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Culturing the Microbiome: A Pain in the Petri Dish

How many times have you spent hours working in the biosafety cabinet, staring down an imposing stack of Petri dishes, streaking samples, and subculturing individual colonies in an attempt to isolate as many different bacterial species as possible—perhaps even find new microbes—from your microbiome samples?

You, like many scientists that rely on traditional isolation and cultivation methods, have likely spent countless hours and expended an untold number of Petri dishes in the quest to study the microbiome but these methods can’t keep up with the demands of microbiome analysis. Complex microbiome samples can contain thousands of bacterial species, and to further complicate this daunting task, many species may be difficult to isolate using typical culture methods, requiring considerable time and effort to generate enough isolates for further study.

Fortunately, there are tools available to help researchers automate and improve the efficiency of their microbial isolation and cultivation efforts.

Traditional Culture Methods: A Painful Process

Traditional, Petri dish isolation and cultivation methods have yielded important discoveries about our microbial neighbors, but this information has taken years to gather, in part, due to the extensive time it takes for some bacteria to grow. Different bacterial species have their own requirements for growth in culture and they tend to grow at different rates, making it difficult to isolate some species. The diversity of species isolated can be increased, however, with the use of multiple media, incubated under different environmental conditions.

Petri dish isolation methods are labor-intensive. Not only do you need to culture directly from the initial sample, but additional (sometimes multiple) subculture steps are required to isolate individual species. It takes a keen eye and a steady hand to separate similar-looking colonies onto individual Petri dishes to obtain pure cultures.

Days after inoculating the original Petri dishes, you may discover that fast-growing microbes have overtaken the plate, leaving no chance for slow-growing or rare species to emerge. The only hope for isolating these species is to dilute the original sample and plate it again, incubate it for days, and hope for the best.

Traditional culture methods cannot be easily scaled to support large microbiome studies or the isolation of bacterial strains from complex samples. In fact, it could take several scientists, hundreds of Petri dishes, multiple subculture events, and months to yield a large, diverse library of isolates.

Overall, traditional Petri dish culture methods are an inefficient system, generating a large amount of wasted media and disposable plastics while consuming precious lab space on the bench, in the biosafety cabinet, and inside laboratory incubators.

Imagine the amount of laboratory and analysis time you could gain if you could reduce the hours of tedious, hands-on time spent manipulating Petri dishes—and what that could mean for your microbiome research.

Automation Can Accelerate Discovery

Isolation Bio’s Prospector® is an automated solution that uses a high-throughput, live-cell cultivation array technology to accelerate microbial isolation and cultivation workflows.

Each array contains 6000+ nanoscale micro-wells, each capable of capturing a single bacterium and enabling the growth of thousands of micro-colonies in parallel. Isolate libraries resulting from one experiment on the Prospector® can equal the output of hundreds of Petri dishes. The Prospector® also replaces manual subculture manipulations by automating the detection of micro-well growth and the transfer of isolates into standard multi-well plates for further study.

The nanoscale micro-well technology enables the capture and cultivation of slow-growing and rare species that may be missed in Petri dish cultures, leading to faster isolation of diverse microbial libraries.

Further, with a compact footprint the Prospector® can be used on the bench, in a biosafety cabinet, or even inside an anaerobic chamber. Less wasted space and fewer consumables streamlines lab workflows.

Large microbiome studies, once limited by the Petri dish, can now be accelerated using modern, automation-driven isolation and cultivation techniques.

Learn how the Prospector® makes microbial isolation and cultivation fast and efficient.