Viral Bacterial Parasites Called Phages Drive Co-Evolution of Gut Microbiome Interview with:

Dr Pauline Scanlan Royal Society-Science Foundation Ireland University Research Fellow/APC Faculty, APC Microbiome Institute, Biosciences, University College Cork, Éire

Dr. Scanlan

Dr Pauline Scanlan
Royal Society-Science Foundation Ireland University Research Fellow/APC Faculty,
APC Microbiome Institute, Biosciences,
University College Cork, Éire What is the background for this study?

Response: The human gut is host to an incredible diversity of microbes collectively known as the gut microbiome. Each of us has a unique collection of bacterial strains that form part of the gut microbiome. This uniqueness is of potentially crucial importance with respect to host health as we know that differences in bacterial strain diversity within species could have a range of positive or negative consequences for the human host. For example, some strains of a given bacteria are harmless whilst another strain of the same bacterial species could kill you. A classic example of such a difference in strain functionality is exemplified by the gut bacterium Escherichia coli – one strain called E. coli Nissle 1917 is used as a probiotic and another, E. coli O157:H7, has been responsible for a number of deadly food-borne pathogen outbreaks. Therefore a better understanding of what drives bacterial strain diversity is not just fundamental to our understanding of the ecology and evolution of microbes but is also highly relevant for improvements in human health and disease prevention. What drives strain diversity in the human gut?

Response: This is a good question – although little known about within-host bacterial evolution and the process of strain diversification in the gut there are a number of possible factors one can consider in this regard. However, I was interested in assessing the evidence for a very particular process known as antagonistic coevolution (AC) between bacteria and their viral parasites, bacteriophages (phages) in driving strain diversity in the gut. Can you explain what bacteriophages are?

Response: Phages are viral parasites of bacteria.

There are two main types of phages – lytic and lysogenic. To infect a bacterial cell, phages bind to specific receptors on the cell. Upon infecting a bacterial cell, lytic phages essentially hijack and replicate inside the bacterial host making multiple viral progeny which they release into the environment upon cell lysis. Lysogenic phages can go through this lytic cycle but can also integrate into the bacterial genome and be passed down to daughter bacterial cells upon cell replication and division. How does coevolution of bacteria and bacteriophages drive diversity of the gut microbiome?

Response: Antagonistic coevolution (AC) is a specific process or type of interaction between bacteria and phages. Because phages can kill their bacterial hosts there is strong selection for bacteria to evolve resistance to phages. Bacterial resistance evolution in turn can select for phage novel infectivity and so on. Over time, this reciprocal selection for resistance and infectivity evolution (antagonistic coevolution) between bacteria and phages drives both bacterial and phage diversity by continuously selecting for novel resistance and infectivity phenotypes. With respect to the gut, these changes in microbial diversity may also have a wide range of functional consequences and ultimately impact on host health. For example, many of the receptors phages bind to are important immune recognition molecules. Therefore, mutations in bacterial cell surface receptors that confer resistance to phages may also increase or decrease bacterial virulence and change how the bacteria interact with the human host immune system.

Response: What are the main findings?  

Response: The main conclusions of this opinion piece is that although research into AC in natural microbial populations, such as the gut microbiome, is in its infancy there is compelling evidence to show that it plays a potentially important role in driving microbial diversity in the human gut. There are a number of lines of evidence to support this. For example, both bacteria and phages are abundant in the gut and many studies have also shown that variation in gene content between strains of many species of gut bacteria is predominantly associated with phage resistance. Temporal analysis of the gut microbiome has also shown that phages are rapidly evolving within individual human hosts over short periods of time (days) which provides a key genomic signature for ongoing phage coevolution with their bacterial hosts. What should readers take away from your report?

Response: Research into the gut microbiome usually takes a static approach with differences in diversity between individuals typically being ascribed to ecological factors (diet, antibiotics etc) rather than evolutionary ones (i.e. coevolution with phages). I hope this opinion piece will provide readers with fresh insight and open up new discussions into how fundamental evolutionary processes, such as coevolution, could potentially shape microbial diversity and functionality in the gut and ultimately impact on host health. What recommendations do you have for future research as a result of this study?

Response: As outlined research into AC in natural populations in general (not just in the gut microbiome) is very much in its infancy and therefore much more work is required to both experimentally validate in vitro and in silico data. Suitable in vitro model systems together with appropriate analysis of native gut microbial communities is key to providing the evidence needed to support the hypotheses outlined in this opinion piece. Thank you for your contribution to the community.


Bacteria–Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality

Scanlan, Pauline D.; Published online: March 22, 2017
Trends in Microbiology , DOI:

Note: Content is Not intended as medical advice. Please consult your health care provider regarding your specific medical condition and questions.

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Last Updated on March 28, 2017 by Marie Benz MD FAAD