Analysis of microbial compositions: a review of normalization and differential abundance analysis.
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ABSTRACT:
SUBMITTER: Lin H
PROVIDER: S-EPMC7710733 | biostudies-literature | 2020 Dec
REPOSITORIES: biostudies-literature
Publications
Analysis of microbial compositions: a review of normalization and differential abundance analysis.
Lin Huang H Peddada Shyamal Das SD
NPJ biofilms and microbiomes 20201202 1
Increasingly, researchers are discovering associations between microbiome and a wide range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on. The first step towards microbiome wide association studies is the characterization of the composition of human microbiome under different conditions. Determination of differentially abundant microbes between two or more environments, known as differential abundance (DA) analysis, is a challenging and an important problem that h ...[more]
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Project description:We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.
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