Deciphering Microbial Mysteries

Some scientific breakthroughs happen with researchers crowded around a high-tech machine in a lab. Some discoveries are made deep in the rainforest, on the ocean floor, or high on a snowy mountaintop. For Basem Al-Shayeb, the moment that changed the course of his career happened in a wetland just a mile from his professor’s house in Northern California.

“We were just passing through on a hike, and Jill said ‘why don’t we take some samples from here,’” Al-Shayeb recalls of that day with his advisor, Jill Banfield, a professor in the Departments of Environmental Science, Policy, and Management, and Earth and Planetary Sciences.

Banfield is a pioneer in metagenomics, a relatively recent field of study that involves reconstructing the genomes of organisms found in natural environments. She and her team often search for samples in unusual places ranging from a hypersaline lake in Australia, to a geyser in Utah, to the gastrointestinal tracts of newborns in an intensive care unit. But on that day in 2017, the only high-tech sampling equipment on hand was a garden spade, which Al-Shayeb plunged deep into the good, clean, West Coast mud.

After scouring a large database of DNA generated from the samples taken that day, along with others the team collected from nearly 30 different Earth environments, Al-Shayeb and his colleagues found hundreds of unusually large, bacteria-killing viruses known as megaphages. The research is just one of many important projects that Al-Shayeb has been involved with during his time as a graduate student at UC Berkeley. Working in the labs of both Banfield and Jennifer Doudna—who shared the 2020 Nobel Prize in Chemistry for her work developing CRISPR, the revolutionary gene-editing tool—Al Shayeb is at the leading edge of one of science’s most exciting frontiers.

Little is known about megaphages so far. Banfield had published a paper in 2019 reporting a set of megaphages, and this new research, published in Nature in 2020, identified 351 of them in total. Through work in Doudna’s lab that was published in Science a few months later, Al-Shayeb was able to demonstrate that the megaphages’ CRISPR systems could be repurposed for gene editing. Although their genomes are hundreds of thousands of DNA letters long, the CRISPR systems of these megaphages are actually smaller than standard CRISPR tools, allowing them to be easily imported into cells, targeting specific regions of a genome in order to perform edits. Even more exciting is the fact that their CRISPR systems can be utilized in animal, plant, or bacterial cells, giving them massive potential for real-world applications in medicine, agriculture, and even the fight against climate change.

“I always wanted to know more,” says Al-Shayeb of his childhood in Egypt. Like a lot of parents of smart kids, his mom wanted him to go into medicine or engineering. “Even as I was taking the GRE, she kept telling me to take the MCAT, saying ‘Maybe you can change your mind later and go into medicine,’” he recalls. His mother’s worry was understandable, Al-Shayeb says, because they didn’t know anybody who had a PhD at the time. “I didn’t know that you could have a career in scientific research so it was kind of a risk for me to go more into biology than medicine.”

Al-Shayeb didn’t come to Berkeley with a specific intent of working with CRISPR. After deepening his passion for research as an undergraduate at the University of Minnesota, he was attracted to Berkeley’s interdisciplinary nature. As a graduate student in the Department of Plant and Microbial Biology (PMB), he began his studies on campus by rotating through various labs, eventually finding a place with both Dr. Banfield and Dr. Doudna. “In Jill’s lab there’s a lot of environmental microbiology and discovery, and in Jennifer’s lab we’re developing tools for biotechnological applications in cells,” he says.

Going back out to the field to follow up on his work with the megaphages, Al-Shayeb and his colleagues made yet another stunning discovery. What they found were exceptionally long strings of extrachromosomal material—up to a million DNA letters long—that seemed to assimilate genetic information from multiple different microbes. With an assist from Banfield’s son, they named their new find “Borgs” after the knowledge-devouring Star Trek characters.

After further study, they discovered that these Borgs could be incorporated into single-celled organisms called archaea, a group of microorganisms that include some of the greatest producers of methane, a greenhouse gas thirty times more potent than carbon dioxide. Some archaea also break down methane, and Al-Shayeb’s work suggested that Borgs could be used to “turbo-boost” archaea’s ability to do just that, potentially offering a powerful new weapon in the fight against climate change. “I haven’t been this excited about a discovery since CRISPR,” tweeted Banfield.

The Borg discovery was highlighted by Nature, Science, and many other news publications. While gene-editing technology is advancing rapidly, part of what motivates Al-Shayeb is how little is still known. Almost eighty percent of the Borg genome consists of proteins that are still completely unknown. The potential for real-world implications is vast, extending beyond methane capture to nitrogen fixation, which is crucial in agriculture and the quest to feed the world’s growing population.

Working with Al-Shayeb to understand what he calls “the dark matter on the genome” is PMB graduate student Luis Valentin-Alvarado, who also works in Banfield’s lab and accompanied them on some of those fateful trips to that unpromising muddy field. Valentin-Alvarado gets excited thinking about the new avenues he and his colleagues can explore. “There are so many questions to answer,” he says. “Can we harness the Borgs and find new ways to improve biotechnology? Can we find new genome editing tools? Can we puzzle out the role of these genomic elements in the evolution of microbial life? Can we look into these enzymes and discover novel chemistry?” His excitement is palpable. “You could do multiple PhDs on this. It’s endless!”

Both Al-Shayeb and Valentin-Alvarado exude an enthusiasm that is as infectious as it is wide-ranging. Like Al-Shayeb, Valentin-Alvarado didn’t expect to land at the center of one of science’s most exciting frontiers. Growing up in Puerto Rico, his first memory of being a scientist was looking at mold on bread and asking his mom what was happening there. “I was always question-driven; my mom would joke and say ‘can you please stop asking so many questions,’” he recalls. Also, like Al-Shayeb, nobody in Valentin-Alvarado’s family worked in the sciences, and he couldn’t even conceive of a career in research. But a high school science project on that moldy bread led him to the Intel Science Fair in San Francisco, and, many years later, to graduate school at Berkeley.

It’s a long way from Puerto Rico to Koshland Hall, but Valentin-Alvarado is still asking questions and figuring things out. “It’s funny, I came to Berkeley to work on bioinorganic chemistry, but I didn’t imagine ending up working on fascinating and collaborative projects involving new lineages of life or mobile genetic elements,” he says. “But I’m a scientist, not just a microbiologist or a chemist. I’m driven by questions, and if I have to learn something new, I’ll do that if it moves me closer to an answer.”

As far back as 2006, Banfield and Doudna frequently shared ideas about CRISPR, and the labs still work closely together today, advancing both the pure science and the practical applicability of their discoveries. Berkeley’s focus on collaboration and interdisciplinary work was not only a draw for both students, but also a key component of their effectiveness here. “Being in two labs feeds my innate curiosity and enables me to make discoveries,” says Al-Shayeb, “but we’re also able to develop technologies that can have a tremendous impact beyond one community.

As if Al-Shayeb isn’t busy enough, his far-ranging interests have recently led him to a side project doing early detection of COVID-19 by sampling wastewater. By sequencing the RNA they find in the sewage, he and his collaborators can determine which variants are surging and even identify the presence of previously undetected strains of the virus. Al-Shayeb also participated in a large-scale study of RNA viruses found in genome repositories around the globe, which was published in Nature in January.

Both Al-Shayeb and Valentin-Alvarado feel strongly about sharing their knowledge with others and about being the kind of scientific role models that they would have appreciated seeing when they were young. Al Shayeb—who was recently featured on the Forbes 30 Under 30 in Science list—translates scientific articles into Arabic and gives talks to young students, in part to help them imagine a future in research for themselves. Valentin-Alvarado talks to middle and high school students every chance he gets. “I want to tell them that you can do field work, you can get dirty and then come back with this cool data that you publish in high-impact journals,” he says.

Whether they find themselves in a muddy field or on the pages of Nature, both of these students have cemented their places as researchers on the leading edge of a world-altering field. When Al-Shayeb talks about life after he finishes his PhD, it’s clear that his experiences at Berkeley have helped instill a lifelong love of research and academia. “To me it’s very rewarding to be able to work on things that I know will help people both here and in the global population, whether it’s genetic diseases, or agriculture, or climate change. These are all things that I know can have a big impact everywhere. And to me, that’s the dream job.”