The impact of gut microbiome on the innate immune response against enteric coronaviruses

Coronaviruses emerge relatively often in pigs, and most commonly cause severe enteric disease in young pigs. Enteric diseases that cause diarrhea in young pigs impact their welfare and are a major source of loss to farmers as there is a high rate of mortality, and those that survive often have reduced growth for the duration of disease and recovery. Often farmers treat young pigs with antibiotics to protect them from bacteria that can cause diarrhea, however this does not protect them from non-bacterial sources of enteric disease, such as viruses, or from disease caused by antibiotic resistant bacteria. There is evidence that commensal microbes that inhabit the guts of animals, the gut microbiome, play a role in priming the immune system to more quickly and efficiently respond to pathogens. Young pigs lack a mature gut microbiome, and treating them with antibiotics further depletes their microbiomes. Given the microbiome's role in priming the immune system to respond to pathogens, introducing microbes that are capable of priming the immune system prior to exposure to pathogens could lead to a more robust immune response to these pathogens and lead to a milder disease, or no disease, as is seen in adult pigs.
I will manipulate the microbiomes of pigs to change the diversity of species present in the gut prior to challenging with Transmissible Gastroenteritis Virus (TGEV). The pigs will be cannulated to allow for access to their ileum microbiome throughout the trial. I will use cutting edge technology to understand how the introduced microbes change the gut microbiome and the pigs' immune responses, and I will identify functional potential in the microbiome that may contribute to changes in the immune response.
I will test candidate bacteria in cells and pig organoids to identify bacteria that trigger changes in homeostatic immune signalling and that impact the response to TGEV infection.
Identifying candidates that protect against TGEV may also be protective more broadly against other enteric coronaviruses and could be used as probiotics to protect pigs from disease.
Overall, this proposal will give important insights into the impact of the gut microbiome on viral diseases of pigs and into microbiome-immune system interactions. This will not only give crucial information on understanding the microbiome's role in pigs' responses to disease but also allow to devise new strategies in combating viral, bacterial, and complex disease, particularly whilst reducing antimicrobial use.

Porcine enteric disease are major concerns of animal health and welfare as well as economic burdens on the pork industry.
There is growing evidence that the composition of the gut microbiome has an impact on the immune response to pathogens. However, in pigs the effect of viral infection on the gut microbiome, and in turn, the effect of the gut microbiome on disease morbidity is poorly understood and understudied. It is well understood that young pigs have substantially higher morbidity and mortality from enteric disease than adults, that young pigs have underdeveloped microbiomes, and that the microbiome has a role in immune development. Recent work has demonstrated that the microbiome impacts immune function in the gut through stimulation of low level interferon-beta expression which primes the immune system to respond to pathogens, and that microbes can affect response to viruses in vitro.
In this project I will manipulate the gut microbiome of cannulated pigs using antibiotics, faecal microbiome transplants and probiotics prior to infection with transmissible gastroenteritis coronavirus (TGEV). I will use long-read sequencing to assemble and characterise the gut microbiome of pigs before, during and after infection. These data will be used to determine how the gut microbiome changes over the course of infection, whether microbiome manipulations persist during infection, and to identify bacteria that may play a functional role in altering morbidity. Additionally I will determine which groups have the lowest morbidity during infection with TGEV, and if increased diversity is associated with lower morbidity in pigs. I will also detect changes in immune signalling between different groups over the course of infection. Bacteria that were enriched pre-infection only in pigs with the lowest morbidity will be tested in vitro in cell lines and enteroids to determine if these bacteria have an impact on immune signalling and improve immune response to TGEV infection.