Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements.

INTRODUCTION: To date, there has been little effort to develop standards for metabolome-based gut microbiome measurements despite the significant efforts toward standard development for DNA-based microbiome measurements. OBJECTIVES: The National Institute of Standards and Technology (NIST), The BioCollective (TBC), and the North America Branch of the International Life Sciences Institute (ILSI North America) are collaborating to extend NIST's efforts to develop a Human Whole Stool Reference Material for the purpose of method harmonization and eventual quality control. METHODS: The reference material will be rationally designed for adequate quality assurance and quality control (QA/QC) for underlying measurements in the study of the impact of diet and nutrition on functional aspects of the host gut microbiome and relationships of those functions to health. To identify which metabolites deserve priority in their value assignment, NIST, TBC, and ILSI North America jointly conducted a workshop on September 12, 2019 at the NIST campus in Gaithersburg, Maryland. The objective of the workshop was to identify metabolites for which evidence indicates relevance to health and disease and to decide on the appropriate course of action to develop a fit-for-purpose reference material. RESULTS: This document represents the consensus opinions of workshop participants and co-authors of this manuscript, and provides additional supporting information. In addition to developing general criteria for metabolite selection and a preliminary list of proposed metabolites, this paper describes some of the strengths and limitations of this initiative given the current state of microbiome research. CONCLUSIONS: Given the rapidly evolving nature of gut microbiome science and the current state of knowledge, an RM (as opposed to a CRM) measured for multiple metabolites is appropriate at this stage. As the science evolves, the RM can evolve to match the needs of the research community. Ultimately, the stool RM may exist in sequential versions. Beneficial to this evolution will be a clear line of communication between NIST and the stakeholder community to ensure alignment with current scientific understanding and community needs.

Elucidating Environmental Fingerprinting Mechanisms of Unconventional Gas Development through Hydrocarbon Analysis.

Hydraulic fracturing is an increasingly common technique for the extraction of natural gas entrapped in shale formations. This technique has been highly criticized due to the possibility of environmental contamination, underscoring the need for method development to identify chemical factors that could be utilized in point-source identification of environmental contamination events. Here, we utilize comprehensive two-dimensional gas chromatography (GC × GC) coupled to high-resolution time-of-flight (HRT) mass spectrometry, which offers a unique instrumental combination allowing for petroleomics hydrocarbon fingerprinting. Four flowback fluids from Marcellus shale gas wells in geographic proximity were analyzed for differentiating factors that could be exploited in environmental forensics investigations of shale gas impacts. Kendrick mass defect (KMD) plots of these flowback fluids illustrated well-to-well differences in heteroatomic substituted hydrocarbons, while GC × GC separations showed variance in cyclic hydrocarbons and polyaromatic hydrocarbons among the four wells. Additionally, generating plots that combine GC × GC separation with KMD established a novel data-rich visualization technique that further differentiated the samples.

The need for multicomponent gas standards for breath biomarker analysis.

Exhaled breath is a non-invasive, information-rich matrix with the potential to diagnose or monitor disease, including infectious disease. Despite significant effort dedicated to biomarker identification in case control studies, very few breath tests are established in practice. In this topical review, we identify how gas standards support breath analysis today and what is needed to support further expansion and translation to practice. We examine forensic and clinical breath tests and discuss how confidence has been built through unambiguous biomarker identification and quantitation supported by gas calibration standards. Based on this discussion, we identify a need for multicomponent gas standards with part-per-trillion to part-per-million concentrations. We highlight National Institute of Standards and Technology gas standards developed for atmospheric measurements that are also relevant to breath analysis and describe investigations of long-term stability, chemical reactions, and interactions with gas cylinder wall treatments. An overview of emerging online instruments and their need for gas standards is also presented. This review concludes with a discussion of our ongoing research to examine the feasibility of producing multicomponent gas standards at breath-relevant concentrations. Such standards could be used to investigate interference from ubiquitous endogenous compounds and as a starting point for standards tailored to specific breath tests.

Enhancing untargeted metabolomics using metadata-based source annotation.

Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.

Forensic tracers of exposure to produced water in freshwater mussels: a preliminary assessment of Ba, Sr, and cyclic hydrocarbons.

Hydraulic fracturing is often criticized due in part to the potential degradation of ground and surface water quality by high-salinity produced water generated during well stimulation and production. This preliminary study evaluated the response of the freshwater mussel, Elliptio complanata, after exposure to produced water. A limited number of adult mussels were grown over an 8-week period in tanks dosed with produced water collected from a hydraulically fractured well. The fatty tissue and carbonate shells were assessed for accumulation of both inorganic and organic pollutants. Ba, Sr, and cyclic hydrocarbons indicated the potential to accumulate in the soft tissue of freshwater mussels following exposure to diluted oil and gas produced water. Exposed mussels showed accumulation of Ba in the soft tissue several hundred times above background water concentrations and increased concentrations of Sr. Cyclic hydrocarbons were detected in dosed mussels and principle component analysis of gas chromatograph time-of-flight mass spectrometer results could be a novel tool to help identify areas where aquatic organisms are impacted by oil and gas produced water, but larger studies with greater replication are necessary to confirm these results.

Detection and removal of biologically active organic micropollutants from hospital wastewater.

The presence of contaminants of emerging concern (CECs), such as antibiotics, antimicrobial disinfectants, nonprescription drugs, personal care products, pharmaceuticals, and steroids, in water resources can impact aquatic and human health. A large portion of the CECs entering regional wastewater treatment plants originate from hospitals. The purposes of this study were to conduct exploratory analytical work to characterize two hospital wastewaters and to evaluate treatment of CECs at hospitals before dilution with domestic wastewater. A 24-h batch reaction with biogenic manganese oxides coated onto coir fiber was used to treat the wastewaters. Organic contaminants in the wastewaters were concentrated by both liquid-liquid extraction (LLE) and solid-phase extraction (SPE). LLE extracts were analyzed by Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry (GC × GC-TOFMS) while SPE extracts were analyzedby UltraHigh Performance Liquid Chromatography/Time-of-Flight Mass Spectrometry (UHPLC-TOFMS). Fifty-two organic micropollutants were detected (26 by GC × GC-TOFMS, 25 by UHPLC-TOFMS, 1 by both) in the wastewaters, while 29 were removed by >90% and six were degraded by <50% after treatment. Control experiments revealed that sorption to coir fiber and oxidation by manganese oxides were the primary contaminant removal mechanisms. Both the LLE and SPE extracts were used to evaluate potential human toxicity of the hospital wastewaters before and after treatment. Twenty-eight human cell-based bioreceptor assays were used to screen the wastewaters, and secondary tests were run to quantify toxicity equivalents to activated receptors. The wastewaters initially contained organic micropollutants that strongly activated the Androgen Receptor, Estrogen Receptor ß, and the Mineralocorticoid Receptor but no bioactive compounds were detected after treatment. Point-of-entry treatment of hospital wastewater should reduce bioactive compounds from entering the environment.

Applications of thermal desorption coupled to comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry for hydrocarbon fingerprinting of hydraulically fractured shale rocks.

Development of shale gas resources through the use of hydraulic fracturing has raised a multitude of environmental concerns and motivated research towards the understanding of shale gas systems. Previous research has demonstrated the potential of utilizing hydrocarbon distributions towards the fingerprinting of a potential environmental contamination event arising from shale gas operations. However, to apply hydrocarbon distributions from shale gas wells towards point-source identification and apportionment, a better understanding of hydrocarbon origins must be achieved. Here we present an efficient and repeatable thermal desorption method, as a sample introduction methodology for GC × GC analysis of shale rock samples that results in comparable chromatograms to those produced by solvent extraction. This novel and robust characterization technique of shale cores from Marcellus and Utica formations by thermal desorption followed by GC × GC enables the understanding of hydrocarbon speciation within the native rock with minimal sample preparation time and solvent use. The detailed shale chemistry gives insight into utilizing hydrocarbon differences towards point-source identification methodologies of environmental contamination events associated with unconventional gas development. Additionally, this analytical technique may provide a more detailed analysis of hydrocarbons than what is currently implemented in the industry to pinpoint the most advantageous areas to exploit by hydraulic fracturing, yet avoiding undesirable areas such as those with a high abundance of sulfur containing compounds.