1. Marianne De Paepe
  2. Marie-Agnès Petit  Is a corresponding author
  1. Micalis Institute, France

Bacteriophages are viruses that prey on bacteria. Also known as phages, they can multiply very quickly—hundreds of new viruses can be produced in a single infected bacterium in less than 30 minutes. However, relatively little is known about the impact of phage predation on human-associated bacteria in general, and even less on bacterial pathogens. Now, in eLife, Andrew Camilli of Tufts University School of Medicine and co-workers in Canada, Haiti and the United States, provide molecular evidence that phages prey on a bacterial pathogen during the course of an infection in humans (Seed et al., 2014).

Vibrio cholerae is the bacterium responsible for cholera. After being ingested, typically by drinking contaminated water, it multiplies in the digestive tract where it releases a toxin. This toxin causes profuse and watery diarrhoea, dehydration and death in 50% of cases if rehydration therapy is not administered.

In the delta region of the river Ganges in Bangladesh and India, cholera epidemics occur every year, and follow regular seasonal cycles. It has been proposed that this seasonal variation might be partly related to phages preying on the V. cholera bacteria—as the so-called vibriophages are most common in environmental waters at the end of the cholera season (Faruque et al., 2005a, 2005b).

Camilli and co-workers—including Kimberley Seed as the first author—report molecular data that indicate that vibriophages may preferentially prey on bacteria in the digestive tract of patients with cholera, rather than in environmental waters (Seed et al., 2014). Seed et al. looked at stool samples from two cholera patients (one from Haiti, one from Bangladesh) who had high viral loads of a type of vibriophage called ICP2. In each sample, they discovered that some of the bacteria were resistant to the phage, while the rest were sensitive to it. Then, Seed et al. sequenced the whole genomes of bacterial clones and discovered that the only differences between the phage-resistant and phage-sensitive isolates in each patient were clustered into a single gene. However, a different bacterial gene was mutated in each patient. Several different mutants of each gene were found. This strongly suggests that these mutations occurred, and were then selected for, in bacteria in the patient during the infection.

In the Haitian patient, almost all (> 99%) of the bacteria isolated were resistant to the phage; and, of the phage-resistant bacteria tested, all had one of six different mutations in a single gene called ompU. The OmpU protein forms a pore in the bacteria’s outer membrane to enable nutrients to be imported into the cell. The bacteria need this protein for their survival both in human hosts and in environmental waters. Since the OmpU mutants are resistant to phage attack, Seed et al.’s findings indicate that the OmpU protein is also used by the vibriophage ICP2 to infect the bacterial cells (i.e. it is also the ‘receptor’ for the ICP2 phage).

Seed et al. show that the selection of OmpU mutants by ICP2 vibriophages is not restricted to this isolated case. Out of a collection of 54 clinical isolates of V. cholerae collected in Bangladesh between 2001 and 2011, 15% have similar phage-resistant mutations in the ompU gene. Seed et al. also found that the changes in the OmpU protein were all in parts of the protein that are exposed on the outside of the bacterial cell; and importantly, that they had very little effect on the fitness of V. cholerae in a range of tests. This is reminiscent of the relationship between the bacterium E. coli and the phage lambda, where mutations in a surface protein can make the bacteria resistant to phage attack. These mutations also occur in a surface-exposed part of the protein and do not affect the other functions of this protein (Gehring et al., 1987; Hofnung, 1995). However, the E. coli/phage lambda studies were performed in the laboratory, whereas this V. cholerae study appears to be the first report that suggests a predator-prey relationship between phage and bacteria in the human intestine.

In the stool sample from the Bangladeshi patient, 22% of bacterial isolates were resistant to the ICP2 phage; and Seed et al. identified four different genetic changes that made the bacteria able to resist this phage attack. All of these mutations were in a gene called toxR, which encodes a protein that regulates the expression of numerous genes, including ompU. Since these ToxR mutants do not produce the phage’s receptor—the OmpU protein—this confers resistance to phage attack. However, the ToxR protein also regulates genes that control the virulence of the bacteria, and the ToxR mutants were unable to start new infections in an animal model of cholera. Therefore, in contrast with the OmpU mutants, it is more difficult to unambiguously assign the selection of ToxR mutants as resulting solely from defending against phage attack. Instead the selection of these non-infectious mutants could also be explained by such mutations making it ‘cheaper’ for these bacteria to grow in the digestive tract at the expense of the virulent clones.

Although it is perhaps counterintuitive, mutations that reduce virulence can have a selective advantage during an infection (Diard et al., 2013). Expressing so-called virulence proteins or factors is costly for an individual bacterium, and mutants that stop making these factors can, therefore, benefit at the expense of other bacteria that continue to do so. This advantage, however, is only short-lived as these less virulent mutants are unable to start new infections themselves. Regardless of the precise mechanism, the selection for the non-infectious ToxR mutants observed by Seed et al. suggests that phage predation may have contributed to the collapse of the infection and the selection of less virulent strains.

Finally, the results of Seed et al., together with the previous work by other groups that it builds on, highlight the important role that phages can play in shaping V. cholerae populations. These findings firmly place these viruses as an important ‘third’ party that must also be considered when trying to understand host–pathogen interactions.


    1. Gehring K
    2. Charbit A
    3. Brissaud E
    4. Hofnung M
    Bacteriophage lambda receptor site on the Escherichia coli K-12 LamB protein
    Journal of Bacteriology 169:2103–2106.

Article and author information

Author details

  1. Marianne De Paepe

    French National Institute for Agricultural Research and AgroParisTech, Micalis Institute, Jouy-en-Josas, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Marie-Agnès Petit

    French National Institute for Agricultural Research and AgroParisTech, Micalis Institute, Jouy-en-Josas, France
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.

Publication history

  1. Version of Record published: September 2, 2014 (version 1)


© 2014, De Paepe and Petit

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.


  • 2,072
  • 82
  • 3

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Marianne De Paepe
  2. Marie-Agnès Petit
Phage Predation: Killing the killers
eLife 3:e04168.
  1. Further reading

Further reading

    1. Microbiology and Infectious Disease
    2. Physics of Living Systems
    Chi Zhang, Rongjing Zhang, Junhua Yuan
    Research Article

    Bacteria in biofilms secrete potassium ions to attract free swimming cells. However, the basis of chemotaxis to potassium remains poorly understood. Here, using a microfluidic device, we found that Escherichia coli can rapidly accumulate in regions of high potassium concentration on the order of millimoles. Using a bead assay, we measured the dynamic response of individual flagellar motors to stepwise changes in potassium concentration, finding that the response resulted from the chemotaxis signaling pathway. To characterize the chemotactic response to potassium, we measured the dose–response curve and adaptation kinetics via an Förster resonance energy transfer (FRET) assay, finding that the chemotaxis pathway exhibited a sensitive response and fast adaptation to potassium. We further found that the two major chemoreceptors Tar and Tsr respond differently to potassium. Tar receptors exhibit a biphasic response, whereas Tsr receptors respond to potassium as an attractant. These different responses were consistent with the responses of the two receptors to intracellular pH changes. The sensitive response and fast adaptation allow bacteria to sense and localize small changes in potassium concentration. The differential responses of Tar and Tsr receptors to potassium suggest that cells at different growth stages respond differently to potassium and may have different requirements for potassium.

    1. Microbiology and Infectious Disease
    Xufeng Xie, Xi Chen ... Yongguo Cao
    Research Article

    Leptospirosis is an emerging infectious disease caused by pathogenic Leptospira spp. Humans and some mammals can develop severe forms of leptospirosis accompanied by a dysregulated inflammatory response, which often results in death. The gut microbiota has been increasingly recognized as a vital element in systemic health. However, the precise role of the gut microbiota in severe leptospirosis is still unknown. Here, we aimed to explore the function and potential mechanisms of the gut microbiota in a hamster model of severe leptospirosis. Our study showed that leptospires were able to multiply in the intestine, cause pathological injury, and induce intestinal and systemic inflammatory responses. 16S rRNA gene sequencing analysis revealed that Leptospira infection changed the composition of the gut microbiota of hamsters with an expansion of Proteobacteria. In addition, gut barrier permeability was increased after infection, as reflected by a decrease in the expression of tight junctions. Translocated Proteobacteria were found in the intestinal epithelium of moribund hamsters, as determined by fluorescence in situ hybridization, with elevated lipopolysaccharide (LPS) levels in the serum. Moreover, gut microbiota depletion reduced the survival time, increased the leptospiral load, and promoted the expression of proinflammatory cytokines after Leptospira infection. Intriguingly, fecal filtration and serum from moribund hamsters both increased the transcription of TNF-α, IL-1β, IL-10, and TLR4 in macrophages compared with those from uninfected hamsters. These stimulating activities were inhibited by LPS neutralization using polymyxin B. Based on our findings, we identified an LPS neutralization therapy that significantly improved the survival rates in severe leptospirosis when used in combination with antibiotic therapy or polyclonal antibody therapy. In conclusion, our study not only uncovers the role of the gut microbiota in severe leptospirosis but also provides a therapeutic strategy for severe leptospirosis.