Correction to: Nature Metabolism https://doi.org/10.1038/s42255-025-01220-1, published online 18 February 2025.

In the version of this article originally published, there were errors in the reporting of population and sample numbers. In the second paragraph of the “Decoy-aware, efficient mapping of food-derived sequences” section, in the sentence now reading “In brief, we generated an average abundance profile of the decoy organisms present in 365 faecal samples from a healthy population of 27 individuals,” the text originally referenced samples from 365 individuals. In the first paragraph of the “Applying MEDI to infant and adult stool metagenomes” section, in the sentence now reading “Adult reference samples were obtained from 365 samples in 27 healthy individuals,” the text originally referenced 351 individuals. In the first paragraph of the “iHMP Project inflammatory bowel disease data” section, in the sentence now reading “This yielded an average abundance profile for non-food-associated taxa in the human gut, representing the full diversity of the 365 samples from a healthy population of 27 healthy individuals,” the text originally referenced 365 individuals. The text has been updated in the HTML and PDF versions of the article.