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High-resolution sweep metagenomics using fast probabilistic inference.

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.

SUBMITTER: Maklin T

PROVIDER: S-EPMC8543175 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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High-resolution sweep metagenomics using fast probabilistic inference.

Mäklin Tommi T Kallonen Teemu T David Sophia S Boinett Christine J CJ Pascoe Ben B Méric Guillaume G Aanensen David M DM Feil Edward J EJ Baker Stephen S Parkhill Julian J Sheppard Samuel K SK Corander Jukka J Honkela Antti A

Wellcome open research 20200101

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 resu ...[more]

PMID: 34746439

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