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Microbial Ecology

, Volume 78, Issue 2, pp 286–298 | Cite as

High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium

  • Andrey O. PlotnikovEmail author
  • Alexander S. Balkin
  • Natalia E. Gogoleva
  • Olivia Lanzoni
  • Yuri A. Khlopko
  • Sergey V. Cherkasov
  • Alexey A. Potekhin
Microbiology of Aquatic Systems

Abstract

Ciliates are the largest group of ubiquitous aquatic bacterivorous protists, and many species are easily cultivated. However, only few studies reported prokaryotic communities naturally associated with ciliate cells. Herein, we analyzed the microbiome composition of several strains of Paramecium (Ciliophora) originating from different locations and belonging to two morpho-species by high-throughput sequencing (HTS) of the 16S rRNA gene. Possible reasons of HTS results bias were addressed comparing DNA libraries obtained using different primers and different number of ciliate cells. Microbiomes associated with ciliates and their environments were always significantly different by prokaryotic taxonomic composition and bacterial richness. There were also pronounced differences between Paramecium strains. Interestingly, potentially pathogenic bacteria were revealed in Paramecium microbiomes.

Keywords

Ciliates Microbiomes Bacterial communities Single cell sequencing Metabarcoding Human pathogens and commensals 

Notes

Funding information

This study was funded by the Russian Science Foundation (grant number 16-14-10157), except the pilot analysis of the P. aurelia samples, which was supported by the Russian Foundation for Basic Research (grant number 14-04-01796).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2019_1321_MOESM1_ESM.xlsx (99 kb)
ESM 1 (XLSX 98 kb)

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Authors and Affiliations

  1. 1.“Persistence of microorganisms” Center of Shared Scientific EquipmentInstitute for Cellular and Intracellular Symbiosis UrB RASOrenburgRussia
  2. 2.Kazan Institute of Biochemistry and BiophysicsKazan Scientific Centre of Russian Academy of SciencesKazanRussia
  3. 3.Institute of Fundamental Medicine and BiologyKazan Federal UniversityKazanRussia
  4. 4.Department of BiologyUniversity of PisaPisaItaly
  5. 5.Laboratory of biomedical technologiesInstitute for Cellular and Intracellular Symbiosis UrB RASOrenburgRussia
  6. 6.Department of Microbiology, Faculty of BiologySaint Petersburg State UniversitySaint PetersburgRussia

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