In November 2014 I found myself drenched in rainwater at the Humacao Nature Reserve collecting soil samples—well, more like mud samples. It was my first morning in Puerto Rico and it had been raining since my arrival. But the University of Puerto Rico students accompanying me were determined to fill their conical tubes with soil, at all costs. Our goal: to discover new antibiotic producers in the soil.
It has been known for decades that soil bacteria produce an incredible array of useful molecules, from fluorescent pigments to enzymes used in detergents to some of the drugs in our medicine cabinets. In fact, more than 70% of the antibiotics we use today originated in the soil. After billions of years of evolution, microbes have figured out clever ways to compete and interact with one another to survive in this complex ecosystem. Grown in a laboratory medium, one bacterial cell reproduces and rapidly spreads across the entire surface of the Petri dish. Yet in the soil, bacteria exist in an intricate balance that microbiologists are only beginning to understand.
The antibiotics crisis
Many antibiotics available today are no longer effective against microbes that have evolved to evade and resist them. This leaves clinicians with fewer and fewer options for treatment. In an effort to revolutionize science education and address the antibiotics crisis, Yale launched the Small World Initiative in 2013. The program offers college students the opportunity to conduct their own research. It aims to promote the recovery of bacteria that produce antibiotics and the study of candidates for new antibiotics more in depth.
At the beginning of the course, students obtain one gram of soil from their surroundings, whether they are in the rainforests of Belize or the marshlands of England. Over the course of the semester, they perform a series of simple experiments to isolate diverse bacteria and characterize those that could be suitable antibiotics. To assess which bacteria have antibiotic potential, students grow them in close contact with safe relatives of some of the most threatening human pathogens, such as Methicillin-resistant Staphylococcus aureus (MRSA), and Acinetobacter baumannii, a common cause of hospital-acquired infections in Puerto Rico. These antibiotic-resistant pathogens are becoming increasingly difficult to treat, making simple surgeries and skin infections just as deadly as they were a hundred years ago, before the age of “miracle drugs.”
Crowdsourcing antibiotic discovery
A few years ago, Jo Handelsman, a microbiology professor at Yale University, currently on leave as science advisor at the White House’s Office of Science and Technology Policy, introduced the idea of “crowdsourcing” antibiotic discovery with college students across the world. In fall 2012, the idea started out small with the “Microbes to Molecules” course at Yale’s Department of Molecular, Cellular and Developmental Biology. After taking the course, students reported being more intellectually stimulated and motivated to pursue science. Moreover, three of six students went on to continue doing research in the summer and one worked on solving the structure of a novel antimicrobial compound. This led to the creation of Small World Initiative – Crowdsourcing Antibiotic Discovery, which was envisioned as a multi-institutional collaborative between instructors and students working towards the same goal.
Over the next year, former postdoctoral associate and microbiologist Tiffany Tsang brought the initiative to reality, building the academic and research infrastructure, as well as the professional network to expand it beyond Yale. I had recently received a B.S. in biology from Dickinson College and worked with Tiffany to develop research protocols and draft all the teaching and research materials needed to run the course.
We trained 25 instructors from universities all over the country in 2013, and the outcome was amazing: 1,000 students around the United States took the course, and many continued to study their antibiotic producers in the hopes of unraveling novel compounds. This first group of professors, the Pilot Partners, helped us train and mentor the next generation of Small World Initiative partners, which now include two institutions in Puerto Rico, as well as institutions in Belize, Malaysia, the UK, and Canada.
Bringing small world initiative to Puerto Rico
It was at the Small World Initiative 2014 summer workshop where I met biology professor Lilliam Casillas Martinez from the University of Puerto Rico – Humacao. Being the only Latinos in the group, we immediately clicked. At the end of the weeklong workshop, she invited me to hold a similar session for her students at Humacao.
I was thrilled to finally visit “La Isla del Encanto.” It was my first time there, even though I had spent nearly half of my life in the neighboring Dominican Republic. Surprised by the wondrous chorus of the coquí frogs that November morning, I was welcomed into a microbiology lab by about a dozen undergraduate students anxious to start this adventure.
Later that day, at the Humacao Nature Reserve, the torrential rain led us to take cover under the canopy of endemic trees. Dr. Casillas pointed at a massive ceiba, and the students huddled around the ancient tree, interested in the microbes associated with its bark and roots. Other students collected soil surrounding a saline pond where they suspected they would acquire anaerobic bacteria.
This was unlike any other sampling experience I had ever had. Back in New Haven, Connecticut, our students rarely worry about collecting under rain but are often had to dig through ice and snow. Despite the new environment and different people in Puerto Rico, some things were very familiar. Just as I had back in New Haven, I watched the students realize that the samples in their hands were not just “dirt”; I saw them come to appreciate that the soil they held contained biological and chemical diversity that could help us one day combat antibiotic resistance.
Over the next couple of days, we diluted the samples in pure water and transferred them to Petri dishes filled with bacterial food—called media—in the lab, and allowed them to grow overnight. One of the students placed leaves and slices of roots directly on the surface of the media in order to grow plant-associated microbes. Another sprinkled soil particles directly on the Petri dish.
Though there was not enough time to test all of the unique isolates and screen them against all the panels of clinically relevant microorganisms, the group was able to observe the great biodiversity of their local soils and store promising bacteria for future testing. In the end, this workshop turned out to be what many students hope their laboratory courses could be: fun, stimulating, interactive, and transformative, changing the way they look and appreciate at the world beneath their feet.
Later this spring, the Small World Initiative will be holding its second annual student symposium at the American Society for Microbiology’s Conference for Undergraduate Education, in Austin, Texas.
Simon A. Hernandez is a Postgraduate Associate in Jo Handelsman’s Lab at Yale University and the Center for Teaching and Learning, Communications Manager of the Small World Initiative (www.smallworldinitiative.org), and a contributor to Ciencia Puerto Rico (www.cienciapr.org). Contact him at firstname.lastname@example.org.
This story was published in Puerto Rico’s newspaper El Nuevo Dia on March 9, 2015, page 41. You can read it in Spanish here.