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Meet the bacteria that are vital to our health

Meet the bacteria that are vital to our health

New research is beginning to uncover how the trillions of bacteria in and on our body are vital to our health. Here's a brief history of microbiomes, past, present and future. 

Early this year, scientists made an extraordinary discovery. They unearthed bacteria from the stomach of a 5,300-year-old mummy preserved in permafrost. The ice man, dubbed Ötzi, was dug up 16 years earlier, but the bacteria had migrated into his ribcage, where it remained hidden until January this year. The finding, although minuscule in size, is gargantuan in significance.

Over millennia, Western lifestyles—characterised by sterile living and a proclivity for the indoors—have changed our gut flora, contributing to modern scourges such as asthma and obesity. Only now are experts realising the extent to which the trillions of bacteria that live in and on us exert an influence on our lives.

These diminutive critters—so tiny that a million laid together would cover a single pinhead—help us digest food, break down toxins, make vitamins and metabolise medicines. They influence our hormones, our immune systems and even our brains. Learning to understand better this relationship may become as critical to modern science and medicine as cracking the genetic code.


Microbiomes in the past

gut bacteria mummy
The mummy known as Ötzi. Scientists have reconstructed his last meal using samples from his stomach and intestines

By gathering data from fossilised faeces and the guts of mummies (including Ötzi), and studying modern hunter-gatherer populations, scientists are recognising that our insides aren’t what they used to be.

“There appears to have been major and very recent changes in our gut microbiome,” points out Dr Christina Warinner, assistant professor of anthropology at the University of Oklahoma. “Both traditional peoples and archaeological populations have more diverse gut microbiomes than people living urban, industrialised lifestyles today.”

Indeed, dwellers of farming communities in Burkina Faso, Malawi and South Africa have a fuller complement of bacteria in their guts than Europeans and North Americans.

One example is treponema, a class of bacteria that’s great at digesting fibre and is believed to reduce inflammation in the gut. It’s still found in Tanzanian and Peruvian hunter-gatherer populations, but it’s virtually absent in urbanised Western society. And there are some gut bacteria that have upped and left completely.

This isn’t good news. Says Professor Warinner, “Reduced gut microbiome diversity is usually associated with conditions such as metabolic disease, along with gastrointestinal disorders.”



“Traditional peoples and archaeological populations
have more diverse gut microbiomes than people living
urban, industrialised lifestyles today.”



Dr Stephanie Schnorr, a researcher in molecular anthropology from the University of Oklahoma, suspects the lost bacteria were also used for “early immune-system training”—that is,
to help humans defend against pathogens.

She says that our gut microbiota continually “engages in cross-talk with the host” to help us develop a robust immune system and healthy metabolism. If these channels of communication are disrupted, the whole system is weakened—rather like trying to govern a country when half the Cabinet has resigned.

We’re “losing touch with our microbial old friends”, the experts warn; a parting hastened by our obsession with hyper-sanitation. We keep babies away from germs, we grow up eating pasteurised, canned or refrigerated food (anything to avoid fermentation). Experts describe this as “starving our microbial selves”.

We douse our hands in antibacterial soaps and, if unwell, we take antibiotics, which rids us of infections but also kills off “good” gut bacteria at the same time.


With asthma, eczema, food allergies, hay fever, autoimmune disease and obesity all on the rise, scientists are looking to redress the balance.

“Sanitisation, antibiotics, soaps and pasteurisation are modern marvels that allow us to live long, healthy adult lives without worrying that a paper cut will kill you,” says Dr Schnorr. “But as with anything, we’ve been blinded to the long-term consequences of the unregulated use of these powerful tools. Now, hindsight is catching up with us.

“The gut ecosystem is like any other—it needs its predators, prey, opportunists and symbionts in all varieties in order to achieve a kind of balance. It’s possible to find some good middle ground so we can have our health and play in the dirt too.”


Microbiomes in the present


The options for redressing the balance are limited to probiotics and, at the extreme end, faecal transplant. Probiotics involve ingesting live bacteria and yeast (usually in drink, yogurt or supplement form) to populate the gut with “friendly” microorganisms.

Research on mice has shown probiotics make rodents’ fur shinier, cause improvements in behaviour and even reduce obesity. In one study, probiotic-fed mice were less anxious and depressed than their peers—evidence of a “gut-brain axis”.

Other studies suggest probiotics help prevent inflammation caused by gastroenteritis and reduce antibiotic-related diarrhoea in patients with Clostridium difficile (C.diff).

But for treating severe antibiotic-resistant bacterial infections, such as C.diff, a “stool transplant” is more effective. The concept dates back to fourth-century China, when a man called Ge Hong recorded administrating a suspension of human faeces by mouth to treat food poisoning or severe diarrhoea.



“We have 25 donors and that makes us the largest stool
bank in the UK, and probably the biggest
donor bank in the world”



Nowadays, Faecal Microbiota Transplant (FMT) involves passing healthy donor stools into the colon via a colonscope, enema or nasogastric pipe. The UK-based Taymount Clinic, (the only dedicated FMT clinic in Europe) has performed over 6,000 procedures. The clinic uses stools from several different donors to maximise diversity, and all are screened to ensure they’re healthy and infection-free.

“We have 25 donors and that makes us the largest stool bank in the UK, and probably the biggest donor bank in the world,” says microbiologist Glenn Taylor, director of science at the clinic.

Relatives aren’t used as donors as their bacterial profiles may be too similar to the patient. Indeed, last year in the US, a woman became obese following a stool transplant from her overweight daughter.

At Taymount, the sample is strained in a sieve stack oscillator down to 20 microns (20 millionths of a millimetre), and the “bacterial pellet” is centrifuged and washed. A rectal catheter infusion is used to implant the FMT directly into the large intestine (colon).

In March 2014, NICE guidelines approved FMT as a treatment of “last resort” in recurrent, antibiotic-resistant C. diff, with studies showing it to be effective. As shown in the case study on p43, FMT can also used to treat inflammatory bowel disease.

But it’s hard to get beyond the yuck factor. Jon Turney, British author of I, Superorganism: Learning to Love Your Inner Ecosystem, likens it to “trying to improve a disease-ravaged, depleted shrubbery by transplanting an entire rainforest, all in one go”.


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