My guide to a healthy microbiota

Our microbiota is our own personal microsystem helping us to digest our food and fight invaders. It is composed of trillions of micro-organisms that populate our body, mostly in our gut. Among them, good and bad species fight for their territories. And the things we eat will feed the species that take over territories in our gut; studies have shown that eating processed food and a lot of sweet stuff is really good at killing off the most beneficial species that help us stay fit and healthy. On the other hand, eating food that will make our most beneficial species grow strong will help us achieve our goals of healthy living. More and more, doctors, nutritionists, naturopaths, (even oncologists), recognize the influence of good bacteria on our health.
What we are struggling with, however, is to know what to do about it. So, what can we do about it?

Here is my ultimate guide for a healthy microbiota. I gathered information and organized it into four sections:

Diet

Fibres - Yes

Why should I pay attention to my fibres intake?

1. Fibres have been advised as part of a healthy diet for years because they help with intestinal transit and make you regular.
2. It is also now known that certain fibres can be prebiotics, i.e. dedicated microbiota food that encourages good bacteria to prosper to help us fight invaders (more on how they do it HERE and why it's essential HERE).
3. Good bacteria help us to keep our colon intact and avoid inflammation (the infamous leaky gut syndrome) (more on this coming soon).

Where can I find fibres?

Apples, bananas, berries, raisins, kiwi, agave, honey, greens, onions, garlic, asparagus, chicory, Jerusalem artichokes, leeks, lentils, chickpeas, beans, brown rice, corn, buckwheat, flaxseed, whole wheat, whole rye, barley, almonds
Please note, foods such as cheese and cereal bars that are labelled ‘prebiotic’ usually have added inulin, a soluble fibre most often extracted from chicory root.

Fermented food - Yes

Fermented food is also an excellent source of goodies for your microbiota.
Sauerkraut; yogurt; soy; natto, miso or tempeh (fermented soy beans with specific species of bacteria); kefir (fermented milk); and kombucha (fermented green/black tea).

What to avoid?

Dietary emulsifiers
A paper published in the highly regarded Nature journal showed that dietary emulsifiers may promote intestinal issues in pre-disposed individuals and metabolic syndrome in anyone (obesity and diabetes). Indeed, carboxymethylcellulose and polysorbate-80 were shown to induce low-grade inflammation with consequences on the gut's mucosal integrity.

Glycoalkaloids?
Some of you who may be familiar with the leaky gut syndrome may have heard that saponins, aka glycoalkaloids, affect the integrity of our colon and should be avoided at all cost.
Saponins are present in spinach, oats, chick peas, beans, asparagus, onions, yams, garlic, tomatoes, and peppers as well as potatoes and tubers, but aren’t present in sweet potatoes. 
Whether these really have an impact on our health, I don't know yet, this will require a more extensive research, which I will carry out very soon.
But what I could find was that cooked potatoes release dietary resistant dextrin that act as prebiotic to modulate positively our microbiota. Moreover, a study in 2015 explained that if potatoes were previously thought to have a negative impact on our health, more research has revealed anti-cancer properties.

Sugar, processed meat, non-organic food are other types of food that are not recommended for a healthy microbiota. However, they do deserve a whole blog post each so, please come back soon to read about their impact on our gut mucosal integrity.

Behavioural habits

Alcool and smoking are clearly bad for you. Both have links to a higher risk of developing diseases including a long list of various cancers. In terms of influence on our microbiota, excessive alcohol intake has been shown to affect our microbial composition (HERE). Giving up smoking has also been shown to have remarkable effect and stimulate a healthier and more diverse microbiota (HERE).

Exercise is also a very good way of promoting a diverse microbiota as signals are sent via the gut-brain axis (HERE). Although admittedly when you exercise you are also more likely to follow a healthy regime, a study in mice showed that exercise alone induces gut microbial changes that are different from changes induced by diet (HERE).


Antibiotics is a subject I've already approached HERE. In brief, antibiotics can save human lives but definitely kill gut microbial lives so overuse is not recommended.

Sanitation is a thing of our generation whereby we absolutely want to get rid of all species on our bodies. But do we really? Too much soap, alcohol, and skin lotions are affecting our skin microbiota, which has been shown to enable bad bacteria to prosper (HERE).

Emotional being

Ever had a gut feeling about something? Ever wondered why we say GUT feeling? Scientists now believe that our microbiota has a major impact on our emotional well-being through the brain-gut axis (HERE). The brain-gut axis is the two-way information highway between our brain and our gut.
Moreover a recently aired TV documentary explained that in all situations, wearing a smile when you feel sad can make you feel better and change your brain signals.
My tips are then to smile, laugh when you can, reduce your daily stress, and accumulate all the beauty sleep you can get.

Maternal influence

Not much we can do about this but certainly you hope your mum had the opportunity to breastfeed you when you were a baby as breast milk is especially conceived to include both pre- and probiotics. And although you don't really have a choice on whether you were born naturally or by C-section, being born naturally and colonized by mum's best microbial starter pack puts you at an advantage in terms of lowered risk of developing diseases compared with C-section babies.
I've already written about this, you can find these articles HERE, HERE, and HERE.

I hope you enjoyed my ultimate guide,

What do you think would be easier to start with? Exercise, diet?

Let me know in the comment section, I'd love to read your stories.

See you next Monday!

Irreversible impact of a low fibre diet on gut flora

Any diet and health book, blog, advice will tell us to increase our intake of fibres. Fibres are essential for a variety of reasons including helping digestion, regulating our metabolism (avoid obesity and diabetes), avoid cardiovascular issues (lowering cholesterol), etc.

But did you know there are two types of fibres? Solubles and insolubles?
Both types behave differently in the gut, but they all end up being munched by our lovely gut flora species.

Those insoluble fibres are essential food for our little bugs. Without them, they are not doing too well. As the diversity in species is key to a healthy you, starving some species off simply results in an unhappy and unhealthy gut. The consequences of which can range from allergies to cancer.

Unfortunately, a recent study on mice showed that by being on a low-fibre highly-processed Western diet, entire species of friendly gut bacteria are starved off and never fully recover - even once back on a healthy high fibre diet.*

What was more worrying though was that this newly balanced gut flora with unhealthy species of bugs was passed on to new generations of mice (mainly from mum to baby as he gets born), and this with even less chance of recovery through healthy eating: some species were in fact completely extinct by generation number four!

This finding, combined with knowing that our Western lifestyle habits such as C-sections, formula feeding, and the overuse of antibiotics results in a poor gut flora diversity, should help us make a definite move towards a healthy life if we don't wish to affect future generations.

Where can I find good fibres, I hear you say: wholemeal bread, nuts, seeds, skin of fruit (apple, grapes, tomato), prunes, dates, popcorn, brown rice, bell peppers, cabbage, onions, lettuce, beans, peas, potato skin, cucumber skin, courgette, cauliflower, celery, avocado, unripe banana.

How do you take your fibres? Do you eat your recommended 30g/day?

Feel free to share your stories in the comments section, I'd love to read them.

See you next Monday1

The study can be found here

Tonsillectomy, breastfeeding, and the risk of obesity

Breast is Best! The NHS hammers that into our head, the WHO too. Recommendations are to exclusively breastfeed your baby for at least 6 months, and yet by saying breast is best, it implies that the alternative is good. This was brought to my attention by science writer Alanna Collen, author of the brilliant book entitled 10% Human.

Although babies’ formulas have been studied extensively these last few years, it is nowhere near as nutritious and protective as mum’s natural milk.

The role of breastfeeding is not only a nutritious one but also a protective one – Would you like to tweet this?

Breast milk contains so many components such as micro-organisms that will colonise the baby’s gut not only to help out with milk digestion but also to help out with immunity (more about it here).

Tonsils are those glands at the back of your throat that contain an army of immune cells. Their job is to investigate any food that comes in in order to educate the immune system on who’s good and who’s bad (wouldn’t want to have an auto-immune reaction against chocolate, now, do we?).

In fact, the tonsils we think are tonsils are only a part of ‘The Tonsils’ but they are the ones that get infected like crazy, and this is due to their surface being formed of deep grooves where bad bacteria can hide and develop leading to frequent infections, sore throats, and respiratory issues.

There is no doubt that in some instances, removing them is the right thing to do (e.g. respiratory obstructions, sleep apnoea); however, those tonsils are essential to educate our immune system, which has an essential role in keeping our heart healthy and controlling our body weight.

The strict recommendations (by the almighty WHO) are to wait until the child turns 7, which is the appropriate age at which the tonsils have had time to educate the immune system on all the stuff it may encounter (outside, school, friends, family, house, shops, etc…)

In fact, many studies have reported children at higher risk of being overweight if they undergo the operation too soon. One of these specifically reported that (adeno)tonsillectomy between 0 and 7 years old was statistically associated with overweight and obesity by 8 years old, and this was not explained by preexisting overweight.*



Coming back to breastfeeding, another study, from 1996 (i.e. we’ve known for a while) showed on the other hand that children undergoing tonsillectomy were less likely to have been breastfed, which effectively means that being breastfed is linked to a lower risk of developing recurrent infections and respiratory issues, which lead to tonsillectomy.**

Risk factors leading to an increased risk of developing each step:

No breastfeeding => Recurrent infections => Tonsillectomy => Obesity

So? Breast is Best? No, it’s the only good option (more about it here) with formula being a back up plan.

Unfortunately, a lot of women encounter difficulties in breastfeeding their baby – And I know what I’m talking about here, having gone through every single difficulty myself! But I believe there is not enough support from: empathic health visitors (who are a bit too rude if you suggest you might try formula), family, or the general public (breastfeeding in public anyone?). Maybe if some steps could be taken there, breastfeeding would be considered the absolute norm (with formula as a back up). Maybe then we would avoid a whole host of future health problems.

Have you undergone tonsillectomy when you were a child? Would you like to share your baby feeding experience?

Feel free to share your thoughts in the comments box, I’d love to read them.

*I got the info on the link between tonsillectomy and obesity from this paper: Wijga AH, et al. Adenotonsillectomy and the development of overweight. Pediatrics 2009; 123: 1095-1101. **And this short article can be found: Pisacane A, et al. Breastfeeding and tonsillectomy. British Medical Journal 1996; 312: 746-747.

Breast is not best, breast is the one and only

As soon as a baby is born, he receives his first germs from his Mum. The way babies are born nowadays, naturally or by C-section, has a massive influence on their initial microbial population, with a risk of long-term consequences such as obesity, asthma, and allergies for babies born by C-section.



During pregnancy, a mother prepares her gut and vagina flora to pass on to baby. The specific germs to be passed on are dedicated to milk digestion and gut immunity training (more about this here and soon to be available here). It becomes worrying therefore that when a child is born by C-section, his first germs are those of his mother’s skin, which are not really super good at helping milk digestion.

When his wife encountered difficulties giving birth to his child, Dr Rob Knight, a specialist in microbiota, didn’t take any chances: after his child was born by emergency C-section, he smeared him with his wife’s vagina secretions.

For those who are a bit grossed at the idea, there is another fantastic tool that women have been equipped with to ensure that baby gets all he needs: breast milk!

Breast milk is ideally (and the only one) conceived for baby, and that includes having a specific set of germs to pass on to baby - Do you want to tweet this?

Germs that will play a role in both nutrition, intestinal tolerance, and immunity. In fact, when looking at mum’s first secreted milk, called colostrum, it is actually full of components to shape baby’s immunity, and less for nutrition.

Breast milk is a savant mix of pre- and probiotics, along with other components, that will help mum provide her child with that famous passive immunity:


Probiotics bacteria by definition are friendly bacteria that have a positive effect. Breast milk's include Lactobacillus rhamnosus, L. gasseri, L. lactis; Leuconostoc mesenteroides, and Bifidobacteria.

Prebiotics are molecules that help our bacteria. In breast milk, they are Lactoferrin, medium-chain saturated fatty acids, long-chain unsaturated fatty acids, lysozyme, or oligosaccharides. Oligosaccharides are forms of sugar that friendly bacteria love. For example, high levels of prebiotics correlates with high levels of Bifidobacterium, an excellent infection protector.

For so many women who encounter lactation issues or other breastfeeding difficulties and for whom the need for formula is their only viable choice, there are just so many more who have forgotten how natural breastfeeding is and are not encouraged enough to pursue it.

Do you think breast is best or really the only one good?

I’d love to read your thoughts and experience, feel free to leave me a comment.

I used this scientific article as my source: Parigi SM, et al. Front Immunol 2015; 19: 415.