Advances in the Study of Metabolomics and Metabolites in Some Species Interactions

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Abstract

In the natural environment, interactions between species are a common natural phenomena. The mechanisms of interaction between different species are mainly studied using genomic, transcriptomic, proteomic, and metabolomic techniques. Metabolomics is a crucial part of system biology and is based on precision instrument analysis. In the last decade, the emerging field of metabolomics has received extensive attention. Metabolomics not only provides a qualitative and quantitative method for studying the mechanisms of interactions between different species, but also helps clarify the mechanisms of defense between the host and pathogen, and to explore new metabolites with various biological activities. This review focuses on the methods and progress of interspecies metabolomics. Additionally, the prospects and challenges of interspecies metabolomics are discussed.

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HMDB 4.0: the human metabolome database for 2018

David Wishart, Yannick Djoumbou Feunang, Ana Marcu … (2017)

Abstract The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Mingxun Wang, Jeremy J. Carver, Vanessa V Phelan … (2016)

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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PubChem Substance and Compound databases

Sunghwan Kim, Paul Thiessen, Evan Bolton … (2015)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.

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George Grant: Role: Academic Editor

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Journal ID (nlm-ta): Molecules

Journal ID (iso-abbrev): Molecules

Journal ID (publisher-id): molecules

Title: Molecules

Publisher: MDPI

ISSN (Electronic): 1420-3049

Publication date (Electronic): 31 May 2021

Publication date Collection: June 2021

Volume: 26

Issue: 11

Electronic Location Identifier: 3311

Affiliations

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China; ruiliu991@ 123456outlook.com (R.L.); bzx357489@ 123456126.com (Z.-X.B.); pjzhao@ 123456ynu.edu.cn (P.-J.Z.)

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[* ]Correspondence: ligh@ 123456ynu.edu.cn ; Tel.: +86-871-6503-2538

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Publisher ID: molecules-26-03311

DOI: 10.3390/molecules26113311

PMC ID: 8197931

PubMed ID: 34072976

SO-VID: 0c5a0198-a77e-4e09-9a44-61424d7a182c

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Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

Advances in the Study of Metabolomics and Metabolites in Some Species Interactions

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Special series on COVID-19 interactions with our Environment

Most cited references 82

HMDB 4.0: the human metabolome database for 2018

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

PubChem Substance and Compound databases

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