The gut microbiota plays an important role in shaping systemic immune responses. In a study published in the journal Science, a team at the University of Chicago identified Bifidobacterium spp. that facilitate anti-PD-L1 treatment in mice using 16S-based metagenomics (Sivan et al. 2015). The crucial clue was the unexpected finding that mice purchased from Jackson Laboratory (JAX) and Taconic Farms/Biosciences (TAC) behave differently against melanoma tumor. The mice raised at JAX showed higher resistance against tumors and facilitated anti-PD-L1 efficacy than those grown at TAC.
In this tutorial, we will use a part of Illumina data published in this study and try to replicate the process of biomarker discovery using EzBioCloud’s MTP cloud. Unlike the original study, we will show you how to discover taxonomic biomarkers at the species-level using EzBioCloud database and EzBioCloud’s MTP pipeline.
Description of the dataset used
10 samples of JAX mice (day 0 & day 14) by Illumina MiSeq V4 region sequencing
10 samples of TAC mice (day 0 & day 14) by Illumina MiSeq V4 region sequencing