Strain identifier

BacDive ID: 6694

Type strain: Yes

Species: Secundilactobacillus similis

Strain Designation: M36

Strain history: CIP <- 2010, JCM <- 1984, M. Seki: strain M36 <- S. Tanasupawat

NCBI tax ID(s): 414682 (species)

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General

@ref: 16808

BacDive-ID: 6694

DSM-Number: 23365

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

description: Secundilactobacillus similis M36 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from fermented cane molasses at alcohol plants.

NCBI tax id

  • NCBI tax id: 414682
  • Matching level: species

strain history

@refhistory
16808<- JCM/RIKEN <- M. Seki <- S. Tanasupawat
67770M. Seki M36 <-- S. Tanasupawat.
122618CIP <- 2010, JCM <- 1984, M. Seki: strain M36 <- S. Tanasupawat

doi: 10.13145/bacdive6694.20230509.8.1

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 similis
  • full scientific name: Secundilactobacillus similis (Kitahara et al. 2010) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus similis

@ref: 16808

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Secundilactobacillus

species: Secundilactobacillus similis

full scientific name: Secundilactobacillus similis (Kitahara et al. 2010) Zheng et al. 2020

strain designation: M36

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29360positive3.5 µm0.5 µmrod-shapedno
69480no93.556
69480positive99.999
122618positiverod-shapedno

pigmentation

  • @ref: 29360
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16808MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
40415MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
122618CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
16808positivegrowth35mesophilic
29360positivegrowth15-37
29360positiveoptimum37mesophilic
40415positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16808anaerobe
16808microaerophile
29360facultative anaerobe
122618obligate aerobe

spore formation

@refspore formationconfidence
29360no
69481no100
69480no99.997
122618no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2936022599arabinose+carbon source
2936028260galactose+carbon source
2936024265gluconate+carbon source
2936017234glucose+carbon source
2936017716lactose+carbon source
2936017306maltose+carbon source
2936028053melibiose+carbon source
29360506227N-acetylglucosamine+carbon source
2936033942ribose+carbon source
2936018222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12261817632nitrate-reduction
12261816301nitrite-reduction

metabolite production

  • @ref: 122618
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29360alpha-galactosidase+3.2.1.22
122618oxidase+
122618catalase-1.11.1.6
122618urease-3.5.1.5

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
16808-----++----+-------------+--+-+-------------------
122618---+/-+/-+/----+/-+/-----------+/------+/--+/-----------------+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16808fermented cane molasses at alcohol plantsThailandTHAAsia
67770Fermented molasses
122618Fermented cane molassesThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Sugary food
#Engineered#Industrial#Plant (Factory)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3919.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_750;97_873;98_2977;99_3919&stattab=map
  • Last taxonomy: Secundilactobacillus
  • 16S sequence: LC071812
  • Sequence Identity:
  • Total samples: 6458
  • soil counts: 256
  • aquatic counts: 475
  • animal counts: 5495
  • plant counts: 232

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
168081Risk group (German classification)
1226181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus similis gene for 16S rRNA, partial sequence, strain: JCM 2765AB289056682ena1423804
16808Lactobacillus similis gene for 16S rRNA, partial sequenceAB2828891528ena1423804
67770Lactobacillus similis gene for 16S ribosomal RNA, partial sequence, strain: JCM 2765LC0718121462ena1423804

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus similis DSM 23365 = JCM 27651423804.4wgspatric1423804
66792Lactobacillus similis DSM 23365 = JCM 27651423804.3wgspatric1423804
66792Secundilactobacillus similis JCM 27652728369669draftimg1423804
66792Secundilactobacillus similis DSM 233652700989125draftimg1423804
67770Secundilactobacillus similis DSM 23365 = JCM 2765GCA_001436595scaffoldncbi1423804
67770Secundilactobacillus similis DSM 23365 = JCM 2765GCA_001311075contigncbi1423804

GC content

@refGC-contentmethod
1680848.5high performance liquid chromatography (HPLC)
2936048.5
6777047genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.166yes
gram-positiveyes97.631yes
anaerobicno90.799no
halophileyes76.546no
spore-formingno85.785no
glucose-utilyes88.846yes
thermophileno99.654no
aerobicno93.392no
flagellatedno95.084yes
glucose-fermentyes86.105no

External links

@ref: 16808

culture collection no.: DSM 23365, JCM 2765, LMG 23904, BCRC 80777, CIP 110209

straininfo link

  • @ref: 76168
  • straininfo: 63892

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
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
Phylogeny35834933Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili.Zhang Z, Wang Y, Dong Y, Xiang F, Zhang Y, Zhang H, Sun Y, Guo ZSyst Appl Microbiol10.1016/j.syapm.2022.1263442022Bacterial Typing Techniques, Base Composition, Carbon, *Cardiolipins, Catalase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycolipids, Nucleic Acid Hybridization, *Pentoses, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, gamma-Aminobutyric Acid/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16808Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23365)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23365
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
29360Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125771
40415Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8043
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
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
76168Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID63892.1StrainInfo: A central database for resolving microbial strain identifiers
122618Curators of the CIPCollection of Institut Pasteur (CIP 110209)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110209