Source: UNIV OF MINNESOTA submitted to NRP
MANAGEMENT OF ORGANIC DAIRY YOUNGSTOCK (MOODY): A NETWORK TO IMPROVE LONG-TERM SUSTAINABILITY OF ORGANIC DAIRY FARMS THROUGH IMPROVED YOUNGSTOCK MANAGEMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
1032792
Grant No.
2024-51300-43145
Cumulative Award Amt.
$3,499,991.00
Proposal No.
2024-03313
Multistate No.
(N/A)
Project Start Date
Sep 1, 2024
Project End Date
Aug 31, 2028
Grant Year
2024
Program Code
[113.A]- Organic Agriculture Research & Extension Initiative
Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
(N/A)
Non Technical Summary
The goal of this project is to support long-term sustainability of organic dairies through improved young cow ("youngstock") liveability and performance. Three objectives support this goal: 1) Optimize youngstock management on organic dairy farms; 2) Identify on-farm source(s) and route(s) of Staphylococcus aureus intramammary infections in organic youngstock; and 3) Provide organic dairy educational materials to U.S. veterinary students.To accomplish these objectives, we assembled a national team spanning the Midwest, Northeast, Mountain West, Pacific Northwest and Southwest; with experts in youngstock health and welfare; organic dairy production; mastitis epidemiology; national farm surveys; and dairy education. The project is guided by an Advisory Board including major stakeholders in organic dairy production.Integrated project activities include national surveys of youngstock management practices; comprehensive on-farm youngstock health assessments; and multi-year data collection to document long-term outcomes that directly impact farm profitability. Innovative statistical and molecularmethods will beused to analyze these information-rich datasets to findrelationships between on-farm practices, youngstock health and performance, and profit-bearing outcomes. Findings are brought back to farmers through practical, evidence-based recommendations and support for youngstock management. Project outcomes address a critical need for organic dairy farmers to optimize youngstock outcomes for sustained herd size.
Animal Health Component
75%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3013410117010%
3073410117020%
3113410117020%
3073410209020%
3113410209010%
3113410110010%
3153410117010%
Goals / Objectives
The long-term goal of this project is to improve the profitability of organic dairy producers through optimal youngstock performance, health and welfare. To acheive this goal, we propose three major objectives,as follows:Objective #1 is to optimize youngstock management on organic dairy farms. To accomplish this, we have 3 sub-objectives: 1a) Establish a network focused on management of organic youngstock ("MOODY"); 1b) Identify management risk factors associated with youngstock health, welfare and performance; and 1c) Provide evidence-based guidance to producers, veterinarians and extension agents to enhance management for optimized youngstock health, welfare and performance.Objective #2 is to identify the on-farm source(s) and route(s) of S. aureus intramammary infections in organic youngstock. We accomplish this through an on-farm research campaign that is integrated with the on-farm activities conducted under objective #1.Objective #3 is to provide organic dairy educational materials to U.S. veterinary schools and students. We will do this through two sub-objectives: 3a) Develop and deliver a modular curriculum focused on veterinary-relevant issues related to organic dairy farms; and 3b) Train veterinary and animal science students to conduct on-farm youngstock health assessments specific to organic dairy farms.
Project Methods
There are several important methods components for Objective #1 activities:The "survey sandwich" method: This term refers to our flipped approach for administering a nationwide survey, and was developed in consultation with key stakeholders. Specifically, our partners reported a notable decrease in survey and research participation by organic dairy farmers over the past 1-2 years. Based on this input, we greatly increased the amount of pre-survey outreach in our approach, leading to the "sandwich method", i.e., pre-survey outreach → survey → post-survey outreach. The pre-survey outreach will significantly increase: 1) farmer participation rates; 2) survey relevance for farmer-drive priorities.Choice of scoping review. The choice of a scoping review (versus a systematic review) was made because we expect that the scope of available relevant literature may not be large enough to support a formal systematic review. However, if sufficient literature is identified, we will define a question for full systematic review.Use of DAGs and target trials analysis. Causal diagrams (such as DAGs) are increasingly used in epidemiological research to better identify true causal relationships between study variables [21]. DAGs have been shown to improve systematic review and survey usability [22] and generate more accurate results from statistical analyses of applied health datasets, particularly when multiple confounders are present [23, 24]. Target trials are also built on a causal inference framework and can be used to emulate a randomized controlled trial using observational "big data" [18]. We decided to use these methods to maximize the utility of the data being collected, and to generate more useful causal inferences from the datasets. While causal inference has made significant headway in human research, it is relatively novel within livestock research.Longitudinal calf-level follow-up. Individual, serial calf measurements are a major portion of our project budget and effort. We decided to make this investment for several key reasons: 1) provides robust data for causal inference methods; 2) allows us to collect prospective health and outcome data, greatly increasing the accuracy of these key metrics; 3) provides an estimate of variability over time and season. Thus, our investment pays off in terms of accuracy and utility.Objective 2 MethodsOn-farm samples will be collected from possible S. aureus sources, includinglactating cows, whole waste milk fed to calves, nurse cows, biting flies, cross-sucking behavior, and skin lesions. All samples will be subjected to culture for S. aureus using standard methods and in-depth strain typing of S. aureus isolates. To obtain strain-level information, we will extract DNA from cultured isolates and subject the DNA to library preparation and short- and long-read whole-genome sequencing (WGS). Resulting data will be analyzed using the Bactopia pipeline, including use of subworkflows specific to S. aureus.We will combine the S. aureus prevalence information with the management and health data collected in Objective #1 to identify farm- and animal-level risk factors for S. aureus. For strains with high enough prevalence, we will conduct a strain-specific risk factor analysis. We will use the WGS strain-level data to identify likely routes of S. aureus transmission to youngstock. Specifically, we will use SNPs as markers for a modified microbial source tracking (MST) analysis, which supports identification of source(s) and sink(s) of specific populations of bacteria (in this case, strains of S. aureus), within a defined environment (in this case, the farm). If not enough strain-specific data exist for MST, we will evaluate phylogenetic clustering patterns to identify strains found across youngstock and environmental samples within a farm, indicating a likely transmission route.Objective 3 MethodsWe will use a four-step process to complete the objective: 1) Information-gathering; 2) Online modules development; 3) Online modules implementation and evaluation; 4) Fine tuning and dissemination.The decision to develop online modules was driven by the realities of dairy education at U.S. institutions of higher education. In essence, individual veterinary or animal science programs are unlikely to possess the requisite students, resources, faculty expertise, or facilities to adequately address the needs of the organic dairy industry on a national scale. Therefore, we decided to pursue a modular online curriculum, which can be an effective education tool for topical areas experiencing faculty shortages; in some cases, such tools even facilitate cross-institutional collaborations.

Progress 09/01/24 to 08/31/25

Outputs
Target Audience:Major outreach efforts during this first reporting period focused on organic dairy producers as the target audience. The goals of these efforts were to: 1) collect input on the national survey that was developed during the reporting period; 2) advertise the project and the survey to organic dairy producers across the U.S.; 3) recruit dairy producers to enroll in on-farm sampling and to complete the survey; 4) connect producers to discuss youngstock management challenges and success stories. We achieved these goals through the following activities: Presentations about the project at major stakeholder events including the Western Organic Dairy Producers Alliance conference and trade show; the Research Roundtable hosted by Organic Valley; andAgNext's Industry Innovation Working Group Meeting. Discussions (video conferences, phone calls)about the project and national survey with key stakeholder groups including Organic Valley, Horizon Organic, and local and regional processors Discussions about the project and on-farm sampling with dairy veterinarians and nutritionists who service a large number of organic dairy farms across all regions represented in the project Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Multiple graduate, undergraduate and veterinary students were trained in sample collection procedures (jugular venipuncture, nasal and rectal sampling), health examinations and on-farm data collection. Four graduate students and three veterinary students were trained in thoracic ultrasonography for assessing lung integrity in cattle. One graduate student was trained in survey development, including use of Qualtrics and survey validation procedures. Four techniciansreceived on-job training in on-farm field activities, lab organization, and parasitology examinations. One graduate student was trained in best practices for data management, including script development using RStudio and GitHub. One post-doc was trained in scoping review protocols and educational module development. Multiple graduate, undergraduate and veterinary students had opportunities for professional development in science communication, through presenting the project at internal student symposia and external conferences. How have the results been disseminated to communities of interest?Organic dairy producers enrolled in the on-farm sampling are receiving individualized farm-level reports after every visit. This allows them to understand the health status of their youngstock over time. Once enough data are collected, we will expand this report to include anonymized and aggregated results across all farms, so that producers can compare their results to the other farms in the study. We have raised awareness about the MOODY project to organic dairy producers across the U.S. through presentations at major stakeholder events at the local, regional and national levels; through mailing lists managed by key value-chain stakeholders; and through individual conversations with organic dairy producers, veterinarians and nutritionists. We started a soft launch of the national survey by sending the survey link to a select group of dairy producers. We have disseminated initial study design and implementation details to other researchers through presentations at scientific conferences and individual video conferences with researchers who have also conducted on- and off-farm surveys. What do you plan to do during the next reporting period to accomplish the goals?For objective #1 goals, we plan to: Conduct an intensive and sustained launch of the national survey (once we have results from the soft launch), to include digital and paper-based mailings and advertisements Enroll at least 18 more farms for the on-farm efforts and continue quarterly visits of all enrolled farms Continue to analyze, summarize and interpret on-farm results, and provide tailored reports back to enrolled farmers Complete a scoping review of organic youngstock management practices Develop a detailed analytical plan for the national survey results For objective #2goals, we plan to: Evaluate the S. aureus status of each farm enrolled in the on-farm activiites as part of Objective #1, and use these results to select a subset of farms for enrollment in Objective #2 Establish detailed protocols for on-farm sample collection, storage and processing for S. aureus Complete on-farm sample collection and begin sample processing For objective #3goals, we plan to: Complete a scoping review of current veterinary-focused educational material related to organic dairy production Outline and begin developing the module content for the proposed educational material Identify subject-matter experts to provide input on module content

Impacts
What was accomplished under these goals? For objective #1, the following accomplishments were achieved during the reporting period: A national survey of organic youngstock practices was developed and beta-tested (using Qualtrics). The survey is now fully launched and responses are being collected. >20 individuals SOPs were developed for on-farm sample collection, on-farm youngstock health exams, and on-farm data collection. These SOPs are supporting standardized on-farm youngstock assessments across all regions. 32 organic dairy farms across 7 U.S. states were enrolled into on-farm sampling and survey. 12 of these farms have been visited 3 times; 12 have been visited twice; and 8 have been visited once so far. At each visit, sample collection and health examshave been performed on youngstock of various ages. Farmers were administered a comprehensive survey at the initial farm visit, and were shown how to collect youngstock health event information in a standardized manner. Health even information is then collected at each subsequent visit. Laboratory results from collected samples are being collected on an ongoing basis. A farm-level summary of laboratory and health exam results was developed and is being used on an ongoing basis tocommunicate individual farm results with producers. A scoping review protocol was developed to guidea peer-reviewed publication on current literature related tomanagement of organic dairy youngstock in the U.S. For objective #2, the following accomplishments were achieved during the reporting period: A literature review was conducted to understand bestpractices to collect and culture fly speciespreviously demonstrated to be sources of Staphylococcus aureus for young dairy cattle. Four species of flies were found to be potentially important for different routes of S. aureus transmission. A pilot project was conducted to develop biting fly collectionmethods. This pilot encompassed 4 different fly collection methods. Preliminary results indicate that nosingle approachworks for all 4 species of flies, and thus multiple collection methods may be needed for a comprehensive collection of fly species on enrolled dairy farms. A series of experiments was conducted to comparemethods for culturingflies to collect S. aureus isolates for strain typing. Preliminary results are pending. For objective #3, the following accomplishments were achieved during the reporting period: A literature review was conducted to catalog the current available resources for veterinary education related toorganic farming that will help to develop the modular curriculum.

Publications