HMN 2025: How Genomes of 24,000 previously unknown microbes are revealed by new tools

QUT researchers have recovered the genomes of more than 24,000 previously unknown microbial species—some from entirely new branches of life that likely evolved before plants and animals. The microbes are detailed in two studies published in Nature Biotechnology and Nature Methods.

Associate Professor Ben Woodcroft, from QUT’s Center for Microbiome Research and School of Biomedical Sciences, based at Brisbane’s Translational Research Institute said microbial communities of bacteria and archaea played vital roles in supporting all life on Earth.

“We know gut microbes are essential for digestion and health, but microbes are just as important in the broader environment—from supporting plant growth in soils to producing the oxygen we breathe in oceans,” Professor Woodcroft said. “Despite decades of research, more than 99% of microbial species remain unknown.

Metagenomics and the search for new life

“A key tool in our toolbox for finding new microbial life is ‘metagenomics,’ where DNA sequence data is extracted directly from environmental samples. The process is very useful because it can be applied almost anywhere in any environment. The challenge lies in processing the data, piecing together the short pieces of DNA we get from metagenomics into full genomes.

“To help close this gap, we developed two software tools to identify and analyze unknown microbes in metagenomics data.”

The first tool, SingleM, quickly scans a microbial sample and identifies what organisms are present—including species that are extremely different from anything seen before. The team applied SingleM to more than 700,000 publicly available metagenomics datasets and found that about 75% of the cells in environmental samples belonged to unknown species.

New software tools uncover hidden species

The second tool, Bin Chicken, dives more deeply into promising samples to reconstruct full genomes from previously uncharacterized microbes.

Lead author and postdoctoral researcher Dr. Sam Aroney said Bin Chicken was affectionately named after the Australian white ibis that rummages through garbage bins for morsels of food, “similar to the way our tool rummages through publicly available metagenomic data.”

“Using Bin Chicken, we reconstructed 24,000 new microbial genomes, including several from entirely new branches of the tree of life,” Dr. Aroney said. “These lineages likely evolved before plants and animals and help us better understand life’s early evolution.”

Implications for climate, biotech and future research

Professor Woodcroft said this expanded genomic catalog was already revealing new insights into global ecosystems. “Microorganisms are central to climate change—they’re the largest producers of methane on Earth,” he said. “We’re now integrating these new genomes into climate modeling and evolutionary studies. They also have broad implications for biotech and health research.”

The research also provided opportunities for the next generation of scientists. QUT undergraduate Joshua Mitchell developed AI methods to predict sample characteristics, such as whether the microbes came from a human host, and has since started a Ph.D. to extend this work.

The full research team includes Associate Professor Woodcroft, Dr. Aroney, Rossen Zhao, Joshua Mitchell, Rizky Nurdiansyah, Dr. Rhys Newell, and Professor Gene Tyson from QUT; and Mitchell Cunningham and Professor Linda Blackall from the University of Melbourne.

The first study, “Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper,” published in Nature Biotechnology is accompanied by a dedicated website.

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