Empowering the first truly planetary-scale tracking of gene flow and antimicrobial resistance through NFDI4Microbiota’s FAIRification efforts

The extensive use of the NFDI4microbiota’s co-funded & co-developed tools metaTraits und Metalog have enabled high-impact, planetary-scale microbiome research on gene flow and antimicrobial resistance.

Learn more about the research and the use of these tools in the publication of

Chan Yeong Kim, Daniel Podlesny, Jonas Schiller, Supriya Khedkar, Anthony Fullam, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Anastasiia Grekova, Michael Kuhn, Peer Bork, “Planetary microbiome structure and generalist-driven gene flow across disparate habitats”, Cell, 2026, https://doi.org/10.1016/j.cell.2025.12.051.

Highlights include:

• Species-based clustering of >85,000 global metagenomes delineates 40 microbial habitat types
• Host and environmental filtering shape planetary microbiome structure
• Generalists facilitate horizontal gene flow across ecologically disparate habitats
• Anthropogenic habitats drive generalist-mediated resistance gene spread

As the abstract states:

Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.