Metagenome, metatranscriptome and 16S rRNA sequencing at multiple intestinal sites of common marmosets

Shotgun metagenomic and metatranscriptomic sequencing were conducted at 3 intestinal locations, caecum, transverse colon, and faeces of 2 marmosets. The gastrointestinal tract of each marmoset was excised, and the luminal content of each gastrointestinal tract site was collected and divided into metagenomic samples and metatranscriptomic samples. DNA extracted from each sample, and RNA extracted from them and reverse transcribed into cDNA were sequenced using the Illumina HiSeq platform. Raw data were filtered to remove low quality, marmoset and feed reads. Using the integrated analytical method proposed in this study, which include assembly, scaffolding and merging steps, we reconstructed reference metagenomes common to all sites. We quantified gene expression levels at each intestinal site. In addition, 16S rRNA sequencing was conducted on 6 marmoset faecal microbiome for comparison with those of other animal model species. DNA extracted from faecal microbiome were amplified and sequenced using Illumina MiSeq platform.