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There comes a time in most of our lives when we’re advised to take antibiotics, which can wipe out good bacteria in your gut as well as bad. Here’s how to restore the balance.

You may be a kefir, kombucha or kimchi convert, but one sure-fire way to disturb your microbiome – gut health devotee or not – is to take a course of antibiotics. They might be life-saving drugs that have revolutionised medicine, but it’s an undeniable fact that antibiotics can do unintentional damage to our guts. And that’s because antibiotics are designed to kill bacteria – all bacteria. 

“There are many kinds of bacteria; some cause disease (pathogens) that we developed antibiotics to kill and thousands of others that are either beneficial or benign to our health,” explains Professor Jack Gilbert, soma peoria il hours award-winning microbiome scientist at the University of California San Diego. 

“The immune system is like a gardener trying to get rid of the weeds (pathogens) and keep the good vegetable and fruit plants growing (beneficial bacteria). But antibiotics don’t discriminate, so they wipe out a lot of the good bugs.”

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Antibiotics can wreak havoc on our guts – especially if you don’t finish the course

Obliterating that good bacteria can have some unwelcome effects. “Not all the good guys repopulate after the course of antibiotics,” explains Jo Cunningham, registered dietitian and clinical director at The Gut Health Clinic. “This can lead to diarrhoea, bloating, abdominal pain, and fatigue.” 

A totally decimated system can have further issues, according to Dr Jenna Macciochi, immunologist and author of Your Blueprint for Strong Immunity. “The downstream impact can include anything from metabolic shifts and (weakened) body barriers like the gut, lung, skin, to the colonisation of bad bacteria – which risks antibiotic resistance.” 

You might be well into your kimchi, but a course of antibiotics can wipe your gut bacteria nonetheless.

That’s not to say you should refuse to take them if your GP advises you to take a course, but Cunningham stresses that it’s always worth discussing with your GP whether they’re absolutely necessary. When they are, take them as directed and always complete the course. If you don’t, Gilbert says: “Pathogens can replicate so fast that new mutations in their genome arise and they can become resistant to antibiotics.”

How to rebuild your gut health after antibiotics

Take the right kinds of probiotics and time them around the antibiotic

You might assume that taking high-strength probiotics would be the best course of action, but the experts we spoke to say the jury is still out over the efficacy and safety of super gut-feeders. 

“There’s some evidence that probiotics may be helpful in preventing diarrhoea and other uncomfortable digestive symptoms, but they may not necessarily help us recover gut microbes that have been killed off by the antibiotics,” says Dr Macciochi.

“In fact, one small study suggested probiotics could slow the recovery of your microbiome.” Dr Macciochi does, however, recommend that people take a targeted strain during and after antibiotics, unless they have a medical reason not to (like inflammatory bowel disease). 

She suggests taking something like lactobacillus rhamnosus GG or saccharomyces boulardii twice a day in between food while on antibiotics and for the 10 days after the course has finished. Take them a few hours after popping the antibiotics “so you don’t cancel them out”, says Professor Tim Spector, author of Spoon Fed and co-founder of ZOE, the personalised nutrition company. 

Cunningham also suggests the research supports these strains, explaining that “not all probiotics have been shown to survive if taken alongside an antibiotic, so the right strain is important to not only see an effect but also to save you wasting money.”

Those strains do have evidence behind them, but rather than popping pills or necking formulated drinks, you should focus on your diet because, as Dr Macciochi puts it: “Throwing probiotics in without also fertilising with the right food is a bit like trying to grow seeds without the soil.” 

Choose plants over pills if you’re after long-term effects

Each of the good ‘bugs’ in our microbiome has different needs and different functions – and food is the best way to support them. “Each microbe in the gut feeds off different types of plant chemicals (polyphenols), and each plant has hundreds of different chemicals in it, so variety is crucial,” Professor Spector tells Stylist

The key is to ensure that the plants you eat contain fibre, so they reach the lower part of the colon. “That’s why real food is better (than supplements),” he says.

Aim to eat 30 plants a week

The sweet spot is to aim to consume 30 types of plants a week. “Eat plenty of prebiotic fibre-filled plant foods”, says Dr Macciochi. They’ll feed the good bacteria you have already built up in your digestive system. Think:

  • Artichokes
  • Asparagus
  • Bananas
  • Berries
  • Garlic 
  • Green vegetables
  • Onions
  • Legumes (beans/peas)
  • Tomatoes 
  • Wholegrain cereals

“Aim for 30g of fibre per day and 30 different plant foods across a week – not just fruit and veg but also nuts, seeds, beans, pulses and herbs and spices,” continues Dr Macciochi. 

Find your fermented favourite

 “Finally, include fermented foods like sauerkraut, kimchi and kefir.” The reason those fermented foods – as well as sauerkraut and Greek yoghurt – are so useful is that, according to Professor Spector, “there are many more different species in fermented food than in probiotic tablets”. Ten billion of one strain sounds good, but isn’t as good as billions of different strains. 

Sleep and stress matter when it comes to rebuilding a strong gut

Of course, it’s not just antibiotics that can knock our guts off-kilter. Those all-important microbes are also impacted more generally by our body clock. “We’ve known for a long time that our gut microbiome is closely connected to our circadian rhythm,” says Professor Spector. “There’s evidence around eating within a time-restricted window of about eight-to-10 hours, to give it a clear break to repair the gut lining.” 

So, eat your dinner, then allow a ‘fast’ of at least eight hours until breakfast. That break reduces inflammation – too much of which can upset the balance of your gut because microbes that like living in inflammation crowd out the good bugs, producing more inflammation themselves and thereby starting a vicious cycle. It’s why it’s a good idea to reduce our intake of ‘pro-inflammatory foods’ like ultra-processed food, excess sugar and alcohol when taking antibiotics. It’s also a good idea to focus on getting good sleep, staying active and reducing stress.

How to tell if your gut is healing

Once you’ve put these principles in place, the next thing to know is when you’re on the right track. How are you supposed to know whether your gut’s repairing? 

“You should have reduced gastrointestinal issues and generally feel more energetic and clear-headed,” says Gilbert. Dr Macciochi adds that beyond this, more noticeable benefits should follow: “Over time, the positive effects will extend beyond your digestion and you may see other improvements in the appearance of skin and better mood.” 

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She also warns of another potential issue post-antibiotics – losing tolerance to dairy or other foods. “Continue eating a very small amount, slowly building up over time,” she advises. “Cutting out foods for good without a medical reason like a diagnosed allergy can worsen food intolerances.”

Because we have a totally personalised gut microbiome, recovery will be totally personal too. “We share 99.5% of our genes, but only about a quarter of our microbes – even in identical twins”, explains Professor Spector. Some people’s gut microbiota may be repopulated within days, for others weeks, but however long it takes “you can be sure that your microbes will be thanking you for feeding them,” says Cunningham. This is the best approach after a course of antibiotics, but it’s a blueprint for good gut health for life. 

Images: Getty

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