Diversity matters, so does redundancy. Functional redundancy (FR) - the difference between taxonomic and functional diversity, describes the extent to which taxonomically distinct organisms can contribute to ecosystem functioning in similar ways.

FR has been shown to be a common event in the human gut microbiome. However, most previous studies of FR in the human microbiome have been conceptual rather than quantitative. The recent advances in deep metaproteomic techniques allow us to construct a protein-content network of human gut microbiomes and quantify the FR on the proteome level (i.e. FR_p).

What does the FR_p metric imply? A decrease in FR_p may be associated with impaired microbiome stability and resilience. We show that naturally occurring protein-content network of gut microbiomes can preserve high taxonomic richness and high FR_p at the same time, while environmental factors such as specific xenobiotics (e.g. antibiotics) and inflammatory bowel disease can significantly decrease the FR_p of an individual’s microbiome.

We still have not fully understood the phenomenon of high FR_p in our gut microbiome. What does it look like in some other diseases? How does it relate to the resistance and resilience of our microbiota? Can we leverage FR_p to combat gut microbiome dysbiosis and diseases? Metaproteomics will continue to facilitate these exciting future explorations, since it opens the door to deepening the understanding of our microbiome functional ecology by examining the proteins – the implementers of microbiome functions.