For years, the prevailing medical wisdom regarding the human microbiome—the trillions of microorganisms living on our skin, in our hair, and deep within our gut—has been centered on the idea of “balance.” The goal of many treatments, from over-the-counter probiotics to clinical fecal microbiota transplants, has been to return the gut to a fixed, ideal state of equilibrium.
However, a new perspective suggests that this pursuit of a static “healthy” state may be fundamentally flawed. Experts now argue that health is not about staying the same, but rather about the system’s ability to change and reorganize without losing its essential functions.
This conceptual shift, detailed in a paper published in the journal Cell Host & Microbe, proposes that the inconsistency seen in microbiome-based interventions isn’t necessarily a failure of the treatment, but a failure of how we define health. By moving away from the idea of a “perfect” microbial composition, researchers hope to unlock more predictable and effective ways to treat digestive and immune disorders.
Beyond the Myth of the ‘Balanced’ Gut
Sahar El Aidy, Professor of Microbiome Engineering at the University of Amsterdam, notes that the scientific community has long relied on terms like “diversity,” “resilience,” and “balance.” While these words are common in health discourse, they often lack a precise, consistent definition across different studies, leading to fragmented results in clinical trials.
To address this, El Aidy collaborated with philosophers to develop a new framework called “Adaptive Coherence.” Rather than viewing the microbiome as a snapshot of specific bacteria that should be present or absent, Adaptive Coherence views it as a dynamic system. In this model, health is defined as the capacity of the microbial community to reorganize itself in response to changing conditions—such as shifts in diet, medication, or immune activity—while continuing to perform the vital tasks the body requires.
“Here’s not about finding the perfect microbiome,” El Aidy explains. “It’s about understanding how the system keeps working, even as it changes.”
The Orchestra Effect: Why Treatments Vary
This new framework helps explain a persistent medical puzzle: why a probiotic or a fecal transplant might cure one patient but have zero effect on another, even if both patients appear to have the same “imbalance.”
Under the Adaptive Coherence model, two people can possess entirely different microbial compositions and both be perfectly healthy. Conversely, a person could have a microbiome that looks “normal” on paper but lacks the ability to reorganize when stressed, leading to functional failure. El Aidy likens this to an orchestra: if one musician drops out, the music does not necessarily stop. The other players adjust their tempo and coordination to ensure the piece continues. The health of the music depends not on the specific musicians present, but on how they coordinate to sustain the sound.
This suggests that the “who” (which species of bacteria are present) is less important than the “how” (how those species interact and adapt).
Rethinking the Role of Stool Samples
For decades, the primary tool for microbiome research has been the stool sample. While non-invasive and highly useful, these samples provide a static trace of past activity. They do not capture the real-time, chaotic dynamics occurring inside the gut, where acidity levels, nutrient availability, and chemical gradients are in constant flux.
The shift toward Adaptive Coherence encourages researchers to ask different questions of the same data. Instead of listing the types of bacteria found in a sample, newer approaches look for “system-level signals.” This involves analyzing the balance between cooperative and competitive interactions among microbes.
By focusing on these organizational patterns, clinicians may be able to distinguish between a healthy state and a diseased state even when the overall composition of the microbiome looks nearly identical in both patients.
Implications for Future Medicine
If health is defined by adaptability rather than stability, the goal of medical intervention must change. Instead of attempting to force a patient’s microbiome back to a predefined “healthy” state—which may not even exist for that specific individual—the focus shifts toward supporting the system’s capacity to adapt.
This approach could fundamentally alter the development of personalized medicine in gastroenterology. Rather than a “one size fits all” probiotic, treatments might be designed to enhance the functional integrity and reorganization capabilities of a patient’s unique microbial ecosystem.
The transition from static snapshots to dynamic indicators of health represents a significant move toward a more nuanced understanding of human biology. “The goal is not to force the microbiome back to a previous state,” El Aidy says. “It’s to support its ability to function and adapt in the face of change. That’s what health looks like.”
Disclaimer: This article is for informational purposes only and does not constitute medical advice. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a medical condition.
As research into functional dynamics continues, the next phase of microbiome science will likely involve the development of new monitoring tools capable of tracking these adaptive shifts in real-time, moving beyond the limitations of traditional stool analysis.
Do you think the way we define “health” needs to change in other areas of medicine? Share your thoughts in the comments or share this article with your network.
