Source: KENTUCKY STATE UNIVERSITY submitted to NRP
TRAINING IN PROTEOMICS, METAGENOMICS AND METABOLOMICS TO DEVELOP AND ENHANCE RESEARCH AND TEACHING CAPACITIES IN ANIMAL AND POULTRY SCIENCES AT KENTUCKY STATE UNIVERSITY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1021804
Grant No.
2020-38821-31110
Cumulative Award Amt.
$99,770.00
Proposal No.
2019-03295
Multistate No.
(N/A)
Project Start Date
Jun 1, 2020
Project End Date
May 31, 2023
Grant Year
2020
Program Code
[EQ]- Research Project
Recipient Organization
KENTUCKY STATE UNIVERSITY
(N/A)
FRANKFORT,KY 40601
Performing Department
CACE
Non Technical Summary
The College of Agriculture, Communities and the Environment (CACE) at Kentucky State University (KSU) is committed to expanding and incorporating new livestock research technologies into established and existing programs. This professional development project will provide the project director (PD) a unique opportunity to acquire knowledge and skills in "-omics" techniques that would enable the profiling of livestock microbial populations, thus providing greater insights into the mechanisms of action of natural antimicrobials (phytobiotics, prebiotics, and probiotics). Natural antimicrobials are known to enhance performance, immune response, and gastrointestinal microbial diversity in livestock and are now popularreplacements forantibiotics in livestock feeding. The "-omics" are a set of emerging technologies that include genomics (study of genes and their functions), proteomics (study of proteins), and metabolomics (study of molecules involved in cellular metabolism). These techniques offer the advantages of rapidly and reliably detecting, measuring, quantifying and comparing thousands of metabolites in a single sample simultaneously and allow numerous significant economic traits associated with livestock production to be assessed routinely, non-invasively, and often at a lower cost than current techniques.This unique training opportunity will be offered by the USDA ARS Animal Biosciences & Biotechnology Laboratory inBeltsville, MD, and the Ruminant Nutrition and Metabolism and the Proteomic and Metabolomic Center Laboratories at Montana State University (MSU) in Bozeman, MT. Research in livestock has been identified as one of the main areas of utmost benefit to KSU's stakeholders, the limited-resource and minority rural and urban farmers of the Commonwealth of Kentucky. The PD is establishing a research program in natural antimicrobials that will incorporate the latest application of "-omics" techniques to improve health and growth performance of pasture-based, small-scale, limited-resource poultry production systems.The specific objective of this project is to build capacity in the use of metagenomics, proteomics, and metabolomics to enhance research in livestock microbiota characterization and quantification. The outcome of this project will help strengthen the PD's capabilities in a cutting edge biotechnology field that will not only benefit the research capacity of KSU livestock and poultry research programs, but will also provide opportunitiesfor experiential learning for students. This professional development project supports one of the major goals of USDA 1890 CBG Program, which is to "enhance and strengthen the quality of research, teaching/education and Extension programs at the 1890 institutions to more readily establish them as full partners in the US FANH sciences higher education system." The project also supports three of NIFA's high-priority areas identified in the FY2019 1890 capacity building grant request for applications: food safety, global food security and agricultural biosecurity, and sustainable agriculture.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30232991010100%
Knowledge Area
302 - Nutrient Utilization in Animals;

Subject Of Investigation
3299 - Poultry, general/other;

Field Of Science
1010 - Nutrition and metabolism;
Goals / Objectives
To build capacity in the use of metagenomics, proteomics and metabolomics to enhance research in livestock microbiota characterization and quantification.
Project Methods
The professional development training will take place at the USDA ARS Animal Biosciences & Biotechnology Laboratory in Beltsville, MD, and at the MSU Ruminant Nutrition and Metabolism Laboratory and the Animal Bioscience Labs and Core Facilities for NMR-MS, Proteomics, Metagenomics, and Metabolomics Research in Bozeman, MT.The training will explore mechanisms of action by which natural antimicrobials may improve health and growth performance of livestock, such as enhancement of specific and non-specific immune responses, production of antimicrobial compounds, competition for nutrients and colonization sites using the latest -omics techniques.Animal Bioscience Biotechnology Laboratory, Beltsville, MDThe PD will learn procedures for a) performing metabolomics analysis in poultry samples; b) construction of DNA libraries for 16s microbial sequencing using the Illumina Mi-Seq instrument; and c) data analysis using Qiime or related software.MSU Animal Bioscience Labs and Core Facilities for NMR-MS, Proteomics, Metagenomics and Metabolomics Research, Bozeman, MTThe PD will learn procedures for a) methods in animal genomics, metagenomics, and metabolomics; b) methods in microbial genomics, metagenomics, and metabolomics; c) procedures for metagenomics profiling of microbial communities in poultry samples; d) high-throughput analysis of targeted and untargeted metabolites via nuclear magnetic resonance (NMR) and NMR/mass spectrometry (MS); and e) multivariate statistical analysis, integration, and quality control.

Progress 06/01/20 to 05/31/23

Outputs
Target Audience:Students that will benefit through training in microbial genomics research methods. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Phase I:The PD participated in workshops, conferences and other related professional development activities organized by the MSU's Department of Animal and Range Sciences. He was also provided with reading and instructional material related to the project goal. Phase II included Field and Laboratory work. Field work included training in local anesthasia and punch biopsy of bovine liver samples for herpatic gene expression. Laboratory training includedRNA extraction cDNA synthesis, immune gene expression using real-time PCR. Blood plasma samples were analyzedfor untargeted metabolome through a commercial laboratory. The PD also received training in metabolomics data analysis and interpretation. How have the results been disseminated to communities of interest?Part of the data generated from the training has been analyzed and results disseminated through a refereed journal article already accepted for publicatrion. Another manuscript is being prepared covering rest of the data genaratedper project objective -see Product Section above. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The outcome of this project will help strengthen the PD's capabilities in a cutting edge biotechnology field that will not only benefit the research capacity of KSU livestock and poultry research programs, but will also provide opportunities for experiential learning for students. This project was accomplished in two phases: Phase I -Fall of 2021 at Montana State University's Animal Bioscience Laboratory, after a year's delay due to the COVID-19 pandemic. The Project Director (PD) received training through workshops and conferences on methods and applications on animal and microbial genomics. Poultry cecal samples from a previous study were outsorced to the Argonne National Laboratory for microbiome analysis due to workload and timing issues resulting from the ovid-19 pandemic. The data hasbeenstatistically analized, collated and an a manuscript is being prapared for publication - see Products Section above. Phase II - Fall 2022 / Spring 2023 This phase of the training at the USDA Animal Bioscience and Biotechnology Laboratory (Beltsville, MD) was transfered to West Virginia University Animal Nutrition& Biotechnology Laboratory (ANBL) dueto delays resulting from the Covid-19 pandemic and thefact that the laboratory was moving into a new facility. Accomplishments West Virginia ANBL included field punch biopsy of bovine liver samples forhepatic gene expression. Laboratory training included RNA extraction,cDNA synthesis and Immune gene expression using real-time PCR. Blood samples (n = 50) weresent out to a commercial lab for untargeted metabolome analysis of plasma samples, after which metabolomics data analysis and interpretation of metabolomics data were conducted.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2023 Citation: Modoluwamu Idowu, Godstime Taiwo, Taylor Sidney, Frederick Bebe, Matthew Wilson, and Ibukun M. Ogunade. 2023. The differential plasma and ruminal metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers. Frontiers in Animal Science.
  • Type: Journal Articles Status: Other Year Published: 2023 Citation: Effect of a phytogenic and synbiotic supplementation on performance, immune response and cecal microbiota of pastured broiler chicken (Under Preparation)


Progress 06/01/21 to 05/31/22

Outputs
Target Audience: Nothing Reported Changes/Problems:The project was negatively impacted by delays due to the Covid-19 pandemic. The first part of the training was achieved last Fall at Montana State University's Animal Bioscience Laboratory. The second phase of the training at the USDA Animal Bioscience abd Biotechnology Laboratory Beltville, MD could not take place this Spring 2022 for similar reasons,and also the fact that the laboratory is moving to a new facililty. The PD may be obliged to suggest another training location/laboratory should it not be possible to achieve full training (as in the project objective) this Fall 2022 at the Beltsville, MD location. What opportunities for training and professional development has the project provided?The PD participated in workshops, conferences and other related professional development activities organized by the MSU's Department of Animal and Range Sciences. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?The PD is in constant communication with Dr. Kate Miskathe responsible mentor(s) at USDAAnimal Bioscience and Biotechnology Laboratory (Beltsville, MD)so as to accomplish the second phase of training in the Fall of this year. Accordingly, The PD will be submitting a formal request for an extension.

Impacts
What was accomplished under these goals? The outcome of this project will help strengthen the PD's capabilities in a cutting edge biotechnology field that will not only benefit the research capacity of KSU livestock and poultry research programs, but will also provide opportunities for experiential learning for students. Part of this project was accomplished lastFall of 2021atMontana State University's Animal Bioscience Laboratory, after a year's delay due to the COVID-19 pandemic. The Project Director(PD) received training through workshops and conferences on methods and applications on animal and microbial genomics.Some of the PD's poultry cecal samples from a previousstudy were outsourced to the Argonne National Laboratory for microbiome analysis due to workload and timing issues.The data has just been received and is being studied, in collaboration with MSU mentors. Meanwhile, training at the USDA Animal Bioscience and Biotechnology Laboratory (Beltsville, MD) in poultry metabolomics, construction of DNA libraries for 16s micriobial sequencing and data analysis using Qiime could not take place this Spring as planned because of delays due to the Covid-19 pandeminc and the fact the laboratory is moving to a new and modern facility this Summer. According to USDA mentor Dr. KateMiska (molecular biologist), trainingmay only be possible in the Fall (2022). Thus, the PD will be requesting another no-cost extension of the grant.

Publications


    Progress 06/01/20 to 05/31/21

    Outputs
    Target Audience: Nothing Reported Changes/Problems:This project was negatively impacted by the COVID-19 pandemic. It was not started. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?The PD is in constant communication with the responsible mentors at USDA Beltsville and Montana State University so as to be able to resume training in the Summer and Fall of this year. Accordingly, The PD will be submitting a formal request for an extension. Hopefully normal operations will soon resume.

    Impacts
    What was accomplished under these goals? The outcome of this project is expected to provide the PD with a unique opportunity to acquire knowledge and skills in proteomics, metagenomics and metabolomics techniques important in improving the health and performance of pasture-based poultry systems in Kentucky, and to provide opportunities for experiential learning for students. This project was supposed to be accomplished in the Summer and Fall of 2020 at the USDA ARS Animal Biosciences & Biotechnology Laboratory in Beltsville, MD and Montana State University's Animal Bioscience Laboratory, respectively. However, work and access to these laboratories were either restricted or closed due to the COVID-19 pandemic.

    Publications