Smoking and the Gut Microbiome

September 23, 2020

Did you know that smoking, in addition to damaging lungs and the cardiovascular system, also harms the gut microbiome? The microbiome, the complex ecosystem of microbes living in your gut and influencing many disease states including diabetes, dementia and Inflammatory Bowel Disease, is damaged by the chemicals in cigarette smoke. In a healthy individual, the gut microbiome typically consists of the Firmicutes and Bacteroides phyla (involved in carbohydrate utilisation), with minor representations from the Proteobacteria (involved in oxygen uptake) and Actinobacteria phyla (involved in immune responses and gut permeability). However, a study by Yoon (2020) found that smokers had decreased levels of Actinobacteria, Proteobacteria and Firmicutes but increased levels of Bacteriodetes, resulting in gut microbiome dysbiosis.

Such dysbiosis can cause an impaired regulation of digestion (e.g. extraction, synthesis, and absorption of nutrients and metabolites), immune function (e.g. inhibition of pathogen colonisation, innate and adaptive immune cells function regulation and maintenance of the intestinal epithelium integrity), development, and homeostasis. Hence, beyond the direct toxicity of the harmful constituents of cigarette smoke on multiple organ systems, smoking’s harmful effects may also be mediated in part through the gut microbiome.

Interestingly, the use of e-cigarettes seemed to have a lesser impact on the gut microbial profiles although this is based only on a single small study. In a study by Stewart et al (2018), ten e-cigarette users with at least 3 years of vaping history, ten tobacco smokers who smoked at least 10 cigarettes per day and ten controls with no smoking history had Prevotella and Bacteroides levels in their faecal samples measured. In the smokers’ cohort, significant increase and reduction in Prevotella and Bacteroides were observed, respectively. However, there were no significant changes in the gut microbial diversity observed in the e-cigarette cohort compared to the non-smokers.

Whilst heated tobacco products, or specifically IQOS manufactured by Philip Morris, is deemed by the US FDA to have ‘reduced exposure’, there is no published literature to the best of our knowledge on the effect of heated tobacco products on the gut microbiome. This would be important to study as the FDA acknowledged that the IQOS system significantly reduces the production of harmful and potentially harmful chemicals and that “switching completely from conventional cigarettes to the IQOS system significantly reduces your body’s exposure to harmful or potentially harmful chemicals”.

Given the growing realization of the importance of the gut microbiome to human health and louder and louder advocacy to switch smokers who cannot or will not stop smoking to e-cigarettes or heated tobacco products (the so-called ‘tobacco harm reduction strategy’), it is important that more independent research is conducted on the effects of these smoking alternatives on the gut microbiome.

Finally, one non-obvious gut-related risk of smoking: smokers have an 80% higher risk of Clostridium difficile infection, a disease that affects half a million Americans annually and causes 29,000 deaths per year. Why? 90% of cigarettes contain Clostridium bacteria species which are introduced into the gut through repeated smoking. Another risk that needs to be reduced!


Benjamin, J. L., Hedin, C. R., Koutsoumpas, A., Ng, S. C., McCarthy, N. E., Prescott, N. J., Pessoa-Lopes, P., Mathew, C. G., Sanderson, J., Hart, A. L., Kamm, M. A., Knight, S. C., Forbes, A., Stagg, A. J., Lindsay, J. O., & Whelan, K. (2012). Smokers with active Crohn’s disease have a clinically relevant dysbiosis of the gastrointestinal microbiota. Inflammatory bowel diseases18(6), 1092–1100.

Biedermann, L., Brülisauer, K., Zeitz, J., Frei, P., Scharl, M., Vavricka, S. R., Fried, M., Loessner, M. J., Rogler, G., & Schuppler, M. (2014). Smoking cessation alters intestinal microbiota: insights from quantitative investigations on human fecal samples using FISH. Inflammatory bowel diseases20(9), 1496–1501. 

Biedermann, L., Zeitz, J., Mwinyi, J., Sutter-Minder, E., Rehman, A., Ott, S. J., Steurer-Stey, C., Frei, A., Frei, P., Scharl, M., Loessner, M. J., Vavricka, S. R., Fried, M., Schreiber, S., Schuppler, M., & Rogler, G. (2013). Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans. PloS one8(3), e59260.

Binda, C., Lopetuso, L. R., Rizzatti, G., Gibiino, G., Cennamo, V., & Gasbarrini, A. (2018). Actinobacteria: A relevant minority for the maintenance of gut homeostasis. Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver50(5), 421–428.

Brestoff, J. R., & Artis, D. (2013). Commensal bacteria at the interface of host metabolism and the immune system. Nature immunology14(7), 676–684.

Chi, L., Mahbub, R., Gao, B., Bian, X., Tu, P., Ru, H., & Lu, K. (2017). Nicotine Alters the Gut Microbiome and Metabolites of Gut–Brain Interactions in a Sex-Specific Manner. Chemical Research In Toxicology, 30(12), 2110-2119. doi: 10.1021/acs.chemrestox.7b00162

Centres for Disease Control and Prevention. (2015). Nearly half a million Americans suffered from Clostridium difficile infections in a single year [Press release].

Faith DP, Reid CAM, Hunter J (2004) Integrating Phylogenetic Diversity, Complementarity, and Endemism for Conservation Assessment. Conservation Biology 18 (1): 255–261

Khosravi, A., & Mazmanian, S. K. (2013). Disruption of the gut microbiome as a risk factor for microbial infections. Current opinion in microbiology16(2), 221–227.

Komaroff, A. (2017). The Microbiome and Risk for Obesity and Diabetes. JAMA317(4), 355. doi: 10.1001/jama.2016.20099

Lee, S., Yun, Y., Kim, S., Lee, E., Chang, Y., & Ryu, S. et al. (2018). Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study. Journal Of Clinical Medicine7(9), 282. doi: 10.3390/jcm7090282

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444(7122), 1022+. Retrieved from

Moon, C., Young, W., Maclean, P., Cookson, A., & Bermingham, E. (2018). Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats. Microbiologyopen7(5), e00677. doi: 10.1002/mbo3.677

Philip Morris Products S.A. (2018). Tobacco Heating System (IQOS) Briefing Document. Retrieved from

Philip Morris Products S.A. Modified Risk Tobacco Product (MRTP) Applications. (2020). Retrieved from

NIDA. (2020) Cigarettes and Other Tobacco Products DrugFacts. Retrieved from 

Ramakrishna, B. (2013). Role of the gut microbiota in human nutrition and metabolism. Journal Of Gastroenterology And Hepatology28, 9-17. doi: 10.1111/jgh.12294

Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G., Gasbarrini, A., & Mele, M. C. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms7(1), 14.

Rogers, M., Greene, M., Saint, S., Chenoweth, C., Malani, P., Trivedi, I., & Aronoff, D. (2012). Higher Rates of Clostridium difficile Infection among Smokers. Plos ONE7(7), e42091. doi: 10.1371/journal.pone.0042091

Sapkota, A. R., Berger, S., & Vogel, T. M. (2010). Human pathogens abundant in the bacterial metagenome of cigarettes. Environmental health perspectives118(3), 351–356.

Savin, Z., Kivity, S., Yonath, H., & Yehuda, S. (2018). Smoking and the intestinal microbiome. Archives Of Microbiology200(5), 677-684. doi: 10.1007/s00203-018-1506-2

Shin, N. R., Whon, T. W., & Bae, J. W. (2015). Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends in biotechnology33(9), 496–503.

St Helen, G., Jacob Iii, P., Nardone, N., & Benowitz, N. L. (2018). IQOS: examination of Philip Morris International’s claim of reduced exposure. Tobacco control27(Suppl 1), s30–s36.

Stewart, C. J., Auchtung, T. A., Ajami, N. J., Velasquez, K., Smith, D. P., De La Garza, R., 2nd, Salas, R., & Petrosino, J. F. (2018). Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study. PeerJ6, e4693.

U.S. Food and Drug Administration. (2020). FDA Authorises Marketing of IQOS Tobacco Heating System with ‘Reduced Exposure’ Information [Press release].

Wexler H. M. (2007). Bacteroides: the good, the bad, and the nitty-gritty. Clinical microbiology reviews20(4), 593–621.

World Health Organisation. (2020). Heated Tobacco Products information sheet [PDF] (2nd ed.). Retrieved from

Yoon, H., Lee, D. H., Lee, J. H., Kwon, J. E., Shin, C. M., Yang, S. J., Park, S. H., Lee, J. H., Kang, S. W., Lee, J. S., & Kim, B. Y. (2020). Characteristics of the Gut Microbiome of Healthy Young Male Soldiers in South Korea: The Effects of Smoking. Gut and liver, 10.5009/gnl19354. Advance online publication.



About the authors

Lim Shu Han is a Biomedical Science student from Temasek Polytechnic. She is currently interning at AMILI.

Dr Jeremy Lim is the co-founder and CEO of AMILI.