The Effect of Antimicrobials on the Gut Microbiome


I believe that it is vitally important to consider the things that adversely affect our gut microbiome.  Most people give very little thought to consuming things that may partially or completely destroy our commensal bacteria.  We know that some antimicrobials adversely affect our gut microbiome, but not enough human research has been done on other antimicrobials.  Those antimicrobials may be greatly impacting our overall health to a degree larger than we anticipate, yet many people don’t even consider that what we put in our mouths every day could be killing us.

Most people understand that antibiotics wreak havoc on the gut microbiome. Antibiotics reduce bacterial diversity while expanding and collapsing membership of specific indigenous taxa according to Dr. Sheetal Modi from Boston University (2014).  In fact, even at the 6-month mark after taking oral antibiotics, the gut still lacks nine common beneficial bacterial species according to researchers (Yoon, 2018).  Because of the reduction in microbial diversity, most doctors recommend probiotics after taking a round of antibiotics.  Since we know definitively that antibiotics alter the gut microbiome composition, it is probable that other antimicrobials would indeed alter the gut species.

What about the antimicrobials that people knowingly or unknowingly consume?  Most Americans consume alcohol, and though some fermented spirits may confer benefit to the microbiome, distilled spirits can destroy most or perhaps all our commensal gut microbiome species.  Alcohol does indeed cause gut microbiome dysbiosis (Qamar, 2019) and this alteration in gut microbiome composition may cause an onslaught of inflammation, brain alteration, and other body system diseases, but very little human research has been done on its direct affects to date.  There is a decent amount of research that gut microbiome dysbiosis causes colorectal cancers (Zou, 2018) and scientists have discovered that this is due to cell stress (TUM, 2018).  It is feasible to consider that alcohol can cause cell stress and colorectal cancers may ensue.

(Read my article: ‘ Young Adults Are Dying Of Colon Cancer – How NOT To Be One Of Them!’ )

Another antimicrobial agent that has been only somewhat studied is pesticides. The gut microbiota is an unintended recipient of pesticides, and some pesticides alteration of the gut microbiome may in fact promote obesity and insulin resistance (Yuan, 2019). Most people that are conscientious about their health are aware of many of the harmful affects of pesticides, and those that can afford organic foods may be able to avoid pesticides altogether.

One antimicrobial agent that has had very little study and is difficult for many people to avoid, is chlorinated drinking water.  Chlorinated drinking water accounts for approximately 64% of all drinking water in the U.S. according to the CDC (2020). Though chlorinating our drinking water was an affective measure for reducing the incidents of Typhoid Fever as well as reducing other harmful bacteria in our drinking water sources, chlorine and other antimicrobial agents are not selective in the species that they kill.  Perhaps this 114-year-old practice that started in Jersey City in 1908 needs to be reconsidered. 

The limited scientific research that has been conducted concerning chlorinated water effect on microbiome includes a few rodent studies and one human study that I can find.  The rodent studies indicate that chlorinated water decontamination of the bedding in rodent facilities does alter their gut microbiome (Bidot, 2018), chlorinated water influences the development of colorectal tumors in mice (Sasada, 2015), and there was a significantly higher developmental weight gain in mice that consumed chlorinated water (Nathan, 2019).  In human studies, a metagenomic analysis of fecal samples from 60 healthy twins sampled from 0–8 months of life reported associations between domestic water sources and associated microbial signatures (Baumann-Dudenhoeffer, 2018). The authors further state that “Domestic water source correlates suggest water may be an underappreciated determinant of microbiome acquisition.”  Still, this limited research indicates an adverse effect that municipal chlorinated drinking water sources have on the gut microbiome.

Given the serious implications of the effects of chlorinated water on gut microbiome composition, this antimicrobial agent needs serious immediate attention.   Human studies need to be conducted to ensure that our so-called clean drinking water is not adversely affecting our health.  Clean drinking water is a human right and chlorinating drinking water may be a violation of those rights.  Individuals that cannot afford bottled spring water or additional filtration of drinking water may be more adversely affected by chlorination, so this is also an equity issue. For these reasons additional research is desperately needed.

Of note, swimming pools contain 2-4ppm chlorine and municipal water sources can contain 9ppm or more when 4ppm is considered ‘safe’ for humans. I would encourage you to consider checking the water quality report of your local municipality and also utilizing refillable containers for getting your water from reputable sources (i.e. Culligan, Glacier Water, etc.) that use filtration and ultra violet (UV) light for water sanitation. I would also recommend the Big Berkey Water Filter. In the mean time, please stop drinking bleach water!

Image Source: Pixabay


Bidot, W. A., Ericsson, A. C., & Franklin, C. L. (2018). Effects of water decontamination methods and bedding material on the gut microbiota. PloS one, 13(10), e0198305.

Modi, S. R., Collins, J. J., & Relman, D. A. (2014). Antibiotics and the gut microbiota. The Journal of clinical investigation, 124(10), 4212–4218.

Nathan, A. (2019). Effect of chlorine water consumption on phenotypic and microbiome development.

Qamar, N., Castano, D., Patt, C., Chu, T., Cottrell, J., & Chang, S. L. (2019). Meta-analysis of alcohol induced gut dysbiosis and the resulting behavioral impact. Behavioural brain research, 376, 112196.

Sasada, T., Hinoi, T., Saito, Y., Adachi, T., Takakura, Y., Kawaguchi, Y., Sotomaru, Y., Sentani, K., Oue, N., Yasui, W., & Ohdan, H. (2015). Chlorinated Water Modulates the Development of Colorectal Tumors with Chromosomal Instability and Gut Microbiota in Apc-Deficient Mice. PloS one, 10(7), e0132435.

Technical University of Munich (TUM). (2018, September 18). Colon cancer is caused by bacteria and cell stress: The microbiota in the intestines fuels tumor growth. ScienceDaily. Retrieved March 21, 2022 from

Water Disinfection with Chlorine and Chloramine | Public Water Systems | Drinking Water | Healthy Water | CDC. (2020, November 17). Centers for Disease Control and Prevention.

Yoon, M. Y., & Yoon, S. S. (2018). Disruption of the Gut Ecosystem by Antibiotics. Yonsei medical journal, 59(1), 4–12.

Yuan, X., Pan, Z., Jin, C., Ni, Y., Fu, Z., & Jin, Y. (2019). Gut microbiota: An underestimated and unintended recipient for pesticide-induced toxicity. Chemosphere, 227, 425–434.

Zou, S., Fang, L., & Lee, M. H. (2018). Dysbiosis of gut microbiota in promoting the development of colorectal cancer. Gastroenterology report, 6(1), 1–12.