Using phages to combat alcohol-related liver damage?

“Treatment options for alcoholic hepatitis, a liver disease associated with heavy alcohol consumption, are limited. Studies in mice show that the microorganisms responsible for this condition can be targeted with a viral treatment.

In 1984, microbiologist Barry Marshall famously used himself as a test subject for his research and drank the contents of a bottle containing the bacterium Helicobacter pylori to show that bacteria cause stomach ulcers1. Duan et al.2, writing in Nature, do not report taking such drastic measures to investigate a bacterial link to a disease. Nevertheless, their careful analysis of a liver disease called alcoholic hepatitis in mouse studies, and their analysis of samples from people with the disease, also provides striking evidence for the involvement of a suspected bacterial culprit.
Alcoholic hepatitis is a poorly understood condition associated with heavy alcohol consumption and is difficult to treat. Previous experiments in mice have shown that the gut bacterium Enterococcus faecalis might be involved3. However, E. faecalis is generally regarded as an old friend that inhabits the intestines of many animals across the evolutionary tree, from humans to nematode worms4, typically accounting for less than 0.1% of all bacteria in stool samples from healthy people5. After antibiotic treatment, however, bacteria of the genus Enterococcus increase in prevalence and become one of the most common types of microbes in the gut6. E. faecalis can infect blood, heart, bladder and brain, as well as teeth that have undergone root canal treatment7,8.

Duan and colleagues analysed human stool samples. They identified E. faecalis in the stool of around 80% of the people with alcoholic hepatitis they tested, and around 30% of E. faecalis strains had genes encoding a toxin called cytolysin. Moreover, people with the disease had almost 3,000 times more E. faecalis in their stool samples than people who did not have alcoholic hepatitis. This is not definitive proof that the disease is caused by this bacterium. However, the authors’ data also show that the presence of cytolysin in stool correlates with mortality—89% of people whose stool samples contained cytolysin died within 180 days of hospitalisation, compared with only 3.8% of people who had alcoholic hepatitis but whose stool samples lacked the toxin.
The authors next investigated the link between E. faecalis and liver disease in mice. The animals were colonised with strains of E. faecalis that either produced cytolysin or did not, and some were then given an alcohol-rich diet while others received an alcohol-free diet. Only the mice colonised with cytolysin-producing E. faecalis developed liver damage (Fig. 1a).

Then, using germ-free mice (which had no natural microorganisms), the authors transplanted stool samples from people with alcoholic hepatitis that contained E. faecalis strains in which cytolysin was either present or absent. Mice on a high-alcohol diet that were colonised with cytolysin-containing stool showed a range of signs of liver damage and liver-cell death, whereas animals on such a diet that were colonised with stool lacking cytolysin showed no major signs of liver damage.

To understand the disease-causing mechanisms, the authors isolated liver cells from the animals and found that cell death in response to cytolysin exposure was dose-dependent. The response to cytolysin was the same regardless of whether the mice had received an alcohol-rich diet or not. This suggests that, rather than alcohol causing alcoholic hepatitis by damaging liver cells, damage occurs because alcohol increases the permeability of the intestinal lining, allowing cytolysin-producing E. faecalis to reach the liver and cause disease symptoms (Fig. 1a).
Given the limited treatment options for alcoholic hepatitis, the authors investigated whether steps could be taken to develop a therapy that exploits bacteria-specific viruses, known as bacteriophages, or phages for short. Phages have the advantage over antibiotics of being highly specific, thereby avoiding the killing of beneficial bacteria as well. Because the surface of a human cell differs substantially from that of a bacterial cell, phages are not thought to infect animal or human cells9.

Phages have been used for almost 100 years to remove Salmonella and Shigella bacteria from infected human intestines10. They have also been used to remove the disease-causing bacterium Clostridium difficile from artificial intestines and from hamsters infected with this bacterium11,12. It has been suggested that one day they could be used in humans or animals to reshape the composition of the community of gut microorganisms (the microbiota) to produce a healthier microbiota, consisting of more bacteria associated with good health and fewer associated with disease13. The potential of E. faecalis-targeting phages to combat human disease is already being discussed7, and phages can kill antibiotic-resistant strains of E. faecalis in the context of human bone and wound infections14,15 and dental caries16. In addition, phages are being developed for use in the food industry to remove E. faecalis from cheese cultures and prevent the production of toxic waste products17.

To test whether a method can be developed to specifically remove cytolysin-producing E. faecalis from mice, the authors identified several phages that target these bacteria (Fig. 1b) while leaving other gut bacteria untouched. Mice that received human stool samples and an alcohol-rich diet and were given E. faecalis-targeting phages had less liver damage than mice that received phages that killed a different bacterium that does not normally occur in animals.
This study shows the benefits of using phages in detective work to investigate the contributions of microbes to disease. The authors show that phages can be used to identify disease-causing bacterial components, and they also highlight the possibility that phages could offer potential treatment options. Further testing, including clinical trials, would be required to assess whether a phage-based approach would make sense in a human context. For example, phage treatment could help to control E. faecalis in the gut before a person receives a liver transplant.

In the study by Duan and colleagues, the phages could treat a disease in which a causal component is a bacterium that normally resides in the gut, even though the site of disease is elsewhere in the body. Although many phage researchers focus on using these viruses to treat diseases associated with antibiotic-resistant bacteria, the work of Duan et al. raises the possibility of a much broader clinical role for them. There is growing evidence that gut microbes can impair the function of certain cells in the brain, and studies are under way to determine whether such microbes play a role in human brain diseases (see go.nature.com/2cp1kfk). Perhaps phages could become part of the next generation of targeted antimicrobial therapies for diseases that are currently difficult to treat. Indeed, there may be many diseases that we do not currently know have a microbial component and that could be combated with phages.”

Source translation: https://www.nature.com/articles/d41586-019-03417-3?WT.ec_id=NATURE-201911&sap-outbound-id=B1DB46EE2E53C2F97DD8759AF0246E5D0F9AD1F4&mkt-key=005056A5C6311ED8AAB34565834CF148
Martha R. J. Clokie is in the Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
Nature 575, 451-453 (2019)
doi: 10.1038/d41586-019-03417-3