Environmental metabolomics is the application of metabolomics to characterise the interactions of organisms with their environment. This approach has many advantages for studying organism–environment interactions and for assessing organism function and health at the molecular level. As such, metabolomics is finding an increasing number of applications in the environmental sciences, ranging from understanding organismal responses to abiotic pressures, to investigating the responses of organisms to other biota. These interactions can be studied from individuals to populations, which can be related to the traditional fields of ecophysiology and ecology, and from instantaneous effects to those over evolutionary time scales, the latter enabling studies of genetic adaptation. This review provides a comprehensive and current overview of environmental metabolomics research. We begin with an overview of metabolomic studies into the effects of abiotic pressures on organisms. In the field of ecophysiology, studies on the metabolic responses to temperature, water, food availability, light and circadian rhythms, atmospheric gases and season are reviewed. A section on ecotoxicogenomics discusses research in aquatic and terrestrial ecotoxicology, assessing organismal responses to anthropogenic pollutants in both the laboratory and field. We then discuss environmental metabolomic studies of diseases and biotic–biotic interactions, in particular herbivory. Finally, we critically evaluate the contribution that metabolomics has made to the environmental sciences, and highlight and discuss recommendations to advance our understanding of the environment, ecology and evolution using a metabolomics approach.

Environmental metabolomics: a critical review and future perspectives

Metabolomics is the analysis of endogenous and exogenous low molecular mass metabolites within a cell, tissue, or biofluid of an organism in response to an external stressor. The sub-discipline of ...

Environmental metabolomics: an emerging approach to study organism responses to environmental stressors

NMR spectroscopy in environmental research: From molecular interactions to global processes

It could be argued that the greatest transformative aspect of the Human Genome Project has been not the sequencing of the genome itself, but the resultant development of new technologies. A host of new approaches has fundamentally changed the way we approach problems in basic and translational research. Now, a new generation of high-throughput sequencing technologies promises to again transform the scientific enterprise, potentially supplanting array-based technologies and opening up many new possibilities. By allowing DNA/RNA to be assayed more rapidly than previously possible, these next-generation platforms promise a deeper understanding of genome regulation and biology. Significantly enhancing sequencing throughput will allow us to follow the evolution of viral and bacterial resistance in real time, to uncover the huge diversity of novel genes that are currently inaccessible, to understand nucleic acid therapeutics, to better integrate biological information for a complete picture of health and disease at a personalized level and to move to advances that we cannot yet imagine.

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What would you do if you could sequence everything

Ecometabolomics, which aims to analyze the metabolome, the total number of metabolites and its shifts in response to environmental changes, is gaining importance in ecological studies because of the increasing use of new technical advances, such as modern HNMR spectrometers and GC-MS coupled to bioinformatic advances. We review here the state of the art and the perspectives of ecometabolomics. The studies available demonstrate ecometabolomic techniques have great sensitivity in detecting the phenotypic mechanisms and key molecules underlying organism responses to abiotic environmental changes to biotic interactions. But such studies are still scarce, and in most cases they are limited to the direct effects of a single abiotic factor or of biotic interactions between two trophic levels under controlled conditions. Several exciting challenges remain to be achieved through the use of ecometabolomics in field conditions, involving more than two trophic levels, or combining the effects of abiotic gradients with intra- and inter-specific relationships. The coupling of ecometabolomic studies with genomics, transcriptomics, ecosystem stoichiometry, community biology and biogeochemistry may provide a further step forward in many areas of ecological sciences, including stress responses, species lifestyle, life history variation, population structure, trophic interaction, nutrient cycling, ecological niche and global change.

Ecological metabolomics: overview of current developments and future challenges

New methods are needed for research into non-model organisms, to monitor the effects of toxic disruption at both the molecular and functional organism level. We exposed earthworms (Lumbricus rubellus Hoffmeister) to sub-lethal levels of copper (10–480 mg/kg soil) for 70 days as a real-world situation, and monitored both molecular (cDNA transcript microarrays and nuclear magnetic resonance-based metabolic profiling: metabolomics) and ecological/functional endpoints (reproduction rate and weight change, which have direct relevance to population-level impacts). Both of the molecular endpoints, metabolomics and transcriptomics, were highly sensitive, with clear copper-induced differences even at levels below those that caused a reduction in reproductive parameters. The microarray and metabolomic data provided evidence that the copper exposure led to a disruption of energy metabolism: transcripts of enzymes from oxidative phosphorylation were significantly over-represented, and increases in transcripts of carbohydrate metabolising enzymes (maltase-glucoamylase, mannosidase) had corresponding decreases in small-molecule metabolites (glucose, mannose). Treating both enzymes and metabolites as functional cohorts led to clear inferences about changes in energetic metabolism (carbohydrate use and oxidative phosphorylation), which would not have been possible by taking a 'biomarker' approach to data analysis. Multiple post-genomic techniques can be combined to provide mechanistic information about the toxic effects of chemical contaminants, even for non-model organisms with few additional mechanistic toxicological data. With 70-day no-observed-effect and lowest-observed-effect concentrations (NOEC and LOEC) of 10 and 40 mg kg-1 for metabolomic and microarray profiles, copper is shown to interfere with energy metabolism in an important soil organism at an ecologically and functionally relevant level.

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'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus

One of the promises of environmental metabolomics, together with other ecotoxicogenomic approaches, is that it can give information on toxic compound mechanism of action (MOA), by providing a specific response profile or fingerprint. This could then be used either for screening in the context of chemical risk assessment, or potentially in contaminated site assessment for determining what compound classes were causing a toxic effect. However for either of these two ends to be achievable, it is first necessary to know if different compounds do indeed elicit specific and distinct metabolic profile responses. Such a comparative study has not yet been carried out for the earthworm Lumbricus rubellus. We exposed L. rubellus to sub-lethal concentrations of three very different toxicants (CdCl2, atrazine, and fluoranthene, representing three compound classes with different expected MOA), by semi-chronic exposures in a laboratory test, and used NMR spectroscopy to obtain metabolic profiles. We were able to use simple multivariate pattern-recognition analyses to distinguish different compounds to some degree. In addition, following the ranking of individual spectral bins according to their mutual information with compound concentrations, it was possible to identify both general and specific metabolite responses to different toxic compounds, and to relate these to concentration levels causing reproductive effects in the worms.

Validation of metabolomics for toxic mechanism of action screening with the earthworm Lumbricus rubellus

'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm -0

Objective: To study the Pattern and Practice of Pediatric neurosurgical procedures during one year among patients presenting to Children Hospital, Faisalabad. Materials and Methods: Retrospective case series of 778 consecutive cases admitted in Pediatric Neurosurgery Department, Children Hospital, Faisalabad over one year (October 2019September 2020). Patients of age less than 15 years, any gender, admitted in Pediatric Neurosurgery ward for management were included and studied for their demographic data hospital stay, a procedure done and outcome. Results: A total of 778 patients who required some neurosurgical intervention were admitted, 725 underwent various types of procedures and the remaining were treated conservatively. 320 (44.14%) were male and 405 (55.86%) were female. The age range was 20 days to 13 years. The most common diagnosis was hydrocephalous, and then was Meningomyelocele (MMC). The first three common procedures performed included monitoring of Cerebrospinal fluid (CSF) in 36% of cases, Placement of shunt (21%), and placement of external ventricular drain (EVD) in 13% of cases of cerebrospinal fluid (CNS) infections in patients of hydrocephalous. Conclusion: Pattern of presentation of pediatric neurosurgical cases take in almost all types of diseases like neural tube defects, hydrocephalous, cranial trauma, tumors, cysts, and infections but surgical procedures in routine practice in Faisalabad district cover mainly hydrocephalous and its complications. Endoscopic or advanced procedures are not commonly practiced due to multiple factors but existing constraints do not prevent the best management of pediatric neurosurgery patients.

Pattern and Practice of Pediatric Neurosurgical Procedures – An analysis of One – Year Initial Experience at Resource Challenged Setup of Children Hospital, Faisalabad

Faisal Rana

Papers

'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus

Validation of metabolomics for toxic mechanism of action screening with the earthworm Lumbricus rubellus

'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm -0

Pattern and Practice of Pediatric Neurosurgical Procedures – An analysis of One – Year Initial Experience at Resource Challenged Setup of Children Hospital, Faisalabad