Cross-feeding in the gut microbiome: ecology and mechanisms

EJ Culp, AL Goodman - Cell host & microbe, 2023 - cell.com
Microbial communities are shaped by positive and negative interactions ranging from
competition to mutualism. In the context of the mammalian gut and its microbial inhabitants …

A decade of advances in transposon-insertion sequencing

AK Cain, L Barquist, AL Goodman, IT Paulsen… - Nature Reviews …, 2020 - nature.com
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS)
methods, which combine genome-wide transposon mutagenesis with high-throughput …

[HTML][HTML] Design, construction, and in vivo augmentation of a complex gut microbiome

AG Cheng, PY Ho, A Aranda-Díaz, S Jain, BY Feiqiao… - Cell, 2022 - cell.com
Efforts to model the human gut microbiome in mice have led to important insights into the
mechanisms of host-microbe interactions. However, the model communities studied to date …

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

SE Klompe, PLH Vo, TS Halpin-Healy, SH Sternberg - Nature, 2019 - nature.com
Conventional CRISPR–Cas systems maintain genomic integrity by leveraging guide RNAs
for the nuclease-dependent degradation of mobile genetic elements, including plasmids and …

Mapping human microbiome drug metabolism by gut bacteria and their genes

M Zimmermann, M Zimmermann-Kogadeeva… - Nature, 2019 - nature.com
Individuals vary widely in their responses to medicinal drugs, which can be dangerous and
expensive owing to treatment delays and adverse effects. Although increasing evidence …

The evolution of the host microbiome as an ecosystem on a leash

KR Foster, J Schluter, KZ Coyte, S Rakoff-Nahoum - Nature, 2017 - nature.com
The human body carries vast communities of microbes that provide many benefits. Our
microbiome is complex and challenging to understand, but evolutionary theory provides a …

Establishing causality: opportunities of synthetic communities for plant microbiome research

JA Vorholt, C Vogel, CI Carlström, DB Müller - Cell host & microbe, 2017 - cell.com
Plant microbiome research highlights the importance of indigenous microbial communities
for host phenotypes such as growth and health. It aims to discover the molecular basis by …

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

M Zimmermann, M Zimmermann-Kogadeeva… - Science, 2019 - science.org
INTRODUCTION The gut microbiota is implicated in the metabolism of many medical drugs,
with consequences for interpersonal variation in drug efficacy and toxicity. However …

An insider's perspective: Bacteroides as a window into the microbiome

AG Wexler, AL Goodman - Nature microbiology, 2017 - nature.com
Over the last decade, our appreciation for the contribution of resident gut microorganisms—
the gut microbiota—to human health has surged. However, progress is limited by the sheer …

Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis

EM Brown, X Ke, D Hitchcock, S Jeanfavre… - Cell host & …, 2019 - cell.com
Sphingolipids are structural membrane components and important eukaryotic signaling
molecules. Sphingolipids regulate inflammation and immunity and were recently identified …