Source: UNIV OF MINNESOTA submitted to NRP
THE MICROBIOME IN ANIMAL PRODUCTION SYSTEMS: INFLUENCE OF MICROBIOME COMPOSITION AND FUNCTION IN ANIMAL EFFICIENCY AND HEALTH
Sponsoring Institution
State Agricultural Experiment Station
Project Status
COMPLETE
Funding Source
STATE
Reporting Frequency
Annual
Accession No.
1017648
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Sep 6, 2018
Project End Date
Jun 30, 2023
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
Animal Science
Non Technical Summary
The trillions of microbes that inhabit animals and their surrounding environments play indispensable roles in their physiological landscapes. These microbiomes, composed of bacteria, fungi, viruses and microeukaryotes, and that colonize environmental surfaces, the animal skin, and their mucosal cavities (respiratory and gastrointestinal) determine disease incidence and regulate nutrient synthesis and animal energetic output. As such, to improve the efficiency of animal production systems it is critical to (i) understand the composition and function of the microbiomes impacting food animals, and (ii) explore ways the microbiome may be manipulated for animal benefit. This proposal focuses on these goals through the execution of 3 main projects: 1) Determine the contribution of intrinsic (genetic - physiological) and extrinsic (dietary - environmental) factors in shaping the composition and function of the animal microbiome; 2) Explore the potential of diverse diets, feed additives and management practices to improve efficiency and health of food animals, through the modulation their gastrointestinal microbiome; and 3) Understand the molecular mechanisms by which microbes interact with diet and the animal host to impact animal physiology. These projects will be executed mainly relying on DNA/RNA-based, next generation sequencing techniques and state of the art bioinformatics, data mining and statistical tools to explore microbial communities. Additionally, the projects seek to offer a system-wide, integral view of animals that not only focuses on the microbes, but also on nutrition, gut health and functional genomics of the animal host. The projects are expected to offer important information for scientists, livestock producers and industry partners on how information of the microbiome can be used to improve health, production and efficiency of food animal systems.
Animal Health Component
40%
Research Effort Categories
Basic
50%
Applied
40%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30540991103100%
Knowledge Area
305 - Animal Physiological Processes;

Subject Of Investigation
4099 - Microorganisms, general/other;

Field Of Science
1103 - Other microbiology;
Goals / Objectives
Objectives: The main objective of this project is to explore the composition and function gut microbiome of food animals (swine and cattle), to improve animal performance and health. Ultimately, the data obtained will be used to inform producers and the industry on how nutritional and management interventions can increase animal productivity through modulation of the animal gut microbiome. To that end, this project will be subdivided in three main subprojects:Determine the factors that shape the early colonization, composition and function of the gut microbiome of food animals;Understand how different feedstuffs and additives are metabolized by microbes in the food animal gut; and,Determine how the gut microbiome interacts with the host to impact physiology.
Project Methods
Determine the factors that shape the early colonization, composition and function of the gut microbiome of food animalsThis project will be conducted in gestating sows and their piglets in pre and post weaning stages, and in different environmental conditions. Briefly, 15 gestating sows will be assigned to two different environments: one in which sanitation and disinfection practices are intensified in the farrowing unit under conventional housing (concrete floor); and one in which sanitation is kept at minimum under an environment that most resembles natural settings (a floor bedding composed by combination of straw and soil). The idea is for both environments to differ significantly in environmental microbial exposures. Samples will be taken from the environment (soil / straw bedding, and swabs from saw skin, the concrete floors, walls, drinking and food sources); and fecal samples from sows, weekly during farrowing, under each condition. At birth, fecal samples (or swabs) will also be taken from piglets biweekly, on day 1 and 5 of every week before weaning, and 20 days after weaning in the same biweekly fashion. After this period, piglets will be sacrificed to collect tissue samples and measure intestinal integrity (organ weight, expression of genes involved in intestinal barrier integrity) in collaboration with Dr. Milena Saqui-Salces (Animal Science Dept. University of Minnesota). DNA will be extracted from all the samples following instructions from commercial environmental and fecal DNA extraction kits (QIAamp Power Soil and Power Fecal, Qiagen, USA). Microbiome composition in each sample will be profiled by sequencing the 16S rRNA gene from bacteria in the Illumina sequencing platform (Illumina, USA), and by shotgun metagenomic sequencing. Additionally, in collaboration with Dr. Chi Chen (Animal Science and Food Science and Nutrition Depts. University of Minnesota) metabolomic analysis (Liquid chromatography / Mass spectrometry) will also be performed in all fecal samples to monitor the metabolic output of the gut microbiome of sows and piglets. Bioinformatics analysis and curation of 16S rRNA, and shotgun metagenomic sequences will be performed using different opensource online software options (QIIME, mothur, KneadData, Spades, Prodigal, Blast and KEGG). Statistical analyses of microbiome and metabolomic data (univariate and multivariate analyses, and mixed models) will be performed using various packages contained in the R statistical language (Team 2014). Briefly, multivariate microbiome and metabolite data will be analyzed using supervised (Principal Least Square Discriminant Analysis) and unsupervised (Principal Coordinates analyses, nonmetric multidimensional scaling) ordination techniques on diverse distance matrices (Bray-Curtis, UniFrac). Machine Learning techniques such as random Forest will be used to select for discriminant microbiome and metabolite features across treatments analyzed. Univariate data (e.g. alpha diversity indices) will be analyzed on mixed models. Gut microbiome composition and function, intestinal integrity and performance data (weight gain) will be compared between sows under different farrowing conditions and monitored on their piglets over time. An option to replicate this experiment across different swine production facilities (farms) will be considered.Understanding how different feedstuffs and additives are metabolized by microbes in the food animal gut. For this project, we will evaluate the mechanisms by which gut microbes metabolize 4 common feedstuffs/additives used or with potential usage in swine and cattle production systems to improve performance, efficiency and health: (i) fiber; (ii) enzymes; and (iii) phenolics/flavonoids/phytogenic extracts; and (iv) microbially derived additives. To that end, the project will rely on in vivo feeding trial/ interventions and on in vitro inoculation of gut contents with the feedstuff/additive of interest. Briefly, feeding trials with each additive will be conducted on at least 15 animals/treatment on a cross-sectional fashion, including the presence of a negative control. Feeding formulation will be conducted in collaboration with Drs. Pedro Urriola, Megan Webb and Alfredo DiCostanzo (Animal Science dept. University of Minnesota). Fecal samples and/or rumen content of each animal will be collected weekly, for at least 2 months under feeding intervention. An additional fecal/rumen samples collected prior to dietary intervention and used for in vitro fermentation trials. Briefly, the in vitro fermentation trials will be conducted in collaboration with Dr. Marshall Stern (Animal Science Dept. University of Minnesota), on a defined set of samples per treatment (n=5) and sampling gut material from the in vitro fermentation system, upon addition of different additive levels and over time (Every 2 hours in a 48 hour span). All molecular (16S rRNA and shotgun metagenomics sequencing and metabolomics), bioinformatics and statistical analyses of microbiome from samples collected will be performed as in subproject 1. Microbiome composition and function will be compared between animals and samples under each dietary intervention, in vivo and in vitro; and microbial metabolic dynamics of each feed additive will be determined to understand which microbes are mainly responsible for metabolic transformations of additives, what microbial enzymatic machineries they use and what metabolites are produced. In collaboration with Dr. Saqui-Salces, a second stage of this project will consist on inoculating gut cells in vitro (e.g. colonocytes) with the metabolites produced by bacteria upon feed transformation, to determine the effect of microbially-derived metabolites on gut health and intestinal integrity.Determine how the gut microbiome interacts with the host to impact physiology. This project will mainly focus on exploring whether bovines with different genetic background, and that have undergone diverse genetic selection strategies, exhibit different gut microbiome composition and function, in connection with different performance parameters. To that end we will study the ProCROSS (Montbeliarde x Red Viking x Holstein) breeds, the unselected (no genetic selection since 1960s) and contemporary pure Holstein breeds from the University of Minnesota. The breeds differ in their production and efficiency traits with the ProCROSS exhibiting the most desired traits. In collaboration with Drs. Marshall Stern, Les Hansen and Brian Crooker, we are currently conducting a pilot study in which rumen fluid of ProCROSS breeds and contemporary and unselected pure Holstein cows, under the same diets and housing conditions, was collected to study the composition and function of the rumen microbiome. The rumen fluid samples were collected and are currently undergoing 16S rRNA and shotgun sequencing as well as metabolomic analyses as described in subproject 1. Microbiome composition and function (metagenomics and metabolomics data) will be compared between animals of both genetic backgrounds as described in subproject 1. Upon determining microbiome features that differ between breeds, we will use genotyping data of the cows to evaluate whether specific genes with production traits of interest are associated with taxa and functions in the microbiome- that is, to explore whether genetic selection also selected for microbiome features that improve efficiency. Additionally, we will evaluate how the microbiome of each breed is modulated by different diets and additives in in vitro fermentation systems and how the rumen functional genomic landscape (through RNA-seq) interact with rumen microbes. In this way, we will determine how genetics and environment converge to select for microbiome features of production interest in dairy systems. The degree of association between production and efficiency traits (e.g. milk yield, feed conversion ratios) and rumen microbiome features will be also determined.

Progress 09/06/18 to 06/30/23

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?Publications: Trudeau, M.P.; Mosher, W.; Tran, H.; de Rodas, B.; Karnezos, T.P.; Urriola, P.E.; Gomez, A.; Saqui-Salces, M.; Chen, C.; Shurson, G.C. Growth Performance, Metabolomics, and Microbiome Responses of Weaned Pigs Fed Diets Containing Growth-Promoting Antibiotics and Various Feed Additives. Animals 2024, 14, 60. https://doi.org/10.3390/ani14010060 Guse, K., Sharma, A., Weyenberg, E., Davison, S., Ma, Y., Choi, Y., Johnson, A.J., Chen, C. and Gomez, A. 2022. Regular Consumption of Lacto-fermented Vegetables has Greater Effects on the Gut Metabolome Compared with the Microbiome. Gut Microbiome. 2023;4:e11. doi:10.1017/gmb.2023.9 Trudeau, M., Mosher, W., Tran, H., de Rodas, B., Karnezos, P., Urriola P.E., Gomez, A., Saqui-Salces, M., Chen, C., and Shurson, G. 2023. Experimental facility had a greater effect on growth performance, gut microbiome, and metabolome in weaned pigs than feeding diets containing subtherapeutic levels of antibiotics: a case study. PloS one, 18(8), p.e0285266. PMC10399857 Medida, R.L., Sharma, A.K., Guo, Y., Johnston, L.J., Urriola, P.E., Gomez, A. and Saqui-Salces, M., 2023. Dietary Zinc Supplemented in Organic Form Affects the Expression of Inflammatory Molecules in Swine Intestine. Animals, 13(15), p.2519. PMC10417787 K Hammers, PE Urriola, A Gomez, L Johnston, M Schwartz. Zinc supplementation in gestating sow diets. National Hog Farmer, 2023. https://wcroc.cfans.umn.edu/news/zinc-supplementation Hammers KL, Law K, Gomez A, Urriola PE, Johnston LJ. 107 Effect of Water Delivery System on Growth Performance of Nursery Pigs. J Anim Sci. 2022 Apr 12;100(Suppl 2):48. doi: 10.1093/jas/skac064.075. PMCID: PMC9003703. Gomez A, Law K. 124 Early Microbiome Development for Gut Health: Intrinsic and Extrinsic Drivers. J Anim Sci. 2022 Apr 12;100(Suppl 2):83. doi: 10.1093/jas/skac064.133. PMCID: PMC9003834. Law, K., Lozinski, B., Torres, I., Davison, S., Hilbrands, A., Nelson, E., Parra-Suescun, J., Johnston, L., & Gomez, A. (2021). Disinfection of Maternal Environments Is Associated with Piglet Microbiome Composition from Birth to Weaning. mSphere, e0066321. PMCID: PMC8550216. DOI: 10.1128/mSphere.00663-21 Kelsey L Hammers and others, 122 Timing of Dietary Zinc Additions During Gestation for Improved Piglet Survival, Journal of Animal Science, Volume 100, Issue Supplement_2, May 2022, Pages 56-57, https://doi.org/10.1093/jas/skac064.090 Omontese, B.O., Sharma, A.K., Davison, S. et al. Microbiome network traits in the rumen predict average daily gain in beef cattle under different backgrounding systems. anim microbiome 4, 25 (2022). https://doi.org/10.1186/s42523-022-00175-y Medida, R., Sharma, A., Guo, Y., Johnston, L., Urriola, P., Gomez, A., & Saqui-Salces, M. (2022). Dietary zinc restriction affects the expression of genes related to immunity and stress response in the small intestine of pigs. Journal of Nutritional Science, 11, E104. doi:10.1017/jns.2022.105 Andres Gomez, Ashok Kumar Sharma, Amanda Grev, Craig Sheaffer, Krishona Martinson (2021) The Horse Gut Microbiome Responds in a Highly Individualized Manner to Forage Lignification, Journal of Equine Veterinary Science, Volume 96, 2021, 103306, ISSN 0737-0806, https://doi.org/10.1016/j.jevs.2020.103306. Michaela Trudeau and others, 257 Young Scholar Presentation: Using an integrated systems biology platform to determine the mode of action of feed additives in nursery pig diets, Journal of Animal Science, Volume 98, Issue Supplement_3, November 2020, Pages 93-94, https://doi.org/10.1093/jas/skaa054.163 Creager CM, Manu H, Sharma A, Baidoo SK, Gomez A. 73 Effects of vegetable and animal protein sources and nutrient specifications on the nursery pig gut microbiome. J Anim Sci. 2019 Jul;97(Suppl 2):41. doi: 10.1093/jas/skz122.073. Epub 2019 Jul 29. PMCID: PMC6666904. Gomez A. 112 Beyond the gut: Systemic effects of the swine gut microbiome. J Anim Sci. 2019 Jul;97(Suppl 2):63. doi: 10.1093/jas/skz122.116. Epub 2019 Jul 29. PMCID: PMC6666576. Medida, Ramya Lekha, et al. "Dietary Zinc Supplementation from Organic and Inorganic Sources Induce Differential Intestinal Gene Expression in Swine." The FASEB Journal 33.S1 (2019): lb547-lb547. Trudeau, M. P., Zhou, Y., Leite, F. L., Gomez, A., Urriola, P. E., Shurson, G. C., Isaacson, R. E. (2018). Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced. Microbiome Changes in Growing Pigs. Frontiers in Veterinary Science, 5, 196. doi: 10.3389/fvets.2018.00196. PMCID: PMC6121748PMID: 30211174 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 trillions of microbes that live with(in) animals and humans, a.k.a. the microbiome, can determine susceptibility to disease, regulate dietary efficiency and impact their welfare and behavior. Thus, understanding the composition and function of these microbiomes under different diets and environments can help improve the efficiency of animal production and advance public health. The information derived from these efforts benefits animal producers, the animal feed and pharmaceutical industry and those involved in public health policy. The major activities of this project were: 1) Studying the factors that determine how bacteria first colonize the animal body and; 2) Exploring how different diets, dietary additives and environments modulate or impact microbes in the animal and human body. These projects were executed by characterizing microbiome composition and function using their nucleic acids (DNA/RNA) and the metabolites (or small chemicals) produced by these microbes. State of the art bioinformatics, data mining and statistical tools were used to interpret the patterns in nucleic acids and metabolites. Work was carried out by graduate students and postdocs in supervision with project lead and collaborating faculty. We have demonstrated that the maternal and post-weaning environment is key in determining which microbes first inhabit the animal body, and that that first microbiome may influence animal health and performance in swine and beef production systems. We have also demonstrated that feed additives of interest in the swine industry, mainly used with the aim of replacing growth-promoting antibiotics (e.g. pre - and probiotics, trace minerals) can modulate the gut microbiome of pigs in early stages of production (nursery) and that such changes can be mediated by incorporating such additives in maternal diets. We have not only assessed effects of feed additives on animal microbiomes but also in intestinal health. Other projects, also in swine production systems, have shown that alternatives to growth promoting antibiotics that seek to improve animal growth performance when fed to animals in later production stages may have mixed effects on their gut microbiome and performance. The impact of this research can change practices as far as considering early stages of development such as pre-and post-weaning, rather than later production stages, as the best windows for microbiome manipulation to improve health and efficiency in food animals. This information is valuable for producers and stakeholders in the animal feed/additive industry to focus on practices and research and development strategies that target the animal at very early stages of animal development. Projects completed on the human health side demonstrated that plant-based fermented foods made from crops of interest in the midwest have the potential to modulate the gut microbiome in ways that these changes can positively impact human health. The main findings indicate that fermented plant foods may positively modulate human health by shifting the functions of the gut microbiome, rather than by changing the identity of the taxonomic microbes themselves. These findings indicate that plant-based, fermented foods, as a regular part of the diet and affordable, easy-to-access foods, can be used for health promotion and prevention of chronic diseases in vulnerable populations. The implications are valuable for public health policy and entities in charge of regulating food systems in the state of Minnesota and the country at large. Our work on the factors that modulate food animal microbiomes benefit the general public as it focuses on animal production strategies that are free from antibiotics for growth promotion, hence making animal production and our food system cleaner and sustainable. The exploration of diets and foods that can modulate the microbiome to improve animal and human health has implications for changing policy on public health and food systems and educating the general public on the importance of the microbiome, a readily modifiable part of our genomes, to sustain health.

Publications


    Progress 10/01/21 to 09/30/22

    Outputs
    Target Audience:Reserachers, industry partners and the general public intersted in agriculture, conservation and health Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We trained 3 undergraduate students, 1 technician and continue training 4 graduate students, 2 of which will be graduating this year. I also teach a course every fall on the influence of the gut microbiome in animal and human physiology, taught to graduate students in animal sciences and food science and nutrition. How have the results been disseminated to communities of interest?Through 15 different publications and 3 products in popular press (youtube videos and podcasts). We have also been guest speakers in 6 different events nationally and internationally. What do you plan to do during the next reporting period to accomplish the goals?Complete pending publications,establish a new research line on the gut-brain axis (microbiome and behavior) and graduate 2 graduate students.

    Impacts
    What was accomplished under these goals? Under these goals, we published 9 different papers and 6 proceedings/abstracts in conferences and meetings. We also collected data for more than 5 papers that we hope to publish in 2023. In meeting these goals, we further prove the significant influence that diet and environment have on shaping the gut microbiome of animals and humans. We also show that early life is a critical period in which microbes are first established in the animal anatomy, which opens a window of opportunityfor manipulation of the microbiome to shape a desired phenotype.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Omontese, B. O., Sharma, A. K., Davison, S., Jacobson, E., DiConstanzo, A., Webb, M. J., & Gomez, A. @ (2022). Microbiome network traits in the rumen predict average daily gain in beef cattle under different backgrounding systems. Animal microbiome, 4(1), 1-15.
    • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Guse, K., Sharma, A., Weyenberg, E., Davison, S., Ma, T., Choi, Y., Johnson, A., Chen, C., & Gomez, A. @ (2022). Regular Consumption of Lacto-fermented Vegetables has Greater Effects on the Gut Metabolome Compared with the Microbiome. In review at Gut Microbiome (Cambridge University Press Journals). Available as preprint at Qeios: https://doi.org/10.32388/MESMZF
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Moussa, D.G., Sharma, A.K., Mansour, T.A., Witthuhn, B., Perdig�o, J., Rudney, J.D., Aparicio, C�. and Gomez, A@�. (2022) Functional signatures of ex-vivo dental caries onset. Journal of Oral Microbiology, 14(1), p.2123624.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Sharma, A.K., Davison, S., Pafco, B., Clayton, J.B., Rothman, J.M., McLennan, M.R., Cibot, M., Fuh, T., Vodicka, R., Robinson, C.J., Petrzelkova, K. & Gomez A@. (2022). The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors. NPJ biofilms and microbiomes, 8(1), pp.1-11.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Gomez, A*@. (2022). Heritable oral microbes and their importance in microbiome research for public health. Cell Host & Microbe, 30(4), 439-443.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Coffey, E. L., Gomez, A. M**., Burton, E. N., Granick, J. L., Lulich, J. P., & Furrow, E. (2022). Characterization of the urogenital microbiome in Miniature Schnauzers with and without calcium oxalate urolithiasis. Journal of veterinary internal medicine, 36(4), 1341-1352.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Medida, R. L., Sharma, A. K., Guo, Y., Johnston, L., Urriola, P. E., Gomez, A., & Saqui-Salces, M. (2022). Dietary zinc restriction affects the expression of genes related to immunity and stress response in the small intestine of pigs. Journal of Nutritional Science, 11, e104.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Mason, B., Petrzelkova, K.J., Kreisinger, J., Bohm, T., Cervena, B., Fairet, E., Fuh, T., Gomez, A., Knauf, S., Maloueki, U. and Modry, D., (2022). Gastrointestinal symbiont diversity in wild gorilla: A comparison of bacterial and strongylid communities across multiple localities. Molecular ecology, 31(15), pp.4127-4145.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Liu, R., Amato, K., Hou, R., Gomez, A., Dunn, D. W., Zhang, J., Garber, P. A., Chapman, C. A., Righini, N., He, G., Fang, G., Li, Y., Li, B., & Guo, S. (2022). Specialised digestive adaptations within the hindgut of a colobine monkey. The Innovation Journal: The Public Sector Innovation Journal, 100207.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Gomez A*@ & Law K. (2022), Early Microbiome Development for Gut Health: Intrinsic and Extrinsic Drivers. Journal of Animal Science 100, 83-83
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Law, K., Garcia, EMR., Hastad, C., Murray, D., Urriola, PE. & Gomez A.@ (2022). Effects of Maternal Parity and Prebiotics on the Microbiome of Nursery Pigs. Journal of Animal Science 100 (Supplement_2), 53-54
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hammers, KL., Law, K., Gomez A., Urriola, PE., Johnston LJ. (2022). Effect of Water Delivery System on Growth Performance of Nursery Pigs. Journal of Animal Science 100, 48-48
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hammers, KL., Urriola, PE., Schwartz, M., Ryu, MS., Gomez, A. & Johnston, LJ. (2022). Timing of Dietary Zinc Additions During Gestation for Improved Piglet Survival. Journal of Animal Science 100 (Supplement_2), 56-57
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Alcheva, A., Elnimeiry, L., Jensen, J., Ruszczak, C., Hatsukami, D., Gomez, A. & Stepanov, I. (2022). Relationship between the oral microbiome and tobacco-induced DNA damage in African American and White persons who smoke. 15th AACR Conference on The Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved. Philadelphia, PA.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Coffey, E. L., Gomez, A. M**., Burton, E. N., Granick, J. L., Lulich, J. P., & Furrow, E. (2022). The Impact of Urine Collection Method on Canine Urinary Microbiota Detection: A Cross-Sectional Study. American Society for Microbiology (ASM) Microbe Annual meeting, Washington DC.


    Progress 10/01/20 to 09/30/21

    Outputs
    Target Audience: Nothing Reported Changes/Problems:The biggest obstacle to overcome this year was related to the logistics complications brought by the COVID-19 pandemic. Because of supply shortage and increases in lab supply costs, we saw significant deviations from research schedule and goals. We also dealt with significant issues with wellbeing (motivation and exhaustion) affecting director students and postdocs. What opportunities for training and professional development has the project provided?Along the execution of these goals, we have trained (and continue training) two graduate students and two postdocs. We have also trained three undergraduate researcherswho have been adjunct to our main lab projects, assisting in different tasks including but not limited to lab techniques and data analyses. How have the results been disseminated to communities of interest?We have presented data from the experiments conducted at scientific Meetings of the American Society of Animal Science (abstracts), besides publishing the results at peer-reviewed journals (mSphere, Journal of Equine Science and animal microbiome (in review)) What do you plan to do during the next reporting period to accomplish the goals?We currently continue to work on exploring the factors that impact microbiomes of food animals at an early age. Specifically we are developing a project that elucidates how early microbial exposures impact immune performance in swine production. That includes microbes in the early environment but also feed additives used at pre-weaning stages. We also have data, (which remains to be analyzed) on how the maternal environment affects microbiome development in beef production. We plan to extend the resolution of these questions to also include the effect of feed quality on shaping early microbiome development. This is in addition to multiple collaborations on other projects that involve the evaluation of feed additives in shaping the gut microbiome of swine and beef production.

    Impacts
    What was accomplished under these goals? We managed to published three papers that recapitulate the main objectives planned and that open the door to answer additional questions about the role that the microbiome plays in the animal physiological landscape. We demonstrated that : Early microbiome colonization, and specifically, microbial exposures at birth,could play a role in shaping early and late physiological development in pigs (Law et al., 2021). We are now putting together a projectthat elucidates the effect of early microbial exposures in regulating immune responses and growth performance. Also at an early age, backgrounding systems significantly impact the rumen microbiome of beef cattle, potentially predicting finishing growth performance. Thus,programingrumenmicrobes at an early age and the way they interact could decide the fate of animal performance later in life (Omontese et al., in review). Changing the composition of feed, and specifically the degree of lignin in forage, has substantial effects on the fecal microbiome of horses. However, we demonstrate that this effect is highly individualized, that is, the effect of feedstuff with different chemical composition is dependent on individual horse. We demonstrate that each horse's microbiome not only responds in an individualized manner to changes in feed, but these responses also reflect the way they digest forage (Gomez et al., 2021).

    Publications

    • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Law, K., Lozinski, B., Torres, I., Davison, S., Hilbrands, A., Nelson, E., Parra-Suescun, J., Johnston, L., & Gomez, A. (2021). Disinfection of Maternal Environments Is Associated with Piglet Microbiome Composition from Birth to Weaning. mSphere, e0066321.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Kayla Law, Brigit Lozinski, Ivanellis Torres, Adrienne Hillbrands, Emma Nelson, Lee Johnston, Andres Gomez. (2021). Maternal Programming of the Piglet Microbiome from Birth to Weaning. Journal of Animal Science, Volume 99, Issue Supplement_1, Pages 5-6, Publisher Oxford University Press.
    • Type: Journal Articles Status: Awaiting Publication Year Published: 2021 Citation: Bobwealth O Omontese, Ashok K Sharma, Samuel Davison, Emily Jacobson, Megan J Webb, Andres Gomez. (2021). Specific rumen microbiome traits predict average daily gain in beef cattle under different backgrounding systems. https://doi.org/10.21203/rs.3.rs-923855/v1
    • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Gomez, A., Sharma, A. K., Grev, A., Sheaffer, C., & Martinson, K. (2020). The Horse Gut Microbiome Responds in a Highly Individualized Manner to Forage Lignification. Journal of Equine Veterinary Science, 103306.


    Progress 10/01/19 to 09/30/20

    Outputs
    Target Audience:The target audience of this project, besides the scientific community involved in microbiome reserach, are dairy, beef and swine producers and industry partners involved in the animal nutition and health field. Changes/Problems:We still have not to initiated or executedour in vitro fermentation systems project to understand how microbes interact with feed additives and diets to metabolize feed in the bovine rumen. We are awaiting for the new dairy nutrition faculty to formally join us to gain expertise on how to use these in vitro system. What opportunities for training and professional development has the project provided?So far, these projects have contributed to training one undergraduatestudent, three graduate students and two postdoctoral researchers How have the results been disseminated to communities of interest?We have published the results of these projects in several scientific meetings and journals of interest, including American Society of Animal Science, The Leman conference The Equine Science Society, The Minnesota Nutrition conference and The Journal of Equine veterinary Sciences. What do you plan to do during the next reporting period to accomplish the goals?The next reporting period should mainly focus on publishing the data that are still pending.

    Impacts
    What was accomplished under these goals? 1. Determine the factors that shape the early colonization, composition and function of the gut microbiome of food animals To accomplish this goal, we have completed five field experiments: Influence of farrowing environmenton piglet microbiome seeding: We have determined that disinfection in farrowing crates affects seeding of the pigletmicrobiome and mother-offspring microbiome exchange, from birth to weaning. The experiment was conducted at the UOMWest Central researchandOutreach Center. Sample collection, sequencing and data analyses have been completed. Two paperconferences were published (Leman conference and Animal Science annual meeting)and a manuscript is being prepared for submission. Development of the microbiome of beef calves: We traced the developmentof the microbiome of beef calves from birth to weaning, including influence of maternal sources. The experiment was conducted at the UoM North Central researchandOutreach Center. Sample collection and sequencing have been completed and data analyses are being conducted. Development of the microbiome of dairy claves: We conducted an experiment at the St. Paul dairy barn, in which we characterized the microbiome ofdairy calves from birth to weaning, and characterized these patterns with those found in theirhutch environment. Resultswere published as a poster for the UoM Undergraduate Research Opportunities Program and a manuscript will be prepared for submission this year. Influence of maternal nutrition (feed additives) on piglet microbiome development:We collaborated with New Fashion Pork (Jackson, MN) to investigate how feeding 4 different feed additives in gestational sows influences microbiome development in piglets. Animal trial, sample collection and sequencing have been completed and data analyses are being conducted. Effect of backgrounding systems on the microbiome and performance of beef cattle. We investigated how different backgrounding systems (after weaning) shape the rumen microbiome of beef cattle at the end of backgrounding. We have completed the animal trial, sample collection, sequencing and data analyses. We published the results in two different conferences (UoM Nutrition conference and Animal Science annual meeting ) and a manuscript is being finalized for submission. 2. Understand how different feedstuffs and additives are metabolized by microbes in the food animal gut To advance this goal, we have completed the following experiments andactivities: Evaluating the effect of feeding alfalfa with different lignin content on the gut microbiome of horses. We characterized the microbiome in fecal samples collected from horses fed alfalfa differing in lignin content, showing that horses have highly individualized responses to the content of lignin in feed. The results were published in three conferences/meetings (The Equine Science Society, Minnesota Nutrition conference and UoM equine conference) and a paper was published on the Journal of Equine Veterinary Sciences. Evaluate the effect of a commercial feed additive derived from a Aspergillus on the gut microbiome and fiber digestibility of pigs. Ileum digesta and fecal samples were collected from cannulated pigs and then used for in vitro fermentation assays. Microbiome composition was characterized in all samples and data analyses are still being conducted. Evaluate the effect of different protein sources (animal and plant origin) and nursery and finisher specification diets on the gut microbiome of pigs. Microbiomes were characterized from colon and cecum samples and data analyses were completed. A manuscript is being prepared for submission. Investigate how diverse alternatives to antibioticsimpact the gut microbiome of pigs. Seven different feed additives used as alternatives of antibiotics were used in contrast with conventional antibiotic sources in nursery pigs. Samples were collected from colon and cecum contents and the microbiomes characterized. Sequencing and data analyses were completed and the results published in the proceedings of the annual meeting of the American Society of animal sciences. A manuscript is being prepared for submission. 3. Determine how the gut microbiome interacts with the host to impact physiology. The following activities were completed to advance this goal: Elucidating the effect of host genetics on the rumen microbiome of dairy cows: We characterized and compared the rumen microbiomes of pure Holstein and UoM ProCROSS breeds (Holstein, Montbeliard and Red Viking) housed in the St Paul barn. Data analyses are still being conducted to evaluate prospects for manuscript submission. Mapping interactions between the host genomic landscape and the rumen microbiome in dairy cows. We conducted an experiment in the St Paul barn to elucidate how dietary changes (high energy and high fiber) influence rumen microbiome composition and gene expression in the rumen epithelia. Data on microbiome composition was generated and analyzed and rumen epithelial samples are awaiting RNAseq.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Gomez, A@., Sharma, A. K., Grev, A., Sheaffer, C., & Martinson, K. (2020). The Horse Gut Microbiome Responds in a Highly Individualized Manner to Forage Lignification. Journal of Equine Veterinary Science, https://doi.org/10.1016/j.jevs.2020.103306
    • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: 1B. Omontese, A.K. Sharma, J. Langlie, J.Armstrong, A. DiCostanzo, M. J Webb, A.Gomez@, PSVI-22 Rumen microbiome of beef cattle is modulated by backgrounding systems. In J. Anim. Sci. 2020. Volume 98, Issue Supplement_3,, Page 220.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2020 Citation: M.Trudeau, H.Tran, B. de Rodas, T. Karnezos, A.Gomez, C. Chen, P. E Urriola, G. C Shurson, 257 Young Scholar Presentation: Using an integrated systems biology platform to determine the mode of action of feed additives in nursery pig diets. In J. Anim. Sci. 2020. Volume 98, Issue Supplement_3, Pages 9394
    • Type: Theses/Dissertations Status: Accepted Year Published: 2020 Citation: Whats in Your Hutch? An evaluation of the microbial community present in diary calf hutches and its relationship with the calf microbiome
    • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: K. Law, B. Lozinsky, I. Torres, A. Hillbrands, E. Nelson, L. Johnston, A. Gomez@. Maternal programing of the piglet microbiome. Presented at: University of Minnesota's Allen D. Leman Swine virtual Conference (Abstract); 2020, September 19-22; Saint Paul, Minnesota, USA.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: K. Law, B. Lozinsky, I. Torres, A. Hillbrands, E. Nelson, L. Johnston, A. Gomez@. Maternal programing of the piglet microbiome. Presented at: ASAS-CSAS-WSASAS Virtual meeting and trade show (Abstract); 2020, July 19-23
    • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Gomez A., Grev, A., Mottet, R., Hathaway, M., Sheaffer, C., Martinson, K. Feeding reduced lignin alfalfa modulates the horse fecal microbiome in an individualized manner. 26th Symposium of The Equine Science Society. Equine biosciences session, Asheville, North Carolina June, 2019
    • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Omontese, B., Kumar, A., Lanlile, A., Diconstanzo., Webb, M and Gomez A. Rumen microbiome of beef cattle is modulated by backgrounding systems. 80th Nutrition conference, Mankato, MN September, 2019.


    Progress 10/01/18 to 09/30/19

    Outputs
    Target Audience:Comodity groups, scientific community Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We are currently training 2 postdoctoral associates (Bob Omontese and Ashok Sharma), 2 grad students (Kayla Law (MsC) and Kylene Guse (PhD)), and three undergraduate research assistants (Emily Jacobson, Emily Weynberg and Ivanellis Torres) How have the results been disseminated to communities of interest?So far we have presented two abstract for Focus area 1 (project A) for the Minnesota nutrition conference. What do you plan to do during the next reporting period to accomplish the goals?Next reporting period we should have one publication for every project cited above. We are also starting new projects, that are complementaryto those presented.

    Impacts
    What was accomplished under these goals? Focus area 1-Determine the factors that shape the early colonization, composition and function of the gut microbiome. Status A) Collection and microbiome analyses for189 rumen samples from beef cattle in from weaning to finishing. All microbiome sequence data has been analyzed and a manuscript is being currently written by Dr. Bob Omontese (postdoc, Gomez lab), in collaboration with Dr. Megan Webb, where weinvestigate if different backgrounding systems (cover crop, perennial pasture and dry lot) simultaneously influence performance and carcass characteristics. The experiment was conducted at theNCROC-UoM. B) Additionally a second stage of the project is being conducted (n=108 samples), where we focus on parasites and fecal microbiomes to have an assessment on how backgrounding systems before finishing affect beef cattle health. C) Collection and molecular analyses for320 samples from beef dams and their offspring have been conducted. Different types of samples (oral vaginal, fecal, milk, skin) were collected in the dam before calving, and then during calving and nursing. In addition, samples from their offspring (fecal, nasal) and from the environment (barns, soil) were also collectedat the same time points. The objective of the study is to investigate the intrinsic (maternal) and extrinsic (environmental)factors that shapeseeding and development of the microbiome in beef systems. DNA from all samples is being extracted and we are awaiting for sequencing.Dr. Bob Omontese (postdoc, Gomez lab), is leading the study, which took place attheNCROC-UoM. D) Collection of 240 fecal samples of dairy Holstein calves - the samples correspond to different time windows of calf development, since birth and periodically after the calves are weaned (day 1- individua hutches, to day 56- when they are kept in groups). Additionally samples from the environment (hutches), colostrum and water have been collected at the same time points. Samples have been collected and they are undergoing molecular analyses. The objective of the study is to investigate the extrinsic (environmental) and developmentalfactors that shapeseeding and development of the microbiome in dairy systems. The study is led by Emily Jacobson, honors thesis student (and UROP grantee) at the Gomez lab. This project was conducted at the St. Paul campus barn, UoM. E)Collection and microbiome analyses for 540 samples for sows and piglets in two different farrowing systems (disinfected vs. not disinfected) have been completed. Samples were collected from the skin, vaginal tract, gut and environment (farrowing crates)of sows and of feces and nasal cavity of piglets, along different time points (pre-farrowing, farrowing, day 7, day 14, day 21, weaningand nursery).The objective of the study is to investigate the intrinsic (maternal), extrinsic (environmental) and developmentalfactors that shapeseeding and development of the microbiome in swine systems.This project is being ked by Kayla Law, masters student in the Gomez lab, and is being conducted in collaboration with Dr. Lee Johnston, at the WCROC, UoM Focus area 2-Understand how different feedstuffs and additives are metabolized by microbes in the food animal gut A) We have collected and processed 168 samples from the rumen of lactating Holstein cows to evaluate the impact of dietary feed composition on rumen microbiome dynamics. The cannulated cows were fed a high starch (high energy) diet anda high fiber diet,in two feeding periods, and samples were collected form rumen fluid to evaluate microbiome composition. DNA sequencing is completed and data analyses are undergoing.Dr. Bob Omontese (postdoc, Gomez lab), is leading the study, in collaboration Dr. Brian Crooker, and ittook place atthe St Paul barn, UoM. B) We have collected and profiled the microbiome of 120 fecal samples of horses fed two different alfalfa kinds (high and low lignin content)- the objective of the study was to evaluate if lignin content in alfalfa hay has an effect on the gut microbiome composition of horses. All data has been analyzed and a manuscript is being currently written. The project was developed in collaboration with Dr. Krishona Martinson. C) In collaboration with Drs Pedro Urriola, we are evaluation the effect of a yeast-enzyme suplemet, on the digestibility, performance and gut microbiome compositiomn of finishing pigs-Samples have been collected and are being analyzed by Jinlong Zhou, Dr. Urriola's PhD student. The Gomez lab role is to provide feedback and support in all microbiome analyses. Focus area 3-Determine how the gut microbiome interacts with the host to impact physiology. A) In connectionwith focus area 3-point A, we also collected rumen biopsies from the lactating Holstein cows feda high starch (high energy) diet anda high fiberdiet, in two feeding periods. The biopsies will undergo RNAseq, to profile patterns of gene expression in the rumen papillae of the cows, and determine how host(at the functional genomics level)and microbiome interact to impact feed efficiency in dairy cows.Dr. Bob Omontese (postdoc, Gomez lab), is leading the study, in collaboration Dr. Brian Crooker, and ittook place atthe St Paul barn, UoM. B) We collected 28 rumen fluid samplesof lactating Holstein and ProCROSS cows to study te influenceof host genetics on rumen microbiome. All data have been collected and analyzed, and an abstract for a meeting is being written.

    Publications


      Progress 09/06/18 to 09/30/18

      Outputs
      Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A graduate student, three undergraduate research assistants and 2 postdocs have been hired to help advance these projects How have the results been disseminated to communities of interest?We will disseminate preliminary results in 3 national conferences (American Society of Animal Sciences, Animal Microbiome congress and Equine Science Society) disseminate these results, and are currently preparing 2 publications What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

      Impacts
      What was accomplished under these goals? 1. Determine the factors that shape the early colonization, composition and function of the gut microbiome of food animals; The first experimental designed to address this aimhas been planned and will start at the UoM swine facilities in Morris, MN in May/2019;We will determine the factors that shape an influence the gut microbiome of swine during the lactation and nursery periods. To that end, we will select three different farrowingenvironments:1) individual, conventional crates; 2) group housing with bedding (straw), and; 3) group housing without bedding. Samples will be taken from skin and gut ofgestating sows, as well as from their built environment to profile microbial communities via 16S rRNA MiSeq sequencing. Upon farrowing (day 0) samples for microbiome analysis will be also collected from the skin, respiratory tract and gut of the piglets, and then again weekly until weaning. Microbiome analyses then will be used to explore how environment and housing system shape the swine microbiome and performance at early life. In the second experiment, we are currently evaluating how backgrounding systems longitudinally shape the rumen microbiome of angus beef cattle in Grand Rapids, MN (n=39), from weaning to harvest. We have collected rumen fluid samples every two months, after weaning, since September 2018. The backgrounding systems being evaluated are: 1) perennial pasture; 2) dry lot, and; 3) cover crops. All samples from three collection periods have been collected and they are awaiting for DNA extraction, once the fourth and sixth sampling dates are completed. After DNA extraction, we will profile microbial communities via 16S rRNA MiSeq sequencing and determine how backgrounding system simultaneously affect ruminal microbiomes and productive parameters in beef cattle. In the third experiment to address this goal, we are characterizing the gut microbiome of dairy calves in a commercial farm near the twin cities, from birth to weaning, including microbial stimuli from the build environment. Collection of rectal swabs for microbiome analyses has started as well as from nursery hutches. Samples will be collected weekly until weaning tom determine the longitudinal dynamics of the calf gut microbiome and the in fluence of the external environment in shaping these microbial communities.. 2. Understand how different feedstuffs and additives are metabolized by microbes in the food animal gut; The first experiment to address this aim, relies on using in vitro fermentation systems to understand how microbes interact with feed additives and diets to metabolize feed. To that end, we will use the continuous batch culture fermentation system in Dr. Marshall Stern's lab and we will incubate rumen fluid collected from three cows currently being fed different diets with diverse levels of fiber; and inoculate a commercial enzyme in the in vitro systems. Rumen fluid samples will be collected via cannula and then the fluid will fill the fermenters. Samples from the fermenters will be collected periodically, during a 30- day fermentation period to determine the metabolic interactions of microbes, additive and feed, via shotgun metagenomics sequencing and metabolomics. The second experiment will involve a commercial feed additive derived from a fungus (Aspergillus) and feed with different levels of fiber; wheat middling and rice bran- and fermentation dynamics in swine. To that end, ileum digesta and fecal samples are being collected from cannulated pigs and then used for in vitro fermentation. Samples will be collected from the fermenters to characterize microbiome composition and metabolomic pools, and contrasted with in vitro digestibility measurements to determine how microbial communities respond to inoculation with feed additives and contribute to the mode of action of the feed additive tested. In the third experiment, in collaboration with Dr. Krishona Martinson, Equine extension, UMN, we evaluated changes on the fecal microbiome when horses were fed to alfalfa with different levels of lignin. Upon sequencing the microbiome of these horses via 16S rRNA MiSeq sequencing, results show that their microbiome responds individually to treatment; that is not all horses respond in the same way to different levels of lining, indicating that microbiome responses are uniquely dependent on individual horse. A publication is being prepared to disseminate this findings. A fourth experiment involved in pigs fed different sources of protein, including animal origin, plant origin as well as nursery and finisher specification diets with specific commercial enzymes and essential oils. Samples from cecum and colon were used to characterize their microbiomes via 16S rRNA MiSeq sequencing and determine how each feed additive and diet altered microbiome composition. No differences in microbiome responses were detected, indicating that protein source (animal or plan) or addition of essential oil and enzymes, in these animals, have no effect in modulating their microbiome at cecum or colon levels and that using either animal or plant protein sources achieves similar performance results. A publication is being prepared to report these findings. A fifth experiment involves evaluate g how seven different alternative to antibiotics modulate the cecal and fecal microbiome of nursery pigs, compared with a conventional antibiotic. In collaboration with Purina Lan O'Lakes, samples have already been collected and DNA was extracted to profile microbial community composition. Sequencing is currently being conducted. A sixth project related to this aim consists on evaluating how a commercial fungal extract, positively modulates the gut microbiome of dairy calves after weaning, to avoid diarrheas. To that end, and in collaboration with colleagues at Colorado State University, we collected rectal swabs samples from calves right after weaning and upon administering commercial electrolytes or the fungal extract, before and after scours episodes. Samples were also collected form health controls. The samples are being processed for DNA extraction and are awaiting sequencing via 16S rRNA MiSeq sequencing to determine the mode of action of the fungal extract. 3. Determine how the gut microbiome interacts with the host to impact physiology. The main project associated with this aim consists on determining the influence of host genetic background, immunity and metabolism on the gut microbiome of dairy cattle. To that end we are currently comparing rumen microbiome composition of pure, contemporary Holstein cows, pure unselected Holstein cows (not under genetic selection since the 1960s) and a PCROSS breed developed in the university of Minnesota (a cross between three dairy breeds: Holstein x red Viking x Montbeliard). We have collected rumen samples and made a preliminary assessment on how their rumen microbiome differs, based on their different genetic background. The preliminary results indicate that based on the microbial communities present in the rumen fluid, there is no evidence that different genetic background influences microbiome composition. However, the next step will be to characterize microbial communities attached to the rumen papillae and characterize both gene expression at the animal immune and metabolic levels and papillae microbiome.

      Publications