What does smoking do to your gut and gut microbiome?

Smoking is associated with changes in the composition of the gut microbiome. In a large Dutch study of more than a thousand people, smoking was one of 126 factors that were measurably linked to how the gut microbiome looked. Which specific bacterial species increase or decrease was not made clear by this study. The effect has therefore been demonstrated, but the details have not yet been fully mapped out.

A more concrete consequence is the increased risk of inflammatory bowel diseases. Smoking raises the likelihood of inflammatory bowel diseases such as ulcerative colitis and Crohn's disease, probably in part because it disrupts the gut microbiome. This is considered probably causal, not merely an association. In addition, smoking is a risk factor for functional dyspepsia: a condition in which you experience pain or a feeling of fullness in the upper abdomen without any physical cause being found.

Smoking also increases the risk of a rare autoimmune disease of the bile ducts in the liver, called primary biliary cholangitis. In people with this condition, the gut microbiome is less diverse. Smoking is one of the environmental factors that can trigger the disease in people who are genetically susceptible to it. Whether smoking directly reduces the diversity of the gut microbiome, or whether this occurs through the disease itself, cannot be stated with certainty on the basis of the available research.

Finally, there is strong evidence that smoking increases the risk of a specific form of oesophageal cancer, particularly in combination with excessive alcohol use. While this does not directly involve the gut microbiome, it shows that the damage caused by smoking affects the entire digestive tract, from the oesophagus to the large intestine.