Progress 03/01/16 to 02/29/20
Outputs
Target Audience:Target audiences reached include researchers involved in ruminant feed efficiency and rumen microbiome research, as well as applied bioinformatics. Other targeted audiences reached include (under)graduate students and members of industry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Extensive computational analysis skills and protocols have been developed and learned by the students on this project. Those involved with this project have been involved with workshop training programs for bioinformatic analysis to further develop the skillsets required for proper analysis and publication of these data. The data continues to provide training for graduate and undergraduate students who have developed skills in sample collection, laboratory analyses, and computational analyses. The PhD student on the project is now a faculty member and presented these data at the international scientific meeting, Plant and Animal Genome Conference, in January of 2019. She has also presented at the Range Beef Cow Symposium to reach a producer audience with the outcomes of this project. How have the results been disseminated to communities of interest?The results have been disseminated in the past year through invited presentations at the Plant and Animal Genome Conference in San Diego and at the Range Beef Cow Symposium. The graduate student primarily associated with this project was also invited to present at the Front Range Microbiome Symposium this past year. Finally, an annual report was generated to provide an update to this research at the Experiment Station level. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This is the final report for this project. In the past year, we have completed further analysis of the sequence data from the rumen fluid at all time points. These data are being included in several manuscripts that are in preparation and will be submitted in the next few months. Data were presented at scientific and producer oriented meetings in an effort to disseminate material to a variety of audiences. All animal and laboratory work have been completed. Bioinformatic analyses have been completed as planned. Additional novel bioinformatic analyses/ tools have recently been developed, and one graduate student continues to work with the data generated from this project to test/refine these new methods.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C. 2019. Maternal influences on the calf rumen microbiome and subsequent impacts on performance and efficiency. Proc. Paper. Range Beef Cow Symposium. Invited.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C., K.J. Austin, and K.M. Cammack. 2019. Maternal influences of the calf rumen microbiome and subsequent host performance. Oral presentation. Plant and Animal Genome Conference XXVII, San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C., K.J. Austin, and K.M. Cammack. 2019. Early colonization of the rumen: What are the contributing factors and why do we care? Front Range Microbiome Symposium, Fort Collins, CO. Invited.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Christensen, T.A., K.J. Austin, K.M. Cammack, and H.C Cunningham-Hollinger. 2019. Metagenomic analysis of rumen population in week old calves as altered by maternal late gestational nutrition and mode of delivery. Proc. Paper. Western Society of American Society of Animal Science, Boise, ID.
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Progress 03/01/16 to 02/11/20
Outputs
Target Audience:Target audiences reached include researchers involved in ruminant feed efficiency and rumen microbiome research, as well as applied bioinformatics. Other targeted audiences reached include (under)graduate students and members of industry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Extensive computational analysis skills and protocols have been developed and learned by the students on this project. Those involved with this project have been involved with workshop training programs for bioinformatic analysis to further develop the skillsets required for proper analysis and publication of these data. The data continues to provide training for graduate and undergraduate students who have developed skills in sample collection, laboratory analyses, and computational analyses. The PhD student on the project is now a faculty member and presented these data at the international scientific meeting, Plant and Animal Genome Conference, in January of 2019. She has also presented at the Range Beef Cow Symposium to reach a producer audience with the outcomes of this project. How have the results been disseminated to communities of interest?The results have been disseminated in the past year through invited presentations at the Plant and Animal Genome Conference in San Diego and at the Range Beef Cow Symposium. The graduate student primarily associated with this project was also invited to present at the Front Range Microbiome Symposium this past year. Finally, an annual report was generated to provide an update to this research at the Experiment Station level. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This is the final report for this project. In the past year, we have completed further analysis of the sequence data from the rumen fluid at all time points. These data are being included in several manuscripts that are in preparation and will be submitted in the next few months. Data were presented at scientific and producer oriented meetings in an effort to disseminate material to a variety of audiences. All animal and laboratory work have been completed. Bioinformatic analyses have been completed as planned. Additional novel bioinformatic analyses/ tools have recently been developed, and one graduate student continues to work with the data generated from this project to test/refine these new methods.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C. 2019. Maternal influences on the calf rumen microbiome and subsequent impacts on performance and efficiency. Proc. Paper. Range Beef Cow Symposium. Invited.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C., K.J. Austin, and K.M. Cammack. 2019. Maternal influences of the calf rumen microbiome and subsequent host performance. Oral presentation. Plant and Animal Genome Conference XXVII, San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C., K.J. Austin, and K.M. Cammack. 2019. Early colonization of the rumen: What are the contributing factors and why do we care? Front Range Microbiome Symposium, Fort Collins, CO. Invited.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Christensen, T.A., K.J. Austin, K.M. Cammack, and H.C Cunningham-Hollinger. 2019. Metagenomic analysis of rumen population in week old calves as altered by maternal late gestational nutrition and mode of delivery. Proc. Paper. Western Society of American Society of Animal Science, Boise, ID.
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Progress 03/01/18 to 02/28/19
Outputs
Target Audience:Target audiences reached include research scientists involved in ruminant feed efficiency and rumen microbe rseearch, as well as applied bioinformatics. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One Ph.D. student completed and successfully completed her dissertation. She presented her dissertation research at several meetings, including one international meeting and one invited presentation. One undergraduate student completed rumen microbial laboratory analysis and competed in the Western Section of the American Society of Animal Science undergraduate poster competition. How have the results been disseminated to communities of interest?Data has been disseminated through conference abstracts, proceedings papers, posters, oral presentations, and Ph.D. dissertation. What do you plan to do during the next reporting period to accomplish the goals?During this next phase, we will complete a comprehensive analysis (functional analysis with metagenomic data, complex multivariate analysis of all existing data) and work on manuscript submissions for all data. All pieces of data have been collected at this point. Further analyses have been planned in order to synthesize and compile all data into an analysis that will address the objectives in a well-rounded and complete fashion. These analyses include correlations of the rumen microbiome profiles with calf VFA profiles, maternal milk profiles and calf performance data.
Impacts
What was accomplished under these goals?
In this past year, we completed the initial analysis of rumen fluid (metagenomic sequencing and VFA profiles) from d 1, 3, 28, post-weaning, and growing-phase feed test. Feed efficiency data collected from GrowSafe was analyzed to determine feed efficiency status. Milk production data analyzed. Data has been disseminated in various abstracts, proceedings, oral and poster presentations, and dissertation of Ph.D. student. Manuscripts are in preparation for publication.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cunningham-Hollinger, H.C., K. J. Austin, and K. M. Cammack. 2019. Maternal influences on the calf rumen microbiome and subsequent host performance. (Abstr.) Oral and Poster Presentation Plant and Animal Genome Conference XXVII. San Diego, CA. January 2019.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2018
Citation:
Cunningham, H. C. 2018. Maternal influence on the calf rumen microbiome and subsequent host performance. University of Wyoming, Department of Animal Science, Dissertation. August 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Austin, K. J., H. C. Cunningham, S. R. Powell, K. T. Carpenter, and K. M. Cammack. 2018. Investigation of maternal breed and rearing type on the calf rumen microbiome from day 28 through weaning. Translational Animal Science. 2:S125-S129. doi:10.1093/tas/txy034. Oral Presentation Western Section American Society of Animal Science.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Powell, S. R., H. C. Cunningham, K. J. Austin, and K. M. Cammack. 2018. Maternal influences on beef calf rumen microbiome in the first 4 weeks of life. Accepted Abstract. Undergraduate Student Poster Competition. (Proc. Western Section of the American Society of Animal Science). Bend, Oregon. June 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Cunningham, H. C., K. J. Austin, S. R. Powell, K. T. Carpenter, and K. M. Cammack. 2018. Potential response of the rumen microbiome to mode of delivery from birth through weaning. Translating Animal Science. 2:S35-S38. doi:10.1093/tas/txy029. Oral Presentation Western Section American Society of Animal Science.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Cunningham, H. C., K. J. Austin, and K. M. Cammack. 2018. Influence of maternal factors on the rumen microbiome and subsequent host performance. Translating Animal Science. 2:S101-S105. doi:10.1093/tas/txy058. Oral Presentation Western Section American Society of Animal Science. Young Scholar Recognition Program.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Cunningham, H. C., K. J. Austin, K. T. Carpenter, S. R. Powell, and K. M. Cammack. 2018. Mode of delivery influence on the early calf rumen microbiome. Accepted. (Abstr.) Poster presented at Rowett-INRA Gut Microbiology: No longer the forgotten organ. June, 2018. Aberdeen, Scotland.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Cammack, K. M., H. C. Cunningham, K. J. Austin, H. C. Barton, and K. T. Carpenter. 2018. Effects of maternal breed on the early calf rumen microbiome. Accepted. (Abstr.) Poster presented at Rowett-INRA Gut Microbiology: No longer the forgotten organ. June, 2018. Aberdeen, Scotland.
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Progress 03/01/17 to 02/28/18
Outputs
Target Audience:Target audiences reached include research scientists involved in ruminant feed efficiency research, as well as applied bioinformatics. Changes/Problems:We are adding one additional feed efficiency test for the calves (described previously). No other major changes to report. What opportunities for training and professional development has the project provided?Two Ph.D. students and 4 undergraduate students were trained in animal handling, sample collection (rumen fluid, body weight, milk, etc.) as well as laboratory protocols (DNA isolation, VFA analysis, etc.). Additionally, conference abstracts have been (and will continue to be) submitted by both graduate and undergraduate students to develop skills in communicating (oral and written) results from this study. Extensive computational analysis skills and protocols have been developed and learned by the students on this project. How have the results been disseminated to communities of interest?To date, results have been disseminated through conference abstracts and presentations. What do you plan to do during the next reporting period to accomplish the goals?An additional feed efficiency test has been designed and will determine feed efficiency status of these calves during the finishing phase. Another rumen fluid sample will be collected along with the Grow Safe performance data and body weight data. This will allow for investigation into long-term effects of genotype, perinatal, or postnatal environment on long-term feed efficiency and performance. Carcass data will also be collected to add the carcass quality component. Analysis software and pipelines have been developed over the last year to allow for complex analysis of the rumen microbiome. These analyses will allow for a description of the rumen microbes as well as functional components. We plan to incorporate the data from the rumen microbiome, VFA analysis, milk profiles, and performance data in order to discuss the results in accordance with the goals of this project in a more comprehensive way.
Impacts
What was accomplished under these goals?
Rumen fluid has been collected from all calves at d 1, 3, 28, post-weaning, and post growing-phase feed test. From these samples volatile fatty acid (VFA) analysis has been completed and DNA has been extracted and sequenced at the University of Missouri DNA Core Facility. Subsequent analysis of VFA and sequencing data is in-progress at the University of Wyoming. Additionally, Grow Safe data generated from the growing phase feed efficiency test has been collected and is in analysis pipelines. Milk profiles are completed on all d 1, 3, 14, 1 month, 2 month, 3 month, and 4 month samples (Virginia Tech). These data will allow for investigation of the goals of the project (to determine relative contributions of the 1) genotype, 2) perinatal maternal environment, and 3) postnatal maternal environment on offspring rumen microbiome and post-weaning feed efficiency status.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2018
Citation:
Tiny but mighty: The role of the rumen microbes in livestock production. J. Anim. Sci. In press.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Cunningham, H. C., K. J. Austin, K. M. Cammack, J. C. McEwan, C. D. Moon, and A. McCulloch. 2018. Effects of mode of delivery on the young calf rumen microbiome. Accepted. (Abstr.) Poster presented at Plant and Animal Genome XXVI. San Diego, CA. January 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Austin, K. J., H. C. Cunningham, K. M Cammack, J. C. McEwan, C. D. Moon, and A. McCulloch. 2018. Potential role of maternal nutrition during late gestation on early calf rumen microbiome. Accepted. (Abstr.) Poster presented at Plant and Animal Genome XXVI. San Diego, CA. January 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Cunningham, H. C., K. J. Austin, K. M. Cammack, G. Conant, and W. R. Lamberson. 2018. The influence of maternal breed on early calf rumen microbiome. Accepted. (Proceedings) 11th World Congress on Genetics Applied to Livestock Production. W.R. Lamberson Presenting. Auckland, New Zealand. February, 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Powell, S. R., H. C. Cunningham, K. J. Austin, K. M. Cammack, and D. C. Rule. 2018. Maternal influences on early calf rumen volatile fatty acid profile. Accepted. (Abstr.) Undergraduate poster competition at Midwest Section of the American Society of Animal Science Annual Meeting. Omaha, NE. March, 2018.
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Progress 03/01/16 to 02/28/17
Outputs
Target Audience:
Nothing Reported
Changes/Problems:We have had numerous changes to the approach for this project. While it had been proposed to use University of Wyoming Angus beef cows for the animal trial, the beef herd at the university had been downsized. We purchased bred Angus and Charolais commercialbeef cows from outside producers for the animal trial. We had a signficant change in the treatments originally proposed for this project. The original treatment groups proposed included: 1) low efficiency control group (Angus calves vaginally born to and raised by their respective dams); 2) high efficiency control group (Charolais calves vaginally born to and raised by their respective dams); 3) high efficiency postnatal environmental group (Angus calves born to Angus dams but reared by Charolais dams); 4) low efficiency postnatal environmental group (Charolais calves born to Charolais dams but reared by Angus dams); 5) low efficiency perinatal environmental group (Angus calves gestated by Angus dams, delivered via caesarian section and then cross-fostered onto Charolais dams for rearing); and 6) high efficiency perinatal environmental group (Charolais calves gestated by Charolais dams, delivered via caesarian section and then cross-fostered onto Angus dams for rearing). However, despite having breeding data on the two groups of dams (Angus and Charolais), the Charolais cows began to calf earlier than the Angus cows. This may be due to breed differences in gestation length or the transportation to a high altitude location (Laramie, WY). The earlier calving by the Charolais breed prohibited successful cross-fostering. Therefore, alternative treatments were developed that will still allow us to answer our research questions. The treatments now include:1) low feed efficiency control group (Angus calves born vaginallyto and raised by their respective dams); 2) high feed efficiency control group (Charolais calves born vaginallyto and raised by their respective dams); 3) caesarian section low feed efficiency group (Angus calves delivered via caesarian section and then raised by their respective dams); 4) caesarian section high feed efficiency group (Charolais calves delivered via caesarian section and then raised by their respective dams); 5) postnatal maternal environment removallow feed efficiency group (Angus calves born vaginally and then reared as bottle calves); and 6) postnatal maternal environment removal high feed efficiency group (Charolais calves born vaginally and then reared as bottle calves). Comparisons of the control treatment groups will allow us to assess overallbreed differences. Comparisons of caesarian section treatment groups with the control treatment groups will allow us to assess the influence of the birth event on progeny rumen microbiome establishment and development. The addition of the bottle-feeding treatment groups will allow usto further assess that influence, and additionally assess the influence of the postnatal maternal environment on progney rumen microbiome. The feed efficiency test will commence as planned this coming spring, and all rumen fluid and milk collections were performed as outlined. Finally, difficulties occured with the caesarian section groups that resulted in losses. Caesarian sections were conducted by the University of Wyoming veterinarian and his staff of veterinarians. Due to the unforeseen complications, it was decided to commence with the procedure despite the Angus caesarian treatment group being incomplete (infections from an unknown source of contamination). At this time, the Angus caesarian treatment group is n = 3. While there will be limitations with the data resulting from this particular treatment group, DNA sequence analysis will still be completed. The are reports in the literature of DNA sequence analysis being conducted on this number of experimental units. While unfortunate, the other five treatment groups are completed, with one treatment group only partially completed. 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?In the next reporting period, we will be finishing the animal component of the project. Finalmilk andcalf rumen fluid samples will becollected postweaning. A postweaning feed efficiency test will be performed on 8 calves from each treatment groupthis coming spring.Laboratoryanalysis of rumen fluid and milk samples will bethe primary focus for this next period. Rumen fluid samples will beprepared for DNA extraction. DNA samples will besent to the University of Missouri for sequence analysis to determine microbial composition and quantification. Milksamples are will be analyzed atVirginia Tech formilk composition data.Volatile fatty acid analysis will be conducted on rumen samples at the University of Wyoming.
Impacts
What was accomplished under these goals?
Feed efficiency is of great economic importance to beef producers, because feed accounts for >65% of production costs. However, genetic improvement of feed efficiency has been hampered by trait measurement difficulty and expense. The rumen microbes, collectively referred to as the rumen microbiome,are responsible for converting feed ingested into energy for the host animal. Therefore, it is logical that the rumen microbiome is important for feed efficiency. Human researchhas shown a strongmaternal influence on theestablishment and development of the gut microbiome in offspring and subsequentoffspring health overtheir lifetime. Our goal is to determine the maternal and genetic influences on rumen microbiome establishment and development in the calf, and how those early influences translate to differences in feed efficiency in the mature animal. Determination of early influences onthe rumen microbial community is a critical step towards understanding feed efficiency and ultimately developing strategies and treatments for trait improvement. Improvements in feed efficiencycould ultimatelylead to 1) less usage of feedresources (less reliance on resources increasingly being shuttled towards human use); and2)improved stocking rates (better use of limited land availability for livestock production). Improved feed efficiency has also been linked to lower methane production, which could lower the environmental footprint of livestock production. These improvements in feed efficiency could be realized through efforts to 1) progress individual genetic merit; 2) use the maternal influence to promote offspring performance; or 3) modify the postnatal environment to enhance microbes favorable for offspring performance. The specific goal of this project is todetermine the relative contributions of the 1) genotype, 2) perinatal maternal environment, and 3) postnatal maternal environment on offspring rumen microbiome and post-weaning feed efficiency status. To accomplish this, two biologically different breeds were used to develop six treatment groups.The literature indicates that theAngus breed is generally less feed efficient, and the Charolais breed more feed efficient. These treatment groups (n = 10 per treatment)include 1) low feed efficiency control group (Angus calves born vaginallyto and raised by their respective dams); 2) high feed efficiency control group (Charolais calves born vaginallyto and raised by their respective dams); 3) caesarian section low feed efficiency group (Angus calves delivered via caesarian section and then raised by their respective dams); 4) caesarian section high feed efficiency group (Charolais calves delivered via caesarian section and then raised by their respective dams); 5) postnatal maternal environment removallow feed efficiency group (Angus calves born vaginally and then reared as bottle calves); and 6) postnatal maternal environment removal high feed efficiency group (Charolais calves born vaginally and then reared as bottle calves). Bred cows were transported to the beef research unit at the University of Wyoming in late spring, with calving beginning in early fall. Rumen fluid samples were collected from calves at d 1, d 3, and 4 wk postbirth; one additional sample will be collected at weaning. Rumen fluid samples will beused for DNA sequencing to determinemicrobial composition and also for volatile fatty acid analysis. Milk sampleswere collected fromall dams at birth, andagainweeklyuntil weaning with exception of the two bottle feeding treatment groups.
Publications
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