Remington Xavier Poulin

Natural products have historically been a rich and diverse source of biologically active compounds. Some of the most interesting members of this category are cyclic and acyclic peptides. Although this structural class has a high potential for development into medicines and application to numerous therapeutic indications, the elucidation of their structures is not always trivial. The occurrence of nonstandard amino acids and extensive overlap of aliphatic ¹ H ^α and amide ¹ H ^N resonances can make the assignment of individual amino acid spin systems and connectivity between them difficult. Experiments like ¹ H– ¹ H TOCSY, ¹ H– ¹³ C HSQC‐TOCSY, and ¹ H– ¹³ C HMBC can be implemented to help disentangle these congested resonances, but the limited spectral dispersion of ¹ H and restricted chemical shift differences in the ¹³ C dimension can limit the effectiveness of these experiments. To circumvent this issue, the larger spectral dispersion of ¹⁵ N (~900 ppm) can be leveraged with the use of ¹ H– ¹⁵ N HSQC‐TOCSY and ¹ H– ¹⁵ N HMBC experiments. Although these NMR experiments have been shown to be effective structure elucidation tools at natural isotopic abundance (0.4%), we demonstrate here that the quality of those data can be significantly enhanced, and their acquisition accelerated, through the production of ¹⁵ N‐labeled analyte.

In the European Union, animal products for human consumption are regulated as products of animal origin (POAO), while those not intended for human consumption are considered animal by‐products (ABPs). Both POAO and ABP are subject to strict regulations to ensure animal and public health, and they are controlled through various EU directives and regulations. Consumer demand for plant‐derived cosmetics, botanicals, and nutraceuticals has also increased sharply over the past decade. Ensuring the origin of ingredients, starting materials, and excipients used in these complex consumer products can be challenging, even when certified reference standards are available. Herein, we report a reliable approach for identifying the origin of cholesterol, a common ingredient in cosmetics and beauty products, using irm‐ ¹³ C NMR and IRMS to differentiate plant versus animal‐derived cholesterol. Further, we show that we can also discriminate semi‐synthetic cholesterol from plant and animal‐derived varieties.

In marine ecosystems, microbial communities often interact using specialised metabolites, which play a central role in shaping the dynamics of the ecological networks and maintaining the balance of the ecosystem. With metabolomics and transcriptomics analyses, this study explores the interactions between two marine microalgae, Skeletonema marinoi and Prymnesium parvum, grown in mono-cultures and non-contact co-cultures. As a growth indicator, the photosynthetic potential, measured via fluorescence, suggested chemical interaction between S. marinoi and P. parvum. Using Liquid Chromatography-Mass Spectrometry (LC-MS) data, we identified 346 and 521 differentially produced features in the endo- and exometabolome of S. marinoi and P. parvum, respectively. Despite limited tandem mass spectrometry data (MS²) for these features, we structurally annotated 14 compounds, most of which were previously under-studied specialised metabolites. Differential gene expression analysis was then performed on the transcriptomes of the microalgae, which uncovered differentially expressed genes involved in energy metabolism and cellular repair for both species. These metabolic changes depict the adaptation of both species in the co-culture. However, further data acquisition and investigation will be necessary to confirm the type of interaction and the underlying mechanisms.

The bacillamides are a class of indole alkaloids produced by the Bacillus genus that possess significant antialgal activity. Incorporation of fluorine into the bacillamides was carried out using a precursor-directed biosynthesis approach, with 4-, 5-, and 6-fluorotryptophan added to growing cultures of Bacillus atrophaeus IMG-11. This yielded the corresponding fluorinated analogues of bacillamides A and C, in addition to new derivatives of the related metabolite N-acetyltryptamine, thus demonstrating a degree of plasticity in the bacillamide biosynthetic pathway. The bacillamide derivatives were tested for activity against bloom-forming algae, which revealed that fluorination could improve the antialgal activity of these compounds in a site-specific manner, with fluorination at the 6-position consistently resulting in improved activity.

In marine ecosystems, microbial communities often interact using specialised metabolites, which play a central role in shaping the dynamics of the ecological networks and maintaining the balance of the ecosystem. With metabolomics and transcriptomics analyses, this study explores the interactions between two marine microalgae, Skeletonema marinoi and Prymnesium parvum , grown in mono-cultures and non-contact co-cultures. As a growth indicator, the photosynthetic potential, measured via fluorescence, suggested chemical interaction between S. marinoi and P. parvum . Using Liquid Chromatography-Mass Spectrometry (LC-MS) data, we identified 346 and 521 differentially produced features in the endo- and exometabolome of S. marinoi and P. parvum , respectively. Despite limited tandem mass spectrometry data (MS ² ) for these features, we structurally annotated 14 compounds, most of which were previously under-studied specialised metabolites. Differential gene expression analysis was then performed on the transcriptomes of the microalgae, which uncovered differentially expressed genes involved in energy metabolism and cellular repair for both species. These metabolic and transcriptomics changes depict the adaptation of both species in the co-culture. However, further data acquisition and investigation will be necessary to confirm the type of interaction and the underlying mechanisms. Importance: Marine microalgae have great ecological importance and biochemical potential. Among these microbes are the diatom Skeletonema marinoi , known for its marine biogeochemical cycling, and the haptophyte Prymnesium parvum , which poses adverse environmental consequences. Given these opposing roles for the two cosmopolitan microalgae, we designed a study using untargeted metabolomics and transcriptomics to acquire a comprehensive snapshot of their interactions, grown as mono-cultures and co-cultures. The statistical analysis of the chlorophyll a fluorescence levels, and the metabolomics and transcriptomics dataset revealed metabolic communication occurring among the two species via specialised metabolites and activated cellular repair mechanisms. These findings reveal the complexity of the interactions within marine microbial ecosystems, offering a foundation for future research to understand and harness marine ecological systems.

In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT‐1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics‐guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real‐time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms.

Since the late 1970s, many ‘omics‐style investigations have advanced our understanding of systems at all levels, from community level, through organismal, to individual cellular processes. Beginning with genomics and progressing through transcriptomics, proteomics and finally to metabolomics, the scope of interest shifts significantly from what is genetically possible to what is currently expressed, produced and measurable in a system. While the ideal goal of any ‘omics investigation is to fully describe a system, loss of information occurs at each decision‐making juncture. These losses are often not considered in the experimental planning stage but, when combined, they drastically affect the power of an investigation and the conclusions that can be drawn from it. Herein we discuss through the analogy of photography many of the decision‐making junctures of metabolomics investigations and the resultant losses of information occurring at each.

Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or –oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner’s cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H₂ as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.

The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC)–mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC)–MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC–MS in comparison to a commonly used unit-mass resolution single-quadrupole GC–MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC–MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC–MS technology for metabolomics studies are shown here.