How antibiotics can ’scar’ your gut microbiome

How antibiotics can ’scar’ your gut microbiome

Antibiotics can have a severely detrimental effect on your gut, depending upon how strong your microbiome is at the outset; lowering good (commensal) bacteria, increasing pathogens, and prompting increased levels of antibiotic and drug resistance.


We have long believed this to be true, but now there’s some serious science.

Just a single course of antibiotics can alter the gut microbiome of a healthy person and it can then take months or even years to recover the volume and diversity of the species.

Antibiotics and your microbiome - much more serious than previously thought

Back in 2018 there we covered research from Memorial Sloan Kettering, where people had 2 drugs, for 4 rounds; then a stem cell transplant, with antibiotics for one month. Just over half of the participants had a fecal transplant from their own stored stools, and this took their microbiome back above 75% of normal healthy levels within a few days. The other participants just followed ‘Standard of care’ and one year later, their microbiome was still just 27% of that of a healthy person (1). 

In 2021 we covered research (2) from the South Australian Health and Medical Research Institute that chemotherapy drugs destroyed the gut microbiome, altering volume and diversity with a reduction in commensal (good) bacteria e.g. Firmicutes, but an increase in gram negative bacteria, Bacteroidetes and Proteobacteria. Basically, this means that when a patient is trying to recover after the chemotherapy and continue to fight cancer, their gut microbiome is helping them less than it was before the chemotherapy and antibiotics. 

As yet, there is no research to detail to what degree outcomes and survival times might suffer. But the first clues may come from recent research on antibiotics.

How antibiotics can promote illness

Francisco Guarner, a digestive system researcher at the University Hospital Vall d’Hebron in Barcelona, has described the gut microbiome as an ecosystem that is perturbed by antibiotics in much the same way as other drugs. He summarised recent studies, "When you take antibiotics, some bacteria in the network disappear, while others overgrow, so the balance is different. Also in this new balance, what you gain are bacteria that are more resistant to antibiotics.” 

Infections caused by antibiotic resistant bacteria are serious. They are known to pose a threat to life. What is now known is that everybody has antibiotic-resistant genes in their gut microbiome. That per se is not a problem. We've come to live with them. But, it becomes a serious problem when the pathogens (the bad bacteria) become antibiotic-resistant - that's when the real problems set in. Recent research (3) from Birmingham, England, showed that, in a gut weakened by antibiotics, antibiotic-resistant genes, which can actually spread by 'Horizontal Gene Transfer', (HGT), are more likely to do so.

No one here is saying that you should not take antibiotics. Just be more careful in your decisions. What we are looking at is how you can get a chain-reaction to them - drugs and/or antibiotics potentially reduce the volume of the microbiome and lower the number of good species; this causes more pathogenic species (as there are less good keeping them in check); and these pathogens may then gain antibiotic resistance. This could clearly promote illness - all in someone who is trying to get better and beat their illness.

Pathogens and Antibiotic- and Drug-Resistance

A little under 5 million deaths across the world in 2019 were associated with this phenomenon (4).  Scientists even know the 6 top pathogens that have gained antibiotic or drug resistance - E coli, Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae,  Pseudomonas aeruginosa and Acinetobacter baumannii.

No such thing as a safe antibiotic - 'Antibiotic scarring'

Research from Sloan Kettering is now showing (5) that good normally healthy bacteria following antibiotics, can pick up antibiotic-resistant genes (ARGs) and these new rogues even help to destroy the antibiotics, further protecting the pathogens! There's no such thing as a safe antibiotic, it's delusional thinking.

Now, the antibiotics are potentially helping your enemies by providing another line of defence. How many times have we heard of patients taking further rounds of antibiotics because their infection came back?

Of course, no one takes an antibiotic if they are well, although we do know that, in the UK, approximately 50% of antibiotics are prescribed for infections they cannot treat (e.g. viral infections such as colds, coughs, flu). WebMD lists the top 5 generic antibiotics as amoxicillin, doxycyclin, cephalexin, ciprofloxacin and clindamycin.

The fact is that people who take antibiotics and/or drugs almost certainly have an issue in their microbiome before the treatment. But.

Another new study (6) where people were separated into four distinct groups, showed that antibiotics affected different people differently, and this may have been due to the strength of the microbiome before taking the antibiotics.

Unfortunately, even after a short spell of antibiotics, the microbiome could still be seriously disturbed in some people 6 months later - three people in the study were described as having a microbiome similar to patients in an ICU, after 6 months! The researchers called it 'antibiotic scarring'! 

In summary, the researchers said that antibiotics can have a major detrimental effect on the microbiome. People are cautioned from taking antibiotics unless they are sure the benefits outweigh the risks and they are certain they have a bacterial infection.

Cancer patients should remember that the US 'Human Microbiome Project' was very clear: 'You gut gets ill first, then you get ill'. And, 'You can't get better until your gut gets better'. Some chap called Hippocrates said much the same thing 2500 years ago, but he did have any research.

Go to: Heal your gut, heal your body




  1. Fecal transplants restore gut microbes after antibiotics; Drs. Ying Taur, Eric Pamer, and Joao Xavier, Science Translational Medicine on September 26, 2018.

  2. Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome; Lito E. Papanicolas, Sarah K. Sims, Steven L. Taylor, Sophie J. Miller, Christos S. Karapetis, Steve L. Wesselingh, David L. Gordon & Geraint B. Rogers; BMC Cancer volume 21, Article number: 591 (2021) 

  3. Horizontal transfer of antibiotic resistance genes in the human gut microbiome; Ross S. McInnes, Gregory E. McCallum, Lisa E. Lamberte, Willem van Schaik;  Current Opinion in Microbiology Vol 53; February 2020, Pages 35-43

  4. Global burden of bacterial antimicrobial resistance in 2019; the Lancet, vol 399, Jan 19 2022

  5. Antibiotic Degradation by Commensal Microbes Shields Pathogens; Mergim Gjonbalaj, James W. Keith, Mytrang H. D, Tobias M. Hohl, Eric G. Pamer, and Simone Becattini; Infect Immun; 2020 Apr; 88(4)

  6. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults;Winston E Anthony et al;   Cell Reports; Volume 39, Issue 2, 110649, April 12 2022



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