Strain identifier

BacDive ID: 5133

Type strain: Yes

Species: Serratia fonticola

Strain Designation: 2.78, 2-78, CUEMT 77-165

Strain history: CIP <- 1978, C. Richard, Inst. Pasteur, Paris, France: strain 2-78 <- H. Leclerc, Inst. Pasteur, Lille, France: strain CUEMT 77-165

NCBI tax ID(s): 1378072 (strain), 47917 (species)

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General

@ref: 1777

BacDive-ID: 5133

DSM-Number: 4576

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Serratia fonticola 2.78 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from water.

NCBI tax id

NCBI tax idMatching level
47917species
1378072strain

strain history

@refhistory
1777<- CIP <- C. Richard; 2.78 <- H. Leclerc; CUETM 77.165
67770Y. Kosako 321 <-- R. Sakazaki 321 <-- ATCC 29844 <-- H. Leclerc.
119420CIP <- 1978, C. Richard, Inst. Pasteur, Paris, France: strain 2-78 <- H. Leclerc, Inst. Pasteur, Lille, France: strain CUEMT 77-165

doi: 10.13145/bacdive5133.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Serratia
  • species: Serratia fonticola
  • full scientific name: Serratia fonticola Gavini et al. 1979 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Serratia glossinae

@ref: 1777

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Serratia

species: Serratia fonticola

full scientific name: Serratia fonticola Gavini et al. 1979 emend. Kämpfer and Glaeser 2015

strain designation: 2.78, 2-78, CUEMT 77-165

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.93
6948099.962negative
119420yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1777NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37710MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
1777TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
119420CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1777positivegrowth28mesophilic
1777positivegrowth30mesophilic
37710positivegrowth30mesophilic
67770positivegrowth37mesophilic
119420positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 119420
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.043

compound production

  • @ref: 1777
  • compound: FSH binding inhibitor (FSH=follicle stimulating hormone)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-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
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
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol+builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol+fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine+degradation18257
68368lysine+degradation25094
68368arginine-hydrolysis29016
119420mannitol+fermentation29864
119420citrate+carbon source16947
119420glucose+fermentation17234
119420lactose-fermentation17716
119420nitrate+reduction17632
119420nitrite+reduction16301
119420malonate+assimilation15792
119420sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 119420
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11942035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11942015688acetoin-
11942017234glucose+

enzymes

@refvalueactivityec
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
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
119420oxidase-
119420beta-galactosidase+3.2.1.23
119420alcohol dehydrogenase-1.1.1.1
119420gelatinase-
119420catalase+1.11.1.6
119420lysine decarboxylase+4.1.1.18
119420ornithine decarboxylase+4.1.1.17
119420phenylalanine ammonia-lyase-4.3.1.24
119420tryptophan deaminase-
119420urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119420-+++-++-+-++++++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1777+-+++------+++++-+++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119420++/--+++-+-++++-+++++-++-+++-+++++--+---++/--+--++++/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119420+++++-+--++++++-++++++++--++++++++++++--+++++-+--++-+++++--+++------+---+--+---++-+---+--+--+++----

Isolation, sampling and environmental information

isolation

@refsample type
1777water
67770Spring water
119420Environment, Spring water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17771Risk group (German classification)
1194201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Serratia fonticola strain CCM 3407 clone d1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; 23S ribosomal RNA gene, partial sequence; and tRNA-Glu gene, complete sequenceGQ332601463ena47917
20218Serratia fonticola strain CCM 3407 clone d3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; 23S ribosomal RNA gene, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceGQ332602602ena47917
20218Serratia fonticola strain CCM 3407 clone d4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; 23S ribosomal RNA gene, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceGQ332603556ena47917
20218Serratia fonticola strain CCM 3407 clone d5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; 23S ribosomal RNA gene, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceGQ332604602ena47917
20218Serratia fonticola 16S rRNA gene (strain DSM 4576)AJ2334291490ena47917
20218Serratia fonticola LMG 7882 16S ribosomal RNA gene, partial sequenceAF2868691457ena47917
20218Serratia fonticola gene for 16S rRNA, partial sequence, strain: NBRC 102597AB6818741466ena47917
1777Serratia fonticola LMG 7882 serratia7882_scaffold293, whole genome shotgun sequenceAVAH010002931773ena1378072

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serratia fonticola DSM 4576GCA_001006005completencbi47917
66792Serratia fonticola LMG 78821378072.3wgspatric1378072
66792Serratia fonticola strain DSM 457647917.8completepatric47917
66792Serratia fonticola strain NCTC1296547917.36wgspatric47917
66792Serratia fonticola LMG 78822602041585draftimg1378072
66792Serratia fonticola DSM 45762636415821completeimg47917
67770Serratia fonticola LMG 7882GCA_000469035contigncbi1378072
67770Serratia fonticola NCTC12965GCA_901482655contigncbi47917

GC content

  • @ref: 67770
  • GC-content: 51.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.1no
flagellatedno53.723no
gram-positiveno98.339no
anaerobicno97.396no
aerobicyes92.302no
halophileno94.452no
spore-formingno94.744no
thermophileno98.993yes
glucose-utilyes95.067no
glucose-fermentyes92.674yes

External links

@ref: 1777

culture collection no.: DSM 4576, ATCC 29844, CIP 78.64, CUETM 77.165, JCM 1242, BCRC 14810, CCM 3407, CCUG 14186, CCUG 37824, CUETM 77-165, IAM 13541, LMG 7882, NBRC 102597, NCTC 12965, IAM 1242

straininfo link

  • @ref: 74625
  • straininfo: 389408

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19667382Serratia glossinae sp. nov., isolated from the midgut of the tsetse fly Glossina palpalis gambiensis.Geiger A, Fardeau ML, Falsen E, Ollivier B, Cuny GInt J Syst Evol Microbiol10.1099/ijs.0.013441-02009Animals, Bacteria, Anaerobic/isolation & purification, Base Composition/genetics, Burkina Faso, Catalase/metabolism, DNA Primers, DNA, Bacterial/chemistry/genetics, Intestines/microbiology, Molecular Sequence Data, Nitrates/metabolism, Phylogeny, Polymerase Chain Reaction, Pupa/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Serratia/classification/genetics/*isolation & purification/metabolism, Trypanosomiasis, African/transmission, Tsetse Flies/*microbiology/pathogenicity, Urea/metabolismMetabolism
Genetics24265499Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater.Carneiro AR, Juca Ramos RT, Barauna RA, de Sa PH, Marinho Almeida D, Barbosa S, Pereira A, Alves A, Egas C, Correia A, Henriques I, Silva AGenome Announc10.1128/genomeA.00971-132013Phylogeny
Phylogeny25667392Serratia glossinae Geiger et al. 2010 is a later synonym of Serratia fonticola Gavini et al. 1979.Kampfer P, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.0001122015Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/isolation & purification, Tsetse Flies/microbiologyGenetics
Metabolism26376471Complete genome sequence of Serratia fonticola DSM 4576 T, a potential plant growth promoting bacterium.Lim YL, Yong D, Ee R, Krishnan T, Tee KK, Yin WF, Chan KGJ Biotechnol10.1016/j.jbiotec.2015.09.0052015Bacterial Proteins/metabolism, DNA, Bacterial/analysis/genetics, Genome, Bacterial/*genetics, Glutamate Synthase/metabolism, Plant Growth Regulators/*metabolism, Sequence Analysis, DNA/methods, Serratia/*genetics/*metabolismGenetics
Phylogeny26537514Serratia aquatilis sp. nov., isolated from drinking water systems.Kampfer P, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0007312015Bacterial Typing Techniques, DNA, Bacterial/genetics, Drinking Water/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Germany, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/isolation & purificationGenetics
Phylogeny28853686Serratia oryzae sp. nov., isolated from rice stems.Zhang CW, Zhang J, Zhao JJ, Zhao X, Zhao DF, Yin HQ, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0020492017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Multilocus Sequence Typing, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1777Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4576)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4576
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
37710Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11015
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
74625Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389408.1StrainInfo: A central database for resolving microbial strain identifiers
119420Curators of the CIPCollection of Institut Pasteur (CIP 78.64)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2078.64