RT Journal Article
SR Electronic
T1 High-resolution sweep metagenomics using fast probabilistic inference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 332544
DO 10.1101/332544
A1 Tommi Mäklin
A1 Teemu Kallonen
A1 Sophia David
A1 Christine J. Boinett
A1 Ben Pascoe
A1 Guillaume Méric
A1 David M. Aanensen
A1 Edward J. Feil
A1 Stephen Baker
A1 Julian Parkhill
A1 Samuel K. Sheppard
A1 Jukka Corander
A1 Antti Honkela
YR 2019
UL http://biorxiv.org/content/early/2019/07/10/332544.abstract
AB 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 method for identifying and estimating the relative 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 method facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.