TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies

Pixu Shi; Cameron Martino; Rungang Han; Stefan Janssen; Gregory Buck; Myrna Serrano; Kouros Owzar; Rob Knight; Liat Shenhav; Anru R Zhang

doi:10.1186/s13059-024-03453-x

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies

Genome Biol. 2024 Dec 19;25(1):317. doi: 10.1186/s13059-024-03453-x.

Authors

Pixu Shi^#^{1

2}, Cameron Martino^#^{3

4

5}, Rungang Han⁶, Stefan Janssen⁷, Gregory Buck^{8

9}, Myrna Serrano^{8

9}, Kouros Owzar¹⁰, Rob Knight^{11

12

13

14

15}, Liat Shenhav^{16

17

18}, Anru R Zhang^{19

20}

Affiliations

¹ Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, USA. [email protected].
² Duke Microbiome Center, Duke University, Durham, NC, USA. [email protected].
³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
⁴ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁵ Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
⁶ Department of Statistical Science, Duke University, Durham, NC, USA.
⁷ Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Giessen, Giessen, Germany.
⁸ Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.
⁹ Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.
¹⁰ Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, USA.
¹¹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. [email protected].
¹² Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. [email protected].
¹³ Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. [email protected].
¹⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. [email protected].
¹⁵ Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA. [email protected].
¹⁶ Institute for Systems Genetics, New York Grossman School of Medicine, New York University, New York, NY, USA. [email protected].
¹⁷ Department of Microbiology, New York Grossman School of Medicine, New York University, New York, NY, USA. [email protected].
¹⁸ Department of Computer Science, New York University, New York, NY, USA. [email protected].
¹⁹ Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, USA. [email protected].
²⁰ Department of Computer Science, Duke University, Durham, NC, USA. [email protected].

^# Contributed equally.

Abstract

Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treats time as a continuous variable, effectively characterizing temporal information and handling varying temporal sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data. In simulations, it achieves 90% accuracy in phenotype classification, significantly outperforming existing methods. In real data, TEMPTED identifies vaginal microbial markers linked to term and preterm births, demonstrating robust performance across datasets and sequencing platforms.

MeSH terms

Algorithms
Female
Humans
Longitudinal Studies
Microbiota*
Vagina / microbiology

Abstract

MeSH terms

Grants and funding