Antibiotics and Microbiomes

As I mentioned in my previous blog “Antibiotic resistance and what we can do about it”, antibiotic resistance is big problem we are currently facing. Every usage of antibiotics contributes to the resistance problem and therefore we need to reduce our use of antibiotics and find alternatives, such as phage therapy. What I have since learnt is that there are more reasons to find alternatives to antibiotics than just antibiotic resistance. Antibiotics can have an impact on our microbiome and that is what I am going to talk about today.


We have a lot of microorganisms in our bodies. The microorganisms I am discussing are mainly bacteria but there are also other microorganisms such as from the Domain Archaea. It has been estimated that there are around 10 times the bacterial cells in our bodies than human cells [1]. More bacteria than you! Microorganisms are found all over and in our bodies. Different areas contain different communities with different organisms. The mouth and gut communities of one person can be more different then the microbes in a reef and prairie [1]. For more information on this watch this video.


Good Bacteria

When we hear about bacteria we may often think about all the ‘bad’ bacteria that cause infections and diseases. However, there is a lot of ‘good’ bacteria that we need to live. For example, some bacteria help us to break down plant fibres [2]. They are also primary sources for some of the nutrients we need. It is thought that bacteria help to ‘prime’ our immune systems while we are children to help prepare for pathogens in later life [2]. In addition, there are many bacteria found on our skin, so many that it may help to prevent other bacteria establishing [2].


What antibiotics do to our microbiomes

Antibiotics are drugs used to kill and treat bacterial infections. They are very commonly used and very important in medicine. The issue with antibiotics is that they are not specific in the type of bacteria that they kill and therefore when used will not just kill the type of bacteria that is being targeted. They will kill bacteria, both good and bad.

As we generally take antibiotics orally the gut microbiome is often affected. It can cause a change in around 30% of the bacteria and can have an impact on the function [3]. Once the antibiotic treatment has stopped the gut tends to revert to its original composition, but does not fully recover [3].

Antibiotic exposure in early life is thought to have the most effect on the microbiome. This is because the microbiome changes the most in early life. The first colonisation of microbes after birth is very important [4]. Interestingly the microbiome is effected by the mode of birth delivery. Caesarean births mean that the baby is not exposed to the vaginal microbes and the babies tend to begin with a gut microbiome like an adult skin microbiome. Whereas vaginally delivered birthed babies tend to have gut microbiomes like an adult vaginal microbiome [1]. This means caesarean births tend to give children with a more unstable microbiome, which may be associated with more allergies, asthma and obesity [4].

Then, in the first two to three years of a child’s life, their microbiome becomes more like an adult microbiome. During this time, they are receiving microbes from places such as food, breast milk and the environment [4]. Delays in the development of the microbiome may be caused by undernutrition or antibiotics [4]. Antibiotics can cause a huge change in the community and the earlier this happens the bigger the effect is likely to be.


So, what can we do to keep our microbiomes healthy?

This, along with antibiotic resistance may make it sound like antibiotics are evil and we should completely avoid them. However, we currently need antibiotics to treat bacterial infections. It is important that we use them only when necessary. As talked about in my previous blog, antibiotics are frequently misused and we need to change this.

To account for the loss in bacteria after using antibiotics probiotics can be used [4]. Probiotics, such as Kombucha, contain live ‘good’ bacteria for our gut and therefore help to replenish it.


Kombucha including the culture (Mgarten, 2007)


The most exciting alternative is using phages! Phages can be used as an alternative to antibiotics as mentioned in my previous blog. Unlike antibiotics phages are specific. This means that they only kill the specific type of bacteria they are targeting eliminating the problem of the microbiome and all the ‘good’ bacteria being killed.

By continuing to do research about phages we are helping to contribute to a future where phage therapy is a widespread alternative to antibiotics. It has been amazing to have had the opportunity to be part of this.



  1. Knight, R., How our microbes make us who we are. 2014, TED Talks.
  2. Ashford, M. Could Humans Live Without Bacteria? 2010; Available from:
  3. Francino, M.P., Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol, 2015. 6: p. 1543.
  4. Langdon, A., N. Crook, and G. Dantas, The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med, 2016. 8(1): p. 39.


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One Response to Antibiotics and Microbiomes

  1. jcturnbullnz says:

    Hi Jenny-Ann, great post! I found it an interesting extention of the discussion on antibiotic resistance, and a good topic for those who may have no idea what the term ‘microbiome’ means. You found some interesting information and presented it well with a nice structure to your post

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