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Building your biome: how to recover from antibiotics and stay healthy

For most of us, the word ‘germ’ is still synonymous with ‘dirty’, ‘dangerous’ – something to be avoided and, if possible, eradicated.

We now know this idea to be outdated and simplistic. There are more microbes living on your hand than people in the world, and these vast populations – known collectively as the human ‘microbiome’ – have a crucial impact on overall health that we are only just beginning to understand.

In addition to the microbes living on us, inside every human cell are pockets of bacterial DNA called mitochondria – the functions of which are incredibly important for cellular energy production and immune regulation.

The problem with antibiotics

Antibiotics have been a painful lesson for medicine, as killing the bad bugs also means killing the good ones. Like a bomb going off in a shopping centre, antibiotics do not differentiate between lone-wolf attackers and law-abiding citizens.

A single week-long course can alter your gut microbiome for up to a year (1). Antimicrobial resistance is so widespread that a “post-antibiotic era” where minor injuries and infections can kill is “far from an apocalyptic fantasy” (2).

As well as avoiding them unless absolutely necessary, there are a few simple things you can do after taking antibiotics to re-build your microbiome and boost your overall immunity.


Start by feeding your ‘good’ gut bacteria with prebiotic fibre. Slippery elm powder is a great soothing prebiotic and anti-inflammatory for the gut – take one heaped teaspoon in warm water twice daily.

Prebiotic foods like onion, leek, asparagus and artichoke will help to increase gut biodiversity, and eating a varied, whole food diet high in fruit and vegetables is a must – ideally 8-10 servings per day.


Get yourself a good multi-strain probiotic supplement from your nearest health shop. These beneficial bacteria help to repopulate the gut, and taking probiotics during as well as after antibiotics may prevent the disruption to gut biodiversity altogether (3).


Natural anti-microbials gently remove ‘bad’ bacteria from the gut without damaging the overall balance of microflora. Swallow a small clove of garlic whole twice a day, and take bitter herbs like barberry, artichoke leaf or milk thistle to kill off bad bugs whilst supporting the liver – the organ that suffers most from continued antibiotic use.

Take antimicrobials on different days to your probiotics. Alternate between the two (3-4 days each) for 6 to 8 weeks to give your intestines a real spring clean, whilst avoiding sugar and refined carbohydrates.

A holistic approach to immunity

A contented mind leads to a contented body – keeping happy, active and de-stressed is as important as eating good food. Rest and good sleep is also essential after illness as it gives your mitochondria a chance to recover.

Becoming more resistant to infection is a gradual process, but one thing is clear – once you have built up your immunity, there is no going back.

1. Zaura et al. (2015) Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term microbial shifts in feces. mBio 6(6):e01693-15
2. WHO (2014) Antimicrobial resistance: global report on surveillance 2014. ISBN: 978 92 4 156474 8
3. Madden et al. (2005) Effect of probiotics on preventing disruption of the intestinal microflora following antibiotic therapy: A double-blind, placebo-controlled pilot study. International Immunopharmacology, Volume 5, Issue 6, Pages 1091-1097

By Poppy Burr
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Poppy Burr, BSc MCPP, is a qualified medical herbalist practising from Aljezur & Praia da Luz. To book a consultation, email [email protected] or call on 282 994 237.

Photo: Illustration by Tom Bund