You Can Do Everything Right and Still Have a Gut Imbalance, Part One: Birth, Antibiotics, Food, and Glyphosate

You had a vaginal birth. You breastfed. You waited to introduce processed food and chose organic whenever you could.

You read ingredient labels. You stopped using antibacterial soap. You replaced the cleaners in your home. You bought the organic cotton pajamas and carefully considered everything that touched your baby’s skin.

And yet, you or your child still developed eczema, constipation, food reactions, recurring infections, anxiety, sleep disruptions, allergies, bloating, picky eating, behavioral issues, or another symptom you couldn’t explain despite everything you were doing to support your family’s health.

If you’ve spent any time here, listened to the podcast, or read our other articles, you already know these aren’t random, disconnected symptoms. They’re different ways an imbalanced gut microbiome can communicate through the skin, digestion, immune system, nervous system, and behavior.

And once you understand that connection, the next question is impossible to ignore.

How could there still be a microbial imbalance?

Because a microbiome isn’t shaped by one decision.

It is shaped by thousands of microbial inputs and disruptions across an entire lifetime, beginning before birth and continuing every day.

You didn’t fail to protect your family.

You’re living in a world that continually disrupts the microbiome, which is why microbial balance now has to be intentionally restored.

Microbial Imbalance Has Become the Modern Baseline

Your microbiome is the enormous ecosystem of bacteria, fungi, viruses, and other microorganisms living throughout your body.

These organisms help digest food, produce important compounds, train and regulate the immune system, protect the intestinal lining, communicate with the nervous system, and prevent opportunistic organisms from gaining too much power.

But this ecosystem depends on balance.

It needs beneficial organisms.

It needs microbial diversity.

It needs minerals and food that allow supportive organisms to flourish.

And it needs regular contact with a diverse microbial world.

Modern life continually interferes with every part of that process.

We’ve removed many of the microbial inputs that once helped build and maintain a diverse microbiome. At the same time, we’ve dramatically increased our exposure to substances that disrupt the microbes we still have.

We eat from a less diverse food supply.

We spend more time indoors.

We have less contact with soil, animals, plants, and natural environments.

We sanitize our hands, countertops, homes, food, water, and public spaces.

We consume antibiotics, medications, pesticides, preservatives, refined sugar, and food additives that were never part of the microbial environment in which humans developed.

We live with chronic stress, contaminated air, treated water, damaged soil, artificial light, disrupted sleep, and buildings where mold can grow behind a wall for years before anyone realizes it’s there.

None of these exposures has to single-handedly destroy your microbiome.

That isn’t how this happens.

Microbial imbalance is built through the cumulative effect of thousands of disruptions and missing inputs over time.

Your Microbiome Was Being Shaped Before You Were Born

No one begins life with a microbiome completely separate from the generations that came before them.

A baby’s early microbial development is influenced by the mother’s microbiome, pregnancy, birth, antibiotics, feeding, the home environment, siblings, animals, food, and everything the baby encounters afterward.

A vaginal birth exposes a baby to maternal microbes during delivery. A C-section creates a different initial microbial experience.

Breast milk supplies microbes and compounds that help feed specific beneficial bacteria. Formula creates a different nutritional and microbial environment.

This doesn’t mean a C-section or formula feeding determines a child’s future.

C-sections save lives. Breastfeeding isn’t possible for every mother. Antibiotics during labor are sometimes medically necessary.

But these experiences help shape the initial microbial ecosystem, and restoration is rarely included in the conversation afterward.

We’re told how to care for the incision, prepare a bottle, or finish the medication.

But no one talks about how the baby’s developing microbiome has also experienced something significant and needs to be intentionally supported.

And this doesn’t begin with one mother.

A woman’s microbiome has already been shaped by her own birth, feeding, childhood diet, illnesses, medications, stress, home, environment, and everything her body has encountered.

She then passes part of that microbial foundation to her baby.

This is how microbial depletion becomes generational.

But this isn’t genetic destiny, and it isn’t something to fear. It explains why a deeply intentional mother can make completely different choices for her baby and still see signs of imbalance.

Her baby’s microbiome didn’t begin with her first feeding decision.

It began inside a much larger microbial story.

Antibiotics Eliminate Bacteria, but They Leave the Microbiome Vulnerable

Antibiotics kill bacteria.

That’s their job.

But they don’t eliminate only the bacteria associated with the infection. They also wipe out beneficial bacteria that protect the gut, regulate the immune system, support digestion, communicate with the brain and nervous system, and prevent harmful organisms from taking over.

This is why the end of an antibiotic prescription isn’t the end of what happens inside the body.

The infection may be gone, but the microbial ecosystem has been disrupted.

Protective bacteria have been depleted. Space has opened inside the microbiome. And yeast, harmful bacteria, and other opportunistic organisms now have an opportunity to multiply without enough beneficial organisms keeping them under control.

This is why women can experience constipation, diarrhea, bloating, anxiety, depression, mastitis, thrush, bacterial vaginosis, yeast infections, or recurring UTIs after taking antibiotics.

These aren’t random symptoms appearing for random reasons.

They’re signs of a microbial ecosystem that was disrupted and never restored.

A woman takes an antibiotic for mastitis. The infection clears, but her beneficial bacteria are depleted. Then the mastitis returns, thrush develops, a vaginal yeast infection appears, her digestion changes, or anxiety begins to feel more consuming.

A child takes an antibiotic for an ear infection. The infection clears, but the protective bacteria aren’t replenished. Then another ear infection develops. Or the next symptom is strep, chronic congestion, constipation, eczema, food reactions, or a cycle of getting sick every few weeks.

The diagnosis changes, so each symptom is treated as a new problem.

But the pattern underneath it never changed.

The infection was treated.

The microbiome was left vulnerable.

And when that ecosystem is left vulnerable, opportunistic organisms have an opportunity to return, multiply, and create the next symptom.

This is how one antibiotic can become the beginning of a repeating pattern.

Antibiotics Aren’t the Only Medications Changing the Gut

Antibiotics are the most obvious medication to include in a microbiome conversation because they’re designed to kill bacteria.

But they aren’t the only medications changing the environment inside the gut.

Acid-suppressing medications reduce stomach acid.

Stomach acid isn’t a digestive inconvenience the body accidentally creates. It helps break down food, release nutrients, and protect the digestive tract from microorganisms entering through food and water.

When stomach acid is repeatedly suppressed, that protection changes. Organisms that would ordinarily encounter a highly acidic environment can survive farther into the digestive tract.

Laxatives and antidiarrheal medications change transit time.

Steroids change immune activity.

Antihistamines influence signaling involved in digestion, motility, and the nervous system.

And commonly used medications, including over-the-counter anti-inflammatory medications can interact directly or indirectly with gut organisms, intestinal permeability, digestive secretions, microbial metabolism, or the immune system surrounding the gut.

This doesn’t mean medications never have an important place.

It means they don’t enter one isolated part of the body, perform one action, and leave everything else untouched.

They enter an interconnected biological system.

A medication can change the symptom it was prescribed for while also changing the microbial environment beneath it.

And when that environment isn’t intentionally supported, you can do everything you were told to do and still find yourself with a new symptom, a recurring symptom, or a body that no longer feels like your own.

Modern Food Is Creating a Different Microbiome

Food does more than provide calories.

It carries nutrients, minerals, fibers, plant compounds, and microorganisms into the gut. And every one of those inputs helps shape the microbial environment inside your body.

But modern food is providing far less of what beneficial bacteria need while delivering far more of what harmful overgrowths can use.

Our food begins in soil that has been repeatedly tilled, chemically treated, and stripped of the microbial diversity and mineral richness that once supported the plants growing within it.

Then the food is harvested, washed, sanitized, processed, refined, preserved, and transported before it ever reaches your kitchen.

The produce may look the same, but it isn’t carrying the same mineral or microbial diversity that food grown in healthy, living soil once carried.

So we are receiving fewer of the beneficial microbial inputs that once came naturally through food.

And at the same time, the modern food system is filling our diets with refined sugar, refined carbohydrates, processed oils, emulsifiers, preservatives, artificial sweeteners, colors, and other additives that create a completely different environment inside the gut.

These foods don’t simply fail to nourish beneficial bacteria.

Many of them provide exactly what harmful bacteria, yeast, and other opportunistic organisms need to continue flourishing.

A “food” can provide calories while providing nothing beneficial bacteria need.

It can fill a stomach while starving the organisms responsible for protecting the gut.

It can be fortified with isolated vitamins while feeding the same microbial overgrowths interfering with digestion, nutrient absorption, immune regulation, appetite, mood, and behavior.

Food literally becomes microbial instruction when it reaches the gut.

Whole, diverse, mineral and microbial-rich foods help create an environment where beneficial bacteria can flourish.

But a diet dominated by refined and ultra-processed foods continually feeds the organisms that have already gained too much power while failing to restore the bacteria needed to keep them under control.

And this is another reason a mother can prepare most meals at home, choose the best ingredients available to her, and still see signs of imbalance in herself or her child.

She is making thoughtful decisions within a food system that has already changed the soil, seeds, plants, animals, processing, and microbial quality of what reaches her kitchen.

Her choices matter deeply.

But they cannot restore everything the modern food system has destroyed.

Refined Sugar Feeds the Microbial Environment That’s Already There

Refined sugar is quickly available.

That matters when harmful bacteria, yeast, fungus, and other opportunistic organisms have already become overgrown.

You’re not simply eating something sweet.

You’re delivering an easily accessible food source into an existing microbial community.

Which organisms benefit depends on what’s already living there.

This is why two children can eat the same cupcake and have completely different experiences.

One child eats it and moves on.

The other becomes bloated, itchy, constipated, hyperactive, emotionally dysregulated, unable to sleep, or desperate for more sugar.

The difference isn’t simply the cupcake.

It’s the microbial environment inside the child’s body.

When the organisms that flourish on sugar already have too much power, their demands become louder. Cravings intensify. Food preferences narrow. The child begins asking for the same refined foods repeatedly while resisting the foods that nourish beneficial bacteria.

This isn’t simply a lack of discipline or a difficult personality.

It’s a microbial environment influencing appetite, cravings, digestion, and behavior.

And it’s another reason a mother can carefully control what comes into her home and still feel like she’s fighting something bigger than the food on her child’s plate.

She is.

She’s working against the microbial environment that food is interacting with.

Glyphosate Belongs at the Center of This Conversation

Most people don’t believe they’re eating Roundup.

They picture glyphosate being sprayed on weeds, driveways, fence lines, and fields.

They don’t picture it as part of the agricultural system producing the food arriving on their child’s plate.

But glyphosate is one of the most widely used herbicides in modern agriculture.

Most genetically engineered crops were specifically developed to tolerate glyphosate. The weeds surrounding the crop can be killed while the crop continues growing.

This dramatically expanded how glyphosate could be used.

But don’t be fooled. Glyphosate isn’t limited to genetically engineered crops.

It’s also used with non-GMO crops for weed control before planting and in certain preharvest applications.

This means non-GMO doesn’t automatically mean glyphosate-free.

And this is where the GMO conversation needs to become more precise.

Genetic engineering is a method used to create many different traits. The microbial concern isn’t simply that a plant was genetically modified.

The deeper concern is the agricultural system created around herbicide-tolerant crops, widespread chemical use, environmental contamination, and the residues that follows food from the field to the body.

One large French study found quantifiable glyphosate in 99.8% of the urine samples it tested. In the United States, nationally representative biomonitoring found glyphosate in 81.2% of people tested. The US study was performed 2014 so we can only imagine what a more recent study would show. Interestingly enough, I couldn’t find one. Hmmmm. I question who is influencing that? 

Needless to say, exposure is widespread.

Glyphosate isn’t limited to farmers, people spraying weeds, or families eating genetically engineered food.

It has become part of the environment nearly everyone is trying to raise a healthy family within.

This is exactly how a mother can buy organic, choose non-GMO, wash every piece of produce, and still have glyphosate detected inside her body.

She didn’t fail to avoid it.

It has become incredibly difficult to avoid.

The Microbiome Cannot Be Left Out of This Conversation

Glyphosate and many of the chemicals used throughout modern agriculture were created to kill, suppress, or interfere with living organisms.

And your body is home to trillions of living organisms.

As you have learned in this article and every Follow Your Gut Podcast episode, your beneficial bacteria help protect your intestinal lining, regulate your immune system, produce essential compounds, support digestion, communicate with your nervous system, and prevent harmful organisms from taking over.

So when chemicals designed to disrupt biological and microbial processes repeatedly enter the food, water, soil, and body, we have to ask what they’re doing to that microbial ecosystem.

They don’t have to kill every organism to create an imbalance.

They only have to weaken enough protective bacteria, interfere with microbial metabolism, or give more resistant organisms an advantage.

Once that happens, the entire environment begins to change.

Beneficial bacteria lose their ability to hold the ecosystem in balance. Harmful bacteria, yeast, fungus, and other opportunistic organisms gain more room to flourish. The compounds being produced inside the gut change, the intestinal lining becomes more vulnerable, and the signals reaching the immune system, brain, and nervous system change with it.

This is why glyphosate exposure is so much bigger than a conversation about residue on food.

It’s a conversation about what happens when a world already depleted of beneficial microbes continually exposes the organisms we have left to chemicals designed to disrupt life.

And it’s another reason you can choose organic, buy non-GMO, wash your produce, prepare your meals at home, and still have a microbial imbalance.

You aren’t making the wrong choices.

You’re making the best choices you can inside an agricultural system that has made microbial disruption almost impossible to avoid.

Why Choosing Organic Matters So Much

Choosing organic is one of the most meaningful ways you can reduce the chemical burden entering your family’s food and support a healthier agricultural system.

Organic farming doesn’t allow genetically engineered seeds or the routine use of most synthetic pesticides and herbicides. Instead, it prioritizes practices that support soil health, biological diversity, natural pest management, and the long-term health of the land where food is grown.

Choosing organic helps reduce the amount of glyphosate and other synthetic agricultural chemicals your family is exposed to through food. It also supports farmers who are growing food without building the entire system around genetically engineered, herbicide-tolerant crops.

This is why organic matters far beyond one piece of produce.

Every organic purchase supports a food system moving away from routine chemical dependence and toward farming practices that protect the biological foundation our food depends on.

But even organic food can’t place your family inside a sealed environment.

Pesticides and herbicides move through air, water, soil, agricultural equipment, processing facilities, and neighboring fields. They don’t stop at the edge of an organic farm.

This means organic food can still encounter residues through environmental drift and contamination.

But let me be very clear, this doesn’t make choosing organic pointless.

In fact, it shows why choosing organic is so important while also explaining why even the most intentional food choices can’t carry the entire responsibility for your family’s microbial health.

Choosing organic can significantly reduce your family’s exposure and support the kind of agricultural system we need more of.

But you can’t shop your way completely outside the modern world.

You Can Make Every Thoughtful Choice and Still Live Within This Food System

Your decisions matter.

Choosing organic matters.

Avoiding unnecessary antibiotics matters.

Preparing food at home, reducing refined sugar, and understanding what different foods are feeding inside the gut all matter.

But these decisions don’t erase the microbial foundation you inherited or completely separate your family from the agricultural and medical systems surrounding you.

You can make the best choices available and still be working with a microbiome shaped by generations of depletion, modern medical interventions, nutrient-depleted food, refined ingredients, pesticides, and an agricultural system built around chemicals designed to disrupt living organisms.

This is why microbial imbalance isn’t proof that you did something wrong.

It’s the cumulative result of living inside a world that has changed the microbial foundation of birth, medicine, soil, agriculture, and food.

And food is only one part of the environment shaping your family.

The water you drink, the air you breathe, the buildings you live in, the products you use, the stress your body carries, and your separation from the natural microbial world are shaping the microbiome too.

That is where Part Two of this conversation begins. Coming next.

Frequently Asked Questions

Why can I have a gut imbalance if I’ve never taken antibiotics?

Antibiotics are one major microbiome disruption, but they aren’t the only one.

Your microbiome has also been shaped by what you inherited from your mother, how you were born and fed, medications, modern food, refined sugar, pesticides, environmental chemicals, and the microbial quality of the soil and food system surrounding you.

Avoiding antibiotics protects the microbiome from one significant disruption. It doesn’t separate you from every other influence shaping it.

Can my child have a gut imbalance if I had a vaginal birth and breastfed?

Yes.

A vaginal birth and breastfeeding provide important microbial inputs, but they don’t determine everything that happens afterward or the microbiome you passed on.

Your child’s microbiome continues responding to food, water, illness, medications, stress, the home environment, outdoor exposure, and everything else the body encounters throughout childhood.

These choices matter deeply, but they can’t guarantee lifelong microbial balance.

How do antibiotics leave the microbiome vulnerable?

Antibiotics don’t eliminate only the bacteria associated with an infection. They also deplete beneficial bacteria that protect the gut, regulate immune activity, support digestion, communicate with the nervous system, and prevent harmful organisms from taking over.

When those protective organisms are depleted, harmful bacteria, yeast, and other opportunistic organisms have more space to multiply.

The infection may be gone, but the microbial environment that allowed the pattern to continue hasn’t been restored.

Can medications other than antibiotics affect the gut?

Yes.

Medications don’t enter one isolated part of the body and leave everything else untouched. They enter an interconnected biological system.

How does modern food contribute to gut imbalance?

Modern food provides less of what beneficial bacteria need while delivering more of what harmful overgrowths can use.

Refined sugar, refined carbohydrates, processed oils, emulsifiers, preservatives, artificial sweeteners, and other additives create a very different microbial environment from diverse, mineral-rich whole foods.

Food doesn’t simply provide calories.

It helps determine which organisms are fed and given the opportunity to flourish.

Does refined sugar feed harmful bacteria and yeast?

Refined sugar provides a quickly available food source inside the gut.

When harmful bacteria, yeast, fungus, and other opportunistic organisms have already become overgrown, refined sugar continues feeding the microbial environment they are flourishing within.

This is why two children can eat the same food and have completely different digestive, skin, mood, sleep, or behavioral responses.

Does non-GMO mean glyphosate-free?

No.

Glyphosate is also used with non-GMO crops for weed control before planting and in certain preharvest applications.

A non-GMO label tells you that the food wasn’t produced using genetic engineering. It doesn’t tell you that the crop was grown without glyphosate or other herbicides.

Non-GMO isn’t a substitute for organic.

Why is choosing organic so important?

Organic farming prohibits genetically engineered seeds and the routine use of most synthetic pesticides and herbicides. It also supports farming practices focused on soil health, biological diversity, and natural pest management.

Choosing organic can reduce your family’s exposure to glyphosate and other synthetic agricultural chemicals while supporting a healthier food system.

But organic farms still exist within the larger environment. Chemical drift and contamination can move through air, water, soil, equipment, and neighboring fields.

Organic matters deeply, but it can’t place your family inside a sealed environment.

Editorial Sources

The Modern and Industrialized Microbiome

Vulnerability of the Industrialized Microbiota
Examines how industrialized living, dietary changes, antibiotics, C-section births, formula feeding, sanitation, and reduced environmental microbial exposure have contributed to the loss of microorganisms associated with traditional human populations. It supports the article’s central teaching that microbial depletion is the cumulative result of modern life rather than one isolated decision.

Industrialization Drives the Gut Microbiome and Resistome of Chinese Populations
Examines microbial differences across populations experiencing different degrees of industrialization. It supports the explanation that industrialization is associated with changes in microbial composition, function, and antibiotic-resistance patterns.

Birth, Antibiotics, and Early Microbial Development

Impact of Mode of Birth and Perinatal Antibiotics on Infant Gut Microbiota and Health: A Systematic Review and Meta-Analysis
Examines how C-section birth and perinatal antibiotic exposure are associated with differences in early gut-microbiome composition and diversity. It also identifies breastfeeding as a factor associated with partial microbial restoration while recognizing that certainty about long-term clinical outcomes remains limited.

Applied Physiology: Gut Microbiota and Antimicrobial Therapy
Reviews how antimicrobial therapies influence gut-microbiota composition, diversity, metabolic activity, and resilience. It supports the distinction between treating an infection and rebuilding the microbial ecosystem afterward.

Public Health Case for Microbiome-Sparing Antibiotics and New Opportunities for Drug Development
Explains the broader effects antibiotics can have on beneficial microbial communities and the growing need for treatments that preserve the microbiome.

Ultra-Processed Food and Food Additives

Ultra-Processed Foods and Food Additives in Gut Health and Disease
Reviews evidence connecting ultra-processed foods and particular additives with the gut microbiome, intestinal permeability, inflammation, and gastrointestinal health. It also distinguishes human observational research from the preclinical evidence available for many individual additives.

Ultra-Processed Food and Gut Microbiota: Do Additives Affect Eubiosis? A Narrative Review
Examines how emulsifiers, sweeteners, preservatives, colors, and other ingredients found in ultra-processed food can interact with microbial balance and the intestinal environment.

Glyphosate, Pesticides, and the Microbiome

Quantifiable Urine Glyphosate Levels Detected in 99% of the French Population, With Higher Values in Men, Younger People, and Farmers
Examined thousands of urine samples collected from participants in France and reported quantifiable glyphosate in 99.8% of those analyzed. It supports the statement that glyphosate exposure is widespread while not establishing that detection alone proves an adverse health effect.

Exposure to Glyphosate in the United States: Data From the 2013–2014 National Health and Nutrition Examination Survey
Used nationally representative U.S. biomonitoring data and detected urinary glyphosate in 81.2% of the population tested. It supports the explanation that glyphosate exposure extends far beyond farmers and people directly spraying herbicides.

Effects of Glyphosate Exposure on Intestinal Microbiota, Metabolism and Microstructure: A Systematic Review
Reviews evidence that glyphosate and glyphosate-based formulations can influence microbial composition, metabolism, intestinal permeability, mucus, microvilli, and other features of the intestinal environment. It also makes clear that much of the available evidence comes from animal studies.

The Effect of Glyphosate on Potential Pathogens and Beneficial Members of Poultry Microbiota In Vitro
Compares the susceptibility of different bacterial organisms to glyphosate under laboratory conditions. It supports the explanation that microbial species don’t necessarily respond to glyphosate equally without establishing that the same pattern definitively occurs inside the human gut.

USDA Pesticide Data Program: 2024 Annual Summary
Reports pesticide-residue findings from foods sampled through the USDA Pesticide Data Program. It supports a precise discussion of pesticide exposure by showing that residues are common across portions of the food supply without claiming that every food contains glyphosate.