Research Article

Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites

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Science  30 Oct 2020:
Vol. 370, Issue 6516, eaay9097
DOI: 10.1126/science.aay9097

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Radioprotective bacteria

A common symptom of radiation treatment for cancer is gastrointestinal disruption. The damage caused can become so severe and debilitating that it interrupts treatment. Guo et al. noticed that mice surviving experimental radiation exposure had distinctive taxonomic representation in their gut microbiota. A similar correlation was also observed in a small group of human subjects. Further experiments in mice revealed that some strains of bacteria produced high levels of short-chain fatty acids, which seemed to be dampening inflammatory responses and alleviating the damage caused by reactive oxygen species released by the radiation. A metabolomics analysis also implicated a role for tryptophan metabolic pathways in radiation survivorship.

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Structured Abstract


The toxicity of high-dose ionizing radiation is associated with the induction of both chronic and acute radiation syndromes that occur after partial or total body radiation and can be further characterized into hematopoietic, gastrointestinal, and cerebrovascular syndromes. The intestine is the major target of radiation and the biggest niche for gut microbiota. Although there are sporadic descriptive studies showing a potential correlation between the gut microbiota and radiation-induced damage, the detailed underpinnings of this relationship remain obscure. In addition, medical intervention to counteract radiation injury is still a global challenge despite decades of rigorous research.


Over the last decade, numerous investigations have demonstrated highly diverse gut microbiota between individuals and significant correlations of gut microbiota with multiple diseases. Gut microbes, as well as microbe-derived metabolites represented by short-chain fatty acids (SCFAs) and tryptophan metabolites, have essential roles in regulating host metabolism and immunity. The imbalance or dysbiosis of a microbial community is associated with potential diseases, risks, or even to the clear onset of clinical symptoms. We have previously corroborated the biological importance of gut microbiota and certain bacteria (e.g., Lachnospiraceae) together with SCFAs in attenuating colitis and obesity. It has also been reported that SCFAs and tryptophan metabolites can reduce proinflammatory cytokines such as tumor necrosis factor-α, interleukin-6, and interferon-γ and promote the anti-inflammatory cytokines, all of which are vital mediators of radiation-induced damage. These findings raise the possibility that the gut microbiota and metabolites play a key role in the regulation of disease susceptibility after radiation challenge.


We found that a small percentage of mice could survive a high dose of radiation and live a normal life span. These “elite-survivors” harbored a distinct gut microbiome that developed after radiation. Taking advantage of this finding, we used a combination of fecal engraftment and dirty cage sharing to demonstrate that the microbiota from elite-survivors provided substantial radioprotection in both germ-free and conventionally housed recipients, characterized by enhanced survival and ameliorated clinical scores. An unbiased microbiome analysis identified Lachnospiraceae and Enterococcaceae as the most enriched bacteria in elite-survivors. Monoassociation analysis provided direct evidence for the protective role of Lachnospiraceae and Enterococcaceae in promoting hematopoiesis and attenuating gastrointestinal damage. Clinical relevance in humans was supported by an analysis of leukemia patients who were exposed to whole-body radiation. The elevated abundance of Lachnospiraceae and Enterococcaceae was associated with fewer adverse effects in a highly statistically significant fashion. Treatment with SCFAs, especially propionate, rendered mice resistant to radiation, mediated by attenuation of DNA damage and reactive oxygen species release both in hematopoietic and gastrointestinal tissues. Further, an untargeted metabolomics study revealed a realm of metabolites that were affected by radiation and selectively increased in elite-survivors. Among these, two tryptophan pathway metabolites, 1H-indole-3-carboxaldehyde (I3A) and kynurenic acid (KYNA), provided long-term radioprotection in vivo.


Our findings emphasize a crucial role for the gut microbiota as a master regulator of host defense against radiation, capable of protecting both the hematopoietic and gastrointestinal systems. Lachnospiraceae and Enterococcaceae, together with downstream metabolites represented by propionate and tryptophan pathway members, contribute substantially to radioprotection. This study sheds light on the pivotal role that the microbiota-metabolite axis plays in generating broad protection against radiation and provides promising therapeutic targets to treat the adverse side effects of radiation exposure.

Gut microbiota and metabolites mediate radioprotection.

Gut microbes, especially Lachnospiraceae and Enterococcaceae along with bacteria-derived metabolites represented by SCFA (propionate) and tryptophan pathway members (I3A and KYNA), tune host resistance against high doses of radiation by facilitating hematopoiesis and gastrointestinal recovery.


Ionizing radiation causes acute radiation syndrome, which leads to hematopoietic, gastrointestinal, and cerebrovascular injuries. We investigated a population of mice that recovered from high-dose radiation to live normal life spans. These “elite-survivors” harbored distinct gut microbiota that developed after radiation and protected against radiation-induced damage and death in both germ-free and conventionally housed recipients. Elevated abundances of members of the bacterial taxa Lachnospiraceae and Enterococcaceae were associated with postradiation restoration of hematopoiesis and gastrointestinal repair. These bacteria were also found to be more abundant in leukemia patients undergoing radiotherapy, who also displayed milder gastrointestinal dysfunction. In our study in mice, metabolomics revealed increased fecal concentrations of microbially derived propionate and tryptophan metabolites in elite-survivors. The administration of these metabolites caused long-term radioprotection, mitigation of hematopoietic and gastrointestinal syndromes, and a reduction in proinflammatory responses.

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