Source: UNIV OF MINNESOTA submitted to NRP
ASSESSING THE MICROBIOME AS A TOOL FOR THE MITIGATION OF VIRAL DISEASE IN NURSERY PIGS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1031642
Grant No.
2020-67015-41527
Cumulative Award Amt.
$237,204.00
Proposal No.
2023-10659
Multistate No.
(N/A)
Project Start Date
Dec 1, 2023
Project End Date
May 31, 2025
Grant Year
2024
Program Code
[A1221]- Animal Health and Production and Animal Products: Animal Health and Disease
Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
(N/A)
Non Technical Summary
Porcine reproductive and respiratory syndrome virus (PRRSV) causes the most costly disease to swine production in the UnitedStates. Disease caused by this virus often involves secondary bacterial pathogens, which exacerbates respiratory disease andincreases antimicrobial administration in young growing pigs. Although commercial vaccines are used to reduce the effects ofPRRSV on swine health, the currently available vaccines are considered inadequate for disease control. Alternative strategiesfor control of PRRSV is needed to maintain swine health and welfare while lessening the economic effects of this disease onpork producers. The goal of this work is to investigate the gut microbiome as an alternative tool for PRRSV control due to itsimpact on the immune system and outcome after infection. Objectives of the work include investigating the effects ofmicrobiome modulation on outcome of swine with respiratory disease and identifying what beneficial microbes are associatedwith improved health. We anticipate the data generated in this project will allow us to characterize and determine the gutmicrobes which improve pig health in the presence of PRRSV. Our goal is to determine how beneficial gut microbes may beused as a preventative medicine tool to reduce the effects of respiratory disease and decrease the need for antimicrobials inswine. The impacts of this work will improve animal welfare and animal health, lessen the economic losses to producersassociated with PRRSV, and reduce the risk of antimicrobial resistance in swine.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3113510110025%
3113510110335%
3113510208015%
3113510109025%
Knowledge Area
311 - Animal Diseases;

Subject Of Investigation
3510 - Swine, live animal;

Field Of Science
1090 - Immunology; 1103 - Other microbiology; 1100 - Bacteriology; 2080 - Mathematics and computer sciences;
Keywords
Goals / Objectives
Project goals are centered on investigating microbiome modulation as a potential tool for mitigating the effects ofpolymicrobial respiratory disease on growing pigs. The major outcome of this project is to understand what gut microbesprovide improved outcomes in pigs using a model of porcine respiratory disease complex. Overall, project outcomes includeidentifying gut microbes for improving the health and welfare of pigs with porcine reproductive and respiratory syndrome(PRRS) and a potential alternative tool for mitigating the effects of respiratory disease in swine. Objectives includedetermining the effects of microbiome modulation on outcome of pigs following co-infection with PRRS virus and porcinecircovirus type 2. We will compare clinical disease, mortality, virus replication, growth performance, pathology, antibodyproduction, cytokine expression, and microbiome characteristics with unmodulated co-infected controls. Gut microbesassociated with beneficial outcomes will be identified.
Project Methods
A randomized controlled viral challenge study will be used to generate data regarding the role and efficacy of fecal microbiome transplantation on swine health and production outcomes. During the trial, multiple tissue samples will be taken longitudinally from study pigs and subjected to several methods including immunological assays (to assess host response) and microbiome assays (to assess microbiome profiles before, during and after challenge and treatments). Pig health and performance will be measured throughout the trial. Data will be analyzed using multivariable time series analysis to understand how treated versus control pigs differ in their response to the viral challenge. Any microbes found to be strongly protective against clinical disease and/or death will be subjected to available culture methods in order to establish an isolate bank of "top candidate" protective microbes.

Progress 12/01/23 to 11/30/24

Outputs
Target Audience:The target audiences reached during this period included >600 attendees of the Allen D. Leman Swine Conference, which includes swine veterinarians and producers from across the U.S. and internationally. The audiences also included attendees of the 2024 Annual Conference for Research Workers in Animal Diseases, which attacts >400 livestock and animal researchers from industry, academia and government. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A post-doctoral researcher was trained in DNA extraction, 16S microbiome analysis and shotgun sequencing analysis. The same post-doctoral researcher was trained in anaerobic culture technique. How have the results been disseminated to communities of interest?We disseminated results at two national conferences, the Allen D. Leman Swine Conference and the annual Conference for Research Workers in Animal Diseases. The project was also included in the keynote lecture given by PI Noyes at theannual Conference for Research Workers in Animal Diseases. What do you plan to do during the next reporting period to accomplish the goals?We will analyze the shotgun metagenomic sequencing data and obtain pure cultures of the potentially beneficial microbe identified through the work completed in the current reportingperiod. We will sequence the pure cultures to initiate a biobank of potentially beneficial microbes for use in pigs during viral infection. We will submit all project results for peer review at a scientific journal, and we will disseminate project findings at national conferences.

Impacts
What was accomplished under these goals? We extracted DNA from all samples collected as part of the fecal microbiome transplant trial, and performed library preparation and 16S rRNA sequencing on the extracted DNA. We analyzed the resulting microbiome data and identified microbiome dynamics associated with improved health and performance outcomes in the pigs. We then used these results to select a subset of samples for more in-depth metagenomic sequencing and analysis. Additionally, we identified a potentially beneficial microbal genuswithin the microbiome and initiated protocol development to culture this anaerobe from banked gastrointestinal samples.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Deng, Y., Khanal, P., Deavours, A., Cino-Ozuna, A. G., Niederwerder, M. C., & Noyes, N. R. (2024, January 20-23). Fecal microbiota transplant (FMT) as a tool for the mitigation of respiratory virus infections in nursery pigs [Poster presentation]. CRWAD 2024, Chicago, IL, United States. https://crwad.org/2024-presentations-and-abstracts/
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2024 Citation: Deng, Y., Khanal, P., Deavours, A., Cino-Ozuna, A. G., Niederwerder, M. C., & Noyes, N. R. (2024, September 21-24). Fecal microbiota transplant (FMT) as a tool for the mitigation of respiratory virus infections in nursery pigs [Poster presentation]. Leman Swine Conference 2024, St Paul, MN, United States.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Noyes NR. Engineering the microbiome: Can we harness the hidden heroes of livestock production? [Keynote Lecture]. Leman Swine Conference 2024, St Paul, MN, United States.