Well Mama Weblog

Our gut bacteria and their influence on our health

by Viviane Höger

Understanding the basics

What is gut microbiota?

Our gut microbiota contains tens of trillions of microorganisms, including at least 1000 different species of known bacteria with more than 3 million genes (150 times more than human genes). Microbiota can, in total, weigh up to 2kg. One third of our gut microbiota is common to most people, while two thirds are specific to each one of us. In other words, the microbiota in your intestine is like a fingerprint.

Where can we find it?

The gut microbiota is harboured in our gastrointestinal tract. Most of our microbes inhabit our large intestine (the colon), whilst the small intestine is where most of our food and energy is absorbed into our blood system.

Why is it important?

Some of the functions we currently understand include:

  • It helps the body to digest certain foods that the stomach and small intestine have not been able to digest.
  • It helps with the production of some vitamins (B and K).
  • It helps us combat aggressions from other microorganisms, maintaining the wholeness of the intestinal mucosa.
  • It plays an important role in the immune system, performing a barrier effect.
  • A healthy and balanced gut microbiota is key to ensuring proper digestive functioning.

How our gut microbiota develops

Taking into account the major role gut microbiota plays in the normal functioning of the body and the different functions it accomplishes, experts nowadays consider it as an “organ”. However, it is an “acquired” organ, as babies are born sterile - intestine colonisation starts right after birth and evolves as we grow. 

Early advantage: a natural birth

Almost immediately after a human being is born, so too is a new microbial ecosystem. In a normal delivery, the baby is exposed to the mother's microbiota as it passes through the birth canal. The new-born’s digestive tract is then quickly colonised by microorganisms from the mother (vaginal, faecal, skin, breast, etc.), or in the case of a Caesarean delivery (C-Section) by other bacteria from environmental sources including health-care workers, air, medical equipment and other new-borns.

This initial colonisation plays a fundamental role in brain development in the early post-natal weeks. How babies are born can also influence the development of food intolerances or allergies. As new-borns traverse the birth canal, they swallow bacteria that will later help them digest milk for example. C-section babies skip this bacterial baptism.

Breast is the best for our microbiota

A 2012 study found that whether babies are fed breast milk or formula influences the composition of their gut bacteria, and in turn, the development of their immune system.

The microbiota of breastfed infants has been reported to be more diverse than formula-fed infants, containing higher proportions of Bacteroides, Clostridium, and Enterobacteriaceae. Babies raised on formula do not get substances in breast milk that nurture beneficial bacteria and limit colonisation by harmful ones.

How our gut bacteria influences our immune system

The vast majority of our immune system (about 80 per cent), the complex system within our bodies that protects us and keeps us healthy, is located in our gastrointestinal tract.

Although researchers are still defining the mechanisms of how our gut microbiota informs and influences our immune system, they have evidence to suggest that our gut affects the mucosal part of our immune system, constantly communicates with our immune system, and even affects growth of certain organs needed for proper immune function.

The problem with antibiotics

The overuse of antibiotics has dire consequences for our gut microbiota and consequently, our immune system. Nevertheless, over the last 30 years the rates of overuse in general practice increased in most countries. 

Whilst they can without a question save lives when used correctly and with a purpose, most of us are unknowing consuming a certain amount of antibiotics with the food we consume, or being prescribed them when we have a viral infection, which cannot be treated by antibiotics in the first place.

Children are particularly vulnerable, and there are numerous studies showing how the over-prescription of antibiotics reduces their proper immune development by lowering the biodiversity of their gut microbiome.

Studies also show that exposure to antibiotics early in life predisposes a child to obesity and other diseases later in life.  Antibiotic levels in conventionally raised livestock may contribute to obesity by reducing the biodiversity of our gut microbiome. This should not be a revelation, as antibiotics have long been known to make livestock fat, so why not humans?

Bacteria and its relationship with our weight

For the now large percentage of the world population that battle with obesity, the main causes of their condition are all too familiar: an unhealthy diet, a sedentary lifestyle and perhaps some unlucky genes.

In recent years, however, researchers have become increasingly convinced that important hidden players literally hide in human bowels: billions on billions of gut microbes.

Evidence that gut microbes might play a role in obesity came from studies comparing intestinal bacteria in obese and lean individuals. In studies of twins who were both lean or both obese, researchers found that the gut community in lean people was like a rain forest brimming with many species but that the community in obese people was less diverse—more like a nutrient-overloaded pond where relatively few species dominate.

Some of the theories of how bacteria may affect our weight include:

Not all calories are created equal

Bacteria have the ability to make various fatty acids out of indigestible carbohydrates (dietary fibre) – these vegetable-loving bacteria then produce fatty acids for the gut and the liver as opposed to producing fatty acids that feed the rest of the body. Therefore, a banana is less likely to make you fat than a bar of chocolate with the same number of calories as the bacteria that produces fatty acids for the liver prefers plant carbohydrates as opposed to chocolate!  


If our microbiome is unbalanced, and the bad bacteria take charge, we start to see an increased presence of a molecule called lipopolysaccharide (LPS), found on the cell surface of bacteria. These molecules trigger the body’s immune defences, producing inflammation.

People suffering from metabolic problems such as obesity, diabetes and high-blood lipid levels normally have increased levels of infection markers in their blood too, a condition often referred to by doctors as ‘subclinical infection’. This understated infection mode can lead to or cause weight gain.

Satiety-signal transmitters

When we feed our gut bacteria what they like to eat, for example, food that reaches the large intestine undigested, they supposedly respond to this by increasing the production of satiety-signal transmitters, thus giving us the feeling of satisfaction, and helping us reduce cravings.

Keeping microbes happy

Fortunately, researchers are beginning to understand the differences between the wrong mix of bacteria and a healthy one, as well as the specific factors that shape those differences. They hope to learn how to cultivate this inner ecosystem in ways that could prevent—and possibly treat—obesity. Could keeping our gut microbes happy could be the elusive secret to weight control?

Why should we look after our microbes?

To put it simply, unbalanced proportions of the different bacteria that inhabit our gut have been detected on those suffering from obesity, malnutrition, nervous diseases, depression, and chronic digestive problems.

When our gut microbiota is functioning optimally and breaking down the food we eat, one of the side benefits we obtain is the production of short-chain fatty acids (SCFAs), these increase mitochondrial function and insulin sensitivity.

However, when the gut microbiota becomes disrupted or wiped out, through such things as antibiotic use and chronic stress, pathogenic bacteria have the opportunity to settle. This can lead to a cascade of catastrophic events such as intestinal hyper-permeability, systemic inflammation, and insulin insensitivity.

Diet is an important factor in shaping the gut ecosystem. A diet of highly processed foods, for example, has been linked to a less diverse gut community in people.

Whether we call it ‘paleo’ or primal eating style, it appears that a diet free of refined grains, flour, sugar, and vegetable oils seems to support a healthy mixture of gut microbes. On the other hand, a typical Western diet – very high in calories from refined carbohydrates but low in overall nutrients – tends to have the opposite effect, contributing to an imbalance in gut bacteria that lends itself further downstream to the development of insulin resistance, diabetes, obesity, and heart disease. 

What the future holds

There’s currently work going on to identify the precise strains of bacteria associated with leanness, determining their roles and developing treatments accordingly. 

Some of the proposals currently being studied include enriching foods with beneficial bacteria and any nutrients needed to establish them in the gut—a science-based version of today's probiotic yogurts. No one in the field believes that probiotics alone will win the war on obesity, but it seems that, along with exercising and eating right, we need to enlist our inner microbial army.

Leading Israeli researchers from the Personalised Nutrition Project (http://newsite.personalnutrition.org) have created bespoke diets using a computer algorithm that learns how individual bodies respond to different foods. Researchers believe the tailored diets could help stem the rising tide of diabetes, heart disease and obesity, by personalising people’s daily meals and so helping them to adopt healthy eating habits. 

The project challenges the idea that general recommendations about healthy foods are suitable for everyone, and instead aims to produce optimised diets based on people’s unique biological make-up.

The study highlights how traditional thinking around diets is flawed in the assumption that people put on weight purely because their meals contain more calories than they burn off.

Looking after our gut’s precious ecosystem

Meanwhile, there is plenty we, as individuals, could be doing to help cultivate our gut’s microbiota, and the recipe is really quite simple, some may even say common sense. Treat yourself to plenty of prebiotic-rich foods, dietary fibre and nutrients, whilst avoiding preservatives, antibiotics, junk food and sugar.

Prebiotic and probiotic

A food that is prebiotic contains ingredients, mostly fibre, that gut bacteria feed on, producing fermentation by-products that benefit health, whilst probiotic-rich foods are prepared by putting them in a slow cooker or a mason jar or otherwise letting the bacteria ferment them naturally.

Common bacteria, like lactobacilli, break down the sugars into acids, preserving the food and imparting a salty, tangy flavour. Fermented foods can provide fibre for our resident gut bacteria as well as a fresh shipment of transient bacteria. The new bacteria enhance the diversity of our gut microbes during their one-way transit and, in ways that scientists are just beginning to unravel, help the resident bacteria do their job better. 


Intermittent fasting is also thought to stimulate friendly microbes. Recent research carried out in laboratory showed that constant calorie restriction in mice was demonstrated to change the composition of their gut flora and promote longevity.

Seven foods that our gut bacteria enjoy:

1. Jerusalem artichokes

Benefits: High in inulin, strong prebiotic potential

Background: Inulin, an insoluble fiber, travels through our bodies from the small to large intestine, our colon. Once this insoluble fiber finds its way to the colon, it ferments into healthy microbiota. Other good sources of inulin include asparagus, leeks, onions, and bananas.

2. Bananas

Benefits: Restores health of the bacterial community, may reduce inflammation

Background: bananas work to maintain harmony among microbes in the bacterial community, known as phyla. This is one reason bananas are a standard prescription for an upset stomach. Bananas may also reduce inflammation, due to high levels of potassium and magnesium.

3. Polenta

Benefits: This high-fiber, corn-based complex carbohydrate has a fermentable component

Background: Polenta’s insoluble fiber travels directly to the colon, where it ferments into multiple strands of gut flora.

4. Broccoli and other cruciferous vegetables (kale, cabbage, and cauliflower)

Benefits: Cruciferous vegetables contain sulfur-containing metabolites, known as glucosinolates, which are broken down by microbes to release substances that reduce inflammation and reduce the risk of bladder, breast, colon, liver, lung, and stomach cancer.

Background: glucosinolates are known to latch onto carcinogenic intruders in our colon and show these pathogens the way out. Studies show people who eat the most cruciferous vegetables reduce their risk of colorectal cancer by 18 percent.

5. Blueberries

Benefits: Can modify the microbiota to enhance immune function

Background: Blueberries are a source of antioxidants, vitamin K compounds, and fiber. Studies continue to show blueberries may help strengthen our memory, improve our immune system, and diversify our gut bacteria.

6. Beans

Benefits: Any legume will help release short-chain fatty acids (SCFA) that strengthen your intestine cells, improve absorption of micronutrients, and help with weight loss.

Background: Beans are favoured by our good gut bacteria, which in turn strengthen our immune system. They are packed with fiber, protein, folate, and B vitamins, which play a role in regulating a healthy gut and a healthy brain.

Bonus: Researchers from Toronto just published a study in the journal Obesity that finds beans (pulses) improve weight loss by enhancing satiety.

7. Fermented plant-based foods: sauerkraut, kimchi, tempeh, and soy sauce

Benefits: Fermented foods, such as beet radish kimchi or pickled ginger sauerkraut, are fashionable for a reason. They directly inoculate your gut with healthy live microorganisms that will crowd out the unhealthy bacteria, improve the absorption of minerals, and improve overall health.

Background: Fermented plant-based foods are probiotics that have been found to improve the health of the intestinal cells, improve immune function, decrease allergies, reduce the risk of colon cancer, and treat diarrhea. You can make fermented foods at home and just as easily pick them up from a local grocery or health food store.

Disclaimer: This blog post contains general information about nutrition, health and diets. The information does not constitute medical advice and should not be treated as such. Before starting any diet, you should speak to your doctor. You must not rely on the information on this website as an alternative to medical advice from your doctor or other professional healthcare provider. If you have any specific questions about any medical matter, you should consult your doctor or other professional healthcare provider.

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