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Warning: May Contain Antibiotics

Antibiotics don’t usually appear on the food label, but they should. We are all exposed to them even if we don’t know it. This is one of the biggest changes to our environment in a million years, but has only had an impact during the last fifty. When the Scot Alexander Fleming, partly by chance, discovered in 1928 a mould that produced anti-bacterial chemicals he had no idea that our modern society would become so addicted to it. We now know it as penicillin.

In fact, Fleming never really saw the massive potential of converting the mould into a medicine. This was left to his colleagues Howard Florey and Ernst Chain, who carried out the essential process, then performed stunning trials on a few patients with normally lethal infections. The penicillin they made was so precious that they went so far as to collect each patient’s urine so that after a bit of cleaning it could be reused for the next. Later, during the Blitz, they left wartime London and started industrial-scale production in the US. The aim was to use the drug for the Allied troops.

Antibiotics were an amazing success, saving millions of lives against the threat of often hitherto fatal bacterial infections. Doctors after the war predicted that antibiotics would herald the end of all human infections.

The DJ and TV-presenting twins Alana and Lisa (the Mac Twins) are twenty-six years old, successful and enjoying life. They are blonde, bouncy Scots, and being genetically identical look very similar. But scratch beneath the surface and they are more different than you might imagine. They are both the same height and similar weight, a healthy 9½ stone (60 kg), but Lisa has slightly bigger hips and once gained 2 stone in six months. Lisa now likes to control her weight with regular exercise, whereas Alana gets no kick from sports and prefers to sweat it off via ‘hot [Bikram] yoga’. Alana finds it easy to do fasting 5:2 diets to control her weight, whereas her twin goes stir-crazy if she doesn’t get regular calories.

Their personalities are also quite different. Alana used to be the shy one, and is much more pragmatic and steady, while Lisa sometimes gets anxious and is prone to bouts of obsessive-compulsive behaviour (OCD). Their father tragically dropped dead of a heart attack on the golf course aged only fifty-eight, and their grief reactions were nearly polar opposites – Alana stoic with episodic but dramatic breakdowns and Lisa in depressed denial. They had never worked out why they were so similar yet so different.

Raised in Scotland, they lived together in the same room for seventeen years and although they fought regularly were best friends. As six-month-old babies they were fragile, both had bronchitis that called for hospital treatment, then later recurrent ear infections and tonsillitis and consequently many courses of antibiotics. At the age of four, Alana had recurrent bladder infections necessitating several long stays in hospital and nearly constant antibiotics for two years. Soon afterwards she developed juvenile arthritis, a genetic auto-immune condition which affected many of her joints, causing painful swelling and stiffness. She was on many medications and managed to carry on a near-normal life, then at sixteen the pains suddenly stopped.

To the surprise of her doctors Lisa never developed any joint problems, but soon after leaving home she had a severe and unexpected late bout of acne. Alana never had acne, which is weird because our twins studies have shown it to be one of the most strongly heritable conditions. It was so severe that doctors put Lisa on several months of the antibiotic minocycline, followed by other, stronger, drugs to eventually clear it up. A year later, Lisa began to have urinary and kidney infections, which have continued to plague her, often calling for monthly courses of antibiotics. The doctors have even suggested she goes on them permanently.

Looking back, one possible reason why they are so different despite identical genes has to do with the antibiotics. Alana might never have developed arthritis if the natural gut microbes she received from her mother hadn’t been decimated by the frequent antibiotics she took for her multiple childhood infections. These will have affected her immune system and maybe even caused her love of ‘hot yoga’. Similarly, Lisa’s late-onset acne, although having a genetic basis was caused by an overgrowth of microbes and an overreaction to them, while her later susceptibility to kidney infections also suggests a disordered gut microbiome as the cause. They both enjoy all foods from pickled eggs to haggis, chips and sushi. But although they used to go to the potty at the same time, they now have very different bowel habits and loo-visiting regimes, despite having identical diets and lifestyles. We tested their microbiomes and they were unalike in many of the normal species. On average they shared only a minority of the same microbes, the same as unrelated people. This suggests that the antibiotics had removed the genetic similarity they started life with.

We now use antibiotics like sweets

In the US alone over 250 million antibiotic courses are prescribed every year, and recent studies in the UK show that despite grave warnings of overuse in general practice, rates are still increasing. Back in 1999 GPs were warned to cut back on prescriptions for mild infections and viruses. The warnings went unheeded – in fact, the situation got much worse. By 2011, rates of use had increased by 40 per cent, and the average GP was giving antibiotics to over half of all patients presenting with coughs or colds. These infections are due to viruses that antibiotics don’t touch. One in ten GPs were even more cavalier, giving them to 97 per cent of their patients, presumably to keep them happy or to get them out of the surgery more quickly.

Global use of antibiotics has been increasing over the last thirty years in virtually every country that has data. Forty per cent of the prescriptions handed over are completely ineffectual, for the reasons just given.1 All countries overuse antibiotics, but those with well-controlled centralised health care systems like Sweden and Denmark use the least – proportionally, half of what America uses. They also use more narrow-spectrum drugs, which select their targets more subtly and cause less microbial damage without any increase in problems.2

Even in rare cases where bacteria are definitely involved, independent overviews show that the benefits of antibiotics are minimal. Treating sore throats or sinus infections early, for example, reduces symptoms by an average of only one day. This might seem worthwhile for some people, but that would be true only if there were no downside.

Treatments to die for

When Arun was two he needed antibiotics for the first time. His mother thought nothing of it as she had been on antibiotics countless times herself as a child, and believed them to be safe and effective. Serious side effects never crossed her mind.

Their ordeal started with what appeared to be a mosquito bite after Arun had been playing outside one evening. When he came in she put anti-itch insect-bite medication on the spot, and put him to bed. By the next day the bite was red and looked infected, and appeared to be spreading slightly up his leg. It was too late in the day to see his own doctor, so his mother took him to A&E at the local hospital where they gave him a shot of Ceftriaxone, which is a powerful type of cephalosporin, an antibiotic widely used to fight multiple unknown bacteria. To be extra sure, he was also given another antibiotic, Bactrim (a combination of two antibiotics), as a syrup, and his mother was told to continue with this course of treatment for ten days.

Shortly after he started taking the antibiotics his leg started healing, but he developed bad diarrhoea. His mother wasn’t too worried as she knew this was a common side effect of antibiotics, but the diarrhoea was severe and persistent and then she noticed blood in his stools. She took him to the doctor’s where a stool test was done, and was later informed that he had tested positive for Clostridium difficile (C. diff) and now had a condition called pseudo-membranous colitis, a nasty inflammatory disorder affecting the colon. His doctor then put him on yet another antibiotic, Flagyl, the first-line treatment for the colitis caused by C. diff. During the first few days of the new treatment his stomach problems improved greatly, but on the last day of the course the original symptoms returned. The doctor prescribed the same course again, and the same pattern recurred.

‘At this point we were referred to a paediatric gastroenterologist,’ Arun’s mother said, ‘but had to wait an agonising week to get an appointment. I was terrified and called my doctor because I could not imagine waiting that long given his dreadful symptoms. He was losing weight rapidly and was visibly ill. In the course of researching his condition I learned about a rare but serious complication that can cause the colon to rupture, and is often fatal. Our own doctor said there was nothing more that he could do, and told me to take my son to the children’s hospital if I became too worried. I was frantic and didn’t sleep for two days. Then, miraculously, he got better – I’ll never know why – but he could easily have died. People need to know of the harm that antibiotics can do.’

Others are not so lucky. Up to half of young children who contract this form of colitis can die, as their gut is so ravaged by the antibiotics that the immune system and gut barrier totally fail. This often begins when a round of antibiotics depletes the natural bacterial flora in the colon, reducing the diversity and power of the usual protective community and allowing a certain aggressive, or pathogenic, type of C. diff bacteria to flourish, replicate and eventually to totally dominate the gut in large numbers. Although horrific, these cases are rare, occurring once in every 10,000 uses of antibiotics. The risks are higher in bottle-fed infants as they lack the diverse and healthy bacteria like the bifidobacteria that come free with prebiotic-loaded breast milk. These extra microbes give them extra infection-fighting properties, as well as reducing allergies.3

Because we now prescribe millions of antibiotic courses annually, mostly of the non-specific broad-spectrum type that kill not only the likely pathogenic bacteria but everything else in their path, these severe C. diff cases, along with antibiotic resistance in general, are increasing. They serve to remind us of the dire and often hidden consequences of overuse, especially for seemingly trivial reasons.

Sterile births and future problems

Remember that the first three years of our lives are the most important in forming our core set of gut microbes whose job it is to maintain our health. Sadly, many drugs are given around birth without any thought for the poor microbes. Giving pregnant mothers antibiotics for mild urinary tract infections is commonplace, and for the last thirty years powerful wide-ranging intravenous antibiotics like cephalosporins have been routinely prescribed for mothers just before caesarean section operations so as to reduce the 1 to 3 per cent risk of post-op infections. This drug crosses the placenta to the baby and affects the breast milk, and may have even worse effects.4

I am all in favour of some C-sections. My life was saved by an emergency C-section when the blood supply to my mother’s placenta suddenly packed up. I was very premature, a thirty-week four-pound weakling, and a few years earlier I would not have survived. I expressed my gratitude when, rather spookily, twenty-five years later I was delivering babies in a small hospital near Colchester and found myself holding a retractor for the very surgeon who had got out of bed to save me at 3 a.m. many years before. I had found his name on some old birth records – but strangely, he didn’t recognise me.

Life-saving emergency operations are one thing, elective operations another.

In Europe there are major differences between countries. Italy, unsurprisingly, led the league table in 2010 with 38 per cent of births being caesareans, and other countries, such as Greece, may be over 50 per cent. Rates in all countries have increased since 2000, and there is a rough north–south European gradient, the UK in the middle with 23 per cent. The lowest C-section rates in Europe – and probably in the developed world, where the situation has hardly changed since the 1980s – are found in the ‘deprived’ countries, led by the Netherlands at 14 per cent, followed closely by the Nordic countries. These probably represent the sensible target levels.

In the US in 1968 only 1 in 25 births ended in an operation, but now it is nearly 1 in 3 and over 1.3 million operations are performed every year.5 But the figures vary tenfold between areas, from as low as 7 per cent in some towns to 50 per cent in New York City and 60 per cent in Puerto Rico.6 The operations are most frequently performed on women at the lowest risk of birth problems, as well as in poor populations that can least afford it such as Brazil (4 per cent) and Mexico (37 per cent). The epidemic has even reached China, with its one-child policy. There, the majority of births are C-sections.7 Cosmetic, financial and cultural reasons are likely to play a role in these differences, but more likely is the key role of the doctors, who no longer have to wake at 2 a.m. and can improve their golf handicaps.

Double trouble

Maria was thirty years old and already had one child and was about to deliver twins. She worked in a hospital, so knew the routine. After some discussion, it had been decided that she would have a C-section at thirty-seven weeks. The day had finally come. She had been fasting, and had been given a small enema to keep everything clean. The operating theatre was full of staff, plus her nervous husband standing there awkwardly in a sterile theatre outfit complete with mask. He and Maria were screened off from the obstetric team down the other end.

She was given a light anaesthetic and an epidural injection into her spine. Maria was relieved when told finally that she had two healthy boys, and glimpsed them briefly before they were whisked away. Thirty minutes later after being stitched up, she was handed her two tiny bundles for the first time. They were smaller than average, but not dangerously so – both were over 2 kg. They looked strikingly similar to each other.

She started breast-feeding and both boys slowly gained weight. At home a week later, the story was different. Juan was not gaining as much weight and seemed to be crying more than Marco. After two months the strain of breast-feeding persuaded Maria to introduce formula milk, which both boys accepted. But still Juan was lagging behind his twin and having more sleepless nights, with episodes of colic. By the age of two, Marco was a chubby, happy baby but Juan was a skinnier, unhappy version. Maria took Juan to the paediatrician several times and was told not to worry.

Eventually it was suggested she try Marco on soy milk as he might be intolerant to lactose. This initially helped him gain weight, but he developed a few strange minor allergies. The family arranged a DNA test for the twins, who were by now markedly different in size. The test confirmed they were identical. The reason for the discrepancy in weight, given that they were genetic clones and had been treated the same way, puzzled both the doctors and the family.

The gut microbiomes of the twins, as for all newborns, started out as blank slates. As the guts of twins become colonised by microbes from both the mother and the environment, they develop gut communities that resemble each other more than do those of fraternal twins or unrelated individuals, but they are not identical. Twins born by C-section, however, are on average more different in their microbes than those born naturally – and sometimes for strange reasons. For example, a few subtle differences in the way they are handled after birth could have a dramatic impact.

Back to Juan and Marco. The actual operation itself was pretty sterile. But when the twins were separated from the placenta they were each handed to a different nurse. The nurses may have looked very clean, but despite scrubbing up and wearing special clothing they were teeming with microbes, constantly shedding them from their hair, their skin and their mouths. In the course of weighing, tagging and cleaning, they were depositing new and different microbes on the fertile ground of the new babies. These ‘foreign’ microbes that found their way to the twins’ mouths and guts were not what evolution had intended. So before they were reintroduced to their mother they already had a distinct microbial signature that not only determined what foods they would tolerate but would shape the rest of their lives.

In normal deliveries the infant gut is first seeded by microbes from the birth canal, including vaginal, urinary and gut microbes, followed by others from the skin. This produces a rich diversity of starting material for the crucial first three years, when, as noted earlier, the character and complex interactions in the gut are formed. These microbial communities are key to our normal development, and particularly in training our immune system, which has to learn from scratch. Vaginal microbes in particular change dramatically during pregnancy in preparation for the birthing process, and when they are altered can trigger early labour. Babies born via C-section are extracted before they can be exposed to the normal microbes from the traditional evolutionary route.

Studies have shown major differences, that happen in the first twenty-four hours, in the gut microbes of C-section babies compared with those in the guts of babies born vaginally. The most obvious difference is the lack of helpful vaginal microbes like lactobacillus, which are replaced by skin microbes like staphylococcus (staph, the cause of most minor skin infections) and corynebacteria.8 We have seen that these don’t all come from the mother, and that sectioned babies get most of their bacteria from the skin of strangers in the operating suite, or sometimes from the Dad if he hasn’t fainted and been removed.

So within the first few hours, changes in these keystone species have been made, and will stay different for at least three years, and maybe for life. The guts of C-section babies are also more resistant to subsequent colonisation by friendly bacteria like lactobacillus and bifidobacteria, even when they start normal breast feeding.9

C-Section babies have more allergies

Just as important, C-section babies, with their disrupted gut microbiome, have also a disrupted immune system that brings with it a greater risk of later immune problems such as coeliac disease and allergies, especially to food.10 Nearly all the epidemiological studies (observational, not trials) published show an average 20 per cent increase in food allergies and asthma in these babies.11 Most studies show the risk is greatest from mothers who have allergies themselves – in such cases the risk may be sevenfold. Most studies uncover similar risks in routine and emergency operations, which makes bias factors less likely and the results more believable.

So this amazing innovation – the opportunity to avoid natural labour and delivery – that one in three humans is now exposed to is messing with powerful evolutionary forces that we hadn’t considered before.

Apart from banning C-sections, which would be unlikely to work, are there any realistic alternatives?

When Rob Knight of the American Gut Project carried out an earlier project comparing C-section births, he suggested something rather strange, on the face of it, to his pregnant wife. If she needed a C-section, he said, could he try to rebalance her natural state? She agreed, and as it turned out she needed a C-section for their daughter. Before she was anaesthetised Rob helped put a large tampon inside her vagina and rubbed it around her bottom. When the healthy baby girl was extracted by the surgeons, Rob immediately wiped the tampon across the face, mouth and eyes of his baby for a few seconds, trying to recreate what nature would have done.

After three years she is none the worse for this and has a natural-looking microbiome. Although her mother’s family are very allergic she has no reported allergies so far, and only one infection that needed antibiotics, a bout of staph laryngitis. I have heard that this novel procedure already goes on unofficially in some Nordic hospitals. Rob and Maria Dominguez-Bello have started a trial of ‘vaginal inoculations’, as the process is now called, in Puerto Rico for women having elective sections, and will be following up the babies long term to see if they can be ‘normalised’ and have their allergies reduced.

Nature has perfected the transfer of helpful nutrients and immune signals from the mother to the next generation not just via her genes but also from her microbes, which are finely tuned by what she eats during pregnancy. The dramatic increases in allergies in the last two generations can be explained by the diminishing diversity of microbes in babies, which is altering their immune systems in ways we don’t yet fully understand. Once the baby is born, the odds are very high that he or she will be given antibiotics within the first three years; most countries now report averages of one to three courses during this time. When this happens, the delicate balance of the carefully forming microbial communities is upset and may never recover.

Of the eight most common adverse effects of prescribed medications in the USA and Europe, five are attributable to antibiotics. When the average American child reaches adulthood, he has already had seventeen courses of these drugs, and as in the UK most of them are unnecessary. Many young kids, of course, have even more than ‘the average’, which as well as reducing their immunity to other infections can have other nasty side effects.

Paediatricians working in developing countries have known for many years that chronic infections stunt child growth, which explains the link between poverty and short stature. A recent review of ten trials of long-term antibiotics given to young children found that they did indeed increase height, by half a centimetre a year, but they had an even greater effect on weight gain.12 In these young Africans and South Americans antibiotics are helpful overall and can reduce malnutrition, presumably killing off many harmful microbes in the process, but this benefit is unlikely to be relevant to the West.

Antibiotics and obesity

Marty Blaser is a New York microbiologist who was one of the first to realise the potential long-term dangers of antibiotics and of our misguided attempts to eradicate microbes without thinking of the side effects. I first heard him talk in 2009 at a genetics meeting on Long Island, New York, and he convinced me of the reality of those dangers. He has now written an excellent book on the subject.13

He had seen, like many of us, a government study of the obesity changes over the last twenty-one years in the American states. The results were presented visually as coloured maps, changing over time, that you can watch like a horror movie.14 The colours change from a light blue (less than 10 per cent obese) in 1985 to dark blue, brown, then red (over 25 per cent obese) – just like the representation of a plague. In 1989 no state had more than 14 per cent of its population obese. By 2010 no state had less than 20 per cent – even the healthiest state, Colorado. The southern US has the highest rates and the west the least. Over a third (34 per cent) of US adults are now obese.

Explaining these changes is not easy. But there are indicators. In 2010 rates of antibiotic use in the same states were published too. The results again showed large differences across the country, which couldn’t be explained by illness or demographics. Amazingly, the same map colours for each state overlapped for antibiotic use and for obesity. The southern states, with the highest rates of antibiotic use, were also the states with the highest obesity rates. California and Oregon showed the lowest use of antibiotics (on average, 30 per cent less than other states), and it was these states that were relatively protected from obesity.

Now we are well aware that studies of national observations such as these can easily mislead. You could, for example, have a similar US map correlating obesity with the use of Facebook or body piercing. So the findings of our two studies were far from proof. Some replication to confirm the antibiotic–obesity hypothesis was needed. The first opportunity came using data from the Avon Longitudinal Study of Parents and Children that I often work with. This follows up 12,000 kids from birth in Bristol, using carefully collected measurements and medical records.15 In this study, exposure to antibiotics in the first six months of life significantly increased – by 22 per cent – the children’s amount of fat and their overall risk of obesity over the next three years. In a later study the effect of antibiotics was found to be weaker, and there was no effect of other medications. This mirrored studies in a Danish birth cohort in which an effect was found between antibiotic use in the first six months and subsequent weight at the age of seven.16

A much larger US study has recently reported the results in 64,000 children. The researchers were able to compare the type of antibiotic used and the precise timing.17 Nearly 70 per cent of kids from Pennsylvania had taken an average of two antibiotic courses before they reached the age of two. They found that broad-spectrum antibiotics given before that age increased the risk of obesity as a toddler by an average of 11 per cent, with greater risk if the drugs were given early.

By contrast, narrow-spectrum targeted antibiotics that kill a more limited range of microbes had no clear effect, and neither did common infections. These ‘epidemiological’ results, although supportive, are not conclusive and could have been caused by some other bias factors, such as children who take antibiotics being different or more susceptible in some other way. So Marty Blaser and his team took this one step further and tested his antibiotic theory in mice.

To mimic the effects of antibiotics on babies in the first three years, they used a group of lab mice pups divided into two sets. He gave one set three shots of antibiotics for five days at the equivalent doses that babies are given for throat or ear infections. The antibiotics were followed in both groups by a generous high-fat diet for five months, at which point they were tested and compared with mice without antibiotics.18 The results were clear and dramatic: in the antibiotic-treated pups there were significant increases in weight and body-fat levels, and the effects were greatest in the mice that had also been fed high-fat diets.

Unless especially lucky, most of us born in the last sixty years won’t have escaped antibiotics as young children, or high-fat diets at some time in our lives, and could potentially be suffering the same effects as these mice. I asked our 10,000 adult twins from around the UK if there were any among them who had never taken antibiotics so that we could study them and their microbes. Sadly, we couldn’t find a single individual. Even if you escaped antibiotics as a child, like me you may not have avoided being born by C-section. After adjusting for other factors, a meta-analysis showed that if you were born by C-section and didn’t get the magic tampon treatment, your risk of obesity probably increases by 20 per cent, likely in my mind to be due to microbes.19

Animal junkies

Most antibiotics produced and sold are not for humans. In Europe around 70 per cent of antibiotics are destined for agriculture, with again big differences between neighbouring countries in their usage. In the US, around 80 per cent of all antibiotics used now are for farming. These are enormous quantities – some 13 million kilograms in 2011 compared to only 50 kg in the 1950s.20 These poor animals must have a lot of sore throats, you might think. In fact the antibiotics are used for other reasons.

Following the war years and into the 1960s, scientists were playing around with ways of making animals grow faster.21 What they eventually discovered, after lots of trial and error, was that adding continuous low doses of antibiotics to the feed of almost any animal increased dramatically its rate of growth, enabling it to be brought to market sooner and thus more cheaply – this was so-called feed efficiency. Moreover, the earlier in their lives you started the ‘special’ feed, the better the results. As antibiotics became cheaper, this made financial sense for the industry. And if this worked so consistently in cattle and poultry, why not in humans?

American farms no longer resemble farms as we know them. US farming today is famous for its enormous industrial-scale feeding stations that they call CAFOs (concentrated animal feeding operations), which can contain up to 500,000 chickens or pigs and up to 50,000 cattle. Cattle are bred super-fast and go from calf to slaughter in around 14 months, by which time they already weigh on average an enormous 545 kg.22 The young cattle are rapidly weaned off natural hay and grass and trained to eat mass-produced corn laced with low-dose antibiotics. The corn is cheap, subsidised and plentiful, and grown in huge pesticide-laden cornfields amounting to a total area equivalent in size to the whole of the UK. Because of their new artificial diet that makes them ill, the overcrowding, the lack of fresh air and inbreeding, these animals are prone to infectious epidemics, so, paradoxically, they benefit from the antibiotics.

The use of only a few antibiotics has been banned from such widespread industrial farming. The US Department of Agriculture has shown little interest in seriously interfering in this lucrative market. In 1998, realising the potential for antibiotics getting into the human food chain and causing drug resistance, the more eco-sensitive European Union banned the feeding of certain antibiotics, valuable to human health, to animals. Then in 2006 they banned all drugs, including antibiotics, used for growth promotion purposes.

This should mean most meat is free of antibiotics in Europe. Sadly this is not the case: illegal use in feed is still rife, as scandals in the Netherlands have shown.23 EU farmers are still legally allowed to use antibiotics when problems occur, and they do this regularly and often using extremely high dosages. Although the EU is trying to restrict which drugs can be used, in reality it has little control. For a farmer with one infected animal in a herd it is cheaper to treat all five hundred than isolate the animal and wait and see. Such huge amounts of antibiotics in both the food chain and the environment lead to increasing microbial resistance, requiring ever stronger antibiotics for the animals, and subsequently for us humans too.

Livestock producers outside Europe fail to abide even by these liberal rules. Furthermore, the European Union imports a lot of outside produce so you don’t always know where your processed meat product comes from, or even if it’s from the same animal declared on the packaging, as the European horsemeat-lasagne scandals revealed.

Over a third of our fish is intensively farmed, whether it’s salmon from Norway or Chile or prawns from Thailand or Vietnam. Antibiotics are now being used in fish farms in ever-increasing amounts, and most of these large suppliers are outside of European or American control. The worse the conditions the fish are kept in, the greater the number of tons of antibiotics that are needed. It has been estimated that over 75 per cent of antibiotics given to farmed fish pass through the cages to other wild fish swimming locally, like cod, and thus get into the food chain that way.24

Can we avoid antibiotics?

So if you are a meat or fish eater you will most likely be ingesting antibiotics with your steak, pork or salmon. Although it is illegal, in many countries small amounts are often detectable in milk. Even if you are a strict vegan and don’t believe in antibiotics, you’re not safe. Particularly in the US, but in other countries as well, contaminated antibiotic-fed livestock manure is used to fertilise plants and vegetables that may end up on your plate. And our water supply is contaminated by the millions of tons of antibiotics flushed down sinks and toilets and by animal waste, and now contains many bacterial colonies possessing antibiotic resistance.

Water companies keep it quiet, but they have no way of monitoring or filtering out either the antibiotics or the resistant bacteria. Large amounts of antibiotics are found in US and European water-treatment plants as well as in reservoirs in rural areas.25 Similar studies have been undertaken in rivers, lakes and reservoirs all over the world, and their findings are very similar.26 The higher the amounts and diversity of the drugs, the more resistant genes were found.27 So wherever you live and whatever you eat, through your water supply you are getting regular doses. Even bottled mineral water may not be safe, as most varieties tested contain bacteria that have been exposed to antibiotics and are resistant to many of them.28

The commercial agriculture industry and the government food and agriculture agencies say that these doses that get into our food chain are totally harmless. But what if these august bodies, with ‘no conflicts of interest’ and concern only for your well-being, are wrong? Could these small doses be harming us? Marty Blaser, again, decided to test it empirically. And what his lab found was that mice fed on even tiny sub-therapeutic doses of antibiotics early in life, or over their lifespan, went on to produce twice the weight and body fat of normal mice and their lipid metabolism had changed.29 The gut microbe contents had shifted significantly; there were many more Bacteroidetes and Prevotella species and fewer lactobacilli.

When the antibiotics were stopped, the microbial composition returned towards that of the untreated group, although it stayed less diverse. But subsequently, even on the same diets, these ex-antibiotic users remained fatter throughout life. The results were always more startling if you added antibiotics to high-fat diets rather than to normal healthy mouse food. Blaser’s lab also found that the immune systems of the antibiotic group was badly impaired. The microbial changes interfered with the normal signalling pathways, and the genes controlling the immune system lining the gut wall and keeping it healthy had been suppressed.

To prove that the results were attributable to the change in the gut microbes and not to some direct toxic effect of the drugs themselves, the research team transplanted the microbes from the guts of the antibiotic-treated mice to the germ-free sterile mice. This produced the same noticeable weight gain, showing conclusively that it was the reduction in the gut flora that was the problem, not the antibiotics. Whether the animals had been fed high- or low-dose antibiotics, both groups also showed increases in the natural gut hormones associated with obesity, such as leptin and a hunger-inducing gut hormone known as PYY, released after signals from the brain that reduce food transit time and permit greater extraction of calories from all kinds of food. This reminds us of the important gut–brain interactions that occur all the time.

Modern babies are facing an onslaught of antibiotics, whether via injections given to the mother before a caesarean section, via short courses for minor infections, or via the mother’s breast milk. And add to this the low-level contamination of tap water and food that we still don’t know the effects of. Antibiotics could be the root of many unrelated and unexpected health problems, such as the recent finding that treatment increases the risk of malaria spread and infection by favouring the uptake of the microbe plasmodia by mosquitoes.30 Antibiotics may be the missing factor, or certainly one of them, explaining the current childhood-rooted obesity epidemic. The diminution in our microbes and our processed, sugary, fatty diets have joined forces to produce the perfect obesity storm.

What’s more, as we become fat and pass our highly selected fat-loving microbes on to our children, a vicious cycle starts: the next generation is exposed to yet more antibiotics and has an even more impoverished microbiome than we had. In other words, the problem of the depleted microbiome is escalating in each generation. This explains why the effects and trends we are observing are magnified in children of obese mums, who themselves started life with a defective microbiome.

Given that antibiotics are so difficult to escape from, is there a solution to this mess? Transforming yourself into a New Age anti-medicine organic vegan might give you and your family and your microbes a slight edge, but a better bet would be community action with a view to reducing the use of these drugs.

The benefits to our children would be greatest if doctors were not pressured into prescribing them. Clearly, for emergencies you need to seek help, but for a minor ailment try waiting an extra day or two to see if it resolves itself. If we all started accepting that we sometimes get ill and put up with a possible extra half-day of symptoms without a prescription we would keep our microbes happy. Governments can make a difference by targeting the worst doctors. This is how, between 2002 and 2006, France managed to stem the tide and reduce its antibiotic prescribing for kids by 36 per cent.

If we really need the drugs we should be using modern genetics to develop more targeted ones, not wiping out the whole microbiome garden with the current medicines. As well as all eating less meat, organic if we can afford it, we should be lobbying government to reduce subsidies for industrial-scale antibiotic-dependent meat production. With antibiotic resistance increasing exponentially globally, we will soon have no drugs left to treat serious infections and we should be working seriously on alternatives. It could mean using natural bacteria-killing viruses that are harmless to us. For this we would need to increase research funding so as to enable us to rapidly identify and eliminate the guilty species.

Are probiotics the cure?

Can yoghurt drinks with added acidophilus or bifidos make any difference? As we already discussed, if you are very young, or old and severely ill, there is increasing evidence that they are beneficial.31 For the rest of us, the reality is that although they do no harm there are as yet no good trials showing benefits in humans. This is probably because we all have very different gut microbes to start with. So not knowing which microbes to replace, it’s a lottery whether such yoghurt drinks will work for you.

Hopefully, the future will produce tailored probiotics for each person that will depend on all of us having our gut microbes measured routinely, which can of course be done.32 Meanwhile, eating microbe-supporting prebiotic-rich foods (like artichokes, chicory, leeks and celeriac) while you are on antibiotics seems sensible, although we are still awaiting data to back this up. And since antibiotics and C-sections have been linked with a rise in allergies, some of the possible culprits being microbe-friendly foods, should we be restricting our diets further to prevent them?