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Metabolic Profiling towards the Development of Antibiotic Management

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Pharmacology and Drug Metabolism".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 7951

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Special Issue Editor

Dr. Cecília R.C. Calado

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Guest Editor

Department of Chemical Engineering, ISEL- Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
Interests: biomarkers discovery; drugs discovery; metabolomics; FTIR spectroscopy; diagnostic; prognosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Given the increase in antibiotic-resistant bacteria, alongside the alarmingly low rate of newly approved antibiotics for clinical usage, we are on the verge of not having effective treatments for many infectious diseases. It is, therefore, urgent to develop strategies to promote antibiotic management, such as methods to detect antibiotic resistance, the characterisation of mechanisms of antibiotic resistance and strategies to overcome these mechanisms. It is also relevant to discover better biomarkers to predict infections and the causative agent. These biomarkers will guide antibiotic application, reducing the use of broad-spectrum antibiotics and the emergence of antibiotic-resistant bacteria strains. Since antibiotic discovery has stagnated at alarmingly low rates, it is also critical to develop new platforms to discover new antibiotics. This Special Issue aims to promote a forum to discuss how metabolic analysis and metabolomics, of the bacteria and of the host, can represent a relevant tool to characterise these types of problems and solutions, towards a better management of antibiotics.

Prof. Dr. Cecília R.C. Calado
Guest Editor

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Keywords

antibiotics
antibiotic resistance
resistance mechanisms
antibiotic discovery
infection biomarkers
metabolic profile
metabolomics

Published Papers (3 papers)

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Research

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13 pages, 2300 KiB

Open AccessArticle

Differential Chemical Profile of Metabolite Extracts Produced by the Diaporthe citri (G-01) Endophyte Mediated by Varying the Fermented Broth pH

by Julio Cesar Polonio, Marcos Alessandro dos Santos Ribeiro, Cintia Zani Fávaro-Polonio, Eduardo Cesar Meurer, João Lúcio Azevedo, Halison Correia Golias and João Alencar Pamphile

Metabolites 2022, 12(8), 692; https://0-doi-org.brum.beds.ac.uk/10.3390/metabo12080692 - 26 Jul 2022

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Abstract

Endophytic microorganisms show great potential for biotechnological exploitation because they are able to produce a wide range of secondary compounds involved in endophyte–plant adaptation, and their interactions with other living organisms that share the same microhabitat. Techniques used to chemically extract these compounds often neglect the intrinsic chemical characteristics of the molecules involved, such as the ability to form conjugate acids or bases and how they influence the solubilities of these molecules in organic solvents. Therefore, in this study, we aimed to evaluate how the pH of the fermented broth affects the process used to extract the secondary metabolites of the Diaporthe citri strain G-01 endophyte with ethyl acetate as the organic solvent. The analyzed samples, conducted by direct-infusion electrospray-ionization mass spectrometry, were grouped according to the pH of the fermented broth (i.e., <7 and ≥7). A more extreme pH (i.e., 2 or 12) was found to affect the chemical profile of the sample. Moreover, statistical analysis enabled us to determine the presence or absence of ions of high importance; for example, ions at 390.7 and 456.5 m/z were observed mainly at acidic pH, while 226.5, 298.3, and 430.1 m/z ions were observed at pH ≥ 7. Extraction at a pH between 4 and 9 may be of interest for exploring the differential secondary metabolites produced by endophytes. Furthermore, pH influences the chemical phenotype of the fungal metabolic extract. Full article

(This article belongs to the Special Issue Metabolic Profiling towards the Development of Antibiotic Management)

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13 pages, 3381 KiB

Open AccessArticle

Genome Features and AntiSMASH Analysis of an Endophytic Strain Fusarium sp. R1

by Yuanyuan Liu, Meijie Xu, Yuqi Tang, Yilan Shao, Hong Wang and Huawei Zhang

Metabolites 2022, 12(6), 521; https://0-doi-org.brum.beds.ac.uk/10.3390/metabo12060521 - 04 Jun 2022

Cited by 8 | Viewed by 3081

Abstract

Endophytic fungi are one of the most prolific sources of functional biomolecules with therapeutic potential. Besides playing an important role in serious plant diseases, Fusarium strains possess the powerful capability to produce a diverse array of bioactive secondary metabolites (SMs). In order to in-depth mine gene clusters for SM biosynthesis of the genus Fusarium, an endophytic strain Fusarium sp. R1 isolated from Rumex madaio Makino was extensively investigated by whole-genome sequencing and in-depth bioinformatic analysis, as well as antiSMASH annotation. The results displayed that strain R1 harbors a total of 51.8 Mb genome, which consists of 542 contigs with an N50 scaffold length of 3.21 Mb and 50.4% GC content. Meanwhile, 19,333 functional protein-coding genes, 338 tRNA and 111 rRNA were comprehensively predicted and highly annotated using various BLAST databases including non-redundant (Nr) protein sequence, nucleotide (Nt) sequence, Swiss-Prot, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), as well as Pathogen Host Interactions (PHI) and Carbohydrate-Active enzymes (CAZy) databases. Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) results showed that strain R1 has 37 SM biosynthetic gene clusters (BGCs), including 17 nonribosomal peptide synthetases (NRPSs), 13 polyketide synthetases (PKSs), 3 terpene synthases (Ts), 3 hybrid NRPS + PKS and 1 hybrid indole + NRPS. These findings improve our knowledge of the molecular biology of the genus Fusarium and would promote the discovery of new bioactive SMs from strain R1 using gene mining strategies including gene knockout and heteroexpression. Full article

(This article belongs to the Special Issue Metabolic Profiling towards the Development of Antibiotic Management)

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Review

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12 pages, 1644 KiB

Open AccessReview

Infection Biomarkers Based on Metabolomics

by Rúben Araújo, Luís F. N. Bento, Tiago A. H. Fonseca, Cristiana P. Von Rekowski, Bernardo Ribeiro da Cunha and Cecília R. C. Calado

Metabolites 2022, 12(2), 92; https://0-doi-org.brum.beds.ac.uk/10.3390/metabo12020092 - 19 Jan 2022

Cited by 12 | Viewed by 3001

Abstract

Current infection biomarkers are highly limited since they have low capability to predict infection in the presence of confounding processes such as in non-infectious inflammatory processes, low capability to predict disease outcomes and have limited applications to guide and evaluate therapeutic regimes. Therefore, it is critical to discover and develop new and effective clinical infection biomarkers, especially applicable in patients at risk of developing severe illness and critically ill patients. Ideal biomarkers would effectively help physicians with better patient management, leading to a decrease of severe outcomes, personalize therapies, minimize antibiotics overuse and hospitalization time, and significantly improve patient survival. Metabolomics, by providing a direct insight into the functional metabolic outcome of an organism, presents a highly appealing strategy to discover these biomarkers. The present work reviews the desired main characteristics of infection biomarkers, the main metabolomics strategies to discover these biomarkers and the next steps for developing the area towards effective clinical biomarkers. Full article

(This article belongs to the Special Issue Metabolic Profiling towards the Development of Antibiotic Management)

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