Strain identifier

BacDive ID: 158378

Type strain: Yes

Species: Trichococcus paludicola

Strain Designation: B7-2

Strain history: <- Yumei Dai, Chengdu Institute of Biology, Chinese Academy of Sciences

NCBI tax ID(s): 2052942 (species)

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General

@ref: 65054

BacDive-ID: 158378

DSM-Number: 104691

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

description: Trichococcus paludicola B7-2 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from From soil.

NCBI tax id

  • NCBI tax id: 2052942
  • Matching level: species

strain history

@refhistory
65054<- Y. Dai; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, P.R. China; B7-2
67771<- Yumei Dai, Chengdu Institute of Biology, Chinese Academy of Sciences

doi: 10.13145/bacdive158378.20230509.8.1

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 paludicola
  • full scientific name: Trichococcus paludicola Dai et al. 2018

@ref: 65054

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Trichococcus

species: Trichococcus paludicola

full scientific name: Trichococcus paludicola Dai et al. 2018

strain designation: B7-2

type strain: yes

Morphology

cell morphology

  • @ref: 65519
  • gram stain: positive
  • cell length: 0.8-1.4 µm
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

  • @ref: 65054
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
65054positivegrowth28mesophilic
65519positivegrowth4-37
65519positiveoptimum25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
65519positivegrowth7.0-10.5alkaliphile
65519positiveoptimum9.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65519facultative anaerobe
67771aerobe

halophily

  • @ref: 65519
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5-4.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6551916004(R)-lactate-growth
65519645522-hydroxybutyrate-growth
65519645522-hydroxybutyrate+growth
65519309162-oxoglutarate-growth
65519370543-hydroxybutyrate-growth
65519739183-O-methyl-D-glucose-growth
65519181014-hydroxyphenylacetic acid-growth
6551930089acetate-growth
6551913705acetoacetate+growth
6551917925alpha-D-glucose+growth
6551973706bromosuccinate+growth
6551917057cellobiose+growth
6551916947citrate+growth
6551918333D-arabitol-growth
6551929990D-aspartate-growth
6551915824D-fructose+growth
6551978697D-fructose 6-phosphate+growth
6551928847D-fucose-growth
6551912936D-galactose+growth
6551918024D-galacturonic acid-growth
655198391D-gluconate+growth
6551914314D-glucose 6-phosphate-growth
6551915748D-glucuronate+growth
6551915588D-malate-growth
6551916899D-mannitol+growth
6551916024D-mannose+growth
6551933801D-saccharate-growth
6551916523D-serine-growth
6551917924D-sorbitol+growth
6551923652dextrin+growth
6551915740formate-growth
6551916537galactarate-growth
6551916865gamma-aminobutyric acid-growth
655195291gelatin-growth
6551928066gentiobiose+growth
6551932323glucuronamide+growth
6551917754glycerol-growth
6551970744glycine-proline-growth
6551917596inosine+growth
6551916977L-alanine-growth
6551916467L-arginine-growth
6551929991L-aspartate-growth
6551918287L-fucose-growth
6551917464L-galactonic acid gamma-lactone-growth
6551929985L-glutamate-growth
6551915971L-histidine-growth
6551915589L-malate+growth
65519L-pyroglutamic acid-growth
6551962345L-rhamnose+growth
6551917115L-serine-growth
6551917716lactose+growth
6551917306maltose+growth
6551928053melibiose+growth
65519320055methyl beta-D-glucopyranoside+growth
6551951850methyl pyruvate+growth
6551917268myo-inositol-growth
6551963153N-acetyl-D-mannosamine+growth
6551928037N-acetylgalactosamine-growth
65519506227N-acetylglucosamine+growth
6551935418n-acetylneuraminate-growth
6551917309pectin+growth
6551917272propionate-growth
6551926490quinate-growth
6551916634raffinose+growth
6551917814salicin+growth
6551917164stachyose+growth
6551917992sucrose+growth
6551927082trehalose+growth
6551932528turanose+growth
6551953423tween 40-growth

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65519C16:025.4
    65519iso-C17:0ω5c4.2
    65519C17:0 anteiso32.9
    65519C18:1ω9c5.9
    65519C18:014.5
    65519C12:0 aldehyde / unknown 10.9287.1
  • type of FA analysis: whole cell analysis
  • incubation medium: TSB
  • incubation temperature: 25
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
67771From soilZoige wetlandChinaCHNAsia
65054Zoige Wetland, soil(33° 56' N, 102°52' E) Qinghai-Tibetan PlateauChinaCHNAsia
65519wetland soilZoige Wetland, Sichuan ProvinceChinaCHNAsia33.9333102.86790 %(w/v) sterilized water with 0.8 %(w/v) chitin flakes3 months25anearobic incubation

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

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: MF407344
  • Sequence Identity:
  • Total samples: 38677
  • soil counts: 4890
  • aquatic counts: 19650
  • animal counts: 13208
  • plant counts: 929

Safety information

risk assessment

  • @ref: 65054
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 65054
  • description: Trichococcus paludicola strain B7-2 16S ribosomal RNA gene, partial sequence
  • accession: MF407344
  • length: 1437
  • database: ena
  • NCBI tax ID: 2052942

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Trichococcus paludicola B7-2GCA_003052295contigncbi2052942
66792Trichococcus paludicola B7-22791354984draftimg2052942

GC content

@refGC-contentmethod
6505446.0
6551946genome sequence analysis

External links

@ref: 65054

culture collection no.: DSM 104691, KCTC 33886

straininfo link

  • @ref: 111182
  • straininfo: 408272

literature

  • topic: Phylogeny
  • Pubmed-ID: 29116035
  • title: Characterization of Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov., isolated from a high-elevation wetland, by phenotypic and genomic analyses.
  • authors: Dai YM, Zhang LL, Li Y, Li YQ, Deng XH, Wang TT, Yang F, Tian YQ, Li N, Zhou XM, Liu XF, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002464
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Carnobacteriaceae/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Wetlands
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65054Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104691Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104691)
65519Yu-Mei Dai, Ling-Li Zhang, Yan Li, Yu-Qian Li, Xiao-Hui Deng, Ting-Ting Wang, Feng Yang, Yong-Qiang Tian, Na Li, Xing-Mei Zhou, Xiao-Feng Liu and Wen-Jun LiCharacterization of Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov., isolated from a high-elevation wetland, by phenotypic and genomic analyses10.1099/ijsem.0.002464IJSEM 68: 99-105 201829116035
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
111182Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408272.1