Bacterial community composition (via 16S rRNA V4 region sequencing) was assessed by amplicon sequencing using the Illumina HiSeq2500 PE250 platform for the six samples. A total of 284,855 high-quality reads were obtained after filtering low-quality reads, chimaeras and trimming adapters, barcodes and primers. All 16S rRNA gene sequences were assigned to 43 bacterial phyla. The ten most abundant taxa at the phylum level are summarized in Fig. 2. Firmicutes were the most abundant phylum and represented between 6.30 and 82.92% of each sample’s reads with an average relative abundance of 42.65%. Proteobacteria were the second most abundant phylum with an average relative abundance of 38.00%. Bacteroidetes comprised 38.09% of all reads in sample NHI.12 but only 3.60 to 7.30% in the other five samples. Other major phyla consisted of the Actinobacteria (1.54–11.58%, average of 4.22%), Chloroflexi (0.13–2.66%, average of 1.04%) and Acidobacteria (0.02–2.13%, average of 0.90%) (Fig. 2a, Supplementary Table 1).Figure 2Relative abundance of the ten most abundant microbial phyla and Venn diagrams showing shared OTU diversity among the six samples. (a) Relative abundance for each sample is shown out of 100%. Bacterial phyla are coloured according to the legend on the right. (b) Relative abundance for each sample is shown out of 100%. Fungal phyla are coloured according to the legend on the right. (c) Bacterial OTUs and (d) fungal OTUs that were shared among samples.