Microbiome Engineering: From Lab to Clinic

Dr. Eric Berg

June 14, 2023

Microbiome Engineering: From Lab to Clinic - Dr. Eric Berg

The human microbiome, with its diverse array of microorganisms inhabiting our bodies, has recently captured the attention of scientists and researchers. As our understanding of the microbiome expands, so does the potential for microbiome engineering—a field dedicated to manipulating the microbiome for therapeutic applications. From faecal microbiota transplantation (FMT) to targeted probiotics and prebiotics, microbiome engineering holds immense promise in revolutionizing medicine and improving human health. This article will explore the exciting realm of microbiome engineering and its journey from the lab to the clinic.

Understanding Microbiome Engineering

Microbiome engineering involves deliberate interventions to modulate the composition and function of the microbiome to promote health or treat diseases. This field leverages the intricate relationships between our microbiota and various physiological processes, aiming to restore balance, enhance beneficial microorganisms, or target harmful ones.

Fecal Microbiota Transplantation (FMT)

One of the most well-known applications of microbiome engineering is faecal microbiota transplantation (FMT). FMT involves the transfer of faecal material from a healthy donor to a recipient with a disrupted or imbalanced microbiome. It has successfully treated recurrent Clostridium difficile infection, a condition notoriously challenging to manage with conventional therapies. FMT is now being explored for other states, including inflammatory bowel disease, irritable bowel syndrome, and even certain metabolic disorders.

Targeted Probiotics and Prebiotics

Probiotics and prebiotics are another avenue of microbiome engineering. Probiotics are live microorganisms that confer health benefits to the host when administered in adequate amounts. They can be specific strains of bacteria or even yeasts. By introducing these beneficial microorganisms, researchers aim to restore microbial imbalances or enhance certain functions in the host’s microbiome.

On the other hand, prebiotics are substances that selectively nourish beneficial bacteria in the gut. These can be dietary fibres or other compounds that fuel specific microbial populations. By providing the right prebiotics, researchers can encourage the growth of beneficial bacteria and promote a healthier microbiome.

Precision Medicine and Personalized Approaches

Microbiome engineering aligns with the concept of precision medicine, which aims to tailor medical treatments to individual patients based on their unique characteristics. Researchers can identify microbial signatures associated with certain diseases or conditions by analyzing an individual’s microbiome composition. This knowledge can pave the way for personalized interventions targeting specific imbalances or dysfunctions within the microbiome.

Challenges and Future Directions

While the potential of microbiome engineering is immense, several challenges lie ahead. Some key areas of ongoing research and development include:

Understanding Microbial Interactions: The microbiome is a complex ecosystem where microorganisms interact with each other and the host. Unravelling these intricate relationships and understanding how changes in one microbial population affect others is crucial for practical microbiome engineering.

Developing Targeted Interventions: As the field progresses, researchers are working towards creating more precise and targeted interventions. This involves identifying specific microbial strains or combinations that can deliver desired therapeutic outcomes and optimizing delivery methods to ensure efficient colonization and persistence in the host.

Safety and Regulatory Considerations: Ensuring microbiome-based interventions’ safety is paramount. Researchers are conducting rigorous studies to assess the long-term effects, potential risks, and unintended consequences of microbiome engineering. Regulatory frameworks are also evolving to establish guidelines for these therapies’ safe and ethical implementation.


Microbiome engineering is an exciting frontier in medical research, harnessing the power of the microbiome to improve human health. From FMT to targeted probiotics and prebiotics, the possibilities for manipulating the microbiome are expanding rapidly. As researchers bridge the gap between the lab and the clinic, microbiome engineering holds tremendous potential for personalized therapies, precision medicine, and innovative approaches to treating various diseases. As we continue to unlock the mysteries of the microbiome, we embark on a transformative journey that will shape the future of medicine and our understanding of human health.