“Unlocking the Unknown: Study Reveals 42% of Bacteria Remain Genomic Mysteries”

Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility situated at Berkeley Laboratory, have released a research paper in Science Advances that examines the present condition of microbial genomic diversity. Utilizing genome sequence data accessible to the public, gathered over the last thirty years, their research evaluates what proportion of the microbial diversity is recognized, proposing a pathway towards curating and nurturing what remains unexplored.

“We conducted an in-depth analysis of more than 1.8 million bacterial and archaeal genomes to determine how much of their diversity we’ve actually documented,” stated co-first author Dongying Wu, a contributor to the Functional Annotation team within the JGI’s Microbiome Data Science group. “It turns out that despite all the genomes we’ve sequenced, we’ve only just begun to scratch the surface.”

The investigation, emphasized co-first author Rekha Seshadri, serves as a clarion call to revive the practice of hands-on microbiology and experimental confirmation.

Microorganisms substantially influence the planet, playing crucial roles in overseeing global nutrient cycles. Insights gained from recognizing the interactions between microbes, hosts, and their surroundings could be beneficial to numerous fields of research such as agriculture, biofuels, bioproducts, and medicine. Sifting through three decades of sequencing data, the team consisting of Wu, Seshadri, Nikos Kyrpides, and Natalia Ivanova conducted a survey of publicly accessible bacterial and archaeal sequences. Kyrpides leads the JGI’s Microbiome Data Science group, while Ivanova directs the Functional Annotation team.

MAGs notably increased the projected diversity of Bacteria and Archaea

Using phylogenetic diversity as a proxy for biodiversity, they employed five universally conserved, protein-coding marker genes across nearly 2 million genomes, including isolates, metagenome-assembled genomes (MAGs) with different quality ratings identifying potential genomes, and almost 44,000 metagenomes. All of the information is publicly accessible in the National Center for Biotechnology Information (NCBI) GenBank collection and on the JGI’s Integrated Microbial Genomes & Microbiomes (IMG/M) database.

From their analysis, the group discovered that bacterial isolate genomes account for 9.73% of the complete estimated diversity within the available datasets. Initiatives to recover MAGs by directly extracting data from environmental specimens over the years have substantially broadened the known diversity of microbial genomes, representing nearly 49% of the estimated bacterial variety. The team conservatively assessed that approximately 42% of the bacterial diversity lacks genomic representation in public databases.

Over the last several decades, improvements in sequencing technologies have resulted in a wealth of microbial genomes being made available to the global research community. In a comparable evaluation for Archaea, the team uncovered that isolate genomes contribute a mere 6.55% while MAGs comprise about 57% of the estimated diversity within the accessible datasets. This leaves 36% of archaeal diversity without genomic documentation.

“Regarding isolate genome data, our real-world reference points, we are merely scratching the proverbial Petri dish,” Seshadri remarked. “It’s a reminder of the urgent need to cultivate new microbial species.”

Focused Investigations for Comprehending the Microbial Realm

The corresponding author Ivanova stated that the JGI continues to advance towards enhancing genomic representation of bacterial and archaeal diversity, illuminating the unexplored microbial realm. Although MAGs have significantly broadened the known variety of microbial genomes in the datasets, the team notes that this information remains computationally derived. Experimental investigations on cultivated isolates are essential to translate potential implications into practical science, contributing towards a sustainable bioeconomy.

“While computationally derived MAGs have emerged as a groundbreaking tool for microbiology, it’s a call for equilibrium,” added Seshadri. She emphasized that the metagenomic datasets utilized in this study could assist researchers in improving their success rate in recovering specific isolate species for culture. “We’ve outlined the treasure map,” she remarked. “Essentially, we can direct attention to environmental samples where researchers can invest time and effort in recovery.”