Erik R. Andersson

Metabolomics is a rapidly growing multidisciplinary field with ever increasing demand and usability, which is attracting a surge of new researchers. While their varied skill sets, scientific questions, and approaches enrich the field with fresh perspectives and innovation, individual investigators also bring wide-ranging levels of metabolomics-specific experience and diverse areas of interest. These factors introduce considerable variability and inconsistency in both the methodology and reporting. A recent comparative literature review of nuclear magnetic resonance (NMR) metabolomics from studies published in 2010 and 2020 revealed significant shortcomings in the reporting of experimental details necessary for evaluating both the scientific rigor and the reproducibility of NMR-based metabolomics experiments. Each stage of metabolomics research contains multiple methodological choices and various optimization parameters, all of which can introduce experimental bias and alter the study results. This emphasizes the need for proper reporting to enhance reproducibility, data reusability, and study comparability. To address these concerns, the NMR Special Interest Group within the Metabolomics Association of North America presents reporting recommendations focused on fundamental aspects of NMR metabolomics research identified from the detailed literature review report. These include specifics with respect to study design, sample preparation, data acquisition, data processing and analysis, data accessibility, and comparability to previous studies. Also presented is a complementary list of seminal papers in the field to guide the study design and implementation of NMR metabolomics experiments. This initiative seeks to enhance the long-term impact of NMR metabolomics by supporting high-quality, reproducible, and impactful data collected from well-executed and thoroughly reported studies.

Coral growth anomalies (GAs) are tumor-like lesions that are detrimental to colony fitness and are commonly associated with high human population density, yet little is known about the disease pathology or calcification behavior. SEM imagery, skeletal trace elements and boron isotopes (δ¹¹B) have been combined as a novel approach to study coral disease. Low Mg/Ca, and high U/Ca, Mo/Ca, and V/Ca potentially suggest a decreased abundance of “centers of calcification” and nitrogen-fixation in GAs. Estimates of carbonate system parameters from δ¹¹B and B/Ca measurements indicate reduced pH (−0.05 units) and [CO₃²⁻] within GA calcifying fluid. We theorize GAs re-allocate resources away from internal pH upregulation to sustain elevated tissue growth, resulting in a porous and fragile skeleton. Our findings show that dystrophic calcification processes could explain structural differences seen in GA skeletons and highlight the use of skeletal geochemistry to shed light on disease pathophysiology in corals.

The field of metabolomics generally lacks standardized methods for the preparation of samples prior to analysis. This is especially true for metabolomics of reef-building corals, where the handful of studies that were published employ a range of sample preparation protocols. The utilization of metabolomics may prove essential in understanding coral biology in the face of increasing environmental threats, and an optimized method for preparing coral samples for metabolomics analysis would aid this cause. The current study evaluates three important steps during sample processing of stony corals: (i) metabolite extraction, (ii) metabolism preservation, and (iii) subsampling. Results indicate that a modified Bligh and Dyer extraction is more reproducible across multiple coral species compared to methyl tert-butyl ether and methanol extractions, while a methanol extraction is superior for feature detection. Additionally, few differences were detected between spectra from frozen or lyophilized coral samples. Finally, extraction of entire coral nubbins increased feature detection, but decreased throughput and was more susceptible to subsampling error compared to a novel tissue powder subsampling method. Overall, we recommend the use of a modified Bligh and Dyer extraction, lyophilized samples, and the analysis of brushed tissue powder for the preparation of reef-building coral samples for ¹H NMR metabolomics.