Your gut is home to thousands of species of bacteria. Most are harmless or helpful, supporting digestion, the immune system and the production of certain vitamins. A smaller number can cause illness when they grow too numerous or turn up where they should not be. Good gut health depends on keeping the helpful species ahead. This guide covers the main types of good and bad gut bacteria, what each does, and what research shows about increasing the good ones.
What is gut bacteria?
Gut bacteria are the microorganisms living in your digestive system, mostly in the large intestine, alongside fungi and viruses. Together they make up your gut microbiome. The exact mix is different for every person, and the species within it compete constantly for food and space.
Species that support digestion, nutrient absorption and the immune system are usually called beneficial, or simply good, bacteria. Species that can cause infections or unpleasant symptoms when their numbers grow are called harmful, or bad, bacteria. Most of the time the beneficial species keep the harmful ones in check by outcompeting them for the available food.
When that balance tips, through illness, a course of antibiotics or a poor diet, harmful bacteria can gain ground. This is one form of gut dysbiosis, an imbalance of gut bacteria that can also involve too few beneficial microbes or a loss of variety overall, and it comes with its own set of symptoms and causes.
Why is gut bacteria important?
Gut bacteria help train your immune system. From early life, contact with these microbes teaches immune cells to tell everyday material apart from genuine threats, and the compounds the bacteria release help keep inflammation under control, as described in a 2016 review in Nature Reviews Immunology.
They also digest what your own body cannot. Beneficial gut bacteria ferment dietary fibre into short-chain fatty acids, compounds that supply energy to the cells lining your gut and influence health well beyond it, according to a 2016 review in Cell. Partly through processes like this, a well-balanced gut microbiome is associated with a lower risk of several long-term conditions.
Some gut bacteria also make nutrients directly. A 2013 review describes how species in the gut produce vitamin K and B-group vitamins, including folate and vitamin B12, and beneficial bacteria more broadly help your body synthesise and absorb essential vitamins and minerals.
Research also connects gut bacteria with the brain, a relationship known as the gut-brain axis. A large 2021 analysis from King's College London, pooling 59 studies, reported that the mix of gut bacteria in people with depression or anxiety differs from the mix in people without, with the anti-inflammatory types in shorter supply. Studies like this cannot show whether the bacteria change before the illness or because of it, and no change to your gut bacteria treats a mental health problem. Anyone struggling with their mood should talk to a GP, and NHS talking therapies accept self-referrals in England.
What is bad bacteria in the gut called?
Harmful gut bacteria are usually called pathogenic bacteria, or informally bad bacteria or bad bugs. Well-known examples include Salmonella, certain types of Escherichia coli and Clostridium difficile. Most cause problems only when they become too numerous or invade parts of the body where they should not be.
Types of good gut bacteria
The two best-known groups of beneficial gut bacteria are Bifidobacterium and Lactobacillus. According to a 2016 review, most of the bacterial strains used in live-culture products belong to these two groups, which is why their names appear on so many supplement and yoghurt labels.
Lactobacillus. Found mainly in the small intestine, these bacteria help digest lactose, the sugar in milk, and produce lactic acid. Lactic acid keeps their surroundings slightly acidic, which makes it harder for harmful bacteria to grow.
Bifidobacterium. Found mainly in the colon, these bacteria ferment dietary fibre into short-chain fatty acids. A 2016 review notes they are among the first bacteria to colonise the gut after birth and are consistently linked with good gut health.
These two groups get most of the attention, but a healthy gut relies on a much wider cast of species working together, most of which never appear on a supplement label. What the beneficial species have in common is that they feed on fibre and crowd out the harmful kinds.
There is a connection with your skin too. A 2021 review found that an imbalanced gut microbiome is associated with skin conditions including eczema, acne and psoriasis, and that Lactobacillus and Bifidobacterium play an important role in skin health.
Types of bad gut bacteria
Bad gut bacteria, while sometimes present in small numbers without causing harm, cause problems when they overpopulate or when the balance of the wider gut microbiome is disturbed. Some include the following.
- Helicobacter pylori, also known as H. pylori. It can live in the stomach without causing symptoms, but it can cause ulcers and has been linked to increasing the risk of stomach cancer.
- Clostridium difficile. This often takes hold after a course of antibiotics has cleared out the bacteria that normally keep it in check. It releases toxins that cause symptoms ranging from diarrhoea to life-threatening inflammation of the colon.
- Pathogenic Escherichia coli. Many E. coli strains are harmless residents of the gut, but some, such as E. coli O157:H7, cause food poisoning, urinary tract infections and other illnesses. In young children, older people and anyone with a weakened immune system, these infections can be serious.
These bacteria are considered harmful because they cause symptoms directly and can disturb the wider balance of your gut bacteria, contributing to poor gut health.
When should you see a GP?
Most everyday digestive upset settles on its own and does not point to a serious infection. See your GP if you have diarrhoea lasting more than seven days, blood in your stool, a fever alongside gut symptoms, severe stomach pain, or symptoms that began during or after travel abroad. Also book an appointment if you have lost weight without trying, if your usual bowel habit has been different for more than three weeks, or if persistent gut symptoms are new and you are over 50. If you have recently taken antibiotics and develop watery diarrhoea that keeps returning, tell your GP, because this can be a sign of a C. difficile infection that needs treatment.
How to starve bad gut bacteria
Starving bad gut bacteria means limiting the foods they thrive on while feeding the species that keep them in check, so most of the work is done through diet. Cutting down on sugar and heavily processed foods removes the easy fuel, and building meals around whole foods gives the advantage back to the beneficial species.
Fibre is the biggest lever. Most UK adults eat around 20g of fibre a day against the NHS recommendation of 30g. That gap matters beyond the gut itself. In a 2019 analysis of 185 studies published in The Lancet, people who ate the most fibre had a 15-30% lower risk of heart disease, type 2 diabetes and bowel cancer than people who ate the least.
Antibiotics kill helpful bacteria along with the ones they are prescribed for. That is not a reason to avoid or cut short a course your GP has prescribed; taking it exactly as directed matters more. Our guide on what antibiotics do to your gut microbiome explains what happens during a course and how the gut recovers afterwards.
How to increase good gut bacteria
Diet and lifestyle changes are the most reliable way to increase good gut bacteria, and none of them needs a supplement.
- Eat a wide variety of plants. A 2018 study of gut samples from more than 10,000 people found that the variety of plants in a person's diet was closely tied to the variety of bacteria in their gut. Vegetables, fruit, whole grains, beans, nuts and seeds all count.
- Add fermented foods that contain live cultures. Yoghurt, kefir, sauerkraut and kimchi are the everyday examples. In a small Stanford trial published in 2021, 36 adults followed either a high-fibre or a high-fermented-food diet for 17 weeks; those eating fermented foods finished with a broader mix of gut bacteria and lower levels of several inflammation markers.
- Include foods that feed good bacteria. Garlic, onions, leeks, asparagus and slightly under-ripe bananas all carry the kinds of fibre beneficial species ferment. Our separate guide explains the difference between Probiotics and Prebiotics and which foods count as each.
- Keep moving. In a 2018 study, 32 adults who took up six weeks of endurance exercise showed measurable changes in the mix of their gut bacteria, and the changes faded once they stopped, which suggests regular activity matters more than any single burst.
- Protect your sleep. A small 2019 study found that people with a more varied gut microbiome slept longer and woke less often during the night, although a correlation like this cannot prove the bacteria are responsible. Aiming for 7-8 hours is a sensible target.
Understanding which foods are good for gut health makes these changes easier to keep up over the long term.
Can a gut microbiome test tell me which bacteria I have?
Yes. A gut microbiome test analyses a stool sample to identify the bacteria present in your gut and how the mix compares with a healthy balance. Feel Gut's test uses shotgun metagenomic sequencing, which reads the DNA in the sample to profile thousands of bacterial species, beneficial and harmful.
A test on its own does not diagnose any illness. It shows which bacteria you carry and whether the balance leans the right way, and results include guidance on what the findings mean and where diet could help. A gut parasite test looks for specific disease-causing organisms instead, covering a number of pathogenic bacteria as well as viruses and parasites.
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