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Protecting and Restoring Your Child’s Gut Health When They Need Antibiotics

Antibiotics are life-saving medications, but on the other hand, they’re overused. Antibiotics are overprescribed, especially in children, for conditions that don’t require or respond to antibiotics, such as viral ear infections and colds. I’m always against the use of antibiotics when they’re unnecessary; however, there are times where they are necessary. 

I anticipated that if my daughter, Maeve, would ever end up with a common childhood illness, like a cold or ear infection, that I’d treat her naturally and encourage her body’s own healing systems, while closely monitoring her symptoms. I’d known that antibiotics, especially early in life,  are damaging to the gut and immune system. Optimizing gut health, especially early in life, is paramount in fostering a robust immune system and preventing chronic disease. When Maeve was just shy of one year old, what I thought was a clogged tear duct, turned out to be periorbital/preseptal cellulitis (an infection of the tissue around the eyelid, typically caused by bacteria).  I know this had the potential to spread to her eye and even her brain if left untreated. After a day of monitoring Maeve and in complete agony over what to do, I came to the decision that she needed the antibiotics she’d been prescribed the day earlier – amoxicillin. I had to ask my mom to give Maeve her first dose. I was in tears and completely devastated. I was relieved in a sense knowing Maeve’s infection would begin to resolve, but so saddened by the harm this medication would cause. Feeling that this decision was necessary, I immediately started working on a supplement regimen and eating plan for Maeve that would augment and prevent some of the damage from the antibiotics. I implemented it the next day. 

I followed this plan with Maeve during the one-week course of her antibiotics, and continued for one month beyond that.


Gut-protecting and gut-healing supplements during and after antibiotic use: grass-fed gelatin, bone broth collagen, organic chicken bone broth, probiotics, L-glutamine, and zinc carnosine. Not pictured: cod liver oil and vitamin D3.

These supplements and dosages were appropriate for my twelve month-old daughter. Dosages will vary based on age and weight of a child, and not all supplements are appropriate for every child. Please consult your child’s physician before giving them any supplements. 


  • 5 billion CFUs, three times per day
  • An infant-specific, multi-strain, refrigerated, and non-milk derived probiotic supplement is best.
  • When taking antibiotics, the gut needs reinoculated with beneficial bacteria.
  • Maeve had been supplementing with probiotics once per day prior to this, but I tripled her dosage to three times per day when she began taking the antibiotics. Be sure to give probiotics at least two to three hours away from antibiotics, so the antibiotics don’t kill the probiotic bacteria.


  • 250mg, twice per day. L-glutamine is generally a safe supplement, and I considered this a safe yet effective dose for my twelve month-old daughter. Please check with your physician before giving your child L-glutamine.
  • L-glutamine is an amino acid that maintains the intestinal barrier function, reduces intestinal permeability due to various stressors (like antibiotics), and is required for enterocyte (small intestine cell) growth, viability, and mucosal protein synthesis.1
  • I mixed this powder in a little breast milk and gave it to Maeve twice per day, away from food. L-glutamine is an amino acid, which is best absorbed and utilized away from consuming protein.

Zinc Carnosine

  • 8mg, once per day. I chose 8mg because this was close to the 7mg UL (tolerable upper intake level) of zinc that is considered safe on a daily basis for children ages 1-3 years.
  • Zinc has been shown to maintain tight junctions between the cells of the small intestines (this prevents leaky gut/intestinal hyperpermeability), through various signaling pathways.2
  • Zinc carnosine is the specific molecular form that is best utilized by the cells lining the gut.

Vitamin D3

  • 400 IU, once per day. It’s recommended that all exclusively breastfed infants supplement 400 IU vitamin D3, daily. Formula is typically fortified with this amount of vitamin D3.3 Breastfed babies are only provided with a sufficient amount of vitamin D3 from breast milk if mom’s vitamin D3 intake is at least 6,400 IU per day.4 My intake/supplementation is not this high, so I give 400 IU per day directly to Maeve.
  • There is evidence that vitamin D modulates the gut microbiome via decreasing pathogenic, inflammation-promoting species of bacteria, and increasing bacterial diversity in the gut.5

Organic, Grass-Fed Bone Broth Collagen & Gelatin

  • ¼ scoop of each, twice per day
  • Bone broth is a rich source of collagen and gelatin proteins, minerals, and other nutrients that promote gut healing. 
  • Collagen and gelatin proteins are especially rich in the amino acids glycine, proline, hydroxyproline, and alanine.6 These amino acids in collagen are utilized to repair tissue in our gut lining; furthermore, healing and preventing ‘leaky gut.’
  • I included gelatin in order to create a ‘jello’ texture in the mixture of Maeve’s supplements!
‘Jello’ full of Maeve’s supplements

Cod Liver Oil

  • The dosage we chose was calculated based on Maeve’s body weight. I used a good ‘maintenance dose’ of omega-3 fatty acids, for a baby her size.
  • Cod liver oil is a great source of omega-3 fatty acids (so is fish oil!).
  • Omega-3 fats have been shown to restore a more beneficial ratio of Firmicutes to Bacteroidetes, increase Bifidobacteria, and decrease Enterobacteria.7 All of these actions reduce endotoxemia and low-grade inflammation in the gut.7

This is the supplement schedule we followed with Maeve throughout the one-week course of the antibiotics, and continued for one month afterwards:

9:00am – Probiotics & L-Glutamine mixed with breast milk (away from food)

2:00pm – Probiotics, Zinc Carnosine, Collagen, & Gelatin mixed in bone broth and refrigerated to make ‘jello’ (with lunch)

6:00pm – Collagen & Gelatin mixed in bone broth and refrigerated to create ‘jello’ (with dinner)

7:30pm – Probiotics, Cod Liver Oil, Vitamin D, & L-Glutamine mixed with breast milk (away from food)


Diet can have profound beneficial or harmful effects on the composition of the gut microbiome, as well as the integrity of the intestinal epithelium (lining). I offered Maeve her usual nutrient-dense foods, but held off on fruits (except avocado), and continued to avoid grains (I haven’t introduced them into her diet, yet). Sugars (even from fruits and low fiber carbohydrates) can unfavorably shift gut microbe populations and microbes’ metabolic activity, within a single day of consumption.8 Additionally, all of her food was cooked in ghee and bone broth. Ghee is clarified butter, and contains high levels of L-butyrate, a short-chain fatty acid that is the primary ‘fuel’ for cells lining the small intestine. Butyrate regulates the pH of the intestinal lumen, which favorably alters intestinal bacteria populations.9 These dietary measures are foundational, in that the supplements will be most beneficial when these dietary guidelines are followed. We followed these dietary guidelines throughout the course of Maeve taking the supplements. Here are some examples of Maeve’s meals:

Wild sardines, organic zucchini & organic shiitake mushrooms sautéed in ghee, and organic seaweed
Wild salmon cooked in bone broth, organic broccoli & organic sweet potato sautéed in ghee, and a few pieces of organic chicken breast
Organic, grass-fed ground beef, organic shiitake mushrooms, organic zucchini, all sautéed in ghee and bone broth, with organic avocado pieces

Lastly, I’d like to note that I continued breastfeeding Maeve (arguably one of the most effective measures to inoculate the gut with healthy bacteria and immunoglobulins), and I made sure we kept to her usual routine regarding sleeping and eating, as to minimize any unnecessary stress. Stress can affect our gut health, too.

This gut-protecting and gut-healing regimen can also be used (with modifications) for older children and adults who have taken oral antibiotics. Keep this information (as well as my contact information) on hand, so if your child ever needs antibiotics, you can be equipped to proactively protect their gut health! Feel free to leave a comment or contact me with any questions.


1. Rao, R., and Samak, G. Role of glutamine in protection of intestinal epithelial tight junctions. Journal of Epithelial Biology and Pharmacology. (2012); 5(Suppl 1-M7):47-54.

2. Shao, Y., Wolf, P.G., Guo, S., et. al. Zinc enhances intestinal epithelial barrier function through the PI3K/AKT/mTOR signaling pathway in caco-2 cells. Journal of Nutritional Biochemsitry. (2017);43:18-26.

3. De Ronne, N., and De Schepper, J. Recommendations for vitamin D supplementation in infants and young children. J Pharm Belg. (2013);3:12-21.

4. Hollis, B.W., Wagner, C.L., Howard, C.R., et. al. Maternal vs infant vitamin D supplementation during lactation: a randomized controlled trial. Pediatrics. (2015);136(4):625-634.

5. Bashir, M., Prietl, B., Tauschmann, M., et. al. Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract. European Journal of Nutrition. (2016);55:1479-1489.

6. Gauza-Wlodarczyk, M., Kubisz, L., and Wlodarczyk, D. Amino acid composition in determination of collagen origin and assessment of physical factors effects. International Journal of Biological Macromolecules. (2017);104(A):987-991.

7. Constantini, L., Molinari, R., Farinon, B., and Merendino, N. Impact of omega-3 fatty acids on the gut microbiota. International Journal of Molecular Science. (2017);18(12):2645.

8. Turnbaugh, P.J., Ridaura, V.K., Faith, J.J., et. al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Science Translational Medicine. (2009);1(6):6ra14.

9. Canani, R.B., Di Costanzo, M., and Leone, L. The epigenetic effects of butyrate: potential therapeutic implications for clinical practice. Clinical Epigenetics. (2012);4(4).


Published by Dr. Alexandra Giuffre

Hello! I’m Dr. Alexandra Giuffre, ND, CNS, CDN (Dr. Alex!). I offer virtual Naturopathic Wellness Consultations. I work with individuals who are either ready to begin, or restructure their healing journey. With my training in clinical science, evidence-based medicine, and natural, holistic therapies, I work with individuals to create a personalized healing plan that is complementary to their current medical care.

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