Strain identifier

BacDive ID: 160592

Type strain: Yes

Species: Paracoccus tegillarcae

Strain Designation: BM15

Strain history: J.-W. Bae; Kyung Hee Univ., South Korea; BM15.

NCBI tax ID(s): 1529068 (species)

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General

@ref: 67500

BacDive-ID: 160592

DSM-Number: 107723

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

description: Paracoccus tegillarcae BM15 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Gut of blood cockle.

NCBI tax id

  • NCBI tax id: 1529068
  • Matching level: species

strain history

@refhistory
67500<- J. Y. Lee, Dept. Biology, Kyung Hee Univ., Seoul, Republic of Korea; BM15 <-
67770J.-W. Bae; Kyung Hee Univ., South Korea; BM15.

doi: 10.13145/bacdive160592.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus tegillarcae
  • full scientific name: Paracoccus tegillarcae Lee et al. 2019

@ref: 67500

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus tegillarcae

full scientific name: Paracoccus tegillarcae Lee et al. 2019

strain designation: BM15

type strain: yes

Morphology

cell morphology

  • @ref: 68004
  • gram stain: negative
  • cell length: 1.50-1.63 µm
  • cell width: 0.78-0.84 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 68004
  • colony color: pale yellow
  • colony shape: circular
  • medium used: Marine agar (MA)

Culture and growth conditions

culture medium

  • @ref: 67500
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
67500positivegrowth25mesophilic
67770positivegrowth20psychrophilic
68004positivegrowth10-30
68004positiveoptimum20psychrophilic

culture pH

@refabilitytypepHPH range
68004positivegrowth5.0-9.0alkaliphile
68004positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 68004
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
68004NaClpositivegrowth0.0-8.0 %(w/v)
68004NaClpositiveoptimum4 %(w/v)

observation

@refobservation
67770quinones: Q-10
68004The predominant respiratory quinone is ubiquinone 10 (Q-10)
68004The polar lipids are consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
680044853esculin+hydrolysis
68004casein+hydrolysis
6800453424tween 20+hydrolysis
6800417632nitrate+reduction
6800416024D-mannose+assimilation
6800417634D-glucose+assimilation
6800430849L-arabinose+assimilation
6800416899D-mannitol+assimilation
6800459640N-acetylglucosamine+assimilation
6800417306maltose+assimilation
6800432032potassium gluconate+assimilation
6800427689decanoate-assimilation
6800417128adipate+assimilation
6800425115malate+assimilation
6800453258sodium citrate-assimilation
6800418401phenylacetate+assimilation
6800428017starch-hydrolysis
6800416199urea-hydrolysis
6800453426tween 80-hydrolysis
6800453425tween 60-hydrolysis
6800453423tween 40-hydrolysis
68004esculin ferric citrate+builds acid from
6800465327D-xylose+builds acid from
6800416988D-ribose+builds acid from
68004potassium 5-dehydro-D-gluconate+builds acid from
6800430849L-arabinose+builds acid from
6800416443D-tagatose-builds acid from
6800417634D-glucose+builds acid from
6800417306maltose-builds acid from
68004potassium 2-dehydro-D-gluconate-builds acid from
6800427082trehalose-builds acid from
6800432528turanose+builds acid from
6800412936D-galactose+builds acid from
6800415824D-fructose+builds acid from
6800417992sucrose+builds acid from
6800417057cellobiose-builds acid from
6800428053melibiose-builds acid from
6800418305arbutin-builds acid from
6800416024D-mannose+builds acid from
6800417814salicin-builds acid from
6800417716lactose-builds acid from
6800416899D-mannitol+builds acid from
6800428087glycogen-builds acid from
6800428017starch-builds acid from
6800417108D-arabinose-builds acid from
680046731melezitose-builds acid from
6800418287L-fucose-builds acid from
6800462345L-rhamnose-builds acid from
6800428066gentiobiose-builds acid from
6800417924D-sorbitol-builds acid from
6800418333D-arabitol+builds acid from
6800462318D-lyxose+builds acid from
6800428847D-fucose+builds acid from
6800417754glycerol-builds acid from
6800459640N-acetylglucosamine-builds acid from
68004320061methyl alpha-D-glucopyranoside-builds acid from
6800417268myo-inositol-builds acid from
6800432032potassium gluconate-builds acid from
6800474863methyl beta-D-xylopyranoside-builds acid from
6800416634raffinose-builds acid from
6800427613amygdalin-builds acid from
6800443943methyl alpha-D-mannoside-builds acid from
6800417113erythritol-builds acid from
6800465328L-xylose-builds acid from
6800415963ribitol-builds acid from
6800417266L-sorbose-builds acid from
6800416813galactitol-builds acid from
6800415443inulin-builds acid from
6800417151xylitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6800435581indoleno
6800416136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6800417234glucose-
6800415688acetoin-

enzymes

@refvalueactivityec
68004catalase+1.11.1.6
68004cytochrome oxidase+1.9.3.1
68004alkaline phosphatase+3.1.3.1
68004esterase (C 4)+
68004esterase Lipase (C 8)+
68004leucine arylamidase+3.4.11.1
68004valine arylamidase+
68004acid phosphatase+3.1.3.2
68004naphthol-AS-BI-phosphohydrolase+
68004alpha-glucosidase+3.2.1.20
68004DNase-
68004lipase (C 14)-
68004cystine arylamidase-3.4.11.3
68004trypsin-3.4.21.4
68004alpha-chymotrypsin-3.4.21.1
68004alpha-galactosidase+3.2.1.22
68004beta-galactosidase-3.2.1.23
68004beta-glucuronidase-3.2.1.31
68004beta-glucosidase-3.2.1.21
68004N-acetyl-beta-glucosaminidase-3.2.1.52
68004alpha-mannosidase-3.2.1.24
68004alpha-fucosidase-3.2.1.51
68004arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68004C16:00.5
    68004C18:04.1
    68004C18:1 w9c0.7
    68004C10:0 3OH2.5
    68004C18:0 iso0.7
    68004C16:1 w7c / C16:1 w6c0.7
    68004C18:1 w7c / C18:1 w6c89
  • type of FA analysis: whole cell analysis
  • incubation medium: MA plates supplemented 2% (w/v) NaCl
  • agar/liquid: agar
  • incubation temperature: 20
  • incubation time: 2
  • software version: Sherlock 6.2
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost speciesgeographic location
67500Gut of blood cockleRepublic of KoreaKORAsia
67770Gastrointestinal tract of a blood cockle, Tegillarca granosaRepublic of KoreaKORAsiaTegillarca granosaforeshore of Beolgyo-eup
68004gastrointestinal tract of a blood cockle, Tegillarca granosa, collected from aforeshoreRepublic of KoreaKORAsiaBeolgyoeup

Sequence information

16S sequences

  • @ref: 67770
  • description: Paracoccus sp. BM15 16S ribosomal RNA gene, partial sequence
  • accession: KJ789958
  • length: 1387
  • database: ena
  • NCBI tax ID: 1529068

Genome sequences

  • @ref: 68004
  • description: Paracoccus tegillarcae BM15
  • accession: GCA_002847305
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1529068

GC content

  • @ref: 67770
  • GC-content: 62.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno87.716yes
gram-positiveno98.013yes
anaerobicno98.579yes
aerobicyes92.716no
halophileyes54.435no
spore-formingno96.486no
thermophileno93.918yes
glucose-utilyes88.012yes
motileno70.56no
glucose-fermentno89.522no

External links

@ref: 67500

culture collection no.: DSM 107723, KCTC 72032, JCM 33289

straininfo link

  • @ref: 112831
  • straininfo: 407014

literature

  • topic: Phylogeny
  • Pubmed-ID: 31251720
  • title: Paracoccus tegillarcae sp. nov., isolated from the gastrointestinal tract of a blood cockle (Tegillarca granosa).
  • authors: Lee JY, Hyun DW, Yun JH, Jung MJ, Shin NR, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003561
  • year: 2019
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cardiidae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
67500Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107723Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107723)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68004June-Young Lee, Dong-Wook Hyun, Ji-Hyun Yun, Mi-Ja Jung, Na-Ri Shin, Jin-Woo BaeParacoccus tegillarcae sp. nov., isolated from the gastrointestinal tract of a blood cockle (Tegillarca granosa)10.1099/ijsem.0.003561IJSEM 69: 2815-2822 2019
112831Reimer, 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-ID407014.1