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.

Kefir and obesity, reduced weight and cholesterol increase

There may be a relationship between kefir and obesity.

kefir and weight loss.
Kefir and weight loss

I’m becoming increasingly convinced of the benefit of fermentation, that enriching beneficial gut bacteria has widespread effects on wellbeing and health. I’m still near the beginning of this journey and learning all the time. I’ve posted a series of articles linked to kefir, not because I’m an expert, but based of the apparent benefits accrued over the last two months from a small glass of kefir each day. I should also say that Maggie has lost a lot of weight over the time she has been drinking kefir, but, she has also been exercising. However weight loss isn’t my only reason for writing about this subject. A few months ago I felt obliged to take a course of antibiotics, I think it was a mistake ( I am aware of the downsides of this kind of medication) but it’s water under the bridge now. The subsequent decline in my overall health was striking. I started to have trouble concentrating and sleeping, I got a cold, suffered from reflux and saw an augmentation in weight.

I didn’t really connect these things with the antibiotics until I noticed that my bowel movements changed significantly. If you are new to the gut bacteria scene you might feel a little uncomfortable around talk about bowel movements, don’t be. A regular healthy bowel movement is one of the signs of a healthy balance in gut bacteria. So when I noticed I wasn’t going to the toilet regularly I though about the possible impact of antibiotics on my gut. I started to take kefir more regularly whilst keeping my usual  prebiotic and probiotic consumption at the same level.  The difference was gradual but pretty much everything started to improve after about five days. Two months later things are back where there were before the antibiotics. I’m much healthier, bowels are back to normal and……..I’ve lost weight without any exercise.

Antibiotics and gut bacteria
Antibiotics and gut bacteria

This isn’t a morality narrative about the harm of antibiotics. I believe antibiotics represent a life saving technology, and in the right place and time are essential. It’s their inappropriate overuse which I think is harmful.

My own anecdote is that I think it took two months to return the state of my gut bacteria to somewhere like normal, and I am a daily consumer of natural prebiotics and probiotics. In all of this story things pretty much fitted my modest understanding of the underlying science except the weight loss. I know that lack of diversity in gut bacteria is correlated with obesity generally but I hadn’t come across any research papers linking kefir to weight loss. If you can improve your gut health and pull your body weight closer to its optimum level this has to be a win-win. So I started to look through the scientific literature. The most recent research is featured here.

Commercial v traditional kefir for weight loss; which is best?

Are their differences in traditional and commercial kefir?

kefir and weight loss.
Kefir and weight loss

This is the second part of the feature, you’ll find part one here.

Despite my scientific training, regular followers of my blogs will have realized I have an established scepticism for extravagant scientific claims. I am a fan of science generally but feel the need to maintain a discriminating eye and treat each scientific claim on its merits. However a recent study into the relationship between kefir and obesity has been worth a closer look.

In a research paper titled Traditional kefir reduces weight gain and improves plasma and liver lipid profiles more successfully than a commercial equivalent in a mouse model of obesity, Bourrie, Cotter and Willing found that kefir appeared able to meditate metabolic health. This study compared the ability of traditional with commercially produced kefir to mediate mouse weight gain, plasma cholesterol, and liver triglycerides. Four traditional and one commercially available kefirs were used in the experiment. Commercial kefir was shown to have no beneficial effect whilst two of the traditional kefirs demonstrated a reduction in the rate of weight gain and increase in blood cholesterol. This was (as far as I know) the first ever study comparing mass produced with traditionally produced kefir, so the research must be regarded as preliminary. It was a study with mice so the extent to which results can be generalised to humans is uncertain.

Traditional kefir may contain a greater diversity of bacteria and yeast

The research concluded that when also considered in relation to the modulation of the gut microbiome, traditional kefir has the potential to mediate obesity through the improvement to metabolic dysfunction.

The report also explained that different forms of traditional kefir do not generate identical microbial populations. It is assumed that this could be linked to variable health benefits. Further that whilst Lactobacillus, Lactococcus, and Leuconostoc would be expected to be found in most forms of kefir, acetic acid bacteria was not found in a majority of commercial products. Research has also suggested that traditional kefir possesses highly complex fungal communities (including, S. cerevisiae, Pichia fermentans, Kazachastania unispora, and Kluyveromyces marxianus and lactis) not always found in commercial products.

In conclusion, three take home points:

  • This is preliminary research, it’s early days!
  • Traditional kefir may support improved cholesterol and fatty acid metabolism.
  • Traditional kefir appear to offer a much greater microbial diversity to the host than commercially produced kefir.

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.

How to start home fermentation

Home fermentation, have you tried the Kilner fermentation set?


Is a home fermentation kit necessary? For the occasional production of sauerkraut I’m not sure that special equipment is essential. Maggie has managed to keep us supplied with our fermented foods simply by using medium sized jam jars, and a range of normal kitchen utensils. The point she always stresses is that everything has to be clean. The fermentation vessel should be thought of as a bacterial incubator. If you incorporate harmful bacteria into the incubator it will inevitably grow quickly. You should throw any tainted product away , clean everything and start again. One of the many appealing aspects of home fermentation is the relatively low cost of fermenting produce. Consider that at current prices a liter of organic sauerkraut can be created for less than 50p (ten bob!).

I know that previous generation of home fermenters from Poland and Germany actually had a range of fermentation pots and tools that were accumulated through the course of married life (I don’t remember seeing any of these is the kitchen of my mother or grandmother).  In particular ceramic pots that were dedicated fermentation vessels. They had necks wide enough that a small plate or large saucer could be accommodated within to keep the  fermented product under the water level.

With the rising interest in home fermentation equipment has passed from specialist shops and online retailers into mainstream retail outlets. We purchased a Kilner fermentation kit at the weekend. Our primary motivation was to increase the volumes of our product. Not only has our own consumption increased but we are also sharing more with our own friends and family. It certainly seems that the public awareness of the benefits of fermentation is growing. The Kilner kit was fairly priced (£18) when compared to similar products and the fermenting jar was around the size we were looking for (3 liters). It all seems OK, we’ll report back when our first batch is ready (cabbage and carrot). We have no particular connection with Kilner, save that we use their 1liter fermentation jars already.

We’d be really interest in what other home fermenters use,  and any equipment related tips would be most welcome. Feel free to leave any suggestions, comments or feedback in the box below.

Probiotics, antibiotics and resistance

The overuse of antibiotics is a major health concern. Probiotics may support the lower consumption of antibiotics by boosting overall health in humans and animals.


I am in the process of writing a basic guide to probiotics, but a general description is,

‘microorganisms contained in some food and supplements that have proven and assumed benefits to human and animal health’.

A key point at the outset is that it is hard to prove causality in such matters. Demonstrating correlation (people that have particular gut bacteria tend to have or not have a particular illness) is much simpler. The evidence linking probiotics and health is both causal and correlational. The point of probiotics is to change (improve) the profile of gut flora so that it has more positive and less negative microorganisms. This is a long road of which we are at the beginning.

Antibiotics are drugs designed to destroy or inhibit the growth of bacteria harmful to humans, animals or other organisms. I acknowledge the potential lifesaving benefits of antibiotics, they are an important part of modern healthcare. But the widespread overuse of antibiotics in industrialized societies is creating superbugs, bacteria that are resistant to all known antibiotics. This problem was the subject of the film Resistance which I recently saw on Netflix. The issue of superbugs is not new and the discoverer of penicillin, Alexander Fleming discussed resistance in the mid 1940s. If you subject bacteria to an effective antibiotics most will die off, but surviving bacteria can develop resistance to that antibiotic. If you repeat the process often enough you risk creating bacteria over time, that become resistant to every antibiotic they have been exposed to.

Sometimes humans are given antibiotics when they are not needed, and so we may carry around bacteria that have a resistance to some antibiotics, this is a problem in itself. A key point that the film Resistance makes is that contemporary farming methods can involve the routine administration of antibiotics to hundreds of millions of animals every year. Antibiotics appear to make some animals grow bigger, thus increasing their cash value. However intensively farmed animals can live in insanitary conditions, exposed to fecal matter for most of their lives. Forcing animals to live in an environment where high levels of dangerous bacteria are present, thus necessitating the use of antibiotics as a routine measure, can be described as a perfect breeding ground for superbugs.

The standards of animal welfare vary from country to country and the use of antibiotics in the EU generally is lower than some other parts of the world. But it’s still  a major problem according to a recent report. Conceptually the idea of eating animals is increasingly unacceptable to many people. However the logic of forcing animals to live in terrible conditions their whole lives, only sustained by large amounts of antibiotics is obviously flawed. Not only are people eating animals that have endured life long suffering underpinned by the consumption of drugs. But this process may also be creating bacteria resistant to those drugs. The use of last-resort antibiotics for humans such as colostin, is increasing according to official data. When colostin is used it can indicate other antibiotics were ineffective against the harmful bacteria.

So what has this got to do with fermentation and probiotics? Firstly antibiotics generally kill and inhibited some good bacteria. Where health is at risk this is clearly an appropriate course of action. However as the importance of gut flora to health becomes better understood we should consider the need to maintain gut bacteria at healthy levels. Secondly the better our overall health the lower the risk of illness and presumably the less need there will be to take antibiotics. Just to be clear, probiotics are not a substitute for antibiotics, there are some very dangerous bacteria in our environment for which antibiotics may be the only cure. My position is to abandon the overuse of antibiotics in animals and humans so that when we (and animals) get really sick we will have antibiotic treatments that continue to work. The third point is eating animals that have lived a life in potentially dangerous bacteria, sustained by routine antibiotic consumption seems irrational.  Wouldn’t it make more sense to maintain animals in healthy conditions, with feed rich in probiotics, reducing the need for antibiotics in all but essential cases?