Atomic Diversity, Molecular Diversity, and Chemical Diversity: The Concept of Chemodiversity

Testa, Bernard; Vistoli, Giulio; Pedretti, Alessandro; Bojarski, Andrzej J.

doi:10.1002/cbdv.200900071

Cited by 9 publications

(4 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Chemodiversity represents the material condition for life to emerge and exist (Testa et al, 2009). Better characterization of DOM ' s chemical diversity could help us understand the biogeochemical processes in soil.…”

Section: Introductionmentioning

confidence: 99%

The chemodiversity of paddy soil dissolved organic matter is shaped and homogenized by bacterial communities that are orchestrated by geographic distance and fertilizations

et al. 2021

Soil Biology and Biochemistry

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

The chemodiversity of paddy soil dissolved organic matter is shaped and homogenized by bacterial communities that are orchestrated by geographic distance and fertilizations

et al. 2021

Soil Biology and Biochemistry

View full text Add to dashboard Cite

“…Chemodiversity analysis In this step, the MetaboDirect pipeline calculates indices that were originally designed for biological species but can be adapted to other organizational levels [61]. These indices are then applied at a macromolecular diversity level [62]. To this end, raw peak intensities are sum-normalized [13] and used to calculate diversity metrics using functions from the R packages vegan [63] and SYNCSA [64].…”

Section: Selection Of the Best Normalization Methodsmentioning

confidence: 99%

“…Diversity metrics, originally designed to study ecological species, have been adapted to analyze other systems, such as metabolites at the macromolecular level [62]. In this case, molecular formulas are akin to individual species, while their peak intensity is used for abundance [84].…”

Section: Metabodirect Pipeline Testingmentioning

confidence: 99%

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

et al. 2023

View full text Add to dashboard Cite

Background Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

show abstract

“…Introduction. -The preceding paper has developed the concepts of moleculardiversity and molecular-property spaces, and has placed them in the broader context of chemodiversity as leading to biodiversity [1]. The present paper deals with computations of conformational space and conformer-dependent properties to explore the lipophilicity space of a database of molecules covering a wide range of flexibility.…”

mentioning

confidence: 99%

Partition Coefficient and Molecular Flexibility: The Concept of Lipophilicity Space

Vistoli

Pedretti

Testa

2009

Chemistry & Biodiversity

Self Cite

View full text Add to dashboard Cite

The rationale of this study was to investigate molecular flexibility and its influence on physicochemical properties with a view to uncovering additional information on the fuzzy concept of dynamic molecular structure. Indeed, it is now known that computed molecular interaction fields (MIFs) such as molecular electrostatic potentials (MEPs) and lipophilicity potentials (MLPs) are conformation-dependent, as are dipole moments. A database of 125 compounds was used whose conformational space was explored, while conformation-dependent parameters were computed for each non-redundant conformer found in the conformational space of the compounds. These parameters were the virtual log P (log P(MLP), calculated by a MLP approach), the apolar surface area (ASA), polar surface area (PSA), and solvent-accessible surface (SAS). For each compound, the range taken by each parameter (its property space) was divided by the number of rotors taken as an index of flexibility, yielding a parameter termed 'molecular sensitivity'. This parameter was poorly correlated with others (i.e., it contains novel information) and showed the compounds to fall into two broad classes. 'Sensitive' molecules are those whose computed property ranges are markedly sensitive to conformational effects, whereas 'insensitive' (in fact, less sensitive) molecules have property ranges which are comparatively less affected by conformational fluctuations. A pharmacokinetic application is presented.

show abstract

Atomic Diversity, Molecular Diversity, and Chemical Diversity: The Concept of Chemodiversity

Cited by 9 publications

References 34 publications

The chemodiversity of paddy soil dissolved organic matter is shaped and homogenized by bacterial communities that are orchestrated by geographic distance and fertilizations

The chemodiversity of paddy soil dissolved organic matter is shaped and homogenized by bacterial communities that are orchestrated by geographic distance and fertilizations

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Partition Coefficient and Molecular Flexibility: The Concept of Lipophilicity Space

Contact Info

Product

Resources

About