Previous preclinical research (here; here) has shown that the gut microbiota helps modulate the host response to influenza infection -germ-free or antibiotic-treated mice usually exhibit weak protection against influenza virus. However, underlying mechanisms mediating this effect and microbial factors involved have not been fully elucidated.

A recent study, led by Dr. Thaddeus Stappenbeck from the Department of Pathology and Immunology at Washington University School of Medicine (St. Louis, USA), has found that a particular gut microbe modulates immune response to influenza infection in mice through breaking down flavonoids naturally found in vegetal foods.

The researchers used a murine model with persistently elevated type I interferons (IFNs) in the absence of exogenous viral infection-named Irgm(-/-) knockout mice-in which the immunity-related guanosine triphosphatase family M member 1 is not expressed. This experimental model was first validated to study host responses to influenza infection in a background of elevated type I IFN in the lung, based on previous research that showed type I IFN signalling is involved in how the gut microbiota responds to viral infections. It was confirmed by several assays that Irgm(-/-) mice had elevated type I IFN in the lungs and were resistant to influenza, whereas control mice that were infected exhibited weight loss and a mortality rate of about 50%. Influenza induced similar mortality and weight loss as controls when Irgm(-/-) mice lacked the type I IFN receptor (IFNAR), which suggests that type I IFN signalling is relevant in mouse protection against influenza infection.

It has also been suggested that microbial metabolites could have a protective role against influenza infection through enhancing type I IFN signalling. Researchers in the current study screened 84 microbial metabolites in a cell-based high-throughput screening assay aimed at identifying small molecules that enhanced the IFN signalling pathway components. 11 metabolites were found to induce type I IFN signalling, which means they improved IFN efficacy and could potentially offer protection against viral infection. Among them, 3 metabolites showed dose-dependent increases in amplification of type I IFN pathways. The metabolite desaminotyrosine (DAT), which is a degradation product of flavonoids from vegetal foods and can also be synthesized by gut bacteria from amino acid metabolism, was recovered in both faeces and serum of wild-type mice. DAT administration alone without antibiotics increased the expression of several type I IFN-stimulated genes in the lungs.

When DAT was given to mice and then the mice were infected with influenza virus, the mice experienced less lung damage than mice not treated with DAT, even though the DAT-treated mice showed levels of viral infection that were identical to those in mice that did not receive the treatment. These data show that DAT protects from influenza infection by enhancing type I IFN signalling before infection. According to Stappenbeck, leading author: “The microbes and DAT didn’t prevent the flu infection itself; the mice still had the virus. But the DAT kept the immune system from harming the lung tissue”. It has also been proven that type I IFN protection from influenza infection was dependent on lung phagocytes, which are well-known innate immune cells involved in protecting the host against bacterial and viral pathogens.

To investigate the role of specific gut bacteria in DAT generation (and subsequent influenza protection), researchers obtained isolates of Clostridium orbiscindens, C. leptum and Enterococcus faecalis, and found that C. orbiscindens was the bacterium that degraded quercetin -a type of flavonoid substrate- most effectively; this was in agreement with a previous study in humans that demonstrated the ability of C. orbiscindens from human faeces to metabolize several flavonoids. C. leptum and E. faecalis did not degrade flavonoids, and mouse caecal contents containing all three bacterial species also degraded the flavonoid substrate, though in a less effective way when compared to C. orbiscindens alone. Besides this, mice were pretreated with vancomycin, neomycin, ampicillin, and metronidazole-antibiotics that enhance influenza-related mortality-and afterwards were gavaged with phosphate-buffered saline, wild-type mouse caecal contents, or isolates of C. orbiscindens, C. leptum and E. fecalis. Both C. orbiscindens and caecal contents protected mice from influenza mortality and morbidity.

Beneficial effects of DAT on the immune system appeared only when it was administered before infection and not in the postinfection period. Both pretreating mice with DAT for 1 week before influenza infection followed by cessation of treatment at the time of infection, and continuous DAT administration, protected mice from infection-related mortality and weight loss to the same extent. However, administration of DAT 2 days postinfection did not have a protective effect.

Finally, the researchers found that DAT exerted its effects by type I IFN signalling amplification via IFNAR and STAT1 -a signalling molecule downstream of IFNAR- rather than through augmentation of type I IFN induction.

In conclusion, gut microbiota protection of the host against influenza infection depends on the generation of the microbial metabolite DAT from C. orbiscindens. DAT enters the bloodstream and triggers type I IFN signalling through a phagocytic-dependent mechanism. Specifically, timing of administration of DAT is relevant as it only confers protection against influenza infection when administered before infection but not when administered postinfection.   



Steed AL, Christophi GP, Kaiko GE, et al. The microbial metabolite desaminotyrosine protects from influenza through type I interferon. Science. 2017; 357(6350):498-502. doi: 10.1126/science.aam5336.