How to preserve your microbiome diversity

Ultra-processed foods, alcohol, and sweeteners—how do they affect our microbiome?

This is the second of a trio of articles on the microbiome–and we’re starting with some top tips to help preserve our microbiomes and keep the bugs productive.

If we think of the microbiome as a city of workers each doing a specialised job, it’s easy to imagine how losing all the teachers or firefighters could wreak havoc. In the same way, our microbiome benefits from a variety of workers doing different things.

Our gut bacteria produce ‘metabolites’, active molecules that can have an effect on our cells, from those in the intestinal wall to our brains.

Good gut bugs create useful metabolites for the physical and cognitive demands of daily life (like butyrate and anti-inflammatory molecules). On the other hand, ‘pathogenic bacteria’ (bad bugs) can produce harmful metabolites. So, when we consider our gut ecosystem as a whole, it’s important to think about the balance of bugs and the metabolites they produce.

Ultra Processed Foods (UPFs) & Emulsifiers

Ultra-processed food is bad news for your gut microbiome.

I mentioned in a previous article a rule of thumb to help identify UPFs. Some are sneakily masquerading as “good for gut health” ( cereal , I'm looking at you).

What makes some UPFs so shelf-stable for a year without falling apart or splitting into water and oil are the lovely chemicals that directly harm the microbiome: emulsifiers .

Emulsifiers bind waters and oils together into an ‘emulsification’. The evidence is stacking up that many of them, particularly polysorbate 80 and carboxymethylcellulose, are harmful to the microbiome.

The jury is out on other emulsifiers (like lethicin), but it seems sensible to minimise highly processed foods, that contain chemicals designed to keep them glued, altogether!

Processed Meats

Sorry, salami-snackers. Processed meats are harmful to health and the evidence behind this is stacking up.

What’s more, our microbiome produces toxic metabolites like trimethylamine (TMA) when we eat red or processed meats, which can damage blood vessels and lead to heart disease. Interestingly, those on consistent plant-based diets may be less able to produce TMA , even when they do eat meat, because they may have fewer bugs that can produce it.

TMA has to be converted to TMAO by the liver to be active and a few colourful compounds like quercetin , found in parsley, may be helpful to slow that conversion down. So, a bright green chimichurri sauce seems like the perfect addition to meat dishes - perhaps explaining its conception and persistence (and deliciousness).

Some of these processed meats also have nitrites added, to prevent spoilage and this may contribute to the health risks associated with high meat consumption.

If you’re looking for an easy way to swap out nitrites—Parma ham is tightly regulated and nitrites are banned!


The process and method of cooking itself can affect your microbiome.

Acrylamide is a fascinating and bad byproduct of high temperature cooking, that occurs when the amino acid asparagine and sugar are heated above 120 degrees Celsius. It is considered harmful to cells in the intestine and microbiome and it tends to be produced when starchy veg (particularly potatoes) have been browned or crisped up (something called the ‘Maillard’ reaction).

The good news is boiling and steaming food hugely reduces its production.

In the third article of this series, we’ll have another look at acrylamide, with a focus on probiotics. Again, we might find that the impact of some of these metabolites depends on the workers you have in your gut…

Artificial Sweeteners

There has been conflicting evidence as to whether artificial sweeteners, like saccharin, sucralose and aspartame, harm the microbiome. One study found that all of them did make significant changes to the gut microbiome of healthy participants.

In this study, the participants were given pure sachets of these sweeteners, below the recommended daily dose. In real life, however, these sweeteners commonly hide inside UPFs and the effects on the microbiome may be even more pronounced.

This is a rapidly expanding research topic, so I’m keeping a close eye on it. In the meantime, I’ve been sticking to honey for sweetness in my cooking!


Alcohol consumption impacts the gut microbiome, with new research suggesting that binge-drinking can particularly affect it. In addition, alcohol consumption impacts sleep ‘architecture’ (the pattern of REM and non-REM sleep) and this too may have a knock-on effect on the microbiome and even our food choices.

Swap a nightcap out for a cuppa to thank your gut bugs for their hard work instead—black tea, green and oolong all have some good evidence to help your microbiome.

These tips should help in preserving the best of our bugs and keep them making useful metabolites for us, whilst keeping food delicious!

Next up, a focus on diversity…

More about Dr Ramy

Dr Ramy Saad is a physician and researcher, focussing on the microbiome and epigenetics.

Ramy studied medicine at UCL and is a medical doctor in Clinical Genetics, with a background in Internal Medicine and Rheumatology.

Ramy’s scientific research has been around the impact of micronutrients, vitamins and polyphenols in inflammation and immunity and he has been published in New England Journal of Medicine and the American Journal of Clinical Nutrition. Ramy also holds academic and industry experience in nutrition, ingredient and supplement development and adapting medical policy.

Ramy is also the co-founder of , creating award-winning fermented sauces for homes and chefs.

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Dr Ramy Saad

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