I Want You: Modelling Microbial Recruitment and Peer-Aiding Bacteria

Image courtesy of Marin Tomic.

Picture yourself sitting down for dinner, perhaps facing a steamy plate of shrimp fried rice. The food on your plate makes its way into your mouth, down your throat, and into your stomach, where it will eventually make its way down the rest of your digestive tract. Picking up your fork for more, it may seem like you are enjoying this delicious meal all alone. In truth, however, you are less alone than you might have thought. From head to toe, microbes are all around and even inside you. 

Microbes play vital roles in the consumption of your favorite dish. These communities of microbes benefit our digestion by keeping our mouths and digestive tracts healthy. Beyond that, they also ensure the food we eat properly develops in the ground long before it even ends up on our plate. In fact, microbes in the gut help process a plethora of complex molecules in our food and play a critical role in immune health and individual reactions to medications. With all these different microbes playing such a vast range of roles, it can be complicated to understand how these separate communities interact.

In a recently published study, Yale ecologists developed a framework for how microbial communities restructure when joined together, providing an understanding of a powerful effect that causes microbes to recruit partners during invasions in a fight for resources and survival. 

Though it can be challenging to visualize the importance of microbes, recent research has showcased an ever-increasing understanding of their role in health and human life. “Right now, we don’t really have a lot of tools to act on how these communities function and operate, but starting to understand how they assemble is the first step to understand how they function,” Juan Díaz-Colunga, first author of the study and postdoctoral associate at Yale, said. The Sanchez lab, where Díaz-Colunga works, is on the cutting edge of this research, helping to develop our understanding of how microbial communities assemble and change in structure. Since microbial health is critical to human health, this understanding is vital in the effort to create therapies that restructure microbial populations and help sick patients.

Their new paper uncovered that there are essentially two realms of microbial community coalescence. The first realm showcases that even a few key species can determine the outcomes of whole communities as they come together and interact. This phenomenon is known as “top-down co-selection” when dominant microbes can influence their partners in the same way a skillful soccer player might amid a team that includes a couple of younger players. Alternatively, the collection of interactions from less abundant species can alter the microbial community significantly. This alternative, known as “bottom-up co-selection,” is when less dominant microbes can determine the composition of their community in the same way that players who arrive earlier at the field – regardless of their level of experience – might get to choose who they want to include in their game. This creates an impactful change in the distribution of resources and determines which species survive. 

A better understanding of this process could be leveraged to engineer healthcare therapies, impact agriculture, food fermentation, and many other technological sectors. “On the single species level, we do have tools to do this,” Díaz-Colunga said. “Strategies like directed evolution allowed humans to select for specific traits and turn wolves into dogs.” 

Engineering microbial communities could increase agriculture yield and nutrition. In fact, it could be used to fortify the nutritional value of rice or to counter the presence of arsenic, which is created as a metabolic byproduct of certain microbes in rice. Seeing the diverse roles that microbes play, from our dinner plate to our gut, showcases all the future opportunities that microbial engineering will be able to impact. 

Although natural microbial communities have a high degree of complexity, analyzing the fundamental interactions of microbial species can allow us to understand how microbes may interact with a vast number of different communities and environmental conditions. This could help set a framework for new technologies and innovations based on microbial recruitment and peer-aiding bacteria.