Microbiome analysis suggests that gut microbial changes in Parkinson’s disease evolve progressively from healthy individuals to genetically at-risk individuals to clinically affected patients, with th...

Background Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized ...

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

The European Nucleotide Archive (ENA) was used as an interface to systematically search the INSDC. Two authors (BV and PCR) screened the databases independently to identify bioprojects including samples from the gut microbiome of South American individuals. For each South...

Here, Valderrama et al., introduced ‘saMBA’, the largest collection of uniformly analyzed microbiome data from South America, the worlds most biodiverse yet less characterized region. The article prop...

Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

These findings suggest that the hormetic effects of physical exercise on cognitive function and neurogenesis are mediated by corresponding changes in the gut microbiota, highlighting a novel mechanist...

Although microbiome meta-analyses are fairly common in the literature, there is a lack of critical discussion on their limitations. This post is my (unsolicited) contribution to that topic.

...and how to successfully avoid it

TL;DR I’ll start a biobliometrics analysis on the Microbiome-Gut-Brain axis field.

Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and N...

The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to whi...

After three postdoc positions, this researcher now sees her skills and knowledge as valuable

Happy Friday and see you next week at MVIF! Gut microbiome The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of negle…

Workflow to build archives of 16s faecal microbiome samples from neglected populations. - Benjamin-Valderrama/saMBA-pipeline

The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to whi...

Acute stress can enhance or impair synaptic plasticity depending on the nature, duration, and type of stress exposure as well as the brain region exam…

DEBIAS-M corrects technical variability in microbiome data in a manner both interpretable and suitable for machine learning. In extensive benchmarks, DEBIAS-M facilitates robust analyses that generali...

Looking for information about Brain, bacteria, and behaviour summer course? Read more about this Radboudumc agenda item

Nature Reviews Gastroenterology & Hepatology, Published online: 03 March 2025; doi:10.1038/s41575-025-01051-1The AI-driven ‘endo-histo-omics’ approach integrates clinical, endoscopic, histological and molecular data to improve management of inflammatory…