A Novel Sparse Compositional Technique Reveals Microbial Perturbations

MSystems
Cameron MartinoKarsten Zengler

Abstract

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 imp...Continue Reading

References

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Citations

May 22, 2020·Environmental Microbiology·Josh L EspinozaChris L Dupont
Sep 24, 2019·GigaScience·Thomas P QuinnTamsyn M Crowley
Apr 2, 2020·Respiratory Research·Jerome BouquetHong Jin
Sep 2, 2020·Nature Biotechnology·Cameron MartinoRob Knight
May 12, 2020·NAR Genomics and Bioinformatics·Marcus W FedarkoRob Knight
Feb 23, 2020·F1000Research·Alexandra Tabrett, Matthew W Horton
Dec 19, 2019·Scientific Reports·Brooke A ClemmonsPhillip R Myer
Jan 1, 2020·BMC Microbiology·Oleg V GoloshchapovBoris V Afanasyev
Feb 11, 2021·Microbial Biotechnology·Cheng WangMingliang Jin
Oct 25, 2020·Nutrients·Tien S DongJonathan P Jacobs
Jan 6, 2021·Nature Methods·Thomas P Quinn, Ionas Erb
Apr 1, 2021·MSystems·Daniel Ruiz-PerezGiri Narasimhan
May 15, 2021·Nature Methods·Zheng SunYang-Yu Liu
Jun 5, 2021·Frontiers in Cellular and Infection Microbiology·Prince Kofi ParbieTetsuro Matano
Jun 11, 2021·Development and Psychopathology·Molly FoxLaura M Glynn
Jun 2, 2021·Cellular and Molecular Gastroenterology and Hepatology·Souradipta GangulyDebanjan Dhar
Jun 15, 2021·Frontiers in Microbiology·Vadim SchützPeter Dörmann
Jun 30, 2021·Genome Biology·Ruochen JiangJingyi Jessica Li

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Methods Mentioned

BETA
PCA
amplicon sequencing
PCR

Software Mentioned

learn
bio
OptSpace
rclr
PERMANOVA
matplotlib
Netflix
Qiita
QIIME
Deblur

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