Microbiome

Pattern recognition (psychology)

Metric (unit)

Salient

Compositional data

Species richness

Bioinformatics

Biology

Gene

Data mining

Curse of dimensionality

Machine learning

Artificial intelligence

Economics

Beta diversity

Ecology

Operations management

Computer science

Dimensionality reduction

Genetics

Robustness (evolution)

mSystems

The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance.

A Novel Sparse Compositional Technique Reveals Microbial Perturbations