Gut Microbiota and Probiotics: a review

Research on the microbial communities in our gut (known as the microbiota) has accelerated dramatically in recent years, thanks to developments in the technologies that allow us to fully enumerate and evaluate the bacterial species and strains that reside there.  We now know emphatically that gut flora plays a significant role in human health and disease, so do probiotics have a role to play?. 

Research has shown depleted or imbalanced gut microbiota is strongly associated with greater risk of disease, including neurological and mental health disorders, whereas having an abundantly diverse, healthy gut microbiota is associated with wellness and a robust immune system.  So it was only a matter of time before a ‘Probiotic’ market would appear, and as research escalates, it looks set to run and run.

Dysbiosis’ is the term used to describe an imbalance in this intestinal ecosystem, the causes of which are numerous.   Favourable alterations to the microbiota and reversal of some conditions can be achieved with some – not all – probiotics, and I’m not referring to the little sweet yoghurt drinks found in most supermarkets.

Our microbial friends

This dynamic microbial ‘organ’ within the gut, weighing around 2 kgs, (the same as our brain), communicates with our brain via the vagus nerve and we now know contributes to various of our metabolic functions.  These microbial communities are termed ‘commensal’, because ‘co’ they’re living closely with us, and ‘mensa’, we’re sharing the same table, effectively they eat what we eat.  They usefully exert an antimicrobial effect – protecting against pathogens, they educate and modulate our immune system, they influence our moods, contribute to glucose tolerance and affect directly or indirectly most of our physiologic functions.  One important digestive contribution is their ability to liberate short chain fatty acids from indigestible vegetable fibers, and these fatty acids are an important energy source for the cells lining our intestines and critical for modulating immune responses and inhibiting tumor development in the gut.

Factors that negatively impact or deplete our microbiota include caesarian birth, bacterially sterile childhoods, environmental toxins, antibiotics and pharmaceutical drug use, chronic stress, as well as the more obvious functional gastrointestinal disorders.  Whereas a vaginal birth, being breastfed, growing up with pets and having plenty of exposure to bugs and dirt, along with a diverse diet with plenty of plant foods, will help shape a strong, diverse, health-protecting gut microbial community.

Gut friendly Diets & fermented foods

It is now accepted that many of our chronic diseases prevalent in the developed world, are associated with our modern diets: highly processed meats, refined carbohydrates, insufficient plant-foods and virtually no fermented foods.  The Mediterranean diet, the traditional Japanese diet, and hunter-gatherer diets on the other hand, are being studied for their health benefits.  Most old, traditional diets originally included many more plant foods and always fermented foods.  Our ancestors – without knowledge of microbes or bacteria – recognized the palatability, preservative, analgesic, and mentally stimulating or sedating qualities of fermented foods and drinks.

The processes required for fermented foods were present on earth when man appeared on the scene… When we study these foods, we are in fact studying the most intimate relationships between man, microbe and foods.’  Prof. Keith H. Steinkraus, Cornell University, 1993

In terms of ancestral diets, as agriculture expanded, so too did intentional fermentation techniques, to preserve foods.  In fact fermentation is the process behind many of our basic staples; bread, cheese, yoghurt, chocolate, coffee, wine and beer.

While artisan fermented products are now becoming trendy amongst health foodies in the UK, people have been harnessing the natural process of fermentation all over the world for thousands of years. Studies now show eating fermented plant foods like Sauerkraut, Tempeh, Kimchi and live yoghurt and drinking probiotic rich drinks like kombucha and kefir, along with a plant-rich diet, is by far the best way to improve the diversity and abundance of our gut bacteria.

Emerging research shows that the bacterial fermentation process can magnify the bioavailability of some food nutrients, and these fermented foods – once consumed – also positively influence our own microbiota.  Most towns now boast a health-food store of sorts, and this is where you’ll find properly fermented foods.  Similarly, ‘Wholefoods’ online will deliver sauerkraut, kombucha and kefir starter cultures: (

Follow this link to read more on fermented foods and their extraordinary and diverse health benefits:

Meanwhile, increasing the variety and quantity of your daily portions of vegetables, remains a great way to improve that ecosystem in your gut.  Feed them what they need!  These ancient friends evolved alongside us when our diets consisted of natural wholefoods, not MacDonald’s.

Probiotic Supplements

There are now many products being marketed as ‘probiotic’ making consumer choice increasingly difficult, and suffice to say, they are not all born equal.  I pride myself on being an evidence-based practitioner and as such, endorse very few probiotic supplements. Evidence has shown it’s not just a numbers game.  Ever greater strength in delivering billions of ‘cfu’ (colony forming units) per capsule will not always translate to therapeutic efficacy. However there are a few researched products that stand out from the crowd.


Manufacturers like Optibac supply specific strains of probiotic bacteria that have been shown in human, placebo controlled clinical trials, to be effective for specific areas of health.  Different ‘strains’ within the same species can have very different properties, and have been shown to migrate to different locations within the human body, and exert different effects.

The Lactobacillus Rhamnosus species, that has many different strains is a good example: Lactobacillus Rhamnosus Rosell- 11 adheres to cells lining the small intestine, where it produces digestive enzymes that help to break down and digest foods, whilst creating a less favourable environment for opportunistic pathogens, so this strain is found in their “For travelling Abroad” product.  Whereas Lactobacillus Rhamnosus GR- 1 has been proven to migrate to, and adhere to cells lining the vaginal tract, where it helps to balance the microflora, acidify the mucosal tissue and make it less favourable for microorganisms involved in thrush infections, cystitis and bacterial vaginosis.  So this strain is found in their “For Women” product.

In their “For your Cholesterol” product, very specific live cultures (‘AB-Life’ Lactobacillus plantarum CECT 7527, Lactobacillus plantarum CECT 7528, Lactobacillus plantarum CECT 7529) were tested in a randomised, double blind, placebo controlled trial, published in the British Journal of Nutrition (2013), and shown to survive environmental stressors and gastric acidity, to survive and reach the gut alive, and shown to significantly lower cholesterol.

For those on antibiotics, taking a probiotic will surely soon become mainstream, as broad spectrum antibiotics indiscriminately kill off so many beneficial, commensal species in our gut, leaving those hardy species that are antibiotic resistant, to then bloom, multiply and fill the newly vacated real estate in the gut.  Optibac “For every day EXTRA strength” is recommended, and I would add a Saccharomyces Boulardii product too, this being a beneficial but transient species that is not affected by antibiotics, and can usefully occupy the newly formed vacuum, on a temporary basis, until probiotic species are replaced.  A bit like using a friendly, reliable house-sitter to reduce the risk of (antibiotic-resistant) squatters!

The bottom line – this is a company that uses robust scientific evidence as a foundation for its strain specific products.  So if you’re perusing the many probiotic supplements now on sale, if only broad category species are named – like L. Acidophilus – on an ingredients list, with no mention of a specific strain, then there may be little or no research behind what’s contained in the product, making any health claim questionable.  Whereas Optibac’s L.Acidophilis NCFM strain, for example, points to research being done at the ‘North Carolina Food Microbiology’ research centre, and a pubmed search of this strain reveals hundreds of published papers.


This is another company that prides itself on using robust research to inform their products.  Their “Infantis” product for example contains 7 specific strains that have been well researched for the following benefits: decrease in diarrhoea, constipation, improvement in symptoms of colic, and severity of eczema.  This is particularly useful for babies born via caesarean section, to introduce the strains of bacteria that would otherwise have inoculated the baby during passage through the birth canal.

It is now well known that the early composition of the gut flora profoundly influences the development of the immune system, and the potential integrity of the gut surface lining, with its all important job of being both an absorptive surface for nutrients, as well as an effective barrier to pathogens and food antigens. Gut bacteria play an enormous part in this function.  A mother’s birth canal provides specific flora designed to do this very job, and her breast milk contains a particular oligosaccharide that feeds and nourishes those strains of bacteria, to ensure they thrive and colonise the infant’s gut. Nature is so clever!  The incidence of allergies, hayfever, and atopic skin disorders in infants is rising exponentially, and is associated with altered, or less diverse gut microflora.

The probiotic “Infantis” also contains vitamin D3 and omega-3 fatty acids, for immunity and brain health, and five of its specific strains have been used in a study/survey involving 33 children diagnosed with Autism Spectrum Disorder (ASD) and gastrointestinal distress.  The results of the caregivers survey indicated an observed 88% improvement in ASD symptoms such as speech/communication, sociability, sensory/cognitive awareness, and health/physical/behaviour in 33 children.  Of course being a survey, there was no control arm of ‘no-treatment’ or placebo.  Accordingly, these survey results need to be validated in controlled clinical trials.  But research has confirmed that a common finding amongst children diagnosed with ASD is altered composition of beneficial gut microflora.


This liquid formulation containing 4 strains of live, active bacteria is also well researched and needs a commitment to a 12 week course, for optimal results.  This product has been shown to be effective in reducing the symptoms of IBS.  A randomised, double-blind, placebo-controlled trial of 186 adult patients with symptomatic IBS, received 12 weeks of treatment with the probiotic drink, or a placebo. The primary measure of effectiveness was the difference in change in the patient’s IBS symptom severity score.

‘Enteric coating’ of probiotic capsules is another persuasive line on the packaging of many probiotic products, claiming to optimise the delivery of live healthy bacteria to the lower gut, because otherwise – supposedly – the bacteria would not survive the acidity of the stomach and therefore fail to reach the intended location of the intestines.  There is also much debate as to the best times of day to take probiotics, and whether it should be with food, or on an empty stomach.

An independent study tested the Symprove drink (no enteric coating there), and seven other market-leading products to explore the comparative health and survival of the formulations at two stages of use; the point of consumption and following exposure to gastric fluid.  Three of them were liquid products and five were freeze-dried products.  Symprove was found to deliver 100% of the claimed colony forming units (CFUs), and 100% of its bacteria survived the gastric tolerance test and then grew in the real-time growth test.

When to take them? Another study examined the optimum time of delivery, in particular whether mealtimes – with the buffering capacity food – actually assisted the survival of probiotic microbes (in a capsule), during passage through the intestine.  They concluded that the best survival of non-enteric coated bacterial probiotics was achieved by taking them with food, or just prior to a meal preferably one containing some fats.  Optibac suggest breakfast is the best time for ensuring optimal survival through gastric acidity, and to avoid taking them with hot drinks.  Most should not need refrigeration, though if the packaging stipulates this, it might be best to comply.

Cautions: Probiotics are not recommended for those with serious medical conditions, those who are immunosuppressed, have pancreatitis, are in the ICU or have a catheter fitted, have malaena or open wounds following surgery, children with short bowel syndrome.

Declaration: At time of writing Eleanor Strang had no professional affiliation with any of the probiotic companies here reviewed.


Patel R & DuPont HL (2015) New approaches for bacteriotherapy: prebiotics, new-generation probiotics, and synbiotics. Clin Infect Dis. 15;60 Suppl 2:S108-21.
Andrew B et al., (2015) The gut microbiome in health and in disease. Curr Opin Gastroenterol. 31(1): 69–75.
Fredua-Agyeman M & Gaisford S (2014) Comparative survival of commercial probiotic formulations: tests in biorelevant gastric fluids and real-time measurements using microcalorimetry. Beneficial Microbes: 6(1):141-151
West R et al., (2013) Improvements in Gastrointestinal Symptoms among Children with Autism Spectrum Disorder Receiving the Delpro® Probiotic and Immunomodulator Formulation. Journal of Probiotics & Health Vol 1(1): 102
Strati F et al., (2017) New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome 5: 24

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