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Antibiotics
Special Issues
Microbiome-Based Therapies: Alternatives to, Complementing or Enhancing Antibiotic Treatments
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Microbiome-Based Therapies: Alternatives to, Complementing or Enhancing Antibiotic Treatments

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Biosynthesis and Combinatorial Approaches in Antimicrobial Discovery".

Deadline for manuscript submissions: 15 June 2024 | Viewed by 6638

Special Issue Editors

Dr. Vitor Cabral

E-Mail Website
Guest Editor
Instituto Gulbenkian de Ciência, Oeiras, Portugal
Interests: microbial communities; biofilms; microbiota; synthetic biology; biotherapies
Dr. Rita A. Oliveira

E-Mail Website
Guest Editor
Duchossois Family Institute, The University of Chicago, Chicago, IL, USA
Interests: gut microbiota; defined bacterial consortia; metabolome; dysbiosis; pathogens; quorum sensing

Special Issue Information

Dear Colleagues,

Antibiotic therapies have been critical in saving lives. However, decades of antibiotics misuse posed a worldwide health burden with the rise of multidrug resistance and collateral damages to the commensal microbial communities that promote host health. This threatens to be the most challenging issues of our generation. Antibiotic treatment still is the most efficient therapy against bacterial infections and inflammatory diseases. Alternatives to antibiotics have been greatly needed although scarce, but also complementing therapies that can be used with antibiotics. These strategies will improve or replace antibiotic treatments, while attenuating their collateral effects on commensal bacteria, hence safeguarding the beneficial and protective effects of the natural microbial communities. Current efforts have been focusing on different strategies towards these aims:

  • Targeting pathogens’ strategies of resistance
  • Novel synthetic antibiotics with narrow spectrum;
  • Novel targets to reduce antimicrobial resistance and robustness;
  • Engineering commensal microbial communities to increase resilience to antibiotics and compete against antimicrobial resistant pathogens;
  • Employing microbial weaponry (bacteriophages, secretion systems, bacteriocins) targeting pathogens with high specificity;
  • Machine learning approaches for in sillico stewardship of antimicrobial resistance research

The aim of this Special Issue is to bridge the gap between these findings and promote a better understanding of the approaches being studied and their successes, fomenting a faster and more sustained advancement of the field to target antibiotic-induced microbiome dysbiosis and rise of antimicrobial resistance in important areas such as human health, agriculture, veterinary medicine, among others.

The discovery and implementation of alternative strategies to the use of antibiotics is very important due to the rise of pathogens resistant to multiple of the current antibiotic treatments. Similarly important are strategies that can complement and enhance antibiotic treatments, either by focusing on different targets, or by protecting commensal bacteria from the collateral effects of antibiotics, therefore aiming their use in the eradication of undesired bacteria while not diminishing the natural protection conferred by the native microbiota. Therefore, this Special Issue fits Antibiotics’s scope in the following parameters:

  • Advances in research on new and current antibiotics and related bioactive medicinal agents
  • Biochemical and genetics studies on microorganisms for improved antibiotics
  • Uses of antibiotics, including in animals and agriculture
  • Antibiotic resistance and misuse
  • Natural antibiotics

Dr. Vitor Cabral
Dr. Rita A. Oliveira
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • antimicrobial resistance
  • microbiome-associated inflammatory diseases
  • microbiota resilience
  • recovery from dysbiosis
  • colonization resistance
  • microbiome therapy
  • probiotics and postbiotics
  • antibiotics alternatives
  • diet and prebiotics
  • mathematical models

Published Papers (3 papers)

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Research

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20 pages, 3284 KiB  
Article
Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region
by Ermias Sissay Balcha, Felipe Gómez, Mesfin Tafesse Gemeda, Fanuel Belayneh Bekele, Sewunet Abera, Barbara Cavalazzi and Adugna Abdi Woldesemayat
Antibiotics 2023, 12(12), 1697; https://doi.org/10.3390/antibiotics12121697 - 04 Dec 2023
Viewed by 1430
Abstract
The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from [...] Read more.
The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance. Full article
(This article belongs to the Special Issue Microbiome-Based Therapies: Alternatives to, Complementing or Enhancing Antibiotic Treatments)
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Review

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19 pages, 945 KiB  
Review
Microbe Interactions within the Skin Microbiome
by Thaís Glatthardt, Rayssa Durães Lima, Raquel Monteiro de Mattos and Rosana Barreto Rocha Ferreira
Antibiotics 2024, 13(1), 49; https://doi.org/10.3390/antibiotics13010049 - 04 Jan 2024
Cited by 1 | Viewed by 2699
Abstract
The skin is the largest human organ and is responsible for many important functions, such as temperature regulation, water transport, and protection from external insults. It is colonized by several microorganisms that interact with each other and with the host, shaping the microbial [...] Read more.
The skin is the largest human organ and is responsible for many important functions, such as temperature regulation, water transport, and protection from external insults. It is colonized by several microorganisms that interact with each other and with the host, shaping the microbial structure and community dynamics. Through these interactions, the skin microbiota can inhibit pathogens through several mechanisms such as the production of bacteriocins, proteases, phenol soluble modulins (PSMs), and fermentation. Furthermore, these commensals can produce molecules with antivirulence activity, reducing the potential of these pathogens to adhere to and invade human tissues. Microorganisms of the skin microbiota are also able to sense molecules from the environment and shape their behavior in response to these signals through the modulation of gene expression. Additionally, microbiota-derived compounds can affect pathogen gene expression, including the expression of virulence determinants. Although most studies related to microbial interactions in the skin have been directed towards elucidating competition mechanisms, microorganisms can also use the products of other species to their benefit. In this review, we will discuss several mechanisms through which microorganisms interact in the skin and the biotechnological applications of products originating from the skin microbiota that have already been reported in the literature. Full article
(This article belongs to the Special Issue Microbiome-Based Therapies: Alternatives to, Complementing or Enhancing Antibiotic Treatments)
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15 pages, 699 KiB  
Review
ESKAPEE Pathogen Biofilm Control on Surfaces with Probiotic Lactobacillaceae and Bacillus species
by Claudio Neidhöfer, Kamni Rathore, Marijo Parčina and Martin A. Sieber
Antibiotics 2023, 12(5), 871; https://doi.org/10.3390/antibiotics12050871 - 08 May 2023
Viewed by 2039
Abstract
Combatting the rapidly growing threat of antimicrobial resistance and reducing prevalence and transmission of ESKAPEE pathogens in healthcare settings requires innovative strategies, one of which is displacing these pathogens using beneficial microorganisms. Our review comprehensively examines the evidence of probiotic bacteria displacing ESKAPEE [...] Read more.
Combatting the rapidly growing threat of antimicrobial resistance and reducing prevalence and transmission of ESKAPEE pathogens in healthcare settings requires innovative strategies, one of which is displacing these pathogens using beneficial microorganisms. Our review comprehensively examines the evidence of probiotic bacteria displacing ESKAPEE pathogens, with a focus on inanimate surfaces. A systematic search was conducted using the PubMed and Web of Science databases on 21 December 2021, and 143 studies were identified examining the effects of Lactobacillaceae and Bacillus spp. cells and products on the growth, colonization, and survival of ESKAPEE pathogens. While the diversity of study methods limits evidence analysis, results presented by narrative synthesis demonstrate that several species have the potential as cells or their products or supernatants to displace nosocomial infection-causing organisms in a variety of in vitro and in vivo settings. Our review aims to aid the development of new promising approaches to control pathogen biofilms in medical settings by informing researchers and policymakers about the potential of probiotics to combat nosocomial infections. More targeted studies are needed to assess safety and efficacy of different probiotic formulations, followed by large-scale studies to assess utility in infection control and medical practice. Full article
(This article belongs to the Special Issue Microbiome-Based Therapies: Alternatives to, Complementing or Enhancing Antibiotic Treatments)
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