Researchers at the University of Virginia and their collaborators, however, have devised a way to understand not just what is happening but why. By combining cutting-edge computer modeling with old-fashioned laboratory legwork, they have developed a crystal ball to predict how microorganisms will interact and the ripple effects those interactions will have. It’s only by understanding this that scientists can hope to manipulate the microbiota, as the organisms are collectively known, to cure disease and improve human health. The new approach developed by the team will change that. Researcher Jason Papin, PhD, stated: “Over the last several years, we have come to appreciate that bacteria living in and on us are critical for a lot of healthy functions. But is far more we don’t know than we do know. Too often, scientists find themselves groping around in the dark, especially when they try to engineer the microbiome to benefit health. Most of what we see is very correlative. We see the presence of the bacteria; what has really been lacking are the actual mechanisms”.
Papin and a PhD student in his lab, Greg Medlock, wanted concrete information: What molecules are being produced by particular bacteria? Which bacteria are then using those molecules? What are the ultimate effects on the populations of different bacteria? The challenge was finding those answers in a system so vast and complex. The solution was starting small; in simple words, you kind of have to take a step back. First Medlock looked at six species of bacteria individually. Then he looked at their interactions in pairs – 15 pairs in total. With this data, the researchers were able to develop a computer simulation. The goal was to be able to predict what would happen: As the different species were grown together, would the molecules they produce and consume match up with what was expected? How would these interactions affect the populations of each species? The researchers then returned to the bench to validate their predictions. The result was hard data that is among the first of its kind, shedding light on the inner workings of the microbiome.
But the importance of the research isn’t just in the findings but in the approach the scientists have created. They call it an “experimental and computational pipeline” and it opens the door to fast, factual research examining many different aspects of the microbiome. The actual research of the team started in 2015 with the publications of several papers until nowadays (almost 10), which concentrated efforts on deciphering how bacterial strains interact metabolically. The have been able to witness how certain metabolites are produced by some strains and actively capitated by others; a sort of “metabolic communication” that could potentially be responsible for the actual human health as it is. In many diseases, infact, there have been accumulating data on the radical changes of microbiota. If some strains are lost and other bacterial strains do not benefit of their presence, this would radically upset the bacterial community. This means that the onset of many human diseases would really find their roots in our guts.
That will have tremendous benefits in the quest to manipulate the microbiome to improve human health. It actually goes beyond personalized medicine, since the earlier understanding of how the “gut citizens” interact each other, would reveal precious data about their behavior, metabolic need and rates of proliferation and capability to maintain health homeostasis. It is like to take continuous “pics” of diaily activities from a satellite, exactly as it happens in the real life. Or, even better, like to hack the bacterial e-mails in order to “spy” regular and unknown intentions of the “citizen” themselves. Since already this happens in the “bigger universe”, scientists performed a “micro-scaled” version of bacterial “Big Brother”. Nothing entertaining for the regular people, that’s for sure, but scientists have their own way to entertain themselves. In the meantime, like psychologists, they acquire information form these “gut citizens” in order to apply intels to the “big folk” counterpart. After all, they came earlier than us and since our health relies on them a lot, these neighbors deserve our “understanding”: in their all possible meanings.
- edited by Dr. Gianfrancesco Cormaci, PhD, specialist in Clinical Biochemistry.
Scientific references
Medlock GL et al. Cell Syst. 2018 Sep 26; 7(3):245-57.
Nussinov R, Papin JA. PLoS Comput Biol. 2017; 13(9).
Liu A et al. PLoS One. 2017 Mar 20; 12(3): e0164919.
Biggs MB et al., Papin JA. ISME J. 2017; 11(2):426-438.
Biggs MB, Papin JA. Bioinformatics. 2016; 32(6):867-74.
Steinway SN et al. PLoS Comput Biol. 2015 Jun 23;11(5).