The Effects of Antibiotics On The Human Gut Microbiome

June 12, 2023 8 min read

The Effects of Antibiotics On The Human Gut Microbiome


This natural life preserving institution sees our internal gut ecosystem become engulfed with billions of tiny bacteria that will provide you with all you need to help you survive. This ranges from breaking down foods that by yourself would be impossible, to producing life sustaining nutrients that are delivered to every part of your body. This amazing feat of mother nature’s engineering is only overshadowed by the true miracle of life itself, yet by no fault of our own, in fact by hoping to extend or advance this amazing gift, man has created a potential disruptor or even destroyer of everything mother nature provided. This comes in the shape of the antibiotic.

Although responsible for the end to many illnesses and diseases, and alleviating absolute pain for many, which is pretty amazing, the antibiotic can also have a very detrimental effect on the human gut microbiome. Not wanting to give up on such a big gun in the battle against illness and disease, more needs to be understood about just how disruptive to us antibiotics can be.

Please join us and read on, as we discuss antibiotics as major disruptors of gut microbiota in this article.

Overview of the gut microbiota

The gut microbiome is a complex yet unique ecosystem residing in your gastrointestinal tract, but predominantly your colon. This abundant population of microorganisms, largely consisting of bacteria but also archaea, fungi, and protozoa, survive by maintaining what’s called a symbiotic relationship with its host, you[i]. That is, a mutually beneficial relationship. These tiny organisms rent a space in your gut by transforming otherwise undigestible foods into magical metabolites your body can use to thrive and survive.

What are antibiotics and how do they work?

Antibiotics are a mainstay of modern medicine, but they’re not as new as you might think. Moulds and plant extracts were used by ancient civilisations to treat infections, but it wasn’t until the early 20th century that antibiotics really became revolutionary. Before that, today’s easily treated infections, like diarrhoea and pneumonia, were the world’s most prolific killers.

The first modern antibiotic was discovered by the German physician, Paul Ehrlich, in 1909. He found that a chemical called arsphenamine was an effective treatment for syphilis. Ehrlich called this ‘chemotherapy’, as he had discovered a chemical that could treat disease. The term ‘antibiotic’ wasn’t used until 30 years later when the Ukranian-American microbiologist Selman Waksman, first used it, and who, incidentally, went on to discover more than 20 antibiotics in his lifetime[ii].

Of course, the most famous discovery is that of penicillin by Alexander Fleming, which has since saved many lives. But what exactly are antibiotics?

In short, antibiotics are medicines that kill or slow down the growth of pathogenic bacteria and prevent them spreading. Doctors most often prescribe them to treat bacterial infections, such as:

  • Chest infections
  • Ear, nose, or throat infections
  • Tooth or gum infections
  • Skin infections[iii]

However, as amazing as antibiotics are, they can also be problematic. For example, antibiotic resistance is a global problem for the medical profession. Simply taking antibiotics when you don’t need them can mean that they might not work for you in the future. That’s because bacteria can change and adapt in response to antibiotics, meaning they can resist their mechanism of action, continue to grow in the body and wreak havoc[iv].

Antibiotic resistance has become a major problem in recent decades, and it is perhaps no wonder, after global antibiotic use rocketed by 65% between 2000 and 2015[v]. Bacteria shouldn’t be underestimated. Despite their microscopic size, they’re pretty clever because they have developed a myriad of mechanisms to evade the effects of antibiotics. For example, the gut microbiota has a huge reservoir of antibiotic resistant genes, sometimes referred to as the gut resistome[vi].

When you take antibiotics, this reservoir of resistance genes increases in the gut but slowly reduces after treatment has finished. There is a risk of spreading antibiotic resistant bacteria from mother to newborns during birth. Every year, antibiotic resistance contributes to around 214,000 infant deaths. This further highlights the devastating impact antibiotic resistance has globally[vii].

What’s the difference between broad and narrow-spectrum antibiotics?

Broad spectrum antibiotics work on two major bacterial groups:

  1. Gram-positive
  2. Gram-negative

They are often effective when the infecting bacteria is unknown. That’s why you may have been prescribed antibiotics such as amoxicillin in the past.

Whereas narrow-spectrum antibiotics only target a few specific types of bacteria. So, Gram-positive or Gram-negative but not both.

Table 1.Examples of broad and narrow spectrum antibiotics.














The impact of antibiotics on the gut microbiota

Although the discovery of antibiotics was a medical breakthrough, antibiotic resistance has become a global burden. So much so, that a 2019 study published in The Lancet discovered that almost 1 million deaths were attributable to antimicrobial resistance across the world[viii]. That’s the most extreme end of the scale but even just one course of antibiotics is enough to perturb the composition of the gut microbiome[ix].

By taking antibiotics, particularly broad-spectrum types, it’s inevitable that the overall diversity of your microbiome will reduce and is likely to even lose some important species. This can have serious consequences for your gut health and can even contribute to antibiotic resistance. A persistent change or imbalance in the gut microbiome is called dysbiosis, and it not only affects the overall composition of this important ecosystem but also its function.

Many studies have identified a link between dysbiosis and the development of recurrent diarrhoea associated with Clostridioides difficile,irritable bowel disease, colorectal cancer, type 2 diabetes, and obesity[x].

Here, using the review by Ramirez et al. (2020) we’ll analyse the effects of antibiotics on the gut microbiota.

Reduced microbial diversity

Taking a course of antibiotics may reduce the abundance of some of the beneficial bacteria species residing in your gut. Some studies show that microbial diversity is restored in children after around 1 month, while in adults it can be up to 1.5 months. Yet, the same study by Palleja et al. (2018) found that nine common species were still absent after 180 days[xi].

The same study also revealed that a combination of antibiotics, including meropenem, gentamicin, and vancomycin lead to an increase in pathobionts or microorganisms, that in the right environment, can cause harm[xii], and a reduction in butyrate-producers. Butyrate is an important metabolite produced by certain gut bacteria. It’s known as a short-chain fatty acid, and is not only the main energy source for cells that line the gut, but also has numerous other benefits for your gut and wider health.

Equally, when you take a course of antibiotics, because the usual microbial diversity within your gut is disturbed, it increases your risk of infections, such as Clostridioides difficile.For example, some research shows that taking antibiotics means you are seven to ten times more likely to contract C. diffinfection[xiii]. That’s because antibiotics can kill off the good bacteria that protect you from illness and disease, allowing pathogenic species or antibiotic resistant ones to rise up and take over your gut empire. How long it takes for your gut to reset after antibiotic use will depend on a variety of factors but can be anywhere from one to six months.

Find out about the antipathogenic effect of HMOs in our blog.

Altered metabolome

Firstly, what is a metabolome?

A metabolome is a complete set of small-molecules found in a cell or biological sample. Although the effects of antibiotics on the gut metabolome are less researched than other areas, there are some studies in mice that show antibiotics increase the fatty tissue and metabolic hormones in the body[xiv].

Further studies have also found that treatment with cefoperazone, a medicine that belongs to the cephalosporin antibiotic family, increased bacterial substrates like sugar alcohols, bile acids, and carbohydrates[xv]. All of these promote the growth of Candida albicans,an opportunistic fungus that’s associated with a variety of infections.

Long term effects of antibiotics on the gut

As well as the more short-term effects, antibiotics can have long-term consequences for your gut, particularly in children. For example, frequent antibiotic use in children has been linked with the development of obesity, asthma, allergies, and IBD in adult life.

Human milk oligosaccharides (HMOs), however, can help to support the health of the gut microbiome and maintain a strong immune system, good brain function, and protect against pathogens. At Layer Origin, our SuperHMO® for Kids Powder is the perfect way to support your little one’s digestive and immune health.

How to support your gut health after antibiotics

Taking antibiotics is unavoidable at some point in our lifetime, but doing so, runs the risk of unbalancing our microbiome. As such, there are certain things you can do to help support the bacterial populations in your gut, such as:

  • Eat polyphenol-rich foods (berries, citrus fruits, olives, turmeric, pomegranate, green tea)
  • Add resistant starch to your diet (cooked and cooled potatoes or rice, raw oats, unripe bananas)
  • Consume plenty of soluble fibre (apples, pears, onions, broccoli, cauliflower, avocado)
  • Experiment with fermented foods (kefir, kimchi, kombucha, sauerkraut)
  • Take prebiotic supplements like GOS, FOS, and HMOs

HMOs, particularly 2’-fucosyllactose (2’-FL) is an effective way to bolster your Bifidobacteria populations, which in turn help to feed other beneficial bacteria species in your gut.

Explore our range of HMOs in our shop.


Antibiotics were a major medical breakthrough in the 20th century and have helped to save millions of lives since their discovery. Yet, their increasing widespread use has contributed to antibiotic resistance and changes to the composition and function of the human gut microbiome.

Written byLeanne Edermaniger, M.Sc. Leanne is a professional science writer who specializes in human health and enjoys writing about all things related to the gut microbiome. 


[i] Malys MK, Campbell L, Malys N. Symbiotic and antibiotic interactions between gut commensal microbiota and host immune system. Medicina. 2015 Mar 24;51(2):69–75. doi:10.1016/j.medici.2015.03.001

[ii] Microbiology Society. The history of antibiotics [Internet]. [cited 2023 Jun 5]. Available from:

[iii] Antibiotics - Overview [Internet]. NHS; 2015 [cited 2023 Jun 5]. Available from:

[iv] Antibiotic resistance [Internet]. World Health Organization; [cited 2023 Jun 5]. Available from:

[v] Klein EY, Van Boeckel TP, Martinez EM, Pant S, Gandra S, Levin SA, Goossens H, Laxminarayan R. Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc Natl Acad Sci U S A. 2018 Apr 10;115(15):E3463-E3470. doi: 10.1073/pnas.1717295115. Epub 2018 Mar 26. PMID: 29581252; PMCID: PMC5899442.

[vi] Matzaras R, Nikopoulou A, Protonotariou E, Christaki E. Gut Microbiota Modulation and Prevention of Dysbiosis as an Alternative Approach to Antimicrobial Resistance: A Narrative Review. Yale J Biol Med. 2022 Dec 22;95(4):479-494. PMID: 36568836; PMCID: PMC9765331.

[vii] Samarra A, Esteban-Torres M, Cabrera-Rubio R, Bernabeu M, Arboleya S, Gueimonde M, Collado MC. Maternal-infant antibiotic resistance genes transference: what do we know? Gut Microbes. 2023 Jan-Dec;15(1):2194797. doi: 10.1080/19490976.2023.2194797. PMID: 37020319; PMCID: PMC10078139.

[viii] Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis. The Lancet. 2022;399(10325):629–55. doi:10.1016/s0140-6736(21)02724-0

[ix] Fessl S. What happens to the gut microbiome after taking antibiotics? [Internet]. 2022 [cited 2023 Jun 6]. Available from:

[x] Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as major disruptors of gut microbiota. Frontiers in Cellular and Infection Microbiology. 2020;10. doi:10.3389/fcimb.2020.572912

[xi] Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018 Nov;3(11):1255-1265. doi: 10.1038/s41564-018-0257-9. Epub 2018 Oct 22. PMID: 30349083.

[xii] Chandra H, Sharma KK, Tuovinen OH, Sun X, Shukla P. Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile. Gut Microbes. 2021 Jan-Dec;13(1):1979882. doi: 10.1080/19490976.2021.1979882. PMID: 34724858; PMCID: PMC8565823.

[xiii] Your risk of C. Diff [Internet]. Centers for Disease Control and Prevention; 2022 [cited 2023 Jun 7]. Available from:,diff%20infection.

[xiv] Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, Li H, Alekseyenko AV, Blaser MJ. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012 Aug 30;488(7413):621-6. doi: 10.1038/nature11400. PMID: 22914093; PMCID: PMC3553221.

[xv] Gutierrez D, Weinstock A, Antharam VC, Gu H, Jasbi P, Shi X, et al. Antibiotic-induced gut metabolome and microbiome alterations increase the susceptibility to candida albicans colonization in the gastrointestinal tract. FEMS Microbiology Ecology. 2019;96(1). doi:10.1093/femsec/fiz187


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