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

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.

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Funding

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).

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Correspondence to Andrey O. Plotnikov.

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Plotnikov, A.O., Balkin, A.S., Gogoleva, N.E. et al. High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium. Microb Ecol 78, 286–298 (2019). https://doi.org/10.1007/s00248-019-01321-x

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Keywords

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