How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome

Abstract

A key component of microbiome research is understanding the role of host genetic influence on gut microbial composition. However, it can be difficult to link host genetics with gut microbial composition because host genetic similarity and environmental similarity are often correlated. Longitudinal microbiome data can supplement our understanding of the relative role of genetic processes in the microbiome. These data can reveal environmentally contingent host genetic effects, both in terms of controlling for environmental differences and in comparing how genetic effects differ by environment. Here, we explore four research areas where longitudinal data could lend new insights into host genetic effects on the microbiome: microbial heritability, microbial plasticity, microbial stability, and host and microbiome population genetics. We conclude with a discussion of methodological considerations for future studies.

Wolbachia impacts microbiome diversity and fitness‐associated traits for Drosophila melanogaster in a seasonally fluctuating environment

“…However, assessing potential constraints on microbial diversity requires better understanding of temporal variation in the microbiome. Developing statistical and theoretical approaches to handle time series data in the microbiome is an active area of research (Coenen et al., 2020 ; Fink et al., 2022 ; Grieneisen et al., 2023 ). Nearly all current approaches require filtering the dataset under different criteria and using different community‐level metrics to essentially define the core microbiome.…”

Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases

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“…Standardized metadata collection and reporting are necessary to integrate and compare data across studies. Establishing standardized metadata standards and guidelines would facilitate data harmonization, improve reproducibility, and enable meta-analyses [373]. Identifying causal mechanisms between specific microbes or microbial functions and infectious diseases remains complex.…”

Long-distance movement dynamics shape host microbiome richness and turnover

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