Progress 11/15/23 to 11/14/24
Outputs
Target Audience:Target audiences reached during this reporting period included: researchers in swine production, microbiomics, food safety and antimicrobial resistance practicing swine veterinarians swine farmers students studying swine production, microbiomics, food safety and antimicrobial resistance. Changes/Problems:We experienced a major delay in obtaining sequence data from the service provider. We have requested a no-cost extension to allow for data analysis of the delayed dataset. What opportunities for training and professional development has the project provided?During this reporting period, a post-doctoral researcher had the opportunity to receive training in machine learning for application to metagenomicdatasets, and presented relevant results at the Symposium on Artificial Intelligence in Veterinary Medicine (SAVY), Cornell University. A graduate student received training in a novel molecular bait enrichment method, and used this training to process a subset of ~150 samples for enriched resistome sequencing. How have the results been disseminated to communities of interest?The results of this project have been presented at numerous conferences, including international conferences attended by swine veterinarians and producers. Of particular note, PI Noyes gave the keynote for the 50th Allen D. Leman Swine Conference, and presented results from this project; the conference was attended by ~750 people, largely practicing swine veterinarians and farmers as well as academics. The project was also presented as an invited presentation at the International Livestock Congress, which is attended by thousands ofinternational producers and veterinarians; and as an invited presentation at the 2023 Annual Meeting of the American Association for Swine Veterinarians, which is attended by thousands of swine veterinarians from across the U.S. What do you plan to do during the next reporting period to accomplish the goals?Our major effort in the next reporting period will be to perform bioinformatic and statistical analysis on the full non-enriched dataset, and to develop these results into multiple manuscripts for submission to peer-reviewed journals. This effort will result in completion ofobjectives #1 and #2.
Impacts
What was accomplished under these goals?
For objectives #1 and #2, we continued to generate the datasets needed to evaluate management modifications on the resistome-microbiome, and to identify microbiome interactions that drive AMR after antibiotic exposures in piglets. To generate more highly-resolved resistome informaiton, we subjected a subset of high-value samples to a molecular bait enrichment workflow to increase sequencing sensitivity for AMR genes. This novel workflow was highly successful, increasing the on-target rate of the resulting sequence data from <1% to >90% across all samples. This enriched dataset is currently being analyzed as we await sequencing results for all of the samples. For objectives #1 and #2, we validated important methodological optimizations for large-scale microbiome-resistome studies in swine populations. Specifically, we demonstrated that pooling samples is a robust method for reflecting individual-level microbiome profiles in pre-weaned swine (paper under review); that a cost-effective "quarter-reaction" library preparation method can be used to generate metagenomic libraries from swine fecal samples; and that swab sampling order does not significantly impact microbiome profiles obtained from pigs. For objective #3, we developed and launched a 5-day short course on microbiome-resistome analysis of metagenomic data. The course is available as an open-source, self-paced tutorial on GitHub (see "Other Products"). The hybrid course was attended by 48 people (21 in-person and 27 online) across 5 countries. Attendees included graduate students, post-docs, faculty and research staff.
Publications
- 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? Allen D. Leman Swine Conference, St. Paul, MN. 21-24 Sept 2024. Keynote.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Noyes, NR. Determinants of Antimicrobial Resistance: From Genes to Ecosystems. Antimicrobial Resistance Conference. West Lafayette, IN. February 27-28, 2024. Keynote.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Noyes, NR. Can we Manage Microbial Populations for Improved Livestock Animal Health, Productivity and Resiliency? International One Health Symposium. Galvaston, TX. April 21-24, 2024. Invited Presentation.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Noyes, NR. Ecology of Antimicrobial Resistance and Implications for Antimicrobial Use and Livestock Management. International Livestock Congress. Houston, TX. February 28-29 2024. Invited Presentation.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Noyes, NR. Modulating the microbiome with feed interventions: Strategies and challenges in swine and livestock production. Annual Meeting of the American Association of Swine Veterinarians. Nashville, TN. February 24-27 2024. Invited Presentation.
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Progress 11/15/22 to 11/14/23
Outputs
Target Audience:Target audiences reached during this reporting period included: researchers in swine production, microbiomics, food safety and antimicrobial resistance practicing swine veterinarians swine farmers students studying swine production, microbiomics, food safety and antimicrobial resistance. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Undergraduate, graduate, DVM students and post-doctoral researchers received training in molecular techniques including automated DNA extraction Graduate DVM/PhD student was trained in resistome analysis We also trained a high school student in DNA extraction, through the StepUp program, which pairs underserved high school students with summer internships within the Twin Cities metro area Post-doctoral researcher was trained in writing conference abstracts; developing scientific presentations; communicating scientific results; and project management. How have the results been disseminated to communities of interest?The results of this project were presented at 3 national conferences attended by scientists, veterinarians and producers. What do you plan to do during the next reporting period to accomplish the goals? Continue to communicate project results and progress to all stakeholders through meetings, seminars and conference presentations Submit a second methods manuscript for peer review at a scientific journal Complete sequencing of all samples Analyze metagenomic data
Impacts
What was accomplished under these goals?
For objectives #1 and #2, we accomplished the following: Completed a formal comparison of pooled versus unpooled sampling approaches(manuscript under review) Completed a formal comparison of sequential sampling andfull- versus 1/4-reaction library preparation methods (manuscript in preparation) Extractedand pooled~12,000 fecal samples Consolidated and validated all metadata related to collected samples Evaluated the effect of commingling and dietary fiber interventions on mortality and average daily gain ofsuckling, weaned and nursery piglets For objective #3, we initiated a GitHub repository and populated it with input files and scripts that accompany the two formal comparisons completed under Objectives #1 and #2.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Gaire T. N., Wehri T., Young J., Schwartz M., Singer R., Pieters M., Noyes, N. Individual samples
provide the most comprehensive profile of the piglet fecal microbiome, but pooled samples accurately
reflect individual-level microbial composition (poster #101). Allen D. Leman Swine Conference,
September 1619, 2023, Saint Paul, Minnesota, USA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Gaire T. N., Wehri T., Brown D., Snow C., Hsu J. C., Diaz Ortiz G. R., Meneguzzi M., Young J., De
Abreu C., Canturri A., Pena Mosca F., Medrano M., Miller L., Li S., Ruch M., Schwartz M., Singer R.,
Pieters M., Noyes N. Effect of Commingling and Dietary Fiber Interventions on Select Performance of
Suckling, Weaned and Nursery Piglets,�SafePork�14(1) (oral presentation), Safe Pork Conference, May
15-17, 2023, New Orleans, USA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Gaire T.N., Wehri T., Brown D., Snow C., Hsu J.C., Slizovskiy I.B., Lopez O.J., Diaz G.R.,
Meneguzzi M., Young J., De Abreu C.F., Canturri A., Pena Mosca F., Medrano M., Miller L., Li S.,
Ruch M., Schwartz M., Singer R., Pieters M., Noyes N.R. Effect of commingling and dietary fiber
interventions on select performance metrics of suckling and weaned pigs (abstract #4). Proceedings of
the 103rd Annual Conference of Research Workers in Animal Disease (CRWAD), January 2224,
2023, Chicago, IL, USA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Gaire T.N., Wehri T., Young J., Schwartz M., Singer R., Pieters M., Noyes N.R. Pooled piglet fecal
samples accurately reflect individual-level fecal microbial composition (abstract #132). Proceedings
of the 103rd Annual Conference of Research Workers in Animal Disease (CRWAD), January 2224,
2023, Chicago, IL, USA
- Type:
Journal Articles
Status:
Submitted
Year Published:
2024
Citation:
Pooled samples accurately reflect the fecal microbiome of individual piglets from the same litter. Tara N. Gaire; Jared Young; Thomas Wehri; Mark Schwartz; Randall Singer; Maria Pieters; Noelle Noyes.
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Progress 11/15/21 to 11/14/22
Outputs
Target Audience:During this reporting period, our target audiences included swine producers and swine worekrs, veterinarians, and researchers in the field of animal microbiome and AMR. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Undergraduate, graduate, DVM students and post-doctoral researchers received training in commercial swine husbandry, handling and production. Undergraduate, graduate, DVM students and post-doctoral researchers were trained in how to collect samples from piglets in a commercial swine farm. Graduate, DVM students and post-doctoral researchers were trained in DNA extraction from rectal swabs, including pooling of raw sample and extracted DNA. Post-doctoral researcher was trained in 16S microbiome bioinformatics and statistical analysis. Post-doctoral researcher was trained in writing conference abstracts; developing scientific presentations; communicating scientific results; and project management. How have the results been disseminated to communities of interest?The results of our study have been disseminated to researchers and key stakeholders through oral presentations at several national and international conferences including International Symposium of Veterinary Epidemiology and Economics (ISVEE) in Canada; International Pig Veterinary Society Congress in Brazil, Conference of Research Workers in Animal Disease (CRWAD) in the US. We have shared our findings with swine producer through on-farm meeting and presentations. We also shared these results with graduate students and faculty members within our College of Veterinary Medicine, which allowed us to receive feedback and input on the project implementations and relevance of our study study to commercial swine productions. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting report, we will: complete DNA extractions from all samples collected during the randomized control trial study, and submit them for metagenomic library preparation and sequencing (Objectives #1 and #2) consolidate all metadata related to this study in order to initiate the data analysis (Objectives #1 and #2) evaluate the effect of commingling and dietary fiber interventions on select performance of suckling, weaned and nursery piglets (Objectives #1 and #2) continue to communicate project results and progress to all stakeholders through meetings, seminars and conference presentations
Impacts
What was accomplished under these goals?
During this reporting period, we: implemented and completed a randomized controlled trial with two interventions, across 3 different commercial facilities (objectives #1 and #2) collected ~12,000 fecal samples from ~800 pigs; each pig was sampled ~15 times from birth to marketing(objectives #1 and #2) optimized our DNA extraction protocol for high-throughput robotic processing(objectives #1 and #2) completed analysis of production data (pig weights and mortality) and analyzed associations between commingling strategy and creep feed fiber levels (objective #1)
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Gaire T.N., Wehri T., Young J., Schwartz M., Singer R., Pieters M., Noyes N. Does the fecal microbiome vary based on individual, composite individual, and pooled DNA samples? A pilot study (Poster abstract # P070). 102nd Conference of Research Workers in Animal Diseases (CRWAD), December 47, 2021, Chicago, IL, USA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gaire T.N., Wehri T., Young J., Schwartz M., Singer R., Pieters M., Noyes N. Does the piglet fecal microbiome vary between individual, composite individual, and pooled DNA samples?: A pilot study. International Symposia on Veterinary Epidemiology and Economics proceedings, Volume ISVEE 16: Proceedings of the 16th Symposium, Halifax, Canada, Issue Oral Presentations, pp 363, Aug 2022
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gaire, T.N., Wehri, T., Young, J., Schwartz, M., Singer, R., Pieters, M., Noyes, N. Does the piglet fecal microbiome vary between individual, composite individual, and pooled DNA samples? A pilot study. Proceedings of the International Pig Veterinary Society Congress. June 2022. Rio de Janeiro, Brazil.
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Progress 11/15/20 to 11/14/21
Outputs
Target Audience:
Nothing Reported
Changes/Problems:We planned to initiate the main sampling campaign during the first reporting period. However, the sow facility where we are going to run the trial experienced a severe PRRS outbreak (as part of the ongoing PRRS 144 outbreak), and therefore we had to delay the start of the sampling campaign. Nothing has changed with the approach, but the timeline has been delayed by ~6 months. What opportunities for training and professional development has the project provided?Undergraduate, graduate, DVMstudents and post-doc researchers were trained in how to collect samples from piglets in a commercial swine farm. Graduate, DVMstudents and post-doc researchers were trained in DNA extraction from rectal swabs, including pooling of raw sample and extracted DNA. Post-doc was trained in 16S microbiome bioinformatics and statistical analysis. Post-doc was trained in writing conference abstracts;developing scientific presentations; communicating scientific results; andproject management. How have the results been disseminated to communities of interest?Results of the pilot work have been communicated to several swine producers through one-on-one meetings. Their input has been integrated into the study design and project implementation in order to ensure applicability of the project results to commercial swine production. What do you plan to do during the next reporting period to accomplish the goals?We will initiate and complete the large randomized longitudinal interventional campaign in the next reporting period, including collection of all samples. All samples will be subjected to total DNA extraction and submitted for metagenomic library preparation and sequencing.
Impacts
What was accomplished under these goals?
We completed a large pilot study, which helped us tofinalize the sample collection and processing protocols for the project that underlies Specific Aims 1, 2 and 3. We established partnership with a commercial swine farm operator and identified a suitable facility in which to conduct the project that underlies Specific Aims 1, 2 and 3. We developed a protocol for implementing the study design, including selection of study animals and executing the plannedinterventions (commingling and diet). We recruited undergraduate, DVM and graduate students to help with sample collection for the large project the underlines Specific Aims 1, 2 and 3.
Publications
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