Strain identifier

BacDive ID: 6436

Type strain: Yes

Species: Secundilactobacillus collinoides

Strain Designation: Cl3a, C13a

Strain history: CIP <- 1987, DSM <- ATCC <- J.G. Carr: strain C13a

NCBI tax ID(s): 33960 (species)

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General

@ref: 8887

BacDive-ID: 6436

DSM-Number: 20515

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

description: Secundilactobacillus collinoides Cl3a is an anaerobe, mesophilic bacterium that was isolated from fermenting apple juice.

NCBI tax id

  • NCBI tax id: 33960
  • Matching level: species

strain history

@refhistory
8887<- ATCC <- J.G. Carr, Cl3a
67770ATCC 27612 <-- J. G. Carr C13a.
118705CIP <- 1987, DSM <- ATCC <- J.G. Carr: strain C13a

doi: 10.13145/bacdive6436.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Secundilactobacillus
  • species: Secundilactobacillus collinoides
  • full scientific name: Secundilactobacillus collinoides (Carr and Davies 1972) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus collinoides

@ref: 8887

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Secundilactobacillus

species: Secundilactobacillus collinoides

full scientific name: Secundilactobacillus collinoides (Carr and Davies 1972) Zheng et al. 2020

strain designation: Cl3a, C13a

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.512
69480100positive
118705nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8887TOMATO JUICE MEDIUM (DSMZ Medium 264)yeshttps://mediadive.dsmz.de/medium/264Name: TOMATO JUICE MEDIUM (DSMZ Medium 264) Composition: Yeast extract 10.0 g/l Casein peptone 10.0 g/l Tomato juice Tween 80 Distilled water
38109MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118705CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41
118705CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8887positivegrowth26mesophilic
38109positivegrowth30mesophilic
50935positivegrowth30mesophilic
67770positivegrowth26mesophilic
118705positivegrowth15-30
118705nogrowth37mesophilic
118705nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50935anaerobe
50935microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.99

murein

  • @ref: 8887
  • 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
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
68371amygdalin-builds acid from27613
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
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
118705nitrate-reduction17632
118705nitrite-reduction16301
118705nitrate+respiration17632

metabolite tests

  • @ref: 118705
  • 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
118705oxidase-
118705alcohol dehydrogenase-1.1.1.1
118705catalase-1.11.1.6
118705lysine decarboxylase-4.1.1.18
118705ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118705-----++---++-+--+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8887----+++-----+---------------+------------------+-+
118705---+++---+/-++---------+/--+/-+--+------------------+-+

Isolation, sampling and environmental information

isolation

@refsample type
8887fermenting apple juice
50935Fermenting apple juice
67770Fermenting apple juice
118705Food, Fermenting apple juice

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_1291.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_750;97_873;98_1020;99_1291&stattab=map
  • Last taxonomy: Secundilactobacillus
  • 16S sequence: LC062900
  • Sequence Identity:
  • Total samples: 11203
  • soil counts: 286
  • aquatic counts: 466
  • animal counts: 10122
  • plant counts: 329

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88871Risk group (German classification)
1187051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus collinoides gene for 16S ribosomal RNA, partial sequenceAB0058931549ena33960
20218Lactobacillus collinoides gene for 16S-23S rRNA intergenic spacer, partial sequence, 300 bp fragment, strain: JCM 1123AB117955298ena33960
20218Lactobacillus collinoides gene for 16S-23S rRNA intergenic spacer, partial sequence, 500 bp fragment, strain: JCM 1123AB117957520ena33960
20218Lactobacillus collinoides gene for 16S rRNA, partial sequence, strain: JCM 1123AB289061689ena33960
20218Lactobacillus collinoides gene for 16S ribosomal RNA, partial sequenceD31683198ena33960
67770Lactobacillus collinoides gene for 16S ribosomal RNA, partial sequence, strain: JCM 1123LC0629001485ena33960

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus collinoides DSM 20515 = JCM 11231423733.4wgspatric1423733
66792Lactobacillus collinoides DSM 20515 = JCM 11231423733.3wgspatric1423733
66792Secundilactobacillus collinoides DSM 205152663762609draftimg1423733
66792Secundilactobacillus collinoides JCM 11232734481918draftimg1423733
67770Secundilactobacillus collinoides DSM 20515 = JCM 1123GCA_001435975scaffoldncbi1423733
67770Secundilactobacillus collinoides DSM 20515 = JCM 1123GCA_001312845contigncbi1423733

GC content

@refGC-contentmethod
888746.0
6777046
6777046.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.305no
gram-positiveyes95.797no
anaerobicno85.057no
halophileyes70.592no
spore-formingno87.365no
glucose-utilyes87.995no
thermophileno99.482yes
aerobicno94.415yes
flagellatedno96.443no
glucose-fermentyes83.557no

External links

@ref: 8887

culture collection no.: DSM 20515, ATCC 27612, NCIB 10925, CCUG 32259, NCIMB 10925, JCM 1123, BCRC 11649, CECT 922, CIP 103008, LMG 11717, LMG 9194, NBRC 107765, NCFB 2805, NCDO 2746

straininfo link

  • @ref: 75910
  • straininfo: 92298

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648343Lactobacillus similis sp. nov., isolated from fermented cane molasses.Kitahara M, Sakamoto M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.011551-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, *Fermentation, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molasses/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharum/*microbiologyMetabolism
Metabolism19760514Lactobacillus collinoides JCM1123(T): effects on mouse plasma cholesterol and isoflavonoids in the caecum.Tamura M, Hori S, Nakagawa HAntonie Van Leeuwenhoek10.1007/s10482-009-9376-x2009Animals, Cecum/*chemistry, Cholesterol/*blood, Colony Count, Microbial, Feces/microbiology, Isoflavones/*analysis, Lactobacillus/*metabolism, *Lipid Metabolism, Male, Mice, Mice, Inbred ICR, Plasma/*chemistry
Phylogeny23919960Lactobacillus silagei sp. nov., isolated from orchardgrass silage.Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima KInt J Syst Evol Microbiol10.1099/ijs.0.053124-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dactylis/*microbiology, Fatty Acids/chemistry, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8887Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20515)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20515
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
38109Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14758
50935Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32259)https://www.ccug.se/strain?id=32259
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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
75910Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92298.1StrainInfo: A central database for resolving microbial strain identifiers
118705Curators of the CIPCollection of Institut Pasteur (CIP 103008)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103008