These microbiome insights are brought to you by Dr. Peter Christey of GALT, Inc., and Arrowhead Publishers. Dr. Christey will be presenting "Driving the Tidal Wave of Microbiome Discovery - a Next Generation Platform for Exploring the Microbiome" at Arrowhead's 4th Annual Translational Microbiome Conference, 18th-20th April, 2018.
I so much enjoy microbiome meetings and continue to be blown away by the speed at which the field is developing and the innovative work being presented. However, there is a sense of frustration with many of the presentations and publications we see in the literature. You would have seen them - studies where samples are taken from healthy patients, samples are taken from diseased patients, next generation sequencing of the microbiome is performed and the results are compared. We get shown lots of charts showing that population x goes up, population y goes down. Then of course PCoA and other statistical charts are presented to demonstrate some point or other. All during the presentation I'm waiting for the punch-line, the insight that helps me understand what is going on. What is the microbiome doing? Who are the key actors? How are they impacting the disease state? What is the underlying biology, chemistry here? Data and insights that quench my curiosity. But no, the presentation ends once the sequencing data analysis is complete - we are left with that empty feeling that something is going on, but it is beyond our ability to understand.
Sequencing is an incredibly powerful tool that has helped illuminate the wonderful complexity and richness of the microbiome. It's one of the few, if not the only, research tools we currently have that scales to the complexity of the microbial systems we are studying. But is it enough? I feel we are doing the equivalent of trying to cure cancer solely by sequencing a million tumor samples. Cancer is being defeated by insights derived from multiple avenues of investigation, including clinical trials, epidemiological data, analysis of the underlying genetics and, critically, wet lab work dissecting the core biological mechanisms and pathways. Wet lab work is critical to test hypotheses and new ideas under controlled conditions - the path to getting from correlation to mechanism. Then we can seriously develop informed interventions to improve the human condition.
Microbiome wet lab work is constrained by the current toolset. Mainstream microbiology technologies were invented over 100 years ago. Core tasks, such as isolating target microbes, creating comprehensive strain collections or studying model ecosystems, are often difficult or impractical. We need new tools to drive microbiome research to the next level.