Discover Biomarkers Facilitating Anti-PD-L1 Efficacy
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
What to prepare in advance
- If you do not have an account at www.ezbiocloud.net, please get one. It is free.
- Since we will use the public database provided by EzBioCloud, we will not need to upload NGS data.
What to do in this video tutorial
You will learn the following in this tutorial. If you want further details about any specific items, please search within help.ezbiocloud.net.
- How to check out the 16S taxonomic profiles (MTPs) from the public database of EzBioCloud. There are >20,000 microbiome samples to choose from including >8,000 human microbiome projects
- How to use the metadata tags to organize your MTPs.
- How to compare and apply statistical testing on alpha-diversity of two groups of mice including the Phylogenetic Diversity Index
- How to apply LefSe analysis to find the biomarkers that are differentially present in JAX or TAC mice
Please follow the below tutorial. If you have any question, please contact us at firstname.lastname@example.org.
- Compare the top 5 species between JAX and TAC mice.
- Compare the Phylogenetic Diversity Indices between JAX and TAC mice.
- Compare the ACE and Chao1 indices between JAX and TAC mice using <Normalization> option.
- Find out which beta-diversity distance matric and options (e.g. species or genus level) separates best between JAX and TAC mice.
- Discuss why JAX mice show more resistance than TAC mice using the data of (1)-(4).
The EzBioCloud team / Last edited on Oct. 9, 2018