Our body has a vast consortium of microbial organisms that live on all of our barrier tissues. The highest density of organisms lives in the intestine, and these organisms provide a tremendous benefit to us (the hosts) via processing complex dietary constituents, such as fibre, into substances we can absorb, in addition to many other enzymatic functions.

Just to give you an idea of this vast universe, 85 per cent of the dried content of the faeces we expel every day is composed of dead and alive bacteria. The dense population of organised and highly specialised microbial communities (“good” bacteria and fungus) also regulates our immunity.

Problems arise when there is a change in this population called commensal microbiota — which lives in our gut peacefully, contributing to our health and causing no damage — caused by food poisoning, acute infectious gastroenteritis, use of antibiotics and other environmental factors such as dietary changes.

Consequently, there is intense interest in manipulation of the composition of commensal microbiota as a therapeutic strategy. Although the public and many physicians may not distinguish this approach from use of probiotics or dietary supplements, large-scale alteration of the intestinal microbiota requires a different set of definitions and requirements, as well as research and the development of live biotherapeutics.

Shall I test my stools to evaluate the composition of my microbiota?

The simple answer is, no!

You may have seen numerous websites encouraging and offering such tests as the basis for help with a dizzying variety of conditions.

You pay their substantial fee, fill in an extensive questionnaire, and pop your poo sample in a package. Typically, you will get an equally extensive report back explaining your “personalised” test results. It might include some harmless data, along with advice your mother could have given you. But don’t be surprised when they suggest you follow their dietary plans — including pills, supplements, etc — and want to track your “progress” with further stool tests and consultations.

But there is a very serious bottom line here, and it comes from the American Gastroenterological Association, a non-profit organisation representing and regulating more than 16,000 gastrointestinal-specialist doctors. The AGA expects that microbiome-based diagnostics will indeed become a routine part of clinical care, but cautions that “there is still a long way to go”.

The update from the American Gastroenterological Association on this topic is:

“Although there is great interest in the microbiome, there is still a long way to go before microbiome-based diagnostics become a routine part of clinical care. Microbiome studies have been enormously valuable both in understanding mechanisms of disease in animal models and finding associations with disease in human beings. A good analogy is machine translation of natural languages: there has been interest since the 1950s, and poorly functioning systems have been available since the 1980s, but only in the past couple of years has it been possible to have a conversation with someone who speaks no common language using a mobile app on a smartphone, or to translate signs or menus from Chinese into English in real time using that smartphone’s camera. In the same way, microbiome testing right now is primarily of interest as a science project. However, there will be rapid progress in the near term to develop better technical capability, including better user interfaces with readouts at the level of bacterial strains, and integration of ecologic dynamic concepts to better understand the transitions from health to illness.”

So, the commercially available tests that are offered nowadays have no use in clinical practice for several reasons that include difficulties in collecting the right amount of stools, homogenising the sample, preserving it, and analysing and interpreting, which incur different results, even for the same patient in different days. Therefore, at the moment, microbiota analyses are exclusively used in research and have not been approved for clinical use.

Can I change the composition of my gut microbiota?

Up to date, the only condition we treat changing the bacterial composition of our gut is a infection cased by a “bad bacteria” called Clostridium difficile. Clostridium difficile infection is caused by enterotoxins, released by vegetative forms of toxigenic bacterial strains that destroy the intestinal epithelium, leading to an intense inflammatory response and secretory diarrhoea.

Although C. difficile is a native of the distal gut, its growth and pathogenic activity normally are held in check by commensal microbiota. Antibiotic use is the main risk factor for CDI. Although specific classes of antibiotics pose different risks for the development of CDI, cumulative exposure to antibiotics over time further increases risk. Notably, antibiotics are also the standard treatment for CDI, but these are broadly active against many members of intestinal microbiota. Therefore, it is likely that successive rounds of antibiotic treatments in patients with recurrent CDI weaken the resistance of the microbiota against C. difficile, which persists in the form of antibiotic-resistant spores.

Despite an instinctive aversion to faecal material, there are records that faecal microbiota transplantation has been used in human civilisation as a therapeutic agent for many centuries. Chinese medicine provided the earliest known documentation of FMT in human beings, referring to various forms of faecal preparations, including fresh, fermented, dried and infant-derived products that were used to treat multiple gastrointestinal maladies. In Europe, for centuries there was widespread belief in medical applications for faecal material. Franz Christian Paullini, a German physician, observed that faecal consumption was common in animals as well as human beings — since manure was used as a fertiliser). In 1696 he published a book, Hailsame Dreck-Apotheke (Salutary Filth-Pharmacy), on medical uses of human and animal faeces.

FMT is highly effective in the treatment of antibiotic-refractory CDI; it is the most direct and radical way to change the composition of a patient’s distal intestinal microbiota and it is done only in patients who have been admitted to hospital.

Shall I take probiotics?

Regulatory agencies such as the US Food and Drug Administration consider any agents given to patients to cure, treat, mitigate or prevent disease to be drugs.

Therefore, their approval for testing and use in patients requires demonstrations of safety and efficacy. In contrast, probiotics are defined as live micro-organisms that might provide health benefits. However, there is no legal definition for probiotics, and these products often are marketed without scientific proof of their claims.

No probiotic product has been able to satisfy the regulatory requirements to be categorised as a drug — a substance intended to cure, mitigate or prevent disease.

The American Gastroenterological Association recommendation regarding probiotics supports use of certain probiotic formulations in three settings:

• For C. difficile infection in adults and children taking antibiotics

• For necrotising enterocolitis in preterm, low-birthweight infants

• For the management of pouchitis, a complication of inflammatory bowel disease

There is insufficient evidence to recommend probiotics for treatment of Crohn’s disease, ulcerative colitis and irritable bowel syndrome. For acute infectious gastroenteritis in children, AGA recommends against the use of probiotics.

However, patients take probiotic products in the belief that they will help to treat their intestinal or systemic diseases.

What can I do to improve my “gut health”?

Modern lifestyle, in particular the increased consumption of fast foods, sugar and decreased consumption of fibre, fruits and vegetables, may contribute to the increase in diseases by disrupting the microbiome from an early age. So read the labels of the products you buy. For instance, emulsifiers, commonly added to foods to improve shelf life, change the composition of gut bacteria and promote chronic inflammation. Chronic alcohol abuse disrupts the intestinal barrier and can modify microbiota composition.

Increasing fibre content in our diet to 50 grams per day and reducing fat can establish a microbiota composition that is low-risk for the development of colorectal carcinoma. This is only a fraction of the dietary effects on the microbiota and health.

Be careful with the overwhelming source of apparently scientific articles that are unreliable. Many of those websites are designed to sell products such as diet books, nutritional supplements — containing probiotics, for example — herbal remedies, gluten-free foods and other special diets, such as low-sugar or antifungal diet, which have no scientific support.

• Suraia Boaventura Barclay, MD is a Consultant Gastroenterologist and Endoscopist, and Fellow of the American Gastroenterological Association