PASTEUR2030
Meteor2: A Major Advance in Multi‑Scale Mapping of the Microbiome
The Institut Pasteur and INRAE unveil an open‑source software that analyzes the intestinal, oral and skin microbiomes with unprecedented precision
A joint team from the Institut Pasteur and INRAE, working within the citizen‑science project Le French Gut, publishes today in Microbiome Meteor2, an open‑source software that redefines the standards of metagenomic analysis. In connection with the four Scientific Priorities of the Pasteur 2030 Strategic Plan, this integrated tool provides, for the first time, a simultaneous and fine‑grained characterization of microbial species, functions and strains, fully exploiting the potential of shotgun‑sequencing data.
The microbiome—especially the gut microbiome—is an extremely complex ecosystem composed of thousands of microorganisms, mainly bacteria, whose analysis remains difficult because of its diversity and the high proportion of non-cultivable bacteria. While shotgun sequencing now generates millions of DNA fragments, existing tools only exploit a single facet of the data: taxonomy, function, or strain diversity. This fragmented view limits our understanding of the precise roles of the microbiome in health. Meteor2 breaks these analytical silos by enabling a multifaceted characterization of the microbiome and its impact on host health.
Using ecosystem‑specific gene catalogues, Meteor2 profiles samples on three levels:
- Species abundances – precise detection, including low‑abundance species;
- Functional potential – metabolic capabilities at the level of the whole sample and of each individual species;
- Genetic variability of strains – identification of single‑nucleotide variants (SNVs) that separate strains and allow measurement of genetic distances between individuals.
All steps—from automatic download of the catalogues to generation of the profiles—are integrated into Meteor2, making it a simple‑to‑use, comprehensive tool that is accessible to any laboratory.
Benchmark tests show that Meteor2 outperforms the reference tools currently used by the scientific community, especially for detecting and quantifying low‑abundance species—an issue that becomes critical when sequencing depth is limited. This increased sensitivity opens new possibilities for large‑scale studies and clinical cohorts.
The current catalogues cover human microbiomes (intestinal, oral and skin) as well as the gut microbiomes of seven animal species used in research, companionship or farming (mouse, rat, cat, dog, chicken, rabbit, pig). These resources will be expanded as the needs of the scientific community evolve.