Probiotics: the definitive guide

Probiotics: the definitive guide

Author Miriam Ferrer, PhD Last updated 1st October 2019

  • Ingredients & Nutrition

Did you know that there are more microorganisms in your body than human cells? Most of these organisms live in your gut, where they play a crucial role in digestion.

Here, we explain why promoting multiple strains of good bacteria in this ‘microbiome’ is an important part of maintaining your wellbeing and explore the best methods for doing so.

What is your microbiome?

Your microbiome (or ‘microbiota’) is the community of tiny microorganisms that live on your skin and inside your body. It consists of thousands of different species and strains, including varieties of virus, bacteria, fungi and archaea (single-celled organisms without a nucleus). Most of these microbes are found in your gastrointestinal tract, forming your ‘gut microbiome’.1

Some of the microorganisms that make up your microbiome are harmful (pathogenic, e.g. the bacteria that make you ill), some subsist on you but don’t do any harm (commensal) , and some are beneficial to you while also subsisting on you (symbiotic).

We have long understood that microbes are important for our wellbeing, but have only recently begun to study the complex web of microbe-microbe and host-microbe interactions that occur in every part of the human body.

By far, the most studied part of the human microbiome is gut flora. We know that the bacteria in our intestines help to process and absorb food as well as to produce essential nutrients, so it’s important to keep it healthy. But scientists have only recently realised how our microbiome can affect our body’s reaction to different foods, pharmaceutical drugs and illnesses. It may affect health issues as wide ranging as how the body reacts to chemotherapy and the likelihood of experiencing particular emotional states.2,3

There is also a correlation between the health of your microbiome and the likelihood you will develop chronic conditions including arthritis, asthma, inflammatory illnesses like IBS, diabetes, cardiovascular problems and even obesity.4,5

Every person’s microbiome is different - even if you’re an identical twin. Studies using identical twins have shown that the bodies of people who are genetically the same react differently to foods that they eat because of differences in their microbiome.6

It’s clear from twin studies that the number of microbes and the variety of species in your microbiome is determined by both genetics and environmental factors.7 Your diet probably has the most direct effect in your microbiome: eating a good diet with a variety of fruits and vegetables will improve your microbiome, but you can harm it with a poor diet or by taking too many antibiotics.

How does an unbalanced gut microbiome affect health?

  1. An upset stomach is a sign that you don’t have a good balance of gut bacteria, as a healthy microbiome helps you to digest your food (although technically the ‘upset’ feeling will stem from microbiome issues in the intestines, not the stomach itself). Symptoms can include diarrhoea, gas, constipation and bloating. Some food intolerances may also be caused by problems with the microbiome.
  2. Poor sleep is linked to a lack of the neurotransmitter seratonin, which is produced in the gut. If you’re tired all the time this can be caused by an imbalance in gut bacteria.
  3. Weight changes that don’t seem to be related to your diet can be caused by a change in your microbiome because it regulates how well your body absorbs nutrients. Changes can also cause sugar cravings, and a diet that is packed with processed sugar products can actually harm your microbiome which creates a vicious cycle.
  4. An unhealthy microbial balance can also underlie conditions like eczema and halitosis (bad breath).
  5. Long-term antibiotic use is certain to damage your microbiome, and these vital drugs unfortunately cannot distinguish between helpful and harmful bacteria.
  6. There is evidence that more serious conditions may be caused by problems with the microbiome. Examples include inflammatory conditions, anxiety and autoimmune issues.

How can I improve my microbiome and gut health?

  • Eat a varied diet. It’s not about eating a lot of healthy food, but eating a range of different fruits and vegetables. Each type of vegetable will support different strains of microbe, and we know that diversity is the key to a healthy microbiome.
  • Eat plenty of fibre, for example from whole grains, bananas, onions and garlic. Fibre acts as a ‘prebiotic’ – a food source for beneficial microbes that helps them to thrive.
  • Fill your diet with polyphenols. These micronutrients are good sustenance for your microbiome. They can be found in large quantities in a wide variety of foods including green tea.8
  • Eat fermented foods that contain live bacteria. Dishes like yoghurt, kefir, sauerkraut, kimchi and miso paste can help to boost the variety of species in your microbiome.
  • Drink in moderation. A little alcohol is known to help your microbiome, but too much will have the opposite effect.
  • Spend plenty of time in the open air. People who live in the countryside, do a lot of outdoor activities or own a dog have healthier microbiomes, whereas those most engaged in modern industrialised lifestyles fare poorly. In fact, a project already exists to try and preserve the unique microbiomes of indigenous peoples before they disappear.9
  • Engaging in exercise may also help to improve your microbiome.10The NHS recommends 150 minutes of moderate aerobic activity a week for adults aged 19-64, plus two sessions of strength exercises (see the NHS website for alternatives).11

You can also try to change negative habits that damage your microbiome:

  • Don’t take medicine unless you need it. Antibiotics don’t distinguish between helpful and harmful bacteria, so they can damage your microbiome. Some over-the-counter medicines can also interfere with microbes. Naturally, you should take any medicine that is recommended to you by your doctor.
  • Take measures to reduce stress. Psychological stress and lack of sleep can affect your microbes too.12
  • Avoid processed foods, as many of the ingredients (e.g. artificial sweeteners like aspartame) are thought to damage your microbiome.13Processed sugars also have a negative effect.

You may also wish to try a probiotic product.

What is a probiotic?

Probiotics are live microorganisms that can be used to support or restore normal physiological processes.

Microorganisms can both disturb and help with the processes in your body, so changes to your microbiome can also make a positive contribution to your health.14 Helpful microbes that will improve your wellbeing when present in your body are called probiotics.

What we have in mind when we think about probiotics, are products that can quickly increase or boost the number of microbes in our gut. Most probiotic products are taken orally, although researchers are looking at probiotic delivery via other methods such as FMT (fecal microbiota transplantation).

When a company creates a probiotic as food supplement, the product development team choose specific strains of microbe that are believed to be useful. These strains originate either from human microbiota or from the environment (e.g. they thrive in the fermentation process that creates food like yoghurt or sauerkraut). A good probiotic supplement will include strains specially for their ability to positively influence disturbed physiological processes, and will be manufactured in an environment that ensures only the correct microbes are contained in the end product.

A good probiotic will also include multiple strains, since diversity is the key to a really healthy microbiome, not just the number of bacteria present.

Common kinds of microbe found in probiotics include lactobacili (usually in yoghurts) and bifidobacteria (from dairy products). These are the most common and studied types because they are known to us from fermented foods and it has long been understood that they can be helpful. Both are believed to aid with digestive issues.

What is the difference between a probiotic and a prebiotic?

Although the names are similar, probiotics and prebiotics are actually completely different things:

  • Probiotics are live microorganisms that can be used to support or restore normal physiological processes.
  • Prebiotics are the food that these microorganisms subsist on. They are usually fibre, for example from garlic, onions, leeks and bananas.

By eating the right prebiotics you can help the right kind of gut bacteria to thrive, which will promote a healthy balance of microorganisms in your body.

What are some common probiotics?

Most probiotics sold in the UK are from two different species:

Lactobacilli convert sugars to lactic acid. They are believed to help protect the body from attack by hostile microorganisms and to treat health issues such as vaginal infections, diarrhoea and skin disorders.

Bifidobacteria are one of the major varieties of bacteria that live in the human digestive tract. They help to convert lactose into useful nutrients and are thought to both support the immune system and help to prevent hostile bacteria from multiplying.

Commerical probiotic products contain different strains of lactobacilli and bifidobacteria that have different benefits. For example, Lactobacillus acidophilus is thought to help with skin issues like acne, vaginal health and diarrhoea where Lactobacillus plantarum is included for its potential anti-inflammatory effects.

Are probiotics safe to take?

The NHS notes that if you have a healthy immune system then it is safe to take probiotics.15

Note that because the majority of probiotics are sold as a food product rather than as a medicine, they are not as tightly regulated. For this reason you should always buy your probiotics from a company that you trust to ensure they are properly manufactured and tested.

A properly manufactured probiotic will contain only the selected helpful strains, and there should be a mechanism to ensure that enough can survive in the digestive system to produce the desired effect.

Different probiotics contain different strains of bacteria. A probiotic that helps with one issue may not help with others, and trying a completely different probiotic may help you where your previous brand had no effect.

How long should it take your probiotic to work?

The most important thing is to follow the directions given by your chosen probiotic.

How long you take a probiotic will probably depend on why you’re taking it and the strength of the particular product. People taking it to aid with diarrhoea are likely to see results much sooner than those looking to simply improve general health.

Further research is needed to understand whether there is an optimal length of time to take a probiotic. Note that there is currently no evidence that long term use causes harm.

You will need to store you probiotic properly to ensure that the microbes are not damaged before you take them. You should also take them before the use by date.

The best probiotics – what to look out for

Different probiotics on the market will have a whole range of effects because they contain different strains of microbe. Note that because most probiotics are sold as a food product rather than a medicine they are not as tightly regulated. For this reason you should always buy your probiotics from a company that you trust to increase the chances that the probiotic will work for you.

There are three especially important considerations when choosing a probiotic:

  • the product needs to contain enough bacteria to have an effect.
  • the bacteria must be able to survive long enough to reach your gut or they will have no effect (intestinal survivability).
  • Since ensuring that you get a variety of microbes is more important than getting a large number of a single variety, you should look for a probiotic supplement that contains multiple strains.

Note that even the best probiotic won’t work for everyone because each person’s microbiome is different. You will need the right strain in the right dose for the right effect. However, you can improve your chances of a positive result by choosing a good-quality product and taking it correctly.


  2. Guthrie L. Gupta S. Daily J. & Kelly L. Effects of regulating intestinal microbiota on anxiety symptoms: A systematic review. npj Biofilms and Microbiomes. Volume 3, Article number: 27 (2017).
  3. Yang B, Wei J, Ju P, et alEffects of regulating intestinal microbiota on anxiety symptoms: A systematic review. General Psychiatry 2019;32:e100056. doi: 10.1136/gpsych-2019-100056.
  4. Tang WH, Kitai T, Hazen SL. Gut Microbiota in Cardiovascular Health and Disease. Circ Res. 2017;120(7):1183–1196. doi:10.1161/CIRCRESAHA.117.309715.
  5. Ottosson F. et al. Connection Between BMI-Related Plasma Metabolite Profile and Gut Microbiota. J Clin Endocrinol Metab. 2018 Apr 1;103(4):1491-1501. doi: 10.1210/jc.2017-02114.
  6. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480–484. doi:10.1038/nature07540.
  7. Kawabata K, Yoshioka Y, Terao J. Role of Intestinal Microbiota in the Bioavailability and Physiological Functions of Dietary Polyphenols. Molecules. 2019 Jan 21;24(2). pii: E370. doi: 10.3390/molecules24020370
  9. Clarke SF et al. Exercise and associated dietary extremes impact on gut microbial diversity. Gut. 2014 Dec;63(12):1913-20. doi: 10.1136/gutjnl-2013-306541.
  11. Karl JP, Hatch AM, Arcidiacono SM, et al. Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota. Front Microbiol. 2018;9:2013. Published 2018 Sep 11. doi:10.3389/fmicb.2018.02013.
  12. Palmnäs MS, Cowan TE, Bomhof MR, et al. Low-dose aspartame consumption differentially affects gut microbiota-host metabolic interactions in the diet-induced obese rat. PLoS One. 2014;9(10):e109841. Published 2014 Oct 14. doi:10.1371/journal.pone.0109841.