About 2 μg DNA per sample was prepared for library construction and then sequenced on the Illumina HiseqX platform. Low quality or contaminated human reads were removed, and the high-quality reads were assembled into contigs using SOAPdenovo (v2.04).79 MetaGeneMark (v2.10)80 was used to predict genes from the assembled contigs. CD-HIT v4.5.881 was used to generate a non-redundant gene catalog. Abundances of the genes were computed by aligning high-quality reads to the reference gene database. For taxonomic identity and functional assignment of unigenes, reads were aligned to the NCBI NR database (e-value≤1e-5) using DIAMOND (v0.9.9).82 The LCA algorithm83 was used to conduct annotation. The detailed methods and results have been presented by our other study.

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