The microbiome is more than just bacteria-what about bacteriophages?

Author: Lorraine Draper, APC Microbiome Ireland
Date: 21st June, 2019
When we think of the microbiome, we usually think of all the bacteria that live inside us, in our digestive system, or live in the soil around us, or in our oceans. But bacteria are not alone, there are many other microorganisms to consider such as, bacteriophages, tiny bacterial viruses that can outnumber bacteria by up to 10-fold in some environments. While bacteriophages are similar in their physical characteristics to human viruses (cold or ‘flu virus for example) in that they consist of a protein shell that contains nucleic acid (e.g. DNA), these viruses can only infect bacteria and are harmless to humans. In fact, there are millions living in gut right now that are actively waging a war on the bacteria. Killing some bacteria and making space for new and different bacteria to flourish. Just like lions and their prey in the Serengeti this is all part of a stable functional ecosystem. Interestingly, bacteriophages are very precise about the bacteria they kill. If we think of an antibiotic, it is like an atomic bomb, obliterating most of the bacteria they come across. Bacteriophages are different, they are like a sniper rifle, with each bacteriophage having a specific bacterial target, leaving the remainder of the microbiome untouched. It is this specialisation that has led to the use of phage in medicine, termed “phage therapy”. Bacteriophages were independently discovered by Frederick Twort in 1915 and Félix d’Hérelle in 1917. d’Hérelle pioneered the concept of ‘phage therapy’ as a treatment for diseases such as typhoid, dysentery and cholera, and infections such as septicaemia. However, when broad spectrum antibiotics were discovered in 1941 and marketed widely, western scientists used phage primarily as research tools. More than 10 Nobel prizes have been awarded for phage research!
Now that many bacteria have developed resistance to antibiotics and are becoming difficult to treat, there is a resurgence in phage therapy research. Only recently we have seen the amazing success stories of how bacteriophages have saved people’s lives. Tom Patterson went on the trip of a lifetime to Egypt in 2015 and fell ill from an infection caused by a bacterium known as Acinetobacter baumannii. Antibiotics were not successful and he fell into a coma. It was only with the treatment of bacteriophages that he was able to recover. A book documenting this story The Perfect Predator: A Scientist’s Race to Save Her Husband From a Deadly Superbug has been written by Patterson and his wife, Steffanie Strathdee, who have also since created iPATH, the first phage therapy centre in North America.
Another example in the UK involved doctors in Great Ormond Street Hospital using phage therapy to treat Isabelle Carnell-Holdaway who was born with cystic fibrosis. This disease causes sticky mucus to develop inside the lungs, which can harbour dangerous infections. This happened to Isabelle and when she became infected with a –bacterium called Mycobacterium abscessus. Potent antibiotics were not able to tackle the infection as the bacterium was resistant to all the antibiotics they tested. Ultimately, the doctors said her chance of survival was less than 1%. However, following administration of a cocktail of three phages, Isabelle began to recover within weeks, and is now back at school. Isabelle continues to have two infusions of the viral cocktail every day to keep the bacteria in check, with hopes of getting a fourth phage added to the mix soon to finally eradicate the infection for good.
These stories show how bacteriophages can be successfully developed as therapeutics to treat even the most difficult bacterial infections, those resistant to antibiotics. Modern medicine will need to rely on new and novel therapeutics such as bacteriophages more and more as these resistant bacterial strains become more prevalent.
For this reason, I suggest that we celebrate and spread the word about bacteriophage this World Microbiome Day. They may very well be our saviours some day!