Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning

IScience
Fedor GalkinAlex Zhavoronkov

Abstract

The human gut microbiome is a complex ecosystem that both affects and is affected by its host status. Previous metagenomic analyses of gut microflora revealed associations between specific microbes and host age. Nonetheless there was no reliable way to tell a host's age based on the gut community composition. Here we developed a method of predicting hosts' age based on microflora taxonomic profiles using a cross-study dataset and deep learning. Our best model has an architecture of a deep neural network that achieves the mean absolute error of 5.91 years when tested on external data. We further advance a procedure for inferring the role of particular microbes during human aging and defining them as potential aging biomarkers. The described intestinal clock represents a unique quantitative model of gut microflora aging and provides a starting point for building host aging and gut community succession into a single narrative.

Citations

Sep 21, 2020·Aging·Maria MitinaAlex Zhavoronkov
Dec 9, 2020·Bioinformatics·Beatriz García-JiménezMark D Wilkinson
Dec 31, 2020·Critical Reviews in Food Science and Nutrition·Zongxin LingShaochang Wu
Jan 30, 2021·Seminars in Cell & Developmental Biology·Albert T Higgins-ChenMorgan E Levine
Jan 11, 2021·Seminars in Cell & Developmental Biology·Annelise A Madison, Janice K Kiecolt-Glaser
Dec 31, 2020·Aging·Garik V MkrtchyanMorten Scheibye-Knudsen
Apr 27, 2021·Frontiers in Genetics·Simone RampelliSilvia Turroni
May 4, 2021·Ageing Research Reviews·Xian XiaJing-Dong J Han
Jun 8, 2021·Journal of Lipid and Atherosclerosis·Amy BottaGary Sweeney
Jun 29, 2021·Frontiers in Genetics·Serena DatoFrancesco Lescai
Jun 23, 2021·Aging·Svetlana YurenevaGennady Sukhikh
Aug 4, 2021·Aging and Disease·Fedor GalkinAlex Zhavoronkov
Aug 21, 2021·Aging Cell·Daniel J Simpson, Tamir Chandra
Sep 7, 2021·Frontiers in Cellular and Infection Microbiology·YuShuang XuZhiFan Xiong

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Datasets Mentioned

BETA
PRJNA289586

Software Mentioned

DNAm
ALE

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