Bacteriophage, Disease, and the Microbiome


A symposium at ASM Microbe 2019 considered some specific examples of how bacteriophage shape the microbiome and also zoomed out for a higher-altitude view of the microbiome.

With the recognition of the microbiome, exploring how bacteriophage shape its environment has become a matter worth investigating. A symposium at ASM Microbe 2019 considered some specific examples and also zoomed out for a higher-altitude view of the microbiome.

Yael Litvak, PhD, from the University of California, Davis, has looked at how bacteriophage participate in the expansion of Shiga toxin-producing bacterial pathogens in the gut. The emergence of more than 2 dozen Shiga toxin-producing strains like Escherichia coli 0157:H7 implies that the production of the toxin provides some fitness advantage to the bacteria. A bevy of experiments performed by Litvak and colleagues using various mouse models has demonstrated a growth benefit of bacteria harboring the toxin. It’s proven to be a complex puzzle to unravel, but the gist is that Shiga toxin causes inflammation of cells, and also enables better access of the bacteria to the vital nutrient of iron. Thus, in the competitive world of the large intestine, Shiga toxin provides a benefit to bacteria, with unfortunate, sometimes catastrophic consequences for us.

Bacteriophage are also at the heart of the misery caused by Vibrio cholerae in the form of cholera. The dominant bacteriophage that preys on V cholerae is ICP1. As discussed by Amelia McKitterick, a PhD student at University of California, Berkeley, there is a complex and intricate dance between V cholerae and ICP1 in the gut. The maestro of the dance is a genetic element of the bacterium called phage-inducible chromosomal island-like element (PLE), which inhibits the production of ICP1. A boatload of research has demonstrated that PLE reduces replication of the phage. It also ramps up lysis of the virus-infected bacteria, which prevents further production of new viruses. The sacrifice of the infected bacteria acts to preserve the remaining population. It boils down to a race between the ability of the bacteriophage to replicate and the ability of the bacteria to respond. Cholera is still very much around, so the phage can definitely be the victor.

Elsewhere, researchers from Harvard University have shown that temperate bacteriophage, which integrate their genomes into the host bacterium’s genome (prophage), with subsequent induction of excision and assembly of new phage, can sensitize bacteria to antibiotics.

The temperate way of phage life is great only so long as the host bacterium is healthy. Bacteriophage work to preserve their bacterial home by their involvement with the SOS response, a system whereby bacteria recognize a threat to their survival, halt cell division, and activate a network of genes to repair the damage. Many antibiotics induce the SOS response.

Using Salmonella typhimurium that lack or contain prophage, Siân Owen, a post-doctoral fellow at Harvard Medical School, demonstrated the influence of the prophage on the survival of bacteria in the presence of ciprofloxacin. The system is exquisitely sensitive, with a marked decrease, not increase, in survival when the level of the antibiotic was bumped up by only 0.3 µg/mL. Further experiments linked this with the SOS response.

The thinking is that by exploiting the SOS response, phage liberate themselves from cells that are destined to die. The bacteria lacking prophage, which will better survival the antibiotic exposure, can then become new homes for the phage. The result over time is increasing bacterial resistance.

A question that follows is whether this is a passive process, or whether the phage drive the evolution of resistance. That’s what occupies Owen currently. Early indications are that the bacteriophage may be more than bystanders in the evolution of ciprofloxacin resistance.

Bacteriophage may also be more than bystanders when it comes to the microbiome, according to Colin Hill, PhD, of the University College Cork in Cook, Ireland. “Do bacteriophage shape or shadow our microbiomes? At the shape end of the spectrum, bacteriophage are responsible for bacterial community structure. At the shadow end, bacteriophage reflect the bacterial community structure. As with many things, the truth likely lies somewhere in between.”

Experiments in mice treated with antibiotics to shift their microbiome showed that re-instilling bacteriophage previously obtained from the mice recovered the microbiome. This and other data pointed to the influence of bacteriophage in actively shaping the structure of the bacterial community.

Data obtained with crAssphage, the most abundant phage in the gut, has indicated that the phage stably co-exist with the host bacterium. This is more of a shadow type of behavior. However, the findings that crAssphage may change the cell function pertaining to increased antimicrobial resistance, suggests that the phage may shape the function of the microbiome.

The collective findings highlight the complexity of the interaction between bacteriophage and bacteria in the gut, and drive home the likely futility of experiments that don’t incorporate this complexity.

The symposium, “Movers and Shakers: How Bacteriophages Influence Health and Disease,” was held June 24, 2019, at ASM Microbe in San Francisco, California.

Brian Hoyle, PhD, is a medical and science writer and editor from Halifax, Nova Scotia, Canada. He has been a full-time freelance writer/editor for over 15 years. Prior to that, he was a research microbiologist and lab manager of a provincial government water testing lab. He can be reached at


Yael Litvak: none

Colin Hill: none

Amelia McKitterick: none

Siân Owen: none


Symposium S387 - Movers and Shakers: How Bacteriophages Influence Health and Disease

  • Shiga toxin-mediated pathogen expansion in the gut; Yael Litvak, PhD, Department of Medical Microbiology & Immunology, University of California, Davis, Davis, California
  • Do bacteriophage shape or shadow our microbiomes?; Colin Hill, PhD, University College Cork, Cork, Ireland
  • Identification of a phage encoded helicase involved in the mobilization of an anti-phage island; Amelia McKitterick, University of California, Berkeley, Berkeley, California
  • Temperate prophage elements sensitise bacteria to antibiotics; Siân Owen, PhD, Harvard Medical School, Boston, Massachusetts
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