Method development for fecal lipidomics profiling

Changes in fecal metabolic and lipidomic features by anti-TNF treatment and prediction of clinical remission in patients with ulcerative colitis

Background

Therapeutic targets for ulcerative colitis (UC) and prediction models of antitumor necrosis factor (TNF) therapy outcomes have not been fully reported.

Objective

Investigate the characteristic metabolite and lipid profiles of fecal samples of UC patients before and after adalimumab treatment and develop a prediction model of clinical remission following adalimumab treatment.

Design

Prospective, observational, multicenter study was conducted on moderate-to-severe UC patients (n = 116).

Methods

Fecal samples were collected from UC patients at 8 and 56 weeks of adalimumab treatment and from healthy controls (HC, n = 37). Clinical remission was assessed using the Mayo score. Metabolomic and lipidomic analyses were performed using gas chromatography mass spectrometry and nano electrospray ionization mass spectrometry, respectively. Orthogonal partial least squares discriminant analysis was performed to establish a remission prediction model.

Results

Fecal metabolites in UC patients markedly differed from those in HC at baseline and were changed similarly to those in HC during treatment; however, lipid profiles did not show these patterns. After treatment, the fecal characteristics of remitters (RM) were closer to those of HC than to those of non-remitters (NRM). At 8 and 56 weeks, amino acid levels in RM were lower than those in NRM and similar to those in HC. After 56 weeks, levels of 3-hydroxybutyrate, lysine, and phenethylamine decreased, and dodecanoate level increased in RM similarly to those in HC. The prediction model of long-term remission in male patients based on lipid biomarkers showed a higher performance than clinical markers.

Conclusion

Fecal metabolites in UC patients markedly differ from those in HC, and the levels in RM are changed similarly to those in HC after anti-TNF therapy. Moreover, 3-hydroxybutyrate, lysine, phenethylamine, and dodecanoate are suggested as potential therapeutic targets for UC. A prediction model of long-term remission based on lipid biomarkers may help implement personalized treatment.

Measurement of neutral ceramidase activity in vitro and in vivo

Neutral ceramidase is a hydrolase of ceramide that has been implicated in multiple biologic processes, including inflammation and oncogenesis. Ceramides and other sphingolipids, belong to a family of N-acyl linked lipids that are biologically active in signaling, despite their limited structural functions. Ceramides are generally pro-apoptotic, while sphingosine and sphingosine-1-phosphate (S1P) exert proliferative and pro-oncogenic effects. Ceramidases are important regulators of ceramide levels that hydrolyze ceramide to sphingosine. Thus, ceramidase inhibition significantly increases the quantities of ceramide and its associated signaling. To better understand the function of ceramide, biochemical and cellular assays for enzymatic activity were developed and validated to identify inhibitors of human neutral ceramidase (nCDase). Here we review the measurement of nCDase activity both in vitro and in vivo.

Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC)

INTRODUCTION

The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research.

OBJECTIVES

This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data.

RESULTS

The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities.

CONCLUSIONS

The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community.

Daily Rice Bran Consumption for 6 Months Influences Serum Glucagon-Like Peptide 2 and Metabolite Profiles without Differences in Trace Elements and Heavy Metals in Weaning Nicaraguan Infants at 12 Months of Age

BACKGROUND

Environmental enteric dysfunction (EED) is associated with chronic gut inflammation affecting nutrient absorption and development of children, primarily in low- and middle-income countries. Several studies have shown that rice bran (RB) supplementation provides nutrients and modulates gut inflammation, which may reduce risk for undernutrition.

OBJECTIVE

The aim was to evaluate the effect of daily RB dietary supplementation for 6 mo on serum biomarkers in weaning infants and associated changes in serum and stool metabolites.

METHODS

A 6-mo randomized-controlled dietary intervention was conducted in a cohort of weaning 6-mo-old infants in León, Nicaragua. Anthropometric indices were obtained at 6, 8, and 12 mo. Serum and stool ionomics and metabolomics were completed at the end of the 6-mo intervention using inductively coupled plasma MS and ultra-high performance LC-tandem MS. The ɑ1-acid glycoprotein, C-reactive protein, and glucagon-like peptide 2 (GLP-2) serum EED biomarkers were measured by ELISA.

RESULTS

Twenty-four infants in the control group and 23 in the RB group successfully completed the 6-mo dietary intervention with 90% dietary compliance. RB participants had higher concentrations of GLP-2 as compared with control participants at 12 mo [median (IQR): 743.53 (380.54) pg/mL vs. 592.50 (223.59) pg/mL; P = 0.04]. Metabolite profiles showed significant fold differences of 39 serum metabolites and 44 stool metabolites from infants consuming RB compared with control, and with significant metabolic pathway enrichment scores of 4.7 for the tryptophan metabolic pathway, 5.7 for polyamine metabolism, and 5.7 for the fatty acid/acylcholine metabolic pathway in the RB group. No differences were detected in serum and stool trace elements or heavy metals following daily RB intake for 6 mo.

CONCLUSIONS

RB consumption influences a suite of metabolites associated with growth promotion and development, while also supporting nutrient absorption as measured by changes in serum GLP-2 in Nicaraguan infants. This clinical trial was registered at https://clinicaltrials.gov as NCT02615886.

Qualitative Characterization of the Rat Liver Mitochondrial Lipidome Using All Ion Fragmentation on an Exactive Benchtop Orbitrap MS

Untargeted lipidomics profiling by liquid chromatography -mass spectrometry (LC-MS) allows researchers to observe the occurrences of lipids in a biological sample without showing intentional bias to any specific class of lipids and allows retrospective reanalysis of data collected. Typically, and in the specific method described, a general extraction method followed by LC separation is used to achieve nonspecific class coverage of the lipidome prior to high resolution accurate mass (HRAM) MS detection . Here we describe a workflow including the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition. We also highlight how, in this method, all ion fragmentation can be used to identify species of lower abundances, often missed by data dependent fragmentation techniques. Here we describe the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition.

Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations

Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.

Reviewing the metabolome coverage provided by LC-MS: Focus on sample preparation and chromatography-A tutorial

Metabolomics has become an invaluable tool for both studying metabolism and biomarker discovery. The great technical advances in analytical chemistry and bioinformatics have considerably increased the number of measurable metabolites, yet an important part of the human metabolome remains uncovered. Among the various MS hyphenated techniques available, LC-MS stands out as the most used. Here, we aimed to show the capabilities of LC-MS to uncover part of the metabolome and how to best proceed with sample preparation and LC to maximise metabolite detection. The analyses of various open metabolite databases served us to estimate the size of the already detected human metabolome, the expected metabolite composition of most used human biospecimens and which part of the metabolome can be detected when LC-MS is used. Based on an extensive review and on our experience, we have outlined standard procedures for LC-MS analysis of urine, cells, serum/plasma, tissues and faeces, to guide in the selection of the sample preparation method that best matches with one or more LC techniques in order to get the widest metabolome coverage. These standard procedures may be a useful tool to explore, at a glance, the wide spectrum of possibilities available, which can be a good starting point for most of the LC-MS metabolomic studies.

Endocannabinoids, endocannabinoid-like molecules and their precursors in human small intestinal lumen and plasma: does diet affect them?

PURPOSE

To determine the small intestinal concentration of endocannabinoids (ECs), N-acylethanolamines (NAEs) and their precursors N-acylphosphatidylethanolamines (NAPEs) in humans. To identify relationships between those concentrations and habitual diet composition as well as individual inflammatory status.

METHODS

An observational study was performed involving 35 participants with an ileostomy (18W/17M, aged 18-70 years, BMI 17-40 kg/m²). Overnight fasting samples of ileal fluid and plasma were collected and ECs, NAEs and NAPEs concentrations were determined by LC-HRMS. Dietary data were estimated from self-reported 4-day food diaries.

RESULTS

Regarding ECs, N-arachidonoylethanolamide (AEA) was not detected in ileal fluids while 2-arachidonoylglycerol (2-AG) was identified in samples from two participants with a maximum concentration of 129.3 µg/mL. In contrast, mean plasma concentration of AEA was 2.1 ± 0.06 ng/mL and 2-AG was 4.9 ± 1.05 ng/mL. NAEs concentrations were in the range 0.72-17.6 µg/mL in ileal fluids and 0.014-0.039 µg/mL in plasma. NAPEs concentrations were in the range 0.3-71.5 µg/mL in ileal fluids and 0.19-1.24 µg/mL in plasma being more abundant in participants with obesity than normal weight and overweight. Significant correlations between the concentrations of AEA, OEA and LEA in biological fluids with habitual energy or fat intakes were identified. Plasma PEA positively correlated with serum C-reactive protein.

CONCLUSION

We quantified ECs, NAEs and NAPEs in the intestinal lumen. Fat and energy intake may influence plasma and intestinal concentrations of these compounds. The luminal concentrations reported would allow modulation of the homeostatic control of food intake via activation of GPR119 receptors located on the gastro-intestinal mucosa.

CLINICAL TRIAL REGISTRY NUMBER AND WEBSITE

NCT04143139; www.clinicaltrials.gov .

1H NMR-Based Fecal Metabolomics Reveals Changes in Gastrointestinal Function of Aging Rats Induced by d-Galactose

d-galactose (d-gal) is widely used to induce aging. However, it is still unclear whether long-term injection of d-gal affects the gastrointestinal functions of aging rats, and how. In this study, we investigated the effects of d-gal on the gastrointestinal functions of aging rats, especially from the perspective of fecal metabolomics. Biochemical and behavioral analyses were performed. Besides, a ¹H NMR-based metabolomics approach was built and applied in combination with multivariate data analysis including principal components analysis (PCA) and orthogonal partial least squares-discriminate analysis (OPLS-DA). Regarding gastrointestinal functions, d-gal significantly decreased the small intestine propulsion rates and prolonged gastrointestinal transit time. In addition, d-gal significantly increased the oxidative damages. PCA results showed that d-gal interrupted the metabolic profiles of endogenous small molecules in aging rats. Furthermore, OPLS-DA showed that 40 metabolites were screened and identified to be involved in the disruption of gastrointestinal functions in aging rats. Accordingly, seven metabolic pathways were recognized as the most influenced pathways associated with gastrointestinal functions of aging rats induced by d-gal, including amino acid metabolism, energy metabolism, intestinal flora metabolism, and metabolism of short chain fatty acids. It is the first report to investigate the effects and underlying mechanisms of d-gal on gastrointestinal functions of aging rats from the perspective of fecal metabolomics. The current results are conducive to further comprehensively understand d-gal-induced aging and will expand the applications of d-gal in pharmacological researches.

Untargeted Profiling of Bile Acids and Lysophospholipids Identifies the Lipid Signature Associated with Glycemic Outcome in an Obese Non-Diabetic Clinical Cohort

The development of high throughput assays for assessing lipid metabolism in metabolic disorders, especially in diabetes research, nonalcoholic fatty liver disease (NAFLD), and nonalcoholic steatohepatitis (NASH), provides a reliable tool for identifying and characterizing potential biomarkers in human plasma for early diagnosis or prognosis of the disease and/or responses to a specific treatment. Predicting the outcome of weight loss or weight management programs is a challenging yet important aspect of such a program’s success. The characterization of potential biomarkers of metabolic disorders, such as lysophospholipids and bile acids, in large human clinical cohorts could provide a useful tool for successful predictions. In this study, we validated an LC-MS method combining the targeted and untargeted detection of these lipid species. Its potential for biomarker discovery was demonstrated in a well-characterized overweight/obese cohort subjected to a low-caloric diet intervention, followed by a weight maintenance phase. Relevant markers predicting successful responses to the low-caloric diet intervention for both weight loss and glycemic control improvements were identified. The response to a controlled weight loss intervention could be best predicted using the baseline concentration of three lysophospholipids (PC(22:4/0:0), PE(17:1/0:0), and PC(22:5/0:0)). Insulin resistance on the other hand could be best predicted using clinical parameters and levels of circulating lysophospholipids and bile acids. Our approach provides a robust tool not only for research purposes, but also for clinical practice, as well as designing new clinical interventions or assessing responses to specific treatment. Considering this, it presents a step toward personalized medicine.

Metabolomics Research Conducted by Nurse Scientists: A Systematic Scoping Review

Metabolomics, one of the newest omics, allows for investigation of holistic responses of living systems to myriad biological, behavioral, and environmental factors. Researcher use metabolomics to examine the underlying mechanisms of clinically observed phenotypes. However, these methods are complex, potentially impeding their uptake by scientists. In this scoping review, we summarize literature illustrating nurse scientists' use of metabolomics. Using electronic search methods, we identified metabolomics investigations conducted by nurse scientists and published in English-language journals between 1990 and November 2019. Of the studies included in the review (N = 30), 9 (30%) listed first and/or senior authors that were nurses. Studies were conducted predominantly in the United States and focused on a wide array of clinical conditions across the life span. The upward trend we note in the use of these methods by nurse scientists over the past 2 decades mirrors a similar trend across scientists of all backgrounds. A broad range of study designs were represented in the literature we reviewed, with the majority involving untargeted metabolomics (n = 16, 53.3%) used to generate hypotheses (n = 13, 76.7%) of potential metabolites and/or metabolic pathways as mechanisms of clinical conditions. Metabolomics methods match well with the unique perspective of nurse researchers, who seek to integrate the experiences of individuals to develop a scientific basis for clinical practice that emphasizes personalized approaches. Although small in number, metabolomics investigations by nurse scientists can serve as the foundation for robust programs of research to answer essential questions for nursing.

Exploring the Lipidome: Current Lipid Extraction Techniques for Mass Spectrometry Analysis

In recent years, high-throughput lipid profiling has contributed to understand the biological, physiological and pathological roles of lipids in living organisms. Across all kingdoms of life, important cell and systemic processes are mediated by lipids including compartmentalization, signaling and energy homeostasis. Despite important advances in liquid chromatography and mass spectrometry, sample extraction procedures remain a bottleneck in lipidomic studies, since the wide structural diversity of lipids imposes a constrain in the type and amount of lipids extracted. Differences in extraction yield across lipid classes can induce a bias on down-stream analysis and outcomes. This review aims to summarize current lipid extraction techniques used for untargeted and targeted studies based on mass spectrometry. Considerations, applications, and limitations of these techniques are discussed when used to extract lipids in complex biological matrices, such as tissues, biofluids, foods, and microorganisms.

N-Acylphosphatidylethanolamines and N-acylethanolamines increase in saliva upon food mastication: the influence of the individual nutritional status and fat type in food

This study aimed to evaluate the influence of the individual nutritional status on the salivary concentration of N-acylethanolamines (NAEs), including linoleoylethanolamide (LEA), oleoylethanolamide (OEA), and palmitoylethanolamide (PEA), and their precursors N-acylphosphatidylethanolamines (NAPEs) upon mastication of biscuits containing different fats. Three types of biscuits were formulated with 10% extra-virgin olive oil (EVOB), 10% palm oil (PALMB) or 10% paraffin oil (0% lipids, CONB). Twenty-five healthy subjects, 12 normal weight (NW, 9 F, 30.4 ± 8.7 years) and 13 obese (OB, 8 F, 35.5 ± 10.7 years) participated in a randomized crossover study. Fasting subjects collected unstimulated saliva (US) and stimulated saliva by masticating a parafilm piece (PP), and CONB, EVOB and PALMB. NAPEs, LEA, OEA and PEA were quantified in saliva samples by liquid chromatography-high-resolution mass spectrometry. The results showed that salivary NAPE and NAE concentrations in OB were higher than in NW in both US (NAPEs: 280.0 ± 45.4 ng mL-1vs. 121.8 ± 24.4 ng mL-1, p = 0.015; NAEs: 10.8 ± 1.4 ng mL-1vs. 4.8 ± 0.8 ng mL-1, p = 0.002, respectively) and PP (NAPEs: 259.8 ± 47.1 ng mL-1vs. 121.7 ± 16.9 ng mL-1, p = 0.049; NAEs: 6.1 ± 0.8 ng mL-1vs. 3.8 ± 0.4 ng mL-1, p = 0.03, respectively). NAPE and LEA levels were similar in US and PP, while the levels of OEA and PEA were lower in PP vs. US. Compared to PP, biscuit mastication increased the salivary NAPEs, LEA, OEA and overall NAEs in NW and OB. NAPEs increased in the order of EVOB = CONB > PALMB in NW and EVOB > CONB = PALMB in OB. LEA, OEA and overall NAEs increased similarly with all the biscuits in NW and in the order of EVOB > PALMB > CONB in OB. In contrast, the PEA concentration did not vary in saliva upon biscuit mastication in NW and neither with EVOB in OB, while it lowered with CONB and PALMB in OB. In conclusion, OB showed higher salivary levels of NAPEs and NAEs than NW. Mastication itself did not vary salivary NAPEs and LEA but reduced OEA, PEA and overall NAEs. Biscuit mastication increased salivary NAPEs and all NAEs, but PEA. Altogether, the data suggested that NAPEs and NAEs were released in saliva from biscuits at levels influenced by the individual nutritional status and biscuit type. These findings may have implications in molecular mechanisms underpinning gustatory processes in humans.

Quantification of diacylglycerol and triacylglycerol species in human fecal samples by flow injection Fourier transform mass spectrometry

The intestinal microbiome plays an important role in human health and disease and fecal materials reflect the microbial activity. Thus, analysis of fecal metabolites provides insight in metabolic interactions between gut microbiota and host organism. In this work, we applied flow injection analysis coupled to Fourier transform mass spectrometry (FIA-FTMS) to identify and quantify lipid species in human fecal samples. Fecal homogenates were subjected to lipid extraction and analyzed by FIA-FTMS. The analysis of different subjects revealed a vast heterogeneity of lipid species abundance. The majority of samples displayed prominent signals of triacylglycerol (TG) and diacylglycerol (DG) species that could be verified by MS2 spectra. Therefore, we focused on the quantification of TG and DG. Method validation included limit of quantification, linearity, evaluation of matrix effects, recovery, and reproducibility. The validation experiments demonstrated the suitability of the method, with exception for approximately 10% of samples, where we observed coefficients of variation higher than 15%. Impaired reproducibility was related to sample inhomogeneity and could not be improved by additional sample preparation steps. Additionally, these experiments demonstrated that compared with aqueous samples, samples containing isopropanol showed higher amounts of DG, presumably due to lysis of bacteria and increased TG lipolysis. These effects were sample-specific and substantiate the high heterogeneity of fecal materials as well as the need for further evaluation of pre-analytic conditions. In summary, FIA-FTMS offers a fast and accurate tool to quantify DG and TG species and is suitable to provide insight into the fecal lipidome and its role in health and disease.

Describing the fecal metabolome in cryogenically collected samples from healthy participants

The chemical composition of feces plays an important role in human metabolism. Metabolomics and lipidomics are valuable tools for screening the metabolite composition in feces. Here we set out to describe fecal metabolite composition in healthy participants in frozen stools. Frozen stool samples were collected from 10 healthy volunteers and cryogenically drilled in four areas along the specimen. Polar metabolites were analyzed using derivatization followed by two-dimensional gas chromatography and time of flight mass spectrometry. Lipids were detected using ultra high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry. 2326 metabolic features were detected. Out of a total of 298 metabolites that were annotated we report here 185 that showed a technical variation of x < 30%. These metabolites included amino acids, fatty acid derivatives, carboxylic acids and phenolic compounds. Lipids predominantly belonged to the groups of diacylglycerols, triacylglycerols and ceramides. Metabolites varied between sampling areas, some were broadly homogeneous, others varied 80%. A LASSO-computed network using metabolites present in all areas showed two main clusters describing the system, DAG lipids and phenyllactic acid. In feces from healthy participants, the main groups detected were phenolic compounds, ceramides, diacylglycerols and triacylglycerols.

A high-throughput platform for detailed lipidomic analysis of a range of mouse and human tissues

Lipidomics is of increasing interest in studies of biological systems. However, high-throughput data collection and processing remains non-trivial, making assessment of phenotypes difficult. We describe a platform for surveying the lipid fraction for a range of tissues. These techniques are demonstrated on a set of seven different tissues (serum, brain, heart, kidney, adipose, liver, and vastus lateralis muscle) from post-weaning mouse dams that were either obese (> 12 g fat mass) or lean (<5 g fat mass). This showed that the lipid metabolism in some tissues is affected more by obesity than others. Analysis of human serum (healthy non-pregnant women and pregnant women at 28 weeks' gestation) showed that the abundance of several phospholipids differed between groups. Human placenta from mothers with high and low BMI showed that lean placentae contain less polyunsaturated lipid. This platform offers a way to map lipid metabolism with immediate application in metabolic research and elsewhere. Graphical abstract.

Assessment of gut microbiota fecal metabolites by chromatographic targeted approaches

Gut microbiota, the specific microbial community of the gastrointestinal tract, by means of the production of microbial metabolites provides the host with several functions affecting metabolic and immunological homeostasis. Insights into the intricate relationships between gut microbiota and the host require not only the understanding of its structure and function but also the measurement of effector molecules acting along the gut microbiota axis. This article reviews the literature on targeted chromatographic approaches in analysis of gut microbiota specific metabolites in feces as the most accessible biological matrix which can directly probe the connection between intestinal bacteria and the (patho)physiology of the holobiont. Together with a discussion on sample collection and preparation, the chromatographic methods targeted to determination of some classes of microbiota-derived metabolites (e.g., short-chain fatty acids, bile acids, low molecular masses amines and polyamines, vitamins, neurotransmitters and related compounds) are discussed and their main characteristics, summarized in Tables.

Food database of N-acyl-phosphatidylethanolamines, N-acylethanolamines and endocannabinoids and daily intake from a Western, a Mediterranean and a vegetarian diet

The contents of N-acylphosphatidylethanolamines (NAPEs), N-acylethanolamines (NAEs) and endocannabinoids (ECs) in 43 food products were assessed and daily intakes, based on consumption of Mediterranean, vegetarian and Western diets, were simulated. NAPEs and NAEs were more abundant in plant-based foods than in animal food products; NAPEs were in the ranges 0-4032 vs 4-398 µg/g dw and NAEs were in the ranges 0-35 vs 0.1-0.7 µg/g dw, respectively while ECs were in the range 0-0.1 vs 0-34 µg/g dw. Daily intakes of NAPEs and NAEs were higher from Mediterranean (263 and 0.25 mg/day) and vegetarian (242 and 0.28 mg/day) diets than the Western diet (163 and 0.08 mg/day). Conversely, ECs intakes were higher from Western and Mediterranean diets (0.17 mg/day) than the vegetarian diet (0.01 mg/day). Future studies will evaluate the physiological role of dietary NAPEs, NAEs and ECs in humans.

"-Omics" workflow for paleolimnological and geological archives: A review

"-Omics" is a powerful screening method with applications in molecular biology, toxicology, wildlife biology, natural product discovery, and many other fields. Genomics, proteomics, metabolomics, and lipidomics are common examples included under the "-omics" umbrella. This screening method uses combinations of untargeted, semi-targeted, and targeted analyses paired with data mining to facilitate researchers' understanding of the genome, proteins, and small organic molecules in biological systems. Recently, however, the use of "-omics" has expanded into the fields of geology, specifically petrology, and paleolimnology. Specifically, untargeted analyses stand to transform these fields as petroleomics, and sediment-"omics" become more prevalent. "-Omics" facilitates the visualization of small molecule profiles from environmental matrices (i.e. oil and sediment). Small molecule profiles can provide improved understanding of small molecules distributions throughout the environment, and how those compositions can change depending on conditions (i.e. climate change, weathering, etc.). "-Omics" also facilities discovery of next-generation biomarkers that can be used for oil source identification and as proxies for reconstructing past environmental changes. Untargeted analyses paired with data mining and multivariate statistical analyses represents a powerful suite of tools for hypothesis generation, and new method development for environmental reconstructions. Here we present an introduction to "-omics" methodology, technical terms, and examples of applications to paleolimnology and petrology. The purpose of this review is to highlight the important considerations at each step in the "-omics" workflow to produce high quality and statistically powerful data for petrological and paleolimnological applications.

Coffee prevents fatty liver disease induced by a high-fat diet by modulating pathways of the gut-liver axis

Coffee consumption is inversely associated with the risk of non-alcoholic fatty liver disease (NAFLD). A gap in the literature still exists concerning the intestinal mechanisms that are involved in the protective effect of coffee consumption towards NAFLD. In this study, twenty-four C57BL/6J mice were divided into three groups each receiving a standard diet, a high-fat diet (HFD) or an HFD plus decaffeinated coffee (HFD+COFFEE) for 12 weeks. Coffee supplementation reduced HFD-induced liver macrovesicular steatosis (P < 0·01) and serum cholesterol (P < 0·001), alanine aminotransferase and glucose (P < 0·05). Accordingly, liver PPAR- α (P < 0·05) and acyl-CoA oxidase-1 (P < 0·05) as well as duodenal ATP-binding cassette (ABC) subfamily A1 (ABCA1) and subfamily G1 (ABCG1) (P < 0·05) mRNA expressions increased with coffee consumption. Compared with HFD animals, HFD+COFFEE mice had more undigested lipids in the caecal content and higher free fatty acid receptor-1 mRNA expression in the duodenum and colon. Furthermore, they showed an up-regulation of duodenal and colonic zonulin-1 (P < 0·05), duodenal claudin (P < 0·05) and duodenal peptide YY (P < 0·05) mRNA as well as a higher abundance of Alcaligenaceae in the faeces (P < 0·05). HFD+COFFEE mice had an energy intake comparable with HFD-fed mice but starting from the eighth intervention week they gained significantly less weight over time. Data altogether showed that coffee supplementation prevented HFD-induced NAFLD in mice by reducing hepatic fat deposition and metabolic derangement through modification of pathways underpinning liver fat oxidation, intestinal cholesterol efflux, energy metabolism and gut permeability. The hepatic and metabolic benefits induced by coffee were accompanied by changes in the gut microbiota.

A systemic workflow for profiling metabolome and lipidome in tissue

Simple metabolome and lipidome sample preparation procedures involving two successive extractions using small pieces of tissue, and a subsequent metabolite identification (MetID) strategy were developed. The sample preparation can significantly circumvent incomplete analysis due to insufficient amounts of tissue as a result of splitting into several aliquots for multiple measurements, with advantages over the similar previously reported methods in metabolite coverage, extraction efficiency, method robustness and friendly experimental operation. A MetID strategy, based on the integration of MS information mining (including adduct ions, in-source CID, MS information from both ESI (+) and ESI (-), characteristic fragmentation ions (CFIs), constant neutral losses (CNLs) and multimers) and in silico MS simulation, was demonstrated. A large number of adduct ions (83 features), in-source CID (123 features), ESI (+/-) ionization (20 features), CFIs& CNLs (more than 120 features) and multimers (17 features) were mined by manually or in silico recognition/filtering, which provide the most suspicious structures for subsequent in silico MS simulation. The unknown features presented the same score distribution as the known (83 features) features with scores ≥25% (geomean score: 52%) and with satisfactory match for the main ions of interest. The MS/MS noise and fragment ions of coeluted quasi-molecular ions of interest are the main reason for the low score in the simulation. Manual check/evaluation is always suggested for the simulation with a score less than 50%. This strategy presents satisfactory performance with 2.5 times more metabolites structurally characterized compared with that of the traditional method based on accurate-mass-based MS and MS/MS library matching. This strategy would be useful for potentially identifying metabolites without available MS/MS information in the library.

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies

The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow.

Cyclocarya paliurus Leaves Tea Improves Dyslipidemia in Diabetic Mice: A Lipidomics-Based Network Pharmacology Study

Hyperlipidemia and hepatic steatosis afflict over 75% of patients with type 2 diabetes, causing diabetic dyslipidemia. Cyclocarya paliurus (CP) leaf is a herbal tea which has long been consumed by the Chinese population, particularly people suffering from obesity and diabetes. CP appears to exhibit a hypolipidemic effect in lipid loaded mice (Kurihara et al., 2003), although the detailed mechanisms and active ingredients for this hypolipidemic effect have not yet been answered. In this study, we investigated the beneficial effects of CP and predicted the mechanisms by utilizing lipidomics, serum-pharmacochemistry and network pharmacology approaches. Our results revealed that serum and hepatic levels of total triglyceride (TG), total cholesterol (T-CHO), low-density lipoproteins (LDL) and high-density lipoproteins (HDL), as well as 30 lipids including cholesterol ester (CE), diglyceride (DG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), and sphingomyelin (SM) in CP-treated mice were improved in comparison with untreated diabetic mice. In parallel, 14 phytochemical compounds of CP were determined in mice serum after CP administration. Mechanistically, the network pharmacology analysis revealed the predicted targets of CP’s active ingredients ALOX12, APP, BCL2, CYP2C9, PTPN1 and linked lipidome targets PLD2, PLA2G(s), and PI3K(s) families could be responsible for the CP effects on diabetic dyslipidemia. In conclusion, this study revealed the beneficial effects of CP on diabetic dyslipidemia are achieved by reducing accumulation of hepatic lipid droplets and regulating circulatory lipids in diabetic mice, possibly through PI3K signaling and MAPK signaling pathways. GRAPHICAL ABSTRACT

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.

Global Fecal and Plasma Metabolic Dynamics Related to Helicobacter pylori Eradication

Background:Helicobacter pylori colonizes the gastric mucosa of more than half of the world's population. There is increasing evidence H. pylori protects against the development of obesity and childhood asthma/allergies in which the development of these diseases coincide with transient dysbiosis. However, the mechanism underlying the association of H. pylori eradication with human metabolic and immunological disorders is not well-established. In this study, we aimed to investigate the local and systemic effects of H. pylori eradication through untargeted fecal lipidomics and plasma metabolomics approaches by liquid chromatography mass spectrometry (LC-MS).

Results: Our study revealed that eradication of H. pylori eradication (i.e., loss of H. pylori and/or H. pylori eradication therapy) changed many global metabolite/lipid features, with the majority being down-regulated. Our findings primarily show that H. pylori eradication affects the host energy and lipid metabolism which may eventually lead to the development of metabolic disorders.

Conclusion: These predictive metabolic signatures of metabolic and immunological disorders following H. pylori eradication can provide insights into dynamic local and systemic metabolism related to H. pylori eradication in modulating human health.

Annotation of the human cerebrospinal fluid lipidome using high resolution mass spectrometry and a dedicated data processing workflow

INTRODUCTION

Due to its proximity with the brain, cerebrospinal fluid (CSF) could be a medium of choice for the discovery of biomarkers of neurological and psychiatric diseases using untargeted analytical approaches.

OBJECTIVES

This study explored the CSF lipidome in order to generate a robust mass spectral database using an untargeted lipidomic approach.

METHODS

Cerebrospinal fluid samples from 45 individuals were analyzed by liquid chromatography coupled to high-resolution mass spectrometry method (LC-HRMS). A dedicated data processing workflow was implemented using XCMS software and adapted filters to select reliable features. In addition, an automatic annotation using an in silico lipid database and several MS/MS experiments were performed to identify CSF lipid species.

RESULTS

Using this complete workflow, 771 analytically relevant monoisotopic lipid species corresponding to 550 unique lipids which represent five major lipid families (i.e., free fatty acids, sphingolipids, glycerophospholipids, glycerolipids, and sterol lipids) were detected and annotated. In addition, MS/MS experiments enabled to improve the annotation of 304 lipid species. Thanks to LC-HRMS, it was possible to discriminate between isobaric and also isomeric lipid species; and interestingly, our study showed that isobaric ions represent about 50 % of the total annotated lipid species in the human CSF.

CONCLUSION

This work provides an extensive LC/HRMS database of the human CSF lipidome which constitutes a relevant foundation for future studies aimed at finding biomarkers of neurological disorders.

Qualitative characterization of the rat liver mitochondrial lipidome using all ion fragmentation on an Exactive benchtop Orbitrap MS

Untargeted lipidomics profiling by liquid chromatography-mass spectrometry (LC-MS) allows researchers to observe the occurrences of lipids in a biological sample without showing intentional bias to any specific class of lipids and allows retrospective reanalysis of data collected. Typically, and in the specific method described, a general extraction method followed by LC separation is used to achieve nonspecific class coverage of the lipidome prior to high-resolution accurate mass (HRAM) MS detection. Here we describe a workflow including the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition. We also highlight how, in this method, all-ion fragmentation can be used to identify species of lower abundances, often missed by data-dependent fragmentation techniques. Here we describe the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition.

Stool phospholipid signature is altered by diet and tumors

Intake of saturated fat is a risk factor for ulcerative colitis (UC) and colon cancer. Changes in the microbiota have been implicated in the development of UC and colon cancer. The host and the microbiota generate metabolites that may contribute to or reflect disease pathogenesis. We used lipid class specific quantitative mass spectrometry to assess the phospholipid (PL) profile (phosphatidylcholine [PC], phosphatidylethanolamine [PE], phosphatidylinositol [PI], phosphatidylserine [PS]) of stool from mice fed a high fat (HFD) or control diet with or without induction of colitis-associated tumors using azoxymethane and dextran sodium sulfate. The microbiota was assessed using qPCR for several bacterial groups. Colitis-associated tumors were associated with reduced bulk PI and PE levels in control diet fed mice compared to untreated mice. Significant decreases in the relative quantities of several PC species were found in colitis-associated tumor bearing mice fed either diet. Statistical analysis of the PL profile revealed distinct clustering by treatment group. Partial least squares regression analysis found that the relative quantities of the PS class profile best predicted bacterial abundance of Clostridium leptum and Prevotella groups. Abundance of selected PL species correlated with bacterial group quantities. Thus, we have described that a HFD and colitis-associated tumors are associated with changes in phospholipids and may reflect host-microbial interactions and disease states.

Ultra-performance liquid chromatography-mass spectrometry as a sensitive and powerful technology in lipidomic applications

Lipidomics, the comprehensive illumination of lipid-based information in biology systems, involves in identifying lipids and profiling lipids and lipid-derived mediators. The development of lipidomics enables the characterization of lipid species and detailed lipid profiling in body fluid, tissue or cell, and allows for a wider understanding of the biological roles of lipid networks. Lipidomic research has been greatly facilitated by recent advances in ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and involved in lipid extraction, lipid identification and data analysis supporting applications from qualitative and quantitative assessment of multiple lipid species. UPLC technique, different mass spectrometry technique, lipid extraction and data analysis in lipidomics are reviewed. Afterwards, examples are provided on the use of UPLC-MS for finding lipid biomarkers in disease, drug, food, nutrition and plant fields. We also discuss the UPLC-MS-based lipidomics for the future perspectives and their potential problems.

Lipidomics applications for discovering biomarkers of diseases in clinical chemistry

Lipids are the fundamental components of biological membranes as well as the metabolites of organisms. Lipids play diverse and important roles in biologicals. The lipid imbalance is closely associated with numerous human lifestyle-related diseases, such as atherosclerosis, obesity, diabetes, and Alzheimer's disease. Lipidomics or lipid profiling is a system-based study of all lipids aiming at comprehensive analysis of lipids in the biological system. Lipidomics has been accepted as a lipid-related research tool in lipid biochemistry, clinical biomarker discovery, disease diagnosis, and in understanding disease pathology. Lipidomics will not only provide insights into the specific functions of lipid species in health and disease, but will also identify potential biomarkers for establishing preventive or therapeutic programs for human diseases. This review presents an overview of lipidomics followed by in-depth discussion of its application to the study of human diseases, including extraction methods of lipids, analytical technologies, data analysis, and clinical research in cancer, neuropsychiatric disease, cardiovascular disease, kidney disease, and respiratory disease. We describe the current status of the identification of metabolic biomarkers in different diseases. We also discuss the lipidomics for the future perspectives and their potential problems. The application of lipidomics in clinical studies may provide new insights into lipid profiling and pathophysiological mechanisms.

Simultaneous, untargeted metabolic profiling of polar and nonpolar metabolites by LC-Q-TOF mass spectrometry

At its most ambitious, untargeted metabolomics aims to characterize and quantify all of the metabolites in a given system. Metabolites are often present at a broad range of concentrations and possess diverse physical properties complicating this task. Performing multiple sample extractions, concentrating sample extracts, and using several separation and detection methods are common strategies to overcome these challenges but require a great amount of resources. This protocol describes the untargeted, metabolic profiling of polar and nonpolar metabolites with a single extraction and using a single analytical platform.

Lipidomics technologies at the end of the first decade and the beginning of the next

The lipidome is composed of all of the biomolecules defined as lipids, which encompass compounds of amazing structural diversity and complexity. It has been ∼1 decade since the study of "lipidomics" was begun in earnest, and the technologies and tools for data analysis have advanced considerably over this period. This workshop summarized the scope of the lipidome and technologies for its analysis, lipidomics databases and other online tools, and examples of the application of lipidomics to nutritional research. The slides from the workshop, online lipidomics tools, and databases are available at http://www.lipidmaps.org.