Minimising The Impact Of Antibiotics On Our Beneficial Microbes


Sneaky Peek

What can we do to support our gut microbiome when we have to take antibiotics? There is a great deal we can do to take advantage of the fantastic power of antibiotics, whilst at the same time minimising the detrimental effects they can have on our gut microbiome. Here are some ideas.


Sometimes, antibiotics are unavoidable, necessary, vital. But it always helps to keep in mind the bigger picture in terms of our health when deciding whether to take them. Broad spectrum antibiotics are indiscriminate about the bacteria they kill and we know that, whilst some people’s gut microbiomes bounce back quickly, others can take months or even years to recover from a course of antibiotics (this is especially true in the young and the old, who tend to have less resilient microbiomes). And in the immediate aftermath of a course of antibiotics, it appears that rapid-growing pathogens may take advantage of the lack of competition. This is why, sometimes, having taken a course of antibiotics, we then have a run of illnesses. I once went from antibiotics for repeated mastitis to an ear infection, a gum infection capped off by a bladder infection – clearly run down after the birth of my young son.

Remember, the issue with antibiotics is not use, it is overuse. Sometimes, pulling back on the microscope to take in the panoramic view of our situation, means we realise that antibiotics are the best health choice. Sometimes, though, taking the mental space to look at the situation in the round enables us to see that antibiotics may actually exacerbate our health issues rather than being some sort of magic bullet. Read about one woman’s story about the challenges of such a choice.

If we do need to take them though, there are things we can do to minimise their impact on our gut microbime.

Firstly, and most importantly, antibiotics don’t work on viruses. Never take antibiotics if you have a virus.

Assuming we suspect a bacterial infection, we can, where appropriate, ask for a swab or sample to be taken and tested. This may enable the doctor to prescribe a narrow spectrum antibiotic rather than a broad spectrum one. As the name suggests, broad spectrum antibiotics will kill a broad range of species within us, whereas narrow spectrum are much more focussed weapons. If the doctor will swab/sample and we can wait for the result, this may result in more directed, more effective and generally less damaging antibiotic use. We will be more likely to be able to target the bacteria causing the problem as opposed to taking out the whole ecosystem.

The fact that we have a bacterial infection may suggest we are run down and vulnerable healthwise. Popping pills without generally trying to support our health often results in being unable to shift the illness or suffering a recurrence within a few days or weeks of the end of the course of antibiotics. I have seen this happen in my family more times than I care to mention.

Adequate sleep is fantastically restorative when we are unwell. It can take real determination to structure our day to ensure we get enough of it, but when we are ill, this is especially important.

Diversity in our diet encourages diversity in our micobial community and scientists believe that microbial diversity is crucial for health, so eating as wide a range of whole, unprocessed foods as possible will help to repopulate our gut with a good range of bacteria. Try to introduce new foods and keep eating them. Having said that, if I feel ill and have no appetite, the best thing I can possibly do is listen to that message and fast.

Fasting whilst ill if I have no appetite is a great way of letting my body use its energy to fight the infection rather than having to digest food. As a family, we often take fluids only when we are poorly. Normally, this only lasts for 24 or 48 hours though – longer than that and I would be concerned.

Opening windows is very important too – this ensures we have fresh air so that the bacteria that we breathe in and out in the air around us gets replaced regularly by a fresh influx. If it feels right, sleep with the window open too.

These behaviour changes are a struggle. It is a challenge to make caring for ourselves a priority in a society where being busy is a status symbol. But it is lunacy, really, to think that we are too busy to care for ourselves. Remember, it is like being on a plane – we have to put our oxygen mask on first before we can help others.



Probiotics are a useful counter-measure to the bacterial decimation caused by antibiotics. Probiotics are the opposite of antibiotics – they add bacteria for health instead of killing bacteria to regain health. VSL3 and Symprove are pretty much the most researched and tested probiotics on the market at the moment. VSL3 is a powder that can be sprinkled on food or in drinks. Symprove is a liquid (and is an acquired taste!). These makes of probiotics are expensive but well respected and recommended by the medical profession. They help to repopulate our gut with beneficial microbes. If our situation doesn’t warrant this financial outlay, I tend to use Culturelle, Optibac, Bio-Kult or Probiotic Plus (Nutri). We try to listen to our bodies and either rotate types or stick to one – there is no one size fits all with probiotics (with anything healthwise in truth) – we are all individual and have our own unique microbiome, so it is trial and error to some extent.

Really, though, I prefer consuming probiotic drinks and foods to repopulate after antibiotics (we consume them all the time, not just when we are ill) – yoghurts with live cultures in them (Yeo Valley, Brown Cow, Total Greek Yoghurt), raw cheeses (Manchego, Reblochon, Parmesan, Gruyere) raw butter (Isigny sur Mer) fermented vegetables such as sauerkraut and kimchi (just ensure that they are fermented with live bacteria and not pickled in vinegar!). But most of all, I swear by my milk kefir. Milk kefir contains 30-50 strains of beneficial lactobacillus and bifidobacteria. If you can’t face making it (which is a very cheap and simple way of getting a constant supply of probiotics), you can buy it in most health food shops now. Be aware, though, that this may not agree with some people – especially those with bowel issues, so start with small amounts to test it out first. Here's my recipe for milk kefir



Eating prebiotic foods, which are foods that selectively encourage the growth of our beneficial bacteria, will help repopulate our gut- whole grains, beans, asparagus, onions,  garlic, leek, endive, artichokes – both globe and jerusalem, bananas (green ones).

Reducing our consumption of sugary foods and drinks and refined foods as much as possible will help too. Sugar supresses the activity of the immune system, which is the last thing we need when we are under the weather.


Vitamin C

Vitamin C, on the other hand, is needed by our immune system in order to function well. Taking a good vitamin C supplement is a great idea when we are ill. Pukka Herbs do a good Vitamin C capsule which is made from naturally-occurring sources. But when one of us is really poorly or on antibiotics, we use Biocare’s Magnesium Ascorbate Powder for a few days as it enables us to take Vitamin C in high doses. Vitamin C is water soluble so it is not possible to overdose on it. If you do, you will just get the runs.



Finally – stress. We know that many illnesses are correlated with inflammation and we also know that the hormone, cortisol, which is an integral part of our hard-wired stress response, causes inflammation. Gut inflammation changes the microbial weather in our gut so avoiding stress, if at all possible when we are ill and attacking our microbes with antibiotics, is a good idea. Again, achieving this involves changing our attitude and daily practices – prioritising rest and relaxation, incorporating mindfulness practice to our day, consistently. Recognising the importance of hobbies and interests outside of the daily grind is crucial too. Hmmm, I continue to work on this area.

Wondergut Wisdom

Remember, antibiotics have unintended effects as well as intended ones.

Ask yourself honesetly, do I need antibiotics or do I need to make some changes around stress, diet, exercise, sleep?

Don't be afraid to take antibiotics if they are genuinely necessary (ideally as evidenced by a swab or test - if there is time). But do what you can to support your body to recover from them.


Spreading straightforward information about the fundamental importance of a healthy gut microbiome.