Dissecting Microbial Communities With Single-Cell Transcriptome Analysis

Authors

Andrew W Pountain
Itai Yanai

Language

English

Publication Date

9-4-2025

Journal

Science

DOI

10.1126/science.adp6252

PMID

40906858

PMCID

PMC12467864

PubMedCentral® Posted Date

9-27-2025

PubMedCentral® Full Text Version

Author MSS

Abstract

Revealing insights into the function of microbial communities requires moving beyond measuring bulk taxonomic composition to detecting interactions between subpopulations. Following the transformative impact of single-cell gene expression profiling techniques on numerous fields of human biology, recent years have seen increased application to microbes. We review progress in the development of these techniques and discuss challenges in applying them to microbial communities. We highlight applications for dissecting the microbiome in human health and disease that reveal functional heterogeneity within gut communities, antibiotic responses, and the dynamics of mobile genetic elements. As single-cell gene expression technologies continue to develop, they are becoming ever more essential for examining and modulating the role of microbial communities in clinical and wider environments.

Keywords

Humans, Anti-Bacterial Agents, Bacteria, Gastrointestinal Microbiome, Interspersed Repetitive Sequences, Single-Cell Gene Expression Analysis, Transcriptome

Published Open-Access

yes

Recommended Citation

Andrew W Pountain and Itai Yanai, "Dissecting Microbial Communities With Single-Cell Transcriptome Analysis" (2025). Faculty, Staff and Student Publications. 6430.
https://digitalcommons.library.tmc.edu/uthgsbs_docs/6430