Strain identifier

BacDive ID: 6284

Type strain: Yes

Species: Serinicoccus profundi

Strain Designation: 0714S6-1

Strain history: CGMCC 4.5582 <-- J. Xu 0714S6-1 (=MCCC 1A05965).

NCBI tax ID(s): 1043205 (strain), 1078471 (species)

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General

@ref: 15653

BacDive-ID: 6284

DSM-Number: 21363

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped

description: Serinicoccus profundi 0714S6-1 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from deep-sea sediment.

NCBI tax id

NCBI tax idMatching level
1043205strain
1078471species

strain history

@refhistory
15653<- J. Xu <- Y.-X. Luo, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen; 0714S6-1
67770CGMCC 4.5582 <-- J. Xu 0714S6-1 (=MCCC 1A05965).

doi: 10.13145/bacdive6284.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Ornithinimicrobiaceae
  • genus: Serinicoccus
  • species: Serinicoccus profundi
  • full scientific name: Serinicoccus profundi Xiao et al. 2011

@ref: 15653

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Ornithinimicrobiaceae

genus: Serinicoccus

species: Serinicoccus profundi

full scientific name: Serinicoccus profundi Xiao et al. 2011

strain designation: 0714S6-1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29748positivecoccus-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21354Corn yellow (1006)10-14 daysISP 2
21354Signal yellow (1003)10-14 daysISP 3
21354Signal yellow (1003)10-14 daysISP 4
21354Signal yellow (1003)10-14 daysISP 5
21354Brown beige (1011)10-14 daysISP 7
21354Ochre yellow (1024)10-14 dayssuter with tyrosine
21354Lemon yellow (1012)10-14 dayssuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21354noISP 2
21354noISP 3
21354noISP 4
21354noISP 5
21354noISP 7
21354noSuter with tyrosine
21354noSuter without tyrosine

pigmentation

  • @ref: 29748
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcomposition
21354ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21354ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21354ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21354ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21354ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21354suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21354suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
29748positivegrowth10-35
29748positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29748positivegrowth06-11alkaliphile
29748positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29748
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29748no
69481no92
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
21354NaClpositivemaximum10 %
29748NaClpositivegrowth0-14 %
29748NaClpositiveoptimum4 %

observation

@refobservation
29748aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2135417234glucose+
2135422599arabinose-
2135417992sucrose-
2135418222xylose+
2135417268myo-inositol-
2135437684mannose+/-
2135428757fructose+
2135426546rhamnose-
2135416634raffinose+
2135462968cellulose-
29748620642,3-butanediol+carbon source
2974821217L-alaninamide+carbon source
29748286442-oxopentanoate+carbon source
2974822599arabinose+carbon source
2974823652dextrin+carbon source
2974828757fructose+carbon source
2974824265gluconate+carbon source
2974817234glucose+carbon source
2974817754glycerol+carbon source
2974828087glycogen+carbon source
2974817596inosine+carbon source
2974824996lactate+carbon source
2974825115malate+carbon source
2974817306maltose+carbon source
2974837684mannose+carbon source
2974815361pyruvate+carbon source
2974851850methyl pyruvate+carbon source
2974816634raffinose+carbon source
2974833942ribose+carbon source
2974830911sorbitol+carbon source
2974830031succinate+carbon source
2974817992sucrose+carbon source
2974817748thymidine+carbon source
2974827082trehalose+carbon source
2974853423tween 40+carbon source
2974853426tween 80+carbon source
2974816704uridine+carbon source
297484853esculin+hydrolysis
2974817632nitrate+reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29748alkaline phosphatase+3.1.3.1
29748catalase+1.11.1.6
29748gelatinase+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21354-+/-++--++-++------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21354+++-+++++++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrycontinentlatitudelongitude
15653deep-sea sedimentIndian OceanIndian OceanAsia-55.249.03
67770Deep-sea (5,368 m) sediment of the Indian Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 15653
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15653
  • description: Serinicoccus profundi MCCC 1A05965 16S ribosomal RNA gene, partial sequence
  • accession: EU603762
  • length: 1490
  • database: ena
  • NCBI tax ID: 1043205

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serinicoccus profundi CGMCC 4.5582GCA_008001015completencbi1078471
66792Serinicoccus profundi strain CGMCC 4.55821078471.4completepatric1078471
66792Serinicoccus profundi CGMCC 4.55822884004160completeimg1078471
67770Serinicoccus profundi MCCC 1A05965GCA_000224715contigncbi1043205

GC content

@refGC-contentmethod
1565372high performance liquid chromatography (HPLC)
2974872

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno93.885yes
flagellatedno98.717no
gram-positiveyes91.056no
anaerobicno99.133no
aerobicyes92.282yes
halophileno75.543no
spore-formingno93.147no
glucose-utilyes90.465yes
thermophileno96.019yes
glucose-fermentno88.69yes

External links

@ref: 15653

culture collection no.: DSM 21363, CGMCC 4.5582, NBRC 110789, MCCC 1A05965, JCM 17740

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20118285Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus.Xiao J, Luo Y, Xie S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.019976-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny20639223Serinicoccus chungangensis sp. nov., isolated from tidal flat sediment, and emended description of the genus Serinicoccus.Traiwan J, Park MH, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.025635-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Genetics22038971Genome sequence of Serinicoccus profundi, a novel actinomycete isolated from deep-sea sediment.Xiao J, Luo Y, Xu JJ Bacteriol10.1128/JB.06119-112011Actinomycetales/*genetics/isolation & purification, Base Sequence, *Genome, Bacterial, Geologic Sediments/*microbiology, Molecular Sequence Data, Seawater/*microbiologyEnzymology
Phylogeny31050624Serinicoccus sediminis sp. nov., isolated from tidal flat sediment.Lee DW, Yoo Y, Lee H, Kwon BO, Khim JS, Yim UH, Kim BS, Kim GH, Kim JJInt J Syst Evol Microbiol10.1099/ijsem.0.0034152019Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32375934Serinicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island.Zhang Q, Ye J, Yu L, Lin D, Tang KInt J Syst Evol Microbiol10.1099/ijsem.0.0041452020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Hydrothermal Vents/*microbiology, Islands, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33174834Ornithinimicrobium pratense sp. nov., isolated from meadow soil.Guo Q, Wang B, Zhou Z, Ke X, Zhang L, Chen M, Lin M, Wang W, Zhang W, Li XInt J Syst Evol Microbiol10.1099/ijsem.0.0045572020Actinobacteria/*classification/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Ornithine/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny36035744Serinicoccus kebangsaanensis sp. nov: A new bacterium isolated from the toxic diatom, Nitzschia navis-varingica.Yusof A, Sahrani FK, Ahmad A, Usup G, Bunawan HNew Microbes New Infect10.1016/j.nmni.2022.1010052022

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15653Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21363)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21363
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
21354Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21363.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29748Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2613028776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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