We all take for granted that if we have a serious infection, antibiotics will come to the rescue. But it’s actually less than a century since the first antibiotic, penicillin, was discovered almost by accident by Alexander Fleming in a London hospital.
This discovery revolutionised the treatment of infectious diseases, which until then had been the single biggest cause of death. The world entered a golden era of antibiotics, where surgery, childbirth and even pneumonia became less feared.
But antibiotics are used to kill harmful bacteria – and these bacteria have fought back. In recent years, we have become all too aware of the rise of antibiotic resistance – where bacteria have evolved to become resistant to the effect of one, two or even several antibiotics.
What’s more, antibiotics can wreak havoc with your gut microbiome – the vast community of bacteria that live in your gut. Antibiotics can be life-savers – but you don’t want to take them unless you really need them.
Why does antibiotic prescribing increase in winter?
It’s hardly surprising that about 8 in 10 prescriptions for antibiotics come from your GP. Quite simply, general practice sees more sick people, with about 370 million appointments a year compared to a maximum of 104 million outpatient appointments yearly in the hospital setting.
Almost half (46%) of antibiotics prescribed in primary care a decade ago were for respiratory tract infections, including tonsillitis, bronchitis, coughs and pneumonia. The second most common reason for prescribing antibiotics is urinary tract infections, which account for under a quarter (22.7%).
In the last decade, prescribing rates for general practice have come down. More patients and doctors now understand that antibiotics are useless against virus infections and that people recover just as quickly from minor coughs without antibiotics. Doctors in primary care usually see more patients with less serious infections. These are more often caused by virus infections, which means prescribing has dropped faster in general practice than in hospitals.
But there are still big seasonal variations, with prescribing much higher in winter – hardly surprising when sore throats, coughs and colds, as well as pneumonia, are so much more common at this time of year.
How do you know when you need antibiotics?
There are dozens of different types of bacterial infection, affecting all different parts of the body. Sepsis is the most life-threatening, when a bacterial infection spreads throughout your body. As an adult, you should always seek emergency medical help if you develop:
- Confusion, slurred speech or significant drowsiness
- Blue, grey, pale, mottled or blotchy skin, lips or tongue
- A rash that doesn’t fade when you press a glass against it
- Extreme shivering
- High fever but cold hands and feet
- Severe muscle pain
- Not passing urine for a whole day
- Severe shortness of breath
- Feeling extremely unwell - including the feeling like you're going to die
If you have asthma, the chronic lung condition COPD or bronchiectasis, your doctor may advise you to seek help at the first signs of a chest infection. Likewise, if your immune system is suppressed (for instance due to cancer, cancer treatment or other medicines that can damp down your immune system system), you should speak to a doctor early.
If you’re otherwise well and have a dry, tickly cough or a mild sore throat that doesn’t stop you from powering on through, it’s highly unlikely antibiotics will help. If, on the other hand, you should definitely seek medical help if your cough is accompanied by:
- Shortness of breath
- High fever
- Chest pain
- Wheezing when you breathe
- Coughing up rust-coloured or bloodstained sputum
- Confusion
For other infections, check NHS 111 online – you can go through a checklist which tells you whether you need antibiotics and/or a medical consultation.
What do antibiotics do to your gut?
The trillions of bacteria that live in your gut – called your gut microbiome – live in a delicate balance. Antibiotics wipe out many of these bacteria – including the healthy ones – leading to an imbalance called dysbiosis. Since your gut microbiome has a huge impact way beyond your gut – including on your risk of heart disease, type 2 diabetes, liver problems, inflammation and your ability to fight off infection – this matters.
Killing off many of the health bacteria that make up your microbiome also makes it easier for some really nasty bacteria – such as clostridioides difficile – to take hold. Infection with C. difficile is uncommon but can be very severe, and it’s usually down to antibiotic use. The bacterium produces toxins that damage your large bowel, and can give rise to severe diarrhoea, fever and tummy pain.
In the past, it was common to prescribe ‘broad spectrum antibiotics’ such as doxycycline, ampicillin, ciprofloxacin and azithromycin, because these worked against a wider selection of bacteria. However, they also carry a higher risk of spreading antibiotic resistance, as well as killing off more of your natural gut microbiome. That’s why if your doctor does need to prescribe antibiotics, they’ll try to choose a narrow spectrum antibiotic that’s aimed at the type of infection you have.
How to support your gut during a course of antibiotics
If your doctor has prescribed antibiotics, that’s likely to be because you really need them. But while that means it’s important to take the whole course as advised, it’s also a very good idea to try and support your gut microbiome while you’re taking them and after you finish the course.
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Focus on fibre. Your gut can’t digest fibre, which is why eating more fibre means bigger, less hard poos. But your gut bacteria will feast on fibre, helping your microbiome to recover. Onions, garlic, leeks, Jerusalem artichokes, oats, soya beans, chicory root and bananas in particular contain inulin, which is a prebiotic fibre. This type of fibre is particularly good for feeding your good bacteria.
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Fermented foods. Many fermented foods contain good bacteria, which can top up your gut microbiome and help crowd out unhealthy bacteria. Examples include sauerkraut, kombucha, kefir, live yoghurt, tempeh and miso.
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Avoid alcohol, which makes you more prone to dysbiosis
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Crowd out ultra-processed foods. Hopefully if you’re focussing on the good stuff, you won’t have room for ultra-processed food anyway. But remember that ultra-processed foods (containing artificial additives, flavours and colours and often high in unrefined carbs) reduce the diversity of your gut microbiome.
Should you take a probiotic alongside antibiotics
One of the common side effects of antibiotics is diarrhoea, with up to 1 in 4 – possibly 1 in 3 - people on antibiotics developing this troublesome side effect. And although C difficile isn’t common, it’s something everyone wants to avoid if they can.
Given the damage antibiotics do to your gut microbiome, it makes sense that replenishing your gut with a supply of healthy bacteria should reduce the risk of antibiotic-associated diarrhoea and support your gut health. This is exactly what dozens of studies have found. In one review of 82 studies involving over 11,000 patients, taking probiotics during a course of antibiotic treatment cut the risk of diarrhoea by well over 1/3 (42%). Importantly, there were no side effects associated with taking the probiotics.
In summary
Antibiotics can be highly effective at treating serious bacterial infection, but they come at a cost. They can disrupt your gut microbiome, leading to diarrhoea of varying severity. What’s more, dysbiosis (an unhealthy balance in the gut microbiome) has been linked to a wide range of chronic health conditions, as well as a reduced ability to fight off infection.
Two in five prescriptions for antibiotics are issued for airways and throat infections, which are all more common in winter. Healthy changes to your diet, as well as taking a probiotic supplement, can all help support your gut health, reducing the risk of dysbiosis and with it the chance of unwanted side effects from antibiotics.
Sources
Clostridium difficile infection: review. Eur J Clin Microbiol Infect Dis. (2019). Link.
Antibiotics in primary care in England: which antibiotics are prescribed and for which conditions? Journal of Antimicrobial Chemotherapy. (2018). Link.
Key facts and figures about the NHS. The King’s Fund. (2025). Link.
Antibiotics and the gut microbiome: Understanding the impact on human health. Medicine in Microecology. (2024). Link.
Antibiotic prescribing trends in primary care 2014–2022. Research in Social and Administrative Pharmacy. (2023). Link.
Cough (acute): antimicrobial prescribing. NICE. (2019). Link.
Prescribing an antibiotic? Pair it with probiotics. J Fam Pract. (2013). Link.
English surveillance programme for antimicrobial utilisation and resistance (ESPAUR). UK Health Security Agency. (2023). Link.
English surveillance programme for antimicrobial utilisation and resistance (ESPAUR) report. UK Health Security Agency. (2024). Link.
Use of antibiotic and prevalence of antibiotic-associated diarrhoea in-patients with spinal cord injuries: a UK national spinal injury centre experience. Spinal Cord. (2017). Link.
