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Related Concept Videos

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Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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Related Experiment Video

Updated: Apr 20, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Séance: reference-based phylogenetic analysis for 18S rRNA studies.

Alan Medlar1, Tuomas Aivelo2, Ari Löytynoja3

  • 1Institute of Biotechnology, University of Helsinki, Helsinki, P.O.Box 56, Finland. alan.j.medlar@helsinki.fi.

BMC Evolutionary Biology
|December 1, 2014
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Summary

Séance is a new open-source pipeline for analyzing 18S rRNA marker gene data using phylogenetic placement. This method improves operational taxonomic unit (OTU) picking and offers accuracy comparable to traditional methods for microbial community analysis.

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Area of Science:

  • Microbial ecology
  • Bioinformatics
  • Phylogenetics

Background:

  • Marker gene studies commonly use short rRNA gene amplicons to analyze environmental microbial communities.
  • Short sequencing reads limit accurate phylogenetic analysis, hindering the study of microscopic eukaryotes where rRNA genes reflect species phylogeny.
  • Phylogenetic placement offers an alternative by inferring a reference phylogeny and extending it with short sequences.

Purpose of the Study:

  • To develop Séance, a community analysis pipeline for 18S marker gene data.
  • To leverage phylogenetic placement for improved analysis of microbial communities.
  • To provide an open-source tool for reference-based phylogenetic analysis of rRNA marker gene studies.

Main Methods:

  • Developed Séance, a pipeline integrating Pagan's alignment extension and phylogenetic placement.
  • Incorporated tools for preprocessing, clustering, and visualizing large datasets.
  • Applied phylogenetic placement to analyze 454 sequencing data from a longitudinal study of mouse lemur intestinal parasites.

Main Results:

  • Demonstrated improved operational taxonomic unit (OTU) picking for 454 data at higher sequence similarity.
  • Showcased the accuracy of phylogenetic placement, comparable to maximum likelihood methods for fewer taxa.
  • Validated Séance's utility in analyzing complex microbial communities.

Conclusions:

  • Séance is an open-source pipeline for reference-based phylogenetic analysis of rRNA marker gene data.
  • The pipeline facilitates accurate community analysis, particularly for 18S rRNA gene studies.
  • The underlying concepts are adaptable for alternative marker genes and reference datasets.