Strain identifier

BacDive ID: 158707

Type strain: Yes

Species: Paracoccus alimentarius

Strain Designation: LB2

Strain history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

NCBI tax ID(s): 2049468 (species)

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General

@ref: 65449

BacDive-ID: 158707

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

description: Paracoccus alimentarius LB2 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from a Korean foodstuff, salted pollack.

NCBI tax id

  • NCBI tax id: 2049468
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

doi: 10.13145/bacdive158707.20230509.8.1

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 alimentarius
  • full scientific name: Paracoccus alimentarius Kim et al. 2018

@ref: 65449

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus alimentarius

strain designation: LB2

type strain: yes

Morphology

cell morphology

  • @ref: 65449
  • gram stain: negative
  • cell length: 0.4-1.0 µm
  • cell width: 0.4-0.6 µm
  • cell shape: coccus-shaped

colony morphology

  • @ref: 65449
  • colony size: 0.7-1.0 mm
  • colony color: greyish yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: marine agar

Culture and growth conditions

culture medium

@refnamegrowth
65449Marine agar (MA)yes
65449marine agar supplemented with nitrateyes

culture temp

@refgrowthtypetemperaturerange
65449positiveoptimum25-30mesophilic
65449positivegrowth10psychrophilic
65449positivegrowth37mesophilic
65449nogrowth4psychrophilic
65449nogrowth40thermophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
65449positiveoptimum7-8
65449positivegrowth5
65449nogrowth4.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65449aerobe
67771aerobe

spore formation

  • @ref: 65449
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65449NaClpositivegrowth0-4 %(w/v)
65449NaClpositiveoptimum0-2 %(w/v)

observation

@refobservation
65449Mg2+ ions are not required for growth
65449the predominant ubiquinone is Q-10
65449the major polar lipids are phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6544916150benzoate-carbon source
65449casein+hydrolysis
6544917057cellobiose-carbon source
6544915824D-fructose+carbon source
6544912936D-galactose-carbon source
6544917634D-glucose-carbon source
6544916024D-mannose-carbon source
6544965327D-xylose-carbon source
654494853esculin+hydrolysis
6544915740formate+carbon source
654495291gelatin-hydrolysis
6544917368hypoxanthine+hydrolysis
6544916411indole-3-acetic acid+carbon source
6544930849L-arabinose-carbon source
6544929985L-glutamate-carbon source
6544915589L-malate+carbon source
6544917895L-tyrosine+hydrolysis
6544917306maltose-carbon source
6544917632nitrate-reduction
6544917814salicin-carbon source
6544953258sodium citrate-carbon source
6544950144sodium pyruvate+carbon source
6544963675sodium succinate+carbon source
6544928017starch-hydrolysis
6544917992sucrose-carbon source
6544927082trehalose-carbon source
6544953426tween 80-hydrolysis
6544916199urea-hydrolysis
6544915318xanthine-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
6544928971ampicillinyesyes10 µg (disc)
654496472lincomycinyesyes15 µg (disc)
6544916869oleandomycinyesyes15 µg (disc)
6544918208penicillin gyesyes20 Unit (disc)
654496104kanamycinyesyes30 µg (disc)
6544917076streptomycinyesyes50 µg (disc)
654498309polymyxin byesyes100 Unit (disc)
6544928368novobiocinyesyes5 µg (disc)
654493542cephalothinyesyes30 µg (disc)
6544917833gentamicinyesyes30 µg (disc)
654497507neomycinyesyes30 µg (disc)
6544927902tetracyclineyesyes30 µg (disc)
654493393carbenicillinyesyes100 µg (disc)
6544917698chloramphenicolyesyes100 µg (disc)

metabolite production

  • @ref: 65449
  • Chebi-ID: 15138
  • metabolite: sulfide
  • production: no

enzymes

@refvalueactivityec
65449catalase+1.11.1.6
65449cytochrome oxidase+1.9.3.1
65449alkaline phosphatase+3.1.3.1
65449esterase (C 4)+
65449esterase Lipase (C 8)+
65449leucine arylamidase+3.4.11.1
65449acid phosphatase+3.1.3.2
65449naphthol-AS-BI-phosphohydrolase+
65449lipase (C 14)-
65449valine arylamidase-
65449cystine arylamidase-3.4.11.3
65449trypsin-3.4.21.4
65449alpha-chymotrypsin-3.4.21.1
65449alpha-galactosidase-3.2.1.22
65449beta-glucuronidase-3.2.1.31
65449alpha-glucosidase-3.2.1.20
65449beta-glucosidase-3.2.1.21
65449N-acetyl-beta-glucosaminidase-3.2.1.52
65449alpha-mannosidase-3.2.1.24
65449alpha-fucosidase-3.2.1.51

fatty acid profile

  • @reffatty acidpercentage
    65449C16:025.7
    65449C18:02.2
    65449C10:0 3OH2.6
    65449C18:1ω7c30.1
    65449C20:2ω6,9c0.6
    6544911-Methyl C18:1ω7c0.7
    65449CycloC19:0ω8c33.3
    6544910-Methyl C19:00.9
    65449C16:1 iso I and/or C14:0 iso 3OH2.7
  • type of FA analysis: whole cell analysis
  • incubation medium: marine
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C16:027.5
    65449C18:02
    65449C10:0 3OH2.7
    65449C18:1ω7c21.4
    65449C20:2ω6,9c0.7
    6544911-Methyl C18:1ω7c0.9
    65449CycloC19:0ω8c39.9
    6544910-Methyl C19:00.9
    65449C16:1 iso I and/or C14:0 iso 3OH2.7
  • type of FA analysis: whole cell analysis
  • incubation medium: marine
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C14:00.6
    65449C16:029.2
    65449C18:02
    65449C10:0 3OH2.8
    65449C18:1ω7c13.5
    65449C20:2ω6,9c0.9
    6544911-Methyl C18:1ω7c1.1
    65449CycloC19:0ω8c45.5
    6544910-Methyl C19:00.8
    65449C16:1 iso I and/or C14:0 iso 3OH2.7
  • type of FA analysis: whole cell analysis
  • incubation medium: marine
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 5
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C14:00.6
    65449C16:030
    65449C18:01.9
    65449C10:0 3OH2.9
    65449C18:1ω7c10
    65449C20:2ω6,9c1
    6544911-Methyl C18:1ω7c1.3
    65449CycloC19:0ω8c47.6
    6544910-Methyl C19:00.8
    65449C16:1 iso I and/or C14:0 iso 3OH2.9
  • type of FA analysis: whole cell analysis
  • incubation medium: marine
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 7
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C16:020.6
    65449C18:02.5
    65449C10:0 3OH2.7
    65449C18:1ω7c68.5
    65449CycloC19:0ω8c2.3
    65449iso-C16:1 Iand/or C14:0 3-OH2.5
  • type of FA analysis: whole cell analysis
  • incubation medium: trypticase soy
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C16:021
    65449C18:01.8
    65449C10:0 3OH2.9
    65449C18:1ω7c65.6
    65449Cyclo C19:0ω8c4
    65449C16:1 iso I and/or C14:0 iso 3OH4
    65449C16:1ω7c and/or C16:1ω6c0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: trypticase soy
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C16:022.5
    65449C18:02
    65449C10:0 3OH2.7
    65449C18:1ω7c63.8
    65449Cyclo C19:0ω8c5.1
    65449C16:1 iso I and/or C14:0 iso 3OH2.5
  • type of FA analysis: whole cell analysis
  • incubation medium: trypticase soy
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 5
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:
  • @reffatty acidpercentage
    65449C16:023.4
    65449C18:01.7
    65449C10:0 3OH2.6
    65449C18:1ω7c60.4
    65449Cyclo C19:0ω8c7.2
    65449C16:1 iso I and/or C14:0 iso 3OH2.6
  • type of FA analysis: whole cell analysis
  • incubation medium: trypticase soy
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 7
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture temperatureisolation procedure
65449a Korean foodstuff, salted pollackGangneungRepublic of KoreaKORAsia30Strain LB2 was isolated by the standard dilution plating technique at 25C on marine agar 2216 (MA; BD Difco) and cultivated routinely at 30 C on MA unless stated otherwise.
67771From Fermented Walleye PollackGangneungRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2
#Host#Fishes
#Engineered#Food production
#Condition#Saline

Sequence information

16S sequences

  • @ref: 65449
  • description: 16S rRNA gene sequence
  • accession: MG269198
  • database: nuccore

GC content

  • @ref: 65449
  • GC-content: 61.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65449

culture collection no.: KCTC 62138, NBRC 113023

literature

  • topic: Phylogeny
  • Pubmed-ID: 29469691
  • title: Paracoccus alimentarius sp. nov., isolated from a Korean foodstuff, salted pollack.
  • authors: Kim YO, Park IS, Park S, Nam BH, Kim DG, Won SM, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002658
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phosphatidylcholines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/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
65449Young-Ok Kim, In-Suk Park, Sooyeon Park, Bo-Hye Nam, Dong-Gyun Kim, Sung-Min Won, Jung-Hoon YoonParacoccus alimentarius sp. nov., isolated from a Korean foodstuff, salted pollack10.1099/ijsem.0.002658IJSEM 68: 1238-1243 201829469691
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc