Publications

Online course materials for researchers: Introduction to statistical analysis of metagenomic sequencing data

Lessons from a course that was conducted in 2020 are available at https://github.com/EnriqueDoster/MEG_intro_stats_course

Public Data Repositories

Scripts and code that accompany published analyses (this code can be re-used to analyze our data or their own data):

Journal Articles

Dean C, Peña-Mosca F, Fernandes LM, T Ray, B Heins, Machado V, Pinedo P, Caixeta L, Noyes NR. 2022. Evaluation of contamination in milk samples pooled from independently collected quarters within a laboratory setting. Accepted at Frontiers in Microbiology. May 2022.
Dean, C.J., Y. Deng, T. C. Wehri, F. Pena-Mosca, T. Ray, B.A. Crooker, S. M. Godden, L. S. Caixeta, N.R. Noyes. The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk. bioRxiv 2023.11.07.566052; doi: https://doi.org/10.1101/2023.11.07.566052
Dean, C.J., I.B. Slizovskiy, K.K. Crone, A.X. Pfennig, B.J. Heins, L.S. Caixeta, N.R. Noyes. 2021. Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches, Journal of Dairy Science, Volume 104, Issue 1,2021,Pages 644-661, ISSN 0022-0302. Available at https://doi.org/10.3168/jds.2020-18277.
Fernandes, L., M.L. Celestino, P.R. Menta, T.H. Silva, D. Paiva, T.L. Ribeiro, L.S. Caixeta, N.R. Noyes, V.S. Machado. Cow-related factors associated with intramammary infections during the 1st week postpartum in primiparous dairy cows in certified organic herds. The Veterinary Journal, Volume 282, 2022. Available at https://doi.org/10.1016/j.tvjl.2022.105822.
Fernandes, L., I. Guimaraes, N.R. Noyes, L.S. Caixeta, V.S. Machado. Effect of subclinical mastitis detected in the first month of lactation on somatic cell count linear scores, milk yield, fertility, and culling of dairy cows in certified organic herds. Journal of Dairy Science, Volume 104, Issue 2, 2021, Pages 2140-2150,
ISSN 0022-0302. Available at https://doi.org/10.3168/jds.2020-19153.

Extension Publications

Dean, C. Peña-Mosca, F., Ray, T., Heins, B., Pinedo, P., Machado, V., Caixeta, L., Noyes, N. 2021. What is the Microbiome and Why is it Important for Organic Livestock Production? eOrganic article. Available at https://eorganic.org/node/34373
Fernandes, L.M., V. Machado. 2021. Intramammary Infections: A challenging issue for organic dairy farmers. Texas Dairy Matters. Texas Agri-Life Extension. February, 2021. Available at https://texasdairymatters.tamu.edu/files/2021/0/Intramammary-Infections-...
Mosca F, Dean C, Machado V, Fernandes L, Pinedo P, Doster E, Heins B, Sharpe K, Baumann C, Ray T, Feijoo V, Antunes A, Wehri T, Noyes NR, Caixeta L. Investigation of intramammary infections in primiparous cows during early lactation on organic dairy farms. In press at Journal of Dairy Science. https://doi.org/10.3168/jds.2022-23036
Peña-Mosca F; Dean CJ; Fernandes LM, Doster E, Sharpe K, Tui R, Feijoo V, Antunes A, Baumann C, Wehri T, Heins B, Pinedo P, Machado V, Noyes NR, Caixeta L. Associations between early lactation intramammary infections and udder health and performance during the first 180 days in milk in first-lactation organic dairy cows. Journal of Dairy Science. 2023. https://doi.org/10.3168/jds.2023-23924
Peña-Mosca, F., Dean, C., Ray, T., Heins, B., Pinedo, P., Machado, V., Caixeta, L., Noyes, N. , Dean, University of Minnesota. 2021. Could Udder Microbiome-based Products be Used as an Alternative Strategy for Mastitis Treatment and Prevention? eOrganic article. Available at https://eorganic.org/node/35010
Peña-Mosca F, Dean C, Machado V, Fernandes L, Pinedo P, Doster E, Heins B, Sharpe K, Ray T, Feijoo V, Antunes A, Baumann C, Wehri T, Noyes N, Caixeta L. Investigation of intramammary infections in primiparous cows during early lactation on organic dairy farms. J Dairy Sci. 2023 Aug 23:S0022-0302(23)00552-0. doi: 10.3168/jds.2022-23036. Epub ahead of print. PMID: 37641314.

Conference Presentations

Baumann, C., C. Dean, L. Fernandes, K. Sharpe, A. Magallhaes Antunes Junior, T. Ray, T. Wehri, B. Heins, P. Pinedo, V. Machado, L. Caxieta, N. Noyes. Milk culture results obtained from early-lactation heifers on organic dairy farms. Proceedings for the 100th Annual Conference of Research Workers in Animal Disease, Chicago IL, November 3, 2019. Abstract 041. Poster Presentation.
Dean, C.J. 2021. Utilizing the power of the microbiome as an interventional tool for mastitis prevention and treatment in organic livestock production. Infographic. Prepared for MOSES Organic Farming Conference eOrganic Virtual Booth. Available here.
Dean, C.J., C. Baumann, L. Fernandes, K. Sharpe, A. Magalhaes Antunes Junior, T. Ray, T. Wehri, B. Heins, P. Pinedo, V. Machado, L. Caixeta, N. Noyes. 2019. Community research and education program to use the microbiome for the advancement of organic livestock production.Proceedings for the 100th Annual Conference of Research Workers in Animal Disease, Chicago IL, November 3, 2019. Abstract 214. Poster Presentation.
Dean, C.J., Peña-Mosca, F., Ray, T., Doster, E., Fernandes, L., Antunes, A., Sharpe, K., Feijoo, V., Baumann, C., Wehri, T., Heins, B.J., Pinedo, P.J., Machado, V.S., Caixeta, L.S., Noyes, N.R. What is the microbiome, and why is it important for organic livestock production? ASA-CSSA-SSSA International Annual Meeting 2020. Organic Management Oral Session: Student eOrganic Competition Winners.
Fernandes, L. 2020. Impact of subclinical mastitis detected in the first month of lactation on milk yield, fertility, and culling of dairy cows on USDA-certified organic herds. American Dairy Science Association Conference Oral Presentation, June 24, 2020. Available at https://virtual2020.adsa.org/oral-sessions/81923.
Fernandes, L., I. Guimaraes, N. Noyes, L. Caixeta, and V. Machado. 2020. Conference of Research Workers in Animal Disease. Poster Presentation.
Heins, B. Chickens and Cows: Best Management Practices for Herd Health" presented at the 2019 Iowa Organic Conference, Nov. 25th 2019, Ames, IA.
Heins, B. Enhancing Livestock Health on Organic Dairy Farms", presented by Bradley Heins at the 2020 Minnesota Organic Conference, Jan. 10th, 2020, St. Cloud, MN.
Peña-Mosca, F., Dean, C., Ray, T., Doster, E., Fernandes, L., Antunes, A., Sharpe, K., Feijoo, V., Baumann, C., Wehri, T., Heins, B., Pinedo, P., Machado, V., Caixeta, L.S., and Noyes, N. “Associations between intramammary infections caused by non-aureus Staphylococci, Streptococcus, Streptococcus-like organisms and Staphylococcus aureus in early lactation on organic dairy cows. 60th Annual National Mastitis Council Meeting. 2021. Oral Presentation.
Peña-Mosca, F., Dean, C.J., Caixeta, L.S., Ray, T., Heins, B., Machado, V.S., Pinedo, P.J., and Noyes, N.R. “Description of the intramammary infections dynamics in early lactation heifer on organic dairy farms.” 54th Annual Conference of the American Association of Bovine Practitioners. 2021. Oral Presentation.
Peña-Mosca, F., Dean, C.J., Heins, B.J., Machado, V.S., Pinedo, P.J., Noyes, N.R., and Caixeta, L.S. “Description of Staphylococcus sp. intramammary infections in early lactation primiparous cows on organic dairy farms”. ADSA Virtual Conference. 2021. Oral Presentation.

Additional Resources

Over the past several years, we have a seen a growing interest by the dairy community to understand the role of the microbiome, and its putative impacts on clinically important diseases affecting dairy cows (e.g., mastitis). For more information about the microbiome and its relationship to mastitis, please see the following journal articles:

Derakhshani, H., Fehr, K.B., Sepehri, S., Francoz, D., Buck, J.D., Barkema, H.W.,Plaizier, J.C., Khafipour, E., 2018. Invited review: Microbiota of the bovine udder: Contributing factors and potential implications for udder health and mastitis susceptibility. Journal of Dairy Science 101, 10605–10625. https://doi.org/10.3168/jds.2018-14860
Kim, D., Hofstaedter, C.E., Zhao, C., Mattei, L., Tanes, C., Clarke, E., Lauder, A., Sherrill-Mix, S., Chehoud, C., Kelsen, J., Conrad, M., Collman, R.G., Baldassano, R., Bushman, F.D., Bittinger, K., 2017. Optimizing methods and dodging pitfalls in microbiome research. Microbiome 5, 52. https://doi.org/10.1186/s40168-017-0267-5
Ma, C., Sun, Z., Zeng, B., Huang, S., Zhao, J., Zhang, Y., Su, X., Xu, J., Wei, H., Zhang, H., 2018. Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis. Microbiome 6, 200. https://doi.org/10.1186/s40168-018-0578-1
Oikonomou, G., Bicalho, M.L., Meira, E., Rossi, R.E., Foditsch, C., Machado, V.S., Teixeira, A.G.V., Santisteban, C., Schukken, Y.H., Bicalho, R.C., 2014. Microbiota of Cow’s Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters. PLOS ONE 9, e85904. https://doi.org/10.1371/journal.pone.0085904
Rainard, P., Foucras, G., 2018. A Critical Appraisal of Probiotics for Mastitis Control. Front Vet Sci 5. https://doi.org/10.3389/fvets.2018.00251