Microbiome, Phytochemicals and Health

April 16th, 2021 | Posted in Info

If you’ve read the blog posts on Microbiome, Diet and Health and Microbiome, Fibre and Fermentation you’ll have some idea of the relationship between what we eat, our microbiome and our health. Here we’ll look at the interactions between phytochemicals and the gut microbiota. Phytochemicals are chemical compounds naturally occurring in plants that don’t come under the definition of macronutrients, vitamins or minerals.

Phenols and Polyphenols

One class of phytochemicals that has been studied extensively is the polyphenols. These act as antibiotics, antioxidants, and signalling molecules affecting body processes. They are often poorly absorbed but it turns out the gut bacteria may increase their bioavailability and bioactivity. They in turn can affect the composition of the gut microbiome. Here’s what research has found out about a few of them:

Thyme – thymol and carvacrol are phenols found in thyme with antibiotic activities. Studies in chickens indicate that these phenols may reduce the numbers of Campylobacter jejuni, Salmonella, spp, E. coli and Clostridium perfringens. The commensal bacteria are largely unaffected by these compounds.

Tea – contains a mixture of polyphenolic compounds dominated by catechins. Tea polyphenols have been shown to have antibacterial, antitoxin and antiviral effects.

Coffee – has been shown to stimulate Bifidobacterium.

Cocoa, strawberries, raspberries, blackcurrants and pomegranates -have all been shown to increase Lactobacillus and Bifidobacterium (1,2).

Flavonoids and Isoflavonoids

Blueberries, blackberries, red apples, red onions and watercress are all sources of quercetin. Studies in rats indicate that quercetin intake reduces gut dysbiosis induced by a high fat diet, possibly leading to reduced weight gain (1,2).

Soy and other legumes contain isoflavones, such as daidzein and genistein. These are thought to have various effects on health including benefits to bone health and anti-cancer properties. Isoflavones have been shown to be converted by certain gut bacteria to equol, which may have even more potent health benefits than the parent compounds (1,2).

Red wine, peanuts, grapes and berries are all sources of resveratrol. Recent reports indicate that resveratrol stimulates growth of Bifidobacterium and Lactobacillus in mice (1,2).

Pomegranate contains elagitannins  that have been shown to stimulate Bifidobacterium and Lactobacillus while inhibiting growth of Bacteroides, Clostridia and Enterobacteriaceae..

Blackcurrants, blueberries, cherries and blackberries contain anthocyanidins, which when fermented increase Bifidobacterium and Lactobacillus (1,2).


There is clearly a bi-directional relationship between dietary phytochemicals and gut microbial communities. Indeed, interactions between phytochemicals and the gut microbiota may be an important contributor to the health promoting properties of many plant foods.  Consumption of phytochemical rich plant foods such as cocoa, tea, wine, soy, fruit and vegetables, and fibres such as inulin, and hemicellulose, have significant effects on the relative abundances of microbes in the gut and the metabolites they produce (2). This in turn has profound effects on our health, metabolism, weight, mood and behaviour.


1. Sheflin AM et al. Linking dietary patterns with gut microbial composition and function, Gut Microbes, 2017, 8:2, 113-129

2. Frame LA et al. Current Explorations of Nutrition and the Gut Microbiome: A Comprehensive Evaluation of the Review Literature. Nutrition Reviews, Oct. 2020; 78, P.798–812,