Behind the Cultures
Cultivating Anaerobic Insights with Compact Microplate Readers
A behind-the-scenes look at how the paper “Cultivating efficiency: high-throughput growth analysis of anaerobic bacteria in compact microplate readers” came to be!
In the Summer of 2021, I took on the task of generating growth curve data for over 100 strains of anaerobic bacteria from the mouse gut microbiome. I had just moved back to the US from Sweden to start a new position as a Research Scientist in the Carini Lab at the University of Arizona. The prospect of collecting optical density (OD=600) data for dozens of gut microbes sans oxygen, was almost as challenging as the 112°F Sonoran Desert heat!
I found myself trying to think of how to generate growth curves without cramming a huge standard-sized plate reader into our anaerobic chamber. Even though our COY chamber is a “double-wide” model and affectionately named Big Ben, it would still be a tight fit to put a normal-size plate reader inside! In my desperation to find a simpler solution, I sent out an SOS to the trusty Twitterverse asking if any of my fellow microbiologist tweeps had any ideas. In less than a day, Professor Rita Tamayo of the University of North Carolina, Chapel Hill, messaged me about her recent success with compact plate readers from Cerillo. It was a eureka moment of sorts, demonstrating the power of social media in fostering scientific collaboration and innovation. Within days we had ordered two of the Stratus microplate readers. Finding accompanying tiny plate shakers that fit in the standard COY incubator was a bit more challenging. The issue was the depth of the incubator was quite shallow, and most plate shakers would not fit. Eventually after some trial and error, we found the perfect match and we were off to the races. Please don’t let anyone tell you that Twitter (X) does not have its uses!
In the world of anaerobic microbiology, researchers often find themselves sweating away in enclosed glove boxes while painstakingly working to maintain sterility. This was certainly the case for two members of the team behind our recent study that developed a workflow for Cerillo's Stratus compact microplate readers.
Our findings were published in Microbiology Spectrum: “Cultivating efficiency: high-throughput growth analysis of anaerobic bacteria in compact microplate readers.” We demonstrated that the Stratus performs as well as standard microplate readers but with the added flexibility of operation inside the confines of an anaerobic chamber. “Working in the anaerobic chamber is tight, and we were constantly worried about contaminating our cultures,” recalls our tenacious undergraduate researcher, Makaela Valencia. “I also have short arms, so I had to get creative and use these super large forceps to reach some things in there!” she says, laughing. A huge fan placed at just the right angle also alleviated our rivers of face sweat and the steaming up of my glasses.
But what motivated us to pursue anaerobic microplate reader validation in the first place? Our goal was to simplify the lives of researchers, like ourselves, who study strict anaerobes. These compact plate readers, aside from being very cute, allow us to perform high throughput growth experiments in an anaerobic chamber. This avoids the hassle of collecting subsamples for OD readings, transporting them out of the chamber to be read in a standard plate reader. Beyond increasing convenience, our work has important implications for advancing our understanding of the anaerobic microbial world - from microbiomes to environmental systems. Being able to efficiently cultivate and monitor the growth of anaerobic isolates in parallel is a real boon for high throughput microbiology and opens avenues for new insights into things like gut microbiome dynamics, biogeochemical cycling of toxins like arsenic and mercury in anoxic ecosystems, syntrophic interactions of anaerobic microbes and much more.
As challenging as our hands-on research was at times, we validated our approach as a new tool for anaerobic cultivation workflows. We had to get pretty creative at points, for example finding ways to maximize our limited space by stacking reservoirs and tubes and using forceps fit for a giant, but in the end, we’re proud to have overcome the obstacles and to establish this capability for our lab and the field. From sweating it out in the chamber to transforming anaerobic cultivation studies, we hope that this behind-the-paper story showcases the work and perseverance that propels scientific advances. We are proud of our team’s published paper, but perhaps more importantly, behind its pages lies a journey of problem-solving, camaraderie, and fastidious dedication to life without oxygen; after all, as Ralphe S. Wolfe famously opined: Study of obligate anaerobes continually provides that extra challenge for all procedures, but for some of us, challenge is what it is all about (Wolfe 1999).
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