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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Research Project #433503

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 Reprint Icon will take you to the publication reprint.)

Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis - (Peer Reviewed Journal)

Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing Reprint Icon - (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. Reprint Icon - (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., Garcia, J.F., Utsunomiya, Y.T. 2021. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle.. Genetics Selection Evolution. 53:40. https://doi.org/10.1186/s12711-021-00633-2.

The effects of artificially dosed adult rumen contents on abomasum transcriptome and associated microbial community structure in calves Reprint Icon - (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),424. https://doi.org/10.3390/genes12030424.

Pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula shaped rumen bacterial communities and co-occurrence networks of post-weaned dairy calves Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (Review Article)
Weimer, P.J., Hall, M.B. 2020. The Potential for Biomimetic Application of Rumination to Bioreactor Design. Biomass and Bioenergy. 143:105822. 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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.

Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach Reprint Icon - (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 Reprint Icon - (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. 103:10161-10174. 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? Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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)

Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection Reprint Icon - (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)

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

The structure, evolution, and gene expression within the caprine leukocyte receptor complex Reprint Icon - (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.

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

Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis - (Peer Reviewed Journal)

Stability of the liquid markers chromium (III) - and cobalt (III) - EDTA in autoclaved, clarified rumen fluid - (Peer Reviewed Journal)

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)

Effect of experimental design on responses to two levels of metabolizable protein in multiparous dairy cows Reprint Icon - (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 Reprint Icon - (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.

Comparative transcriptomics analysis in rumen and liver from young calves treated with artificial dosing of rumen content from adult donor cow - (Peer Reviewed Journal)

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 Reprint Icon - (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)

The effect of high-fat diet feeding and associated transcriptome changes during mid lactation - (Peer Reviewed Journal)

Postpartum supplementation of fermented ammoniated condensed whey improves feed efficiency and metabolic profile Reprint Icon - (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.

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)

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)