Environmental Metabolomics: A SWOT Analysis (Strengths, Weaknesses, Opportunities, and Threats)

Urbanisation-associated shifts in the avian metabolome within the annual cycle

While organisms have evolved to cope with predictable changes in the environment, the rapid rate of current global change presents numerous novel and unpredictable stressors to which organisms have had less time to adapt. To persist in the urban environment, organisms must modify their physiology, morphology and behaviour accordingly. Metabolomics offers great potential for characterising organismal responses to natural and anthropogenic stressors at the systems level and can be applied to any species, even without genomic knowledge. Using metabolomic profiling of blood, we investigated how two closely related species of passerine bird respond to the urban environment. Great tits Parus major and blue tits Cyanistes caeruleus residing in urban and forest habitats were sampled during the breeding (spring) and non-breeding (winter) seasons across replicated sites in southern Sweden. During breeding, differences in the plasma metabolome between urban and forest birds were characterised by higher levels of amino acids in urban-dwelling tits and higher levels of fatty acyls in forest-dwelling tits. The suggested higher rates of fatty acid oxidation in forest tits could be driven by habitat-associated differences in diet and could explain the higher reproductive investment and success of forest tits. High levels of amino acids in breeding urban tits could reflect the lack of lipid-rich caterpillars in the urban environment and a dietary switch to protein-rich spiders, which could be of benefit for tackling inflammation and oxidative stress associated with pollution. In winter, metabolomic profiles indicated lower overall levels of amino acids and fatty acyls in urban tits, which could reflect relaxed energetic demands in the urban environment. Our metabolomic profiling of two urban-adapted species suggests that their metabolism is modified by urban living, though whether these changes represent adaptative or non-adaptive mechanisms to cope with anthropogenic challenges remains to be determined.

Approaches and methods to study wildlife cancer

The last few years have seen a surge of interest from field ecologists and evolutionary biologists to study neoplasia and cancer in wildlife. This contributes to the One Health Approach, which investigates health issues at the intersection of people, wild and domestic animals, together with their changing environments. Nonetheless, the emerging field of wildlife cancer is currently constrained by methodological limitations in detecting cancer using non-invasive sampling. In addition, the suspected differential susceptibility and resistance of species to cancer often make the choice of a unique model species difficult for field biologists. Here, we provide an overview of the importance of pursuing the study of cancer in non-model organisms and we review the currently available methods to detect, measure and quantify cancer in the wild, as well as the methodological limitations to be overcome to develop novel approaches inspired by diagnostic techniques used in human medicine. The methodology we propose here will help understand and hopefully fight this major disease by generating general knowledge about cancer, variation in its rates, tumour-suppressor mechanisms across species as well as its link to life history and physiological characters. Moreover, this is expected to provide key information about cancer in wildlife, which is a top priority due to the accelerated anthropogenic change in the past decades that might favour cancer progression in wild populations.

Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches

The remediation of emerging contaminants presents a pressing environmental challenge, necessitating innovative approaches for effective mitigation. This review article delves into the untapped potential of soil microbial communities in the bioremediation of emerging contaminants. Bioremediation, while a promising method, often proves time-consuming and requires a deep comprehension of microbial intricacies for enhancement. Given the challenges presented by the inability to culture many of these microorganisms, conventional methods are inadequate for achieving this goal. While omics-based methods provide an innovative approach to understanding the fundamental aspects, processes, and connections among microorganisms that are essential for improving bioremediation strategies. By exploring the latest advancements in omics technologies, this review aims to shed light on how these approaches can unlock the hidden capabilities of soil microbial communities, paving the way for more efficient and sustainable remediation solutions.

Evidence of interregional similarity in crayfish metabolomes at reference sites: Progress towards the metabolome as a biomonitoring tool

It has been proposed that biomonitoring may benefit from the use of metabolomics (the study of all small molecules in an organism) to detect sub-lethal organism stress through changes in the metabolite profile (i.e., the metabolome). However, to integrate the metabolome into biomonitoring programs the amount of natural variability among and within populations of indicator taxa must be established prior to generating a reference condition. This study determined variation in the metabolome among ecoregion and stream of origin in the northern crayfish (Faxonius virilis) and if that variation inhibited detection of stressor effects at sites exposed to human activities. We collected crayfish from seven minimally disturbed streams (i.e., reference streams), distributed across three level II ecoregions in central Canada and compared their metabolomes. We found ecoregion and stream origin were poor predictors of crayfish metabolomes. This result suggests crayfish metabolomes were similar, despite differing environmental conditions. Metabolomes of crayfish collected from three stream sites exposed to agricultural activity and municipal wastewater (i.e., test sites) were then compared to the crayfish metabolomes from the seven reference streams. Findings showed that crayfish metabolomes from test sites were strongly differentiated from those at all reference sites. The consistency in the northern crayfish metabolome at the studied reference streams indicates that a single reference condition may effectively detect impacts of human activities across the sampled ecoregions.

Metabolomics revealed disruptions in amino acid and antioxidant biochemistry in Daphnia magna exposed to industrial effluents associated with plastic and polymer production

Industrial wastewater effluents are a major source of chemicals in aquatic environments, and many of these chemicals may negatively impact aquatic life. In this study, the crustacean Daphnia magna, a common model organism in ecotoxicity studies, was exposed for 48 h to nine different industrial effluent samples from manufacturing facilities associated with the production of plastics, polymers, and coating products at a range of dilutions: 10, 25, 50, 100% (undiluted). A targeted metabolomic-based approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantify polar metabolites from individual daphnids that survived the 48 h exposure. Multivariate analyses and metabolite changes revealed metabolic perturbations across all effluent samples studied, with non-monotonic responses and both up and downregulation relative to the unexposed control. Pathway analyses indicated the disruption of similar and distinct pathways, mostly connected to protein synthesis, amino acid metabolism, and antioxidant processes. Overall, we observed disruptions in Daphnia biochemistry that were similar across the effluent samples, but with unique features for each effluent sample. Additionally, non-monotonic heightened responses suggested additive and/or synergistic interactions between the chemicals within the industrial effluents. These findings demonstrate that targeted metabolomic approaches are a powerful tool for the biomonitoring of aquatic ecosystems in the context of complex mixtures, such as industrial wastewater effluents.

Metabolomic analysis of honey bee (Apis mellifera L.) response to glyphosate exposure

Glyphosate is among the world's most commonly used herbicides in agriculture and weed control. The use of this agrochemical has unintended consequences on non-target organisms, such as honey bees (Apis mellifera L.), the Earth's most prominent insect pollinator. However, detailed understanding of the biological effects in bees in response to sub-lethal glyphosate exposure is still limited. In this study, 1H NMR-based metabolomics was performed to investigate whether oral exposure to an environmentally realistic concentration (7.12 mg L-1) of glyphosate affects the regulation of honey bee metabolites in 2, 5, and 10 days. On Day 2 of glyphosate exposure, the honey bees showed significant downregulation of several essential amino acids, including leucine, lysine, valine, and isoleucine. This phenomenon indicates that glyphosate causes an obvious metabolic perturbation when the honey bees are subjected to the initial caging process. The mid-term (Day 5) results showed negligible metabolite-level perturbation, which indicated the low glyphosate impact on active honeybees. However, the long-term (Day 10) data showed evident separation between the control and experimental groups in the principal component analysis (PCA). This separation is the result of the combinatorial changes of essential amino acids such as threonine, histidine, and methionine, while the non-essential amino acids glutamine and proline as well as the carbohydrate sucrose were all downregulated. In summary, our study demonstrates that although no significant behavioral differences were observed in honey bees under sub-lethal doses of glyphosate, metabolomic level perturbation can be observed under short-term exposure when met with other environmental stressors or long-term exposure.

Identification of Metabolomic Biomarkers of Long-Term Stress Using NMR Spectroscopy in a Diving Duck

Human-induced environmental changes that act as long-term stressors pose significant impacts on wildlife health. Energy required for maintenance or other functions may be re-routed towards coping with stressors, ultimately resulting in fluctuations in metabolite levels associated with energy metabolism. While metabolomics approaches are used increasingly to study environmental stressors, its use in studying stress in birds is in its infancy. We implanted captive lesser scaup (Aythya affinis) with either a biodegradable corticosterone (CORT) pellet to mimic the effects of a prolonged stressor or a placebo pellet. 1D ¹H nuclear magnetic resonance (NMR) spectroscopy was performed on serum samples collected over 20 days after implant surgery. We hypothesized that CORT pellet-induced physiological stress would alter energy metabolism and result in distinct metabolite profiles in ducks compared with placebo (control). Quantitative targeted metabolite analysis revealed that metabolites related to energy metabolism: glucose, formate, lactate, glutamine, 3-hydroxybutyrate, ethanolamine, indole-3- acetate, and threonine differentiated ducks with higher circulatory CORT from controls on day 2. These metabolites function as substrates or intermediates in metabolic pathways related to energy production affected by elevated serum CORT. The use of metabolomics shows promise as a novel tool to identify and characterize physiological responses to stressors in wild birds.

Assessing Dietary Pesticide Intake and Potential Health Effects: The Application of Global Metabolomics Analysis

Scientific information is not yet available to provide insight into how individual metabolome might be affected by the presence of pesticides in regular diets. This study aimed to evaluate the perturbation of metabolomic pathways in children who switched their diets from conventional foods to mostly organic foods for five consecutive days. We selected 46 child-matched spot urine samples with distinct differences of urinary pesticide metabolite levels between the conventional and organic eating days and then analyzed those urine samples on three analytical platforms to perform global metabolomics analysis. We found statistically significant perturbations of metabolic pathways relevant to inflammation, oxidative stress, and the demands of xenobiotic detoxification when children switched their conventional diets to mostly organic foods. The outcomes of this study allow us to extend the current understanding beyond organophosphate pesticides' acute toxicity of cholinesterase inhibition to the perturbation of metabolic pathways at dietary intake levels.

Environmental Metabolomics Promises and Achievements in the Field of Aquatic Ecotoxicology: Viewed through the Pharmaceutical Lens

Scientists often set ambitious targets using environmental metabolomics to address challenging ecotoxicological issues. This promising approach has a high potential to elucidate the mechanisms of action (MeOAs) of contaminants (in hazard assessments) and to develop biomarkers (in environmental biomonitoring). However, metabolomics fingerprints often involve a complex mixture of molecular effects that are hard to link to a specific MeOA (if detected in the analytical conditions used). Given these promises and limitations, here we propose an updated review on the achievements of this approach. Metabolomics-based studies conducted on the effects of pharmaceutical active compounds in aquatic organisms provide a relevant means to review the achievements of this approach, as prior knowledge about the MeOA of these molecules could help overcome some shortcomings. This review highlighted that current metabolomics advances have enabled more accurate MeOA assessment, especially when combined with other omics approaches. The combination of metabolomics with other measured biological endpoints has also turned out to be an efficient way to link molecular effects to (sub)-individual adverse outcomes, thereby paving the way to the construction of adverse outcome pathways (AOPs). Here, we also discuss the importance of determining MeOA as a key strategy in the identification of MeOA-specific biomarkers for biomonitoring. We have put forward some recommendations to take full advantage of environmental metabolomics and thus help fulfil these promises.

Metabolite profiling of the post-ovulatory oocytes of the common carp, Cyprinus carpio: A 1H NMR-based metabolomics approach

A metabolomics study was conducted to investigate the molecular bases of oocyte over-ripening in common carp, Cyprinus carpio from a metabolic point of view. The ovulation was induced in fish brooders by intramuscular injection of pituitary extract and oocytes were collected four times post-ovulation with 30 min intervals. A set of 32 metabolites were identified on the NMR spectra of the oocytes, which mainly included energy-linked metabolites, amino acids, methylated metabolites and citric acid cycle (TCA) intermediates. PCA and PLS-DA models clearly separated the post ovulations times, indicating the effects of post-ovulation time on oocyte metabolome content. Based on the loading plot outputs, 15 metabolites including tryptophan, cysteine, AMP, tyrosine, valine, creatine phosphate (PCr), ATP, leucine, inosine, malate, acetate, TMAO, glucose, fumarate and lysine had more effects on the separation of post ovulation times. According to the results of metabolite profiling, the concentrations of glutamine, alanine, tryptophan, lysine and cysteine mostly significantly (P < 0.01) increased at 90 and 120 min post-ovulation. The concentrations of PCr, ATP, inosine and guanosine were relatively stable until 60 min post-ovulation, while significantly (P < 0.01) decreased at 90 and 120 min post ovulation. The TCA metabolites succinate, malate and fumarate significantly (P < 0.01) elevated at 90 and 120 min post-ovulation. AMP concentrations remained relatively unchanged until 30 min and then progressively decreased with time post ovulation (P < 0.01). The concentrations of lactate showed significant elevations at 90 and 120 min post ovulation (P < 0.01). In conclusion, the energetic potentials of the oocytes reduced with time post ovulation. There were apparent elevations in the concentrations of free amino acids, which may be associated with the onset of proteolytic activities in the post ovulatory oocytes. In addition, we found some changes in the apoptotic-related metabolites, which may support the results of previous studies regarding the oxidative stress and following apoptosis in post ovulatory oocytes of fish.

An NMR-based metabolomics study on sea anemones Exaiptasia diaphana (Rapp, 1829) with atrazine exposure

Sea anemones have been recommended as critical bioindicators for marine environmental stressors; however, the understanding of the biological effects in response to sublethal pollutant exposure is still limited. In this study, NMR-based metabolomics was performed to investigate the effects of atrazine on Exaiptasia diaphana with concentrations ranging from 3 to 90 ppb. As a result, the metabolic profiling of E. diaphana was significantly affected after 70 ppb treatment while a partial perturbation was observed as early as 3 ppb treatment. Glutamate was significantly changed at low atrazine concentrations with increased upregulation in concentrated atrazine experiments which is a potential biomarker for E. diaphana exposed to atrazine stressors. The TCA intermediates succinate and malate as well as the TCA cycle-related metabolites such as alanine, glycine, and taurine downregulated after atrazine treatment which also indicated the lower energy supply of E. diaphana. In summary, our study demonstrated that significant metabolic level perturbation could be detected at low atrazine concentrations before a physical change could be observed, and glutamate or the nitrogen metabolism may be the initial target for sea anemones by atrazine. The study may provide pioneering results for using E. diaphana to predict the impacts of exposure to atrazine toxin in marine systems.

Metallic oxide nanomaterials act as antioxidant nanozymes in higher plants: Trends, meta-analysis, and prospect

Improving plant resistance against various environmental stresses is crucial to gain higher agricultural productivity for meeting future food demands of the fast-growing global population. Nanozymes, nanomaterials (NMs) with enzyme-like activity, have shown the potential to defend environmental stresses via scavenging reactive oxygen species (ROS) and augmenting the inherent antioxidant functions of plants. However, several studies confirmed that NMs could cause oxidative damage triggered by excessive ROS. In this study, the conversion mechanism between antioxidant and oxidant activities of metallic oxidative nanozymes was systematically reviewed and evaluated using meta-analysis approach. Moreover, our work attempts to seek the optimal dose and physicochemical property of antioxidant-functionalized NMs and put forward future research directions. The meta-analysis results indicated that NMs at a low dose (below 20 ppm) exhibited antioxidant activity which could scavenge ROS and alleviate their deleterious impacts. Conversely, their oxidant activity was activated at the exposure dose above 200 ppm which might induce ROS overproduction and lead to oxidative stress. Further, root exposure tends to stimulate the oxidant activity of NMs, and the NMs modification is highly promising for improving their bioavailability. A SWOT analysis was conducted to evaluate the strengths, weaknesses, opportunities, and threats of agro-applied nanozymes. Therefore, the rational design and development of nanozymes for better antioxidant potential will be beneficial to their applications in agriculture.

Direct analysis of metabolites in the liver tissue of zebrafish exposed to fiproles by internal extractive electrospray ionization mass spectrometry

Exploring the metabolic disturbance of fipronil and its derivatives in aquatic organisms may provide a more comprehensive understanding of the impact of fipronil on the ecological environment. In this work, internal extractive electrospray ionization mass spectrometry (iEESI-MS) was used to directly analyze metabolites in the liver tissue of zebrafish exposed to fipronil and its three derivatives. Partial least squares-discriminant analysis (PLS-DA) revealed that 32 signals were considered as differential signals in zebrafish after the exposure treatment of fipronil and its derivatives, including phosphatidylcholines (PCs), lysophosphatidylcholines (LPCs), phosphatidylethanolamines (PEs), fatty acids and so on. The pathway analysis result showed that both fipronil and its derivatives have a significant impact on the glycerophospholipid metabolism of zebrafish. Besides, the intensities of PC signals in the liver samples of each group showed such a trend: mixed fiprole exposed group > fipronil sulfone exposed group ≈ fipronil sulfide exposed group > fipronil exposed group > fipronil desulfinyl exposed group > control group, indicating that mixed exposure of fipronil and its derivatives exhibited more significant metabolic disturbance in zebrafish. Taken together, iEESI-MS is applied to environmental toxicology and investigating the metabolic disturbance induced by fipronil and its derivatives in aquatic organisms, providing a new analytical method for this field.

Crayfish tissue metabolomes effectively distinguish impacts of wastewater and agriculture in aquatic ecosystems

Environmental metabolomics has been proposed as a tool for biomonitoring because organisms regulate production or consumption of metabolites in response to environmental conditions. We evaluated the efficacy of the metabolome of three tissues (hepatopancreas, gill, and tail muscle) from the northern crayfish (Faxonius virilis) to detect and differentiate between impacts of human activities (i.e., reference, municipal wastewater, and agriculture). We conducted a reciprocal transfer study exposing crayfish for 1 or 2 weeks in three streams with different amounts and types of human activities in southern Manitoba, Canada. Tissue samples were analyzed using nuclear magnetic resonance spectroscopy to generate a metabolic profile. Findings indicated the gill tissue metabolome best detected and differentiated between human activities. In particular, the gill metabolome was able to rapidly integrate abrupt changes in environmental conditions associated with municipal wastewater activity. In contrast, the tail metabolome best differentiated between crayfish collected at the reference site from those collected at the two impacted sites. Metabolites extracted from hepatopancreas tissue showed limited and inconsistent detection of among site differences. Based on our findings, we conclude that the metabolome of the northern crayfish can be an effective biomonitoring tool, but monitoring purpose will dictate tissue selection. Indeed, we recommend the gill metabolome be used for short-term assays aimed at detecting acute effects, whereas the tail be applied for survey monitoring aimed at detecting deviations in ecological condition at test sites from reference site conditions.

Microscale extraction versus conventional approaches for handling gastrointestinal extracts in oral bioaccessibility assays of endocrine disrupting compounds from microplastic contaminated beach sand

The unified bioaccessibility method (UBM) was harnessed to assess in vitro oral bioaccessibility pools of dialkyl phthalate congeners (with methyl, -ethyl, -butylbenzyl, -n-butyl, -2-ethylhexyl, and -n-octyl moieties) and bisphenol A at the 17 μg g^-1 level in beach sand contaminated with polyethylene microplastics. A variety of sample preparation approaches prior to the analysis of the UBM gastrointestinal extracts, including traditional methods (protein precipitation, liquid-liquid extraction, and solid-phase extraction) and dispersive liquid-liquid microextraction (DLLME) were comprehensively evaluated for clean-up and analyte enrichment. DLLME was chosen among all tested approaches on account of the high extraction efficiency (73-95%, excluding bis(2-ethylhexyl)phthalate and di-n-octyl phthalate), high sample throughput (∼7 min per set of samples), and environmental friendliness as demonstrated by the analytical eco-scale score of 83, and the green analytical procedure index pictogram with green/yellow labeling. The release of the less hydrophobic plastic-laden compounds (dimethyl phthalate, diethyl phthalate and bisphenol A) from the contaminated sample into the body fluids was significant, with bioaccessibility values ranging from 30 to 70%, and from 43 to 74% in gastric and gastrointestinal fluids, respectively, and with relative standard deviation < 17% in all cases. The majority of the compounds were leached during gastric digestion, likely as the combined action of the low pH and the gastric enzymes. The risk exposure analysis revealed that accumulation/concentration in the body fluids is potentially relevant for dimethyl phthalate, diethyl phthalate and bisphenol A, with relative accumulation ratios ranging from 1.1 ± 0.1 to 2.6 ± 0.4. The average daily intake values for the suite of compounds, corrected with the bioaccessibility fraction, ranged from 60 to 430 ng kg of body weight^-1·day^-1, in all cases, far below the tolerable daily intakes, thus indicating the lack of children health risk by ingestion of microplastic-laden sand with elevated concentrations of plasticizers.

Immunological Responses of Marine Bivalves to Contaminant Exposure: Contribution of the -Omics Approach

The increasing number of data studies on the biological impact of anthropogenic chemicals in the marine environment, together with the great development of invertebrate immunology, has identified marine bivalves as a key invertebrate group for studies on immunological responses to pollutant exposure. Available data on the effects of contaminants on bivalve immunity, evaluated with different functional and molecular endpoints, underline that individual functional parameters (cellular or humoral) and the expression of selected immune-related genes can distinctly react to different chemicals depending on the conditions of exposure. Therefore, the measurement of a suite of immune biomarkers in hemocytes and hemolymph is needed for the correct evaluation of the overall impact of contaminant exposure on the organism's immunocompetence. Recent advances in -omics technologies are revealing the complexity of the molecular players in the immune response of different bivalve species. Although different -omics represent extremely powerful tools in understanding the impact of pollutants on a key physiological function such as immune defense, the -omics approach has only been utilized in this area of investigation in the last few years. In this work, available information obtained from the application of -omics to evaluate the effects of pollutants on bivalve immunity is summarized. The data shows that the overall knowledge on this subject is still quite limited and that to understand the environmental relevance of any change in immune homeostasis induced by exposure to contaminants, a combination of both functional assays and cutting-edge technology (transcriptomics, proteomics, and metabolomics) is required. In addition, the utilization of metagenomics may explain how the complex interplay between the immune system of bivalves and its associated bacterial communities can be modulated by pollutants, and how this may in turn affect homeostatic processes of the host, host–pathogen interactions, and the increased susceptibility to disease. Integrating different approaches will contribute to knowledge on the mechanism responsible for immune dysfunction induced by pollutants in ecologically and economically relevant bivalve species and further explain their sensitivity to multiple stressors, thus resulting in health or disease.

Metabolomic insights into the lasting impacts of early-life exposure to BDE-47 in mice

Early-life exposure to toxicants may have lasting effects that adversely impact later development. Thus, although the production and use of a toxicant have been banned, the risk to previously exposed individuals may continue. BDE-47, a component of commercial penta-BDEs, is a persistent organic pollutant with demonstrated neurotoxicity. To investigate the persistent effects of BDE-47 and the mechanisms thereof, we employed a metabolomics approach to analyze the brain, blood and urine of mice exposed to BDE-47 for 28 days and then 3 months post-exposure. In the brain, BDE-47 was detectable just after exposure but was below the limit of detection (LOD) 3 months later. However, the metabolomic alterations caused by early-life exposure to BDE-47 persisted. Potential biomarkers related to these alterations included phosphatidylcholine, lysophosphatidylcholine, sphingomyelin and several amino acids and biogenic amines. The metabolic pathways involved in the response to BDE-47 in the brain were mainly those related to glycerophospholipid metabolism, sphingomyelin metabolism and neurotransmitter regulation. Thus, our study demonstrates the utility of metabolomics, as the omics most closely reflecting the phenotype, in exploring the mechanisms underlying the lasting effects induced by early-life BDE-47 exposure.

Multifactorial Analysis of Environmental Metabolomic Data in Ecotoxicology: Wild Marine Mussel Exposed to WWTP Effluent as a Case Study

Environmental metabolomics is a powerful approach to investigate the response of organisms to contaminant exposure at a molecular scale. However, metabolomic responses to realistic environmental conditions can be hindered by factors intrinsic to the environment and the organism. Hence, a well-designed experimental exposure associated with adequate statistical analysis could be helpful to better characterize and relate the observed variability to its different origins. In the current study, we applied a multifactorial experiment combined to Analysis of variance Multiblock Orthogonal Partial Least Squares (AMOPLS), to assess the metabolic response of wild marine mussels, Mytilus galloprovincialis, exposed to a wastewater treatment plant effluent, considering gender as an experimental factor. First, the total observed variability was decomposed to highlight the contribution of each effect related to the experimental factors. Both the exposure and the interaction gender × exposure had a statistically significant impact on the observed metabolic alteration. Then, these metabolic patterns were further characterized by analyzing the individual variable contributions to each effect. A main change in glycerophospholipid levels was highlighted in both males and females as a common response, possibly caused by oxidative stress, which could lead to reproductive disorders, whereas metabolic alterations in some polar lipids and kynurenine pathway were rather gender-specific. This may indicate a disturbance in the energy metabolism and immune system only in males. Finally, AMOPLS is a useful tool facilitating the interpretation of complex metabolomic data and is expected to have a broad application in the field of ecotoxicology.

Bioleaching for resource recovery from low-grade wastes like fly and bottom ashes from municipal incinerators: A SWOT analysis

Bioleaching (or microbial leaching) is a biohydrometallurgical technology that can be applied for metal recovery from anthropogenic waste streams. In particular, fly ashes and bottom ashes of municipal solid waste incineration (MSWI) can be used as a target material for biomining. Globally, approximately 46 million tonnes of MSWI ashes are produced annually. Currently landfilled or used as aggregate, these contain large amounts of marketable metals, equivalent to low-grade ores. There is opportunity to recover critical materials as the circular economy demands, using mesophile, moderately thermophile, and extremophile microorganisms for bioleaching. A Strengths, Weaknesses, Opportunities and Threats (SWOT) analysis was developed to assess the potential of this biotechnology to recover critical metals from MSWI wastes. Bioleaching has potential as a sustainable technology for resource recovery and enhanced waste management. However, stakeholders can only reap the full benefits of bioleaching by addressing both the technical engineering challenges and regulatory requirements needed to realise and integrated approach to resource use.

Metabolomics approach reveals disruption of metabolic pathways in the marine bivalve Mytilus galloprovincialis exposed to a WWTP effluent extract

Conventional wastewater treatment plants (WWTPs) discharge a highly diverse range of organic contaminants in aquatic environments, including marine waters. The health of marine ecosystems could be threatened by contaminants release. Environmental metabolomics can be helpful to assess the effects of multi-contamination on marine organisms without any a priori information since it is able to provide meaningful information on the biochemical response of organisms to a stress. The aim of the present study was to evaluate the potential of metabolomics to highlight key metabolites disrupted by a WWTP effluent extract exposure and then elucidate the biological effects of such exposure on Mediterranean mussels (Mytilus galloprovincialis). Exposed male mussels showed numerous metabolites altered in response to WWTP effluent exposure. The highlighted metabolites belong mainly to amino acids metabolism (e.g. tyrosine, phenylalanine, leucine, proline, etc.), neurohormones (dopamine and a serotonin metabolite), purine and pyrimidine metabolism (e.g. adenosine, adenine, guanine, uracil etc.), citric acid cycle intermediates (e.g. malate, fumarate), and a component involved in oxidative stress defense (oxidized glutathione). Modulation of these metabolites could reflect the alteration of several biological processes such as energy metabolism, DNA and RNA synthesis, immune system, osmoregulation, byssus formation and reproduction, which may lead to a negative impact of organism fitness. Our study provided further insight into the effects of WWTP effluents on marine organisms.

Metabolite tracking to elucidate the effects of environmental pollutants

The purpose of this study was to determine whether behavioral tests and metabolic profiling of organisms can be promising alternatives for assessing the health of aquatic systems. Water samples from four potential pollution sources in South Korea were collected for toxicity evaluation. First, conventional acute toxicity test in Daphnia magna and behavioral test in zebrafish was conducted to assess water quality. Second, metabolomic analysis was performed on zebrafish exposed to water samples and on environmental fish collected from the same source. Acute toxicity test in D. magna showed that none of the water samples exerted significant adverse effects. However, activity of zebrafish larvae exposed to samples from the zinc smelter (ZS) and industrial complex (IND) sites decreased compared to those exposed to samples from the reference site (RS). Metabolomic analysis using the Manhattan plot and Partial Least Square (PLS)/Orthogonal PLS Discriminant Analysis (OPLS-DA) showed differences in metabolic profiles between RS and ZS, and between IND and abandoned mine site (M). Interestingly, applying the same metabolomic analysis to environmental fish revealed patterns similar to those for zebrafish, despite the uncontrollable variables involved in environmental sampling. This study shows that metabolomics is a promising tool in assessing the health of aquatic environments.

Metabolic characteristics revealing cell differentiation of nasopharyngeal carcinoma by combining NMR spectroscopy with Raman spectroscopy

Background

The staging system of nasopharyngeal carcinoma (NPC) has close relationship with the degree of cell differentiation, but most NPC patients remain undiagnosed until advanced phases. Novel metabolic markers need to be characterized to support diagnose at an early stage.

Methods

Metabolic characteristics of nasopharyngeal normal cell NP69 and two types of NPC cells, including CNE1 and CNE2 associated with high and low differentiation degrees were studied by combining ¹H NMR spectroscopy with Raman spectroscopy. Statistical methods were also utilized to determine potential characteristic metabolites for monitoring differentiation progression.

Results

Metabolic profiles of NPC cells were significantly different according to differentiation degrees. Various characteristic metabolites responsible for different differentiated NPC cells were identified, and then disordered metabolic pathways were combed according to these metabolites. We found disordered pathways mainly included amino acids metabolisms like essential amino acids metabolisms, as well as altered lipid metabolism and TCA cycle, and abnormal energy metabolism. Thus our results provide evidence about close relationship between differentiation degrees of NPC cells and the levels of intracellular metabolites. Moreover, Raman spectrum analysis also provided complementary and confirmatory information about intracellular components in single living cells. Eight pathways were verified to that in NMR analysis, including amino acids metabolisms, inositol phosphate metabolism, and purine metabolism.

Conclusions

Methodology of NMR-based metabolomics combining with Raman spectroscopy could be powerful and straightforward to reveal cell differentiation development and meanwhile lay the basis for experimental and clinical practice to monitor disease progression and therapeutic evaluation.

Electronic supplementary material

The online version of this article (10.1186/s12935-019-0759-4) contains supplementary material, which is available to authorized users.

Developing metabolomics-based bioassessment: crayfish metabolome sensitivity to food and dissolved oxygen stress

There is a need to develop bioassessment tools that can diagnose the effects of individual stressors that can have multiple ecological effects. Using nuclear magnetic resonance (NMR)-based metabolomics, our experiments aimed to identify the sensitivity of metabolites to changes in food availability and dissolved oxygen (DO) concentrations, and compare these results to identify metabolites that may differentiate between the effects of these two stressors. Forty-eight, laboratory-raised, red swamp crayfish (Procambarus clarkii) were randomly assigned and exposed to one of three food availability or DO treatment levels (high, normal, low). Starved crayfish had lower amounts of amino acids than fed crayfish, suggesting catabolic effects of starvation on tail muscle tissue for energy requirements. In contrast, crayfish exposed to hypoxic conditions experienced changes in abundance of metabolites primarily associated with energy metabolism. Tail muscle was the only tissue sensitive to food and DO stress, suggesting the need to select tissues for monitoring appropriately. Our evaluation of environmental metabolomics as a tool for bioassessment indicates that several identified metabolites in crayfish tail muscle may be able to diagnose food and oxygen stress. Further study is required to determine if these metabolic effects are linked with changes of individual fitness and higher levels of biological organization, such as population size.

In-Vivo NMR Spectroscopy: A Powerful and Complimentary Tool for Understanding Environmental Toxicity

Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning. With in-vivo NMR it is possible to use the same organisms for control and exposure studies (controls are the same organisms prior to exposure inside the NMR). As such individual variability can be reduced while continual data collection over time provides the temporal resolution required to discern complex interconnected response pathways. When multidimensional NMR is combined with isotopic labelling, a wide range of metabolites can be identified in-vivo providing a unique window into the living metabolome that is highly complementary to more traditional metabolomics studies employing extracts, tissues, or biofluids.

Influence of exposure to pesticide mixtures on the metabolomic profile in post-metamorphic green frogs (Lithobates clamitans)

Pesticide use in agricultural areas requires the application of numerous chemicals to control target organisms, leaving non-target organisms at risk. The present study evaluates the hepatic metabolomic profile of one group of non-target organisms, amphibians, after exposure to a single pesticide and pesticide mixtures. Five common-use pesticide active ingredients were used in this study, three herbicides (atrazine, metolachlor and 2,4-d), one insecticide (malathion) and one fungicide (propiconazole). Juvenile green frogs (Lithobates clamitans) were reared for 60-90days post-metamorphosis then exposed to a single pesticide or a combination of pesticides at the labeled application rate on soil. Amphibian livers were excised for metabolomic analysis and pesticides were quantified for whole body homogenates. Based on the current study, metabolomic profiling of livers support both individual and interactive effects where pesticide exposures altered biochemical processes, potentially indicating a different response between active ingredients in pesticide mixtures, among these non-target species. Amphibian metabolomic response is likely dependent on the pesticides present in each mixture and their ability to perturb biochemical networks, thereby confounding efforts with risk assessment.

Environmental metabolomics with data science for investigating ecosystem homeostasis

A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.

Gene-metabolite profile integration to understand the cause of spaceflight induced immunodeficiency

Spaceflight presents a spectrum of stresses very different from those associated with terrestrial conditions. Our previous study (BMC Genom. 15: 659, 2014) integrated the expressions of mRNAs, microRNAs, and proteins and results indicated that microgravity induces an immunosuppressive state that can facilitate opportunistic pathogenic attack. However, the existing data are not sufficient for elucidating the molecular drivers of the given immunosuppressed state. To meet this knowledge gap, we focused on the metabolite profile of spaceflown human cells. Independent studies have attributed cellular energy deficiency as a major cause of compromised immunity of the host, and metabolites that are closely associated with energy production could be a robust signature of atypical energy fluctuation. Our protocol involved inoculation of human endothelial cells in cell culture modules in spaceflight and on the ground concurrently. Ten days later, the cells in space and on the ground were exposed to lipopolysaccharide (LPS), a ubiquitous membrane endotoxin of Gram-negative bacteria. Nucleic acids, proteins, and metabolites were collected 4 and 8 h post-LPS exposure. Untargeted profiling of metabolites was followed by targeted identification of amino acids and knowledge integration with gene expression profiles. Consistent with the past reports associating microgravity with increased energy expenditure, we identified several markers linked to energy deficiency, including various amino acids such as tryptophan, creatinine, dopamine, and glycine, and cofactors such as lactate and pyruvate. The present study revealed a molecular architecture linking energy metabolism and immunodeficiency in microgravity. The energy-deficient condition potentially cascaded into dysregulation of protein metabolism and impairment of host immunity. This project is limited by a small sample size. Although a strict statistical screening was carefully implemented, the present results further emphasize the need for additional studies with larger sample sizes. Validating this hypothesis using an in vivo model is essential to extend the knowledge towards identifying markers of diagnostic and therapeutic value.

Human cells challenged with a bacterial toxin show more signs of energy deficiency when flown in space than when cultured on the ground. Rasha Hammamieh from the US Army Center for Environmental Health Research in Frederick, Maryland, and colleagues exposed human endothelial cells in spaceflight to lipopolysaccharide, an immune response-triggering part of the bacterial membrane. They then collected nucleic acids, proteins and metabolites 4 and 8 h later, and saw a molecular architecture consistent with increased energy expenditure compared to matched control cells grown on Earth. Combined with the researchers’ previous finding that microgravity can induce an immunosuppressive state, the results suggest that energy imbalances potentially lead to problems with protein metabolism that ultimately impair the immune system. The authors propose that reversing this energy depletion could help enhance the immune health of astronauts.

Omics tools: New challenges in aquatic nanotoxicology?

In recent years, the implication of genomics into ecotoxicological studies has been studied closely to allow a better understanding of organism's responses to environmental contaminants including engineering nanomaterials (ENMs). ENMs are increasingly produced for various applications including cosmetics, electronics, sports equipment, biomedicine and agriculture. Because of their small size, ENMs possess chemical or physical characteristics improved compared to the corresponding macro-sized material. As their application expend, the release of manufactured ENMs into the environment is likely to increase and concern over impacts for the aquatic ecosystem is growing. Several studies reported deleterious effect of ENMs to aquatic organisms, but there is little information about the molecular mechanisms of toxicity. The development of ecotoxicogenomic approaches will improve the characterization of cellular and molecular modes of action of ENMs to aquatic organisms and allow a better prediction of contaminants toxicity. This paper presents an overview of transciptomic/proteomic studies in freshwater and marine organisms exposed to ENMs. Overall, induction of gene expression in relations to defense mechanisms, immune responses, growth and reproduction were measured after ENMs exposures of organisms, but with different patterns depending on exposure duration and concentrations used. In addition, some studies reported a positive correlation between gene expression and cellular modifications, but not at the individual level.

In vivo tissue sampling using solid-phase microextraction for non-lethal exposome-wide association study of CYP1A1 induction in Catostomus commersonii

Fish are widely used for monitoring aquatic ecosystem health and water contamination by organic toxicants from natural and anthropogenic sources. However, most of these studies only focused on the measurement of specific toxicants and did not examine the impact of chemical mixtures. In this study, we examined whether the tissue exposome captured in vivo with solid-phase microextraction (SPME) without lethal sampling and analyzed by liquid chromatography-high resolution mass spectrometry can detect differences between Catostomus commersonii exhibiting a significant induction of CYP1A1, through case/control comparisons, controlling for false discovery rates. We observed the presence of environmental toxicants in induced case fish known as potential inducers of CYP1A1. We also found significant changes in the levels of anti-oxidants, short-lived oxysterols and other lipids associated with CYP1A1 induction, possibly due to oxidative stress, lipid peroxidation and free fatty acids mobilization to maintain homeostatic state. In vivo SPME opens the way to perform repeated sampling on the same animal over the time and explore the individual internal exposome trajectory for better characterization of the links between toxicant load and health effects, at the individual scale.

Metabolic adaptations in a range-expanding arthropod

Despite an increasing number of studies documenting life‐history evolution during range expansions or shifts, we lack a mechanistic understanding of the underlying physiological processes. In this explorative study, we used a metabolomics approach to study physiological changes associated with the recent range expansion of the two‐spotted spider mite (Tetranychus urticae). Mite populations were sampled along a latitudinal gradient from range core to edge and reared under benign common garden conditions for two generations. Using gas chromatography–mass spectrometry, we obtained metabolic population profiles, which showed a gradual differentiation along the latitudinal gradient, indicating (epi)genetic changes in the metabolome in association with range expansion. These changes seemed not related with shifts in the mites’ energetic metabolism, but rather with differential use of amino acids. Particularly, more dispersive northern populations showed lowered concentrations of several essential and nonessential amino acids, suggesting a potential downregulation of metabolic pathways associated with protein synthesis.

Urinary metabolomics revealed arsenic internal dose-related metabolic alterations: a proof-of-concept study in a Chinese male cohort

Urinary biomonitoring provides the most accurate arsenic exposure assessment; however, to improve the risk assessment, arsenic-related metabolic biomarkers are required to understand the internal processes that may be perturbed, which may, in turn, link the exposure to a specific health outcome. This study aimed to investigate arsenic-related urinary metabolome changes and identify dose-dependent metabolic biomarkers as a proof-of-concept of the information that could be obtained by combining metabolomics and targeted analyses. Urinary arsenic species such as inorganic arsenic, methylarsonic acid, dimethylarsinic acid and arsenobetaine were quantified using high performance liquid chromatography (HPLC)-inductively coupled plasma-mass spectrometry in a Chinese adult male cohort. Urinary metabolomics was conducted using HPLC-quadrupole time-of-flight mass spectrometry. Arsenic-related metabolic biomarkers were investigated by comparing the samples of the first and fifth quintiles of arsenic exposure classifications using a partial least-squares discriminant model. After the adjustments for age, body mass index, smoking, and alcohol consumption, five potential biomarkers related to arsenic exposure (i.e., testosterone, guanine, hippurate, acetyl-N-formyl-5-methoxykynurenamine, and serine) were identified from 61 candidate metabolites; these biomarkers suggested that endocrine disruption and oxidative stress were associated with urinary arsenic levels. Testosterone, guanine, and hippurate showed a high or moderate ability to discriminate the first and fifth quintiles of arsenic exposure with area-under-curve (AUC) values of 0.89, 0.87, and 0.83, respectively; their combination pattern showed an AUC value of 0.91 with a sensitivity of 88% and a specificity of 80%. Arsenic dose-dependent AUC value changes were also observed. This study demonstrated that metabolomics can be used to investigate arsenic-related biomarkers of metabolic changes; the dose-dependent trends of arsenic exposure to these biomarkers may translate into the potential use of metabolic biomarkers in arsenic risk assessment. Since this was a proof-of-concept study, more research is needed to confirm the relationships we observed between arsenic exposure and biochemical changes.

Metabolomic, behavioral, and reproductive effects of the aromatase inhibitor fadrozole hydrochloride on the unionid mussel Lampsilis fasciola

Androgen-induced masculinization of female aquatic biota poses concerns for natural population stability. This research evaluated the effects of a twelve day exposure of fadrozole hydrochloride on the metabolism and reproductive status of the unionid mussel Lampsilis fasciola. Although this compound is not considered to be widespread in the aquatic environment, it was selected as a model aromatase (enzyme that converts testosterone to estradiol) inhibitor. Adult mussels were exposed to a control and 3 concentrations of fadrozole (2μg/L, 20μg/L, and 50μg/L), and samples of gill tissue were taken on days 4 and 12 for metabolomics analysis. Gills were used because of the variety of critical processes they mediate, such as feeding, ion exchange, and siphoning. Daily observed mussel behavior included female mantle display, foot protrusion, siphoning, and larval (glochidia) releases. Glochidia mortality was significantly higher in the 20μg/L treatment. Fewer conglutinate (packets of glochidia) releases were observed in the 50μg/L treatment, and mortality was highly correlated to release numbers. Foot protrusion was significantly higher in females in nearly all treatments, including the control, during the first 4days of observations. However, this sex difference was observed only in the 50μg/L treatment during the last 8days. Generally, metabolites were significantly altered in female gill tissue in the 2μg/L treatment whereas males were mostly affected only at the highest (50μg/L) treatment. Both sexes also revealed significant reductions in fadrozole-induced metabolic effects in gill tissue sampled after 12days compared to tissue sampled after 4days, indicating time-dependent mechanisms of disruptions in metabolic pathways and homeostatic processes to compensate for such disruptions.

Integrated analysis of seaweed components during seasonal fluctuation by data mining across heterogeneous chemical measurements with network visualization

Biological information is intricately intertwined with several factors. Therefore, comprehensive analytical methods such as integrated data analysis, combining several data measurements, are required. In this study, we describe a method of data preprocessing that can perform comprehensively integrated analysis based on a variety of multimeasurement of organic and inorganic chemical data from Sargassum fusiforme and explore the concealed biological information by statistical analyses with integrated data. Chemical components including polar and semipolar metabolites, minerals, major elemental and isotopic ratio, and thermal decompositional data were measured as environmentally responsive biological data in the seasonal variation. The obtained spectral data of complex chemical components were preprocessed to isolate pure peaks by removing noise and separating overlapping signals using the multivariate curve resolution alternating least-squares method before integrated analyses. By the input of these preprocessed multimeasurement chemical data, principal component analysis and self-organizing maps of integrated data showed changes in the chemical compositions during the mature stage and identified trends in seasonal variation. Correlation network analysis revealed multiple relationships between organic and inorganic components. Moreover, in terms of the relationship between metal group and metabolites, the results of structural equation modeling suggest that the structure of alginic acid changes during the growth of S. fusiforme, which affects its metal binding ability. This integrated analytical approach using a variety of chemical data can be developed for practical applications to obtain new biochemical knowledge including genetic and environmental information.

Potential input from metabolomics for exploring and understanding the links between environment and health

Humans may be exposed via their environment to multiple chemicals as a consequence of human activities and use of synthetic products. Little knowledge is routinely generated on the hazards of these chemical mixtures. The metabolomic approach is widely used to identify metabolic pathways modified by diseases, drugs, or exposures to toxicants. This review, based on the state of the art of the current applications of metabolomics in environmental health, attempts to determine whether metabolomics might constitute an original approach to the study of associations between multiple, low-dose environmental exposures in humans. Studying the biochemical consequences of complex environmental exposures is a challenge demanding the development of careful experimental and epidemiological designs, in order to take into account possible confounders associated with the high level of interindividual variability induced by different lifestyles. The choices of populations studied, sampling and storage procedures, statistical tools used, and system biology need to be considered. Suggestions for improved experimental and epidemiological designs are described. Evidence indicates that metabolomics may be a powerful tool in environmental health in the identification of both complex exposure biomarkers directly in human populations and modified metabolic pathways, in an attempt to improve understanding the underlying environmental causes of diseases. Nevertheless, the validity of biomarkers and relevancy of animal-to-human extrapolation remain key challenges that need to be properly explored.

Gas chromatography-mass spectrometry based metabolomic approach for optimization and toxicity evaluation of earthworm sub-lethal responses to carbofuran

Despite recent advances in understanding mechanism of toxicity, the development of biomarkers (biochemicals that vary significantly with exposure to chemicals) for pesticides and environmental contaminants exposure is still a challenging task. Carbofuran is one of the most commonly used pesticides in agriculture and said to be most toxic carbamate pesticide. It is necessary to identify the biochemicals that can vary significantly after carbofuran exposure on earthworms which will help to assess the soil ecotoxicity. Initially, we have optimized the extraction conditions which are suitable for high-throughput gas chromatography mass spectrometry (GC-MS) based metabolomics for the tissue of earthworm, Metaphire posthuma. Upon evaluation of five different extraction solvent systems, 80% methanol was found to have good extraction efficiency based on the yields of metabolites, multivariate analysis, total number of peaks and reproducibility of metabolites. Later the toxicity evaluation was performed to characterize the tissue specific metabolomic perturbation of earthworm, Metaphire posthuma after exposure to carbofuran at three different concentration levels (0.15, 0.3 and 0.6 mg/kg of soil). Seventeen metabolites, contributing to the best classification performance of highest dose dependent carbofuran exposed earthworms from healthy controls were identified. This study suggests that GC-MS based metabolomic approach was precise and sensitive to measure the earthworm responses to carbofuran exposure in soil, and can be used as a promising tool for environmental eco-toxicological studies.

A metabonomic investigation of the effects of 60 days exposure of rats to two types of pyrethroid insecticides

Type I and II pyrethroid insecticides display different neurotoxicity. To investigate the long-term (60 days exposure) metabolic effect of the two types of pyrethroid insecticides deltamethrin and permethrin, (1)H nuclear magnetic resonance (NMR) spectroscopy-based metabonomics was used to analyze the biochemical composition of urine and serum samples from rats administrated daily with deltamethrin or permethrin for 60 consecutive days, and principal component analysis used to visualize similarities and differences in the resultant biochemical profiles. Rats treated with either deltamethrin or permethrin displayed increased levels of urinary acetate, dimethylamine, dimethylglycine, trimethylamine and serum free amino acids, and decreased urinary 2-oxoglutarate, all of which are indicative of kidney lesions and nephrotoxicity. The reduced excretion of tricarboxylic acid cycle intermediates, together with increased 3-D-hydroxybutyrate, acetate, and lactate in treated rats could suggest disturbance of the energy metabolism, including an increased rate of anaerobic glycolysis, enhanced fatty acid β-oxidation and ketogenesis. These results show that these two types of insecticides have similarities in the urine and serum spectra, indicating that similar metabolic pathways are perturbed by the insecticides, which induced hepatotoxicity and nephrotoxicity. This approach may lead to the discovery of novel biomarkers of pyrethroids toxicity and thereby provide new insights into the toxicological mechanisms of pesticides pyrethroids.

Metabolomics in plant environmental physiology

Changes in plant metabolism are at the heart of plant developmental processes, underpinning many of the ways in which plants respond to the environment. As such, the comprehensive study of plant metabolism, or metabolomics, is highly valuable in identifying phenotypic effects of abiotic and biotic stresses on plants. When study is in reference to analysing samples that are relevant to environmental or ecologically based hypotheses, it is termed 'environmental metabolomics'. The emergence of environmental metabolomics as one of the latest of the omics technologies has been one of the most critically important recent developments in plant physiology. Its applications broach the entire landscape of plant ecology, from the understanding of plant plasticity and adaptation through to community composition and even genetic modification in crops. The multitude of novel studies published utilizing metabolomics methods employ a variety of techniques, from the initial stages of tissue sampling, through to sample preservation, transportation, and analysis. This review introduces the concept and applications of plant environmental metabolomics as an ecologically important investigative tool. It examines the main techniques used in situ within field sites, with particular reference to sampling and processing, and those more appropriate for use in laboratory-based settings with emphasis on secondary metabolite analysis.

Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems

Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated.

Clinical laboratory as an economic model for business performance analysis

Aim

To perform SWOT (strengths, weaknesses, opportunities, and threats) analysis of a clinical laboratory as an economic model that may be used to improve business performance of laboratories by removing weaknesses, minimizing threats, and using external opportunities and internal strengths.

Methods

Impact of possible threats to and weaknesses of the Clinical Laboratory at Našice General County Hospital business performance and use of strengths and opportunities to improve operating profit were simulated using models created on the basis of SWOT analysis results. The operating profit as a measure of profitability of the clinical laboratory was defined as total revenue minus total expenses and presented using a profit and loss account. Changes in the input parameters in the profit and loss account for 2008 were determined using opportunities and potential threats, and economic sensitivity analysis was made by using changes in the key parameters. The profit and loss account and economic sensitivity analysis were tools for quantifying the impact of changes in the revenues and expenses on the business operations of clinical laboratory.

Results

Results of simulation models showed that operational profit of €470 723 in 2008 could be reduced to only €21 542 if all possible threats became a reality and current weaknesses remained the same. Also, operational gain could be increased to €535 804 if laboratory strengths and opportunities were utilized. If both the opportunities and threats became a reality, the operational profit would decrease by €384 465.

Conclusion

The operational profit of the clinical laboratory could be significantly reduced if all threats became a reality and the current weaknesses remained the same. The operational profit could be increased by utilizing strengths and opportunities as much as possible. This type of modeling may be used to monitor business operations of any clinical laboratory and improve its financial situation by implementing changes in the next fiscal period.

Genetics of age at menarche: a systematic review

BACKGROUND

Menarche is the first menstrual period of a girl at puberty. The timing of menarche is important for health in later life. Age at menarche is a complex trait and has a strong genetic component. This review summarizes the results of the genetic studies of age at menarche conducted to date, highlights existing problems in this area and outlines prospects of future studies on genetic factors for the trait.

METHODS

PubMed and Google Scholar were searched until May 2011 using the keywords: 'menarche', 'puberty' and 'age at menarche' in combination with the keywords 'polymorphism', 'candidate gene', 'genome-wide association study' and 'linkage'.

RESULTS

Our search yielded 170 papers, 35 of which were selected for further analysis. Several large-scale genome-wide association studies along with a powerful meta-analysis of their aggregated data identified about 50 candidate genes for the trait. Some genes were replicated in different studies of Caucasians (e.g. LIN28B, TMEM38B) or in different ethnicities (e.g. SPOCK, RANK and RANKL). However, despite the large volume of results obtained, there is a huge gap in relevant data on ethnic groups other than Caucasians.

CONCLUSIONS

The reviewed studies laid a solid basis for future research on genetics of age at menarche. However, as yet specific genes for this trait have not been identified consistently in all ethnicities and types of studies. We suggest expanding the research to different ethnicities and propose several methodologies to increase the efficiency of studies in this area, including a systems approach, which combines existing high-throughput methods in a single pipeline.

Metabolic responses of Eisenia fetida after sub-lethal exposure to organic contaminants with different toxic modes of action

Nuclear magnetic resonance (NMR)--based metabolomics has the potential to identify toxic responses of contaminants within a mixture in contaminated soil. This study evaluated the metabolic response of Eisenia fetida after exposure to an array of organic compounds to determine whether contaminant-specific responses could be identified. The compounds investigated in contact tests included: two pesticides (carbaryl and chlorpyrifos), three pharmaceuticals (carbamazephine, estrone and caffeine), two persistent organohalogens (Aroclor 1254 and PBDE 209) and two industrial compounds (nonylphenol and dimethyl phthalate). Control and contaminant-exposed metabolic profiles were distinguished using principal component analysis and potential contaminant-specific biomarkers of exposure were found for several contaminants. These results suggest that NMR-based metabolomics offers considerable promise for differentiating between the different toxic modes of action (MOA) associated with sub-lethal toxicity to earthworms.

A practical approach to detect unique metabolic patterns for personalized medicine

Information-rich technologies have advanced personalized medicine, yet obstacles limit measurement of large numbers of chemicals in human samples. Current laboratory tests measure hundreds of chemicals based upon existing knowledge of exposures, metabolism and disease mechanisms. Practical issues of cost and throughput preclude measurement of thousands of chemicals. Additionally, individuals are genetically diverse and have different exposures and response characteristics; some have disease mechanisms that have not yet been elucidated. Consequently, methods are needed to detect unique metabolic characteristics without presumption of known pathways, exposures or disease mechanisms, i.e., using a top-down approach. In this report, we describe profiling of human plasma with liquid chromatography (LC) coupled to Fourier-transform mass spectrometry (FTMS). FTMS is a high-resolution mass spectrometer providing mass accuracy and resolution to discriminate thousands of m/z features, which are peaks defined by m/z, retention time and intensity. We demonstrate that LC-FTMS detects 2000 m/z features in 10 min. These features include known and unidentified chemicals with m/z between 85 and 850, most with <10% coefficient of variation. Comparison of metabolic profiles for 4 healthy individuals showed that 62% of the m/z features were common while 10% were unique and 770 discriminated the individuals. Because the simple one-step extraction and automated analysis is rapid and cost-effective, the approach is practical for personalized medicine. This provides a basis to rapidly characterize novel metabolic patterns which can be linked to genetics, environment and/or lifestyle.

Advances in NMR-based biofluid analysis and metabolite profiling

Significant improvements in NMR technology and methods have propelled NMR studies to play an important role in a rapidly expanding number of applications involving the profiling of metabolites in biofluids. This review discusses recent technical advances in NMR spectroscopy based metabolite profiling methods, data processing and analysis over the last three years.

Metabolomic analysis of human disease and its application to the eye

Metabolomics, the analysis of the metabolite profile in body fluids or tissues, is being applied to the analysis of a number of different diseases as well as being used in following responses to therapy. While genomics involves the study of gene expression and proteomics the expression of proteins, metabolomics investigates the consequences of the activity of these genes and proteins. There is good reason to think that metabolomics will find particular utility in the investigation of inflammation, given the multi-layered responses to infection and damage that are seen. This may be particularly relevant to eye disease, which may have tissue specific and systemic components. Metabolomic analysis can inform us about ocular or other body fluids and can therefore provide new information on pathways and processes involved in these responses. In this review, we explore the metabolic consequences of disease, in particular ocular conditions, and why the data may be usefully and uniquely assessed using the multiplexed analysis inherent in the metabolomic approach.