Analysis of microbial compositions: a review of normalization and differential abundance analysis

Huang Lin,Shyamal Das Peddada

doi:10.1038/s41522-020-00160-w

Abstract

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 has received considerable interest during the past decade. It is well documented in the literature that the observed microbiome data (OTU/SV table) are relative abundances with an excess of zeros. Since relative abundances sum to a constant, these data are necessarily compositional. In this article we review some recent methods for DA analysis and describe their strengths and weaknesses.

Highlights

Human oral and gut microbiome are estimated to have 45.6 million genes, which is ~2000-fold more genes than human genes1, the microbiome is sometimes referred to as the “second genome”, or another “organ” of human body2–4
The goal of differential abundance (DA) analysis described in this paper is to identify taxa whose mean absolute abundances, per unit volume, of an ecosystem are significantly different with changes in the covariate of interest
As new scientific questions emerge, so do new statistical and computational methods of analysis. This is a very rapidly growing area of research with new statistical methods being developed on a regular basis

Summary

INTRODUCTION

Human oral and gut microbiome are estimated to have 45.6 million genes, which is ~2000-fold more genes than human genes, the microbiome is sometimes referred to as the “second genome”, or another “organ” of human body. The fraction of the taxon observed in the feature table relative to the sum of all taxa in the sample Unobserved absolute abundance of ith taxon in a unit volume of ecosystem of jth sample. Unobserved absolute relative abundance of ith taxon in a unit volume of ecosystem of jth sample. Observed abundance of ith taxon in a random specimen taken from a unit volume of ecosystem of jth sample. Observed relative abundance of ith taxon in a random specimen taken from a unit volume of ecosystem of jth sample. The goal of DA analysis described in this paper is to identify taxa whose mean absolute abundances, per unit volume, of an ecosystem are significantly different with changes in the covariate of interest (e.g. study groups).

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Method

METHODS

12 DISCUSSION

Findings

CODE AVAILABILITY