Multi-omics tools for studying microbial biofilms: current perspectives and future directions DOI

Chaminda Jayampath Seneviratne,

Tanujaa Suriyanarayanan, Armelia Sari Widyarman

et al.

Critical Reviews in Microbiology, Journal Year: 2020, Volume and Issue: 46(6), P. 759 - 778

Published: Oct. 8, 2020

The advent of omics technologies has greatly improved our understanding microbial biology, particularly in the last two decades. field biofilms is, however, relatively new, consolidated 1980s. morphogenic switching by microbes from planktonic to biofilm phenotype confers numerous survival advantages such as resistance desiccation, antibiotics, biocides, ultraviolet radiation, and host immune responses, thereby complicating treatment strategies for pathogenic microorganisms. Hence, mechanisms governing can result efficient directed specifically against molecular markers mediating this process. application studying is less explored holds great promise furthering biology. In review, we provide an overview tools transcriptomics, proteomics, metabolomics well multi-omics approaches current literature. We also highlight how use at various stages biological information flow, genes metabolites, be integrated via platforms a holistic view Following this, propose future artificial intelligence-based platform that predict pathways associated with different phenotypes.

Language: Английский

Validation of in-vitro bioassay methods: Application in herbal drug research DOI
Gunawan Indrayanto, Galih Satrio Putra,

Farida Suhud

et al.

Profiles of drug substances, excipients, and related methodology, Journal Year: 2020, Volume and Issue: unknown, P. 273 - 307

Published: Aug. 27, 2020

Language: Английский

Citations

347
Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics—Standardization, Coverage, and Throughput DOI Creative Commons

Evelyn Rampler,

Yasin El Abiead, Harald Schoeny

et al.

Analytical Chemistry, Journal Year: 2020, Volume and Issue: 93(1), P. 519 - 545

Published: Nov. 28, 2020

RETURN TO ISSUEPREVReviewNEXTRecurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics—Standardization, Coverage, ThroughputEvelyn RamplerEvelyn RamplerDepartment of Analytical Chemistry, Faculty University Vienna, Währinger Str. 38, 1090 AustriaVienna Center (VIME), Althanstraße 14, AustriaUniversity AustriaMore by Evelyn RamplerView Biographyhttp://orcid.org/0000-0002-9429-7663, Yasin El AbieadYasin AbieadDepartment AbieadView Biography, Harald SchoenyHarald SchoenyDepartment SchoenyView Biographyhttp://orcid.org/0000-0001-8696-481X, Mate RuszMate RuszDepartment AustriaInstitute Inorganic Straße 42, RuszView Felina HildebrandFelina HildebrandDepartment HildebrandView Veronika FitzVeronika FitzDepartment FitzView Gunda Koellensperger*Gunda KoellenspergerDepartment Austria*Email: [email protected]. Phone: +43-1-4277-52303.More KoellenspergerView Biographyhttp://orcid.org/0000-0002-1460-4919Cite this: Anal. Chem. 2021, 93, 1, 519–545Publication Date (Web):November 28, 2020Publication History Published online28 November 2020Published inissue 12 January 2021https://doi.org/10.1021/acs.analchem.0c04698Copyright © 2020 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoicewith CC-BYlicenseArticle Views7341Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum full text article downloads since 2008 (both PDF HTML) across all institutions individuals. These metrics regularly updated to reflect usage leading up last few days.Citations number other articles citing this article, calculated Crossref daily. Find more information about citation counts.The Altmetric Attention Score is a quantitative measure attention that research has received online. Clicking on donut icon will load page at altmetric.com with additional details score social media presence for given article. how calculated. Share Add toView InAdd Full Text ReferenceAdd Description ExportRISCitationCitation abstractCitation referencesMore Options onFacebookTwitterWechatLinked InReddit (5 MB) Get e-AlertsSUBJECTS:Lipids,Metabolomics,Metabolism,Fungi,Materials e-Alerts

Language: Английский

Citations

133
Implementation of liquid chromatography–high resolution mass spectrometry methods for untargeted metabolomic analyses of biological samples: A tutorial DOI
Julian Pezzatti, Julien Boccard, Santiago Codesido

et al.

Analytica Chimica Acta, Journal Year: 2020, Volume and Issue: 1105, P. 28 - 44

Published: Jan. 2, 2020

Language: Английский

Citations

120
Metabolomic Biomarkers in Gestational Diabetes Mellitus: A Review of the Evidence DOI Open Access
Simon Alesi,

Drishti P. Ghelani,

Kate Rassie

et al.

International Journal of Molecular Sciences, Journal Year: 2021, Volume and Issue: 22(11), P. 5512 - 5512

Published: May 24, 2021

Gestational diabetes mellitus (GDM) is the fastest growing type of diabetes, affecting between 2 to 38% pregnancies worldwide, varying considerably depending on diagnostic criteria used and sample population studied. Adverse obstetric outcomes include an increased risk macrosomia, higher rates stillbirth, instrumental delivery, birth trauma. Metabolomics, which a platform analyse characterise large number metabolites, increasingly explore pathophysiology cardiometabolic conditions such as GDM. This review aims summarise metabolomics studies in GDM (from inception January 2021) order highlight prospective biomarkers for diagnosis, better understand dysfunctional metabolic pathways underlying condition. We found that most commonly deranged amino acids (glutathione, alanine, valine, serine), carbohydrates (2-hydroxybutyrate 1,5-anhydroglucitol), lipids (phosphatidylcholines lysophosphatidylcholines). also possibility using certain metabolites predictive markers developing GDM, with use highly stratified modelling techniques. Limitations metabolomic research are evaluated, future directions field suggested aid integration these findings into clinical practice.

Language: Английский

Citations

80
The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management DOI Creative Commons
Yandong Xia, Junang Liu,

Cang Chen

et al.

Microorganisms, Journal Year: 2022, Volume and Issue: 10(5), P. 1072 - 1072

Published: May 23, 2022

Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens even promote development In this review, we focus on biological control diseases, aiming elucidate contribution key roles endophytes their field with latest research information. Metabolites synthesized are part disease management, application endophyte induce resistance is very promising. Furthermore, multi-omics should be fully utilized plant-microbe research, especially mining novel bioactive metabolites. We believe utilization for management meaningful promising direction lead new breakthroughs effective ecosystem-friendly insecticides fungicides modern agriculture.

Language: Английский

Citations

69
Secondary Metabolites Produced by Plant Growth-Promoting Bacterial Endophytes DOI Creative Commons
Zareen Narayanan, Bernard R. Glick

Microorganisms, Journal Year: 2022, Volume and Issue: 10(10), P. 2008 - 2008

Published: Oct. 11, 2022

There is an increasing interest in the use of beneficial microorganisms as alternatives to chemically synthesized or plant-derived molecules produce therapeutic agents. Bacterial endophytes are plant-associated that can colonize different parts living plants without causing any diseases. Diverse endophytic bacteria possess ability synthesize a wide range secondary metabolites with unique chemical structures have been exploited for their anti-microbial, antiviral, anti-cancer, and anti-inflammatory properties. Additionally, production these bioactive compounds also benefit host plant they may play significant role plant's interaction environment adaptation defense. As result impact curative precursors new drugs, biotechnological possibilities derived from immense.

Language: Английский

Citations

68
Metabolomic Insights Into Endophyte-Derived Bioactive Compounds DOI Creative Commons
Sushma Mishra,

Priyanka Singh,

Shilpi Sharma

et al.

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: March 2, 2022

Among the various plant-associated microbiota, endophytes (the microbial communities inhabiting plant endosphere without causing disease symptoms) exhibit most intimate and specific association with host plants. Endophytic microbes influence aspects of responses (such as increasing availability nutrients, tolerance against biotic abiotic stresses, etc.) by modulating primary secondary metabolism host. Besides, endophytic produce a diverse array bioactive compounds, which have potential applications in pharmaceutical, food, cosmetic industries. Further, there is sufficient evidence for endophyte-derived metabolites, could be pursued alternative sources commercially important metabolites. The field bioprospecting, discovery novel chemistries, endophyte-mediated production metabolites witnessed boom advent omics technologies (especially metabolomics) endophyte research. high throughput study small at particular timepoint or tissue forms core metabolomics. Being downstream to transcriptome proteome, metabolome provides direct reflection phenotype an organism. contribution metabolomics answering fundamental questions plant-endophyte interaction, such effect inoculation on metabolome, composition impact environmental stressors (biotic abiotic), etc., also been discussed.

Language: Английский

Citations

52
Molecular networking as a natural products discovery strategy DOI Creative Commons
Mi Zhang, Kouharu Otsuki, Wei Li

et al.

Acta Materia Medica, Journal Year: 2023, Volume and Issue: 2(2)

Published: April 25, 2023

The rapid development of bioinformatics tools has recently broken through the bottleneck in natural products research. These advances have enabled researchers to rapidly separate and efficiently target discover previously undescribed molecules. Among these advances, tandem mass spectrometry molecular networking is a promising method for de-replicating complex mixtures, thus leading an accelerated revolution “art isolation” field. In this review we describe current networking-based metabolite analysis methods that are widely applied or implementable discovery research, metabolomics, related fields. main objective was summarize strategies can be implemented as alternative de-replication approaches efficient list examples successful applications combine with other techniques.

Language: Английский

Citations

35
Biological biomarkers of oral cancer DOI Creative Commons
Allan Radaic, Pachiyappan Kamarajan,

Alex Cho

et al.

Periodontology 2000, Journal Year: 2023, Volume and Issue: 96(1), P. 250 - 280

Published: Dec. 10, 2023

The oral squamous cell carcinoma (OSCC) 5 year survival rate of 41% has marginally improved in the last few years, with less than a 1% improvement per from 2005 to 2017, higher rates when detected at early stages. Based on histopathological grading dysplasia, it is estimated that severe dysplasia malignant transformation 7%-50%. Despite these numbers, does not reliably predict its clinical behavior. Thus, more accurate markers predicting progression cancer would enable better targeting lesions for closer follow-up, especially stages disease. In this context, molecular biomarkers derived genetics, proteins, and metabolites play key roles oncology. These signatures can help likelihood OSCC development and/or have potential detect disease an stage and, support treatment decision-making responsiveness. Also, identifying reliable detection be obtained non-invasively enhance management OSCC. This review will discuss emerged different biological areas, including genomics, transcriptomics, proteomics, metabolomics, immunomics, microbiomics.

Language: Английский

Citations

30
Multiplatform Untargeted Metabolomics DOI Creative Commons

Micah J. Jeppesen,

Robert Powers

Magnetic Resonance in Chemistry, Journal Year: 2023, Volume and Issue: 61(12), P. 628 - 653

Published: April 3, 2023

Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize hundred metabolites at best. The uncertainty in metabolite identification commonly encountered untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple techniques) approach improve upon the number reliably detected and correctly assigned. This be further improved by applying synergistic sample preparation along with use combinatorial sequential non-destructive destructive techniques. Similarly, peak detection strategies that employ multiple probabilistic approaches have led better annotation decisions. Applying these also addresses issues reproducibility found single platform methods. Nevertheless, analysis large data sets from disparate presents unique challenges. While general processing workflow is similar across platforms, many software packages are fully capable types instrument. Traditional statistical methods such as principal component were not designed handle multiple, distinct sets. Instead, multivariate requires multiblock other model for understanding contribution instruments. review summarizes advantages, limitations, recent achievements metabolomics.

Language: Английский

Citations

28