Using the SHIME (an in vitro simulator of the human gut microbiome) we studied changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). 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. Samples were collected before, during, and after inoculation of the reactors with LGG. This dataset includes untargeted metabolomics data. Shallow shotgun metagenomic sequencing data 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: Resource Title: Batch normalized metabolite peak area data File Name: metabolites_individual_samples_batch_norm_non_imputed.csv Resource Title: Sample metadata File Name: LGG2_metadata.csv

Data and supplemental figures for manuscript titled "Net release and uptake of xenometabolites across intestinal, hepatic, muscle, and renal tissue beds in healthy conscious pigs." We used a catheterized conscious pig model to estimate inter-organ flux of xenometabolites, derivatives, and bile acids using LC/MS. Female pigs (n=12; 2-3 months old; 25.6 ± 2.2 kg) had surgically-implanted catheters across portal-drained viscera (PDV), splanchnic area (SPL), liver, kidney, and hindquarter muscle. Overnight fasted arterial and venous plasma was collected simultaneously in a conscious state and stored at -80°C. Thawed samples were analyzed by liquid chromatography-mass spectrometry. Plasma flow was determined with para-aminohippuric acid dilution technology and used to calculate net organ balance for each metabolite. This repository contains the LC/MS data and supplemental figures for the submitted manuscript.

Stilbenoid levels in resistant (Freedom) and susceptible (O39-16) grapevine rootstock roots, in plants that were healthy or infected with root knot nematodes (RKN).

High-resolution mass spectrometry is advantageous for monitoring physiological impacts and contaminant biotransformation products in fish exposed to complex wastewater effluent. We evaluated this technique using skin mucus from male and female fathead minnows (Pimephales promelas) exposed to control water or treated wastewater effluent at 5%, 20%, and 100% levels for 21 d, using an onsite, flow-through system providing real-time exposure. Both sex-specific and non-sex-specific responses were observed in the mucus metabolome, the latter suggesting the induction of general compensatory pathways for xenobiotic exposures. Altogether, 85 statistically significant treatment-dependent metabolite changes were observed and 30 of those annotated with probable structures. The mummichog software package was used to elucidate impacted biochemical pathways and enhance metabolite annotation. Partial least squares regression models revealed relationships between the mucus metabolomes and upregulated hepatic mRNA transcripts reported previously for these same fish. These regression models suggest that mucus metabolomic changes reflected, in part, processes by which the fish biotransformed xenobiotics in the effluent. Further, we detected a phase II transformation product of bisphenol A in the skin mucus of male fish. Collectively, these findings demonstrate the utility of mucus as a minimally invasive matrix for simultaneously assessing exposures and effects of real-world mixtures of contaminants. This dataset is associated with the following publication: Mosley, J., D. Ekman, J.E. Cavallin, D. Villeneuve, G. Ankley, and T. Collette. High‐resolution mass spectrometry of skin mucus for monitoring physiological impacts and contaminant biotransformation products in fathead minnows exposed to wastewater effluent. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 37(3): 788-796, (2018).

Maternal high-fat diet (HFD) and obesity can increase the susceptibility of offspring to inhaled pollutants. In this study, we examined the influence of maternal HFD on metabolic responses to ozone in young Long-Evans rat offspring. F0-females began control (CD; 10%kcal from fat) or high-fat diet (HFD; 60%kcal from fat) at post-natal day (PND)-30. Rats were bred on PND-72 and allowed to give birth. Dietary regimen was maintained until PND-30 and then all offspring were switched to CD. On PND-40, female and male offspring-F1 (n=10/group) were exposed to air or 0.8-ppm ozone for 5h and within 1h serum samples were collected for neuroendocrine hormones and global metabolomic analysis. Offspring from HFD-dams had increased body fat and weight relative to CD, however, no major changes in circulating hormones were noted. Metabolomic analysis revealed significant sex, diet, and exposure-related changes in metabolites. Maternal HFD increased free fatty acids and decreased phospholipids (female>male). Also, microbiome-associated histidine and tyrosine metabolites were increased in both sexes of offspring, while 1,5-anhydroglucitol levels decreased in males. Ozone exposure increased free fatty acids in males from CD-dams but decreased in females from HFD-dams. Ozone also decreased monohydroxy fatty acids and acyl carnitines in females (HFD>CD). Moreover, it increased pyruvate along with TCA cycle intermediates in females suggesting an increase in glucose utilization. Ozone increased various amino acids, polyamines and metabolites of gut microbiota in HFD female offspring. Collectively, these data suggest that maternal HFD increases offspring susceptibility to metabolic alterations in a sex-specific manner when challenged with environmental stressors. This dataset is associated with the following publication: Snow, S., K. Broniowska, E. Karoly, A. Henriquez, P. Phillips, A. Ledbetter, M. Schladweiler, C. Miller, C. Gordon, and U. Kodavanti. Offspring Susceptibility to Metabolic Alterations Due to Maternal High Fat Diet and the Impact of Inhaled Ozone Used as a Stressor. Scientific Reports. Nature Publishing Group, London, UK, 1, (2020).

The purpose of this study was twofold. First, we sought to identify candidate markers of exposure to antiandrogens by analyzing endogenous metabolite profiles in the urine of male fathead minnows (mFHM, Pimephales promelas). Based on earlier work, we hypothesized that unidentified lipids in the urine of mFHM were selectively responsive to exposure to androgen receptor antagonists,which is otherwise difficult to confirm using established fish toxicity assays. A second goal was to evaluate the feasibility of non-lethally and repeatedly sampling urine from individual mFHMs over the time course of response to a chemical exposure. Accordingly, we exposed mFHM to the model anti-androgens vinclozolin or flutamide. Urine was collected from each fish at 48 hour intervals over the course of a 14 day exposure. Parallel experiments were conducted with mFHM exposed to bisphenol A or control water. The frequent handling/sampling regime did not cause apparent adverse effects on the fish. Endogenous metabolite profiling was conducted with gas chromatography–mass spectrometry (GC–MS), which exhibited lower variation for the urinary metabolome than was found in earlier work with nuclear magnetic resonance (NMR) spectroscopy. Specifically, for inter- and intra-individual variations, the median spectrum-wide relative standard deviation (RSD) was 32.6% and 33.3%, respectively, for GC–MS analysis of urine from unexposed mFHM. These results compared favorably with similar measurements of urine from other model species, including the Sprague Dawley rat. In addition, GC–MS allowed us to identify several lipids (e.g., certain saturated fatty acids) in mFHM urine as candidate markers of exposure to androgen receptor antagonists. The dataset that is uploaded here is the complete processed data from GC-MS instrument. This dataset is associated with the following publication: Collette , T., D. Skelton, J. Davis , J. Cavallin , K. Jensen , M. Kahl , G. Ankley , G. Ankley , D. Martinovic-Weigelt, and D. Ekman. Metabolite profiles of repeatedly sampled urine from male fathead minnows (Pimephales promelas) contain unique lipid signatures following exposure to anti-androgens. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY - PART D: GENOMICS AND PROTEOMICS. Elsevier BV, AMSTERDAM, NETHERLANDS, 19: 190-198, (2016).