All sequences were analysed using Quantitative Insights into Microbial Ecology (QIIME2). Alpha and beta diversity analyses were also performed using QIIME2. Heatmap analysis was performed using the MetaboAnalyst website (https://www.metaboanalyst.ca/MetaboAnalyst/ModuleView.xhtml, accessed on November 2020). The data were normalised by the median, transformed by log transformation, and scaled by the centred mean. Heat tree analysis and linear discriminant analysis (LDA) effect size were performed using the MicrobiomeAnalyst website (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/upload/OtuUploadView.xhtml, accessed on December 2020). The low count filter was a 20% prevalence filter, whereas the low-variance filter was based on the inter-quantile range. The data were normalised using total sum scaling. Differences were regarded significant at p < 0.05.

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