High-resolution sweep metagenomics using fast probabilistic inference

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 bacteri...

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Bibliographic Details
Published in:Wellcome open research 2021, Vol.5, p.14
Main Authors: Mäklin, Tommi, Kallonen, Teemu, David, Sophia, Boinett, Christine J., Pascoe, Ben, Méric, Guillaume, Aanensen, David M., Feil, Edward J., Baker, Stephen, Parkhill, Julian, Sheppard, Samuel K., Corander, Jukka, Honkela, Antti
Format: Article
Language:English
Subjects:
Accuracy
Antimicrobial agents
Bacteria
Clustering
Collections
Experiments
Genomes
Peer review
Performance evaluation
Pipelines
Taxonomy
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Summary: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.
ISSN:2398-502X
2398-502X
DOI:10.12688/wellcomeopenres.15639.1