Small molecule metabolites: discovery of biomarkers and therapeutic targets

S Qiu, Y Cai, H Yao, C Lin, Y **e, S Tang… - Signal Transduction and …, 2023 - nature.com
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite
accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite …

[HTML][HTML] Rethinking healthy eating in light of the gut microbiome

AM Armet, EC Deehan, AF O'Sullivan, JF Mota… - Cell Host & Microbe, 2022 - cell.com
Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary
recommendations are fundamentally important for health promotion. Despite the importance …

The person-to-person transmission landscape of the gut and oral microbiomes

M Valles-Colomer, A Blanco-Míguez, P Manghi… - Nature, 2023 - nature.com
The human microbiome is an integral component of the human body and a co-determinant
of several health conditions,. However, the extent to which interpersonal relations shape the …

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

A Blanco-Míguez, F Beghini, F Cumbo, LJ McIver… - Nature …, 2023 - nature.com
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome

L Chen, DV Zhernakova, A Kurilshikov… - Nature medicine, 2022 - nature.com
The levels of the thousands of metabolites in the human plasma metabolome are strongly
influenced by an individual's genetics and the composition of their diet and gut microbiome …

High-throughput microbial culturomics using automation and machine learning

Y Huang, RU Sheth, S Zhao, LA Cohen… - Nature …, 2023 - nature.com
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in
microbiome research, and traditional methods to isolate individual bacteria from complex …

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

X Zhou, X Shen, JS Johnson, DJ Spakowicz… - Cell Host & Microbe, 2024 - cell.com
To understand the dynamic interplay between the human microbiome and host during
health and disease, we analyzed the microbial composition, temporal dynamics, and …

EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

YX Liu, L Chen, T Ma, X Li, M Zheng, X Zhou, L Chen… - Imeta, 2023 - Wiley Online Library
It is difficult for beginners to learn and use amplicon analysis software because there are so
many software tools to choose from, and all of them need multiple steps of operation. Herein …

Utilization of the microbiome in personalized medicine

K Ratiner, D Ciocan, SK Abdeen, E Elinav - Nature Reviews …, 2024 - nature.com
Inter-individual human variability, driven by various genetic and environmental factors,
complicates the ability to develop effective population-based early disease detection …

Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma

JR Björk, LA Bolte, A Maltez Thomas, KA Lee… - Nature Medicine, 2024 - nature.com
Multiple clinical trials targeting the gut microbiome are being conducted to optimize
treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these …