The specific primers 515F and 806R were used for the sequencing of the V4 hypervariable region, as suggested by the Earth Microbiome Project [21 (link)] and as previously described [22 (link)]. DNA libraries was sequenced at the Sequencing Unit in the National Institute of Genomic Medicine (INMEGEN) by an Illumina Miseq 2 × 250 platform (Illumina, San Diego, CA, USA) [23 (link)].
Processing of the Illumina fastq reads was performed using the QIIME 1.8.(16). The UCHIME algorithm was used for detection and removal of chimeric sequences. The Greengenes database was used as the reference 16S database. Taxonomy was assigned by the Ribosomal Database Project (RDP) classifier using a threshold of 80% [24 (link)]. The taxonomic composition of the gut microbiota was analyzed by METAGENassist.
Processing of the Illumina fastq reads was performed using the QIIME 1.8.(16). The UCHIME algorithm was used for detection and removal of chimeric sequences. The Greengenes database was used as the reference 16S database. Taxonomy was assigned by the Ribosomal Database Project (RDP) classifier using a threshold of 80% [24 (link)]. The taxonomic composition of the gut microbiota was analyzed by METAGENassist.
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