Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Turn on the news and it’s easy to feel overwhelmed. Political division. Environmental crises. Artificial intelligence advancing at breakneck speed. Rising rates of obesity, diabetes, anxiety, and other chronic diseases. Many of us have the sense that the world is becoming increasingly fragmented, uncertain, and difficult to understand.

After years of studying nutrition, chronic disease, and the gut microbiome, I’ve become increasingly convinced that many of life’s most important questions are less about isolated parts and more about relationships. In the microbiome, health emerges not from any single microbe, nutrient, or hormone, but from countless interactions among them. The same principle seems to appear throughout biology, ecosystems, human societies, and even the technologies we create.

Viewed through this lens, the story of the universe becomes surprisingly coherent. From the smallest particles to the rise of artificial intelligence, complexity seems to emerge whenever independent things begin interacting in new ways. This perspective doesn’t solve every problem, but it may offer something many of us need right now: a reason for hope.

From Particles to Possibility

At the beginning of the universe, there were no planets, trees, animals, or people. There were only fundamental particles interacting according to simple physical rules. When those particles formed stable relationships, atoms emerged. When atoms formed new relationships, molecules emerged. And when molecules formed increasingly complex relationships, life emerged. The remarkable thing is that the individual components never disappeared. They simply became part of something larger.

Hydrogen and oxygen are not water. Yet when they relate in a particular way, something entirely new appears. The same pattern repeats throughout nature. The whole becomes more than the sum of its parts because relationships create possibilities that isolated components cannot access alone.

Life Is a Relationship Machine

Biology is perhaps the most striking example of this principle. Your body is not a single organism in the traditional sense, but a vast community of trillions of cells working together. Every heartbeat, thought, and breath depends on cooperation among countless components. The same is true of your microbiome. The microbes in your gut are not merely passengers. They form relationships with one another, with your diet, and with your immune system. Through those relationships they produce metabolites that influence metabolism, inflammation, appetite, and even mood.

Health itself may be less about individual parts and more about the quality of relationships among those parts. This helps explain why simple solutions often disappoint. Biology is rarely controlled by a single nutrient, hormone, gene, or microbe. Instead, it emerges from networks of interactions. The healthiest systems are often not the most optimized, but the most balanced.

The Hidden Power of Human Relationships

Humans took this principle to an entirely new level. Language allowed ideas to connect. Trade connected communities. Science connected discoveries across generations. Civilization itself emerged because humans learned to cooperate beyond immediate family groups. No individual built modern society. It emerged from billions of relationships accumulated over generations.

Every meal we eat, every book we read, and every medical treatment we receive represents the combined efforts of countless people we will never meet. The modern world can sometimes make us feel isolated, yet our lives are more interconnected than at any point in history.

Why the World Feels Like It’s Falling Apart

If relationships create complexity, why does the world often feel so divided?

Partly because relationships are powerful enough to create both order and disorder. Social media can connect people across continents, but it can also amplify conflict. Modern agriculture can feed billions of people, yet it has also contributed to environmental degradation and diets increasingly disconnected from the biological systems that shaped human health. Medicine can treat disease more effectively than ever before, yet chronic illnesses continue to rise. Global trade can lift millions from poverty, but it can also spread instability. Artificial intelligence can accelerate discovery while creating uncertainty.

Every major technological advance increases the number and speed of relationships within the system. More relationships create more opportunities, but also more friction. Periods of rapid change often feel chaotic because existing relationships are being reorganized into new patterns.

Nature has gone through similar transitions before. Evolution itself is a story of disruption followed by the emergence of new forms of order.

What About Artificial Intelligence?

Many people fear AI because it appears so different from anything that came before. Yet viewed through a relational lens, AI may represent another step in a familiar process. Human intelligence emerged from relationships among neurons. Science emerged from relationships among minds. The internet emerged from relationships among computers. AI itself emerges from relationships among vast amounts of information.

Whether AI ultimately benefits humanity will depend less on intelligence itself and more on the relationships we build between humans, institutions, technology, and values. The challenge is not simply creating smarter machines, but creating healthier relationships between intelligence and wisdom.

Wisdom in a Relational World

This perspective also changes how we think about wisdom. Wisdom is not simply accumulating facts, but understanding relationships. A wise person recognizes that actions have consequences beyond the present moment. They understand that trust often creates greater value than exploitation and appreciate that short-term gains can sometimes undermine long-term flourishing.

In many ways, wisdom is the ability to see the larger network. The more relationships we can perceive, the more accurately we can navigate reality.

Why Complexity Keeps Emerging

What gives me hope is that throughout the history of the universe, systems built on broader and more productive relationships have repeatedly outperformed those built on isolation. Atoms are more capable than particles alone. Living cells are more capable than molecules alone. Multicellular organisms are more capable than individual cells alone. Civilizations are more capable than isolated individuals alone.

At each step, progress emerged not because competition disappeared, but because cooperation expanded. Systems that successfully integrated more perspectives, more capabilities, and more relationships gained access to possibilities unavailable to their individual parts.

Destructive forces will always exist. Conflict, exploitation, and self-interest are recurring features of nature and human society. Yet these forces are often limited by their narrow focus. They extract value from existing systems but rarely create entirely new forms of value.

Constructive forces operate differently. They connect ideas, people, communities, and resources in ways that allow new possibilities to emerge. In doing so, they often become more resilient, adaptive, and enduring than the forces working against them.

This does not mean progress is inevitable or that every generation moves smoothly forward. History is full of setbacks, collapses, and periods of uncertainty. A forest takes decades to grow, but a wildfire can destroy it in hours. Yet over Earth’s history, forests keep returning.

The same pattern appears throughout nature. Not because destruction disappears, but because systems that successfully build broader, richer relationships gain access to possibilities that simpler systems never had. That pattern is visible in atoms, life, ecosystems, civilizations, science, and perhaps even the future relationship between humans and AI.

Why This Gives Me Hope

Today’s challenges are real. Climate change, political polarization, chronic disease, and AI all present serious risks. Yet they may also reflect something deeper: humanity is participating in one of the most interconnected periods in history.

The same forces creating instability are also creating opportunities for entirely new forms of cooperation, discovery, and understanding. Advances in microbiome science, nutrition, computing, communication, and artificial intelligence are helping us better understand relationships that were previously invisible. Problems once viewed in isolation are increasingly being understood as connected parts of larger systems.

If history teaches us anything, it is that periods of disruption often precede the emergence of new forms of order. The universe has repeatedly transformed apparent chaos into new possibilities. The future is not guaranteed to improve, but neither is it destined to decline.

The next chapter will be shaped by the relationships we choose to build, strengthen, and sustain. That is true for our health, our communities, our technologies, and our planet. The story of complexity is still unfolding, and each of us has the opportunity to contribute to what comes next.

Five Ways to Practice a Relational Perspective

First, invest in relationships before outcomes. Healthy relationships often generate opportunities that cannot be predicted in advance.

Second, focus on contribution rather than control. Complex systems are rarely controlled by any one person, but they can be influenced by many small actions.

Third, think in decades rather than days. The most important effects of our actions often emerge slowly.

Fourth, seek connection across differences. New ideas frequently emerge when previously separate worlds interact.

Fifth, remember that flourishing is contagious. Acts of generosity, curiosity, mentorship, and cooperation often spread through networks in ways we never directly observe.

The Bigger Story

Perhaps the most hopeful realization is this: you do not have to solve the world’s problems alone. No atom created life. No cell created an organism. No individual created civilization. Progress has always emerged through relationships.

Every time we strengthen a family, mentor a student, support a community, improve a technology, prevent disease, restore an ecosystem, or help another person thrive, we contribute to a process much larger than ourselves. The future is not guaranteed. But if history is any guide, the forces that build, connect, teach, heal, and cooperate will continue to create opportunities that destructive forces alone cannot.

In a world that often feels fragmented, that may be the most important truth of all. The future is not built by isolated individuals. It is built through the relationships we create, strengthen, and sustain.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Further Reading

Many of the ideas explored in this essay draw inspiration from thinkers working across physics, evolution, complexity science, microbiome research, systems thinking, human cooperation, and artificial intelligence. Readers interested in exploring these themes more deeply may enjoy the following books.

Physics, Emergence, and Complexity

These books explore how order, complexity, and meaning emerge from simpler building blocks and why cooperation and self-organization have repeatedly shaped the history of the universe and life itself.

• Sean Carroll, The Big Picture
  Physics, emergence, and meaning.

• John Maynard Smith and Eörs Szathmáry, The Major Transitions in Evolution
  How increasing cooperation gave rise to new levels of biological complexity.

• Stuart Kauffman, At Home in the Universe
  Self-organization and the emergence of order.

Human Cooperation and Civilization

These works examine how culture, shared knowledge, and cooperation allowed human societies to accomplish things no individual could achieve alone.

• Joseph Henrich, The Secret of Our Success
  Culture, cooperation, and cumulative knowledge.

• Yuval Noah Harari, Sapiens
  Human history and the power of shared stories.

• Robert Wright, Nonzero
  Why increasing interconnectedness repeatedly creates new opportunities and forms of complexity.

Networks, Systems, and Innovation

These authors emphasize that creativity, resilience, and innovation often emerge from relationships and interactions rather than from isolated parts.

• Steven Johnson, Where Good Ideas Come From
  How innovation emerges from networks and connections.

• Donella H. Meadows, Thinking in Systems
  Seeing the world through relationships rather than isolated parts.

• Fritjof Capra, The Web of Life
  Systems biology and the interconnected nature of living systems.

Microbiome and Human Health

These books illustrate how human health depends not only on our own cells, but also on our microbial partners and the ecosystems we inhabit.

• Martin J. Blaser, Missing Microbes
  The microbiome and modern chronic disease.

• Justin and Erica Sonnenburg, The Good Gut
  Microbiome ecology and the importance of nourishing our microbial partners.

Technology and the Future

These works explore how periods of disruption often accompany the emergence of new technologies, new forms of organization, and new opportunities.

• Melanie Mitchell, Artificial Intelligence: A Guide for Thinking Humans
  Artificial intelligence and what it means to be human.

• Carlota Perez, Technological Revolutions and Financial Capital
  Why periods of disruption often accompany the emergence of new forms of order.

• Peter Turchin, End Times
  Historical cycles, social instability, and periods of transformation.

Life as an Interconnected System

These books take an even broader view, emphasizing that organisms, societies, and the Earth itself are interconnected systems whose properties emerge through relationships.

• James Lovelock, Gaia: A New Look at Life on Earth
  Earth as a self-regulating, interconnected system.

• David Sloan Wilson, This View of Life
  Evolution, cooperation, and multilevel selection.

Taken together, these books point toward a common theme that runs throughout this essay: throughout nature and human history, some of the greatest sources of creativity, resilience, and progress have emerged not from isolation, but from connection.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Walk through any grocery store and you’ll find yourself surrounded by some of the most sophisticated products ever created by modern industry. Not computers. Not smartphones. Food.

For most of human history, food existed within the constraints of nature. Plants contained fiber. Fruits contained polyphenols. Meals required effort to prepare and consume. Hunger and satiety evolved over millions of years as tightly regulated biological systems designed to help us survive. Today, many of those natural signals are increasingly being challenged by foods engineered not simply to nourish us, but to maximize consumption.

This isn’t a conspiracy. It’s economics. The primary responsibility of a publicly traded company is to sell products and generate returns for shareholders. Without strong social guardrails, the natural tendency of any competitive market is to optimize for what drives sales. In the food industry, that often means creating products that are highly palatable, convenient, inexpensive, and difficult to stop eating. The unintended consequence may be that we are increasingly living in an environment that works against many of the biological systems that once helped regulate appetite and metabolic health.

The Science of “More”

Food companies spend billions studying consumer behavior, sensory science, flavor chemistry, and reward pathways. The goal is simple: create products people want to buy again. One strategy is increasing what scientists call hyper-palatability—the combination of salt, sugar, fat, texture, aroma, and flavor that drives reward and encourages continued consumption.

Many ultra-processed foods contain:

• Higher levels of salt

• Refined carbohydrates that digest rapidly

• Concentrated fats

• Artificial or natural flavor systems designed to amplify taste

• Textures engineered for maximum enjoyment

• Long shelf life and convenience

At the same time, many contain substantially less of the components that naturally promote fullness and metabolic regulation:

• Fiber

• Polyphenols

• Intact plant structures

• Fermentable substrates that feed beneficial gut microbes

The result is often food that delivers a powerful reward signal without generating the same degree of satiety that traditionally accompanied eating. In other words, more pleasure per bite and less biological braking.

Many researchers believe this effect extends beyond the food itself. Fiber and polyphenols help nourish the gut microbiome, which in turn produces compounds that influence satiety hormones and metabolic health. As diets become increasingly dominated by ultra-processed foods, we may be losing not only the nutrients that support fullness, but also the microbial signals that help regulate appetite. In this way, some foods may be amplifying reward while simultaneously weakening the biological systems designed to tell us we’ve had enough.

When Biology Meets Industry

Humans evolved in environments where calories were scarce. Our brains developed reward systems that encouraged us to seek energy-dense foods when they were available, and this system worked remarkably well for most of human history.

Then modern food technology arrived.

Suddenly, foods capable of delivering intense reward signals became available 24 hours a day, 365 days a year. The reward system that once protected us from starvation now operates in an environment overflowing with engineered abundance. Viewed through this lens, the result is not a failure of willpower as much as a mismatch between ancient biology and modern incentives.

The Rise of Chronic Disease

Over the last several decades, societies around the world have experienced dramatic increases in:

• Obesity

• Type 2 diabetes

• Fatty liver disease

• Cardiovascular disease

• Certain cancers

• Autoimmune disorders

• Neurodegenerative diseases such as Alzheimer’s disease

These conditions are complex and multifactorial, and no single factor explains their rise. However, few scientists would dispute that dietary patterns, sedentary lifestyles, poor sleep, chronic stress, environmental exposures, and increasing consumption of ultra-processed foods are important contributors.

Our modern environment often pushes biological systems away from equilibrium and toward chronic metabolic dysfunction. While the precise causes vary from disease to disease, many appear to share common roots in disrupted metabolism, chronic inflammation, and lifestyles increasingly disconnected from the conditions under which human physiology evolved.

Then Came the GLP-1 Revolution

The most fascinating twist in this story may be the emergence of GLP-1 medications. Drugs such as semaglutide and tirzepatide have demonstrated unprecedented effectiveness for weight loss and metabolic disease, helping many individuals achieve results that were previously difficult to attain.

What do they do? At their core, they amplify signals related to satiety. In many ways, they help restore a message that modern food environments may have weakened:

“You’ve had enough.”

Patients frequently report:

• Reduced hunger

• Earlier fullness

• Less food noise

• Reduced cravings

• Lower interest in highly rewarding foods

Some researchers and clinicians describe the experience as finally feeling in control around food. The irony is difficult to ignore. For decades, portions of the food industry invested enormous resources into making products that encouraged people to eat more. Now one of the most successful classes of drugs in history helps people want to eat less.

In some respects, GLP-1 medications can be viewed as an antidote to a food environment that has spent decades weakening natural satiety signals. While that comparison is imperfect, it highlights an extraordinary reality: one of the most powerful therapies for metabolic disease works by restoring fullness and reducing desire.

The Promise and Limitations of GLP-1 Drugs

These medications represent a major medical breakthrough. For many individuals, they reduce suffering, improve metabolic health, lower cardiovascular risk, and dramatically improve quality of life. They may ultimately prove beneficial for a range of conditions linked to metabolic dysfunction, including heart disease, neurodegenerative disease, and potentially even some cancers.

Yet they are not without tradeoffs.

Common side effects include:

• Nausea

• Constipation

• Vomiting

• Gastrointestinal discomfort

More serious complications can occur, including severe gastrointestinal slowing and, in rare cases, gastroparesis. Another concern is that rapid weight loss can include loss of lean muscle mass if individuals are not prioritizing resistance training and adequate protein intake. Nutrient deficiencies may also emerge when food intake drops substantially without attention to dietary quality.

Importantly, these medications help manage disease, but they do not fundamentally transform the food environment that contributed to the problem. They are powerful tools, but they do not address the root causes that continue to drive chronic disease throughout society.

A Deeper Question: What Happens to Desire?

One of the most intriguing observations emerging from GLP-1 therapy is that some individuals report changes extending beyond food.

Researchers are investigating reports of:

• Reduced alcohol cravings

• Reduced interest in addictive substances

• Lower compulsive behaviors

• Changes in reward-seeking behavior

These findings are generating excitement because they may offer new approaches to treating addiction. By influencing fundamental reward systems in the brain, GLP-1 medications may help reduce cravings not only for food but for a variety of compulsive behaviors.

At the same time, some patients and their partners report something more complicated. Some describe a general dampening of desire—not just for unhealthy foods, but sometimes for other pleasures as well. Food feels less exciting. Alcohol becomes less appealing. Shopping impulses decline. Some individuals even report changes in sexual interest.

The science is still evolving, and experiences vary widely from person to person. But these observations raise fascinating questions about the relationship between appetite, reward, motivation, and meaning. The systems that drive unhealthy cravings may also be connected to some of the drives that make life feel rich and engaging.

The Real Goal Is Neither More Drugs Nor More Processed Food

The lesson is not that processed foods are evil. Nor is it that medications are bad. Both have delivered enormous benefits.

Food processing has improved food safety, affordability, preservation, and convenience. Modern pharmaceuticals have reduced suffering and extended millions of lives. The challenge arises when either becomes a substitute for addressing root causes.

A society built around hyper-palatable foods and sedentary lifestyles will inevitably require more medical intervention. A society focused on restoring metabolic health may reduce the need for those interventions in the first place.

The future should not be a battle between food and medicine. It should be a collaboration aimed at restoring human health.

A Better Alignment of Incentives

Money moves the world. Companies respond to incentives. Governments respond to incentives. Consumers respond to incentives.

The question is not whether profit exists. The question is whether profit can be aligned with long-term human flourishing. When healthier choices become the easier choices, the market adapts. When consumers demand better products, companies innovate. When policy rewards long-term health instead of short-term gains, systems evolve.

The challenge before us is not technological. It is cultural, economic, and political. We already know many of the levers that promote metabolic health:

• Whole foods

• Fiber-rich diets

• Physical activity

• Sleep

• Stress management

• Social connection

• Reduced consumption of ultra-processed foods

The question is whether we are willing to build environments that make these choices easier.

What Could Be Done?

Governments

• Incentivize production and affordability of minimally processed foods.

• Improve front-of-package labeling transparency.

• Fund independent nutrition and microbiome research.

• Restrict marketing of hyper-palatable foods to children.

• Design cities that encourage physical activity and active transportation.

• Align healthcare reimbursement with prevention, not just treatment.

• Support school nutrition programs focused on whole-food dietary patterns.

Food Companies

• Increase fiber content in products without sacrificing accessibility.

• Preserve beneficial plant compounds and polyphenols where possible.

• Develop foods that promote satiety rather than maximizing overconsumption.

• Invest in long-term health outcomes as a business metric.

• Increase transparency around ingredients and formulation strategies.

• Measure success not only by sales volume but by consumer health impact.

Healthcare Systems

• Emphasize prevention alongside pharmaceutical treatment.

• Pair GLP-1 therapies with nutrition, exercise, and behavioral support.

• Promote resistance training and muscle preservation during weight loss.

• Expand access to lifestyle medicine programs.

• Educate patients about the root causes of metabolic disease.

Individuals

• Prioritize whole and minimally processed foods when possible.

• Increase dietary fiber through fruits, vegetables, legumes, nuts, and whole grains.

• Consume a diverse range of colorful plant foods to support microbiome health.

• Engage in regular resistance and aerobic exercise.

• Protect sleep and stress management as pillars of metabolic health.

• View medications as tools, not substitutes for foundational lifestyle habits.

• Vote with purchasing decisions and support companies that prioritize long-term health.

The ultimate goal is not simply to live longer. It is to create a world in which our food, our biology, our economy, and our healthcare systems work together rather than against one another.

When we align those forces, we move closer to something medicine alone can never provide: a society that makes health the default rather than the exception.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Imagine two fish tanks. One is a vibrant coral reef with clear water, diverse life, and a system that largely regulates itself. Fish move easily, feed naturally, and exist in a stable environment where balance is maintained by the ecosystem itself. The other tank is overgrown with algae. The water is cloudy, oxygen is low, and the fish are sluggish. They struggle to see, to feed, and to function in a system that is no longer supporting them.

Now add a small amount of chlorine to each tank. In the algae-filled tank, the effect feels almost restorative. The water clears, the fish begin to move more freely, and they can “breathe” and feed again. Function returns, and the change feels dramatic. In the healthy reef tank, the exact same intervention is disruptive. Coral bleaches, fish become stressed, and the system begins to break down. The difference is not the chlorine. It is the condition of the system it is being added to.

Why GLP-1 Feels Like a Panacea

GLP-1 medications feel powerful because they act on fundamental biology. They enhance satiety signaling, slow gastric emptying, and improve aspects of metabolic regulation that are often dysregulated in modern life. In a setting shaped by ultra-processed foods, sedentary routines, chronic stress, and disrupted sleep, these effects can feel transformative.

Appetite decreases, weight drops, and people often find it easier to move, think clearly, and engage with daily life. What is happening in many cases is not the creation of a new system, but the partial restoration of a strained one. The drug helps clear some of the “algae,” allowing underlying physiology to function more effectively. The improvement feels dramatic because the starting point was so far from optimal.

The Role of Baseline Health

If we shift the baseline, the picture changes. In a setting where people eat mostly whole foods, move regularly as part of daily life, sleep consistently, and maintain strong social and environmental connections, the system is already closer to balance. Appetite regulation, energy use, and metabolic signaling are functioning within a healthier range.

In that context, adding a supraphysiologic GLP-1 signal is less likely to feel like a solution and more likely to feel like an intrusion. The same mechanisms that provide benefit in a dysregulated system can manifest as side effects when the system is already working well. Nausea, vomiting, constipation, diarrhea, delayed gastric emptying, muscle loss, and nutrient gaps become more prominent. The intervention stands out because there is less dysfunction to offset.

Relative Health vs. True Health

This highlights an important distinction between relative and true health. GLP-1 medications can move someone from a more impaired state to a less impaired one, and that shift can be meaningful and clinically valuable. But it is still improvement within the context of an underlying system that may remain suboptimal.

Feeling better after an intervention does not necessarily mean the system is fully restored. It often means that one constraint has been reduced. The clarity that follows can make it easier to recognize how compromised the baseline had been. The contrast is what creates the sense of a “panacea.”

From Clearing the Water to Building the Reef

GLP-1 medications have an important role. They can reduce friction, create momentum, and help people re-engage with behaviors that support health. For many, they open a door that had previously felt closed. But they are best understood as part of a broader process rather than the endpoint.

A more durable solution looks like rebuilding the reef rather than continually correcting the water. That includes dietary patterns centered on whole and minimally processed foods, adequate protein and nutrient density, and fiber and microbiome-supporting compounds. It includes regular movement, especially resistance training to preserve lean mass, as well as consistent sleep, time outdoors, and attention to stress. These inputs do not act as a single lever. They work together to restore system-level balance.

The Takeaway

GLP-1 can help clear the water in a system that has become overwhelmed. That benefit is real and, for many, meaningful. But the larger goal is to create an environment where the system can maintain clarity independently.

The opportunity is not just to feel better within a compromised system, but to build one that does not require constant correction in the first place. That shift, from intervention to prevention, is where the most durable improvements in health are likely to come from.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

For decades, we’ve treated calories as if they are perfectly measurable units of energy. Eat 200 calories, absorb 200 calories. Simple. But biology is not that simple. In reality, the structure of food changes how many calories we actually absorb. Some foods deliver energy rapidly and efficiently, while others “hide” part of their calories inside cellular structures that our digestive enzymes are not able to fully break down. This is especially true for many whole plant foods, and it may help explain why whole foods and ultra-processed foods behave so differently in the body even when their calorie counts look similar on paper.

Plants are built differently than animal foods. Much of their energy is stored inside rigid cell walls made from fibers like cellulose, hemicellulose, and pectin. These structures protect nutrients from the gut environment and regulate how quickly they are released. Humans cannot fully break down many of these plant cell walls, meaning that some starches, fats, and other nutrients remain physically trapped during digestion. Instead of being absorbed in the small intestine, portions of these nutrients continue farther down the digestive tract into the colon, where gut microbes begin metabolizing them.

Whole Foods Feed More Than Just Us

Once these leftovers reach the colon, microbes take over. Some fibers and resistant starches are fermented into short-chain fatty acids like butyrate that help support the gut lining, immune system, metabolism, and mitochondrial function. Polyphenols that escape absorption can also be transformed by microbes into bioactive metabolites that may influence inflammation and cardiometabolic health throughout the body. And some energy simply exits the body as waste.

Whole foods are not inefficient. They are metabolically buffered. Part of their energy is slowed, shared with the microbiome, or never fully extracted at all. In many ways, whole foods evolved to distribute calories gradually rather than flood the body with rapidly absorbable energy.

What Almonds Reveal About Calories

Almonds provide one of the clearest demonstrations that food structure matters. Studies consistently show that whole almonds deliver significantly fewer absorbable calories than predicted using standard calorie calculations. Depending on the preparation method, humans may absorb roughly 30% fewer calories from whole almonds than expected because much of the fat remains trapped inside intact plant cell walls.

One study found that a serving of whole almonds provided approximately 129 absorbable calories rather than the 170 calories predicted on nutrition labels using standard Atwater calculations — roughly 25% fewer absorbed calories. But processing changes this dramatically. Roasting, chopping, grinding into flour, or turning almonds into almond butter progressively disrupts cellular structures and exposes more fat to digestive enzymes. As a result, more calories become bioavailable. The calories were always present. Processing simply made them easier for the body to access.

Grains Behave The Same Way

Grains show a remarkably similar pattern. Whole intact grains contain starch granules enclosed within fibrous plant structures that slow digestion and limit how rapidly enzymes can access carbohydrates. Milling grains into fine flour dramatically changes this relationship. Grinding increases surface area, disrupts cellular architecture, accelerates starch digestion, and increases caloric availability.

This helps explain why steel-cut oats, intact barley, or minimally processed kernels tend to produce slower glucose responses and greater fullness than finely milled flours made from the exact same grain. Even particle size matters. The smaller and more disrupted the food structure becomes, the easier it is for the body to rapidly extract calories. A whole kernel of wheat and finely milled white flour may originate from the same plant, but metabolically they behave very differently.

Humans Evolved Through Processing

Ironically, processing itself is not unnatural. Humans have been processing food throughout nearly all of evolutionary history. Cooking with fire may have been one of the most important metabolic innovations our species ever developed. Heat softens fibers, denatures proteins, gelatinizes starches, and breaks down cellular structures, dramatically increasing caloric availability. Without cooking, humans likely could not have supported our large energy-demanding brains.

Grinding grains into flour represented another major leap in energy extraction. Fermentation partially breaks down fibers and proteins while improving preservation at the same time. Churning milk into butter, fermenting dairy into yogurt, pressing olives into oil, soaking legumes, and nixtamalizing corn are all forms of processing that helped humans obtain more usable energy and nutrients from food. In many ways, processing helped humans survive scarcity.

Modern Ultra-Processing Changed The Equation

The problem is that modern food systems no longer operate in a world defined by scarcity. Modern ultra-processing goes far beyond traditional cooking or fermentation. Instead of gently modifying whole foods, many ultra-processed foods break ingredients down into highly purified components such as starches, sugars, refined oils, protein isolates, flavor compounds, emulsifiers, electrolytes, and added vitamins. These ingredients are then recombined into foods engineered for shelf stability, convenience, hyper-palatability, and low manufacturing cost.

The result is food that is extraordinarily easy to digest and absorb. The cellular structures are largely gone. The natural slowing mechanisms are reduced. Calories become rapidly bioavailable. For each calorie consumed, the body may extract and absorb a greater percentage of usable energy compared with intact whole foods.

Fiber And Polyphenols Are More Than “Extras”

At the same time, many of the non-nutritive compounds that normally accompany those calories are diminished. For years, nutrition science focused heavily on macronutrients: fat, carbohydrate, and protein considering the other compounds in plants anti-nutrients. But foods contain another layer of biology that may be just as important.

Fiber helps regulate how quickly nutrients are absorbed, alters satiety hormones, slows gastric emptying, feeds microbes, and changes how food moves through the intestine. Polyphenols interact with gut microbes, inflammation, mitochondrial signaling, and metabolic pathways throughout the body. These compounds are not simply passive passengers inside plants. They help regulate the metabolic response to the calories packaged alongside them. In many ways, they act like metabolic instructions.

The Problem Isn’t Processing — It’s Imbalance

Ultra-processed foods often preserve the calories while stripping away much of the structural and signaling system that once balanced them. The result is food that delivers energy rapidly but often with fewer of the microbial and metabolic signals that help regulate appetite, fullness, and energy handling.

Importantly, this does not mean processing itself is bad. Without processing, humanity may never have survived. Cooking, grinding, fermenting, preserving, and culturing foods helped build civilization, and many traditional forms of processing remain incredibly beneficial today. Fermentation, for example, not only preserves food but also creates bioactive compounds and partially breaks down fibers and proteins in ways that may support metabolic health.

Maybe The Future Is Smarter Processing

The real issue is degree. Modern food engineering became exceptionally good at palatability and maximizing calories while paying far less attention to preserving the structural and microbial context food evolved within. Calories are now easier to absorb than ever before, while many foods contain fewer of the fibers, polyphenols, and intact structures that once slowed absorption and communicated with our microbiome.

The answer may not be eliminating processing altogether. It may be rediscovering older forms of processing that work with human health rather than against it — fermentation, intact grains, minimally refined foods, preservation of fiber structures, and polyphenol-rich ingredients — while designing future foods that restore the signals modern processing removed. Because the healthiest foods may not simply be the ones with the fewest calories. They may be the ones that deliver calories at the right speed, in the right structure, with the right instructions attached.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Modern nutrition debates often frame diet as a choice between opposing camps: plant-based versus animal-based, carbs versus fat, glucose versus ketones. But evolution probably never forced humans to permanently choose one over the other. For most of human history, food availability shifted with the seasons. Wet seasons or summers often brought berries, tubers, honey, legumes, and fibrous plants, while dry seasons or winters likely pushed humans toward hunting, marrow, fat, and animal protein. Rather than existing in one stable nutritional state, humans probably moved back and forth between these environments repeatedly over thousands of generations.

This may explain why humans evolved such remarkable metabolic flexibility. Instead of specializing like strict carnivores or herbivores, we appear built to adapt. Our biology can shift fuel sources, digestive priorities, microbial activity, and even gene expression depending on what foods are available. In many ways, the defining feature of human metabolism may not be commitment to a single diet, but the ability to transition between them.

The Hadza Diet Offers a Glimpse Into the Past

One of the clearest modern examples comes from the diet patterns of the Hadza hunter-gatherers in Tanzania. Their food intake naturally changes throughout the year depending on rainfall, plant growth, and hunting success. During some seasons they consume large amounts of fibrous tubers, berries, baobab, and honey, while during other times meat intake rises substantially.

What makes this especially fascinating is that their microbiome changes alongside their diet. Certain microbial species expand during plant-rich seasons and then decline during more animal-based periods, only to return again when fibrous foods reappear. Their gut ecosystem itself appears metabolically flexible, adapting to changing food environments much like the human body does. This seasonal oscillation may resemble how humans ate for much of evolutionary history.

Our Cells Can Literally Run on Different Fuels

This flexibility is reflected deep within our biology. When carbohydrate intake is high, the body primarily relies on glucose for energy. But when carbohydrates become scarce and fat intake or fasting increases, the liver begins producing ketones like beta-hydroxybutyrate from fat. Remarkably, even the brain, one of the body’s most energy-demanding organs, can transition between these fuel systems.

That ability is extraordinary from an evolutionary perspective. Most tissues throughout the body, including muscle, liver, heart, and immune cells, can alter how they generate energy depending on what foods are available. Scientists refer to this as metabolic flexibility: the ability to efficiently switch between fuel sources rather than becoming locked into a single metabolic mode. This likely evolved because human food environments were rarely stable for long.

Plants and Animals Engage Different Parts of Our Biology

Plant-heavy and animal-heavy diets do not simply provide different calories. They activate different digestive and metabolic systems. Animal foods are relatively easy for the body to digest and absorb. Meat and fat are rapidly broken down by stomach acid and digestive enzymes, with much of their nutrients absorbed early in the small intestine.

Plants work differently. Plant cells are surrounded by fibrous cell walls that human digestive enzymes cannot fully break apart. As a result, substantial portions of plant material travel into the lower intestine, where gut microbes begin fermenting and transforming them. In many ways, a plant-rich diet recruits the microbiome as an additional metabolic organ.

These microbes help break down fiber and resistant starches into short-chain fatty acids like butyrate. They also transform polyphenols and other plant compounds into bioactive metabolites that humans may not efficiently produce on their own. While the microbiome likely plays a smaller role during heavily animal-based dietary periods, it becomes critically important during plant-rich periods where microbial fermentation helps unlock nutrients and signaling molecules from otherwise inaccessible plant material.

Carnivores, Herbivores, and Humans

This difference is reflected across the animal kingdom. Carnivores generally have relatively short digestive tracts and small colons because meat is energy-dense and rapidly absorbed. Herbivores are the opposite. They often possess long intestines and large colons or foreguts, fermentation chambers designed to support extensive microbial breakdown of fibrous plants. Animals like cows rely heavily on microbial fermentation to extract energy from grasses humans could never digest on their own.

Humans appear built somewhere in the middle. Our digestive tract is longer than a carnivore’s but far shorter than a dedicated herbivore’s. Our teeth also reflect this mixed strategy. We have incisors and canines capable of tearing food, but also broad molars designed for grinding plants. As omnivores, we seem to possess elements of both systems, allowing us to shift between them depending on environmental conditions and food availability.

The Microbiome May Have Helped Bridge Nutritional Gaps

One fascinating possibility is that the microbiome helped humans obtain nutrients from plants that were otherwise more directly available in animal foods. Gut microbes can synthesize certain vitamins and unlock micronutrients trapped within plant structures. During seasons when meat was less available, microbial metabolism may have helped compensate for some of these nutritional differences.

But the microbiome may have done something even more important than nutrient extraction. It may have functioned as a signaling system that helped regulate metabolism itself. Many microbial metabolites do not simply provide calories. They act as molecular instructions that influence inflammation, mitochondrial activity, energy production, and gene expression.

One of the clearest examples is butyrate, a short-chain fatty acid produced when microbes ferment dietary fiber. Butyrate is not only a fuel source for colon cells. It also functions as an epigenetic signaling molecule that influences HDAC enzymes involved in metabolic regulation and mitochondrial function.

Butyrate and Beta-Hydroxybutyrate: Two Parallel Signals

What makes this especially interesting is that butyrate shares some functional similarities with beta-hydroxybutyrate, the ketone body produced during ketosis. At first glance they seem completely different. One emerges largely from plant fiber fermentation by microbes, while the other comes from fat metabolism during fasting or carbohydrate restriction.

Yet both molecules appear capable of influencing mitochondrial function, inflammation, oxidative stress, and epigenetic signaling pathways. In other words, both may help shift the body into a more stress-resistant and metabolically adaptive state. One pathway emerges from a fiber-rich plant environment, while the other emerges from fat metabolism and ketosis.

This kind of redundancy appears throughout biology. Evolution often preserves multiple ways to activate important survival pathways. Humans may have evolved overlapping systems that allowed periods of plant-rich microbial fermentation and periods of ketosis to both support metabolic resilience under different environmental conditions.

Why Ketogenic Diets May Sometimes Help

This broader evolutionary perspective may help explain why ketogenic diets can sometimes produce meaningful metabolic improvements, particularly in carefully supervised medical settings. Ketosis may temporarily activate ancient pathways associated with fasting, scarcity, cellular repair, and mitochondrial stress resistance. For some individuals, this metabolic reset may improve insulin sensitivity, appetite regulation, or neurological function.

But that does not necessarily mean humans evolved to remain in ketosis permanently. More likely, humans cycled between metabolic states depending on season, geography, migration, hunting success, illness, and food availability. Periods of lower carbohydrate intake may have alternated with periods rich in fibrous plants that nourished both humans and their microbiome.

That distinction matters. A metabolically restorative phase may not be the same thing as an ideal permanent state. Evolutionary health may have depended less on staying in one mode continuously and more on maintaining the flexibility to transition between them.

The Bigger Evolutionary Picture

Modern diets often remove the natural oscillations our biology may have evolved around. Ultra-processed foods provide continuous refined carbohydrates, concentrated fats, constant availability, and very little nourishment for the microbiome. Seasonal variation largely disappears, and the body may become metabolically locked into a narrow range of inputs.

But our biology still appears designed for variation. Variation in fuel sources. Variation in microbial activity. Variation in fasting and feeding. Variation in plant and animal intake. Rather than being optimized for one extreme dietary philosophy, humans may have evolved to move fluidly between nutritional environments depending on circumstance.

The goal may not be choosing one metabolic state forever. It may be preserving the flexibility to do both.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

For decades, nutrition and medicine have excelled at identifying what is missing when something goes wrong, guided in part by frameworks like Koch’s postulates and, in nutrition, by Casimir Funk’s early insight that specific diseases could be traced to missing nutrients. A single pathogen causes infection. A single deficiency causes disease.

This reductionist approach has been powerful. It gave us antibiotics, vitamins, and life-saving treatments. But it also shaped how we look for problems: one cause, one effect.

The microbiome does not work that way. It is not a single organism. It is a system, as understood in systems biology, and systems are harder to see, especially when they are buffered by redundancy.

The Invisible Safety Net

For most of human history, the gut microbiome was remarkably resilient. Diets were naturally rich in fiber and polyphenols, and diverse plant foods continuously fed microbial communities.

If one pathway faltered, another could compensate. If one species declined, others could fill the gap. This redundancy acted like a biological safety net.

Even when diets varied or stressors appeared, the system held. Because of that, there was no obvious deficiency disease for low fiber or low polyphenols, and no single microbe to point to and blame.

So we missed it. Not because it was unimportant, but because it was protected.

Why Fiber and Polyphenols Stayed in the Background

Fiber and polyphenols do not act like traditional nutrients. They are not primarily absorbed to nourish us directly, but instead nourish our microbes, which generate metabolites that regulate inflammation, metabolism, and immunity.

Their effects are indirect, distributed, and context-dependent. That makes them difficult to study using frameworks designed for single nutrients and single outcomes.

So while we measured vitamins, minerals and macronutrients with increasing precision, the compounds that fed the system itself remained in the background.

When Redundancy Breaks

What was once a strength is now becoming a vulnerability. The modern environment is applying multiple, simultaneous pressures on the microbiome, including diets low in fiber and polyphenols, increasing reliance on ultra-processed foods, widespread antibiotic exposure, changes in birth practices, and reduced environmental microbial diversity.

Each of these alone might be manageable. Together, they are not.

Redundant pathways begin to disappear, functional overlap shrinks, and the system becomes less flexible, less stable, and more prone to dysfunction. This is what system failure looks like, not a sudden collapse, but a gradual loss of resilience.

The One-Two Punch

At the same time, two forces are converging. First, we are removing the inputs that sustain the microbiome, fiber and polyphenol-rich foods.

Second, we are increasing exposures that disrupt it, including ultra-processed foods, additives, and other environmental pressures. This creates a compounding effect.

It is not just that beneficial inputs are missing. It is that disruptive inputs are replacing them. A one-two punch: deprivation and disruption.

From Deficiency to Depletion

We are used to thinking about nutrition in terms of deficiency. But what we are seeing now is different.

This is not the absence of a single nutrient. It is the depletion of a system, a gradual erosion of microbial diversity, metabolic capacity, and functional redundancy.

And unlike classic deficiencies, the consequences are diffuse, including metabolic disease, immune dysregulation, and neurodegenerative diseases. No single cause and no single fix.

The microbiome challenges us to think differently. Not in terms of isolated nutrients, but relationships, and not in terms of single causes, but interacting systems.

Fiber and polyphenols are not just components of food. They are inputs into a larger network that converts diet into biological signals.

What we missed was not just the microbiome itself. We missed the importance of maintaining the system that makes nutrition work.

A Shift Forward

The solution is not to chase individual microbes or single compounds. It is to restore the conditions that allow the system to function.

This includes high quality, diverse, fiber-rich plant foods, polyphenol-rich dietary patterns, minimizing unnecessary disruption, and supporting early-life microbial development.

In other words, rebuilding redundancy. Because resilience is not created by precision alone, it is created by overlap, diversity, and balance.

The Takeaway

We did not miss the microbiome because it was too small. We missed it because it had built in back up.

Only now, as that resilience erodes, are we beginning to see what it was doing all along. And why it matters.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

If you’ve ever felt hungry soon after eating, the issue may not be how much you ate, but what was missing from it. For years, nutrition advice has focused on what to remove. Cut carbs, avoid fat, reduce calories, eliminate sugar. While each of these ideas contains some truth, they share a common limitation. They frame health as a process of subtraction rather than balance. But what if the bigger issue is not just what we are eating too much of, but what we are no longer getting enough of?

Modern diets are not only high in certain nutrients. They are also depleted of others. Highly processed foods tend to concentrate refined carbohydrates, sodium, and certain fats while stripping away fiber, potassium, and plant-derived compounds like polyphenols that normally travel with them. This creates what you might think of as a nutrition gap, not just excess, but absence. And those relationships matter, because physiology responds to how nutrients interact within a meal, not just to individual components in isolation.

Why Restriction Often Fails

Avoidance-based approaches can unintentionally widen the very gap they are trying to close. When we focus only on removing foods, the diet may become lighter, but it does not become more complete. What is missing remains missing and our cravings grow bigger.

Biologically, that gap matters. When fiber, protein, potassium, and phytonutrients are underrepresented, satiety signaling is weaker and metabolic responses are less stable. Hunger does not disappear. It often returns sooner and stronger.

In this way, restriction can amplify the cycle of craving and overeating, not resolve it.

Reframing the Question

A more effective approach is to shift the question. Instead of asking what to remove, we can ask what to add back to restore balance. This is not about abandoning the foods you enjoy, but about pairing them with foods that complement what is missing.

When balance improves, something else changes as well. Meals tend to satisfy more. Hunger stabilizes. Cravings often diminish, not because of willpower, but because the underlying nutritional gaps are being filled.

Everyday Examples of Balance

This approach can be applied in simple, practical ways. Potato chips with a yogurt-based dip. A hot dog with turkey chili. Pizza with a fiber-rich salad. Chocolate with almonds. Cake with berries.

Each pairing adds back something that is lacking in the original food, improving the overall nutritional balance of the meal or snack. Importantly, these combinations also tend to be more satisfying. By adding protein, fiber, and potassium-rich foods, they support fullness and sustained energy, which can naturally help you reduce portion size and the urge to keep eating or to snack again soon after.

A Closer Look: Cake & Berries

Consider chocolate cake on its own. It is energy dense and high in refined carbohydrate and fat, while providing very little fiber or micronutrient density. This creates imbalance across key nutrient relationships such as carbohydrate to fiber and calories to weight. It is also easy to over consume because it delivers energy without strongly engaging satiety pathways.

Reducing the portion of cake and adding a generous serving of mixed berries lowers simple carbohydrates and saturated fats while adding fiber, micronutrients, and a wide range of healthy plant compounds. Fiber, and plant compounds help slow digestion and enhance gut–brain signaling pathways that regulate fullness.

This helps rebalance key nutrient ratios and improve satiety.

The result is not a perfect food, but a more complete and satisfying one. You are more likely to feel full sooner and stay full longer, reducing both portion size and the likelihood of reaching for more food shortly after.

Measuring Balance

Balance can be difficult to see, but it can be measured. The Nutrient Consume Score evaluates how well key nutrient ratios are aligned within a food, meal, or dietary pattern, incorporating relationships such as carbohydrate to fiber, saturated to unsaturated fat, sodium to potassium, and calories to weight.

Foods that are imbalanced on their own often improve when paired thoughtfully, and those improvements are reflected in higher scores. This provides a practical way to connect food choices with both nutrient quality and lived experience, helping remove guesswork and guide better decisions over time.

Making It Practical

Understanding balance is one thing. Applying it consistently is another. Tools that provide real-time feedback can help bridge that gap.

Smart Bites allows you to scan foods, score meals, and track how combinations influence overall balance. Barry, the in-app assistant, suggests complementary additions that can improve what you are already eating.

Instead of guessing, you can see in real time how small additions change the overall balance of a meal. This shifts the experience from restriction to optimization, helping you build meals that are both more balanced and more satisfying.

The Takeaway

Nutrition often gravitates toward extremes because they are easy to communicate, but biology tends to favor balance. Health is not built by removing every imperfect food from the diet. It is built by consistently restoring what is missing.

When balance improves, satisfaction tends to follow. Hunger stabilizes. Cravings diminish. And the path forward becomes both more effective and more sustainable.

In that sense, you really can have your cake and eat it too. You just might find you are more satisfied when you have your berries with it.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

We’re used to thinking about food pairing in terms of just taste. Wine with cheese, peanut butter with chocolate, tomatoes with basil. But pairing matters for another reason that’s far more consequential: biology.

Foods are rarely eaten alone. They are combined into meals, layered into recipes, and repeated as patterns over time. When foods are combined, their effects on metabolism, the gut microbiome, and appetite are not simply additive. They synergize.

This means that the health impact of a food depends not just on what it is, but what it’s eaten with.

Foods Don’t Act Alone

Nutrition science has traditionally evaluated foods one at a time by measuring calories, sugar, fat, or protein, then assigning value accordingly. This approach is practical, especially for labeling. But it misses how people actually eat.

A slice of bread on its own affects the body differently than bread eaten with olive oil, vegetables, or protein. A cookie alone is one thing; a cookie eaten after a fiber-rich meal is another. These combinations shape how quickly nutrients are absorbed, how full we feel, and how our metabolism responds.

Some pairings improve balance. Others amplify imbalance.

Refined carbohydrates paired with fat, for example, can increase energy intake and reduce satiety signals, making it easier to overconsume. In contrast, pairing carbohydrates with fiber-rich foods slows absorption, moderates blood sugar, and supports microbial fermentation in the gut.

The difference is not just in the foods. It is in the relationship between them.

Biology Runs on Ratios

At a deeper level, this idea reflects a fundamental principle of biology: systems operate through balance and proportion.

Cells maintain gradients of sodium and potassium across their membranes using the sodium–potassium pump. This process is essential for nerve signaling, muscle contraction, and cellular stability. It is not sodium or potassium alone that matters, but their ratio.

Cell membranes also depend on a balance of fats. Saturated fats provide structure, while unsaturated fats provide fluidity. Together, in the right proportions, they create membranes that are both stable and flexible and capable of adapting to changing conditions.

Plants follow similar principles. Fiber provides structure to plant cells, while starch serves as stored energy. When we eat whole plant foods, we consume both structure and fuel together, which slows carbohydrate absorption and shapes downstream metabolism. When foods are refined, these elements are often separated.

Nutrition works the same way. Ratios like carbohydrate to fiber, saturated to unsaturated fat, and sodium to potassium shape how foods function in the body. These relationships influence digestion, metabolism, and microbial activity in ways that single nutrients cannot.

Food as Signal, Not Just Fuel

Food does more than provide energy. It sends signals.

Fiber signals fullness and feeds gut microbes that produce short-chain fatty acids. Protein influences satiety hormones and muscle metabolism. Fats alter membrane composition and inflammatory signaling. Minerals like sodium and potassium regulate fluid balance and cellular communication.

When foods are combined, these signals interact.

A meal rich in refined starch and low in fiber sends a different signal than one where those same carbohydrates are embedded in a matrix of intact plant structure. Adding potassium-rich foods like vegetables or legumes can help offset the physiological effects of sodium. Including fats alongside carbohydrates can either stabilize or destabilize intake depending on the broader context.

In this sense, meals are not just collections of nutrients. They are coordinated signals to the body, patterns that can be reflected in a new approach to food quality scoring systems designed to evaluate how foods work together rather than in isolation.

Pairing for Better Balance

Understanding food pairing shifts the goal of nutrition. It moves us away from asking whether a single food is good or bad and toward asking how foods work together.

Some simple patterns emerge:

• Pair carbohydrates with fiber-rich foods to support more stable metabolism

• Balance fats toward unsaturated sources while maintaining structural diversity

• Combine sodium-containing foods with potassium-rich plants

• Build meals around intact foods that retain their natural structure

These are not rules of elimination, but principles of composition—patterns that can be measured and improved in real time when meals are viewed as integrated systems rather than individual parts.

From Foods to Patterns

This perspective helps explain why traditional dietary patterns such as Mediterranean, Japanese, or other plant-forward cuisines are associated with better health. They are not defined by single superfoods, but by combinations that create balance across meals.

It also highlights a limitation of many modern food environments. Highly refined foods often separate components that were once naturally paired, removing fiber from carbohydrates, altering fat composition, and increasing sodium relative to potassium. The result is not just different foods, but different biological signals.

If we want to improve health, the focus should not only be on choosing better individual foods, but on building better combinations—something that can now be quantified, guided, and refined using new tools to better understand how these relationships shape metabolism and the microbiome.

Because in the end, nutrition is not just about what we eat. It is about how what we eat works together.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Front-of-package nutrition labels are having a moment. The FDA is proposing to require front of package nutrition labeling and a recent report in the Journal of the American College of Cardiology calls for clearer, more effective labeling to improve cardiovascular health. The premise is straightforward: make it easier for people to identify healthier options at a glance and guide better decisions at scale.

It is a meaningful step forward. But it also highlights a deeper limitation in how we think about food and health, one that becomes clear when we look beyond individual nutrients and consider how we actually eat.

What Are We Measuring?

Most labeling systems evaluate foods one at a time. They focus on components like sugar, fat, sodium, and calories, then translate those into a simplified score or symbol. This reduction makes complex information easier to interpret, particularly in fast-paced environments like grocery stores.

But this approach assumes that foods are consumed in isolation. In reality, they are almost always part of meals, recipes, and broader dietary patterns. Butter, oil, bread, rice, and even a cookie are rarely eaten alone. Each may appear unbalanced when viewed on its own. Oils are energy-dense and refined, carbohydrate-rich foods may lack fiber, and processed foods may concentrate salt or sugar, but these snapshots miss the context in which they are actually consumed.

Approaches that evaluate nutrients and foods in context, rather than in isolation, can help bridge this gap and better reflect how people actually eat.

Foods & Nutrients Don’t Act Alone

Health is not determined by individual nutrients or foods, but by how they are combined. Nutrition, at its core, is a problem of balance, how nutrients relate to one another within a meal and across the diet as a whole. Looking at nutrients in isolation captures only part of the picture.

Ratios such as carbohydrate to fiber, saturated to unsaturated fat, and sodium to potassium, and energy to weight begin to reflect this deeper structure. They capture quality within categories and balance across them. These relationships also align more closely with how the gut microbiome interprets diet, responding not to isolated nutrients but to the overall pattern of inputs that arrive together and shape its function.

What Traditional Diets Understood

Long before nutrition labels or nutrient databases, traditional cuisines arrived at balance through experience. Food combinations evolved over generations, shaped by how people felt, functioned, and maintained health over time.

Meals like pasta with tomato sauce, rice with seaweed or legumes, and tortillas with beans or avocado reflect this accumulated knowledge. These pairings balance refined and intact components, energy and fiber, and sodium and potassium. Without formal scoring systems, they created dietary patterns that supported both human biology and the gut microbiome.

From Foods to Patterns

Modern labeling systems are designed to evaluate foods, but what we ultimately need is a way to evaluate diets. This requires shifting from a focus on individual components to the relationships that define overall balance.

The Nutrient Consume Score is one framework that assesses this gap. Instead of asking whether a single food is “good” or “bad,” it evaluates how foods and combinations of foods contribute to dietary balance. It measures key nutritional ratios, including the carbohydrate to fiber ratio, the saturated to unsaturated fat ratio, the protein to energy ratio, and the sodium to potassium ratio.

The ratios are evaluated individually, and these are then combined into an overall score, not by simple averaging, but by integrating how each dimension contributes to overall balance.

Because it focuses on nutrition ratios and relationships, it can be applied across levels, from individual foods to meals, recipes, and overall dietary patterns, better reflecting how people actually eat. It is available as a public-good mobile app that allows quick scanning of foods, meals, and recipes, providing overall scores and suggestions for improvement.

A Shift in Perspective

This perspective shifts how we think about food, from labeling nutrients as good or bad to focusing on context. Nutrition has long swung between extremes, vilifying fat, then carbohydrates, and now elevating protein, but these shifts reflect changing narratives more than biology. Carbohydrates, fats, and proteins are not opposing forces, but parts of a broader system that can be combined to support balance.

In this framework, a single food does not define a diet. A traditional sugar cookie on its own may be unbalanced, but paired with a fiber-rich food like a carrot, the overall pattern improves. The focus shifts from elimination to composition, from avoiding ingredients to building balanced snacks and meals that shape metabolism, satiety, and the microbiome.

The Bigger Picture

Front-of-package labels remain a valuable tool. They simplify complex information and can help guide better decisions, particularly at the point of purchase. But they are only one piece of a larger puzzle.

If we want to meaningfully improve health, we need to move beyond evaluating foods in isolation and toward understanding diet as a system, one defined by balance, relationships, and context. Food quality is not just about what a food contains, but how foods fit together to shape biology, the microbiome, and long-term health.

Tools that evaluate how foods work together, not just on their own, can help translate this perspective into everyday choices when shopping, cooking, or building meals.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

Food additives are suddenly back in the headlines. Regulators are phasing out artificial dyes, companies are reformulating ingredients, and consumers are paying closer attention to long ingredient lists. Much of the conversation assumes a simple story: additives are harmful, so removing them should solve the problem.

The science suggests something more nuanced. Some additives may indeed have effects that were not detected in traditional safety testing, in part because most evaluations historically focused on direct toxicity, while giving less attention to whether these compounds might alter the gut microbiome that helps regulate metabolism, immunity, and inflammation.

But the microbiome perspective also reveals a deeper issue. Ultra-processed foods influence the gut ecosystem in more than one way. They introduce compounds the microbiome did not evolve to encounter in these combinations while also removing many of the plant fibers and phytochemicals that normally nourish it.

The result is a one-two punch. If the gut microbiome is an ecosystem, ultra-processed foods can act like both pollution and deforestation at the same time.

Not all additives are created equal

Food additives include emulsifiers, sweeteners, preservatives, colors, stabilizers, and thickeners. Many likely have little impact on the gut microbiome at typical exposures, while others raise more credible concerns. Viewed through a microbiome lens, current evidence points most strongly toward certain emulsifiers and sweeteners.

Emulsifiers stabilize fat-water mixtures and create the smooth textures expected in foods such as salad dressings, sauces, ice cream, and packaged baked goods. Experimental studies show that some emulsifiers can alter microbial communities, thin the intestinal mucus barrier, and promote low-grade inflammation. Human evidence now supports some of these concerns. In a controlled feeding study, the emulsifier carboxymethylcellulose altered the gut microbiome and metabolome and, in some individuals, allowed bacteria to encroach into the mucus layer.

Evidence for non-nutritive sweeteners also depends on the specific molecule. Some artificial sweeteners such as saccharin and sucralose have been shown in several studies to alter the gut microbiome and influence glucose metabolism. Human trials indicate that these responses vary between individuals and may depend on the composition of the existing microbiome. In contrast, many naturally derived compounds such as monk fruit, stevia, and allulose, appear to have less adverse impact on the gut microbiome at typical intake levels, although evidence remains limited.

Other additives such as carrageenan, titanium dioxide, and some synthetic dyes show signals in experimental models but limited human evidence. Additives therefore remain an important area of study. But focusing only on what gets added to food misses an equally important part of the story.

The story’s missing half

Ultra-processed diets likely affect the microbiome through both added compounds and missing food components. Some additives may directly stress the gut ecosystem. But industrial processing also removes many of the features of foods that normally support microbial communities.

Whole plant foods contain complex fibers, intact cellular structures, and diverse phytochemicals that shape microbial ecology. Polyphenols are especially important. These compounds, abundant in berries, tea, cocoa, coffee, herbs, spices, and colorful vegetables, often reach the colon where microbes transform them into smaller metabolites that influence inflammation, metabolism, and gut barrier function.

When processing strips away these compounds, the microbiome loses an important source of ecological support. Diets dominated by ultra-processed foods therefore deliver a double effect: they introduce novel compounds while simultaneously removing many of the nutrients and structures that normally sustain microbial diversity and resilience.

Reducing problematic additives addresses part of the issue, but restoring whole plant foods helps rebuild the habitat the microbiome depends on.

Nature’s built-in additives

An ironic twist is that many additives exist because manufacturers must recreate properties that whole foods naturally provide but that are removed by industrial processing.

Plants contain pigments such as anthocyanins and carotenoids that produce vibrant colors. Polyphenols contribute flavor complexity and antioxidant stability. Herbs and spices contain antimicrobial phytochemicals that help slow spoilage.

Whole foods also contain natural thickeners and stabilizers. Plant fibers, pectins, and starches influence texture and water retention, helping foods maintain structure without the need for synthetic stabilizers.

Traditional cuisines relied on these naturally occurring compounds to shape flavor, appearance, and shelf life. Industrial processing often removes many of these natural compounds and structures, then reintroduces additives designed to recreate their functions.

Processing by fermentation

Processing itself is not inherently harmful. Fermentation is also a form of processing, long used for preservation, flavor enhancement, and nutrient enhancement, but it works very differently from industrial processing.

Fermentation uses microbes to transform foods. Their metabolism generates organic acids that preserve, aromatic molecules that build flavor, and molecules such as glutamate that deepen savory taste. These microbiomes can also synthesize certain vitamins, including B vitamins and vitamin K, and make minerals like iron more available, increasing the nutritional value of some foods.

Traditional food systems relied heavily on fermentation. Fermented vegetables like cabbage were preserved as kimchi or sauerkraut through fermentation-driven acidity. Cocoa fermentation created the characteristic flavor of chocolate. Cheeses, yogurts, and breads similarly depend on microbial activity.

Rather than simplifying food, fermentation increases biological complexity by generating new metabolites and microbial signals that stabilize the gut ecosystem and metabolic processes in the body.

Industrial processing frequently moves in the opposite direction. Natural food structures are broken down and many biological signals are removed, while flavor, color, and texture are rebuilt using refined ingredients and additives.

Putting perspective into practice

In summary, the microbiome perspective suggests that additives, particularly some emulsifiers and non-nutritive sweeteners, warrant closer scrutiny, while evidence for others remains mixed. But additives alone do not explain the effects of ultra-processed foods. What processing removes matters just as much. Fibers, polyphenols, plant structures, and fermentation-derived compounds help shape the gut ecosystem and total health.

In practice, this means:

• Build meals around intact plant foods such as vegetables, legumes, whole grains, nuts, and seeds that deliver fermentable fiber and plant structures.

• Include polyphenol-rich foods regularly such as berries, herbs, spices, tea, coffee, and colorful fruits and vegetables.

• Add fermented foods when possible including yogurt, kefir, kimchi, sauerkraut, or other traditionally fermented foods.

• Be mindful of long ingredient lists, which often signal highly formulated foods with multiple additives and fewer intact plant structures.

• Consider a food quality scoring tool to quickly assess foods and compare options, especially when navigating packaged products.

The goal is not simply to remove additives from food. It is to rebuild diets that restore the biological signals the gut microbiome evolved to recognize.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

GLP-1 has changed the conversation around metabolism. Once a relatively obscure gut hormone, it now seems impossible to open an article about nutrition, weight, or metabolic health without seeing GLP-1 in the headline.

Medications that amplify GLP-1 signaling can meaningfully reduce food intake, lower body weight, and improve the metabolic dysfunction underlying many chronic diseases. For many patients, these medications are a true game changer.

But beneath the headlines sits an important physiological reality. GLP-1 was never meant to work alone.

In normal human biology, GLP-1 is just one component of a coordinated signaling system involving multiple hormones, microbiome signals, and nerve pathways.

If metabolism were an orchestra, GLP-1 would be one important instrument but not the conductor. Food itself coordinates the performance, and food quality still matters even in the era of powerful GLP-1 therapies.

Pharmacology vs Physiology

GLP-1 medications work by producing sustained activation of the GLP-1 receptor at levels the body would not normally generate in the brain, gut, and endocrine organs. This pharmacologic signal suppresses appetite, slows stomach emptying, and improves how our bodies process sugar.

Physiology works differently. After a meal, the intestine releases a cascade of signals including nutrients, factors produced by our microbiome, and a set of gut hormones: GLP-1, GIP, and PYY. Circulating hormone levels are typically far lower than those produced by medications, but the system functions as a coordinated regulatory network rather than a single dominant signal.

Many of these signals act locally within the gut. The vagus nerve, the gut’s information highway, relays this information to the brain, stomach, and other organs. As a result, their effects are not necessarily reflected by generating highest hormone concentrations in the bloodstream. In fact, less processed foods often produce lower GIP and GLP-1 levels in the blood while generating a more coordinated and sustained response within the gut and through vagal signaling.

The Ileal Brake

One of the most important mechanisms in this network is the ileal brake.

When nutrients reach the lower small intestine (the ileum) and colon, they trigger feedback signals that slow stomach emptying and appetite. Specialized cells release hormones such as GLP-1 and PYY that signal through the vagus nerve to the brain. Together these signals slow digestion and help limit further intake.

Rather than producing a high spike in circulating hormones, this system functions as a gradual and subtle braking mechanism that helps regulate appetite over time. How strongly it activates depends largely on what foods reach the lower intestine.

Evidence for the importance of the break comes from weight loss surgery. Gastric bypass leads to more rapid delivery of less-digested nutrients to the lower intestine, strongly activating GLP-1, PYY, and other satiety signals. This enhanced stimulation of the distal gut and improved appetite control is thought to be a key reason these surgeries are so effective for weight loss and metabolic disease.

Food Structure and Composition Determines What Reaches the Brake

Food processing also strongly influences how much intact nutrient material reaches the distal gut, often in the opposite direction.

Minimally processed foods retain structural complexity such as plant cell walls, intact fibers, and resistant starches. These structures slow digestion and allow portions of food to travel further down the intestine before absorption.

Food composition also matters. Components common in less processed foods such as fibers, polyphenols, and unsaturated fats can independently slow digestion and absorption by inhibiting digestive enzymes and slowing glucose absorption.

Highly processed foods often disrupt both structure and composition. Industrial processing breaks down plant structures and concentrates refined carbohydrates and saturated fats while removing fibers, polyphenols, and unsaturated fats. It allows calories to be absorbed rapidly in the upper intestine before the distal gut’s braking signals are fully engaged.

The Microbiome: Fiber and Polyphenols

The microbiome adds another important layer to this system.

Fibers, resistant starches, and many polyphenols escape digestion in the upper gastrointestinal tract and reach the colon, where microbes transform our food’s leftovers into biologically active metabolites.

Fermentation of fiber produces short-chain fatty acids such as butyrate that interact with specialized cells that produce hormones like GLP-1 and neural pathways involved in appetite regulation. Many polyphenols are also transformed into metabolites that influence hormone signaling and inflammation within the gut.

Microbial fermentation therefore acts almost like a slow-release capsule for satiety. While nutrients absorbed earlier in digestion create short-term signals, microbial metabolism provides a longer and steadier signal that helps extend fullness and stabilize appetite. Dietary patterns rich in diverse plant foods tend to strengthen this microbial signaling system.

Food Quality in the Era of GLP-1 Therapy

GLP-1 medications reduce appetite effectively, but they do not automatically determine what foods people choose to eat.

Some studies suggest that individuals using these medications shift modestly toward healthier foods because smaller portions feel more satisfying. Reduced appetite alone, however, does not guarantee adequate protein, micronutrients, or microbiome-supporting foods.

This matters because rapid weight loss without attention to nutrition can contribute to loss of lean muscle mass, nutrient deficiencies, and reduced metabolic resilience. Research supports the important of working with nutrition professionals during GLP-1 therapy so that reduced appetite translates into higher-quality food choices rather than simply lower food intake.

Simple tools that help people measure and score the quality of foods, meals, and recipes can also make this process easier by helping individuals quickly identify whole and better-for-you processed options that support metabolic health.

Principles That Support Physiologic Satiety

Several dietary components consistently support the gut’s natural satiety systems:

• Diverse fermentable fibers from intact plant foods

• Polyphenol-rich foods such as berries, herbs, spices, tea, coffee, and colorful produce

• Whole-food protein paired with fiber and healthy fats

• Unsaturated fats from foods such as nuts, seeds, olive oil, and fish

• Reduced reliance on ultra-processed foods

These components increase the likelihood that digestion, microbial fermentation, and distal gut signaling work together to regulate appetite.

A Practical Perspective

GLP-1 medications represent an important advance in treating metabolic disease because they can meaningfully reduce appetite and help many patients achieve weight loss that was previously difficult to sustain.

At the same time, the deeper biology of appetite regulation still depends on the interaction between food structure, digestion, microbial metabolism, and gut–brain signaling. Medications can amplify one part of the system, but food still conducts the orchestra.

For that reason, improving food quality and having practical tools to quantify and track that quality in everyday eating remain powerful ways to support metabolic health whether GLP-1 therapy is part of the plan or not.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

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If you’re coming over from Gut Bites, welcome. If you’re new, this is where I translate microbiome science into practical decisions about food and health.

For decades, nutrition debates have played out like rival sports fandoms. Keto versus carbs. Vegan versus carnivore. Low-fat versus low-carb. Each camp comes armed with studies, success stories, and unwavering conviction.

And yet, a curious pattern keeps emerging: two people can follow the same diet, with the same discipline, and get completely different results. One feels energized and loses weight; the other feels bloated, fatigued, and frustrated. This isn’t failure or lack of willpower. It’s biology.

I’m a gastroenterologist and professor at the University of Washington, where I study how diet interacts with the gut microbiome, the trillions of microbes living in our digestive tract. Increasingly, research suggests that many diet debates aren’t about which diet is “right,” but about which diet is right for whom. And one of the biggest reasons may be the microbial ecosystem each of us carries.

The same food, different biology

Nutrition science historically treated the human body as if it responded predictably to nutrients: carbohydrates raise blood sugar, saturated fat affects cholesterol, protein supports muscle. That framework helped solve nutrient deficiencies and transform public health.

But it missed a critical layer. Food doesn’t just feed us. It feeds our microbiome. And that microbiome acts like a metabolic translator, transforming what we eat into bioactive compounds that influence inflammation, metabolism, appetite, and even mood. Diet is one of the most powerful forces shaping microbiome composition and function.

Because each person’s microbiome is different, the same diet can produce very different internal chemistry. This might help explain why diet “tribes” form in the first place. People aren’t imagining their success. They’re experiencing a real biological response, one that may not translate to someone else.

Where personalization is already happening

We’re not starting from scratch, several areas of nutrition already show how differences in the microbiome shape how people respond to food.

In gastrointestinal care for irritable bowel syndrome (IBS), this pattern is already visible in clinical practice. Dietary approaches such as low-FODMAP eating patterns can shift the microbiome and improve symptoms in some patients, and baseline microbial features may help predict who benefits most. Breath testing and microbiome-informed strategies are increasingly used to tailor dietary advice, offering a real-world example of personalization already in practice.

Metabolic research shows the same principle at work in blood sugar regulation. Landmark studies demonstrate that individuals have highly personalized blood sugar responses to identical foods and fibers, and that adding microbiome data significantly improves the ability to predict those responses. In clinical trials, personalized dietary recommendations built from these models lowered post-meal glucose levels, reinforcing a simple idea: carbohydrate responses aren’t universal, they’re microbiome-dependent.

Weight-loss research tells a similar story. In randomized trials, people with certain baseline microbiome profiles, particularly a higher Prevotella-to-Bacteroides ratio, lost significantly more weight and body fat on higher-fiber diets than those without that profile. In other words, the same “healthy” diet can produce different satiety signals and metabolic outcomes depending on how an individual’s microbes process it.

What about a keto versus plant-based diets?

What about keto versus carbs? This is where the science is still emerging, but there are some intriguing signals. Different dietary patterns, including ketogenic diets and plant-based diets, consistently reshape the gut microbiome, and people vary widely in their metabolic and symptomatic responses to these approaches.

Early evidence suggests that while baseline microbiome composition may not predict weight loss in low-carb vs. low-fat diet, how the microbiome responds to diets dynamically does correlate with with sustained weight loss.

The same principles driving IBS diet tailoring, personalized glycemic response, and fiber responsiveness could apply to macronutrient patterns like keto versus higher-carb diets. Diet wars may be arguments over population averages in a world of biological individuality.

As nutrition enters the era of GLP-1 therapies, ultra-processed food debates, and personalized health tracking, this variability is becoming impossible to ignore.

You’re not crazy, and neither is your friend

One of the most striking clinical patterns I see is how differently people respond to the same dietary changes. One patient feels dramatically better when they reduce carbohydrates, while another becomes sluggish and constipated. One thrives on plant-rich, fiber-heavy meals, while another develops bloating and discomfort.

These reactions often leave people wondering if something is wrong with them, but what if both responses are valid? Each person’s microbiome is shaped over time by early life exposures, antibiotics, environment, diet history, geography, and stress. As a result, two people may share only a fraction of microbial species, meaning they’re not starting from the same metabolic baseline when they try a new diet. What feels energizing, satiating, or gut-friendly for one person may not land the same way for another.

Diet debates often frame disagreement as ignorance, noncompliance, or bias. Viewed through a microbiome lens, though, those differences look less like confusion and more like biological diversity.

From diet debates to precision nutrition

Instead of asking whether keto is better than carbohydrates, the more useful question may be who benefits from carbohydrate restriction, and why. Likewise, rather than assuming all fibers are universally beneficial, we should be asking who truly thrives on which fibers and what biological factors explain this response.

The real challenge is learning how to identify these differences earlier, before people cycle through diets that leave them frustrated or discouraged. Precision-nutrition research is already moving in this direction, focusing on inter-individual variability rather than average effects. A growing number of new companies are now building services around these insights. The future of nutrition may look less like universal rules and more like microbiome-informed personalization.

How to personalize now, before the science catches up

You don’t need a microbiome sequencing report to begin applying this idea.

1. Keep a food journal. Track what you eat alongside energy, mood, digestion, sleep, and hunger.

2. Use a structured tool. A food-quality scoring app or tracker can reveal patterns between what you eat and how you feel over time.

3. Listen to your gut. Persistent bloating, fatigue, or crashes after certain foods are signals, not weaknesses.
   

4. Experiment systematically. Try small, structured changes. Reduce refined carbs for two weeks, increase fiber gradually, or shift fat sources, and observe how you respond.
   

5. Focus on food quality first. Minimally processed foods consistently support healthier microbial ecosystems.
   

The end of diet tribes?

Nutrition may be entering a phase similar to medicine’s shift toward personalization. We no longer expect the same drug to work identically for every patient. Diet may follow the same path.

The goal isn’t to pick a winning diet. It’s to understand the biological individuality behind why different diets work for different people, and to use that insight to help everyone eat in a way that supports their own metabolism, microbiome, and well-being.

You’re not crazy if keto works for you. You’re not wrong if carbs work better. You’re human. And your microbiome is part of what makes your nutritional needs uniquely yours. That’s the future Gut Bites will be exploring.

What have you noticed works best for your body—lower carb, higher fiber, higher fat, or something else?

Now, the rise of GLP-1–based medications has added another layer; highlighting just how powerfully appetite, metabolism, and food intake are regulated by biology, not just willpower.

The problem isn’t a lack of information. It’s that we’re often asking the wrong question. Instead of debating nutrition camps, the more useful question is:
What actually changes metabolism in everyday life?

Again and again, the answer comes back to one core driver: food quality.

The missing link: microbiome → metabolism → appetite

What we eat doesn’t just provide calories and nutrients. It shapes:

• the gut microbiome

• metabolic signaling

• inflammation

• appetite hormones like GLP-1

• energy stability

Different foods create different biological environments. Some support microbial ecosystems that produce beneficial metabolites and help regulate appetite and metabolism. Others push toward volatility: spikes, crashes, cravings, and long-term metabolic strain.

This is why two people can eat “the same diet” on paper and feel completely different. It’s not just the label. It’s how the foods interact with the body.

GLP-1 medications have made this visible. They work by altering appetite and metabolic signaling, but these pathways are also influenced every day by what we eat, how food is processed, and how the microbiome responds.

Food is not a drug. But it does shape the same biology.

Why Gut Bites exists

As a gastroenterologist and microbiome researcher, I see this disconnect constantly. Patients aren’t failing nutrition advice. Nutrition advice is often too abstract, too polarized, or too disconnected from real life. People don’t need more rules. They need clearer signals.

Gut Bites exists to translate credible science into practical insight:

• how food shapes the gut microbiome

• how the microbiome shapes metabolism and appetite

• how metabolic signaling affects everyday health

Not as theory. As decisions you can use while choosing foods, building meals, and noticing how you feel.

What you’ll find here

This publication focuses on the patterns that consistently matter:

• why food quality often beats diet labels

• how different foods influence appetite, energy, and digestion

• how microbiome activity connects to metabolic health

• how GLP-1 biology fits into everyday eating

• how small, repeatable changes outperform extreme diets

• how to make better choices without moralizing food

The goal isn’t perfection. It’s clarity.

From ideas to tools

Over time, this work is also moving beyond writing. Gut Bites connects to a broader effort to make healthier eating easier in daily life, translating science into tools that help people:

• evaluate food quality

• refine meals

• see patterns between what they eat, appetite, and energy

This includes emerging tools that bring food quality, microbiome, and nutrition science into everyday decisions.

Because insight matters most when it changes what happens at the grocery store, in the kitchen, and across the week.

A different tone for nutrition

Nutrition doesn’t need more arguments. It needs better translation.

Less:

• rigid camps

• moral language

• one-size-fits-all advice

More:

• biological understanding

• practical guidance

• personalization over time

The future of nutrition will likely look less like universal rules and more like understanding how different people respond to different foods, and using that information earlier, before metabolic problems compound.

GLP-1 therapies are part of this shift. They’re not the whole story, but they’re a clear signal that metabolism is governed by biology we can influence, not just calories we count.

The simple starting point

Before sequencing the microbiome, starting a medication, or following a specific diet, most people benefit from the same first move. Focus on food quality.

Minimally processed foods, fiber diversity, and metabolically supportive patterns consistently create more stable signals: for the microbiome, for appetite regulation, and for metabolism. That foundation makes everything else work better.

If you care about:

• energy that lasts

• appetite that makes sense

• digestion that feels predictable

• health that compounds over time

You’re in the right place.

MD-authored gut health literature digests and first-in-class food quality app to power your microbiome.

Ultra-processed foods have received quite a lot of press, and a bit of a bad rap, recently, and perhaps rightfully so. They’ve been linked to expanding waistlines, declining brain health, and even higher risks of cancer.

But what exactly is an ultra-processed food—and are they all equally harmful? How do they affect the body in such adverse ways, and what role might the microbiome—the trillions of bacteria and viruses living in our digestive tract—play in this process?

My name is Chris Damman, and I’m a professor of gastroenterology at the University of Washington, where I see patients and study the microbiome. I’m also a former Gut Health and Microbiome Program Officer at the Bill & Melinda Gates Foundation, where I helped develop next-generation supplemental foods for women and children facing malnutrition.

The Forgotten Upside of Processing

We don’t often consider that food processing helped address hunger in many parts of the world and remains essential for famine relief today. Early nutritional science, understanding macronutrients like protein, fat, and carbohydrates, along with micronutrients such as vitamins and minerals, allowed us to prevent devastating deficiencies like kwashiorkor (deficient protein), pellagra (deficient vitamin B3), and scurvy (deficient vitamin C).

Modern ultra-processed foods grew out of this reductionist approach to food. And while the science initially helped address nutrient deficiencies, processed foods have since taken on a Frankenstein life of their own, meticulously engineered to co-opt our taste buds and reward pathways. The right combination of sugar, salt, fat, and flavor additives keeps us coming back for more.

What’s Missing Matters as Much as What’s Added

What’s less discussed is what’s been removed from ultra-processed foods rather than what’s been added. For every nutrient that’s concentrated, refined carbohydrates, sodium, saturated fats, there are missing components: potassium, micronutrients, fiber, healthy fats from nuts and fish, and phytochemicals like polyphenols from plants.

These missing ingredients are critical for both nutritional balance and for feeding our microbiome, which in turn supports our immune system, metabolism, and even mood. The health harms of ultra-processed foods arise not just from excess sugar or salt, but also from the absence of microbiome-accessible nutrients that whole foods naturally contain.

The Microbiome: The Missing Piece of the Puzzle

For decades, these “other” components—fiber, which give plants their structure, and polyphenols, which give plants their color—were thought to be unnecessary waste streams of food processing. But we now know they’re essential substrates for our gut microbes, which ferment fiber into short-chain fatty acids like butyrate and transform polyphenols into postbiotic compounds like urolithin A that regulate metabolism, immunity, and even mitochondrial function.

This missing microbial perspective has reshaped our understanding of nutrition: we weren’t just feeding ourselves. We were meant to feed our microbes too.

What Do We Mean by “Ultra-Processed”?

The term “ultra-processed food” was coined by Dr. Carlos Monteiro and colleagues at the University of São Paulo, Brazil, who developed the NOVA food classification system.

In short, ultra-processed foods (NOVA Group 4) are industrial formulations made mostly from refined ingredients and additives—sugar, starches, oils, protein isolates, and artificial flavorings—with few intact whole-food components. These foods are designed for long shelf life, convenience, and sensory appeal, not for microbiome nourishment.

Monteiro’s focus was on the ingredients added and intensified—not necessarily on what was lost. Yet the omissions may be just as harmful. Much like the macronutrient deficiencies of the early 20th century, today we face “microbiome nutrient deficiencies”—missing fiber, polyphenols, and healthy fats—linked to modern conditions such as obesity, diabetes, cancer, autoimmune disease, and neurodegeneration.

Can We Make Processed Foods Healthier?

Given the importance of processed foods for feeding the world, the question isn’t how to eliminate them, but how to make them incrementally better. The answer lies in restoring the natural balance once found in whole foods.

This means adding back fiber, healthy fats, micronutrients, and polyphenols—often lost as industrial waste streams—a practice now called “upcycling.” Ironically, our waste is becoming a new wellness commodity.

These reformulated products are not as healthy as whole foods, but they can be healthier than conventional ultra-processed ones, offering better nutrition, shelf stability, and flavor. After all, who doesn’t enjoy a good Oreo or bag of Doritos? The real question is: can we make a healthier Oreo or Dorito?

Empowering Consumers

Food companies are beginning to explore this space, but it’s difficult for consumers to know which claims: “Good for gut health,” “High in fiber” are credible.

Countries like France and Australia have introduced front-of-pack labeling systems such as Nutri-Score and the Health Star Rating to help distinguish better options. These tools work well for separating whole from processed foods, but they’re less effective at identifying the healthier processed foods within that category.

To address this, I developed a nutrient balance scoring system that targets the core nutritional imbalances in modern foods—ratios like sodium to potassium, carbohydrate to fiber, saturated to unsaturated fat, and artificial additives to phytochemicals.

This system has been integrated into a smartphone app that lets users scan foods in grocery aisles and see a score instantly. The hope is that widespread use will not only improve individual health, but also drive industry change by shifting consumer demand toward better products.

A Path Forward

Healthier ultra-processed foods may initially cost more and be considered an add on feature, just like power steering or power locks once did, but with scale, these innovations can become standard.

Just as we have significantly reduced nutritional deficiencies like pellagra, kwashiorkor, and scurvy, we can now address the microbiome-related nutrient deficiencies underlying many modern diseases—cancer, obesity, autoimmune disease, and Alzheimer’s.

With better science, smarter design, and informed consumers, even ultra-processed foods can evolve from part of the problem to part of the solution.

MD-authored gut health literature digests and first-in-class food quality app to power your microbiome.

MD-authored gut health literature digests and first-in-class food quality app to power your microbiome.

The post Ultra-Processed Foods: What the Media & Consumers are Missing appeared first on Gut Bites MD.

Colorectal cancer is steadily rising. Learn how diet & the gut microbiome affect risk, and which dietary practices & tools might reduce it.

Chances are you know someone impacted by colorectal cancer. The disease is on the rise, especially in young adults, with rates increasing 50% over the past 30 years. In another 5 years, it is projected to become the leading cause of cancer deaths in adults under 50. 

Contributing to this rise, more than 1 in 4 people ages 45-50 already have precancerous polyps, a figure that climbs to over 1 in 3 people for people after age 50. That is why 45 is the new 50 for starting colon cancer screening, to ideally catch the polyps early before they become cancer. But what’s behind this alarming trend? 

I’m Chris Damman, a gastroenterologist at the University of Washington, where I perform colorectal cancer screening colonoscopies, and study the microbiome’s impact on gut health. Over my 15 years in practice, I’ve personally witnessed an unsettling rise in early colorectal cancer.  Growing evidence suggests that the microbes in your gut may play a key role

.

Colon Cancer‘s Microbial Suspects

Modern changes in diet and lifestyle have been repeatedly linked to rising rates of colorectal cancer. Factors include ultra-processed diets, reduced physical activity, obesity, increased stress, as well as exposure to frequent, broad-spectrum antibiotics. 

One lesser-known, but increasingly studied factor is our gut microbiome–30 trillion plus bacteria, viruses and fungi that live in our colon and help regulate immunity and metabolism as well as protection from bad acting microorganisms. 

While a diverse microbiome can protect our health and may help prevent the development of colon cancer, some unsavery components of the microbiome can attach to the colon lining, cause inflammation, and even alter DNA, transforming healthy colon cells into cells that may become cancerous. 

The same lifestyle factors that influence colon cancer risk also disrupt the microbiome: processed foods, sedentary lifestyles, obesity, stress, and antibiotics. They reduce protective butyrate producers and promote inflammatory species.

These data raise the intriguing question of how much well-known lifestyle factors act directly on the colon versus indirectly through their effects on the microbiome.

Bad Actors at Play in the Colon

Research shows that certain strains of bacteria—with well-known names like E. coli and lesser-known ones like Fusobacterium nucleatum and Bacteroides fragilis—produce toxins and other factors that over time disrupt normal cell function and promote uncontrolled growth. 

Combinations of tests to detect these various strains are being used to develop new colorectal cancer diagnostics and prognostics. Ongoing research is also exploring whether these bacteria are merely associated bystanders or active instigators in cancer development.

Findings from animal model studies suggest the later may be true. In these experiments, researchers introduce specific microbes into germ-free or antibiotic-treated mice and directly observe whether tumors develop—offering the experimental control needed to demonstrate cause and effect in ways that human studies cannot.

Some human clinical studies suggest that these bacteria can also promote cancer cells spreading to other parts of the body, and may even hitch a ride with cancer cells during metastasis.

The Many Biotics Being Studied

This naturally raises the question: can colorectal cancer be treated or prevented by targeting bacteria?

There is precedent for targeting bacteria to treat GI cancers. Dr. Barry Marshall famously proved that H. pylori causes stomach ulcers by infecting himself and then curing the infection with antibiotics, a discovery that later helped establish H. pylori as a cause of certain stomach cancers and earned him the 2005 Nobel Prize.

The colon, however, is far more complex, containing thousands of bacterial species. Proving that any one type or collection of unhealthy bacteria causes cancer (rather than simply coexisting with it) is more challenging. Still, early trials are testing whether selective antibiotics, combined with standard chemotherapy treatments, might improve colorectal cancer treatment outcomes.

Other studies are exploring probiotics (beneficial bacteria) and prebiotics (the food that nourishes them) to reduce inflammation and potentially lower cancer risk, though data remains too preliminary for any formal recommendations

A Healthy Diet for Good Microbes

In the absence of strong evidence supporting various biotics for colorectal cancer prevention, the best approach is to focus on proven lifestyle measures for general health: eat well, exercise regularly, and manage stress. Recent research adds an important dimension to this advice—nurturing a healthy gut microbiome. 

The microbiome transforms components of food we can’t digest, such as fiber (which gives plant foods their structure) and polyphenols (which give them their color), into beneficial metabolites like butyrate and microbiome-modified polyphenols. These compounds can help reduce unhealthy bacteria and inflammation in the colon and may play a key role in preventing colorectal cancer.

Recent research also supports the use of calcium-rich dairy products and/or fermented dairy products, as well as increased omega-3 rich fish consumption as potentially protective in colon cancer and supportive of the microbiome.

Microbiome-supportive eating largely boils down to choosing more whole plants, dairy, and fish, but we all have our sweet and salty packaged food vices. Some packaged foods contain more fiber and polyphenols, less sugar and salt, and are more microbiome-friendly than others. I developed this public service smart app to help you find them.

Hazards For Microbial Dysbiosis

And what not to do? Smoking and most alcohol, especially hard alcohol and beer, disrupt the microbiome and are strongly associated with higher colorectal cancer risk (Group 1, definite carcinogens).

Current medical guidelines recommend avoiding both tobacco & alcohol altogether, but if you are going to consume alcohol, an occasional glass of wine may be the least associated with colorectal cancer risk.

Likewise, it is best to avoid processed meats—like hot dogs, bacon, sausage, deli meats, jerky (Group 1 carcinogens)—and limit red meats like beef, pork, lamb, and goat, (Group 2A carcinogens). The heme iron that gives red meat its color disrupts the microbiome and can promote the formation of precancerous polyps.

Meats charred at high temperatures during grilling also contain polycyclic aromatic hydrocarbons and heterocyclic amines, compounds that damage DNA, disrupt the microbiome, and raise colon cancer risk.

45 is the New 50 for Screening

And if lifestyle measures aren’t adequate, screening helps catch colorectal cancer early—or ideally prevent it altogether. Most people should start at age 45, or possibly earlier if there’s a family history of cancer or large polyps.

If you notice blood in your stool, change in your bowel habits, or unexplained abdominal pain or weight loss, check in with your primary doctor to see if further testing is needed.

A colonoscopy is the gold standard test, done about every 10 years if normal, or sooner if precancerous polyps are found. It involves drinking a prep solution the day before to clean the colon, sedating medications during the procedure, and usually a quick recovery by the next day.

Stool-based tests are noninvasive and done at home. They check for hidden blood or abnormal DNA—annually for FIT and gFOBT, and every three years for stool DNA tests (like Cologuard). If any test is positive, a colonoscopy is needed to follow up.

A Prescription for Prevention

In short, consume more plants, dairy, and fish and less processed/red meat, alcohol, and tobacco to support a healthy microbiome & colon. As for all the packaged items at the store, tools like this app with barcode scanner can help you choose the most microbiome-supportive foods. Beyond diet, exercise regularly, manage stress, and remember, 45 is the new 50 for screening. Here is a short list of the do’s and don’ts:

Dietary Do’s:

• Increase whole grains, beans, nuts, seeds, fruits and vegetables

• Increase fermented and unfermented dairy products & fish

• Try a scanner to explore the more microbiome-friendly foods

Dietary Dont’s:

• Avoid processed meat: hot dogs, bacon, sausage, deli meats, jerky

• Limit red meat, especially grilled beef, pork, lamb, and goat

• Avoid tobacco & alcohol, especially hard alcohol and beer

Additional Do’s:

• Get daily physical activity-at least 30 minutes of moderate/day.

• Manage stress through meditation, mindfulness, and quality sleep

• Discuss colon cancer screening strategy with your primary doctor

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington

MD-authored gut health literature digests and first-in-class food quality app to power your microbiome.

The post Why Colorectal Cancer is Rising–The Microbiome, Diet & How to Lower Your Risk appeared first on Gut Bites MD.

Is the old adage “calories in, calories out” true? The short answer is yes, but the full story is more nuanced.

From the moment food touches your tongue to the time it leaves your body, your digestive system and gut microbiome work to extract its nutrients. Enzymes in your mouth, stomach and small intestine break down food for absorption, while microbes in your large intestine digest the leftovers.

“Calories in, calories out” refers to the concept that weight change is determined by the balance between the calories you consume and calories you expend. This includes not only the number of calories you eat due to appetite and absorb via digestion, but also how well those absorbed calories are burned through metabolism.

Recent research indicates that a significant factor influencing people’s variable appetites, digestion and metabolism are biologically active leftover components of food, known as bioactives. These bioactives play a key role in regulating the body’s metabolic control centers: your brain’s appetite center, the hypothalamus; your gut’s digestive bioreactor, the microbiome; and your cells’ metabolic powerhouses, the mitochondria.

I’m a gastroenterologist who has spent the past 20 years studying the gut microbiome’s role in metabolic disease. I’ll share how dietary bioactives help to explain why some people can eat more but gain less and offer some dietary tools to improve metabolism.

Ruminating on appetite and digestion

Research has shown that consuming whole foods still “packaged” in their original fibers and polyphenols – the cellular wrappers and colorful compounds in plants that confer many of their health benefits – leads to more calories that pass through to your stool, when compared to processed foods that have been “predigested” by factories into simple carbs, refined fats and additives.

This is one way calorie-free factors influence the “calories in, calories out” equation, which can be beneficial in a society where calorie intake often exceeds needs. Eating more whole foods and less processed foods simply lets you eat more because more of those unprocessed calories go to your microbiome and out the other end.

Fiber and polyphenols also help regulate your appetite and calorie intake through the brain. Your microbiome transforms these leftover bioactives into metabolites – molecular byproducts of digestion – that naturally decrease your appetite. These metabolites regulate the same gut hormones that first inspired the popular weight loss drugs Wegovy, Ozempic and Monjaro, controlling appetite through your brain’s satiety center, the hypothalamus.

Processed foods lack these bioactives and are further formulated with salt, sugar, fat, and additives to be hyperpalatable, causing you to crave them and eat more.

Mitochondrial maestros in the middle

A full accounting of calories also depends on how effectively your body burns them to power your movement, thoughts, immunity and other functions – a process largely orchestrated by your mitochondria.

Healthy people typically have high-capacity mitochondria that easily process calories to fuel cellular functions. People with metabolic diseases have mitochondria that don’t work as well, contributing to bigger appetites, less muscle and increased fat storage.

Healthy folks also have less of a mitochondria-rich type of fat called brown fat. Rather than storing calories, this fat burns them to produce heat. Less brown fat may help explain why some people with obesity can have lower body temperatures than those who aren’t obese, and why there has been a decline in average body temperature in the U.S. since the industrial revolution.

Healthy mitochondria that burn more calories might also help explain why some people can eat more without gaining weight. But this raises the question: why do some people have healthier mitochondria than others?

Your mitochondrial health is ultimately influenced by many factors, including those usually associated with overall well-being: regular exercise, adequate sleep, stress management and healthy eating.

Who turned off the metabo-lights

The latest nutrition research is revealing the roles previously underappreciated dietary factors play in mitochondrial health. Beyond the essential macronutrients – fat, protein and carbohydrates – and micronutrients like vitamins and minerals, other leftover factors in food, including fibers, polyphenols, bioactive fats and fermentation products are also key for metabolism.

Unlike a Western diet, which often lacks these bioactives, traditional diets like the Mediterranean and Okinowan diets are rich in foods – nuts, seeds, fruits, vegetables, whole grains and fermented foods – replete with these factors. Many bioactives pass undigested through the small intestine to the large intestine, where the microbiome converts them into activated metabolites. These metabolites are then absorbed, influencing the number of mitochondria in cells and how they function.

At the most fundamental level of cell biology, metabolites turn on and off molecular switches in your genes through a process called epigenetics that can affect both you and your offspring. When the metabolic “lights” are turned on, they enliven the mitochondria responsible for a faster metabolism, effectively increasing the calories you use.

Please mind the microbiome gap

A healthy microbiome produces a full range of beneficial metabolites that support calorie-burning brown fat, muscle and metabolic health. But not everyone has a microbiome capable of converting bioactives into their active metabolites.

Long-term consumption of processed foods, low in bioactives and high in salt and additives, can impair the microbiome’s ability to produce the metabolites needed for optimal mitochondrial health. Overuse of antibiotics, high stress and lack of exercise can also adversely impact microbiome and mitochondrial health.

This creates a double nutrition gap: a lack of healthy diet and a deficiency in the microbes to convert its bioactives. As a result, well-studied nutritional approaches like the Mediterranean diet might be less effective in some people with an impaired microbiome, potentially leading to gastrointestinal symptoms like diarrhea and negatively affecting metabolic health.

In these cases, nutrition research is exploring the potential health benefits of various low-carb diets that may bypass the need for a healthy microbiome. While the higher protein in these diets can reduce the microbiome’s production of beneficial metabolites, the lower carbs stimulate the body’s production of ketones. One ketone, beta-hydroxybutyrate, may function similar to the microbiome metabolite butyrate in regulating mitochondria.

Emerging microbiome-targeting approaches might also prove helpful for improving your metabolic health: butyrate and other postbiotics to provide preformed microbiome metabolites, personalized nutrition to tailor your diet to your microbiome, intermittent fasting to help repair your microbiome, and the future possibility of live bacterial therapies to restore microbiome health.

Tools to transform fat into fuel

For most people, restoring the microbiome through traditional diets like the Mediterranean diet remains biologically achievable, but it is not always practical due to challenges such as time, cost and taste preferences. In the end, maintaining metabolic health comes back to the deceptively simple healthy lifestyle pillars of exercise, sleep, stress management and nutritious diet.

Some simple tips and tools can none-the-less help make nutritious diet choices easier. Mnemonics like the 4 F’s of food – fibers, polyphenols, unsaturated fats and ferments – can help you focus on foods that best support your microbiome and mitochondria with “leftovers.”

Bioactive-powered calculators and apps can also aid in selecting foods to control your appetite, digestion and metabolism to rebalance your calorie “ins and outs.”

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington

This article is republished from The Conversation under a Creative Commons license. Read the original article.

More Resources:

Gutbites.org — where you’ll find more practical food & microbiome digests to improve gut and overall health.

Gut Microbiome Nutrition App — to help in gut healthy food choice and meal preparation.

MD-authored gut health literature digests and first-in-class food quality app to power your microbiome.

The post Beyond calories in, calories out: your gut microbes, mitochondria & last meal’s leftovers count in metabolism appeared first on Gut Bites MD.

When milliseconds can mean the difference between silver and gold, endurance athletes in sports like marathon running, cycling, rowing and swimming optimize every aspect of their physiology for a competitive edge.

Many of these efforts result in enhancing the performance of mitochondria, the tiny but mighty energy-generating powerhouses within your cells. Carefully calibrated doses of exercise combined with beneficial stress – altitude, cold and heat – and optimized recovery in the form of nutrition, meditation and sleep, positively affect the number and health of mitochondria in the cells of your muscles, heart and brain.

But there is another aspect of endurance training that may have largely been overlooked by athletes and trainers – the role of the gut microbiome in optimizing your mitochondrial health and fitness.

I am a physician-scientist and gastroenterologist who has studied how food affects the gut microbiome’s role in health and disease for over 20 years. While research evaluating food’s effects on the microbiome and mitochondria is improving our understanding of conditions like obesity, cancer, rheumatoid arthritis and Alzheimer’s disease, it might also help athletes achieve new levels of performance through innovative approaches to nutrition.

Of microbiomes and mitochondria

The gut microbiome, a hidden factory of highly collaborative microorganisms in your intestines, ensures that your metabolism, immune system and brain run smoothly. Some researchers liken it to another organ that senses nutritional inputs, manufactures signaling molecules and prepares your body to respond appropriately.

Research has shown that endurance athletes have different gut microbiomes compared with the general population. Their microbiome’s composition and function, like increased production of a short-chain fatty acid called butyrate, are associated with increased VO₂ max, a fitness benchmark that measures your ability to consume oxygen during intense exercise. One organism in particular, Veillonella is found in some elite runners and may help raise lactate threshold, a fitness metric closely linked to mitochondrial function and how long an athlete is able to sustain intense effort.

A healthy microbiome communicates with the mitochondria, the tiny structures within your cells that convert calories into the raw cellular energy required for muscle contraction and other essential functions. It does this by transforming undigested food components of a healthy diet – like fiber, polyunsaturated fats and polyphenols – into molecules that increase the number and health of your mitochondria.

Some of these metabolites – butyrate, conjugated linoleic acid and urolithin A among them – have been shown to specifically improve muscle strength and endurance. Combining exercise with diets high in fiber, polyphenols – a chemical compound from plants – and healthy fats may thus augment mitochondrial fitness and improve exercise performance.

Nutritional gaffes and gaps

Healthy diets are critical for microbiome and mitochondrial health. Conversely, ultra-processed diets have been linked to conditions ranging from obesity and cancer to autoimmune disease and Alzheimer’s disease. Some people believe athletes are protected from the adverse health effects of ultra-processed diets due to the beneficial effects of exercise. While this may partially be true, it’s important to consider other factors in diet beyond just the calories burned.

Additives used to improve the taste and appearance of food, like emulsifiers, can negatively affect the gut microbiome, compromising the gut barrier and causing systemic inflammation, an unhealthy state linked to metabolic disease, cancer, autoimmune conditions and neurodegenerative diseases. Ultra-processed foods have also removed key factors like fiber, polyphenols and healthy fats found in whole foods that support gut health and signal to the mitochondria that there are calories to be metabolized.

The drinks, shakes, bars and gels used for endurance sports are processed foods formulated to provide concentrated and accessible energy during intense exercise. While unhealthy in other contexts, they can be key for enhancing performance during long endurance events when your body depletes its own version of accessible carbohydrates called glycogen.

But it’s important to complement these energy supplements with a healthy diet in the recovery hours following exercise. The combination of an unhealthy baseline diet with high-intensity exercise could compromise your gut barrier and increase inflammation. This has been linked to various training-related issues including gastrointestinal upset, musculoskeletal injuries and respiratory illnesses.

Performance-enhancing microbes

Reintroducing a diet rich in foods that positively affect your microbiome — beans, nuts, seeds, whole grains, fruits and vegetables — during the recovery phase of training can help most people prevent the adverse effects of high-intensity exercise and optimize performance.

However, due to antibiotic misuse and processed diets, some people lack key microbes and metabolic machinery needed to convert fibers and polyphenols into useful molecules the body can use. This shortage may explain why some healthy foods and diets might not be beneficial or tolerated by everyone.

Healthy diets might then benefit from reintroducing key microbes into the gastrointestinal tract. Research has shown that specific strains of probiotic bacteria can improve barrier function, reduce systemic inflammation and potentially enhance athletic performance by mitigating the side effects of high-intensity exercise. An alternative approach is to increase consumption of fermented foods, such as yogurt and pickled vegetables, which can increase microbiome diversity and decrease systemic inflammation.

In some cases, healthy foods might also be complemented by directly providing the body the key metabolites that microbes produce. Research shows that these metabolites – also called postbiotics or exercise mimetics – enhance muscle strength and exercise performance. Some postbiotics also function as prebiotics that fuel the growth of healthy microbes and help restore a damaged microbiome.

From research to podium

While the benefits of nutrition targeting your microbiome and mitochondria for general health are increasingly clear, this approach is still in the early days of exploration in endurance sports.

For the occasional exerciser and weekend warrior, whole nutrition strategies that support the microbiome and mitochondria could be quite helpful. These strategies have the potential to improve performance, protect against adverse training effects and prevent chronic health conditions like obesity, cancer and Alzheimer’s disease.

For elite athletes seeking even the smallest of improvements in an already finely tuned training regimen, further research into the gut microbiome’s influence on performance might be invaluable. In a highly competitive field where nothing can be left off the table — or in the cupboard — such interventions might just be the deciding factor between finishing on the podium or off it.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

More Resources:

Gutbites.org — where you’ll find more practical food & microbiome digests to improve gut and overall health.

Gut Microbiome Nutrition Calculator — to help in gut healthy food choice and meal preparation.

MD-authored gut health literature digests and first-in-class food quality app to power your microbiome.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

The post Athletes looking for a competitive edge may find it within their gut microbiome appeared first on Gut Bites MD.

Microbiome research to date has been much like the parable of the blind men and the elephant. How much can be said about an elephant by examining just its tail? Researchers have studied what is most readily available – stool rescued from a flush down the toilet – but have been missing the microbial masterminds upstream in the small intestine. Until recently.

Likened by some scientists to another human organ, your microbiome is collectively the tens of trillions of microorganisms that live in interconnected populations on and in your body. They serve as miniature sentinels that help protect your body’s surfaces from pathogenic invaders. In the upper intestine, distinct microbial populations also aid in digestion, metabolism and even immunity.

I am a gastroenterologist who has spent the past 20 years studying the microbiome’s role in health and disease. Advances in technology are helping scientists investigate the small intestine microbiome and the promise it holds for better understanding and treating many diseases.

Big transformations come from small places

Certain members of the small intestine microbiome are linked to obesity and overweight, while other microbial members are linked to a healthy metabolic state. Indeed, small intestine microbes aid in digestion by turning certain simple carbohydrates into the molecular building blocks of a healthy gut and body.

While analogous in function to the colon, small intestine metabolites can be quite distinct from the fiber-derived metabolites of the large intestine microbiome. Some small intestine metabolites help regulate the upper gut’s production of GIP, a sister molecule to the lower gut hormone GLP-1, which makes up the weight loss and type 2 diabetes drugs Wegovy and Ozempic. Together, with another lower gut hormone called PYY, this triumvirate is critical for coordinating your body’s response to food by regulating your appetite and blood sugar.

Monjaro is an incrementally more powerful combination of GIP and GLP-1 compared with Wegovy and Ozempic. The full complement of these hormones is naturally stimulated by the breakdown of products from both the large and small intestine microbiome.

The upshot on gut breakdown

Research has linked a disrupted small intestine microbiome to diseases of the gut. These include irritable bowel syndrome (IBS), small intestinal bacterial overgrowth (SIBO), Crohn’s disease and Celiac disease.

These diseases are thought to arise partly from disturbances in the way the microbiome breaks down food. Celiac disease, for example, is associated with the small intestine microbiome’s decreased ability to digest gluten. IBS and SIBO are linked to the opposite: the small intestine microbiome’s ability to too readily ferment fibers and sugars.

Foods like wheat, garlic, onion, beans and certain processed products that are high in FODMAPs – a set of fermentable short-chain carbohydrates – have been shown to contribute to symptoms in individuals with SIBO and IBS. Lactose-rich dairy is a high FODMAP food group implicated in lactose intolerance and linked to an overzealous small intestine microbiome.

The body’s not-so-diplomatic immunity

Diseases associated with the small intestine microbiome aren’t limited to metabolism and the gut. In the gut’s lining resides a virtual embassy of immune cells that remain in an ever-vigilant state surveying the motley stream of microbial and nutritional antigens passing through your gut.

Compromise in the security systems that separate the fecal stream from the rest of the body and the processes that keep immune responses in check are hypothesized to play a role in triggering various autoimmune conditions in which the body becomes confused as to who’s friend and who’s foe.

Studies have linked inflammatory changes in the small intestine microbiome to type 1 diabetes, where the body’s circulating immune cells attack insulin-producing cells in the pancreas, and to the extra-intestinal symptoms of Celiac disease, where immune cells can lead to destructive processes in the body’s eyes, skin and joints.

Lights shed in and on the tunnel

Up until very recently, small intestinal research has moved slowly. Scientists relied on upper endoscopy procedures, which involve sedation and inserting a small camera at the end of pinky-thick tubes through the mouth into the very first part of the small intestine.

One of the few alternatives to endoscopies has been studying patients who have had intestinal surgeries that leave direct portals into their small intestine via a hole in their abdominal wall.

Newly developed technologies are removing the need for sedating medications and unique anatomical situations by allowing scientists to more easily sample the furthest reaches of the gut. Such technologies include camera capsules tethered to angel-hair-thin filaments and other even more streamlined devices that create minimally invasive direct lines of access to the small intestine. Researchers have also developed capsules with sample compartments that open when they reach certain acidity levels in the body.

These new sampling techniques have unlocked unprecedented access to the upper gut, paving the way for new insights and therapies. In a real-life parallel to a childhood favorite, “The Magic School Bus, Inside the Human Body,” researchers can now ride along through the gut like Ms. Frizzle and her class, shining light on the microbial secrets held within.

Accrued alliance in a still-crude science

Therapies based on early understandings of the gut microbiome have included approaches ranging from probiotics to fecal transplants and prebiotics to fermented foods.

But new treatments for gut health are still in their early days. Studying the small intestine could provide insights to improve therapeutic development. A couple of promising future possibilities include partnering small intestine bacteria with their preferred prebiotics and personalized combinations of low FODMAP prebiotics designed to avoid small intestine fermentation.

Treatments that partner food and the microbiome are likely early harbingers of what’s to come in the rapidly developing field of microbiome medicine. Researching the small intestine – and not only the gut’s tail end – might just be microbiome medicine’s most pioneering upstream start.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

MD-authored food & microbiome digests and first-in-class food quality app to power your microbiome.

The post Gut Health’s Final Frontier: Voyages Into The Small Intestine Microbiome appeared first on Gut Bites MD.

People have been using salt since the dawn of civilization to process, preserve and enhance foods. In ancient Rome, salt was so central to commerce that soldiers were paid their “salarium,” or salaries, in salt, for instance.

Salt’s value was in part as a food preservative, keeping unwanted microbes at bay while allowing desired ones to grow. It was this remarkable ability to regulate bacterial growth that likely helped spark the development of fermented foods ranging from sauerkraut to salami, olives to bread, cheese to kimchi.

Today, salt has become ubiquitous and highly concentrated in increasingly processed diets. The evidence has mounted that too much salt – specifically the sodium chloride added to preserve and enhance the flavor of many highly processed foods – is making people sick. It can cause high blood pressure and contribute to heart attacks and stroke. It is also associated with an increased risk of developing stomach and colon cancer, Ménière’s disease, osteoporosis and obesity.

How might a substance previously thought worth its weight in gold have transformed into something many medical institutions consider a key predictor of disease?

Salt lobbyists may be one answer to this question. And as a gastroenterologist and research scientist at the University of Washington School of Medicine, I want to share the mounting evidence that microbes from the shadows of your gut might also shed some light on how salt contributes to disease.

Blood pressure cookers

Sodium’s role in blood pressure and heart disease results largely from its regulating the amount of water inside your blood vessels. In simple terms, the more sodium in your blood, the more water it pulls into your blood vessels. This leads to higher blood pressure and subsequently an increased risk for heart attack and stroke. Some people may be more or less sensitive to the effects salt has on blood pressure.

Recent research suggests an additional way salt may raise blood pressure – by altering your gut microbiome. Salt leads to a decrease in healthy microbes and the key metabolites they produce from fiber. These metabolites decrease inflammation in blood vessels and keep them relaxed, contributing to reduced blood pressure.

With the exception of certain organisms that thrive in salt called halophiles, high levels of salt can poison just about any microbe, even ones your body wants to keep around. This is why people have been using salt for a long time to preserve food and keep unwanted bacteria away.

But modern diets often have too much sodium. According to the World Health Organization, healthy consumption amounts to less than 2,000 milligrams per day for the average adult. The American Heart Association recommends less than 2,300 milligrams per day.

While the specific sodium needs may vary by individual, by the amount of potassium in the diet, and specific medical conditions like heart failure, the global mean intake of 4,310 milligrams of sodium has likely increased the amount of salt in the gut over healthy levels for most adults.

Lowering sodium has been associated with and causally linked to increases in healthy members of the microbiome and their metabolites.

Salt of the girth

Sodium is connected to health outcomes other than blood pressure, and your microbiome may be playing a role here, too.

High sodium diets and higher sodium levels in stool are significantly linked to metabolic disorders, including elevated blood sugar, fatty liver disease and weight gain. In fact, one study estimated that for every one gram per day increase in dietary sodium, there is a 15% increased risk of obesity.

A gold-standard dietary study from the National Institutes of Health found that those on a diet of ultraprocessed foods over two weeks ate about 500 more calories and weighed about 2 pounds more compared with those on a minimally processed diet. One of the biggest differences between the two diets was the extra 1.2 grams of sodium consumed with the ultraprocessed diets.

A leading explanation for why increased salt may lead to weight gain despite having no calories is that sodium increases cravings. When sodium is combined with simple sugars and unhealthy fats, these so-called hyperpalatable foods may be linked to fat gain, as they are particularly good at stimulating the reward centers in the brain and addiction-like eating behaviors.

Salt may also connect to cravings via a short circuit in the gut microbiome. Microbiome metabolites stimulate the release of a natural version of weight loss drugs Wegovy and Ozempic, the gut hormone GLP-1. Through GLP-1, a healthy microbiome can control your appetite, blood sugar levels and your body’s decision to burn or store energy as fat. Too much salt may interfere with its release.

Other explanations for salt’s effect on metabolic disease, with varying amounts of evidence, include increased sugar absorption, increased gut-derived corticosteroids and a sugar called fructose that can lead to fat accumulation and decreases in energy use for heat production.

Desalin-nations

While many countries are implementing national salt reduction initiatives, sodium consumption in most parts of the world remains on the rise. Dietary salt reduction in the United States in particular remains behind the curve, while many European countries have started to see benefits such as lower blood pressure and fewer deaths from heart disease through initiatives like improved package labeling of salt content, reformulating foods to limit salt and even salt taxes.

Comparing the nutrition facts of fast-food items between countries reveals considerable variability. For instance, McDonald’s chicken nuggets are saltiest in the U.S. and even American Coke contains salt, an ingredient it lacks in other countries

.

The salt industry in the U.S may have a role here. It lobbied to prevent government regulations on salt in the 2010s, not dissimilar from what the tobacco industry did with cigarettes in the 1980s. Salty foods sell well. One of the key voices of the salt industry for many years, the now-defunct Salt Institute, may have confused public health messaging around the importance of salt reduction by emphasizing the less common instances where restriction can be dangerous.

But the evidence for reducing salt in the general diet is mounting, and institutions are responding. In 2021, the U.S. Department of Agriculture issued new industry guidance calling for a voluntary gradual reduction of salt in commercially processed and prepared foods. The Salt Institute dissolved in 2019. Other organizations such as the American Frozen Food Institute and major ingredient suppliers such as Cargill are on board with lowering dietary salt.

From add-vice to advice

How can you feed your gut microbiome well while being mindful of your salt intake?

Start with limiting your consumption of highly processed foods: salty meats (such as fast food and cured meat), salty treats (such as crackers and chips) and salty sneaks (such as soft drinks, condiments and breads). Up to 70% of dietary salt in the U.S. is currently consumed from packaged and processed foods.

Instead, focus on foods low in added sodium and high in potassium such as unprocessed, plant-based foods: beans, nuts, seeds, whole grains, fruits and vegetables. Fermented foods, though often high in sodium, may also be a healthier option due to high levels of potassium, short-chain fatty acids, fiber, polyphenols.

Indeed, it’s important to consider the ratio of sodium and potassium as a dietary guide. While sodium helps keep fluid in your blood vessels, potassium helps regulate sodium levels in your blood and stool. Here’s a calculator tool to help maintain the healthiest balance.

And remember, while all advice is best taken with a grain of salt, your microbiome gently asks that it just not be too large.

Christopher Damman, Associate Professor of Gastroenterology, School of Medicine, University of Washington. Editor-in-Chief of Gut Bites MD.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

MD-authored gut health literature digests & first-in-class food quality app to power your microbiome.

The post How Salty Diets Might Harm Your Microbiome Contributing to Metabolic Disorders & Obesity appeared first on Gut Bites MD.