... and the other one that discovers that shifts in the gut microbiome linked to urbanization impact host gene expression (in collaboration with @blekhman.bsky.social & @fluca2406.bsky.social):

www.biorxiv.org/content/10.1...

This work is accompanied by two other studies, one showing that industrialization drives convergent microbial and physiological shifts in the human metaorganism:

www.biorxiv.org/content/10.1...

These findings show that gut bacteria are not passive passengers — they are actively evolving with their human hosts, mirroring the ecological pressures of their industrialized or non-industrialized host environments.

... as well as: within- and between-species convergent positive selection in key functions; within- and between-species convergent allelic variants in stress-response, cell-envelope, and metabolic genes

Across species of Bacteroides, Parabacteroides, and Blautia, strains from industrialized hosts show: larger proteomes, associated with recent increases in gene transfer and more fluid pangenomes...

Isolate genomes revealed richer functional content and mobile genetic elements than paired MAGs from the same hosts and species, allowing us to detect fine-scale evolutionary changes.

We built a collection of 6,000 cultured gut bacterial genomes from 9 countries included in the GMbC cohort, and compared their evolution across host lifestyles.

... and the other one that discovers that shifts in the gut microbiome linked to urbanization impact host gene expression (in collaboration with @blekhman.bsky.social & @fluca2406.bsky.social):

www.biorxiv.org/content/10.1...

This work is accompanied by 2 other studies, one showing that industrialization drives parallel genomic adaptations in gut bacteria:

www.biorxiv.org/content/10.1...

Our results highlight the need for globally inclusive microbiome research to ensure discoveries translate across all human populations.

These shifts occur independently of other determinants of the microbiome, such as host genetics, geography, and diet.
Microbiome-based disease models trained on industrialized populations also fail to generalize globally.

We uncover convergent microbial and immune responses to industrialized lifestyles - specifically a loss of microbial diversity, the homogenization of gut communities, reduced community stability, elevated gut stress markers and increased IgA secretion, and altered immune-microbe interactions

Generating new data from >1,000 participants across 12 countries and 35 localities worldwide, we combined gut metagenomics, host genotyping, IgA-seq, lifestyle, diet, and biomarkers to build a multidimensional picture of the human metaorganism — the host and its gut microbiome together.