Tag Archives: antibiotics

The Decline of Probiotics in a Germophobic World (part 2)


 Ponder the above statement for a minute. What does it mean exactly? Essentially that humans are actually made up of 90% microorganisms and only about 10% human cells.

How can that be, you might ask? Because humans evolved to live symbiotically with microorganisms. We provide them with food and shelter, and they in turn help us digest components of our food that we lack the enzymes to digest ourselves. They also synthesize certain vitamins, help regulate our immune systems, and prevent invasion from harmful microorganisms that can make us sick12. Their survival is dependent on us, and our survival is dependent on them. When the balance of good germs and bad germs is thrown off, the result is termed intestinal dysbiosis1.

How do these microorganisms get inside of us in the first place?

We inherit our gut flora from our mothers. Babies in the womb are completely sterile, meaning that they have no gut flora at all3. As they pass through the birth canal they “pick up” microorganisms that are present in their mother’s vaginal tract (which is representative of the microorganisms present in her gut)9. This could be why babies that are born via cesarean section have been found to have higher rates of asthma, allergies, obesity, coeliac disease, and diabetes than babies who are born vaginally8. Recent research has also linked cesarean deliveries to an increased rate of autism but it is unsure yet as to whether c-sections raise the chances of having a child with autism or if giving birth to a baby predisposed to autism raises the chances of requiring an emergency c-section4. Babies who are born vaginally and exclusively breastfed have also been found to have more “beneficial” gut microbiota compared to babies who are born via c-section and formula-fed8.  Now that doesn’t mean that if your baby was born via cesarean he or she will be doomed to develop some sort of illness. It just means that you need to ensure your baby develops a healthy gut flora via other methods (breastfeeding, eating fermented foods, and staying away from antibiotics unless absolutely necessary).

Breastfeeding and its role in developing healthy gut flora

 Breastfeeding helps babies’ immune systems “learn” to be tolerant to different foods and things in the environment to avoid allergic reactions8. Breastmilk also contains prebiotics12 which help the probiotics in the baby’s gut flourish.  If you are unable to breastfeed there are now many probiotic formulas available to promote good gut health in your baby. Even women who breastfeed are not necessarily passing on the best probiotics to their babies unless they themselves have good gut health (although they will still pass on many other molecules that are crucial to developing healthy gut flora). Babies can be given probiotic foods when they start weaning to introduce more “good germs” into their bodies. They will also naturally pick up germs from their environment, which is good for their gut flora.  Just as long as you don’t over-sanitize everything in their environment. 

Newborns and small infants should however be kept away from sick people since their immune systems are still developing (sick people harbour pathogens, the harmful kind of microbes that you don’t want invading your baby’s body). 

What is happening to our gut health?

 The cumulative overuse of antibiotics across multiple generations is resulting in our children lacking healthy gut flora1. Add to that the negative effect that birth control pills and vaccinations have on our gut flora, and its no wonder that we seem to be getting sicker and sicker. Each generation is passing on less beneficial microbes to the next. There are scientists who are studying and saving microbes found in fecal samples from people living in the amazon and villages who have had little to no contact with the modern world and also have not contracted our modern diseases3. The hope is that some of the beneficial microbes that have gone extinct in our bodies can one day be salvaged from those people and reintroduced into our bodies to protect or even cure us of our modern diseases3. If you are interested in reading more about how and why beneficial microbes are going extinct and why they are so important, I highly recommend this book by Dr. Martin Blaser.  

What happens when we don’t have good gut health? 

The beneficial microorganisms in the gastrointestinal tract directly affect the immune system, therefore the absence of “good germs” in the gut can lead to inflammatory diseases due to a lack of regulation of the immune system11. Microorganisms in the gut also influence how a potentially toxic environmental chemical is metabolized by your body (if its absorbed or excreted)7.  Basically, good germs in your gut can protect you from bad chemicals.  Antibiotic use has even been linked to coeliac disease10  which infers that the bacteria in your gut are crucial for proper digestion of food. It is very likely that antibiotics alter gut flora to the extent of causing disease.

So what does all of this research mean?

It means that we need to be more conscious of nurturing the trillions of “good germs” in our bodies that have such a profound impact on our health. We need to be mindful that when we get vaccinated and take antibiotics or other medications, we also need to restore the good germs that may have been lost. In order to maintain optimal health we also need to maintain the health of all of our microfriends living inside of us. This is where probiotics and prebiotics come in (read more about them in my previous post here).

All of the above information DOES NOT mean that we shouldn’t get vaccinated or take antibiotics and other medications when necessary. Without them, infectious diseases would still be the number one cause of death in humans as it was prior to their invention. We just need to be aware of the effect that they have on our gut microbiota and take measures to reverse that effect. So if you get bronchitis and have to take antibiotics, follow up with a round of probiotic supplements or increase the amount of fermented foods in your diet. The same logic applies to other medications and vaccinations.

For pregnant women, probiotic foods are a must and I cannot emphasize enough the importance of maintaining a healthy gut during pregnancy. Babies who have gut dysbiosis from birth are essentially immunocompromised and will react differently to vaccinations and antibiotics or medications than babies with healthy gut flora. Any medical intervention can end up being the straw that breaks the camels back when it comes to already immunocompromised infants and children, possibly resulting in disorders like asthma, diabetes, autism, obesity, coeliac disease, and others.

Let me be perfectly clear. I am in no way saying that the above listed illnesses are caused by medical interventions. I am saying that they can be triggered by them in babies and children who are already immunocompromised due to gut dysbiosis.  Those medical interventions are necessary and can be life saving.

Think about it this way; if children with gut dysbiosis can be triggered by certain medical interventions, that’s not to say that avoiding them completely will prevent them from being triggered. Those children can also be triggered by a virus or environmental exposure to a toxic chemical, basically anything that their immune system is not equipped to handle. So avoiding medical interventions isn’t the answer, it will only delay the onset of illnesses and disorders that some children are bound to contract as long as their gut microbiota are unbalanced. The answer is to heal their immune systems by healing their guts.

Or, if possible, give them the best start in life by ensuring they are born with healthy gut flora so that they don’t need to be healed in the first place.

I wish I had known all of this when I was pregnant as I could have possibly prevented a lot of my daughter’s “gut issues” (acid reflux, gas and overall stomach discomfort, irritability, poor eating habits) that caused her to be such a fussy baby. I’m grateful that I at least know it now so I can work on balancing her gut microbiota by feeding her plenty of fermented foods. Hopefully this post will help other parents recognize their children’s gut issues. And even better, I hope it will reach expecting mothers who may have unbalanced gut flora themselves, so that they can fix the imbalance before delivery to ensure that their babies have healthy guts from birth.

There are studies that show a correlation between good gut flora and having older siblings, possibly due to daily exposure to germs from other kids. However, I have my own theory as to why children with older siblings are more likely to have healthy gut flora compared to first-born or only children:


1. Blaser, Martin J. Antibiotics Overload Is Endangering Our Children. Time.com. 5/9/2014, p1-1. 1p

2. Blaser, Martin; Bork, Peer; Fraser, Claire; Knight, Rob; Wang, Jun. The microbiome explored: recent insights and future challenges, Nature Reviews Microbiology. Mar2013, Vol. 11 Issue 3, p213-217. 5p. DOI: 10.1038/nrmicro2973

3. Blaser, Martin J. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Holt. 2014. 288p

4. Curran, E. A., O’Neill, S. M., Cryan, J. F., Kenny, L. C., Dinan, T. G., Khashan, A. S. and Kearney, P. M. (2014), Research Review: Birth by caesarean section and development of autism spectrum disorder and attention-deficit/hyperactivity disorder: a systematic review and meta-analysis. Journal of Child Psychology and Psychiatry. doi: 10.1111/jcpp.12351

5. Dong, H., Rowland, I., Tuohy, K. M., Thomas, L. V., & Yaqoob, P. (2010). Selective effects of Lactobacillus casei Shirota on T cell activation, natural killer cell activity and cytokine production. Clinical & Experimental Immunology, 161(2), 378-388. doi:10.1111/j.1365-2249.2010.04173.x

6. Dotterud, C. K.; Storr, O.; Johnsen, R.; Øien, T. Probiotics in pregnant women to prevent allergic disease: a randomized, double-blind trial. British Journal of Dermatology. Sep2010, Vol. 163 Issue 3, p616-623. 8p. DOI: 10.1111/j.1365-2133.2010.09889.x

7. Holtcamp, Wendee. Gut Check: Do Interactions between Environmental Chemicals and Intestinal Microbiota Affect Obesity and Diabetes? Environmental Health Perspectives. Mar2012, Vol. 120 Issue 3, pA123-A123. 3/5p.

8. Isolauri, Erika. Journal of Paediatrics & Child Health. Development of healthy gut microbiota early in life. Jun2012 Supplement, Vol. 48, p1-6. 6p. DOI: 10.1111/j.1440-1754.2012.02489.x

9. John Penders, MSca, Carel Thijs, MD, PhDa,b, Cornelis Vink, PhDc, Foekje F. Stelma, MD, PhDc, Bianca Snijders, MScb, Ischa Kummeling, MScb, Piet A. van den Brandt, PhDa, Ellen E. Stobberingh, PhDc. Factors Influencing the Composition of the Intestinal Microbiota in Early Infancy. PEDIATRICS Vol. 118 No. 2 August 1, 2006 pp. 511 -521 (doi: 10.1542/peds.2005-2824)

10. Mårild, Karl; Weimin Ye; Lebwohl, Benjamin; Green, Peter H. R.; Blaser, Martin J.; Card, Tim; Ludvigsson, Jonas F. Antibiotic exposure and the development of coeliac disease: a nationwide case-control study. BMC Gastroenterology. 2013, Vol. 13 Issue 1, p1-9. 9p. 1 Diagram, 2 Charts. DOI: 10.1186/1471-230X-13-109

11. Round, June L.; Mazmanian, Sarkis K. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology. May2009, Vol. 9 Issue 5, p313-323. 11p. 3 Diagrams, 3 Charts. DOI: 10.1038/nri2515.

12. Wallace, Taylor C; Guarner, Francisco; Madsen, Karen; Cabana, Michael D; Gibson, Glenn; Hentges, Eric; Sanders, Mary Ellen. Human gut microbiota and its relationship to health and disease. Nutrition Reviews. Jul2011, Vol. 69 Issue 7, p392-403. 12p. 2 Charts. DOI: 10.1111/j.1753-4887.2011.00402.x.