cellobiose 2.0 g/l Trypticase peptone 2.0 g/l Na-thioglycolate 1.0 g/l Yeast extract 1.0 g/l Sodium resazurin 0.0005 g/l Charcoal-filtered, natural seawater Distilled water

culture temp

@refgrowthtypetemperaturerange
43495positivegrowth10-40
43495positiveoptimum25-30mesophilic
43019positivegrowth28mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43495positivegrowth6.3-8.8alkaliphile
43495positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43495obligate anaerobe
67771anaerobe

nutrition type

  • @ref: 43495
  • type: chemoorganoheterotroph

halophily

@refsaltgrowthtested relationconcentration
43495NaClpositivegrowth1-7 %
43495NaClpositiveoptimum2-3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4349516150benzoate-growth
4349516899D-mannitol-growth
4349516236ethanol-growth
4349529806fumarate-growth
4349517754glycerol-growth
4349529991L-aspartate-growth
4349515361pyruvate-growth
4349516634raffinose-growth
4349517057cellobiose+growth
4349515824D-fructose+growth
4349512936D-galactose+growth
4349517634D-glucose+growth
4349516024D-mannose+growth
4349517924D-sorbitol+growth
4349529985L-glutamate+growth
4349562345L-rhamnose+growth
4349517716lactose+growth
4349517306maltose+growth
4349528017starch+growth
4349530031succinate+growth
4349517992sucrose+growth

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4349517334penicillinyesyes50 µg/mL
4349517698chloramphenicolyesyes50 µg/mL
434956104kanamycinyesyes50 µg/mL
4349528915fosfomycinyesyes50 µg/mL
4349528077rifampicinyesyes50 µg/mL

enzymes

@refvalueactivityec
43495catalase-1.11.1.6
43495cytochrome oxidase-1.9.3.1
43495caseinase-3.4.21.50

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43019coastal marine sedimentsTongyeong-SiRepublic of KoreaKORAsia34.8464128.466
43495coastal marine sedimentsTongyeong-SiRepublic of KoreaKORAsia
67771From coastal marine sedimentsTongyeong-SiRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_38111.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1926;96_18027;97_22239;98_27972;99_38111&stattab=map
  • Last taxonomy: Oceanispirochaeta sediminicola subclade
  • 16S sequence: LT821384
  • Sequence Identity:
  • Total samples: 877
  • soil counts: 17
  • aquatic counts: 795
  • animal counts: 52
  • plant counts: 13

Safety information

risk assessment

  • @ref: 43019
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 43019
  • description: Spirochaeta sp. SY2 partial 16S rRNA gene, strain SY2
  • accession: LT821384
  • length: 1491
  • database: ena
  • NCBI tax ID: 1969108

GC content

@refGC-contentmethod
4301953.5high performance liquid chromatography (HPLC)
6777153.5

External links

@ref: 43019

culture collection no.: DSM 104770, KCTC 15593, KEMB 3001-381

straininfo link

  • @ref: 96688
  • straininfo: 408173

literature

  • topic: Phylogeny
  • Pubmed-ID: 28875893
  • title: Description of Oceanispirochaeta sediminicola gen. nov., sp. nov., an obligately anaerobic bacterium isolated from coastal marine sediments, and reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov.
  • authors: Subhash Y, Lee SS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002130
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Spirochaetaceae/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
43019Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104770Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104770)
43495Y. Subhash, Sang-Seob LeeDescription of Oceanispirochaeta sediminicola gen. nov., sp. nov., an obligately anaerobic bacterium isolated from coastal marine sediments, and reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov.10.1099/ijsem.0.002130IJSEM 67: 3403-3409 201728875893
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/
96688Reimer, 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-ID408173.1