Metabolomics and Proteomics to Understand Fuel Use in Rat Model of High and Low Exercise Capacity.

In humans, exercise capacity strongly associates with morbidity, mortality, and disease-risk. Maximal exercise capacity is a heritable trait, and rats selectively bred for high and low exercise capacity mimic phenotypes observed in humans: high capacity running rats (HCR) have lower metabolic-disease risk and increased longevity compared to low capacity running rats (LCR). In prior in vitro studies HCR skeletal muscle was shown to have higher fatty acid (FA) oxidizing capacity than LCR. We hypothesized that HCR would have enhanced FA utilization during in vivo exercise. In this study we use metabolomics and proteomics approaches to test this hypothesis and to explore metabolic differences between HCR and LCR during an increasing-intensity treadmill protocol (speed increasing 1 m/min every 2 min). Using indirect calorimetry, we found that during exercise HCR maintain high FA utilization, while LCR primarily utilize carbohydrates. Skeletal muscle and plasma were collected at rest, at 10 min of exercise (near exhaustion for LCR), and at 45 min of exercise (near exhaustion for HCR). Metabolite profiles showed HCR have increased muscle long-chain acyl-carnitines from rest to 10 min of exercise, indicating increased FA entry into the mitochondria of HCR. In contrast, LCR showed accumulation of short- and medium-chain muscle acylcarnitines from rest to 10 min of exercise, indicating inefficient substrate metabolism. We quantified muscle mitochondrial proteins and protein post-translational modifications (phosphorylation and acetylation) at rest and at 10 min of exercise. At rest, HCR have greater expression of enzymes within FA and branched-chain amino acid (BCAA) metabolic pathways than LCR. Compared to LCR, HCR have lower mitochondrial protein acetylation at rest and show protein deacetylation with 10 min of exercise, specifically in oxidative phosphorylation, citric acid cycle, FA and BCAA metabolic pathways. Consistent with a functional role of increased protein expression and lower protein acetylation within the BCAA pathway, HCR have greater BCAA metabolism during 10 min of exercise as measured by flux of intraperitoneally injected U-13C15N valine into catabolic intermediates. This study suggests enhanced FA and BCAA metabolism supports high running capacity and provides evidence for FA and BCAA pathway protein expression and acetylation in mediating enhanced fuel utilization.PHDMolecular and Integrative PhysiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/110359/1/kappacoo_1.pd

Water-soluble saponins accumulate in drought-stressed switchgrass and may inhibit yeast growth during bioethanol production

Background: Developing economically viable pathways to produce renewable energy has become an important research theme in recent years. Lignocellulosic biomass is a promising feedstock that can be converted into second-generation biofuels and bioproducts. Global warming has adversely affected climate change causing many environmental changes that have impacted earth surface temperature and rainfall patterns. Recent research has shown that environmental growth conditions altered the composition of drought-stressed switchgrass and directly influenced the extent of biomass conversion to fuels by completely inhibiting yeast growth during fermentation. Our goal in this project was to find a way to overcome the microbial inhibition and characterize specific compounds that led to this inhibition. Additionally, we also determined if these microbial inhibitors were plant-generated compounds, by-products of the pretreatment process, or a combination of both. Results: Switchgrass harvested in drought (2012) and non-drought (2010) years were pretreated using Ammonia Fiber Expansion (AFEX). Untreated and AFEX processed samples were then extracted using solvents (i.e., water, ethanol, and ethyl acetate) to selectively remove potential inhibitory compounds and determine whether pretreatment affects the inhibition. High solids loading enzymatic hydrolysis was performed on all samples, followed by fermentation using engineered Saccharomyces cerevisiae. Fermentation rate, cell growth, sugar consumption, and ethanol production were used to evaluate fermentation performance. We found that water extraction of drought-year switchgrass before AFEX pretreatment reduced the inhibition of yeast fermentation. The extracts were analyzed using liquid chromatography–mass spectrometry (LC–MS) to detect compounds enriched in the extracted fractions. Saponins, a class of plant-generated triterpene or steroidal glycosides, were found to be significantly more abundant in the water extracts from drought-year (inhibitory) switchgrass. The inhibitory nature of the saponins in switchgrass hydrolysate was validated by spiking commercially available saponin standard (protodioscin) in non-inhibitory switchgrass hydrolysate harvested in normal year. Conclusions: Adding a water extraction step prior to AFEX-pretreatment of drought-stressed switchgrass effectively overcame inhibition of yeast growth during bioethanol production. Saponins appear to be generated by the plant as a response to drought as they were significantly more abundant in the drought-stressed switchgrass water extracts and may contribute toward yeast inhibition in drought-stressed switchgrass hydrolysates

Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation

SummaryMaximal exercise-associated oxidative capacity is strongly correlated with health and longevity in humans. Rats selectively bred for high running capacity (HCR) have improved metabolic health and are longer-lived than their low-capacity counterparts (LCR). Using metabolomic and proteomic profiling, we show that HCR efficiently oxidize fatty acids (FAs) and branched-chain amino acids (BCAAs), sparing glycogen and reducing accumulation of short- and medium-chain acylcarnitines. HCR mitochondria have reduced acetylation of mitochondrial proteins within oxidative pathways at rest, and there is rapid protein deacetylation with exercise, which is greater in HCR than LCR. Fluxomic analysis of valine degradation with exercise demonstrates a functional role of differential protein acetylation in HCR and LCR. Our data suggest that efficient FA and BCAA utilization contribute to high intrinsic exercise capacity and the health and longevity benefits associated with enhanced fitness

Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut.

The molecular bases of how host genetic variation impacts the gut microbiome remain largely unknown. Here we used a genetically diverse mouse population and applied systems genetics strategies to identify interactions between host and microbe phenotypes including microbial functions, using faecal metagenomics, small intestinal transcripts and caecal lipids that influence microbe-host dynamics. Quantitative trait locus (QTL) mapping identified murine genomic regions associated with variations in bacterial taxa; bacterial functions including motility, sporulation and lipopolysaccharide production and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and caecal levels of ornithine lipids. Follow-up in vitro and in vivo studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that ornithine lipids have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits including Atf3, which encodes for a transcription factor that plays vital roles in modulating metabolism and immunity. Collectively, these results suggest that ornithine lipids are potentially important for A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes

The dental calculus metabolome in modern and historic samples.

INTRODUCTION: Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens. OBJECTIVE: We present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach. METHODS: Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC-MS/MS for further characterization of metabolites and lipids. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss. RESULTS: Dipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples. CONCLUSIONS: The results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies

Metabolomic Biomarkers Differentiate Soy Sauce Freshness under Conditions of Accelerated Storage

Naturally fermented soy sauce is one of the few globally valued food condiments. It is complex in its substrate, manufacturing processes, and chemical profile of salts and organic compounds, resulting from spontaneous, enzymatic and biochemical reactions. The overall chemical character of soy sauce has a few rivals relative to its chemical and bioactive complexity. Resulting from this complexity are unique sensory attributes contributing to the characteristic soy sauce flavor as well as potentiating other sensory sensations. Soy sauce is susceptible to deterioration after bottling during storage. This work examined soy sauces over an eight-month period using descriptive sensory methods and the discovery of metabolomic biomarkers with high resolution mass spectrometry, wherein samples were derivatized to enable volatility and identification of polar analytes. While several thousand metabolites were detected, only organic acids, amino acids, and various glycosylated metabolites were statistically defensible biomarkers of storage time. The relationships between sensory and metabolomic data were assessed using Kendall rank-based correlations to generate Kendall Tau correlation coefficients. A second approach filtered the data based on correlation significance and grouped molecules based on hierarchical clustering. Mass spectrometry analyses discovered several thousand unique analyte peaks with relevant changes denoted as significant relative to the fresh samples using volcano depictions of p values versus changes in compound abundances. We present a metabolomic approach for the analysis of complex food systems capable of differentiating a quantifiable extrinsic variable, which is, in this case, storage time with a correlation coefficient of 0.99. We further demonstrate that changes in soy sauce resulting from storage are characterized by sensory decreases in fruity/grape and nutty/sesame aroma and increases in methional/potato aroma and astringent attributes with concomitant changes in the concentrations of several key biomarkers

Impact of anesthesia and euthanasia on metabolomics of mammalian tissues: studies in a C57BL/6J mouse model.

A critical application of metabolomics is the evaluation of tissues, which are often the primary sites of metabolic dysregulation in disease. Laboratory rodents have been widely used for metabolomics studies involving tissues due to their facile handing, genetic manipulability and similarity to most aspects of human metabolism. However, the necessary step of administration of anesthesia in preparation for tissue sampling is not often given careful consideration, in spite of its potential for causing alterations in the metabolome. We examined, for the first time using untargeted and targeted metabolomics, the effect of several commonly used methods of anesthesia and euthanasia for collection of skeletal muscle, liver, heart, adipose and serum of C57BL/6J mice. The data revealed dramatic, tissue-specific impacts of tissue collection strategy. Among many differences observed, post-euthanasia samples showed elevated levels of glucose 6-phosphate and other glycolytic intermediates in skeletal muscle. In heart and liver, multiple nucleotide and purine degradation metabolites accumulated in tissues of euthanized compared to anesthetized animals. Adipose tissue was comparatively less affected by collection strategy, although accumulation of lactate and succinate in euthanized animals was observed in all tissues. Among methods of tissue collection performed pre-euthanasia, ketamine showed more variability compared to isoflurane and pentobarbital. Isoflurane induced elevated liver aspartate but allowed more rapid initiation of tissue collection. Based on these findings, we present a more optimal collection strategy mammalian tissues and recommend that rodent tissues intended for metabolomics studies be collected under anesthesia rather than post-euthanasia

Principal component analysis of untargeted metabolomics data from tissues collected using different methods of anesthesia.

<p>Two-dimensional PCA score plots reveal separation in metabolite profiles induced by different methods of anesthesia and euthanasia in C57BL/6J mice. Tissues analyzed were a) skeletal muscle, b) heart, c) liver, d) white adipose and e) serum. Methods of anesthesia and euthanasia were: CD, cervical dislocation euthanasia (red); CO2, Carbon dioxide euthanasia (green); Iso-Cont, continuous isoflurane anesthesia (dark blue); Iso-OD, isoflurane overdose euthanasia (light blue); Ket, ketamine anesthesia (pink); Pent, pentobarbital anesthesia (orange). Ellipses represent the 95% confidence interval.</p