A massive nationwide effort led by Johns Hopkins University geneticists is cataloging the soil microbiome across the United States, revealing more than 1,000 new bacterial strains and previously unknown microbes. The BioDiversity and Informatics for Genomics Scholars (BioDIGS) consortium taps advanced DNA-analysis technology, particularly long-read sequencing, to probe the genetic makeup of soil microorganisms. As Michael Schatz, senior author of the paper published in Nature Genetics, notes, “This scientific void we’re trying to fill on microbial diversity could only be accomplished by having this network of scientists and students across the United States.”
The project involves about 150 researchers from more than 40 sites, including many students, who analyze soil for genetic relationships linking microbes, environments, and human health. Long-read sequencing enables the team to identify patterns in the microbial “dark matter,” an estimated 99% of soil microorganisms that remain unstudied. “The soil is the most biologically active environment on the planet, yet we’ve sampled only a tiny fraction of the life that lives inside it,” Schatz explains.
BioDIGS builds on efforts like the MetaSUB Consortium, which studied urban subway microbes globally, but focuses on soil’s vast biodiversity, home to millions of bacteria, archaea, bacteriophages, and other species critical to ecological functions and antimicrobial resistance. Students play a central role, not just in gathering samples but in building reference genomes, scanning sequences, and identifying genes. “Students can be very sophisticated data scientists,” Schatz says. “They were involved with sample collection and now we’re leaning on them to help build out the reference genomes of the microbes, to scan and ID genes—everything.”
The consortium strengthens genetics education at participating institutions, with over 100 student researchers already contributing and more expected as the work grows. At United Tribes Technical College in North Dakota, research faculty member Emily Biggane highlights how BioDIGS engages students with their local land: “Our students have a deep connection to the land and this project offered an opportunity to explore the properties of something celebrated and honored.” By expanding access to genomics tools and training, the project fosters the next generation of scientists while illuminating soil’s hidden microbial world.
The project involves about 150 researchers from more than 40 sites, including many students, who analyze soil for genetic relationships linking microbes, environments, and human health. Long-read sequencing enables the team to identify patterns in the microbial “dark matter,” an estimated 99% of soil microorganisms that remain unstudied. “The soil is the most biologically active environment on the planet, yet we’ve sampled only a tiny fraction of the life that lives inside it,” Schatz explains.
BioDIGS builds on efforts like the MetaSUB Consortium, which studied urban subway microbes globally, but focuses on soil’s vast biodiversity, home to millions of bacteria, archaea, bacteriophages, and other species critical to ecological functions and antimicrobial resistance. Students play a central role, not just in gathering samples but in building reference genomes, scanning sequences, and identifying genes. “Students can be very sophisticated data scientists,” Schatz says. “They were involved with sample collection and now we’re leaning on them to help build out the reference genomes of the microbes, to scan and ID genes—everything.”
The consortium strengthens genetics education at participating institutions, with over 100 student researchers already contributing and more expected as the work grows. At United Tribes Technical College in North Dakota, research faculty member Emily Biggane highlights how BioDIGS engages students with their local land: “Our students have a deep connection to the land and this project offered an opportunity to explore the properties of something celebrated and honored.” By expanding access to genomics tools and training, the project fosters the next generation of scientists while illuminating soil’s hidden microbial world.