Strain identifier

BacDive ID: 13720

Type strain: Yes

Species: Paracoccus seriniphilus

Strain Designation: LS-1, MBT-A4

Strain history: CIP <- 2002, DSMZ <- R. Pukall: strain MBT-A4 <- M. Laroche

NCBI tax ID(s): 184748 (species)

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General

@ref: 5564

BacDive-ID: 13720

DSM-Number: 14827

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Paracoccus seriniphilus LS-1 is a mesophilic, Gram-negative bacterium that was isolated from Bugula plumosa .

NCBI tax id

  • NCBI tax id: 184748
  • Matching level: species

strain history

@refhistory
5564<- R. Pukall; MBT-A4 <- M. Laroche
122570CIP <- 2002, DSMZ <- R. Pukall: strain MBT-A4 <- M. Laroche

doi: 10.13145/bacdive13720.20230509.8.1

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 seriniphilus
  • full scientific name: Paracoccus seriniphilus Pukall et al. 2003

@ref: 5564

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus seriniphilus

full scientific name: Paracoccus seriniphilus Pukall et al. 2003

strain designation: LS-1, MBT-A4

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
122570negativecoccus-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5564BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
40708Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122570CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5564positivegrowth28mesophilic
40708positivegrowth30mesophilic
122570positivegrowth25-41
122570nogrowth5psychrophilic
122570nogrowth10psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
122570NaClpositivegrowth4-6 %
122570NaClnogrowth0 %
122570NaClnogrowth2 %
122570NaClnogrowth8 %
122570NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1225704853esculin-hydrolysis
12257017632nitrate+reduction
12257016301nitrite-reduction

metabolite production

  • @ref: 122570
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122570
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
122570oxidase+
122570beta-galactosidase+3.2.1.23
122570alcohol dehydrogenase-1.1.1.1
122570gelatinase-
122570amylase-
122570DNase-
122570caseinase-3.4.21.50
122570catalase+1.11.1.6
122570tween esterase+
122570lecithinase-
122570lipase-
122570lysine decarboxylase-4.1.1.18
122570ornithine decarboxylase-4.1.1.17
122570protease-
122570tryptophan deaminase-
122570urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122570-+---++-+-+-+--+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122570+-+-+-+-------+---+-------+-+-+-++---+--+---------+---+-----+-+--+-----+--++----------+-+++--++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
5564Bugula plumosa (Bryozoa)Bugula plumosa;BryozoaHelgolandGermanyDEUEurope
122570Bugula plumosaGermanyDEUEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Moss

taxonmaps

  • @ref: 69479
  • File name: preview.99_12636.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_610;98_3341;99_12636&stattab=map
  • Last taxonomy: Paracoccus seriniphilus
  • 16S sequence: AJ428275
  • Sequence Identity:
  • Total samples: 87
  • soil counts: 7
  • aquatic counts: 52
  • animal counts: 27
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55641Risk group (German classification)
1225701Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5564
  • description: Paracoccus seriniphilus partial 16S rRNA gene, strain MBT-A4
  • accession: AJ428275
  • length: 1416
  • database: ena
  • NCBI tax ID: 184748

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus seriniphilus DSM 14827GCA_900199195contigncbi184748
66792Paracoccus seriniphilus strain DSM 14827184748.24wgspatric184748
66792Paracoccus seriniphilus DSM 14827 (v2)2737471638draftimg184748
66792Paracoccus seriniphilus DSM 14827GCA_028553745completencbi184748

GC content

  • @ref: 5564
  • GC-content: 63.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno66.902no
flagellatedno84.12no
gram-positiveno98.491no
anaerobicno97.366no
aerobicyes85.682no
halophileno58.961no
spore-formingno96.43no
glucose-fermentno83.628no
thermophileno95.972yes
glucose-utilyes87.481no

External links

@ref: 5564

culture collection no.: DSM 14827, CIP 107400, NBRC 100798

straininfo link

  • @ref: 82904
  • straininfo: 100847

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710610Paracoccus seriniphilus sp. nov., an L-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa.Pukall R, Laroche M, Kroppenstedt RM, Schumann P, Stackebrandt E, Ulber RInt J Syst Evol Microbiol10.1099/ijs.0.02352-02003Animals, Base Sequence, Bryozoa/*microbiology, L-Serine Dehydratase/*biosynthesis, Marine Biology, Molecular Sequence Data, Paracoccus/*classification/enzymology/genetics/ultrastructure, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Serine/*metabolismGenetics
Phylogeny19329608Paracoccus aestuarii sp. nov., isolated from tidal flat sediment.Roh SW, Nam YD, Chang HW, Kim KH, Kim MS, Shin KS, Yoon JH, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65759-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny23546859Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract.Liu Y, Xie QY, Hong K, Li L, Zhao YM, Tang YL, An JY, Zhu PP, Xu CHAntonie Van Leeuwenhoek10.1007/s10482-013-9894-42013Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fishes/*microbiology, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28741997Paracoccus hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus).Lin P, Yan ZF, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0019902017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny30737708Paracoccus indicus sp. nov., isolated from surface seawater in the Indian Ocean.Lin D, Zhu S, Chen Y, Huang Y, Yang J, Chen JAntonie Van Leeuwenhoek10.1007/s10482-019-01226-22019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Indian Ocean, Paracoccus/classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny35939379Paracoccus salsus sp. nov., a novel slightly halophilic bacterium isolated from saline lake sediment.Gao L, Fang BZ, Liu YH, Huang Y, Wang S, Jiang HC, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0054732022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lakes, *Paracoccus, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5564Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14827)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14827
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
40708Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4831
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82904Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100847.1StrainInfo: A central database for resolving microbial strain identifiers
122570Curators of the CIPCollection of Institut Pasteur (CIP 107400)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107400