Missing Microbes


Missing Microbes

Missing Microbes is a book by Martin Blaser. He is the director of the NYU Human Microbiome Project which is part of a wider collaboration of research projects investigating the links between the microbes which colonise our bodies and how they impact on our health.


Modern Plagues

Historically, plagues took the form of infectious diseases which spread between people and wiped out millions. There was nothing to affectively treat them so preventative measures to reduce the acquisition of these infectious diseases was the best bet for surviving an outbreak. With the dawn of antibiotic treatment, many previously deadly infections became trivial annoyances. The bubonic plague of the 14th century which killed half of the population of Europe could now be easily treated with a short course of doxycycline.


For years, antibiotics have been seen as a panacea for all infections. Coughs, colds, sticky eyes, earache and upset stomachs were all seen as good reasons to give a course of these immensely powerful drugs which decimate the bacterial populations living upon and inside us. Barring the occasional allergic reaction or lose bowel motion, antibiotics were seen to be fairly safe drugs with little chance of serious side effects.


Martin Blaser outlines the theories explaining why the failure to consider our microbial populations has lead to the creation of ‘modern plagues’. These plagues take a much more surreptitious form. Until now, many theories have been put forward as to why certain conditions are on the rise, often neglecting to look at the bigger picture. Could it be possible that the rise of these conditions can all be explained by one unifying theory?


The modern plagues of western civilisation include obesity, diabetes, asthma, eczema, hay fever, food allergies, oesophageal reflux, autism, cancer and Alzheimer’s. The Human Microbiome Project is looking at the possibility that the rise in these conditions could be linked to a change, and often loss, in the microbes that colonise our bodies. The cause of this change in microbiome is the product of changes in lifestyle, medical practice and behaviour which have only existed for the past hundred or so years. Before then, microbes and human beings evolved in parallel, symbiotically benefiting one another and promoting the continuing health and propagation of our species.


Helicobacter Pylori

H.pylori is a bacteria that lives in the stomach. It is present in over half the people in the world. An Australian doctor called Barry Marshall came up with the theory that instead of stress and spicy foods, stomach ulcers and gastritis were caused by the h.pylori bacteria. He managed to prove this through a series of experiments and won the nobel prize for medicine in 2005 for his troubles. It is now common practice to test patients who are suffering from gastritis symptoms, such as epigastric pain and nausea, for the presence of h.pylori, and then treat them with a course of antibiotics and acid suppressing medication called PPIs. This all seems fine and dandy until you stop and wonder why h.pylori might be there in the first place. Since the implication of h.pylori in the  cause of gastritis, gastric ulcers and indeed stomach cancer rates have reduced considerably. But an unexpected consequence of h.pylori eradication was that the incidence of oesophageal reflux disease and oesophageal cancer started to increase. H.pylori is present in the human stomach for a very good reason. The low-level of gastritis it causes actually helps to regulate the amount of acid produced by the cells in the stomach wall. If h.pylori is eradicated, the acid production increases. This increased acidity causes problems if the acid is allowed into the oesophagus, primarily by causing increased inflammation which can ultimately lead to cancer. Unfortunately it seems that in reducing the amount of stomach cancer, we have increased the amount of oesophageal cancer. Both cancers are terribly destructive and aggressive and it would be trivialising their seriousness to arbitrarily chose one over the other. But maybe our focus should be to embrace the presence of a bacteria which has evolved with us for millennia and maybe look at other ways to stop a mild gastritis turning into a peptic ulcer, rather than trying to eliminate gastritis all together.



It’s becoming more and more widely accepted that using antibiotics willy-nilly for any slight feeling of indisposition is not a responsible way to practice medicine. Weekly stories pop up the news about antibiotic resistance and the threat of returning to the dark ages of incurable infectious diseases.  But little is mentioned about how using antibiotics can interfere with normal bacterial populations within the body. Human are supposed to have bacteria and fungi living on our skin, in our guts and in our airways. The developing immune system of children is the most delicately balanced and most susceptible to dysfunction if the populations of bacteria which should be present, are missing.


This can be caused by antibiotics and also by excessively sanitary living conditions. When the immune system does not become primed to the presence of the pathogens which it should commonly encounter, we see an over-reaction and excessive response which manifests in the form of eczema, asthma, hay fever and food allergies. Unfortunately, the children who present with these conditions are often misdiagnosed and treated with antibiotics which only serves to exacerbate the problem.


It is also postulated that antibiotics cause weight gain. Farmers have been using antibiotics for decades as a cheap way of increasing the weight of their herds. Antibiotics are cheaper than cattle feed and cause greater weight gains for the money spent. For some reason, until now, this widely known effect has never been extrapolated and applied to humans.


Caesarian Section

 Roughly one in four births in the UK are by Caesarian section. C-section is a marvellous operation which is a hugely important part of the obstetrician’s repertoire when it comes to safely delivering a baby. However, many people fail to consider that there might be detrimental affects to delivering children differently to the way nature intended. I know from my time working on the labour ward, aside from the ‘too posh to push’ cohort, that a c-section is often performed as a knee jerk reaction to any sign of fetal distress. I don’t mean to belittle the important decisions that obstetricians have to make every day, but compare the UK’s 25% Caesarian  rate to Sweden’s 4% Caesarian rate, with no difference in foetal mortality, and you can see that some Caesarian sections in the UK must be taking place unnecessarily.


It’s widely known that delivering a baby via Caesarian section increases the rate of neonatal breathing difficulties. But what is not commonly known, is the longterm consequences of the bacterial microbiome of the growing baby. The female vagina contains a very specific population of bacteria. The most prevalent is a species called Lactobacillus Prevotella. As the name implies, this bacteria helps to break down lactose. Lactose is found in breast milk in the form of galactose. Unless the feeding baby has acquired a thriving population of lactobacilli, the breast milk is not easily digested.  Babies born by Caesarian section, tend to become colonised by bacteria found on human skin such as Staphylococcus and Corynebacterium .


The Importance of our Microbiome

The study of how microbes interact with out bodies is still in its infancy, but this book really sheds some interesting light on the possibilities within this new field of science. This is just a brief overview of the points which stood out to me as the most salient, but there’s plenty more to get your teeth into if it’s something which interests you.  It never fails to amaze me that the more we learn about our bodies, the more we realise that the way we’ve lived for most of our existence provides the clues we need to continue to thrive in the modern world. Whenever science provides us with a cure, we must always consider what effect the changes we make might have and why, over the course of millions of years, our bodies haven’t evolved that way by themselves. As Angelo Coppola most eloquently puts it; ‘Humans are not broken by default’.

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