The Influence of Antibiotics on our Microbiome

AntibioticsMicrobiomeJacquie Eubanks RN BSN



While science has yet to discover the total impact of one’s unique and diverse microbiome on health and function, we do know that trillions of microbial cells directly influence each person’s most fundamental processes. Every individual’s ecosystem is composed of distinct colonies of microbes that inhabit different parts of the body and play essential specialized roles in digestion and absorption of nutrients, immune health, weight, sleep, mood and even our behavior. What’s really interesting is that similar to fingerprints, no two microbiomes are identical. This diversity may help to explain why some of us are prone to allergies, illness or anxiety, while others seem to fair far better.

Dr. Martin Blaser, microbiologist and director of the Human Microbiome Program at N.Y.U., describes the microbiome as, “all the organisms that call us home, that live in us and interact with each other and ourselves.” The fact is, bacterial cells vastly outnumber bodily cells ten to one, and have a combined weight of about three pounds. Many microbes are beneficial and some are deleterious, such as viruses, pathogens and harmful bacteria. Often referred to as colonies, microbes live in specific niches, and make their homes on our skin and in our nose, throat, lungs, mouth, stomach, intestines, and genitals. The study of the microbiome continues to evolve, as science strives to determine just how significantly these microbes affect our biological processes, and if microbes can be manipulated to support health and prevent disease.

We know that microbes have existed since the dawn of time and that animals, humans and microbes evolved together over millions of years. We know that the womb is sterile, and that babies acquire their first dose of microbes during the birthing process as they pass through the birth canal. Science now shows that babies born by caesarean section have very different microbiota than vaginal birth babies and have a higher risk of developing allergies and obesity. By the age of three, toddlers will have acquired the majority of their microbiome, which is still vastly different from the more stabilized one they will have by adulthood. Over a period of years, it is largely our age, genetics, environment, antibiotic usage and diet that shape our gut microbiome, beginning with breast milk in infancy, and continuing as we are introduced to solid foods and the world. While the composition of our microbiota slowly evolves over time, many microbes are persistent and stay with us throughout our lifetimes.

Research shows that those with a healthy, balanced gut microbiome have normal digestion and absorption of nutrients, better overall immune function, and a properly regulated metabolism. Evidence shows that an imbalanced gut flora, or dysbiosis, contributes to autoimmune diseases, obesity, type 2 diabetes and depression. Diets that are low in fermentable fibers and high in refined carbs, added sugars and processed foods directly contribute to an overgrowth of unhealthy gut flora. Of huge concern is the abundant use of antibiotics in both our medical care and our food supply. The ongoing exposure to antibiotics is considered particularly harmful to our beneficial intestinal microflora. Studies show that intervention is often necessary to restore a healthy balance of friendly bacteria after antibiotic use for illness, infection or surgery.

Using data and studies, Dr. Blaser has hypothesized that our obesity epidemic may be directly related the loss of certain microflora species over generations, largely in the last 20 years. While the discovery of antibiotics was no less than miraculous, currently the most commonly dispensed medications in the U.S. are outpatient antibiotics. Expectant women, children and the elderly are most often exposed to antibiotic use, varied by region and by country, though not by increased bacterial infections. When food producers discovered that antibiotics played a role in metabolism, growth and development, it led to an abundant and misappropriate use of antibiotics in industrial meat and poultry production, creating a huge problem for human overexposure and the rise of antibiotic resistant superbugs.

A study led by Brian Swartz, professor of environmental health services at the Johns Hopkins Bloomberg School of Health and published in the International Journal of Obesity, showed that antibiotic exposure in children could lead to long term weight gain. Significantly, they found that when antibiotics wipe out existing microbes, they are replaced by other less beneficial species that may adversely affect weight. According to Professor Schwartz, growing evidence shows that “A single course of antibiotics can wipe out an entire intestinal microbiome.” With infrequent use the microbiome can recover. However, “excessive antibiotics” can have a lasting impact on the microbiome and permanently change the ecology of the intestinal tract.

While there is certainly a time and a place for antibiotics, they should be used sparingly and only when necessary. Avoiding food products that may contain antibiotics by choosing meat and dairy products raised without antibiotics and hormones will reduce your exposure. Along with antibiotics, diet is believed to have the have largest impact on the microbiome. As both long and short term diet can influence the microbiome, support your own good health with a whole food, nutritious, fiber-filled, largely plant-based diet. Many high quality strands of probiotic supplements can aid in restoring, supporting and maintaining a healthy microbiome.

Professional Supplement Center carries many high quality products that provide various strains of viable probiotics:

Bio-Bifidus Complex by American BiologicsBio-Bifidus™ by American Biologics® – This patented dairy-free probiotic complex powdered formula is designed for optimal transplanting into the gastrointestinal tract and provides one billion CFU of beneficial microorganisms per serving. Gluten, soy and dairy free formulation.


UltraFlora Balance (HEAT SENSITIVE PRODUCT) by MetagenicsUltra Flora Balance® by Metagenics – This nutraceutical is formulated to promote daily gastrointestinal and immune health, and provide multiple levels of intestinal support, intestinal integrity and digestive function with a blend of pure, viable beneficial probiotic strains. Gluten, dairy and soy free formulation.


Complete Probiotics by Dr. MercolaComplete Probiotics by Dr. MercolaOn Sale 12% OFF! Each power packed dose of Complete Probiotics provides multiple strains of highly researched beneficial microorganisms to promote an optimal environment for colony growth, and provide critical immune and complete digestive support. Gluten and soy free.


FloraMend Prime Probiotic (SF811) by Thorne ResearchFloraMend Prime Probiotic by Thorne Research – This dairy and allergen free proprietary blend provides three essential strains of natural, stable, stomach acid-resistant probiotics to help replenish intestinal flora and promote overall digestive and immune health. Gluten, soy and dairy free formulation.


Saccharomyces Boulardii by Ortho MolecularSaccharomyces Boulardii by Ortho Molecular – Well studied for its use in supporting gastrointestinal disturbances often associated with antibiotic use, this product supplies 5 billion CFU of S. boulardii per capsule. No refrigeration necessary, making this a great traveler’s aid.  Gluten free.


Body Bugs: 5 Surprising Facts About Your Microbiome.
ASM’s Microbes After Hours.
Too Many Antibiotics May Make Children Heavier.
What To Do About The Antidepressants, Antibiotics And Other Drugs In Our Water.
Impact of diet and age on the gut microbiota.

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