Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

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

Evaluation of three collection protocols to determine urine output and urinary urea nitrogen excretion in dairy cows in response to dietary salt supplementation - (Peer Reviewed Journal)

Crude protein oscillation in diets adequate and deficient in metabolizable protein: effects on nutrient digestibility, nitrogen balance, plasma amino acids, and greenhouse gas emissions - (Peer Reviewed Journal)

Methane emission, nutrient digestibility, and rumen microbiota in Holstein heifers fed 14 different grass or clover silages as the sole feed - (Peer Reviewed Journal)
Parian-Khajehdizaj, F., Noel, S., Johansen, M., Weisbjerg, M., Hellwing, A., Hojberg, O., Hall, M., Lund, P. 2023. Methane emission, nutrient digestibility, and rumen microbiota in Holstein heifers fed 14 different grass or clover silages as the sole feed. Journal of Dairy Science. 106(6):4072-4091. https://doi.org/10.3168/jds.2022-22638.

Production performance of Holstein cows at four stages of lactation fed four dietary crude protein concentrations - (Database / Dataset)
Letelier, P., Zanton, G.I., Wattiaux, M.A. 2022. Production performance of Holstein cows at four stages of lactation fed four dietary crude protein concentrations. Zenodo. 105:9581–9596. https://doi.org/10.3168/jds.2022-22146.

Invited review: Corrected milk: Reconsideration of common equations and milk energy estimates - (Literature Review)
Hall, M. 2023. Invited review: Corrected milk: Reconsideration of common equations and milk energy estimates. Journal of Dairy Science. 106(4):2230-2246. https://doi.org/10.3168/jds.2022-22219.

Production performance of Holstein cows at 4 stages of lactation fed 4 dietary crude protein concentrations - (Peer Reviewed Journal)
Letelier, P., Zanton, G.I., Wattiaux, M.A. 2022. Production performance of Holstein cows at 4 stages of lactation fed 4 dietary crude protein concentrations. Journal of Dairy Science. 105(12):9581-9596. https://doi.org/10.3168/jds.2022-22146.

Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2 - (Peer Reviewed Journal)
Ortega, M.S., Bickhart, D.M., Lockhart, K.N., Null, D.J., Hutchison, J.L., McClure, J.C., Cole, J.B. 2022. Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2. Journal of Dairy Science. 105(11):9001-9011. https://doi.org/10.3168/jds.2022-21853.

Estimation and energy implications of flux of hexose through glycogen in fermentations of sugars in vitro with mixed ruminal microbes from dairy cows - (Abstract Only)
Hall, M., White, R.R. 2022. Estimation and energy implications of flux of hexose through glycogen in fermentations of sugars in vitro with mixed ruminal microbes from dairy cows. EAAP International Symposium on Energy and Protein Metabolism and Nutrition. 13(2022):262-263.

Methane and carbon dioxide production of lactating Holstein cows with different crude protein feeding strategies - (Abstract Only)

Effect of 2-hydroxy-4-(methylthio)butanoate (HMTBa) on milk fat, rumen environment and biohydrogenation, and rumen protozoa in lactating cows fed diets with increased risk for milk fat depression - (Peer Reviewed Journal)
Baldin, M., Garcia, D., Zanton, G.I., Hao, F., Patterson, A.D., and Harvatine, K.J. 2022. Effect of 2-hydroxy-4-(methylthio)butanoate (HMTBa) on milk fat, rumen environment and biohydrogenation, and rumen protozoa in lactating cows fed diets with increased risk for milk fat depression. Journal of Dairy Science. 105(9):7446–7461. https://doi.org/10.3168/jds.2022-21910

Supporting data for "Plasma essential amino acid concentration and profile are associated with performance of lactating dairy cows as revealed through meta-analysis and hierarchical clustering" - (Database / Dataset)
Letelier, P., Zanton, G.I., Dorea, J.R., Wattiaux, M.A. 2022. Supporting data for "Plasma essential amino acid concentration and profile are associated with performance of lactating dairy cows as revealed through meta-analysis and hierarchical clustering". Zenodo. https://doi.org/10.5281/zenodo.6453183.

Effects of dietary crude protein level and feeding pattern on milk production - (Abstract Only)

Effects of dietary crude protein level and feeding pattern on nitrogen balance and nutrient digestibility - (Abstract Only)

Plasma essential amino acid concentration and profile are associated with performance of lactating dairy cows as revealed through meta-analysis and hierarchical clustering - (Peer Reviewed Journal)
Letelier, P., Zanton, G.I., Dorea, J.R., Wattiaux, M.A. 2022. Plasma essential amino acid concentration and profile are associated with performance of lactating dairy cows as revealed through meta-analysis and hierarchical clustering. Journal of Dairy Science. 105(6):5044-5061. https://doi.org/10.3168/jds.2021-21028.

Substitution of cane molasses for corn grain at two levels of degradable protein. I. Lactating cow performance, nutrition model predictions, and potential basis for butterfat and intake responses - (Peer Reviewed Journal)
Hall, M., Zanton, G.I. 2022. Substitution of cane molasses for corn grain at two levels of degradable protein. I. Lactating cow performance, nutrition model predictions, and potential basis for butterfat and intake responses. Journal of Dairy Science. 105(5):3939-3953. https://doi.org/10.3168/jds.2021-21241.

An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome - (Peer Reviewed Journal)
Davenport, K.M., Bickhart, D.M., Worley, K.C., Murali, S.C., Salavati, M., Clark, E.L., Cockett, N., Heaton, M.P., Smith, T.P., Murdoch, B.M., Rosen, B.D. 2022. An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome. Gigascience. 11. Article giab096. https://doi.org/10.1093/gigascience/giab096.

Substitution of molasses for corn grain at two levels of degradable protein. II. Effects on ruminal fermentation, digestion, and nitrogen metabolism - (Peer Reviewed Journal)
Zanton, G.I., Hall, M. 2022. Substitution of molasses for corn grain at two levels of degradable protein. II. Effects on ruminal fermentation, digestion, and nitrogen metabolism. Journal of Dairy Science. 105(5):3954-3968. https://doi.org/10.3168/jds.2021-21240.

The rumen liquid meta-transcriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula - (Peer Reviewed Journal)
Park, T., Cersosimo, L.M., Radloff, W.J., Zanton, G.I., Li, W. 2022. The rumen liquid meta-transcriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula. Animal Microbiome. 4. Article 4. https://doi.org/10.1186/s42523-021-00142-z.

FLC MidWest Regional Technology Transfer Award - (Abstract Only)

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities - (Peer Reviewed Journal)
Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology. 40:711-719. https://doi.org/10.1038/s41587-021-01130-z.

Novel facets of the liver transcriptome are associated with the susceptibility and resistance to lipid-related metabolic disorders in periparturient Holstein cows - (Peer Reviewed Journal)
Pralle, R., Li, W., Murphy, B., Holdorf, H.T., White, H. 2021. Novel facets of the liver transcriptome are associated with the susceptibility and resistance to lipid-related metabolic disorders in periparturient Holstein cows. Animals. 11(9). Article 2558. https://doi.org/10.3390/ani11092558.

Investigating the effect of positional variation on mid-lactation mammary gland transcriptomics in mice fed either a low-fat or high-fat diet - (Peer Reviewed Journal)
Cheng, A., Li, W., Hernandez, L. 2021. Investigating the effect of positional variation on mid-lactation mammary gland transcriptomics in mice fed either a low-fat or high-fat diet. PLoS ONE. 16(8): e0255770. https://doi.org/10.1371/journal.pone.0255770.

Effect of natural pre-luteolytic prostaglandin F2a pulses on the bovine luteal transcriptome during spontaneous luteal regression - (Peer Reviewed Journal)
Mezera, M., Li, W., Liu, L., Meidan, R., Penagaricano, F., Wiltbank, M. 2021. Effect of natural pre-luteolytic prostaglandin F2a pulses on the bovine luteal transcriptome during spontaneous luteal regression. Biology of Reproduction. 104(5):1016-1029. https://doi.org/10.1093/biolre/ioab123.

Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis - (Peer Reviewed Journal)
Naren, G., Li, W., Gelsinger, S., Murphy, B., Li, S. 2021. Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis. Metabolites. 11(7). Article 414. https://doi.org/10.3390/metabo11070414.

Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing - (Pre-print Publication)
Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2021. Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing. bioRxiv. https://doi.org/10.1101/2021.05.04.442591.

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle - (Peer Reviewed Journal)
Trigo, B.B., Utsunomiya, A.T., Fortunato, A., Milanesi, M., Torrecilha, R.B., Lamb, H., Hayes, B., Nguyen, L., Ross, E., Padula, R.C., Sussai, T.S., Zavarez, L.B., Cipriano, R.S., Caminhas, M.M., Lopes, F.L., Lung, L.H., Pelle, C., Leeb, T., Bannasch, D., Bickhart, D.M., Smith, T.P.L, Garcia, J.F., Utsunomiya, Y.T. 2021. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution. 53. Article 40. https://doi.org/10.1186/s12711-021-00633-2.

Rumen volatile fatty acid molar proportions, rumen epithelial gene expression, and blood metabolite concentration responses to ruminally degradable starch and fiber supplies - (Peer Reviewed Journal)
Beckett, L., Gleason, C.B., Bedford, A., Liebe, D., Yohe, T.T., Hall, M., Daniels, K.M., White, R.R. 2021. Rumen volatile fatty acid molar proportions, rumen epithelial gene expression, and blood metabolite concentration responses to ruminally degradable starch and fiber supplies. Journal of Dairy Science. https://doi.org/10.3168/jds.2020-19622.

The effects of artificially dosed adult rumen contents on abomasum transcriptome and associated microbial community structure in calves - (Peer Reviewed Journal)
Narengaowa, F., Li, W., Murphy, B., Cox, M., Suen, G. 2021. The effects of artificially dosed adult rumen contents on abomasum transcriptome and associated microbial community structure in calves. Genes. 12(3). Article 424. https://doi.org/10.3390/genes12030424.

Pregnancy-induced changes in the transcriptome of the bovine corpus luteum during and after embryonic interferon-tau secretion - (Peer Reviewed Journal)
Mezera, M., Li, W., Meidan, R., Wiltbank, M. 2021. Pregnancy-induced changes in the transcriptome of the bovine corpus luteum during and after embryonic interferon-tau secretion. Biology of Reproduction. 105(1):148-163. https://doi.org/10.1093/biolre/ioab034.

Pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula shaped rumen bacterial communities and co-occurrence networks of post-weaned dairy calves - (Peer Reviewed Journal)
Park, T., Cersosimo, L.M., Li, W., Radloff, W.J., Zanton, G.I. 2021. Pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula shaped rumen bacterial communities and co-occurrence networks of post-weaned dairy calves. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2021.625488.

Development of polymorphic markers in the immune gene complex loci of cattle - (Peer Reviewed Journal)
Bakshy, K., Heimeier, D., Schwartz, J.C., Glass, E.J., Wilkinson, S., Skuce, R.A., Allen, A.R., Young, J., McClure, J.C., Cole, J.B., Null, D.J., Hammond, J.A., Smith, T.P.L., Bickhart, D.M. 2021. Development of polymorphic markers in the immune gene complex loci of cattle. Journal of Dairy Science. 104(6):6897-6908. https://doi.org/10.3168/jds.2020-19809.

Investigating the complex interplay between genotype and high-fat-diet feeding in the lactating mammary gland using the Tph1 and Ldlr knockout models - (Peer Reviewed Journal)
Cheng, A., Li, W., Walker, T., Silver, C., Ardendt, L., Hernandez, L. 2021. Investigating the complex interplay between genotype and high-fat-diet feeding in the lactating mammary gland using the Tph1 and Ldlr knockout models. American Journal of Physiology. 320(3):E438-E452. https://doi.org/10.1152/ajpendo.00456.2020.

Big data from small cells: Metagenome assembly of ruminant microbial communities - (Abstract Only)
Bickhart, D.M. 2020. Big data from small cells: Metagenome assembly of ruminant microbial communities. Meeting Abstract. US Dairy Forage Research Center Webinar Series. November 18, 2020. Virtual.

Improving metagenome assemblies with long read sequence data - (Abstract Only)
Bickhart, D.M., Koren, S., Kolmogorov, M., Watson, M., Pevzner, P., Phillippy, A.M., Smith, T.P. 2020. Improving metagenome assemblies with long read sequence data. Cold Spring Harbor Meeting. October 20-24, 2020. Virtual Meeting.

The Potential for Biomimetic Application of Rumination to Bioreactor Design - (Review Article)
Weimer, P.J., Hall, M. 2020. The Potential for Biomimetic Application of Rumination to Bioreactor Design. Biomass and Bioenergy. 143. Article 105822. https://doi.org/10.1016/j.biombioe.2020.105822.

Relative availability of metabolizable methionine from two sources of ruminally protected methionine fed to lactating dairy cattle - (Peer Reviewed Journal)
Ardalan, M., Vargas-Rodriguez, C., Zanton, G.I., Vazquez-Anon, M., Bradford, B., Tigemeyer, E. 2020. Relative availability of metabolizable methionine from two sources of ruminally protected methionine fed to lactating dairy cattle. Journal of Dairy Science. 104(2):1811-1822. https://doi.org/10.3168/jds.2020-19042.

The Bovine Pangenome Consortium - (Abstract Only)
Bickhart, D.M., Rosen, B.D., Smith, T.P. 2020. The Bovine Pangenome Consortium. Meeting Abstract. Biodiversity Genomics Conference October 5-9, 2020, Virtual Meeting.

metaFlye: scalable long-read metagenome assembly using repeat graphs - (Peer Reviewed Journal)
Kolmogorov, M., Bickhart, D.M., Behsaz, B., Gurevich, A., Rayko, M., Shin, S.B., Kuhn, K.L., Yuan, J., Polevikov, E., Smith, T.P.L., Pevzner, P.A. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nature Methods. 17:1103-1110. https://doi.org/10.1038/s41592-020-00971-x.

Reassembly of cattle immune gene clusters for quantitative analysis - (Abstract Only)

Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads - (Abstract Only)
Bickhart, D.M., Kolmogorov, M., Medema, M.H., Korobeynikov, A., Mizrahi, I., Pevzner, P., Smith, T.P. 2020. Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads. Cold Spring Harbor Laboratory's Microbiome Conference. October 20-23, 2020. Virtual Meeting.

Identifying and linking antimicrobial resistance genes in metagenomes with new DNA sequencing technologies - (Abstract Only)
Bickhart, D.M. 2020. Identifying and linking antimicrobial resistance genes in metagenomes with new DNA sequencing technologies. Meeting Abstract. LabRoots Microbiology Virtual Week, September 8-10, 2020. Virtual Meeting.

Cobalt (III)-EDTA dissociates and chromium (III)-EDTA is slightly more stable under in vitro reducing conditions comparable to those in the rumen - (Peer Reviewed Journal)
Van Soest, P.J., Hall, M.B. 2020. Cobalt (III)-EDTA dissociates and chromium (III)-EDTA is slightly more stable under in vitro reducing conditions comparable to those in the rumen. Journal of Dairy Science. 103(11):10152-10160. https://doi.org/10.3168/jds.2020-18945.

Contributions of dairy products to environmental impacts and nutritional supplies from United States agriculture - (Peer Reviewed Journal)
Liebe, D.L., Hall, M.B., White, R.R. 2020. Contributions of dairy products to environmental impacts and nutritional supplies from United States agriculture. Journal of Dairy Science. 103(11):10867-10881. https://doi.org/10.3168/jds.2020-18570.

Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents - (Peer Reviewed Journal)
Li, W., Edwards, A., Murphy, B., Cox, M., Raabis, S., Skarlupka, J., Steinberger, A. 2020. Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents. Physiological Genomics. 52:333-346. https://doi.org/10.1152/physiolgenomics.00005.2020.

Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach - (Peer Reviewed Journal)
Young, J.N., Skarlupka, J.H., Resende, R.T., Fischer, A., Kalscheur, K., Mcclure, J.C., Cole, J.B., Suen, G., Bickhart, D.M. 2020. Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach. Applied and Environmental Microbiology. 86(17). Article e00861-20.. https://doi.org/10.1128/AEM.00861-20 .

The effects of 2-hydroxy-4-methylthio-butanoic acid supplementation on the rumen microbial population and duodenal flow of microbial nitrogen - (Peer Reviewed Journal)
Jenkins, C., Fernando, S., Anderson, C., Aluthge, N., Castillo-Lopez, E., Zanton, G.I., Kononoff, P. 2020. The effects of 2-hydroxy-4-methylthio-butanoic acid supplementation on the rumen microbial population and duodenal flow of microbial nitrogen. Journal of Dairy Science. 103(11):10161-10174. https://doi.org/10.3168/jds.2019-17664.

How does nitrogen and forage harvest affect belowground biomass and non-structural carbohydrates in dual use Kernza intermediate wheatgrass? - (Peer Reviewed Journal)
Sakiroglu, M., Dong, C., Hall, M., Jungers, J., Picasso, V. 2020. How does nitrogen and forage harvest affect belowground biomass and non-structural carbohydrates in dual use Kernza intermediate wheatgrass?. Crop Science. 2020;60:2562-2573. https://doi.org/10.1002/csc2.20239.

Klason lignin is a nutritionally heterogeneous fraction unsuitable for the prediction of neutral-detergent fibre digestibility in ruminants - (Peer Reviewed Journal)
Van Soest, P.J., Robertson, J.B., Hall, M., Barry, M.C. 2020. Klason lignin is a nutritionally heterogeneous fraction unsuitable for the prediction of forage neutral-detergent fibre digestibility in ruminants. British Journal of Nutrition. 1-8. https://doi.org/10.1017/S0007114520001713.

High-throughput Phenotyping of Rumen Microbial Contents Using Buccal Swabs - (Abstract Only)

Improving metagenome assemblies with long read sequence data - (Abstract Only)

An improved pig reference genome sequence to enable pig genetics and genomics research - (Peer Reviewed Journal)
Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Giron, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Shwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P., Archibald, A.L. 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience. 9(6):giaa051. https://doi.org/10.1093/gigascience/giaa051.

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle - (Peer Reviewed Journal)
Low, W., Tearle, R., Liu, C., Koren, S., Rhie, A., Bickhart, D.M., Rosen, B.D., Kronenberg, Z.N., Kingan, S.B., Tseng, E., Thibaud-Nissen, F., Martin, F., Billis, K., Ghurye, J., Hastie, A.R., Lee, J., Pang, A., Heaton, M.P., Phillippy, A.M., Hiendleder, S., Smith, T.P., Williams, J.L. 2020. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications. 11:2071. https://doi.org/10.1038/s41467-020-15848-y.

Influence of hydrolyzed soybean meal on glycogen production by mixed ruminal microbes - (Abstract Only)

High-throughput Phenotyping of Rumen Microbial Contents Using Buccal Swabs - (Abstract Only)

Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: implications for selection of RT-qPCR reference genes - (Peer Reviewed Journal)
Mezera, M., Li, W., Edwards, A., Koch, D., Beard, A., Wiltbank, M. 2020. Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: implications for selection of RT-qPCR reference genes. Journal of Dairy Science. 103(5):4846-4857. https://doi.org/10.3168/jds.2019-17526.

Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection - (Review Article)
Bickhart, D.M., McClure, J.C., Schnabel, R.D., Rosen, B.D., Medrano, J.F., Smith, T.P.L. 2020. Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. Journal of Dairy Science. 103(6):5278-5290. https://doi.org/10.3168/jds.2019-17693.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Abstract Only)

Development of feed composition tables using a statistical screening procedure - (Peer Reviewed Journal)
Tran, H., Schlageter-Tello, A., Caprez, A., Miller, P.S., Hall, M., Weiss, W.P., Kononoff, P.J. 2020. Development of feed composition tables using a statistical screening procedure. Journal of Dairy Science. https://doi.org/10.3168/jds.2019-16702.

Bioinformatics training workshop: Introduction to Unix and Advanced Command Line tutorial - (Abstract Only)

Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis. - (Peer Reviewed Journal)
Li, W., Gelsinger, S., Edwards, A., Riehle, C., Koch, D. 2019. Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis.. Scientific Reports. 9. Article 18967. https://doi.org/10.1038/s41598-019-54055-8.

The structure, evolution, and gene expression within the caprine leukocyte receptor complex - (Peer Reviewed Journal)
Schwartz, J.C., Sanderson, N.D., Bickhart, D.M., Smith, T.P., Hammond, J.A. 2019. The structure, evolution, and gene expression within the caprine leukocyte receptor complex. Frontiers in Immunology. 10:2302. https://doi.org/10.3389/fimmu.2019.02302.

Microbial inoculum composition and pre-weaned dairy calf age alter the developing rumen microbial environment - (Peer Reviewed Journal)
Cersosimo, L.M., Radloff, W.J., Zanton, G.I. 2019. Microbial inoculum composition and pre-weaned dairy calf age alter the developing rumen microbial environment. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.01651.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Peer Reviewed Journal)
Bickhart, D.M., Watson, M., Koren, S., Panke-Buisse, K., Cersosimo, L.M., Press, M.O., Van Tassell, C.P., Van Kessel, J.S., Haley, B.J., Kim, S., Heiner, C., Suen, G., Bakshy, K., Liachko, I., Sullivan, S.T., Myer, P.R., Ghurye, J., Pop, M., Weimer, P., Phillippy, A., Smith, T.P. 2019. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology. 20:153. https://doi.org/10.1186/s13059-019-1760-x.

A modified method for preparing the lithium salt of chromium EDTA and comparison to the Binnerts method - (Peer Reviewed Journal)
Hall, M., Van Soest, P.J. 2019. A modified method for preparing the lithium salt of chromium EDTA and comparison to the Binnerts method. Animal Feed Science And Technology. https://doi.org/10.1016/j.anifeedsci.2019.05.002.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Abstract Only)

Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations - (Abstract Only)

Stability of the liquid markers chromium (III) - and cobalt (III) - EDTA in autoclaved, clarified rumen fluid - (Peer Reviewed Journal)
Hall, M., Van Soest, P.J. 2019. Stability of the liquid markers chromium (III) - and cobalt (III) - EDTA in autoclaved, clarified rumen fluid. Journal of Dairy Science. https://doi.org/10.3168/jds.2018-15768.

From sequence of dominette to 10K and 50K SNP chips - (Abstract Only)

Cattle variant-detection modelling using selective-sequencing experimental design and statistical learning - (Abstract Only)

Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis - (Peer Reviewed Journal)
Li, W., Arnold, S., Edwards, A., Riehle, C. 2019. Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis. Scientific Reports. 9. Article 4744. https://doi.org/10.1038/s41598-019-40375-2.

Effect of experimental design on responses to two levels of metabolizable protein in multiparous dairy cows - (Peer Reviewed Journal)
Zanton, G.I. 2019. Effect of experimental design on responses to two levels of metabolizable protein in multiparous dairy cows. Journal of Dairy Science. https://doi.org/10.3168/jds.2018-15730.

Physicochemical and enzymatic hydrolysis characteristics of glycogen granules isolated from ruminal protozoa that are relevant to their analysis and digestion - (Peer Reviewed Journal)
Hall, M. 2019. Physicochemical and enzymatic hydrolysis characteristics of glycogen granules isolated from ruminal protozoa that are relevant to their analysis and digestion. Journal of Dairy Science. https://doi.org/10.3168/jds.2018-15758.

Effects and immune responses of probiotic treatment in ruminants - (Literature Review)

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity - (Peer Reviewed Journal)
Yee Low, W., Tearle, R., Bickhart, D.M., Rosen, B.D., Kingan, S.B., Swale, T., Thibaud-Nissen, F., Murphy, T., Young, R., Lefevre, L., Hume, D., Collins, A., Ajmone-Marsan, P., Smith, T.P., Williams, J. 2019. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications. 10:260. https://doi.org/10.1038/s41467-018-08260-0.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Abstract Only)

Selection of cattle SNP markers using selective-sequencing experimental design and statistical learning - (Abstract Only)

Postpartum supplementation of fermented ammoniated condensed whey improves feed efficiency and metabolic profile - (Peer Reviewed Journal)
Oliveira, R.C., Sailer, K.J., Holodorf, H.T., Seeley, C.R., Pralle, R.S., Hall, M., Bello, N.M., White, H.M. 2019. Postpartum supplementation of fermented ammoniated condensed whey improves feed efficiency and metabolic profile. Journal of Dairy Science. https://doi.org/10.3168/jds.2018-15519.

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow - (Peer Reviewed Journal)
Li, W., Edwards, A., Riehle, C., Cox, M., Raabis, S., Steinberger, A., Skarlupka, J., Walling, J.G., Bickhart, D.M., Suen, G. 2019. Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow. Scientific Reports. 9. Article 790. https://doi.org/10.1038/s41598-018-37033-4.

Microbiome – improving production and controlling disease - (Abstract Only)

The application of long-read sequencing and assembly to livestock genomics and metagenomics - (Abstract Only)

Microbiome – Improving production and controlling disease - (Proceedings)

Effect of high-fat diet feeding and associated transcriptome changes in the peak lactation mammary gland in C57BL/6 dams - (Peer Reviewed Journal)
Cheng, A., Hernandez, L., Li, W. 2018. Effect of high-fat diet feeding and associated transcriptome changes in the peak lactation mammary gland in C57BL/6 dams. Physiological Genomics. 50(12):1059-1070. https://doi.org/10.1152/physiolgenomics.00052.2018.

Contiguity of the goat genome assembly enables comparative analyses and gene discovery within the repetitive immune-related regions - (Abstract Only)

Goat and sheep KIR have independently expanded compared to cattle and a unique subtype is unusually expressed - (Abstract Only)

Use of RAPTR-SV to identify SVs from read pairing and split read signatures - (Book / Chapter)

Microbial inocula alter the ruminal environment and animal performance of post-weaned dairy calves - (Abstract Only)
Cerosimo, L.M., Radloff, W.J., Zanton, G.I. 2018. Microbial inocula alter the ruminal environment and animal performance of post-weaned dairy calves. J.Dairy Sci. 101(Suppl. 2): i.

Haplotype resolution of MHC in cattle through targeted enrichment and SMRT sequencing - (Abstract Only)

Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis - (Peer Reviewed Journal)
Li, W., Bickhart, D.M., Ramunno, L., Lamartino, D., Williams, J., Liu, G. 2018. Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis. Data in Brief. 19:236-239.

Buccal swabs as a noninvasive proxy for rumen microbial content - (Abstract Only)

What if we got rid of livestock? - (Popular Publication)
Hall, M., White, R.R. 2018. What if we got rid of livestock?. Hoard's Dairyman. 163(12):403.

Effects of microbial inoculum composition on rumen microbial ecology of dairy calves - (Abstract Only)
Cerosimo, L.M., Radloff, W.J., Zanton, G.I. 2018. Effects of microbial inoculum composition on rumen microbial ecology of dairy calves. Journal of Dairy Science. 101(Suppl. 2): 310.

Physiological effects of low rumen pH in calves before, during and after weaning - (Abstract Only)
Gelsinger, S.L., Zanton, G.I. 2018. Physiological effects of low rumen pH in calves before, during and after weaning. Journal of Dairy Science. 101(Suppl. 2): 335.

Effects of molasses and corn grain at 2 levels of ruminally degradable protein on lactating cow ruminal fermentation and rumen content mass - (Abstract Only)
Zanton, G.I., Hall, M. 2018. Effects of molasses and corn grain at 2 levels of ruminally degradable protein on lactating cow ruminal fermentation and rumen content mass. Journal of Dairy Science. 101(Suppl. 2): 94.

Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle - (Peer Reviewed Journal)
Li, W., Bickhart, D.M., Ramunno, L., Iamartino, D., Williams, J., Liu, G. 2018. Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics. https://doi.org/10.1016/j.ygeno.2018.02.018.

Adverse Maternal Environment Increases Fetal Liver Hydroxymethylation and Alters the Transcriptome - (Abstract Only)

Reply to Van Meerbeek and Svenning, Emery, and Springmann et al.: Clarifying assumptions and objectives in evaluating effects of food system shifts on human diets. - (Other)
White, R.R., Hall, M. 2018. Reply to Van Meerbeek and Svenning, Emery, and Springmann et al.: Clarifying assumptions and objectives in evaluating effects of food system shifts on human diets.. Proceedings of the National Academy of Sciences. Proc. National Academy of Sci. 115(8):E1706-E1708.

New-world quail population genomics reveal structure, divergence, and evidence for selection - (Abstract Only)

Chromosome-level assembly of the water buffalo genome - (Abstract Only)

Long-read sequencing enables the accurate annotation of immune gene clusters in goat - (Abstract Only)

Copy number variation in dairy cattle using next-generation sequencing - (Abstract Only)

Reassembly of cattle immune gene clusters for quantitative analysis - (Abstract Only)

Breeding cattle for improved disease resistance - (Abstract Only)

Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle - (Abstract Only)