Recent work in Gut has highlighted multi-kingdom interactions between gut bacteria and bacteriophage (‘phage’) as contributors to Crohn’s disease.1 Whether similar alterations characterise colorectal ...

Coupled with well-characterized host genetic and environmental risk factors, alterations of gut microbial communities contribute to risk and severity …

WAAFLE 1.5 has been updated to utilize the chocophlan.v202210_202403 SGB database, which is compatible with all bioBakery 4 tools utilizing SGB pangenomes (e.g., MetaPhlAn4 and HUMAnN4, see details Me...

Nature Metabolism, Published online: 02 July 2025; doi:10.1038/s42255-025-01318-6High-resolution multi-omic profiling indicates widespread gut dysbiosis in individuals with MASLD, also affecting the virome, and reveals microbial signatures that can classify MASLD and its subtypes.

Nature Metabolism, Published online: 02 July 2025; doi:10.1038/s42255-025-01300-2The gut microbiome is pivotal to the development of liver diseases in multifaceted ways. A recent study uses a multi-omics, multi-kingdom approach to analyse the gut dysbiosis in metabolic dysfunction-associated steatotic liver disease, highlighting a substantial role for oral-typical microorganisms and their associated metabolites.

Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.

Applying WAAFLE to metagenomic data from human samples reveals over 100,000 putative LGTs not currently found in reference genomes, highlighting an underappreciated microbiome phenomenon.