High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review: 1 approved, 1 approved with reservations]

Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J. Boinett, Ben Pascoe, Guillaume Méric, David M. Aanensen, Edward J. Feil, Stephen Baker, Julian Parkhill, Samuel K. Sheppard, Jukka Corander, Antti Honkela

Research output: Contribution to journalArticlepeer-review

Abstract

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

Original languageEnglish
Pages (from-to)1-20
Number of pages20
JournalWellcome Open Research
Volume5
DOIs
Publication statusPublished - 2021

Keywords

  • bacterial strain identification
  • metagenomics
  • microbial communities
  • plate sweeps
  • probabilistic modeling

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology(all)

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