Strain identifier

BacDive ID: 2280

Type strain: Yes

Species: Trichococcus pasteurii

Strain Designation: KoTa2

Strain history: CIP <- 1995, P.H. Janssen, Max Planck Inst., Marburg, Germany: strain KoTa2 <- B. Schink

NCBI tax ID(s): 43064 (species)

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General

@ref: 1063

BacDive-ID: 2280

DSM-Number: 2381

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

description: Trichococcus pasteurii KoTa2 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from sewage digester sludge.

NCBI tax id

  • NCBI tax id: 43064
  • Matching level: species

strain history

@refhistory
1063<- B. Schink, KoTa2
121624CIP <- 1995, P.H. Janssen, Max Planck Inst., Marburg, Germany: strain KoTa2 <- B. Schink

doi: 10.13145/bacdive2280.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Trichococcus
  • species: Trichococcus pasteurii
  • full scientific name: Trichococcus pasteurii (Schink 1985) Liu et al. 2002

  • synonyms

    @refsynonym
    20215Ruminococcus pasteurii
    20215Lactosphaera pasteurii

@ref: 1063

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Trichococcus

species: Trichococcus pasteurii

full scientific name: Trichococcus pasteurii (Schink 1985) Liu et al. 2002

strain designation: KoTa2

type strain: yes

Morphology

cell morphology

  • @ref: 121624
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1063TRYPTICASE 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
1063RUMINOCOCCUS PASTEURII MEDIUM (DSMZ Medium 300)yeshttps://mediadive.dsmz.de/medium/300Name: RUMINOCOCCUS PASTEURII MEDIUM (DSMZ Medium 300) Composition: Sodium tartrate 2.0 g/l Na2CO3 1.5 g/l Yeast extract 1.0 g/l NaCl 1.0 g/l KCl 0.5 g/l Biotin 0.4 g/l MgCl2 x 6 H2O 0.4 g/l Na2S x 9 H2O 0.36 g/l NH4Cl 0.25 g/l KH2PO4 0.2 g/l CaCl2 x 2 H2O 0.15 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
39053MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121624CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1063positivegrowth30mesophilic
39053positivegrowth30mesophilic
53647positivegrowth34-37mesophilic
121624positivegrowth10-30
121624nogrowth37mesophilic
121624nogrowth41thermophilic
121624nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1063anaerobe
53647anaerobe
121624facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
121624NaClpositivegrowth0-2 %
121624NaClnogrowth4 %
121624NaClnogrowth6 %
121624NaClnogrowth8 %
121624NaClnogrowth10 %

murein

  • @ref: 1063
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
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
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121624esculin+hydrolysis4853
121624nitrate-reduction17632
121624nitrite-reduction16301

metabolite production

  • @ref: 121624
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 121624
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
121624oxidase-
121624beta-galactosidase+3.2.1.23
121624alcohol dehydrogenase-1.1.1.1
121624gelatinase-
121624DNase-
121624caseinase+3.4.21.50
121624catalase-1.11.1.6
121624tween esterase-
121624lecithinase-
121624lipase-
121624lysine decarboxylase-4.1.1.18
121624ornithine decarboxylase-4.1.1.17
121624urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    53647C12:01.612
    53647C14:011.114
    53647C16:016.616
    53647C18:02.418
    53647C16:1 ω7c4.315.819
    53647C16:1 ω9c17.215.774
    53647C17:1 ω5c ISO116.461
    53647C18:1 ω9c16.217.769
    53647C18:2 ω6,9c/C18:0 ANTE1517.724
    53647Unidentified1.49.745
    53647Unidentified110.745
    53647Unidentified0.811.744
    53647Unidentified0.712.742
    53647Unidentified6.113.742
    53647Unidentified2.213.854
    53647Unidentified2.514.742
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121624--++------+++-+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121624---+++---++++-++-++-+++++++++++++-+---++------+/--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121624---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
1063sewage digester sludge
53647Sewage digester sludge
121624Environment, Anoxic digester sludgeKonstanzGermanyDEUEurope1983

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation
#Engineered#Waste#Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_24449.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_12252;97_14862;98_18388;99_24449&stattab=map
  • Last taxonomy: Trichococcus
  • 16S sequence: L76599
  • Sequence Identity:
  • Total samples: 38677
  • soil counts: 4890
  • aquatic counts: 19650
  • animal counts: 13208
  • plant counts: 929

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
10631Risk group (German classification)
1216241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactosphaera pasteurii small subunit ribosomal RNA (16S rDNA) geneL765991435ena43064
1063L.pasteurii 16S rRNA geneX871501554ena43064

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Trichococcus pasteurii DSM 2381GCA_900112935scaffoldncbi43064
66792Trichococcus pasteurii strain DSM 238143064.15wgspatric43064
66792Trichococcus pasteurii DSM 23812619618823draftimg43064

GC content

  • @ref: 1063
  • GC-content: 45.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes55.529no
flagellatedno66.909no
gram-positiveyes88.803no
anaerobicno77.768no
aerobicno91.7yes
halophileno53.812no
spore-formingno80.307no
glucose-fermentyes76.129no
thermophileno98.814yes
glucose-utilyes89.252no

External links

@ref: 1063

culture collection no.: DSM 2381, ATCC 35945, CCUG 37395, CIP 104580

straininfo link

  • @ref: 71838
  • straininfo: 41382

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism8590685Lactosphaera gen. nov., a new genus of lactic acid bacteria, and transfer of Ruminococcus pasteurii Schink 1984 to Lactosphaera pasteurii comb. nov.Janssen PH, Evers S, Rainey FA, Weiss N, Ludwig W, Harfoot CG, Schink BInt J Syst Bacteriol10.1099/00207713-45-3-5651995Anaerobiosis, Base Sequence, Carbohydrate Metabolism, DNA, Ribosomal/genetics, Enzyme Activation, Fermentation/physiology, Fructosediphosphates/metabolism, Gram-Positive Cocci/*classification/genetics/growth & development/*metabolism, Hydrogen-Ion Concentration, L-Lactate Dehydrogenase/metabolism, Lactates/*metabolism, Lactic Acid, Molecular Sequence Data, Oxidation-Reduction, Oxygen Consumption, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsPhylogeny
Phylogeny12148615Emended description of the genus Trichococcus, description of Trichococcus collinsii sp. nov., and reclassification of Lactosphaera pasteurii as Trichococcus pasteurii comb. nov. and of Ruminococcus palustris as Trichococcus palustris comb. nov. in the low-G+C gram-positive bacteria.Liu JR, Tanner RS, Schumann P, Weiss N, McKenzie CA, Janssen PH, Seviour EM, Lawson PA, Allen TD, Seviour RJInt J Syst Evol Microbiol10.1099/00207713-52-4-11132002Bacteria/*classification/genetics/metabolism/ultrastructure, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1063Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2381)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2381
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
39053Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16504
53647Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37395)https://www.ccug.se/strain?id=37395
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
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
71838Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41382.1StrainInfo: A central database for resolving microbial strain identifiers
121624Curators of the CIPCollection of Institut Pasteur (CIP 104580)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104580