Growth regulation mechanisms of core bacteria in human gut microbiome 

Mechanisms to suppress rival subtypes observed among subtypes of Akkermansia muciniphila

Researchers at the Korea Food Research Institute (KFRI) have identified key growth regulation mechanisms within the human gut microbiota, focusing on the bacterial species Akkermansia muciniphila – a leading candidate for microbiome-based therapies.

A. muciniphila is known to be abundant in the gut of healthy individuals, where it plays a vital role in maintaining physiological balance through the modulation of immune responses and insulin sensitivity.

The study, led by Dr Young-Do Nam at KFRI, was conducted in collaboration with Professor Kwang-Soon Kim at Pohang University of Science and Technology (POSTECH) and the biotech company EnteroBiome. Using large-scale gut microbiome datasets from individuals in South Korea, the team discovered that A. muciniphila comprises four distinct clades (I–IV), with typically only one clade present in any given individual.

The researchers hypothesised that the subtypes compete for dominance within the gut environment. Through comparative genomic and physiological analysis, in vitro co-culturing, and gnotobiotic experiments in germ-free mice, they confirmed this theory. Clade II (AmII), which exhibits limited mucin-degrading ability, was shown to secrete extracellular vesicles containing proteins that specifically target and lyse cells of clade I (AmI), a more efficient mucin utilising variant.

These vesicles disrupt AmI cell walls, effectively eliminating the competition. Moreover, the vesicles were found to stimulate AmII-specific immunoglobulin A (IgA) responses, further enhancing AmII colonisation within the host.

The findings indicate that certain A. muciniphila subtypes have evolved mechanisms to suppress rival subtypes using extracellular vesicles, thus compensating for metabolic disadvantages. This discovery represents a novel adaptive strategy among gut bacteria.

Dr Nam commented that the research, by clarifying competitive interactions among A. muciniphila clades based on Korean microbiome data, could support the design of precision nutritional interventions aimed at selectively modulating gut microbial composition.

For further reading please visit: 10.1038/s41467-025-57631-x