Coffee & Microbiome

Posted On: January 6, 2020
Categories:The Health Series,


The microbiomes of regular coffee drinkers were substantially healthier
than those who consumed little to no coffee.

By Ross Pelton, RPh, PhD, CCN
Scientific Director, Essential Formulas

In recent years, numerous studies have demonstrated associations between coffee consumption and lowered health risks of all sorts—from type 2 diabetes to certain cancers to Parkinson’s disease.i Also, accumulating evidence suggests that the composition of the gut microbiome has profound regulatory effects on human health. In general, a healthy microbiome reduces risks to a wide variety of health problems.ii

Recently, results from a new study reported that the microbiomes of regular coffee drinkers were substantially healthier than those who consumed little to no coffee. The new findings were announced at the 2019 American College of Gastroenterology annual meeting held in San Antonio, Texas.

In previous studies, scientists assessed people’s microbiome by examining stool samples. In this study, scientists took gut microbiome samples directly from various parts of the colon during colonoscopies

In this study, 34 participants who drank two or more cups of coffee daily throughout the previous year exhibited better gut microbiome profiles than those who consumed less or no coffee.

The bacterial species in heavy coffee drinkers were more abundant and more evenly distributed throughout the large intestine. The bacteria in coffee drinkers were also strains that provided stronger anti-inflammatory properties, and those strains were also considerably less likely to be strains of bacteria that are associated with metabolic abnormalities and obesity.

Scientists still do not completely understand the mechanisms behind coffee’s impact on the microbiome. However, coffee is rich in polyphenols and other antioxidants. These are naturally occurring compounds found in plant foods, that may be contributing to healthier microbiomes.

MY COMMENTS: Mycotoxins, which are toxins produced by fungi, have been found to be present in coffee beans from many countries. One study analyzed samples of coffee beans (84 from Africa, 60 America and 18 samples from Asia) and found mycotoxins in 106 of the 162 samples tested.iii

Mycotoxins are extremely toxic, and the study referenced above shows that many commercial coffee products contain traces of mycotoxins. Hence, I strongly recommend that people only purchase organically grown coffee beans. Also, the health benefits from drinking coffee pertain to drinking coffee alone, without added milk or cream and without sugar or artificial sweeteners.

I have previously posted an article on my blog about the wide-ranging health benefits from drinking coffee, such as reduced risks to type 2 diabetes and heart disease. My article is available at: (scroll down the index and click on Coffee).

Healthy coffee provides significant health benefits. It is the milk, cream, sugar and/or artificial sweeteners that cause health problems. And, be sure to purchase high-quality organically grown coffee (or coffee beans) to avoid pesticides, herbicides, and mycotoxins from mold.

i Bidel S and Tuomilehto J. The Emerging Health Benefits of Coffee with an Emphasis on Type 2 Diabetes and Cardiovascular Disease. Eur Endocrinol. 2013 Aug;9(2):99-106.
ii Liang D, et al. Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities. Gut Pathog. 2018 Jan 25;10:3.
iii Romani S, et al. Screening on the Occurrence of Ochratoxin A in Green Coffee Beans of Different Origins and Types. J. Agric. Food Chem. 2000, 48, 8, 3616-3619