Probiotics and the Microbiome

post immuno microbiotic

The microbiome is one of the hottest topics in health research now!

The term microbiome was coined by the Nobel laureate Joshua Lederberg. Strictly speaking, it refers to the combined genetic material of all the microbes that we are host to, whereas the actual trillions of microbes themselves are called your microbiota. But we will use the word microbiome because that is the term used by the Human Microbiome Project completed in 2011.

Your microbiome is unique
Like your DNA, your microbiome is unique to you and made up of bacteria on your skin, in your mouth and crucially in your digestive system.

The digestive system or gut

Your digestive system (also referred to as the “gut”) comprises the:

  • STOMACH - breaks down and digests food
  • SMALL INTESTINE - about 20 feet long, where most nutrients are absorbed
  • COLON/LARGE INTESTINE - removes water from digested food and creates stools
Human gastrointestinal tract

Two astonishing facts


Trillions of tiny benevolent ‘good’ bacteria live in our intestines and they metabolise the food that the stomach will have partially digested, extracting the nutrients we need.

Weighing a total of about 2kg, they help to defend us against and ‘crowd out’ bad (pathogenic) bacteria which can produce toxins that are absorbed into the bloodstream and cause disease. Good health depends on the right balance between ‘good’ and ‘bad’ bacteria.
So your gut health determines your immune system health. And your immune system health determines how well you resist not just colds and flu, but long developing diseases like cancer.


The enteric nervous system has been dubbed ‘your second brain’ by researchers. It comprises about 500 million neurons (nerve cells) lining the long tube of the gastrointestinal system.
Originally the enteric nervous system was thought to only direct the process of digestion. It does that, but we now know that it also produces hormones and chemically communicates directly to the brain – conveying emotions and affecting mood.

‘Butterflies in the stomach’ are part of our stress response originating in the second brain.
A ‘gut feel’ that we don’t trust someone is literally our brain below communicating to our brain above.
And we’ve all eaten something that ‘didn’t agree with us’ – and later our gut brain ‘knew’ to avoid that same food again.

Relation of human brain and guts, second brain

Vital for mood balance

The enteric nervous system (ENS) uses over 35 neurotransmitters in a similar way to the brain and an extraordinary 95% of the body’s serotonin is found in the gut.

Serotonin is the ‘feel-good’ neurotransmitter responsible for maintaining a stable mood balance – a sense of wellbeing. Researchers are finding that an alteration in the balance between ‘good’ and ‘bad’ intestinal bacteria can directly alter mood, anxiety and even confidence.

Irritable Bowel Syndrome (IBS) is now thought to be caused – at least in part – by a gut infection or stress in a child’s early years. This affected the normal production of serotonin and therefore the normal development of the neurons in the ENS. Recent research showed that some 87% of people with IBS had antibodies in their circulation that were attacking neurons in the gut.

The new science of neuro-gastroenterology

So important is this communication from the gut to the brain that a new science of neuro- gastroenterology is emerging.
Scientists in the field confirm that our mental health is influenced by the health of our gut. Michael Gershon at Columbia-Presbyterian Medical Center, New York states that:

“A lot of the information that the gut sends to the brain affects well-being, and doesn’t even rise to consciousness.”

Pankaj Pasricha, Director of the Johns Hopkins Center for Neuro-gastroenterology in Baltimore, believes that a fuller understanding of the role of the ‘second brain’ can help us control all sorts of conditions, from obesity and diabetes to mental issues like depression, and even Alzheimer’s and Parkinson’s.

Mental health and gut health

Research has shown that depression is frequently associated with gastrointestinal inflammation – a common symptom of food intolerance. And significantly the characteristic plaques or tangles found in the brains of people with Alzheimer’s are present in neurons in their guts, too.

Recent studies have demonstrated that a healthy microbiome has a direct role in mental health, with people who regularly consume probiotics having less anxiety and depression. When their saliva was tested it contained lower levels of cortisol – the stress hormone – than control patients. Lower levels of anxiety may also be because the amino-acid tryptophan is created during fermentation triggered by probiotics. And tryptophan synthesises serotonin which alleviates anxiety.


If – as the researchers now say – health issues like chronic fatigue, depression, poor skin and inflammatory diseases are all affected by gut health, then a major health objective must be to increase the proportion of good bacteria in your microbiome.

Improve the balance between good and bad bacteria

Your gut contains both beneficial and harmful bacteria and these antagonists have been battling it out for billions of years! Health researchers suggest that the balance of gut flora should be approximately 85 percent good bacteria and 15 percent bad bacteria. If this ratio becomes unbalanced – a condition known as dysbiosis – the result is a compromised immune system and ill health.

Dysbiosis can have especially detrimental effects on older people. Overgrowth of unhealthy bacteria in the small intestines is called Small Intestinal Bacterial Overgrowth (SIBO). This can cause ‘leaky gut syndrome’ where toxins leak into the bloodstream. This powerfully stimulates inflammation throughout the body including the brain, which in turn can lead to depression, anxiety and impaired memory.

Now we know that the gut–brain axis is so influential, scientists are speculating that a deficiency of probiotics in older people can contribute to memory loss and disorientation.

By consuming the right probiotic food and supplements you can help bring the ratios of healthy bacteria back into balance. To over-simplify – more ‘good’ bacteria leave less room for the ‘bad’ ones.

Data from the Human Microbiome Project shows that the average microbiome of someone living in a western industrialised country has fewer beneficial probiotic bacteria, and crucially less
variety of probiotics, than those in rural and non-industrialised countries. It also shows that a wider range of probiotics is strongly linked to better health.

Probiotics are critical to health – indeed the derivation is pro (for) and biotic (life). But probiotics on their own are not enough. Probiotics are living beneficial bacteria and like any living thing, they need their own food supply. This ‘food’ is called prebiotics.

Probiotics need prebiotics

Prebiotics are non-digestible plant fibres that bacteria break down and feed on. The two most common subtypes of prebiotics are the closely related inulin and fructo-oligosaccharides or FOS. A third subtype galacto-oligosaccharides or GOS are synthesised from lactose in milk by enzymatic activity within the body. GOS are also present in several nondairy foods such as grains, legumes and cruciferous vegetables.

Every culture has had to rely on fermentation to preserve foods in the non-growing seasons. Germans developed sauerkraut, Bulgarians kefir and yoghurt, Asian cultures created tempeh, kimchi, natto and miso, and Russians ‘raw’ yoghurt.

These all contain many strains of probiotics and many of them are naturally based on foods that contain a lot of prebiotics, too. For instance, sauerkraut is based on cabbage, which contains GOS.

♦ See more details about the top probiotic foods.

What disturbs the microbial balance?


One of the main culprits for the reduction in beneficial probiotics is antibiotics. Although the development of antibiotics is amongst the greatest medical advance of the 20th century, they have a flaw. Antibiotics may well kill a pathogenic bacterium, but they also attack good bacteria along the way – internal ‘friendly fire’.

The reduction in number and range of protective probiotic bacteria that inevitably follows a course of antibiotics is why antibiotics can cause nausea and upset stomachs – and encourage candida yeast infections. The imbalance can last up to a year or more.

By killing good as well as ‘bad’ bacteria, antibiotics can cause gastrointestinal inflammation and vulnerability to pathogens like C. difficile. Salmonella can cause infection at a dose 1,000 times lower if the patient is on antibiotics!

This is why you should only take an antibiotic when really necessary and always complete the dose. If you do not complete the course it is quite possible that some of the original pathogens will be left and they can and will develop resistance. It’s one reason we have an antibiotic crisis, and why we are seeing a massive evolutionary change in bacteria – the rise of the super-bugs that make a visit to a hospital a risky trip.


Unfortunately it’s not only the course of antibiotics prescribed by a doctor that causes the problem. We also ingest antibiotics indirectly as they can be residual in non- organic meats and milk. Indeed the over-use of antibiotics in animals is far greater than that in humans.


A decrease in healthy bacteria can also be caused by stress and elevated cortisol.
Antacids and acid lowering drugs also negatively alter the bacterial balance and can increase the level of disease, encouraging bacteria like C. difficile, which can cause severe illness.
Other causes of dysbiosis include some artificial sweeteners, pesticide residue and importantly too much sugar. Sugar promotes unhealthy bacteria and yeasts in the gut.