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Missing Microbes: How Killing
Bacteria Creates Modern Plagues
Martin Blaser
Oneworld Publications

Review by Frank Armstrong

The overuse of antibiotics in humans and other animals combined with other medical interventions such as Caesarian sections presages disaster according to a new book by Martin Blaser, Professor of Translational Medicine and Director of the Human Microbiome Program, at NYU.

Antibiotic treatments act on bacteria which have colonised every corner of the earth, including our bodies, and have been around for nearly four billion years.

We have 30 trillion cells of our own, but play host to more than 100 trillion bacterial and fungal cells. This might lead us to wonder who we really are. Indeed, the evolution of our resident bacteria has probably been just as important as the evolution of our own cells according to Blaser.

The welfare of a person’s microbiome, the collective term for resident bacteria, plays a critical role in health and the last seventy years has seen a progressive weakening of these crucial organisms. Blaser links their impoverishment to the onset of a host of modern plagues including obesity, diabetes, heart-burn and GORD (gastro-oesophageal reflux disease), asthma, a host of allergies, IBS (irritable bowel syndrome) and even autism.

A parallel problem is the widespread resort to Caesarian sections which deny new-born babies vital sources of bacteria available through conventional birth. But according to Blaser the main source of the microbiome’s decline has been the invention and subsequent over-use of antibiotics the force of which he likens to that of the atomic bomb. Moreover, their over-use in humans and in animal agriculture is giving rise to superbugs such as MRSA that are already killing thousands each year.

Moulds were used in Ancient Egypt, China and Central American Indians for centuries to treat infections before Alexander Fleming discovered the anti-bacterial effects of penicillium moulds in 1928. This gave Western medicine access to a life-saving medicine first tested on a nurse called Anne Miller in 1942. Antibiotics have saved millions of lives, and many surgical procedures would not be possible without them.

However, their use by doctors and dentists has surged in most Western countries to the extent that in most Western countries the average twenty-year-old has taken almost 20 courses, in many cases unnecessarily. Research in 2012 found antibiotic use in Ireland to be in the mid- to high- range in comparison to other EU countries.


The fault does not lie entirely with doctors most of whom are aware of the dangers of over-use. Recent research into their use in Ireland showed that 50% of patients request antibiotics when they visit a doctor with upper respiratory infections (colds and sore throats), an area of over-use identified by Blaser. Embattled general practitioners need more support in terms of patient education to stem this demand.

These infections are mainly caused by viruses which do not respond to antibiotics, but the problem is that a throat may already be colonised by bacteria that are not causing the disease.

Usually the reason doctors reflexively prescribe antiobiotics for sore throats is out fear of rheumatic fever which typically occurs two or three weeks after an untreated strep infection, and can be fatal.

According to Blaser: “Before antibiotics, about one child in three hundred with a strep infection developed rheumatic fever or, if the strep strains were very ‘hot’, one in thirty. Nowadays doctors prescribe an antibiotic for strep throat not to shorten the duration of the infection, because it doesn’t much, but to ward off rheumatic fever”.

He asserts that: “Until doctors can readily distinguish viral from bacterial throat infections, they will always follow the safer course”. He also acknowledges they are pressed for time and fearful of being sued.

Another problem is the use of antibiotics in animal agriculture. As in humans, untreatable bacterial infections are emerging in farm animals, and are passing the species barrier into human populations.

Often farmers use antibiotics not to treat disease but to expedite growth. The practice of using sub-therapeutic doses is now banned in the EU but the law is not enforced.

The Department of Agriculture, Food and the Marine does not collect data on antibiotic usage on Irish farms, and according to research by journalist Ella McSweeney antibiotic sales for large animals in Ireland are increasing.

Antibiotics of course cause the same weight gains in humans. Blaser connects their over-use to the obesity pandemic with compelling evidence from his laboratory experiments; and this is born out in studies showing obese individuals manifesting smaller ranges of bacterial strains compared to individuals of normal weight. An NHS study, the Avon Longitudinal Study of Parents and Children, showed that children who received antibiotics in the first six months of life were likely to have a higher body-mass index.

Controversially, Blaser hypothesises a link with autism the incidence of which appears to have risen considerably since the development of antibiotics. Today one in sixty-five children is diagnosed as autistic or on its spectrum, a condition that was only identified in 1943. Many of the microbes in the gut also make chemicals that the developing brain needs to function normally and these are being compromised by over-use of antibiotics. That there should be crucial interactions is perhaps unsurprising considering there are as many neurons in our guts as our brains.

Today most bacterial infections are treated with broad-spectrum antibiotics. According to Blaser: “It is not profitable for companies to go to the trouble and enormous expense of developing new antibiotics”. Targeted antibiotics only applicable in a small number of cases make little sense for companies concerned by their bottom line.

Fundamental to the understanding of our relationship with bacteria is the concept of amphibiosis: ‘the condition in which two life-forms create relationships that are either symbiotic or parasitic, depending on the context’.

This is apparent in the case of a bacterial strain called Helicobacter pylori (H. pylori) which has been discovered in our stomachs, and which Blaser has spent much of his career pursuing.

In 1982 two Australian doctors Dr Robert Warren and Dr Barry Marshall won a Nobel prize for showing for the first time that ulcers could be treated with antibiotics that removed H. pylori. Later it was discovered that individuals with H. pylori were also susceptible to stomach cancer. This led to all out war against a strain that was already declining due to increased sanitation.

But H. pylori performs other roles in our bodies. According to Blaser: “it appears that H. pylori is having some general effect on immunity, on people’s ability to turn off an allergic response”: this may explain the increasing incidences of potentially fatal food allergies. It also controls the regulation of the hormones ghrelin and leptin which are both produced in the stomach and are involved in the storage and use of energy. This implies those without it are often more susceptible to obesity.

Having H. pylori in our stomachs increases the risk of stomach cancer but this is only likely to arise in our 70s or 80s, while we may be losing its beneficial effects for most of our lifetimes. That is amphibiosis in action. Lifestyle changes, especially refraining from consumption of red and processed meat, would make far more sense.

According to recent studies normal individuals have lost 15-40 percent of their microbial diversity. Blaser warns that: “unless we are change our ways we are facing an antibiotic winter … a worldwide plague that we cannot stop”. The problem is not only with the potential for super bugs but also ‘a degraded ecosystem’ could make it more difficult for us to stave off infection.

But Blaser shows that there are ways in which we can begin to recover lost ground. Doctors can be far more selective in their prescriptions, armed with rapid tests enabling them to sample blood, sputum, exhaled air or urine to look for the chemical signature of particular organisms; and pharmaceutical companies could be compelled to develop more targeted antibiotics. Governments, including our own, can be far more rigorous in ensuring that antibiotics are not used as growth-promoters in animal agriculture.

Moreover, a raft of new treatments enhancing our microbiome could be introduced, including targeted prebiotics and probiotics, and the transfer of bacterial strains between individuals.

Unfortunately Blaser does not give significant attention to the extent to which diet, especially consumption of fermented foods,  can help our resistance to disease and enhance the health of the microbiome,.

Just like nuclear energy, the development of antibiotics presented humans with astonishing power, which alas they have mishandled. There is sufficient time for this technology to be recovered and for it to be used only in circumstances when it works to our benefit. In the meantime the human microbiome remains a discreet battleground. •