Strain identifier

BacDive ID: 140623

Type strain: Yes

Species: Sedimentitalea todarodis

Strain Designation: KHS03

Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; KHS03.

NCBI tax ID(s): 1631240 (species)

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General

@ref: 43147

BacDive-ID: 140623

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

description: Sedimentitalea todarodis KHS03 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from intestinal tract of a Japanese flying squid.

NCBI tax id

  • NCBI tax id: 1631240
  • Matching level: species

strain history

  • @ref: 67770
  • history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; KHS03.

doi: 10.13145/bacdive140623.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Sedimentitalea
  • species: Sedimentitalea todarodis
  • full scientific name: Sedimentitalea todarodis Kim et al. 2016

@ref: 43147

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Sedimentitalea

species: Sedimentitalea todarodis

strain designation: KHS03

type strain: yes

Morphology

cell morphology

  • @ref: 43147
  • gram stain: negative
  • cell length: 2.4-3.0 µm
  • cell width: 0.6-0.9 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43147
  • colony color: beige
  • colony shape: circular
  • incubation period: 2 days
  • medium used: MA

Culture and growth conditions

culture medium

  • @ref: 43147
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43147positivegrowth4-30
43147positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43147positiveoptimum7
43147positivegrowth6.0-10.2alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43147
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43147NaClpositiveoptimum1-2 %(w/v)
43147NaClpositivegrowth0.6-8.0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4314717632nitrate+reduction
4314717754glycerol+builds acid from
4314733942ribose+builds acid from
431474853esculin+builds acid from
4314762318D-lyxose+builds acid from
4314716443D-tagatose+builds acid from
4314718287L-fucose+builds acid from
43147581435-dehydro-D-gluconate+builds acid from
4314765327D-xylose+builds acid from
4314765328L-xylose+builds acid from
4314728757fructose+builds acid from
4314728847D-fucose+builds acid from
4314718333D-arabitol+builds acid from
4314775146monomethyl succinate+carbon source
4314730089acetate+carbon source
431478295beta-hydroxybutyrate+carbon source
43147309162-oxoglutarate+carbon source
4314724996lactate+carbon source
4314773786L-alanylglycine+carbon source
4314729985L-glutamate+carbon source
4314716523D-serine+carbon source
4314718287L-fucose+carbon source
4314727605D-psicose+carbon source
4314716947citrate+carbon source
4314728087glycogen+carbon source
4314751850methyl pyruvate+carbon source
43147645522-hydroxybutyrate+carbon source
43147167632-oxobutanoate+carbon source
4314717196L-asparagine+carbon source
4314773784glycyl-l-glutamate+carbon source
4314729991L-aspartate+carbon source
4314773804glycyl L-aspartic acid+carbon source
4314717295L-phenylalanine+carbon source
4314717203L-proline+carbon source
4314716857L-threonine+carbon source
4314715824D-fructose+carbon source
4314712936D-galactose+carbon source
4314717925alpha-D-glucose+carbon source
4314716024D-mannose+carbon source
43147143136succinamate+carbon source
4314721217L-alaninamide+carbon source
4314715570D-alanine+carbon source
4314716977L-alanine+carbon source
4314717748thymidine+carbon source
4314717754glycerol+carbon source
4314715729L-ornithine+carbon source
4314717115L-serine+carbon source
4314716865gamma-aminobutyric acid+carbon source
4314730849L-arabinose+carbon source
4314716301nitrite-reduction
4314717634D-glucose-fermentation
431475291gelatin-hydrolysis
4314717113erythritol-builds acid from
4314715963ribitol-builds acid from
4314774863methyl beta-D-xylopyranoside-builds acid from
4314727922sorbose-builds acid from
4314717268myo-inositol-builds acid from
4314730911sorbitol-builds acid from
4314743943methyl alpha-D-mannoside-builds acid from
43147320061methyl alpha-D-glucopyranoside-builds acid from
43147506227N-acetylglucosamine-builds acid from
4314727613amygdalin-builds acid from
4314718305arbutin-builds acid from
4314717814salicin-builds acid from
4314717306maltose-builds acid from
4314717716lactose-builds acid from
4314728053melibiose-builds acid from
4314717992sucrose-builds acid from
4314727082trehalose-builds acid from
4314715443inulin-builds acid from
431476731melezitose-builds acid from
4314716634raffinose-builds acid from
4314728017starch-builds acid from
4314728087glycogen-builds acid from
4314728066gentiobiose-builds acid from
4314732528turanose-builds acid from
4314718403L-arabitol-builds acid from
4314724265gluconate-builds acid from
43147309162-oxoglutarate-builds acid from
4314740585alpha-cyclodextrin-assimilation
4314723652dextrin-assimilation
4314728037N-acetylgalactosamine-assimilation
43147506227N-acetylglucosamine-assimilation
4314715963ribitol-assimilation
4314717113erythritol-assimilation
4314717268myo-inositol-assimilation
4314736219alpha-lactose-assimilation
4314716899D-mannitol-assimilation
4314728053melibiose-assimilation
43147320061methyl alpha-D-glucopyranoside-assimilation
4314716634raffinose-assimilation
4314762345L-rhamnose-assimilation
4314717924D-sorbitol-assimilation
4314717992sucrose-assimilation
4314732528turanose-assimilation
4314717151xylitol-assimilation
4314718024D-galacturonic acid-assimilation
431478391D-gluconate-assimilation
4314717784D-glucosaminic acid-assimilation
4314715748D-glucuronate-assimilation
4314717240itaconate-assimilation
43147286442-oxopentanoate-assimilation
4314715792malonate-assimilation
4314726490quinate-assimilation
4314733801D-saccharate-assimilation
4314741865sebacic acid-assimilation
4314732323glucuronamide-assimilation
43147hydroxy-L-proline-assimilation
4314715603L-leucine-assimilation
4314718183L-pyroglutamic acid-assimilation
4314717126DL-carnitine-assimilation
4314717148putrescine-assimilation
43147620642,3-butanediol-assimilation
4314729042glucose 1-phosphate-assimilation
4314714314D-glucose 6-phosphate-assimilation
4314716000ethanolamine-assimilation
431474853esculin-hydrolysis
4314717108D-arabinose-builds acid from
4314729864mannitol-builds acid from
4314737684mannose-builds acid from
4314726546rhamnose-builds acid from
4314717057cellobiose-builds acid from
4314717151xylitol-builds acid from
4314730849L-arabinose-builds acid from
4314728260galactose-builds acid from
4314717234glucose-builds acid from
4314753423tween 40-carbon source
43147167244-hydroxybutyrate-carbon source
4314716704uridine-carbon source
4314717272propionate-carbon source
4314773706bromosuccinate-carbon source
4314715971L-histidine-carbon source
4314727248urocanic acid-carbon source
4314753426tween 80-carbon source
4314730031succinate-carbon source
4314717596inosine-carbon source
4314718333D-arabitol-carbon source
431476359lactulose-carbon source
4314716383cis-aconitate-carbon source
4314715895D-galactonic acid lactone-carbon source
43147181014-hydroxyphenylacetic acid-carbon source
4314717057cellobiose-carbon source
4314717306maltose-carbon source
4314727082trehalose-carbon source
4314715740formate-carbon source

metabolite production

  • @ref: 43147
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43147catalase+1.11.1.6
43147cytochrome oxidase+1.9.3.1
43147alkaline phosphatase+3.1.3.1
43147esterase (C 4)+
43147esterase Lipase (C 8)+
43147leucine arylamidase+3.4.11.1
43147valine arylamidase+
43147cystine arylamidase+3.4.11.3
43147acid phosphatase+3.1.3.2
43147naphthol-AS-BI-phosphohydrolase+
43147lipase (C 14)-
43147trypsin-3.4.21.4
43147alpha-chymotrypsin-3.4.21.1
43147alpha-galactosidase-3.2.1.22
43147beta-galactosidase-3.2.1.23
43147beta-glucosidase-3.2.1.21
43147alpha-glucosidase-3.2.1.20
43147N-acetyl-beta-glucosaminidase-3.2.1.52
43147alpha-mannosidase-3.2.1.24
43147alpha-fucosidase-3.2.1.51
43147beta-glucuronidase-3.2.1.31
431476-phospho-beta-galactosidase-3.2.1.85
43147arginine dihydrolase-3.5.3.6
43147urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43147C16:02.7
    43147C17:00.5
    43147C18:00.8
    43147C18:1ω7c82.5
    4314711-methyl-C18:1ω7c2
    43147C10:0 3OH4.3
    43147C12:0 3OH2
    43147C16:0 2OH2.7
    43147C18:0 2OH0.3
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 6.2B
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
43147intestinal tract of a Japanese flying squidthe East Sea in KoreaKoreaKORAsia
67770Intestinal tract of a Japanese flying squid, Todarodes pacificusRepublic of KoreaKORAsiaTodarodes pacificus

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_23694.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_97;97_2136;98_17836;99_23694&stattab=map
  • Last taxonomy: Sedimentitalea todarodis subclade
  • 16S sequence: KP172215
  • Sequence Identity:
  • Total samples: 419
  • soil counts: 23
  • aquatic counts: 355
  • animal counts: 38
  • plant counts: 3

Sequence information

16S sequences

  • @ref: 43147
  • description: 16S rRNA gene sequences
  • accession: KP172215
  • length: 1393
  • database: ena
  • NCBI tax ID: 1631240

GC content

@refGC-contentmethod
4314759.9Thermal denaturation, fluorometry
6777059.9thermal denaturation, midpoint method (Tm)

External links

@ref: 43147

culture collection no.: KCTC 42412, JCM 31160

literature

  • topic: Phylogeny
  • Pubmed-ID: 27226032
  • title: Sedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid.
  • authors: Kim HS, Hyun DW, Lee JY, Kim PS, Whon TW, Kang W, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001188
  • year: 2016
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Decapodiformes/*microbiology, Fatty Acids/chemistry, Intestines/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, 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
43147Hyun Sik Kim, Dong-Wook Hyun, June-Young Lee, Pil Soo Kim, Tae Woong Whon, Woorim Kang and Jin-Woo BaeSedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid10.1099/ijsem.0.001188IJSEM 66: 3293-3298 201627226032
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/