,R scripts and associated data used to select the sweetpotato core sets described in: Slonecki, T. J., Rutter, W. B., Olukolu, B. A., Yencho, G. C., Jackson, D. M., & Wadl, P. A. (2023). Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.1022555,Resources in this dataset:,Title: Sweetpotato_phenotype_classification_scripts File name: SP_phenotype_classification_scripts_7-29-21.R Description: R Scripts used to format, classify, and retain individuals with 'rare' phenotypes into the core collections, generating the reduced 508 accession dataset from which the core sets were selected,Title: Sweetpotato_core_set_selection_scripts File name: Core_set_selection_permutations_8-24-20.R Description: Core set sampling scripts derived from previous R scripts and data generated in "SP_phenotype_classification_scripts",Title: Original Phenotype data File name: Core_Sets_VanRaden_Complete_Passport_Phenotype_July_2021.xlsx Description: Phenotype data downloaded from GRIN sweetpotato collection and used for core set selection,Title: SP_core_selection_Rdata File name: SP_core_selection_data_7-30-21.zip Description: Data sets used in conjunction with Rscripts from Slonecki et. al. 2022,

,Using the SHIME (an in vitro simulator of the human gut microbiome) we tracked the fate of the probiotic Lacticaseibacillus rhamnosus GG (LGG) over time and across colonic regions. Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Community composition before, during, and after inoculation of the reactors with LGG as well as short chain fatty acid concentrations representing microbiome metabolic outputs. This dataset includes short-chain fatty acid concentrations and qPCR-based cell concentrations. Raw 16S rRNA amplicon sequencing of the V1-V2 regions can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635.,Resources in this dataset:,

Log10 fecal score ratios for eligible microbial source tracking qPCR assays. This dataset is associated with the following publication: Brumfield, K.D., J.A. Cotruvo, O. Shanks, M. Sivaganesan, J. Hey, N.A. Hasan, A. Huq, R.R. Colwell, and M.B. Leddy. Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed. Frontiers in Water. Frontiers, Lausanne, SWITZERLAND, 3: 626849, (2021).

Acetylene (C2H2) is a molecule rarely found in nature, with few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs, however we hypothesized that there may be yet unrecognized diversity of acetylenotrophs in nature. In this study, we expanded this diversity by isolating an aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethene (TCE)-contaminated soils undergoing bioremediation. TCE-contaminated soils from the NASA Ames Research Center in California were used to establish soil microcosms with acetylene as the primary carbon substrate and acetylene uptake was tracked over time and reported in T1_soil_microcosm_v2.0.csv. DNA was extracted from soil microcosm samples for microbial community analysis based on 16S rRNA gene sequencing; the resulting operational taxonomic units are presented in T2_soil_OTU_v2.0.csv. Bradyrhizobium sp. strain I71 was isolated from the soil microcosms and acetylene uptake and cell growth data for the isolate over time are shown in T3_soil_isolate_v2.0.csv. Nitrogen fixation assays for the pure culture of Bradyrhizobium sp. strain I71 are reported in T4_N2_fixation_v2.0.csv. Acetylene concentrations and cell densities from acetylenotrophic and heterotrophic growth assays for Bradyrhizobium sp. strain I71 are reported in T5_GrowthCurve_v2.0.csv

The fasta files (Genome_Set01.zip) contain the reference-assisted de novo assemblies (as contigs) of three Escherichia coli isolates. The table contains rows as isolates (yellow) and columns as attributes (green) for each individual genome. This dataset is associated with the following publication: Gomez-Alvarez, V., and J. Hoelle-Schwalbach. Draft Genome Sequences of Antibiotic-Resistant Escherichia coli Isolates from U.S. Wastewater Treatment Plants. Microbiology Resource Announcements. American Society for Microbiology, Washington, DC, USA, 8(23): e00351-19, (2019).

,Protein predictions using Augustus web for the fungi Neonectria coccinea and N. faginata, as well as protein prediction of closely related species N. ditissima, and Corinectria fuckeliana.,,

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes Proliferative Kidney Disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. We present data that was used to determine assay sensitivity, specificity and to define the limits of detection and quantification.