Optimize Your Child’s Gut Flora

Optimize Child's Gut Flora

Optimizing your children’s gut flora is not that difficult, once you know what to avoid and how to replenish and maintain beneficial microbes.

How to Replenish and Maintain Healthy Gut Flora

It’s important to eat a healthy diet with a diversity of organic whole plant foods that are rich in fiber. You need both prebiotics and probiotics. A great way to build and maintain a healthy microbiome is to eat these foods every day. Try to get a variety of different prebiotic and probiotic foods with every meal.


Beneficial microbes (the good bugs) thrive on nutrients called prebiotics, which are found in a high-fiber, plant-based diet.  Prebiotics are non-digestible food ingredients that feed and stimulate the activity of beneficial bacteria. Here are some foods that are exceptionally high in prebiotics:

  • Jerusalem Artichoke
  • Dandelion greens
  • Radicchio
  • Frisee
  • Endive
  • Onions
  • Leeks
  • Apples
  • Asparagus
  • Bananas
  • Plantains
  • Chicory
  • Jicama root
  • Yacon root
  • Garlic
  • Barley
  • Flaxseeds
  • Oat bran
  • Wheat bran


The prebiotics should be eaten with probiotics. Probiotics are the live, beneficial bacteria and other microbes that are needed in the gut to maintain immunity. It’s best to add a variety of fermented foods to the diet.

Fermented Foods

Fermented foods, if  made properly, contain hundreds of strains of beneficial bacteria. Fermented foods are easy to make and can be more cost-effective than buying supplements. Fermenting foods will also improve digestion by breaking down your food into a more easily digestible form. Fermented foods keep for a long time without losing the nutrients so you can make big batches that will keep in the fridge.

The key is diversity. Eating only one type, like sauerkraut, all the time won’t give you the diversity needed to build a healthy microbiome. Try to give your child a bite or two of several types every day. Here are some of the different types of fermented foods. If buying these foods in a store, make certain they are not pasteurized.

  • Sauerkraut
  • Kefir (coconut kefir is great)
  • Kimchi
  • Pickles
  • Vegetables (onions, beets, cabbage, carrots or any vegetable can be fermented)
  • Kombucha
  • Natto
  • Miso
  • Raw, unpasteurized cheese (goat milk, sheep milk and some cow cheeses aged 6 months or more)
  • Yogurt (organic, unpasteurized, grass-fed)

Here is a great resource for learning to make your own fermented foods, purchasing live starter cultures and other equipment:


Probiotic Supplements

There are many probiotic supplements on the market that you can buy in health food stores, online, and from health practitioners. Probiotic supplements are considered safe to give to babies and children. They are available in powders, capsules, and liquids.

It’s important that the probiotic supplement you use contains multiple strains and has adequate numbers of colony forming units (CFUs).  10-30 billion CFUs per day are recommended amounts for babies and children. The number of CFUs in a probiotic supplement can vary a lot between brands. Quality is a big issue and many preparations don’t contain the number of viable CFUs claimed on the label. Probiotic supplements need to stay alive during processing and shelf life, and they are sensitive to oxygen, moisture and heat. Most probiotic supplements should be kept refrigerated. They must also survive stomach acid and digestion in order to colonize in the digestive tract and remain viable to do what they need to do.

Here are some good probiotics:

Klaire Labs Ther-Biotic Children’s Chewable

Klaire Labs Ther-Biotic Infant Formula

UltraFlora Children’s Chewable by Metagenics

Orthobiotic powder by OrthoMolecular

What to Avoid:

Processed Foods and Sugar

Bad bacteria thrive on sugar and there’s a lot of added sugar in processed food.


Antibiotics do not discriminate; they will kill both the good and the bad bacteria and disrupt the balance of gut flora. Babies given antibiotics in their first year tend to have higher rates of asthma, and children who take frequent rounds of antibiotics are prone to further infections. Using antibiotics for minor infections is unnecessary and can create more frequent infections. But there are some bacterial infections that can be serious and require antibiotics. If you must use antibiotics, be sure to replace the beneficial bacteria by giving your child probiotics and fermented foods.

Antibacterial Soaps, Cleansers, Hand Sanitizers and Wipes

If you use these products frequently, you may be destroying the good with the bad. The skin is loaded with good bacteria necessary to immunity, and using antibacterial wipes and sanitizers could inadvertently disrupt the development of immunity by depleting the good bugs. Additionally, using antibacterial household products might lead to strains of bacteria resistant to antibiotics. This means more powerful bugs that antibiotics are no longer able to deal with.

Products that can be infused with antibacterial chemicals include furniture, mattresses, toys, plastic kitchen tools, cutting boards, highchairs, and bedding. None of this is necessary and could be harmful to health.

There’s no evidence that antibacterial products provide any health benefits. They have no effect on viruses such as cold or flu, and there’s no evidence that using antibacterial soaps or wipes are any better than simply washing hands with normal soap and water.

Two chlorinated antimicrobials – Triclosan and Triclocarban – are the most commonly used, and are associated with endocrine, thyroid, and reproductive changes. These chemicals are absorbed into the body, and also washed down the drain, into lakes, rivers and water supplies.

Dr. Stuart B. Levy, of the Tufts University School of Medicine, warns about antibacterial household products:

“The recent entry of products containing antibacterial agents into healthy households has escalated from a few dozen products in the mid-1990s to more than 700 today. Antibacterial products were developed and have been successfully used to prevent transmission of disease-causing microorganisms among patients, particularly in hospitals. They are now being added to products used in healthy households, even though an added health benefit has not been demonstrated. Scientists are concerned that the antibacterial agents will select bacteria resistant to them and cross-resistant to antibiotics. Moreover, if they alter a person’s microflora, they may negatively affect the normal maturation of the T helper cell response of the immune system to commensal flora antigens; this change could lead to a greater chance of allergies in children. As with antibiotics, prudent use of these products is urged. Their designated purpose is to protect vulnerable patients.”

The following report from the National Coalition Against the Misuse of Pesticides goes into detail about common antibacterial agents in hundreds of consumer products. There’s a list of products containing these chemicals. The report also provides alternatives and the proper way to wash hands.

View the report here:

The Ubiquitous Triclosan: A common antibacterial agent exposed

You don’t have to try to kill the germs, just wash them away with nontoxic soap and water. This is the best way to prevent exposure while keeping your children’s environment healthy.