Use of a Timely Topics Web Tool to Enhance Research-Based Extension Program Impact

Developing creative, impactful methods for delivering research-based Extension educational material is often challenging. However, options have increased as technological advancement has made online learning accessible to stakeholders, producers/farmers, and the general public alike. An interactive timely topics web tool (TTW) can enhance interaction with a program home page to aid Extension professionals in effectively disseminating relevant information to users. Use of an equine program TTW broadened the reach of programmatic resources to national and international scales and increased new and repeat contacts with the educational website. Providing opportunities for interactive web-based learning may enhance implementation of recommended practices and reportable outcomes within Extension programs

Effects of Red Clover Isoflavones on Tall Fescue Seed Fermentation and Microbial Populations \u3cem\u3eIn Vitro\u3c/em\u3e

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo

Rumen and Serum Metabolomes in Response to Endophyte-Infected Tall Fescue Seed and Isoflavone Supplementation in Beef Steers

Fescue toxicosis impacts beef cattle production via reductions in weight gain and muscle development. Isoflavone supplementation has displayed potential for mitigating these effects. The objective of the current study was to evaluate isoflavone supplementation with fescue seed consumption on rumen and serum metabolomes. Angus steers (n = 36) were allocated randomly in a 2 × 2 factorial arrangement of treatments including endophyte-infected (E+) or endophyte-free (E−) tall fescue seed, with (P+) or without (P−) isoflavones. Steers were provided a basal diet with fescue seed for 21 days, while isoflavones were orally administered daily. Following the trial, blood and rumen fluid were collected for metabolite analysis. Metabolites were extracted and then analyzed by UPLC-MS. The MAVEN program was implemented to identify metabolites for MetaboAnalyst 4.0 and SAS 9.4 statistical analysis. Seven differentially abundant metabolites were identified in serum by isoflavone treatment, and eleven metabolites in the rumen due to seed type (p \u3c 0.05). Pathways affected by treatments were related to amino acid and nucleic acid metabolism in both rumen fluid and serum (p \u3c 0.05). Therefore, metabolism was altered by fescue seed in the rumen; however, isoflavones altered metabolism systemically to potentially mitigate detrimental effects of seed and improve animal performance

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics—in addition to the traditional considerations when conducting an animal science study—makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type

Rumen biogeographical regions and their impact on microbial and metabolome variation

The rumen microbiome is a complex microbial network critical to the health and nutrition of its host, due to their inherent ability to convert low-quality feedstuffs into energy. In rumen microbiome studies, samples from the ventral sac are most often collected because of the ease of access and repeatability. However, anatomical musculature demarcates the rumen into five sacs (biogeographical regions), which may support distinct microbial communities. The distinction among the microbes may generate functional variation among the rumen microbiome, thus, specialized tasks within different sacs. The objective of this study was to determine the rumen liquid metabolome and epimural, planktonic, and fiber-adherent bacterial communities among each rumen biogeographical region. It was hypothesized that differences in bacterial species and metabolome would occur due to differing anatomy and physiology associated with the respective regions. To assess this variation, epithelial and content microbial-associated communities were evaluated, as well as the metabolites among various rumen biogeographical regions. A total of 17 cannulated Angus cows were utilized to examine the fiber-adherent (solid fraction), planktonic (liquid fraction), and epimural microbial communities from the cranial, dorsal, caudodorsal blind, caudoventral blind, and ventral sacs. Metagenomic DNA was extracted and sequenced from the hypervariable V4 region of the 16S rRNA gene. Reads were processed using packages ‘phyloseq’ and ‘dada2’ in R. Untargeted metabolomics were conducted on rumen liquid from each sac using UHPLC-HRMS and analyzed in MetaboAnalyst 5.0. An analysis of variance (ANOVA) revealed 13 significant differentially abundant metabolites with pairwise comparisons against the five rumen sacs (P < 0.05). Within the bacterial communities, neither alpha nor beta diversity determined significance against the rumen sacs (P > 0.05), although there was significance against the fraction types (P < 0.05). Utilizing multivariable association analysis with MaAslin2, there were significant differential abundances found in fraction type × location (P < 0.05). Knowledge of similarities among fiber-adherent microbial communities provides evidence that single sac sampling is sufficient for this fraction. However, future projects focusing on either planktonic or epimural fractions may need to consider multiple rumen sac sampling to obtain the most comprehensive analysis of the rumen. Defining these variabilities, especially among the rumen epimural microbiome, are critical to define host-microbiome interactions

Interactive Web-Based Tool for Nutritional Microbiology in Applied Agriculture Outreach

The interconnection of microbiology, biology, and agriculture poses unique challenges for dissemination of basic science research data in an applied format. Further, audiences including the general public, stakeholders, agricultural commodity producers, and students to which information is directed often possess various backgrounds and educational training. In response to technological advances, and the benefits of web-based learning tools to deliver complex information, an integrative approach to deliver microbial content information was developed. Through the constructed web-based interface, an interactive format to highlight the microbe of interest consisted of a main image with strategically placed hotspots to illuminate the location/environment/organ where the microbe can be found. As each hotspot is accessed, an additional image and description of the role and function of the microbe at the location is presented. To encourage regular user access with the learning tool, monthly features were created to focus on various concepts in nutritional microbiology. Monthly themes were selected by the educator to cover a specific microbe, environment, and physiological or nutritional function. Facilitation of educator operation of the interface was achieved through development of an easy-to-use dashboard, allowing for uploading of main, monthly, and hotspot images, along with information on the overview of microbe function and with details contained within the hotspot descriptions. Additionally, an archive feature was created to allow access to information that was previously covered within the learning tool. Application of this web-based interface can span across classroom settings, outreach educational events, adult and youth learning within Extension, student recruitment, and many other non-traditional learning settings to impact production agriculture with research-driven microbiological and biological concepts.

Improving Education in Agricultural Biosciences through Studying Abroad in the United States

Studying abroad in agricultural biosciences can develop students’ cultural, academic, and communication skills, and enhance employability. However, discussions in the United States of study abroad are limited to either one-way directionality (US students to other countries) or to the experiences of international students in the US for degree programs. We analyzed the perspectives and experiences of studying abroad by Zamorano University (Honduras) students, who completed an agricultural bioscience pasantia (four-month internship) during the final year of their undergraduate program. We used mixed methods to collect data via key informant interviews with Zamorano pasantia coordinators, and focus group discussions and a survey with Zamorano students who had completed a pasantia in 2017. Study abroad experiences were compared between students who completed their pasantia in the United States (37%) versus those who completed their pasantia in any of 17 other countries worldwide. Significant relationships were identified (P < 0.05) between: doing a pasantia in the US (compared to going elsewhere) and improving science and theoretical knowledge; having a hands-on experience and science and theory improvement; improving communication and confidence in using scientific methods. The Zamorano pasantia model provides a different model that may influence brain “gain, drain and exchange”, and lends insights into the value of study abroad upon agricultural bioscience education

Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided. For more information, see “Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers” P.R. Myer, M. Kim, H.C. Freetly, T.P.L. Smith (2016) [1]. Keywords: 16S rRNA gene, MiSeq, Pacific Biosciences, Rumen microbiom