There is growing recognition that the microorganisms which live in and on us ― our microbiome ― are crucial to our health. Anything that disrupts the delicate balance in which we live with them could cause disease. But what about when medical intervention is the cause of this disruption? Here Dr Brenda Kwambana, a postdoctoral researcher the MRC Unit The Gambia, tells us about her work investigating the microbiome and child health. From the time when bacteria were first viewed under a microscope in the 17th century to today, microbiology has seen its fair share of paradigm shifts. From thinking that humans outnumbered microbes, and that all microbes were germs to be avoided and destroyed, we now know that they are an integral part of our biology.

It is staggering to think that there are an estimated 100 trillion bacterial cells in the human body, 10 times the number of human cells. Of more than 100,000 different species inhabiting the body, only a tiny fraction is known to cause disease in humans.

The term ‘human microbiome’ describes the microbial communities that colonise the human body and their genes. Microbes colonise most surfaces of the body including the skin and surfaces inside the body such as the gut and respiratory tract.

Microbial genes outnumber human genes by a factor of 100 and invariably play an important role in the maintenance of health. In a way, we can think of the microbiome as our second genome.

We need microbes to develop strong immune systems, to have a balanced metabolism and to digest and absorb nutrients among many other things. For example, butyrates, fatty acids which are essential food for colon cells, are produced exclusively by bacteria that live in the colon called Bifidobacteria and Eubacteria. If colon cells are starved of butyrates, they die.

There is some evidence that imbalances in the microbiome may be associated with a wide range of diseases such as eczema, obesity, colon cancer, Crohn’s disease, cystic fibrosis, type 2 diabetes, oral cancer and bacterial vaginosis.

Now that we’ve begun to appreciate our microbial cohabitants and the need to keep the microbiome balanced, we’re also thinking about medical interventions and daily activities that have the potential to destabilise it. Using antibiotics, vaccination and even dietary supplements has the potential to cause changes in the microbiome with significant implications for health, either by killing off useful bacteria or by creating conditions which allow damaging bacteria to flourish.

At the MRC Unit in the Gambia, these are exactly the sorts of issues we are looking at.

For example, the nasopharynx is a surface at the back of the nose colonised by many of the pathogens that cause pneumonia, meningitis and sepsis. We are investigating how some of the vaccines and micronutrient supplements routinely given to young children to prevent disease may cause unwanted changes in the nasopharyngeal microbiome.

The pneumococcus bacterium which colonises the back of the nose of up to 90 per cent of children in The Gambia is a leading cause of pneumonia, meningitis and sepsis. However, because the pneumococcus is so common in this country, we would like to know what the effects of eliminating or reducing its populations by vaccination are among young children. Imagine a forest with several animals such as lions, cheetahs, zebras and buffalos; what would happen if the number of lions was suddenly reduced?

Presumably there would be some important measurable changes in the entire animal population after some time. The questions we are asking are actually ecological, just at a ‘micro’ scale.

If changes do occur in the microbial communities of vaccinated children, the next step will be to determine whether they are clinically important. If adverse effects are found, we may need to start finding ways to protect ourselves from disease, without changing the natural balance of our microbial communities.

I think we have to work towards finding that elusive and intricate balance between controlling the few microorganisms that cause disease without disturbing the trillions of friendly bacteria we need to function.

Brenda Kwambana

This article was first published on the MRC's http://www.insight.mrc.ac.uk/2014/11/04/bugs-are-us/.

Brenda Kwambana became the first MRC and London School of Hygiene and Tropical Medicine http://www.insight.mrc.ac.uk/2014/11/04/bugs-are-us/ in July this year.