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Sequencing the Soil Microbiome 20 Years after the Human Genome Project

In April 2003, scientists announced the completion of an international, highly collaborative effort that took 13 years to complete and cost almost $3 billion: the Human Genome Project. The goal was to sequence the human genome—the DNA blueprint that contains the necessary information to “build” a human.

The famous double-helix structure of the molecule was published in Nature just 50 years prior, in April 1953, thanks to work done by Dr. Rosalind Franklin. Setting out to sequence the full human genome was a groundbreaking venture with impacts in fundamental genetics research, biological data sharing, and how scientists work together on large-scale projects.

In the 20 years since, DNA sequencing has entered public awareness with applications to human health, ancestry, and criminal forensics. This has been made possible by incredible advances in DNA sequencing technology that have made it dramatically cheaper, faster, and more accessible to applications outside of scientific research. This new type of sequencing is called Next Generation Sequencing (NGS); today’s NGS market was valued at $6.37 billion in 2021 and is projected to grow to $24.48 billion by 2030. Today with NGS, a human genome can be sequenced for less than $1000, with new startup Ultima Genomics promising a cost of less than $100

Shortly after the Human Genome Project was completed, Poornima Parameswaran was starting her Ph.D. at Stanford University and was inspired by the potential of DNA sequencing, especially for the field of microbiology. Similar to the Human Genome Project, scientists can do Whole Genome Sequencing (WGS) of any organism. By looking at their DNA sequences, we are able to differentiate microorganisms that may look identical under a microscope or on a petri dish. Bolstered by the development of NGS technology, scientists started sequencing entire communities of microorganisms at once—a process called metagenomics.

This spark of inspiration pushed Dr. Parameswaran’s career, ultimately leading her to co-found Trace Genomics in 2015 with fellow Stanford alumna, Dr. Diane Wu. With the power of DNA sequencers made by market-leader Illumina, Trace analyzes the soil microbiome through metagenomics and translates the information into actionable insights that can be used for measuring soil health, making decisions on soil fertility, pathogen management, and more. 

Today at Trace, our team of genomics R&D scientists are developing innovative methods to decrease the cost and turnaround time of delivering metagenomics data to customers without compromising scientific accuracy. Thanks to innovations in DNA sequencing made during the Human Genome Project, Trace is standing on the shoulders of giants to apply sequencing technology to sustainable practices in agriculture for a better world.

About the author: Dr. Tuesday Simmons is the Science Writer at Trace Genomics. She earned her Ph.D. in Microbiology from the University of California, Berkeley, studying the root microbiome of cereal crops.