Strain identifier

BacDive ID: 14650

Type strain: Yes

Species: Staphylococcus succinus

Strain Designation: AMG-D1

Strain history: CIP <- 2001, DSMZ <- ATCC <- R.J. Cano, strain: AMG-D1

NCBI tax ID(s): 61015 (species)

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General

@ref: 5411

BacDive-ID: 14650

DSM-Number: 14617

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

description: Staphylococcus succinus AMG-D1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from plant and soil inclusions within 25-35 million-year-old Dominican amber.

NCBI tax id

  • NCBI tax id: 61015
  • Matching level: species

strain history

@refhistory
5411<- ATCC <- R.J. Cano; AMG-D1
123368CIP <- 2001, DSMZ <- ATCC <- R.J. Cano, strain: AMG-D1

doi: 10.13145/bacdive14650.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Staphylococcus
  • species: Staphylococcus succinus
  • full scientific name: Staphylococcus succinus Lambert et al. 1998

@ref: 5411

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus succinus

full scientific name: Staphylococcus succinus Lambert et al. 1998

strain designation: AMG-D1

type strain: yes

Morphology

cell morphology

  • @ref: 123368
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 123368

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5411COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
5411TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
35496MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123368CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5411positivegrowth30mesophilic
5411positivegrowth25mesophilic
35496positivegrowth37mesophilic
123368positivegrowth30-41
123368nogrowth10psychrophilic
123368nogrowth22psychrophilic
123368nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123368
  • oxygen tolerance: obligate aerobe

murein

  • @ref: 5411
  • murein short key: A11.02
  • type: A3alpha L-Lys-Gly5-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose-builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123368hippurate+hydrolysis606565
123368nitrate-reduction17632
123368nitrite-reduction16301
68375urea+hydrolysis16199
68375arginine-hydrolysis29016
68375ornithine-degradation18257
68375esculin+hydrolysis4853
68375D-glucose+fermentation17634
68375D-fructose+fermentation15824
68375D-mannose+fermentation16024
68375maltose+fermentation17306
68375lactose+fermentation17716
68375trehalose+fermentation27082
68375D-mannitol+fermentation16899
68375D-ribose-fermentation16988
68375sucrose+fermentation17992
68375N-acetylglucosamine+fermentation59640
68375turanose-fermentation32528

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12336835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837515688acetoin-
12336815688acetoin-

enzymes

@refvalueactivityec
68375beta-glucuronidase+3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase+3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase+3.2.1.23
68375beta-glucosidase+3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease+3.5.1.5
123368oxidase-
123368beta-galactosidase+3.2.1.23
123368alcohol dehydrogenase-1.1.1.1
123368gelatinase-
123368amylase-
123368DNase-
123368caseinase-3.4.21.50
123368catalase+1.11.1.6
123368coagulase-
123368tween esterase-
123368gamma-glutamyltransferase-2.3.2.2
123368lecithinase-
123368lipase-
123368lysine decarboxylase-4.1.1.18
123368ornithine decarboxylase-4.1.1.17
123368phenylalanine ammonia-lyase-4.3.1.24
123368urease+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
123368-++--+----+---+-+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123368---++/-+---+/-++-----++--+-++++-+-++------+----------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
5411+--+++++++++-++-+-+-+++--+
5411+--++++++++-----+-+-+++-++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123368++-+---+---++---+++-++---------+-+--+----------------++-+--++-+--+---------+----------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5411plant and soil inclusions within 25-35 million-year-old Dominican amberDominican RepublicDOMMiddle and South America
55943Plant and soil inclusions within amber
123368Plant, And soil inclusions within old amberDominican RepublicDOMNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_63.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_63&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AF004220
  • Sequence Identity:
  • Total samples: 26921
  • soil counts: 930
  • aquatic counts: 1554
  • animal counts: 23674
  • plant counts: 763

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
54111Risk group (German classification)
1233681Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus succinus subsp. succinus strain DSM 14617 16S ribosomal RNA gene, partial sequenceAY688103464ena224030
5411Staphylococcus succinus 16S ribosomal RNA gene, complete sequenceAF0042201548ena224030

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus succinus subsp. succinus DSM 14617GCA_001006765contigncbi224030
66792Staphylococcus succinus subsp. succinus DSM 14617GCA_002902045scaffoldncbi224030
66792Staphylococcus succinus subsp. succinus strain DSM 14617224030.5wgspatric224030
66792Staphylococcus succinus subsp. succinus strain DSM 14617224030.8wgspatric224030
66792Staphylococcus succinus succinus DSM 146172917463979draftimg224030
66792Staphylococcus succinus succinus DSM 146172639763042draftimg224030

GC content

  • @ref: 5411
  • GC-content: 35
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno87.03no
gram-positiveyes89.562no
anaerobicno99.456no
halophileyes95.904no
spore-formingno91.345no
glucose-utilyes89.979no
aerobicyes93.943no
thermophileno99.853yes
motileno88.226no
glucose-fermentyes82.623yes

External links

@ref: 5411

culture collection no.: DSM 14617, ATCC 700337, CIP 107307, CCUG 43571, CCM 7157

straininfo link

  • @ref: 83777
  • straininfo: 43883

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731292Staphylococcus succinus sp. nov., isolated from Dominican amber.Lambert LH, Cox T, Mitchell K, Rossello-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJInt J Syst Bacteriol10.1099/00207713-48-2-5111998*Amber, Anti-Bacterial Agents/pharmacology, Base Composition, Base Sequence, Cell Wall, DNA, Bacterial/analysis, Dominica, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Staphylococcus/*classification/drug effects/isolation & purification/ultrastructureGenetics
Phylogeny12421073Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese.Place RB, Hiestand D, Burri S, Teuber MSyst Appl Microbiol10.1078/0723-2020-001302002Bacterial Typing Techniques, Cell Wall/chemistry, Chaperonin 60/*genetics, Cheese/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, Staphylococcus/*classification/*genetics/isolation & purification/metabolismBiotechnology
Phylogeny14657137Staphylococcus nepalensis sp. nov., isolated from goats of the Himalayan region.Spergser J, Wieser M, Taubel M, Rossello-Mora RA, Rosengarten R, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.02646-02003Altitude, Animals, DNA Fingerprinting, Geography, Goats/*microbiology, India, Microbial Sensitivity Tests, Molecular Sequence Data, *Phylogeny, Polymerase Chain Reaction, Staphylococcus/*classification/genetics/isolation & purification/physiologyGenetics
Genetics28126945Draft Genome Sequence of Staphylococcus succinus subsp. succinus Type Strain DSM 14617, Isolated from Plant and Soil Inclusions within 25- to 35-Million-Year-Old Dominican Amber.Zhou H, Yao Z, Shi H, Wang B, Li D, Hou J, Ma SGenome Announc10.1128/genomeA.01521-162017Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5411Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14617)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14617
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35496Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4729
55943Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43571)https://www.ccug.se/strain?id=43571
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)
68371Automatically annotated from API 50CH acid
68375Automatically annotated from API ID32STA
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
83777Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43883.1StrainInfo: A central database for resolving microbial strain identifiers
123368Curators of the CIPCollection of Institut Pasteur (CIP 107307)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107307