Did you know that the health of your baby’s microbiome during the first year of life can determine whether or not they experience certain health issues years down the road?

Scientists have discovered a “window of opportunity” during the first 12 months after birth when the microbes in our gut are actually programming our baby’s immune system, training it on what sorts of things to react to and not react to as well as the appropriate amount of immune response.

Recent studies indicate that certain exposures during this window of opportunity such as antibiotics, cesarean section delivery, and formula feeding can cause the wrong types of microbes to colonize our baby’s gut, setting in place potentially permanent immune programming that can increase their risk for developing immune-related issues later on like autoimmunity, eczema, allergies, type 1 diabetes, and more.

Given this fact, it’s important that we do everything we can as parents to optimize our baby’s gut microbiome, particularly in the first year of life since the microbes present in our baby’s gut at this point in time have strong influences on the development and training of their immune system, which can have lasting effects on their health.

But what exactly is happening and, even more importantly, what can we do about it?

Keep reading to find out what you can do to mitigate these risks and improve your child’s health.

Table of Contents

What is happening?

The microbes that colonize our body strongly influence the development of our immune system.

Scientists have discovered a critical period during early development in which disruption of our microbiome can lead to persistent and even permanent immune system abnormalities:

• According to a study, “the immune influences induced by the microbiota during this early period of life may be durable, creating a “window of opportunity” for proper (or improper) immune education to occur and resistance (or susceptibility) to disease in later life” [1].
• These microbe-immune interactions happen even in the earliest days of life, and it appears that any disruption to this process by means of C-section delivery, formula feeding, antibiotic exposure, etc. can possibly cause long-lasting immune dysfunction that manifests as childhood diseases like allergies, eczema, asthma, autoimmunity, and more
• Numerous epidemiological studies suggest that early development of the infant gut microbiota influences the risk of allergic diseases later in life, which they attribute to an inappropriate development of the gut microbiome and associated disruption of immune homeostasis during the first year of life [2].

Some Examples

• Antibiotic use within the first 6 months of life has been associated with an increased susceptibility to allergies and asthma at 6 years of age.
• Antibiotic exposure during the first year of life is associated with the development of wheezing and eczema at 8 years of age.
• Antibiotic exposure during the first year of life is associated with an increased risk for the development of inflammatory bowel disease (IBD), obesity, and type 2 diabetes later in life.
• Children born via C-section have an altered gut microbiome and may be more susceptible to obesity, type 1 diabetes, allergies, and asthma during childhood and adulthood [1].
• Perhaps the most convincing finding is that the fact that mode of delivery (C-section vs vaginal delivery) has been shown to impact health issues throughout adulthood, while the differences in the gut microbiomes of C-section delivered babies compared to vaginally-delivered babies virtually disappears after the first 6-12 months of life.

This means that even though the microbiomes between C-section babies and vaginally-birthed babies ends up being identical after a period of time, there was distinct immune programming  between the two that led to completely different health outcomes well into adulthood [2].

This finding highlights the importance of early gut microbiota in the development and programming of our immune system.

Why does this happen?

This happens because the microbes that populate our gut are responsible for the development and programming of our immune system, instructing it on things like which microbes to attack or not attack, how to mount an appropriate immune response, etc.:

• According to scientists, a continuous dialogue must occur between our gut microbes and our immune system in order for the immune programming to take place.
• Therefore, dysbiosis — overgrowths of opportunistic and/or pathogenic microbes in the gut combined with low levels of beneficial microbes — present in our gut during this window can disrupt this dialogue, resulting in long-lasting physiological effects and health issues.
• This crosstalk between our microbiota and our body takes place during the earliest days of life, suggesting that disease risk is programmed during early life.
• Animal studies have repeatedly shown the importance of the gut microbiota in determining the levels of immune cells and their recruitment to various tissues as well as the development of immune tolerance [2].

In addition, our microbiome during this time period is highly vulnerable to change from environmental inputs like diet, antibiotics, etc., which is why is imperative that we strive to make sure we are doing everything we can to give our babies a healthy gut microbiome.

Specific Health Issues Resulting from Early Gut Microbiome Disruption

Allergies and Asthma

• One study found a reduced abundance of bifidobacteria and Faelcalibacterium in 3 month old infants who later developed atopic disease (eczema, hay fever, asthma, etc.), determined at 2 and 4 years of age.
• Another study found a correlation between a low microbiota diversity at 1 week of age in infants who developed eczema at 12 and 18 months of age.
• Antibiotic-induced dysbiosis of early microbiomes of lab animals has been shown to increase the risk of allergic asthma.
• Epidemiological studies show a link between perinatal antibiotic exposure and risk of subsequent allergic disease development.
• Recent evidence suggest that the risk of developing asthma is higher in infants who exhibited dysbiosis of the gut microbiome during the first 100 days of life.
• One study took bacteria from the guts of infants who had asthma and placed them into germ-free mice. Inoculation of these bacteria in the germ-free mice reduced airway inflammation, suggesting that some microbes have a causative role in the development of asthma.
• A reduced gut microbiome diversity during the first month of life is associated with a higher prevalence of asthma in 7-year old children [2].

Obesity

• It has been suggested that certain factors that disturb the microbial balance during early life play a pivotal role in the development of obesity in children later in life.
• Such factors include nutrition, maternal obesity, delivery mode, intestinal permeability, pathogenic infections, and antibiotic use.
• Epidemiological studies in humans have also demonstrated that antibiotic exposure is associated with long-term metabolic effects, including weight gain and obesity in children and adults.
• Certain gut microbiota referred to as obesogenic microbiota, are associated with obesity. They have been found to regulate metabolism.
• Scientists have found that higher levels of bifidobacteria in infants at 6 and 12 months is inversely associated with obesity in 7-year old children.
• One study investigating the effects of antibiotics on the early microbiome found that the negative effects on host metabolism were sustained over time, even after the alterations to the microbiome had disappeared after stopping antibiotic treatment.
• This highlights the importance of microbiota-immune interactions during the early life window of opportunity [2].

Other Diseases

• Early infant dysbiosis has also been associated with other chronic health issues that manifest later in life including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and type 1 diabetes (T1D).
• Experiments in mice have shown that early-life perturbations to the microbiome — mainly by low-dose antibiotic therapy — alter the immune system, increasing the risk of T1D and accelerate T1D development in non-obese, diabetic mice.
• Recent findings in human trials have shown that microbiota perturbations during early infancy may generate a proinflammatory environment that facilitates the development of autoimmune disease [2].

Top Things That Damage the Infant Microbiome

The best known risk factors for developing an unhealthy infant microbiome include:

1. C-section delivery – Babies born via C-section tend to have less diverse microbiomes and increased rates of obesity, autoimmune disease, asthma, allergies, and eczema.
2. Prenatal and perinatal antibiotic use – Antibiotic use is well-known to damage the gut microbiome, reducing diversity and allowing the overgrowth of pathogenic and opportunistic microbes. Use of antibiotics by pregnant and nursing moms both lead to damage of the baby’s microbiome.
3. Formula feeding – Formula-fed infants have less diversity and abundance of beneficial bacteria like bifidobacteria compared to breast fed infants.

How to Create a Healthy Microbiome for Your Baby

The following items are the most important factors affecting which type of microbes colonize our baby’s gut:

1. The health of mom’s microbiome – This will largely determine which microbes are passed to the baby.
2. Mode of delivery – The first microbes to colonize our baby’s gut will either come from our mother in the case of a vaginal delivery or the hospital environment in the case of cesarean section.
3. Feeding practices – Breast feeding and formula feeding lead to very different outcomes in regard to which microbes grow in the baby’s gut.
4. Antibiotic exposure – Antibiotic exposure has a devasting impact on the microbiome and can set the stage for which microbes will colonize the gut long term.
5. Environmental toxin exposure – Environmental toxins like microplastics, heavy metals, pfas, mold toxins, phthalates, and pesticides can kill off beneficial bacteria, cause leaky gut, and encourage the growth of pathogenic microbes.

Therefore, in order to create the healthiest microbiome we can for our baby, we must strive to do the following:

1. Improve the health of the mother’s microbiome
2. Strive for a vaginal birth
3. Use vaginal seeding to mitigate effects of C-section delivery
4. Breast feed over formula
5. Try to avoid giving your baby antibiotics
6. Restore your baby’s microbiome after antibiotics
7. Opt for organic whole foods when transitioning your baby’s diet
8. Reduce environmental toxin exposure
9. Use prebiotics/probiotics/postbiotics to improve the microbiome

1. Improve the mother’s microbiome

The health of the mother’s microbiome plays a critical role in shaping the newborn’s microbiome, immune system, metabolic health, and neurodevelopment, whose effects often last into childhood and beyond [3].

The mother can make significant beneficial shifts in her microbiome by implementing the following changes:

1. Improve your diet
   • Remove ultra-processed foods. This includes foods containing refined sugar, flour, hydrogenated seed and vegetable oils, high fructose corn syrup, artificial flavors, sweeteners, and dyes, and preservatives. These foods are linked to a decrease in microbial diversity, lower levels of beneficial bacteria, and an increase in pro-inflammatory microbes [6].
   • Increase soluble fiber and prebiotics. Eat foods high in prebiotic fiber like asparagus, dandelion greens, garlic, Jerusalem artichokes, leeks, onions, apples, bananas, and berries. Polyphenols are also act as prebiotics, feeding beneficial bacteria that will begin to crowd out bad bacteria. Foods high in polyphenols include green tea, cacao, pomegranate, and berries. Make sure that whichever foods you decide to include are not causing you any food sensitivities as this cause inflammation in the body, undermining the steps you are trying to take to improve your gut health [7].
   • Emphasize animal fat and protein. Our body needs adequate amounts of animal protein and fat in order to thrive. Animal foods are extremely nutrient dense, with nutrients already in a form our body can use. Make sure the majority of your calories come from organic meats including beef, pork, lamb, chicken, fish, eggs, and raw dairy [8].
   • Add fermented foods. Fermented foods are a good source of beneficial bacteria and prebiotic fiber that improve our microbiome and nourish our gut lining. Include foods like raw yogurt, sauerkraut, kimchi, kefir, and kombucha. Be sure that these products are unpasteurized as we want all the original probiotic bacteria present as opposed to individual strains added in later [7][9]. 
   • Drink bone broth – Bone broth is full of nutrients like gelatin, collagen, amino acids, and healthy fats, which are essential for repairing and rebuilding the gut lining. Regularly consuming bone broth and meat stock can help heal and seal a damaged gut lining. In addition, bone broth contains easily digestible minerals like sodium, calcium, and magnesium. Dr. Natasha Campbell McBride has been using meat stock and bone broth as part of the GAPS diet to treat patients with gut dysfunction for decades with incredible success.
2. Avoid antibiotics. Only use antibiotics if your life or the life of your child is at risk. These substances are just too damaging to the gut to take without a good reason to do so. It can take months to years to rebuild the microbiome after a round of antibiotics [10][11].
   • There are safer, natural alternatives for treating things like Group B Strep and UTIs that conventional medicine typically treats with antibiotics.
   • Family Nurse Practitioner and Prenatal expert, Dr. Cece Brooks, says that Lactobacillus rhamnosus administered vaginally for approximately 10 days is highly effective at eradicating GBS in the vaginal canal [72].
   • For UTIs, D-mannose combined with cranberry extract has shown good efficacy and is safe for the microbiome.
   • Herbs like juniper berry, uva ursi, bidens pilosa, and corn silk are very effective at treating UTIs as well.
3. Take spore-based probiotics – Spore-based probiotics like this one have been shown to reduce leaky gut, improve dysbiosis, and reduce inflammation.
   • They have had profound effects on me including reduced food sensitivities, improved mood and outlook, more energy, more resilience, and just increased overall vitality. I cannot emphasize enough how beneficial these probiotics have been for me.
   • They are superior to other types of probiotics because they are able to survive stomach acid, reaching the intestines alive, where they can activate and colonize.
   • Spore-based probiotics use quorum sensing to increase microbial diversity, encourage the growth of beneficial bacteria, and reduce pathogens. They can remain active in the gut for 21–28 days, reconditioning the microbiome rather than just repopulating it [12][13].

2. Strive for a vaginal birth

The method we choose to deliver our baby has a tremendous impact on the establishment of their microbiome, as the moment of birth is the first opportunity for large-scale bacterial colonization [16].

For example:

• It has been clearly documented that babies delivered vaginally have higher abundance and diversity in beneficial bacteria compared to babies born via C-section.
• This is because babies born vaginally acquire their microbes from the mother’s vaginal canal and fecal matter as they travel through and out of the birth canal, while those born via C-section receive microbes primarily from skin and the hospital environment, resulting in lower microbial diversity and delayed colonization by protective species [5][4][16][14].
• This means that babies born vaginally end up with a microbiome that’s very similar to their mother’s microbiome, emphasizing the importance of making sure the mom has a healthy microbiome prior to giving birth.
• This deviation in microbiome development in the C-section babies is linked to long-term effects on metabolism and impaired immune development.
• One study found that infants born by cesarean section (C-section) obtain microbes derived from the hospital environment and mother’s skin such as Staphylococcus, Corynebacterium, Propionibacterium, while infants born vaginally have more amounts of Bifidobacterium species.
• Differences in the microbiomes between C-section and vaginally-born infants have even been detected at 7 years of age [4].
• Some studies report that birth mode effects on the microbiota can be absent as little as 6–8 weeks after birth or as late as the first 2 years of life [16].
• However, as we’ve already pointed out earlier, regardless of the how similar the microbiomes end up being between the two birth modes, babies born via C-section have a much higher risk of developing T1D, obesity, asthma, allergies, and other health issues [4][16].

3. Use vaginal seeding to mitigate effects of C-section delivery

We understand it’s not always an option for mothers to deliver vaginally, so for those moms who have a medical reason to deliver via C-section (e.g. a high risk pregnancy due to a breached baby), consider vaginal seeding to help restore your baby’s microbiome.

Vaginal seeding is the practice of transferring a birthing parent’s vaginal bacteria to their newborn after a C-section delivery to help restore the baby’s microbiome to a more healthy composition and reduce risks of allergies, asthma, and other immune-related disorders.

Benefits:

• Some studies suggest that vaginal seeding provides modest changes to gut microbiome in C-section infants but doesn’t fully replicate natural microbial transfer [44].
• However, other results suggest that vaginal seeding causes the microbiome to resemble the microbiome of the mother, suggesting more than a partial recovery.
• One small study found that for 30 cesarean-born infants who underwent vaginal seeding, fecal and skin microbiota more closely resembled vaginal-born infants throughout the first year [43].
• Another study found that the microbiomes of C-section-born babies who received vaginal seeding aligned more closely with vaginally born babies than with C-section babies who did not receive vaginal seeding [45].

How Vaginal Seeding is Performed

1. Before the C-section: A healthcare provider inserts a sterile cotton gauze or swab into the mother’s vagina for about an hour to collect fluids and beneficial bacteria.
2. During the C-section: The gauze is carefully removed and stored in a sterile container to avoid contamination.
3. Right after birth: The healthcare provider gently rubs the gauze on the baby’s mouth, nose, eyes, ears, and skin to transfer the maternal vaginal microbiome to the newborn.

Our recommendation:

For healthy, low risk pregnancies:

• Opt for a vaginal birth over a C-section.

For moms who must have a C-section:

• Ask your doctor or midwife about vaginal seeding to mitigate the negative effects on your baby’s microbiome.

4. Breast feed over formula

Breast milk is superior to formula for several reasons including its unique composition, health benefits for the baby, and additional benefits for the mother.

Breast milk contains numerous beneficial bioactive compounds including:

• Immunoglobulins – Also known as antibodies, these are specialized proteins produced by B cells and plasma cells that play a vital role in the immune system by identifying and neutralizing foreign invaders like bacteria and viruses.
• Lactoferrin – A protein with antiviral and antibacterial properties that helps the body absorb iron and plays a vital role in microbiome development.
• Lysozyme –  An antimicrobial enzyme that forms a critical part of the body’s innate immune system, rapidly defending against bacteria and other pathogens.
• Antimicrobial peptides – Small, naturally occurring proteins that act as a key part of the innate immune system, found in nearly all forms of life. AMPs can directly kill a wide range of pathogens, including bacteria (both Gram-positive and Gram-negative), viruses, fungi, and even some cancer cells.
• Growth factors – Compounds that support infant growth, organ development, gut maturation, and immune system regulation. They are associated with improved gastrointestinal development, enhanced resistance to infection, and optimal organ maturation in infants.
• White blood cells – Essential components of the immune system that defend the body against infections and foreign substances.
• Stem cells -Unspecialized cells that have the unique ability to self-renew (make copies of themselves) and differentiate (develop into various specialized cell types). They serve as the foundation for the growth, development, and repair of tissues and organs in the body throughout life.
• MicroRNAs – MicroRNAs in breast milk support infant immune defenses, brain development, metabolism, and gut health.
• Human milk oligosaccharides (HMOs) – A group of complex, structurally diverse sugar molecules that are the third most abundant solid component in human breast milk after lactose and fat. They serve as prebiotics, promoting the growth of beneficial gut bacteria, especially Bifidobacteria. They also act as decoy receptors that block harmful pathogens from binding to the infant’s gut cells, reducing infections.
• Essential fatty acids like DHA and EPA – These are the main two omega-3 fatty acids that are crucial for brain development, cognitive function, vision, and inflammation reduction.

These components play a vital role in the development of the immune system, protecting against pathogens, and supporting the baby’s overall growth and development [15].

Benefits of Breast Milk

Nutritional and Health Benefits:

• Immune support – It is a living fluid that adapts to the baby’s changing needs, containing natural antibodies and immune-boosting components that formula cannot replicate.
• Digestibility – It’s more easily digested, resulting in fewer cases of constipation and gas.
• Adaptability – It provides the perfect, dynamic balance of nutrients tailored to the baby’s developmental stage.
• Nutrient absorption – It supports better nutrient absorption (e.g. iron absorption rates are higher with breast milk).
• Cognitive health – Breast milk may also supports better cognitive and neurological development due to nutrients like DHA.
• Long-term health – It may protect against conditions like obesity, diabetes, and allergies later in life.
• Reduced health risks – Breastfed babies a lower risk of ear infections, respiratory infections, asthma, obesity, type 2 diabetes, and sudden infant death syndrome (SIDS) compared to formula-fed babies.
• Disease incidence – In one study comparing breast-fed to bottle-fed babies, breast-fed babies had a reduced risk of infection, improved cognitive development, decreased occurrence of celiac disease, asthma, and high cholesterol, decreased occurrence of type 2 diabetes and obesity later in life [5][17][18][19][20][21].

Microbiome Benefits:

• Breast milk helps to shape developing core gut microbiota – such as bifidobacteria – that can improve growth and neurodevelopment and decrease the risk of many long-term, immune related health issues [4].
• Breastfed infants generally contain a more complex and diverse Bifidobacterium microbiota – a two-fold increase – and a lower number of C. difficile and E. coli than formula-fed infants [3][4].
• Bifidobacteria are responsible for digesting components of breast milk (like HMOs and other prebiotics) and turning them into gut-nourishing short-chain fatty acids (SFCAs)[4].
• Bifidobacterium species are greatly reduced through formula feeding [5].
• Breast milk contains dozens of structurally distinct human milk oligosaccharides (HMOs) that support a balanced growth of beneficial microbes compared to formula which generally contains one or two types of HMOs (such as 2′FL or LNnT), encouraging overgrowths of single strains [2].
• Lactoferrin present in breast milk has been shown to play an important role in the initiation, development, and composition of the infant microbiome, contributing to immune system maturation and well-being of new born infants, particularly pre-term infants [4].
• The HMOs present in breast milk selectively feed a broad range of beneficial microbes, creating a healthy microbiome composition.
• HMOs in breast milk use competitive exclusion, anti-microbial production, and alteration of the gut environment to crowd out bad bacteria, protecting the baby’s microbiome [16].
• The HMOs in breast milk have antimicrobial effects, with studies showing that group B strep stops growing in the presence of HMOs [2].
• HMOs prevent pathogens from colonizing the gut by blocking the attachment sites that bad bacteria use to take hold [2].
• Breast milk contains prebiotics (e.g., human milk oligosaccharides) and beneficial bacteria that help counteract some antibiotic-induced disruptions, offering a protective effect compared to formula-fed infants.

Benefits for the mother:

• Bonding and mental health – The skin-to-skin contact and release of oxytocin during breastfeeding can enhance bonding and reduce postpartum depression.
• Physical health – Breastfeeding promotes faster postpartum weight loss, reduces the risk of breast and ovarian cancer, and may lower the risk of type 2 diabetes[17][18][19][20][21].

Formula

In contrast to breast milk, formula has several downsides:

1. It provides a standardized nutrient profile but lacks the dynamic, immune-enhancing properties of breast milk since it is a static product made from cow’s milk or other bases, processed to be safe for infants.
2. Most formulas contain virtually no animal fats, which are crucial for a developing brain.
3. Instead, most formula’s contain highly processed seed oils, which promote oxidative stress, damage our cell membranes and mitochondria, and lead to chronic inflammation [46][47][48][49][50][51].

Formula is a viable alternative when breastfeeding isn’t possible, but it definitely does not match the benefits of breast milk.

5. Avoid giving your baby antibiotics if possible

Antibiotics administered early in life can have a devastating effect on the microbiome, killing off beneficial bacteria and reducing diversity, potentially interfering with immune system programming and leading to health issues later in life including autoimmunity, obesity, type 1 diabetes, allergies, eczema, asthma, and more [1][2][22][23][24].

Key Effects of Antibiotics on Infant Microbiome:

• Disruption of diversity – Antibiotics reduce the overall diversity and abundance of beneficial bacteria (e.g., Bifidobacterium and Lactobacillus) in an infant’s gut. These microbes are crucial for immune system development and protection against pathogens.
• Increased growth of bad bacteria – Antibiotics given directly for infections or indirectly via breast milk from a mother taking antibiotics can alter the initial colonization process of the baby’s microbiome, reducing the growth of beneficial microbes and allowing opportunistic and pathogenic microbes to proliferate.
• Impaired Immune System Development – Antibiotics given in the first year of life has been associated with a higher risk of abnormal immune system training and development, setting the stage for long-term health issues like autoimmunity, ear infections, asthma, allergies, eczema, and other immune-related issues later in life.
• Possibility of delayed recovery – Sometimes, changes in microbiome composition can persist for up to a year or longer after a round of antibiotics.
• Duration and timing matter – Early antibiotic exposure, especially during the first week or months of life, has a more pronounced and lasting effect compared to later treatments [22][23][24].

While antibiotics are life-saving medications, their use in infants disrupts the developing gut microbiome by reducing beneficial bacteria, promoting resistant pathogens, and potentially influencing long-term immune and metabolic health.

The effects are most pronounced when antibiotics are given early in life, during critical periods of microbiome establishment, and can persist for months or even longer, potentially impacting immune development and increasing risks of allergies, asthma, and other conditions.

However, there are some steps we can take to help restore the microbiome after antibiotic use.

6. Restore your baby’s microbiome after antibiotics

If you have to give your baby antibiotics for any reason, there are some things you can do that have proven efficacy at helping to repair some of the damage caused by the antibiotics.

Recovery of our baby’s microbiome after antibiotics depends on several factors like:

• The type/duration of antibiotics – Broad-spectrum antibiotics target and kill a wide range of bacterial species, including both pathogenic and beneficial bacteria. This can cause widespread destruction of the microbiome, severely reducing its diversity and function. Narrow-spectrum antibiotics are designed to target only a specific, limited range of bacteria. By preserving most of the commensal, or “good,” bacteria, they cause much less disruption to the overall microbiome. Obviously the longer the course of antibiotics, the more damage can occur [25][26].
• The infant’s age at the time of exposure – Early-life exposure, particularly in the first months, is associated with more severe disruption of microbial diversity and a slower recovery of the gut microbiome [27][28].
• Diet (breast milk vs. formula) – Breast milk can accelerate the recovery of the microbiome by providing a range of human milk oligosaccharides (HMOs) that act as prebiotics, feeding beneficial bacteria like Bifidobacterium, by supplying live probiotics that can directly colonize the infant’s gut, by supplying other components, including glutamine — which has direct antimicrobial effects against certain pathogens — supporting the gut’s immune defenses, by triggering increased production of short-chain fatty acids — which help maintain the integrity of the intestinal barrier, reduce inflammation, and protect the colon — , and by promoting the maturation of the immune system which is crucial for protecting against infections and re-establishing a healthy gut microbiome after antibiotic exposure [29].
• Supplementation with pre/probiotics – Certain prebiotics and probiotics have the ability to protect the microbiome during antibiotic exposure and help accelerate the recovery of the microbiome post-exposure.

Here are the most effective ways to rebuild your baby’s microbiome after antibiotic exposure:

1. Continue breastfeeding – As we have discussed, breast milk provides a range of compounds that are instrumental in healing the microbiome, the gut lining, and the immune system post antibiotic treatment. Continue giving this nectar to your baby to help heal their gut during and after antibiotics.
2. Give your baby saccharomyces boulardii during their course – S. boulardii is a probiotic yeast that has been shown to help mitigate the negative changes to the microbiome from antibiotics [30].
   1. S. boulardii administration during antibiotic treatment reduces the proliferation of bad bacteria that tend to grow due to antibiotic treatment and promotes the growth of beneficial microbes [31].
   2. It has also been shown to inhibit candida overgrowth, which is common during antibiotic treatment [32]. Aim to take this during the entire course of antibiotics as well as 1-2 weeks after.
3. Introduce probiotics – Supplementing with multispecies probiotics—especially those containing Bifidobacterium and Lactobacillus—has consistently shown the best results in restoring microbiota disturbed by antibiotics in infants.
   1. Studies show that multi-strain probiotics containing specific Bifidobacterium and Lactobacillus species appear to have the highest efficacy — especially when combined with breastfeeding — to support colonization.
   2. These formulations have been shown to increase beneficial bacteria, reduce antibiotic resistance genes, suppress pathogens, and normalize microbial diversity and function closer to that of unexposed infants [33][34][35].
4. Introduce prebiotics – Prebiotics, particularly human milk oligosaccharides (HMOs), fructaoligosaccharides (FOS), and galactoligosaccharides (GOS), play a critical role in restoring the infant gut microbiome after antibiotic exposure by selectively promoting the growth of beneficial bacteria like Bifidobacterium and Lactobacillus while suppressing pathogenic bacteria.
   1. Clinical data links HMO-enhanced infant formula feeding to microbiome profiles with higher bifidobacteria abundance and reduced antibiotic use later in infancy, suggesting HMOs contribute to immune protection and microbiome recovery.
   2. Bifidobacteria are known to produce protective metabolites like acetate that support gut barrier function and immune maturation, contributing to the restoration of a balanced microbiome post-antibiotics [39][40].
   3. Studies in infants have shown that FOS supplementation increases fecal Bifidobacterium levels, supporting microbial recovery even after antibiotics. Effects are generally greater with higher doses (>5 g) and longer supplementation (>4 weeks) [41].
   4. Animal models combining FOS with other prebiotics (such as GOS) and infant-type bifidobacteria demonstrated partial recovery of microbiota disrupted by antibiotics, including reductions in harmful bacteria and improvements in gut tissue health [42].
   5. FOS has been demonstrated to increase production of short-chain fatty acids like acetate and butyrate, which help maintain gut barrier function and inhibit pathogenic bacteria proliferation post-antibiotics [41][42].
   6. GOS, which are derived from lactose, have been shown to boost populations of beneficial bifidobacteria and restore SCFA production, strengthening the gut barrier and reducing inflammation [36][37][38].

If your baby has transitioned to whole foods:

1. Add fermented foods – Fermented foods are loaded with prebiotics and probiotics that will help restore the gut microbiome and repair the gut lining, reducing inflammation and restoring immune and metabolic health. This can include things like raw kefir, raw yogurt, raw sauerkraut, kimchi, and raw kombucha.
2. Add bone broth or meat stock – In her book Gut and Psychology Syndrome: Natural Treatment for Autism, Dyspraxia, A.D.D, author Dr. Natasha Campbell-McBride describes how the addition of meat stock and broth gives our gut a plethora of nourishing compounds that it needs to repair and seal a damaged gut lining including gelatin, collagen, proline, glycine, glutamine, and nutrient-dense animal fats. She emphasizes that these essential nutrients and building blocks aid in healing and sealing the gut lining, describing them as critical for repairing a damaged intestinal tract, including conditions like leaky gut which are highly likely with antibiotic use [48].

7. Opt for organic whole foods when transitioning your baby’s diet

When transitioning from milk to solid foods, try your best to only give your baby organic, whole foods and avoid feeding them ultra-processed foods.

Ultra-processed foods are defined as foods that are primarily composed of chemically modified substances and additives, which are intended to increase their palatability and shelf-life.

Some common examples include carbonated soft drinks, cereal, snacks, breads, ice cream, pastries, chips, cookies, cakes, fast food, candy, and many others.

These foods are high in toxic oils, sugars, food additives, heavy metals, pesticides, and immune triggering substances but low in prebiotic fiber, vitamins, and bioactive compounds.

Ultra-processed foods have been shown to damage the gut microbiome by:

• Reducing microbial diversity
• Increasing pro-inflammatory bacteria
• Leading to a state of intestinal dysbiosis
• Weakening the intestinal barrier, leading to “leaky gut” and chronic inflammation
• Leading to metabolic dysfunction [52][53][54]

This occurs due to the low fiber content, high levels of hydrogenated fats, sugars, and artificial food additives, which create a pro-inflammatory environment and alter the balance of beneficial vs. harmful bacteria.

In addition to avoiding ultra-processed foods, try to choose organic foods over non-organic foods due to the rampant use of pesticides like glyphosate, which is known to decimate the gut microbiome and even lead to cancer.

Glyphosate has been shown to:

• Selectively kill beneficial commensal bacteria
• Reducing microbial diversity
• Promote the growth of opportunistic pathogens [56][57]

One review shows evidence from animal studies, which indicates that early-life exposure to glyphosate, even at EPA-approved levels, adds risk for altered neonatal gut microbiome development, potentially affecting immune tolerance and increasing susceptibility to autoimmune conditions [55].

8. Reduce environmental toxin exposure

We live in a world full of environmental toxins like heavy metals, mold, pesticides, plastics, PFAS, flame retardants, food additives, phthalates, and many other chemicals that can wreak havoc on our microbiome.

For example:

• BPA from plastic has been shown to alter the gut microbiome in rodents and rabbits, increasing oxidative stress and inflammation, and causing metabolic dysfunction.
• Phthalates, which are plasticizers and stabilizers found in vinyl flooring, clothing, detergents, personal care products, and children’s toys, given to newborn infants at medically relevant doses altered the gut microbiota and decreased bacterial diversity, increasing the risk of imbalanced immune responses later in life.
• Persistent organic pollutants, which are found in things like such as pesticides/insecticides, fast-food packaging, nonstick coatings for cookware, and heat exchange fluids, have been shown in animal studies to increase gut permeability, alter genes relate to certain inflammatory markers, increase intestinal and systemic inflammation, and reduce microbial abundance in the gut.
• Heavy metals like lead, arsenic, mercury, and cadmium have been shown to cause significant damage to the intestinal lining and changes in the microbiome, leading to oxidative stress and impairing detoxification systems.
• Pesticides like glyphosate, aldicarb, atrazine, and many others are known to cause enormous damage to the gut through increased pathogenicity of certain bacteria, increased oxidative stress, DNA damage, inflammation in the intestines, reduced richness and diversity of microbiota, hepatic lipid metabolism disorder, liver damage, delayed maturation of intestinal barriers, increased gut permeability, increased lipopolysaccharide levels, and increased pathogenic bacteria levels [57].

It’s impossible to completely avoid environmental toxins, but there is a lot we can do to minimize our exposure and thus minimize our baby’s risk of damage to their gut.

The best ways to minimize our baby’s toxic exposure are to:

1. Filter the water your baby drinks and bathes in using a whole-home water filter or a very effective under-the-sink/countertop filter like this one.
2. Only feed your baby organic foods.
3. Avoid feeding your baby food or milk from plastic. Instead use glass bottles and storage containers (for daycare friendly bottles, use these).
4. Avoid plastics (receipts, bottled water, cling film, plastic tupperware, etc.
5. Avoid cooking in non-stick cooking pans. Opt for brands like Carraway that use ceramic coating as opposed Teflon.
6. Avoid spraying your yard with weed killers and insecticides.
7. Use non-toxic brands of cleaning and personal care products for your baby.
8. Avoid commercial sunscreens. Use safer brands like Sky and Sol or Primally Pure.
9. Add an UltraHEPA air purifier like this one to your home to remove toxins and purifier your home.

9. Use prebiotics/probiotics/postbiotics to improve the microbiome

Once your baby has transitioned to whole foods and their microbiome becomes more established, you might consider supplementing with things that can protect their microbiome against the inevitable exposures that are to come as well as make them more resilient when they do come into contact with these things.

Prebiotics, probiotics, and postbiotics can all be very effective at protecting our baby’s microbiome by:

1. Selectively encouraging the growth of beneficial bacteria like Bifidobacteria and Lactobacillus
2. Killing off pathogenic and opportunistic microbes
3. Creating an anaerobic environment in the gut that is inhospitable to pathogenic bacteria
4. Increasing the production of short chain fatty acids that heal the gut lining discourage the growth of pathogenic bacteria
5. Using quorum sensing to interfere with the communication between pathogenic bacteria, leading to improved microbiome composition
6. Reducing the production of toxic bacterial metabolites like LPS that lead to inflammation and health issues
7. Improving the immune response, leading to enhanced microbiome resilience
8. Increasing mineral absorption
9. Increasing antioxidant activity, reducing oxidative stress
10. Stimulating cancer cell apoptosis, thereby reducing colorectal cancer
11. Improving digestion
12. Alleviating constipation and diarrhea
13. Protecting against infections and autoimmune disease
14. Improving gut barrier function
15. Maintaining luminal pH, inhibiting pathogen growth
16. Influencing intestinal motility, which improves bowel movement regularity and prevents constipation and SIBO [59]

Prebiotics

Prebiotics include any form of soluble fiber that feed bacteria in the gut, promoting the production of beneficial compounds like short chain fatty acids like protect the gut barrier, encourage the growth of health-promoting bacteria, and discourage the growth of pathogenic bacteria.

These compounds are highly resistant to gastrointestinal enzymes and stomach acid, which allows them to pass through the upper gastrointestinal tract without being digested, until they reach the colon where they are metabolized by beneficial bacteria like Bifidobacterium and Lactobacillus, where they in turn product beneficial SCFAs like butyrate.

Some common prebiotics include:

• Human milk oligosaccharides (HMOs) – Present in breast milk and very effective at selectively feeding beneficial bacteria and crowding out pathogenic bacteria. We like this brand.
• Fructaoligosaccharides (FOS) – Found in honey, banana, artichokes, chicory, onions, leeks, garlic, and asparagus, FOS has been shown to increase levels of bifidobacteria, aid in the inhibition of harmful bacteria, enhance mineral absorption, promote digestive health, and boost immunity [58]. We like this brand.
• Galactoligosaccharides (GOS) – GOS enhances short-chain fatty acids (SCFAs) production, reduces levels of pathogenic bacteria, and promotes optimal intestinal function, and stimulates the production of bifidobacteria. GOS also plays an important role in alleviating lactose intolerance and preventing constipation by softening stools and reducing transit time [60]. We like this brand.
• Xylooligosaccharides (XOS) – XOs are known to improve digestion and absorption of nutrients, decrease the pH of the gut environment — preventing the growth of pathogenic bacteria —, increase the proliferation and colonization of beneficial bacteria, prevent gastrointestinal infections, maintain healthy stool water levels, and prevent diarrhea. In addition XOs are very effective at increasing the production of SCFAs and suppressing inflammation in the intestines, making them a potentially better option compared to other types of prebiotics like FOS and GOS [61]. We like this brand.
• Polyphenols – Found in foods like cacao powder, green tea/matcha, pomegranate, cranberries, and blueberries, polyphenols are a newer class of prebiotic that travel through our digestive system undigested until they reach the colon where they are metabolized by our microbes. Recent studies show that polyphenols are effective at increasing levels of beneficial microbes like Akkermansia, Faecalbacterium, Bifidobacterium, and Lactobacillus. In addition, polyphenols have an antimicrobial effect, suppressing the growth of many pathogens [62]. We like this brand and this brand.

High-prebiotic foods:

• Asparagus
• Artichoke
• Brussels sprouts
• Chicory root
• Dandelion greens
• Garlic
• Leeks
• Onions
• Potatoes
• Butternut squash
• Pumpkin
• Berries (blueberries, raspberries, strawberries)
• Cranberry
• Pomegranate
• Matcha
• Cacao
• Cherries
• Kiwi
• Pears
• Dates
• Figs

Our recommendation:

1. Feed your baby high prebiotic fruits and vegetables, making sure that they can tolerate them without any reactions.
2. Supplement them with prebiotic powders, experimenting with different types and watching for any changes in bowel function or potential reactions.

Probiotics

Probiotics have been shown to improve microbial diversity and protect against microbiome damage from C-section birth and antibiotics in infants [63].

They also may play a foundational role in supporting a healthy microbiome and healthy digestive function for your child.

A recent review found that probiotics balance the immune system, improve intestinal barrier function, suppress pathogenic bacteria, increase levels of healthy bacteria, reduce inflammation and oxidative stress, possess anti-cancer properties, act as anti-obesity agents, and have anti-diabetic effects [64].

Additionally, they may also help manage bloating, diarrhea, and abdominal pain and may improve overall digestive function [65].

There are a few different types of probiotics:

1. Lactobacillus/Bifidobacteria – These are the lactic-acid producing bacteria that are the most well researched for promoting gut health. They have been shown to promote optimal gastrointestinal tract function, a healthy immune response, and the ability to support a healthy and balanced microbiome. In addition, they have been shown to reduce bacterial overgrowths, gas production, and abdominal pain in the small intestine. These strains do not colonize the gut but rather exert their beneficial effects during their transit through our GI tract [69].
2. Spore-based probiotics – These strains are known as spore-forming or soil-based because they are found everywhere in soil and water, and they often spend part of their life cycle in a dormant “spore” state. These bacteria do colonize our gut and may help replace missing bacteria due to our reduced contact with soil and natural environments. These bacteria are superior in that their tough spore coat allows them to survive stomach acid and reach the intestines alive, as opposed to other strains they may be killed off by stomach acid. Spore-based probiotics have been shown to improve overall gut diversity, boost beneficial strains like Akkermansia and Bifidobacterium, suppress overgrown or pathogenic bacteria, produce prebiotic compounds to feed good microbes, reduce leaky gut by repairing and strengthening the gut lining, and improve immune signaling — dampening overactive inflammation and increasing resilience against infection [66][67][68][69].
3. Saccharomyces boullardii – Another well-researched probiotic, the strain is a beneficial yeast that has the ability to protect against fungal infections, improve symptoms of IBS, help treat Crohn’s disease and ulcerative colitis, and help correct dysbiosis. This strain does not appear to colonize the gut [69].

Our recommendation:

• We believe spore-based probiotics are superior for the following reasons:
  • Unlike other strains, spore-based strains survive the stomach acid and make it to the colon alive.
  • They have the ability to use quorum sensing to detect the balance of microbes in the gut and will specifically act to decrease the populations of pathogenic or overgrown bacteria while encouraging beneficial species to grow.
  • They produce potent antimicrobial substances that directly inhibit pathogenic and overgrowth bacteria, acting as natural antibiotics within the gut ecosystem.
  • The spores use competitive exclusion where they compete with harmful microbes for nutrients and adhesion sites, limiting their ability to thrive or colonize.
  • Spore-based probiotics can acidify the gut microenvironment, making conditions less hospitable for pathogens while supporting beneficial bacteria like Lactobacillus and Bifidobacterium.
  • They interact with the gut-associated lymphoid tissue (GALT), helping the host immune system more effectively recognize and eliminate pathogenic microbes [70].
• JustThrive and MegaSporeBiotic are our personal favorites for spore-based probiotics.
• However, everyone is unique and will experience different effects so we recommend trying each type of probiotic on your baby and pay attention to any changes in bowel habits, digestive function, skin health, and even mood changes.

Postbiotics

Postbiotics are compounds produced by microbial fermentation of dietary fiber.

They are the output of the process of our bacteria consuming the prebiotics that we consume and metabolizing them.

The most studied and most powerful of the postbiotics is a short-chain fatty acid called butyrate.

Butyrate has a precursor called tributyrin that when consumed can provide profound benefits to our gut including:

• Strengthening tight junctions and healing leaky gut
• Regulation of gut motility (speed)
• Supporting healthy mucosal layers
• Increasing microbial diversity
• Inhibiting the growth of pathogenic bacteria
• Reverse dysbiosis
• Ameliorating antibiotic-induced intestinal damage
• Reducing levels of toxic microbial metabolites like LPS
• Reducing levels of proinflammatory cytokines
• Increase the production of other SCFAs
• Improving symptoms of MCAS and histamine intolerance [71]

A lot of people have negative reactions to prebiotics or consuming more fiber like increasing bloating, gas, constipation, or abdominal pain.

This makes tributyrin a great option since it skips the fiber metabolism and gives us the direct source of the beneficial effects that eating fiber gives us, without the digestive upset.

Our recommendation:

• Experiment giving your baby tributyrin and take note of any changes in bowel habits, digestive function, mood, behavior, skin, etc.
• Our favorite brand of tributyrin is HealthyGut.

The first 12 months after our baby is born is an important window of opportunity for us as parents to try and create the healthiest microbiome for our baby so that it will support proper immune programming and set them up for good health for years to come.

It’s important that we don’t stress about what we can’t control. If you have to have a C-section, give your baby a round of antibiotics, or use formula, there are always ways we can mitigate the damage from those things.

The important thing is that you are well informed and can make the best decision possible for you and your family.