Researchers have unlocked the genetic secrets of soil’s hidden bacteria, discovering hundreds of previously unknown genomes and two promising new antibiotics.
Most bacteria cannot be cultured in the lab – and that has been a big hurdle for medicine. Many of our frontline antibiotics originated from microbes, yet as antibiotic resistance spreads and drug pipelines run dry, the earth’s soil is a vast hidden reservoir of untapped compounds.
Now, researchers at Rockefeller University have developed a way to access this microbial goldmine. Their approach, published in Nature Biotechnology, bypasses the need to grow bacteria in the lab by extracting very large DNA fragments directly from soil. This can then piece together the genomes of previously hidden microbes – and then mine resulting genomes for bioactive molecules.
From a single forest sample, the team generated hundreds of complete bacterial genomes never seen before, as well as two new antibiotic leads. The findings offer a scalable way to find unculturable bacteria for new drug leads – and expose the uncharted microbial world contained within the soil.
“We finally have the technology to see the microbial world that have been previously inaccessible to humans,” says Sean F. Brady, head of the Laboratory of Genetically Encoded Small Molecules at Rockefeller. “And we’re not just seeing this information; we’re already turning it into potentially useful antibiotics. This is just the tip of the spear.”
Soil: a treasure trove of microbes
When looking for bacteria, soil is an obvious choice. It’s the largest, most biodiverse reservoir of bacteria on the planet – a single teaspoon may contain thousands of different species. Many important therapeutics, including most of our antibiotic arsenal, were discovered in the tiny portion of soil bacteria that can be grown in the laboratory.
When looking for bacteria, soil is an obvious choice. It’s the largest, most biodiverse reservoir of bacteria on the planet
We still know very little about the millions of microbes packed into the earth. Scientists suspect that these hidden bacteria hold not only an unexplored opportunity for new therapeutics but also clues as to how microbes shape climate, agriculture and the larger environment.
“All over the world there’s this hidden ecosystem of microbes that could have dramatic effects on our lives,” Brady adds. “We wanted to finally see them.”
To find bioactive molecules with the potential to become new drugs less prone to antibiotic resistance, the researchers sequenced bacterial DNA extracted from soils from Rockefeller’s field center in upstate New York. Credit: Laboratory of Genetically Encoded Small Molecules at The Rockefeller University
A new approach to ancient soil
Getting that glimpse involved combining several approaches. First, the team optimised a method for isolating large, high-quality DNA fragments directly from soil. Pairing this with emerging long-read nanopore sequencing gave the researchers continuous stretches of DNA that were tens of thousands of base pairs long – 200 times longer than any previously existing technology could manage.
“It’s easier to assemble a whole genome out of bigger pieces of DNA, rather than the millions of tiny snippets that were available before,” Brady says. “And that makes a dramatic difference in your confidence in your results.”
Unique small molecules, like antibiotics, that bacteria produce are called ‘natural products.’ To convert the newly found sequences into bioactive molecules, the team applied a synthetic bioinformatic natural products (synBNP) approach. They bioinformatically predicted the chemical structures of natural products directly from the genome data and then chemically synthesised them in the lab. With the synBNP approach, the team managed to turn the genetic blueprints from uncultured bacteria into actual molecules – including two potent antibiotics.
Brady describes the method, which is scalable and can be adapted to virtually any metagenomic space beyond soil, as a three-step strategy that could kick off a new era of microbiology.
Two new antibiotic leads
Applied to their single forest soil sample, the team’s approach produced 2.5 terabase-pairs of sequence data – the deepest long-read exploration of a single soil sample to date. Their analysis discovered hundreds of complete contiguous bacterial genomes, more than 99 percent of which were entirely new to science and identified members from 16 major branches of the bacterial family tree.
The two lead compounds discovered could translate into potent antibiotics.
The two lead compounds discovered could translate into potent antibiotics. One, called erutacidin, disrupts bacterial membranes through an uncommon interaction with the lipid cardiolipin and is effective against even the most challenging drug-resistant bacteria. The other, trigintamicin, acts on a protein-unfolding motor known as ClpX – a rare antibacterial target.
Brady emphasises that these discoveries are only the start. The study demonstrates that previously inaccessible microbial genomes can now be decoded and mined for bioactive molecules at scale without culturing the organisms. Unlocking the genetic potential of microbial dark matter may also provide new insights into the hidden microbial networks that sustain ecosystems.
“We’re mainly interested in small molecules as therapeutics, but there are applications beyond medicine,” Burian says. “Studying culturable bacteria led to advances that helped shape the modern world and finally seeing and accessing the uncultured majority will drive a new generation of discovery.”