Antibiotics and their effect on the Microbiome

Dr Charles Akle

I need to use antibiotics – what effect do they have on my microbiome?

This is a great and important question. Antibiotics have been a fantastic discovery and millions upon millions of lives have been saved by them. Initially, they were thought of as the magic bullet and could treat most conditions but, as time passed, we soon realised that there was going to be trouble ahead.

Firstly, bacteria are really smart and soon learned to develop resistance against antibiotics. Initially not a major issue as our pharmaceutical experts kept finding new agents and tried to keep one step ahead of the bugs. Scouting parties were sent all over the world to look for new bacteria from which to create new antibiotics and some were found in amazing places.

Cephalosporins were discovered off the coast of Sardinia near a sewage discharge pipe! Another was found in Easter Island (Rapa Nui) in the Pacific. 

Yet another area of assault involves viruses that can kill bacteria, so-called bacteriophages, and which were the hope before penicillin was developed. They are still used in Eastern Europe and their use generally is being resurrected.

Secondly, we knew that bacteria were a great source of agents to kill other bacteria, but we did not realise till recently that they are also a great source of resistance! A set of bacteria found at the bottom of a cave in New Mexico in 2012 shocked the profession. This cave is millions of years old and the water takes thousands of years to percolate to it. The organisms are thought to be at least 30,000 years old and are resistant to almost every modern antibiotic!

This is typical of Mother Nature. You never get a single effect without a response to go with it. If you can attack, then others learn to defend!

The “antibiotic apocalypse” is worrying many but mankind lived for hundreds of thousands of years without antibiotics and is well equipped to deal with infection provided good health is maintained. This is why the microbiome is so critical to any intelligent person who wants to avoid antibiotic use. That is not to say you should not use them to save life but you should use them judiciously and with care and then compensate as I will explain below.

An especially critical time is when we are very young and still “tuning” our immune system to look after us. We derive all our bacteria at birth from our mother and the natural process of birthing usually results in the mother’s faecal matter and skin bacteria inoculating the baby. We used to think this was a bad thing but now we know better. In many countries, the midwives actually take some faeces from the mother and contaminate the baby, especially after a Caesarian Section. They also rub the baby on the mother’s abdomen to get good skin to skin transmission.

The mother’s first milk (called colostrum) contains large amounts of secreted antibodies from her which protect the baby until it has developed its own immunity – this is why breast feeding even if only for a few days is so critical. We do know that milk contains bacteria also and it may well be there are other agents.

{Teaching point: Did you know that an entire group of bacteria has only been discovered in the last fifteen years and is just beginning to be classified? These bacteria are extremely difficult to culture and study and the work has been based on DNA analysis. They are thought of as the “Dark Matter” of the bacterial world because they seem to account for between 25 and 50% of ALL bacterial species on Earth! We know almost nothing about them or what effect they may have on our lives but I would hazard a bet that they will have some important link in the network that is Nature and Life! Watch this space! If you want to learn more, look up “Candidate Phyla Reaction”.]

What should I do during my antibiotic treatment?

The first thing is not to worry too much. Just make sure you discuss with the doctor to see if there are any alternatives and if not, then take them as advised. Often, antibiotics are used almost as a placebo in situations where they will not help – this is to be discouraged and you should not try and force your doctor into prescribing them unnecessarily.

During the course of therapy, make sure you keep a close eye on replenishing your microbiome diversity because it is this that suffers especially with antibiotics. Make sure you are “farming” properly and feeding and restoring this diversity. 

Once the course is finished, you must carry on for some days so that restoration takes place – don’t stop when the antibiotics stop! Other supplements might be worth taking such as extra vitamin B, C and D for a couple of weeks after.

You are also aware of how important Au+ is in this equation and you should keep taking that as there is no evidence of any drug interaction and you do want everything going for you in terms of immune responses.