Microbiome-Based Medicinal Products: The Next Frontier in Medicine

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 14540

Special Issue Editor

Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France
Interests: Crohn’s disease; metabonomics; gut microbiota

Special Issue Information

Dear Colleagues,

The recent discovery of the importance of microbiomes in health has revolutionized the way we think about disease management and therapies. As a consequence, a number of microbiome-based medicinal products (MMPs) are now being developed to address a range of diseases. The objective of this Special Issue is to collect state-of-the-art articles that broadly cover the full range of microbiome-derived therapies. These may include original results or reviews discussing the development of any MMPs, such as fecal material transplants, bacterial consortia, single strain live biotherapeutic products, bacteriophages, postbiotics, and generally any molecules targeting human-associated microbiomes. Since many of these therapies rely on precise characterization of microbiome signatures, the collection will also include articles reporting on the development of diagnostic assays. Reflections on manufacturing challenges and the regulatory landscape surrounding the MMP development field are also welcome.

Dr. Sandrine P. Claus
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

  • microbiome-based medicinal products
  • live biotherapeutics products
  • microbiome
  • drugs

Published Papers (4 papers)

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Research

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16 pages, 878 KiB  
Article
Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required
by Márton Szoboszlay, Laetitia Schramm, David Pinzauti, Jeanesse Scerri, Anna Sandionigi and Manuele Biazzo
Microorganisms 2023, 11(3), 804; https://doi.org/10.3390/microorganisms11030804 - 21 Mar 2023
Cited by 9 | Viewed by 6000
Abstract
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the [...] Read more.
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants. Full article
(This article belongs to the Special Issue Microbiome-Based Medicinal Products: The Next Frontier in Medicine)
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14 pages, 1643 KiB  
Article
Topical Administration of Lactiplantibacillus plantarum (SkinDuoTM) Serum Improves Anti-Acne Properties
by Christine Podrini, Laetitia Schramm, Giulia Marianantoni, Jagienka Apolinarska, Colin McGuckin, Nico Forraz, Clément Milet, Anne-Laure Desroches, Pauline Payen, Maria D’Aguanno and Manuele Biazzo
Microorganisms 2023, 11(2), 417; https://doi.org/10.3390/microorganisms11020417 - 07 Feb 2023
Cited by 5 | Viewed by 2869
Abstract
The tailoring of the skin microbiome is challenging and is a research hotspot in the pathogenesis of immune-mediated inflammatory skin diseases such as acne. Commonly encountered preservatives used as functional ingredients have an impact on the skin microbiota and are known to inhibit [...] Read more.
The tailoring of the skin microbiome is challenging and is a research hotspot in the pathogenesis of immune-mediated inflammatory skin diseases such as acne. Commonly encountered preservatives used as functional ingredients have an impact on the skin microbiota and are known to inhibit the survival of skin commensal bacteria. The selected species is Lactiplantibacillus plantarum, formulated with natural enhancers for topical use (SkinDuoTM). Ex vivo human skin models were used as a test system to assess the strain viability which was then validated on healthy volunteers. SkinDuoTM showed increased viability over time for in vitro skin models and a stable viability of over 50% on healthy skin. The strain was tested on human primary sebocytes obtained from sebaceous gland rich areas of facial skin and inoculated with the most abundant bacteria from the skin microbiota. Results on human ex vivo sebaceous gland models with the virulent phylotype of Cutibacterium acnes and Staphylococcus epidermidis present a significant reduction in viability, lipid production, and anti-inflammatory markers. We have developed an innovative anti-acne serum with L. plantarum that mimics the over-production of lipids, anti-inflammatory properties, and improves acne-disease skin models. Based on these results, we suggest that SkinDuoTM may be introduced as an acne-mitigating agent. Full article
(This article belongs to the Special Issue Microbiome-Based Medicinal Products: The Next Frontier in Medicine)
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14 pages, 2586 KiB  
Article
Human Fecal Bile Acid Analysis after Investigational Microbiota-Based Live Biotherapeutic Delivery for Recurrent Clostridioides difficile Infection
by Romeo Papazyan, Nicky Ferdyan, Karthik Srinivasan, Carlos Gonzalez, William D. Shannon, Ken Blount and Bryan C. Fuchs
Microorganisms 2023, 11(1), 135; https://doi.org/10.3390/microorganisms11010135 - 05 Jan 2023
Cited by 7 | Viewed by 2799
Abstract
Microbiome-based therapeutics are increasingly evaluated as a strategy to reduce recurrent Clostridioides difficile infection (rCDI), with proposed mechanisms including restoration of the microbiota and microbiota-mediated functions, such as bile acid (BA) metabolism. This study reports a quantitative and sensitive assay for targeted metabolomic [...] Read more.
Microbiome-based therapeutics are increasingly evaluated as a strategy to reduce recurrent Clostridioides difficile infection (rCDI), with proposed mechanisms including restoration of the microbiota and microbiota-mediated functions, such as bile acid (BA) metabolism. This study reports a quantitative and sensitive assay for targeted metabolomic assessment, and the application of the assay to profile BA composition in a Phase 2 trial of the investigational microbiota-based live biotherapeutic RBX2660 for reduction of rCDI. A liquid chromatography tandem mass spectrometry method was developed to extract and quantify 35 BAs from 113 participant stool samples from 27 RBX2660-treated rCDI participants in the double-blinded, placebo-controlled clinical trial. The results demonstrate a high-confidence assay as represented by sensitivity, linearity, accuracy, and precision. Furthermore, the assay enabled the observation of primary BAs as the dominant BA species at baseline in stool samples from clinical trial participants, consistent with the expected loss of commensals after broad-spectrum antibiotic treatment. After RBX2660 administration, there was a significant drop in primary BAs concurrent with increased secondary BAs that sustained through 24 months post-RBX2660. Taken together, we describe a robust assay that demonstrates altered BA metabolism in rCDI patients treated with RBX2660 administration. Full article
(This article belongs to the Special Issue Microbiome-Based Medicinal Products: The Next Frontier in Medicine)
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Review

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18 pages, 1591 KiB  
Review
Advances in Lactobacillus Restoration for β-Lactam Antibiotic-Induced Dysbiosis: A System Review in Intestinal Microbiota and Immune Homeostasis
by Ying Shi, Jiaqi Luo, Arjan Narbad and Qihe Chen
Microorganisms 2023, 11(1), 179; https://doi.org/10.3390/microorganisms11010179 - 11 Jan 2023
Cited by 5 | Viewed by 2122
Abstract
A balanced gut microbiota and their metabolites are necessary for the maintenance of the host’s health. The antibiotic-induced dysbiosis can cause the disturbance of the microbial community, influence the immune homeostasis and induce susceptibility to metabolic- or immune-mediated disorders and diseases. The Lactobacillus [...] Read more.
A balanced gut microbiota and their metabolites are necessary for the maintenance of the host’s health. The antibiotic-induced dysbiosis can cause the disturbance of the microbial community, influence the immune homeostasis and induce susceptibility to metabolic- or immune-mediated disorders and diseases. The Lactobacillus and their metabolites or components affect the function of the host’s immune system and result in microbiota-mediated restoration. Recent data have indicated that, by altering the composition and functions of gut microbiota, antibiotic exposure can also lead to a number of specific pathologies, hence, understanding the potential mechanisms of the interactions between gut microbiota dysbiosis and immunological homeostasis is very important. The Lactobacillus strategies for detecting the associations between the restoration of the relatively imbalanced microbiome and gut diseases are provided in this discussion. In this review, we discuss the recently discovered connections between microbial communities and metabolites in the Lactobacillus treatment of β-lactam antibiotic-induced dysbiosis, and establish the relationship between commensal bacteria and host immunity under this imbalanced homeostasis of the gut microbiota. Full article
(This article belongs to the Special Issue Microbiome-Based Medicinal Products: The Next Frontier in Medicine)
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