News

Correcting Batch Effects in Microbiome Data

Batch Effects in 16S Datasets Complicate Cross-Study Comparisons

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses.

You can read more about this work in our recent PloS Computational Biology article.

The code for running percentile normalization is available on github and can be applied as a QIIME2 plugin.

Recent Articles

  • ‘1 in 1,000:’ Dr. Sean Gibbons Named Highly Cited Researcher for 2023

    ISB Associate Professor Dr. Sean Gibbons was named a Highly Cited Researcher for 2023. It is the second consecutive year Gibbons has earned the distinction. The Highly Cited Research list is generated annually by Clarivate, which says: “Of the world’s population of scientists and social scientists, Highly Cited Researchers are 1 in 1,000.”

  • 2023 ISB Virtual Microbiome Series

    2023 ISB Virtual Microbiome Series Registration Now Open!

    On October 11-13, 2023, ISB will host a virtual course and symposium on how the ecology of our guts protects us from pathogens. Both events are virtual and free. The intended audience for these events are graduate students, postdocs, principal investigators, industry scientists, educators, clinicians, or any other variety of microbiome-curious person from across the globe.

  • Lab awarded a Global Grant for Gut Health to study healthy aging

    Revealing the unique signatures of healthy guts as we age The Gibbons lab at the Institute for Systems Biology in Seattle, US, and collaborators will use their Global Grant for Gut Health to explore the unique gut microbial compositional signatures, gut microbial functional gene signatures, and associated blood metabolites in healthy elderly people.