Defining the relationship between MAG abundances and WLZ
The procedures used for shotgun sequencing of faecal DNA and preprocessing of the resulting reads, plus MAG assembly and quantification are described in the Linear mixed-effects models were used to relate the abundances of MAGs identified in each trial participant to WLZ using the formula:Our data normalization strategies before linear modelling did not include a consideration of MAG assembly length. We therefore analysed the TPM (reads per kilobase per million) output of kallisto (v.0.43.0) by applying a filter requiring each MAG’s abundance to be >5 TPM in >40% of the 707 faecal samples collected at timepoints at which anthropometry was also measured. This filtering approach yielded 837 MAGs. We then returned to the unfiltered count output from kallisto, performed a variance-stabilizing transformation (VST, DESeq2