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Raw count and FPKM data for jejunum transcriptome analysis in sheep bred for host resistance and susceptibility in response to Trichostrongylus colubriformis infections

Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a 12.8-fold reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P = 1.12 x 10-14; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.

The global gene correlation pattern between the RES and SUS phenotypes in sheep bred for parasite resistance (RES) and susceptibility (SUS) obtained using Spearman rank-based analysis in the DGCA package

Ascaris roundworms impair human and swine health. While treatments using anthelmintic drugs are generally effective in eliminating worms, their effects on the gut microenvironment remain poorly understood. Here we took an integrated multi-omics approach to investigate pathophysiological implications of drug-mediated worm clearance in a swine-Ascaris model. We also validated key findings using in vitro aerobic and anaerobic cultures. Our data show that Ascaris suum infection altered microbial composition and dysregulated 182 serum and fecal metabolites, including histamine and p-cresol sulfate. Compared to time-matched healthy controls, the infected and anthelmintic treated pigs differed markedly in gut microbial composition thirteen days after successful fenbendazole treatments that eliminated worms from the gut. Eleven pathways were enriched in successfully treated pigs, including peptidoglycan biosynthesis and histidine metabolism, suggesting that infection-induced alterations can be long-lasting. Interactions between parasite proteins and fenbendazole strongly increased histamine production by Lactobacillus reuteri in vitro by 83.7% (P < 0.05). Host microbiota modified swine-Ascaris interactions by producing metabolites regulating host gene expression, such as TFF2 and IL8. Our findings demonstrated that host microbiota modifies swine-Ascaris interactions via different mechanisms. Microbiota-derived metabolites directly regulate host gene expression. Microbiota plasticity allows the exploitation of the niche differentiated upon infection, resulting in blossom of certain Lactobacillus strains in treated animals. Designing functional anthelminthics will require attention to the complex interactions between parasites, drugs, and the gut microbiota.

This data set supports an article under review at Forests titled: "Cold tolerance assay reveals evidence of climate adaptation among American elm (Ulmus americana L.) genotypes" by authors: John R Butnor, Cornelia Wilson, Melike Bakir, Athony D’ Amato, Charles Flower, Chris Hansen, Stephen R Keller, Kathleen S Knight, Paula F Murakami

The supplementary material contains data used for the publication "Relationships between individual animal variation in dry matter intake and animal performance and feed efficiency" (DOI: 10.15232/aas.2024-02583). This manuscript presents associations between animal variation in dry matter intake with growth performance, feed efficiency indexes, and carcass characteristics.

These files are programs generated by Campbell Scientific's Short Cut software for operating the "simple DTA prototype" with a Campbell Scientific CR23X logger. They support a manuscript in preparation for submission to HardwareX journal titled "A simple prototype for assessing plant cold hardiness with differential thermal analysis" by John R Butnor, USDA Forest Service, Northern research Station, Burlington, VT USA

These are sensory data, composition, starch properties, and amylase activities of 15 sweetpotato genotypes that were used in the manuscript " Baked Sweetpotato Textures and Sweetness: An Investigation into Relationships Between Physicochemical and Cooked Attributes " by Allan, Johanningsmeier, Nakitto, Guambe, Abugu, Pecota, and Yencho.

Dataset describes Kentucky bluegrass production and height throughout two growing seasons in a rangeland system in the northern Great Plains. One year of sampling was during a drought year and one year had average precipitation. 2017 was a drought year and 2018 was an average precipitation year. Dataset also includes the nutritive value of Kentucky bluegrass throughout the season. Dataset can be used for modeling or for grazing planning. 2017 was a drought year and 2018 was an average precipitation year. Some plots were mowed before the growing season to simulate early defoliation. Sampling occurred at the USDA Northern Great Plains Research Laboratory near Mandan, ND (46.7673 N, 100.9184 W) The 6-hectare pasture is at an altitude of 502 m above sea level and is within the temperate steppe ecoregion of the United States. This region is characterized by long, cold winters and short, hot summers. Predominant soil types include Temvik-Wilton silt loams (fine-silty, mixed, superactive, frigid Typic and Pachic Haplustolls). The pasture is on a loamy ecological site (site ID 054XY030ND) and is managed as a native grassland with no fertilization or irrigation. The average soil texture is a clay loam (31% clay, 49% silt, and 20% sand). Average soil chemical characteristics were: pH (H2O) = 6.4; OM = 7.4% LOI; Na (ppm) = 8.25; K (ppm) = 362.4; Ca (ppm) = 1925.4; Mg (mmolc/dm3) = 417.6; CEC (me/100 g) = 17.5; S (ppm) = 8.3; Cu (ppm) = 0.74; Fe (ppm) = 33.7; Mn (ppm) = 18.5; and Zn (ppm) = 9.7.

Ceja et al. - J. Dairy Sci. - Supplementary Figures 1, 2 and 3