Total DNA was extracted from feces and SI contents using QIAamp DNA stool mini kits (Qiagen) in accordance with the manufacturer’s instructions. For bacterial PCR amplification, primers targeting 341 F and 805 R were used. The amplified product was purified and sequenced by Chunlab (Seoul, South Korea) with an Illumina Miseq Sequencing system (Illumina). The processing of raw reads started with a quality check and filtering of low-quality (60 (link) After chimeric filtering, reads that were not identified to the species level (with <97% similarity) in the EzBioCloud database were compiled. Operational taxonomic units with single reads (singletons) were omitted from further analysis. The alpha diversity (Shannon index) and beta diversity for the sample difference were estimated. A taxonomic cladogram was generated using LEfSe with a threshold of 2 on the logarithmic LDA score.61 (link) A relationship based on a Pearson correlation between gut microbiota and SCFAs was visualized using Calypso software.62 (link)
Free full text: Click here
