The human microbiome; helping to prevent obesity, asthma and much more

Your diet can play a significant role in your chances of becoming obese, suffering from asthma or a range of other illnesses.


Discovery, a general science programme from the BBC World Service, has put together a helpful three part guide to the human microbiome. It is made for the wider World Service audience so it presents the issues in an interesting but accessible way. The discussion of the subject matter is engaging, and important contributions are made by leading scientists in the field such as Prof Rob Knight, from the University of California and Prof Tim Spector from Kings.

The show provides a general outline broken down into three parts; Manipulating Our Hidden Half, Dirt and Development and Gateway to the Mind. The idea that humans (in common with other animals) have not one but two genomes is central to this mini series. Our human genome is the one handed down to us through our parents, set in stone at conception. The so called second genome is made up of a vast pool of genetic diversity present in the microbes found throughout and within our bodies. The Human Microbiome Project has begun the process of analyzing the large number of microbes present in us. Two key issues that have started to excite scientists in recent years are,

  • the extent to which microbes can influence human health and experience.
  • the ability of individuals to alter their own microbial profile.

For example, it is generally observed that increased diversity of different kinds of helpful bacteria in the gut, is correlated with improved wellness. Studies in obesity, allergies, asthma and auto immunity suggest that gut bacteria may have a crucial role in meditating our health. This opens up the prospect that lifestyles remedies such as changes to diet may offer us significant potential benefits. It also raises the question about the long term benefits of medication known to have a detrimental affect on gut bacteria such as antibiotics.

This then takes us back to the discussion of probiotic and prebiotic food and drinks. When you consume products rich in helpful bacteria (probiotics) or the soluble fibre known to support microbial diversity in the large intestine (prebiotics), you are likely to be improving your health in a number of ways. It cannot yet be said that there is a direct causal relationship between your diet and certain illnesses. However the scientists are starting to think of gut bacteria as increasing or decreasing the chances of suffering from particular health problems.

At the time of writing all three programmes were freely available online or to download here.

Understanding fermentation and health

What is fermentation and how is it related to health and well being?


The growing area of study linking human microbiota to health and wellbeing is seeing the development of new learning opportunities. The extent to which microorganisms on our skin and in our bodies meditate our lived experience can be understood through a free Coursera module, Gut check; exploring your microbiome. Maggie and I have completed the first two weeks, I thought potential future students might be interested in hearing more about what this course entails.

This MOOC is produced by the University of Colorado Boulder and the tutors are all linked to the institution; Professor Rob Knight, Dr. Jessica L. Metcalf and Dr. Katherine R. Amato.

As you might expect week one offers an overview of the subject area. Explanations are given for what microbes are in relation to each other (Bacteria, Archaea, Eukaryotes and Viruses) and all living organisms. The role of microbes more generally is explained before looking at how microbes and humans interact. Definitions include the distinction between human microbiota (a community of microbes), and the microbiota (the total genes in the microbiota).

The material highlights a number of interesting microbiome facts including that whilst humans share 99.99% of the same DNA, two humans may only have 10% of their microbiomes in common. This is one of the reasons why gut bacteria is thought to be influential in how we experience life. Although the majority of our microbes live in our gut, there are communities all over us (mouth, skin, vagina). We are born sterile and then communities of microbiota become established at a very early age, changes to these communities happen throughout our lives. The module material clearly illustrates that the microbes we are exposed to have an import role in our lives.

The first week provides a useful introduction to the subject and offers a context for later material. Beyond week 1, the course follows a much stronger academic path. Explaining the science behind the study of microbiota and moving onto subjects such as alpha diversity and ‘fuzzy microbes’. If you’ve tried the MOOC what do you think?

Understanding gut health

A basic guide to gut health, key terms defined and explained.


Understanding gut health; 1 the basics

The scientific investigation of gut bacteria and its relationship to wellbeing is at a very early stage. There are discoveries every week that support, coexist with or contradict earlier findings. It’s a rapidly developing and dynamic area of human knowledge. The good news is, there are many resources available to anyone who wants to understand and take control of their own health through diet.

As a starting point there are a few concepts that are best understood at the outset. Not everyone uses these terms in the same way but try these definitions as a starting point.

Microorganism is widely used in talking about gut health, it is a general description for any organism that is too small to see with the naked eye. Some scientists prefer not to use the word but you are likely to come across it widely if you start reading about gut bacteria. Bacteria, viruses, archaea and fungi are all typically included in the term.

Microbiota  is generally used to denote the population of microbes in any given community or system. Flora appears to have largely the same meaning as microbiota and appears interchangeably. For example gut flora means the same thing as gut microbiota.

The aggregate of all the genes of an entire population of microorganisms  in any environment is described as a microbiome.

Typically scientists divide human microbiota into populations linked to their environment, such as skin, mouth, nose, digestive tract, and in females also the vagina. The largest population of microbes occur in the digestive tract, also known as the gut. Bacteria are the largest type of microbe in the human gut and bacteria reflects the dominant interest of scientific research. Gut bacteria are the main recipients of the benefits of prebiotics and probiotics, that is why the term gut bacteria and gut health is so prominent in media accounts of research findings. Technically speaking the plural of bacteria is bacterium but you will rarely see this outside of science journals, bacteria is typically used as the singular and plural form in most everyday situations.

A key point to make is that the gut has an important two way communication system with the human brain. That means to think of fermented food and drinks as only involved in what happens in the intestinal tract is a mistake. What we eat and drink has has the potential to exert a widespread influence across a number of systems.

Free course; bacteria and your health

As science begins to unravel the importance of gut bacteria to health and wellbeing, there’s never been a better time to learn about human microbiota.

gut bacteria
bacteria – crucial to your health

So what’s the big deal about the fermentation of food and drink? Why is there such an interest in it now when it’s been around for thousands of years? The growing ability of science to study microorganisms has opened up research linking the human microbiome to a range of health and wellbeing benefits. Even though this research is at an early stage, there are signs that our understanding of the human condition is entering a new era. Fermentation has a central role in this process, prebiotics and  probiotics may be able to make a significant contribution to the quality of our lives and the state of our health.

The awareness that fermented foods may be beneficial is a useful starting point, but there are resources available for anyone wanting to know more. Maggie and I have signed up for the Coursera MOOC, Gut Check; Exploring Your Microbiome. MOOCs are multiple open online courses; essentially short samples of higher and further education. They are typically free and offered by experts in their fields. All materials are available online, and a  study commitment of three to five hours for between four to eight weeks are required by students. There is usually an assessment required to complete a MOOC and a verified certificate may be available for a fee.

We will provide a weekly report of the Gut Check MOOC. But for anyone considering signing up for the course, it starts with a basic outline of the microbiome and microbiota (What is the human microbiome? What’s in your gut and how is the human microbiome studied?). It takes a little effort, but it is accessible to most people with a desire to learn and a basic knowledge of biology. This course is offered on the Coursera platform, there are other MOOC providers and free courses available in the same or similar areas of study. We welcome feedback about this or similar resources, feel free to enter your comments in the box below.

Gut bacteria and obesity; eating yourself thin

There is growing evidence that gut bacteria is linked to obesity. Preliminary experiments with mice appear to be supported by human studies.


Ongoing research into the role of the microbiome (bacteria in the gut) in human wellbeing is at a very early stage. But the frequency of media headlines linking gut bacteria to health is growing. As with all areas of science, claims which have not been verified in clinical trials and subsequently replicated must be treated with caution. Nevertheless the evidence of a relationship between gut microbiome diversity and obesity has been repeatedly demonstrated in mice.

The microbiome is a term used to describe all of the genetic material of a microbiota, the entire range of microorganisms present in a particular context, in this case the human gut.

There have been a number of studies which show that obese mice tend to have fewer different types of gut bacteria than thin mice. The thinking is that a greater range of gut bacteria is likely to positively influence the way that the digestive system breaks down food. Having more (types of) bacteria is linked to efficient processing of what we eat, with the results of a tendency not to be obese. Recent research reported in The Independent looked at the weight gained by 1,632 female twins over nine years. The study calculated that only 41% of the weight increase could be explained by genetic factors.

On closer inspection it was estimated that becoming slimmer or maintaining the same weight was connected to the consumption of dietary fibre (typically found in whole grains, fruit and vegetables). The study also discovered that the women who had gained weight, had a lower diversity of gut bacteria. These findings were in line with similar studies with mice. Although not yet conclusive the overall evidence linking the shape of our body and the composition of our microbiome is growing.

How your food directly affects your brain

There is a two way communication system between the gut and brain, this is one way that gut microbiota mediate our health.

gut bacteria
bacteria – crucial to your health

The growing excitement over the role of gut bacteria is being fuelled, in part, by the realisation of the potential role of the gut – brain axis. The gut-brain axis is the hard wiring between the digestive tract and the brain. That is to say a direct communication link passing information between neural, hormonal and immune systems. A key point to make is that the communication is bi-directional, that means the brain talks to the gut and that the gut talks to the brain. Thus the microbiota (gut bacteria) and metaboloites (small molecules that are the product of metabolism) may be in reciprocal communication with different parts of the brain. While this has a direct and obvious impact on processes related to eating and digesting, there is rising evidence that our gut flora may be significant factors in physical and mental health.

The relationship between emotions and  the digestive system is one of which we are intuitively aware. For example, feelings of love often manifest as ‘butterflies’ in the stomach. Engaging in team sports enables you to observe pre-match nerves in both yourself and others; the digestive system often plays an obvious role in how some people deal with tension! There is evidence that stress is a mediating component in gut microbiota, perhaps through increasing or decreasing the optimal conditions for certain types of bacteria to flourish.

New studies are suggesting that individual microbiota may be influential in functions as apparently disparate as memory and fear. It is not known what the basis of the relationship is, where the causality can be found. But that there is a correlation between what is in our gut and how we experience life in terms of mental and physical well being. The take home point is that many of the things we eat and drink are able to positively and negatively influence our health. By taking more interest in what goes into your stomach you might do yourself a power of good.

Gut bacteria and your health

Outstanding lecture from Prof Simon Carding, how gut bacteria mediates both physical and mental health


Emerging research is demonstrating a profound relationship between the bacteria in our gut and how well we are, our lived experience. In this outstanding lecture  Prof. Simon Carding offers insights, new and old into ideas about our gut bacteria. Warning you may see the world a little differently after watching the video!

“A potential life changer and life saver”

Gut bacteria and mind control by Prof. Simon Carding.