Category Archives: IBD

The Human Microbiome: A Teeming Ecosystem Within Your Own Body

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Meet the neighbours: here’s Paul, Sandra, Jack, Lily, and so on and so on

“Why have you stopped speaking about sleep?”

“I can have other interests!”

“I don’t know man, you’ve changed. Why should I care about anything you have to say now?”

“…”

What is a microbiome? That’s a very good question. For a start, it’s not some artificial eco-project which is attempting to save the world or even, I’m sorry to disappoint you, some form of miniaturised food either. The microbiome refers to the different ecosystems of microbes which we have all over our body. These microbes use us as their home and in turn can benefit us, live mutually alongside us, or cause us problems. They form a complex and important addition to the multitude of cells which make up our own bodies and recent estimates suggest there are as many microbial cells as there are cells which make us up. One particularly well studied microbiome requires us to get to the bowels of every one of us. Quite literally. This ecosystem is the one we find in the human gut. This microbiome has also attracted a lot of interest because of its impact on the brain known as the gut-brain axis (more of this in the next article). In general, microbiome research is still in its infancy and everyone wants a piece of it. This is likely because it seems to play an important role in a number of different mental and physical functions and there is even talk of this ecosystem containing our ‘second genome’. So, what does this all really mean and why should we care?

The ecosystem of microbes (e.g. bacteria, fungi and viruses) which live alongside us help to break down food, protect us from invaders and produce nutrients necessary for our health. One good example of the benefits of the gut microbiome is evident in looking at babies and breast milk. There is a particular group of complex sugars known as human milk oligosaccharides (HMOs) which make up a considerable amount of breast milk. However, despite their prevalence in mother’s milk babies do not have the ability to break them down. This should make them rather useless to the baby and a waste of resources for the already energy-stretched mother. Indeed, this finding initially stumped scientists as breast milk has evolved to be the perfect nutrition for an infant – why should it contain something a baby cannot digest? However, it seems that a specific HMO, B. infantis, in the infant’s gut is the intended target of this sugar instead. B. infantis can break down the complex sugar and in turn flourish in its presence. Why is this a good thing? Well it is hypothesised that the healthy colony of B. infantis force out more harmful bacteria from making their home in the infant and act as decoys for potential pathogens keen on harming the bleary eyed newborn. Moreover, this rather nifty bacterium promotes gut health and has anti-inflammatory properties. The mother’s breast milk helps ensure this positive bacterium survives and in turn the bacterium ensures the baby is more likely to survive.

How about in adulthood though? What are some of the functions of our microbiomes scattered around our body? Well the ‘second genome’ seems to play an important role in our behaviour and health. For example, in a series of experiments which looked at the effects of transferring human bacteria from obese and lean twins to germ-free mice. The researchers found that when the mice were given the bacteria from the lean twin they stayed the same weight; however, when the bacteria were from an obese twin they gained weight. This is despite the mice all being given the same amount of food to eat. Furthermore, it seems that lean mice which live together with obese mice have the capacity to transfer their ‘healthy’ microbiome. Yet, the obese mice could not transfer their bacteria to the lean mice. This, it is argued, was because the obese mice have a lower diversity of bacteria within their gut microbiome and this leaves space for new species (found in the lean mice) to colonise and flourish. The bacteria of the lean mice tend to win in these situations. However, the positive effect of the transfer of bacteria on the obese mice is not universal. It requires that the obese mice have the right diet in the first place. If the obese mice were fed a westernised diet high in junk food and saturated fats then the positive impact of the bacteria from lean mice was non-existent. The positive effect was seen only if the obese mice were eating a healthier diet from the start. It could be speculated that this is because the high-fat diet does not promote the survival of the bacteria found in the lean mice’s gut. This opens up the exciting possibility that our gut bacteria are having an important role in our weight and health. It is possible that a particular diet might be able to promote the colonisation of new species of bacteria within our microbiome and, in turn, help promote weight-loss.

The human microbiome has also been linked to illnesses characterised by disruption of the normal functioning of the immune system. It has been argued that autoimmune conditions such as crohn’s disease and ulcerative colitis may be linked to a failure of the gut microbiome to develop appropriately during childhood. It’s claimed that this is because of the increased use of antibiotics and high-fat, low-fibre, diets which characterise the western world. The presence of these environmental factors reduces the diversity of the gut microbiome and interferes with the normal process of teaching the immune system how to function. In addition, certain species of bacteria appear to have anti-inflammatory effects which researchers are trying to capitalise on as treatment possibilities for inflammatory bowel diseases (IBD).

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Understanding the gut microbiome holds promise for the treatment of IBD.

So, it looks like the gut microbiome can have profound effects on our health. With this in mind, can we change our gut bacteria? Well, there are a lot of potential problems with this. Our gut microbiome seems to be influenced by the microbes which our mother and father impart upon us at birth (particularly from our mother). However, during infancy we go through a fluctuating development of our microbiota and the constituent microbes change considerably as we progress to adulthood. This is why some researchers believe that it is during early childhood that any attempts to modify the microbiome will be most effective. It is during this period of flux for our plucky neighbours that attempts to modify the microbiome are likely to be most effective and long-lasting. If there is a link between our gut microbiome and autoimmune disorders it is likely that this stage of our development is critical to reduce the risk of IBD. However, during adulthood there is more stability of our microbiome. The gut microbiome appears resilient to change following diet in the short-term but it is possible that long-term dietary changes might create a more favourable environment for new microbial species. For example, when the initial gut bacteria colonise an area they change the environment so it is more beneficial to their survival compared to other species. Therefore, although there is an obvious benefit to improving our diet, whether this boosts our microbiome is not quite known yet.

The human microbiome is not confined to our guts but our mouths, throats, noses, genitals and skin, to name but a few, are also examples of microbiota within the human body. For example, we contain our own signature of gut bacteria on our hands although there is considerable variation between individuals and even between our own two hands. It is not known exactly what is responsible for this variation but a mixture of genetic and environmental (e.g. hand-washing, climate, sex, etc.) factors seem to be important. It is also possible to shift the microbial constitution of someone else’s hand through direct contact – a handshake. How long the changes remain, however, is not clear and it is likely that the ecosystem carved out by your own skin microbiome favours the microbes usually residing on and in your skin. This is perhaps something to keep in mind when meeting your hero and desperately trying to shake their hand. It may be that greatness can rub off on others through a firm handshake. Also, in a similar manner to the gut microbiome, the composition of microbes on the skin has also been linked to health and disease. A good example of this is psoriasis which involves the development of plaques on the skin of those affected. In a similar manner to the gut microbiome, it is likely that a wider diversity of the skin microbiome has anti-inflammatory properties which are protective against auto-immune disorders such as psoriasis.

So, does this mean that all of us need to alter our eating habits to ensure that our gut bacteria are working at their best? Probably not for the time being. This is the nature of any research in its infancy and beware of any book or news article which claims that changing your microbiome through diet will improve your health. Despite all the excitement surrounding the microbiome at the moment we need to be aware of the limitations of research which seems to be ‘in vogue’. There is plenty of high-quality research which is being carried out in this area but much of this research is conducted in mice and the human research is largely correlational. It’s currently difficult to infer cause and effect – does poor health causes changes in our microbiome or vice-versa or, more likely, is it a mixture of the two? We need to be aware of how little we really know about the microbiome at this current moment. For example, we don’t know what a healthy microbiome looks like. Is there one individual ‘optimal’ combination of microbes to strive for or is it that a greater diversity, in general, is best? There seems to be some evidence of ‘types’ of stable microbiomes in adults but this work is still in development. There is also some evidence which links a healthier, fibre-rich, diet to a greater diversity of microbes within the gut microbiome but it is unclear what impact this has on health and behaviour. Currently, the Human Microbiome Project is trying to understand what the normal limits of the microbial ecosystems look like and how they might be implicated in health and disease. Although they started in 2008 and have received considerable funding there is still a long way to go before we see these findings directly influencing health. There is plenty of excitement about the microbiome but it is still early days for this field. For now, the human microbiome holds a plethora of secrets yet to be unlocked about the teeming, fluctuating, and enigmatic organisms we share our body with.

Image Credits:

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References / Recommended Reading:

http://www.nature.com/news/bacteria-from-lean-cage-mates-help-mice-stay-slim-1.13693#/ref-link-1

https://www.nature.com/articles/srep32484

http://www.nytimes.com/2013/05/19/magazine/say-hello-to-the-100-trillion-bacteria-that-make-up-your-microbiome.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535073/

https://www.nature.com/cti/journal/v5/n4/full/cti201612a.html

http://www.nature.com/news/scientists-bust-myth-that-our-bodies-have-more-bacteria-than-human-cells-1.19136

http://hmpdacc.org/ (Human Microbiome Project Website)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577372/

https://www.ncbi.nlm.nih.gov/pubmed/20668239/

http://www.newyorker.com/tech/elements/breast-feeding-the-microbiome (An extract from the amazing Ed Yong’s book, ‘I contain multitudes’)

http://www.radiolab.org/story/funky-hand-jive/ (A hilarious and brilliant podcast on this topic)

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Filed under General Interest, IBD, Microbiome, Psychology