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?
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.
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.
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?
Show someone your love by taking an interest in their long-term health and wellbeing. Fermentation is a game changer.
The media (traditional and social) are full of valentine news, view and suggestions. Local traders, shops and supermarkets have an overwhelming array of products linked to St Valentine’s day. However the way in which you decide to treat your loved one says a lot about you. Whilst chocolates, Champagne or roses spring immediately to mind they may by simple clichés of what people are supposed to give, rather than lasting indications of love.
Perhaps a different approach would be to offer your partner (and yourself) something likely to offer nourishment and a lasting health benefit. It is easy to overstate the qualities of naturally fermented probiotics. But we can feel confident that they are likely to make a long lasting contribution to wellbeing in a number of ways. Evidence is starting to emerge that positive gut flora, may be correlated with, stable weight, and generally improved physical and mental health across a number of measures.
Clearly probiotics are not just for February the 14th, and moving towards a healthy diet is a long term project. But talking about fermented foods or trying them for the first time, may be a great way of showing your partner that you really care, and that you want them to enjoy the best possible health. When you create fermented foods at home, not only are your own family exposed to the product, but the idea and your positive actions can influence a wide circle of friends. Something that can’t be said of a bottle of fizz or a bunch of roses.
Whatever you do, and whoever you do it with have a great day.
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.
There is a two way communication system between the gut and brain, this is one way that gut microbiota mediate our 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.