Research Project: Developing Strategies to Improve Dairy Cow Performance and Nutrient Use Efficiency with Nutrition, Genetics, and Microbiology

Location: Cell Wall Biology and Utilization Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

In vitro evaluation of selected compounds affecting ruminal fermentation and methane production - (Peer Reviewed Journal)
Peres Assumpção, A., Young, J.D., Ferreira, I., Rodrigues, A., Anderson, R.C., Suen, G., Mantovani, H.C. 2026. In vitro evaluation of selected compounds affecting ruminal fermentation and methane production. Journal of Dairy Science. https://doi.org/10.3168/jds.2026-28405.

Rumen microbial protein—Supply, efficiency, and measurement. Future needs: Methodologies, key questions, and modeling. - (Abstract Only)

Looking beyond the rumen: Uncovering opportunities to improve health and performance by considering the whole gastrointestinal tract - (Review Article)
Costello, M.K., Mcclure, J.C., Olson, E.G., Mantovani, H.C., Ricke, S.C. 2026. Looking beyond the rumen: Uncovering opportunities to improve health and performance by considering the whole gastrointestinal tract. Microbiology and Molecular Biology Reviews. https://doi.org/10.1128/mmbr.00057-25.

Cow-level evaluation of plasma essential amino acid clusters and their association with lactating dairy cow performance - (Peer Reviewed Journal)
Menezes, G.L., Letelier, P., Dorea, J.R., Sullivan, M.L., Reinhardt, L.A., Zanton, G.I., Wattiaux, M.A. 2026. Cow-level evaluation of plasma essential amino acid clusters and their association with lactating dairy cow performance. Journal of Dairy Science. https://doi.org/10.3168/jds.2025-27455.

The microbiota of wooden cheese ripening boards is a rich source of antimicrobial-producing bacteria against Listeria monocytogenes - (Peer Reviewed Journal)
Chen, Y., Zuniga Chaves, I., Mcclure, J.C., Suen, G., Huynh, T.N. 2026. The microbiota of wooden cheese ripening boards is a rich source of antimicrobial-producing bacteria against Listeria monocytogenes. Applied and Environmental Microbiology. https://doi.org/10.1128/spectrum.02936-25.

Meta-analysis of supplemental methionine effects on plasma amino acid concentrations in dairy cows - (Peer Reviewed Journal)
Zanton, G.I. 2026. Meta-analysis of supplemental methionine effects on plasma amino acid concentrations in dairy cows. Journal of Dairy Science Communications. https://doi.org/10.3168/jdsc.2025-0804.

Assessing the impact of oscillating dietary crude protein on the stability of the rumen microbiome in dairy cattle - (Peer Reviewed Journal)
Viquez-Umana, F., Erickson, M., Young, J.D., Zanton, G.I., Wattiaux, M., Suen, G., Mantovani, H. 2025. Assessing the impact of oscillating dietary crude protein on the stability of the rumen microbiome in dairy cattle. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1568112.

Correlating the oral swab microbial community with milk production metrics in holstein dairy cows - (Peer Reviewed Journal)
Skarlupka, J.H., Cox, M.S., Steinberger, A.J., Sbardellati, D.L., Mcclure, J.C., Bickhart, D., Scheftgen, A.J., Zuniga-Chaves, I., Paget, E., Skadron, C., Attipetty, N., Suen, G. 2025. Correlating the oral swab microbial community with milk production metrics in holstein dairy cows. mSphere. https://doi.org/10.1128/msphere.00167-25.

Pipeline for antimicrobial resistance gene quantification from host tissue - (Peer Reviewed Journal)
Svaren, L.M., Li, W. 2025. Pipeline for antimicrobial resistance gene quantification from host tissue. Current Protocols in Bioinformatics. https://doi.org/10.1002/cpz1.70116.

The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process - (Peer Reviewed Journal)
Costello, M.K., Mcclure, J.C., Brown, J.A., Mantovani, H.C., Ricke, S.C. 2025. The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.02599-24.

Effect of second iron injection on growth performance, hematological parameters, and fecal microbiome of piglets fed different dietary iron levels - (Peer Reviewed Journal)
Johnson, A., Li, W., Dittrich, B., Cole, A., Prodell, M., Fritz, S., Fregulia, P., Chen, C., Kown, C., Jang, D.Y. 2024. Effect of second iron injection on growth performance, hematological parameters, and fecal microbiome of piglets fed different dietary iron levels. Journal of Animal Science. https://doi.org/10.1093/jas/skae371.

Comparison of 2-pool and 3-pool digestion kinetic model predictions of neutral detergent fiber digestibility of forages from commercially available data - (Peer Reviewed Journal)
Barry, M.C., Hall, M. 2024. Comparison of 2-pool and 3-pool digestion kinetic model predictions of neutral detergent fiber digestibility of forages from commercially available data. Journal of Dairy Science. 108:2371-2380. https://doi.org/10.3168/jds.2024-25284.

Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color - (Peer Reviewed Journal)
Skarlupka, J.H., Cox, M.S., Steinberger, A.J., Sbardellati, D.L., Mcclure, J.C., Bickhart, D.M., Scheftgen, A.J., Zuniga-Chavez, I., Wolfe, L.A., Paget, E., Skadron, C., Attipetty, N., Suen, G. 2024. Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2024.1466375.

Estimates of optimal supplies of animal-sourced foods differ by food system goal and socioeconomic context - (Peer Reviewed Journal)
White, R.R., Hall, M. 2024. Estimates of optimal supplies of animal-sourced foods differ by food system goal and socioeconomic context. Proceedings of the National Academy of Sciences (PNAS). https://doi.org/10.1073/pnas.2319011121.

Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves - (Peer Reviewed Journal)
Fregulia, P., Park, T., Cersosimo, L., Zanton, G.I., Li, W. 2024. Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves. Scientific Reports. https://doi.org/10.1038/s41598-024-65685-y.

Production responses of dairy cows to protein and amino acid supplementation - (Proceedings)

Effects of altering diet carbohydrate profile and physical form on zoo-housed giraffe Giraffa camelopardalis reticulata - (Peer Reviewed Journal)
Kearney, C.C., Ball, R., Hall, M. 2024. Effects of altering diet carbohydrate profile and physical form on zoo-housed giraffe Giraffa camelopardalis reticulata. Journal of Animal Physiology and Animal Nutrition. https://doi.org/10.1111/jpn.13957.

Feed efficiency starts in the rumen - (Proceedings)
Hall, M. 2024. Feed efficiency starts in the rumen. Proceedings. https:/DOI.org//www.naaic.org/Meetings/National/2024meeting/45-Sullivan.pdf.

Impact of alternative methods on measurement of NDF compared to the official method - (Abstract Only)
Hall, M. 2024. Impact of alternative methods on measurement of NDF compared to the official method. American Dairy Science Association Abstracts. 107 (Supplement 1):176.

Behavioral and hair cortisol responses of heifers raised in barn or on pasture - (Abstract Only)
Hall, M., Jaramillo, D.M., Kalscheur, K., Camisa Nova, C.P., Disalvo, A. 2024. Behavioral and hair cortisol responses of heifers raised in barn or on pasture. Journal of Dairy Science. 107 (Supplement 1):155.

Effects of microbial inoculum on the transcriptome and meta-transcriptome of rumen, reticulum, omasum, and abomasum epithelium in calves - (Abstract Only)
Fregulia, P., Zanton, G.I., Li, W. 2024. Effects of microbial inoculum on the transcriptome and meta-transcriptome of rumen, reticulum, omasum, and abomasum epithelium in calves. American Dairy Science Association Abstracts. 107 (Supplement 1):28.

Meta-transcriptome analysis reveals temporal dynamics on the active rumen microbiome in transition Holstein cows - (Abstract Only)
Fregulia, P., Zanton, G., Li, W. 2024. Meta-transcriptome analysis reveals temporal dynamics on the active rumen microbiome in transition Holstein cows [abstract]. Journal of Dairy Science. 107 (Supplement 1):28.

Metabolic and transcriptomic responses to dietary-induced milk fat depression and balanced amino acid supplementation in lactating dairy cows - (Abstract Only)
Ruh, K.E., Millerby, M., de Souza, G.M., Benn, A.D., Cohan, E.M., Krueger, A., Coelho Ribeiro, L.A., Larsen, A.M., Hoppmann, A. Sherlock, D.N., Li, W., Arriola Apelo, S.I. 2024. Metabolic and transcriptomic responses to dietaryinduced milk fat depression and balanced amino acid supplementation [abstract]. Journal of Dairy Science. 107 (Supplement 1):115.

In search of a better way: Exploring the impact of enrichment and DNA extraction on long-read sequencing of rumen protozoa. - (Abstract Only)
McClure, J., Panke-Buisse, K. Lai, E., deHegedus, R.A., Zanton, G., French, E., Smith, T., Suen, G., Bickhart, D. 2024. In search of a better way: Exploring the effects of enrichment and DNA extraction on long-read sequencing of rumen protozoa [abstract]. Journal of Dairy Science. 107 (Supplement 1):268

Impact of ruminally pulse-dosed calcium acetate, butyrate, their combination, or limestone on milk composition - (Abstract Only)
Hall, M.B. 2024. Impact of ruminally pulse-dosed calcium acetate, butyrate, their combination, or CaCO3 on milk composition [abstract]. International Symposium on Ruminant Physiology. Paper No. 57.

Whole blood transcriptome and meta-transcriptome changes in transition cows - (Abstract Only)
Fregulia, P., Zanton G., Li, W. 2024. Whole blood transcriptome and microbial abundance changes in transition cows [abstract]. International Symposium on Ruminant Physiology. Paper No. 26.

Blood transcriptome and its microbial community in young claves with prolonged ruminal acidosis - (Abstract Only)
Larsen, A., Li, W. 2024. Blood transcriptome and its microbial changes in young calves with feed-induced ruminal acidosis [abstract]. International Symposium on Ruminant Physiology. Paper No. 74.

Metabolic responses to AA infused along different energy sources - (Abstract Only)
Killerby, M., de Souza, G.M., Ruh, K., Larsen, A., Cohan, E., Hoppmann, A., Danes, M., Li, W., Ariolla Apelo, S.I. 2024. Metabolic responses to amino acids infused with different energy sources [abstract]. International Symposium on Ruminant Physiology. Paper No. 36.

Defining the pre-harvest bovine gastrointestinal tract microbiome after lairage at a USDA processing facility - (Abstract Only)

Rumen microbial inoculation effects on the liver transcriptome and meta-transcriptome in weaned calves - (Abstract Only)
Fregulia, P., Zanton, G., Li, W. 2024. Rumen microbial inoculation effects on the liver transcriptome and meta-transcriptome in weaned calves [abstract]. International Symposium on Ruminant Physiology. Paper No. 27.

Investigating the impact of feed-induced acidosis on the rumen transcriptome and metatranscriptome in young calves at 8- and 17-weeks of age - (Peer Reviewed Journal)
Li, W., Larsen, A., Freguila, P. 2024. Investigating the impact of feed-induced acidosis on the rumen transcriptome and metatranscriptome in young calves at 8- and 17-weeks of age. Frontiers in Veterinary Science. https://doi.org/10.3389/fvets.2024.1328539.

Systematic review and meta-analysis of dairy cow responses to rumen-protected methionine supplementation before and after calving - (Peer Reviewed Journal)
Zanton, G.I., Toledo, M.Z. 2024. Systematic review and meta-analysis of dairy cow responses to rumen-protected methionine supplementation before and after calving. Journal of Dairy Science Communications. 5:293-298. https://doi.org/10.3168/jdsc.2023-0512.

The liver microbiome in calves with feed induced acidosis - (Abstract Only)

Dose-dependent effects of supplementing a two-strain Bacillus subtilis probiotic on growth performance, blood parameters, fecal metabolites, and microbiome in nursery pigs - (Peer Reviewed Journal)
Smith, A., Hernandez, S., Wenner, S., Fregulia, P., Larsen, A., Li, W., Jang, Y., Duddeck, K., Petersen, T., Adkins, H.J., Yao, D., Chi, C. 2023. Dose-dependent effects of supplementing a two-strain Bacillus subtilis probiotic on growth performance, blood parameters, fecal metabolites, and microbiome in nursery pigs. Animals. https://doi.org/10.3390/ani14010109.

Whole genome sequences of two nitrate-reducing strains of Selenomonas ruminantium isolated from the rumen - (Abstract Only)
Costello, M.K., Ricke, S.C., McClure, J., Anderson, R.C. 2024. Whole genome sequences of two nitrate-reducing strains of Selenomonas ruminantium isolated from the rumen [abstract]. Journal of Animal Science. 102 (Supplement 2):269. https://doi.org/10.1093/jas/skae102.306.

Liver microbial community and associated host transcriptome in calves with feed induced acidosis - (Peer Reviewed Journal)

Genome-wide copy number variation and structural variation: A novel tool for improved livestock genomic selection - (Book / Chapter)
Li, W. 2023. Genome-wide copy number variation and structural variation. A novel tool for improved livestock genomic selection. In: Mukhopadhyay, C.S., Choudhary, R.K., Panwar, H., Malik, Y.S., editors. Biotechnological interventions Augmenting Livestock Health and Production. Livestock Diseases and Management. Singapore: Springer. p.75-87. https://doi.org/10.1007/978-981-99-2209-3_5.

Liver and muscle transcriptomes differ in mid-lactation cows divergent in feed efficiency in the presence or absence of supplemental rumen-protected choline - (Peer Reviewed Journal)
Caputo, M., Li, W., Kendall, S., Larsen, A., Weigel, K., White, H. 2023. Liver and muscle transcriptomes differ in mid-lactation cows divergent in feed efficiency in the presence or absence of supplemental rumen-protected choline. Metabolites. https://doi.org/10.3390/metabo13091023.

Dynamic lactation responses to dietary crude protein oscillation in diets adequate and deficient in metabolizable protein in Holstein cows - (Peer Reviewed Journal)
Erickson, M., Zanton, G.I., Wattiaux, M.A. 2023. Dynamic lactation responses to dietary crude protein oscillation in diets adequate and deficient in metabolizable protein in Holstein cows. Journal of Dairy Science. 106:8774–8786. https://doi.org/10.3168/jds.2023-23603.

Characterization of rumen microbiota in lactating Holstein cows fed molasses versus corn grain at two levels of rumen degradable protein - (Peer Reviewed Journal)
Guduk, E., Hall, M., Zanton, G.I., Steinberger, A.J., Weimer, P.J., Suen, G., Weigel, K.A. 2023. Characterization of rumen microbiota in lactating Holstein cows fed molasses versus corn grain at two levels of rumen degradable protein. Frontiers in Microbiomes. 2. Article 1204988. https://doi.org/10.3389/frmbi.2023.1204988.

A meta-analysis of liver microbiome in beef and dairy cattle using metatranscriptome sequencing reads - (Other)

Supplemental methionine effects on plasma amino acid concentrations - (Abstract Only)

Effects of level and oscillation of dietary crude protein on ruminal conditions - (Abstract Only)

Comparison of neutral detergent fiber methods - (Abstract Only)

Microbial inoculum alters the rumen epithelial transcriptome and associated meta-transcriptome in calves - (Abstract Only)

Comparison of alternative neutral detergent fiber methods to the AOAC definitive method - (Peer Reviewed Journal)
Hall, M., Mertens, D.R. 2023. Comparison of alternative neutral detergent fiber methods to the AOAC definitive method. Journal of Dairy Science. 106(8):5364-5378. https://doi.org/10.3168/jds.2022-22847.