Helping Whole Biome Advance Microbiome Research

A main concern of any science team in the microbiome is being left behind technologically. In order to stay ahead of the competition, teams need to constantly be on the lookout for, and integrating, the newest tech. A person who understands the power of new tech more than most is Whole Biome’s founder and CEO, Dr. Colleen Cutcliffe. Loop sat down with Colleen to go over some of the things that her team are working on and how she has found Loop’s kits to be helpful.

Whole Biome is in many ways an original microbiome company (despite only being a 4 year old startup). Their founders were scientists from UC Berkeley, Harvard and Johns Hopkins who worked together at PacBio and saw an opportunity to make a platform technology to analyze human gut microbiome samples to find clinically relevant insights. “The mission of the company is to improve people’s health through microbiome intervention,” said Colleen. By all means, the Whole Biome team is onto some amazing insights with products currently in clinical trial with hopes of selling products directly to patients.

However, they understand the shortcomings of the traditional characterization methods for microbiome - short read, single variable region 16S data. “The problem is that it turns out [the 16S variable regions] are actually not so variable,” she said. “You can get a sequence of that which actually matches to a whole bunch of different strains. People are starting to realize, you can’t actually get a very accurate classification.”

What Colleen appreciates about LoopSeq is the departure from dependency on just one variable region and entering an era of full length 16S. “Full length gives you a better ability to classify because now if just that V1 region looks the same [as another microbe], the chances of the V1 region and the V4 region looking exactly the same is much less.” Given that Loop provides all the variable regions, the probability of having V1-V9 identical and being different species is right next to zero.

Accurate classification can mean the difference between having a pipeline that will lead to a clinical insight and one that doesn’t. “When you’re trying to really understand what are the small differences in somebody’s microbiome, you need tools in place that help you get clarity at a high resolution, and also high specificity of what those different microbes are.” So if the data leads to mischaracterization of the species present, then it can lead a team in the wrong direction. Having the right analysis tools can mean greater success. “My hope is that the quality of [Loop’s] data will enable us to be very precise, and specific about the kinds of interventions that we’d all develop.”

Some companies might be a bit hesitant to bring on new technology, given they have an established pipeline. But at Whole Biome, Colleen and her team understand that staying ahead is what makes them different. “LoopSeq and Whole Biome see a world in which the next step is going to be wanting more comprehensive information. And there are no other sample prep / analytic products out there today that give you better data quality than LoopSeq.”

Whole Biome and Loop are excited about the future of microbiome research and the potential of full length 16S. The newest technology will push their team to more meaningful insights and success.

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