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Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic...
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Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 20530

Special Issue Editor

Dr. Walid Mottawea

E-Mail Website
Guest Editor
School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Interests: gut microbiome; inflammatory bowel diseases; 16S rRNA sequencing; brain-gut axis; probiotics; metagenomics; gut homeostasis; systems biology; bacterial genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past two decades, advances in omics technology have allowed comprehensive characterizations of the gut microbiome in many health disorders. Gut microbiomes interact with the host through their metabolites, defense against pathogens and/or immunological promotion. Perturbation of host–microbiome crosstalk has been associated with different health disorders, including irritable bowel syndrome, inflammatory bowel diseases, diabetes, Clostridium difficile infection and mental health disorders. Therefore, the focus of interest of the current wave of microbiome research is to investigate how to manipulate the gut microbiome consortium to promote human health. Manipulation of the gut microbiome can be achieved through restoring microbiota diversity and composition or by inducing certain functional activities. Several targeted and non-targeted approaches are being tested for their efficiency in modulating the microbiome balance. These approaches include fecal microbiota transplant (FMT) and prebiotic, probiotic and CRISPR-Cas9-engineered phage. The purpose of this Special Issue is to create a collection of scientific reports that help us to understand the microbiome’s therapeutic potential in different disorders. We invite original articles and extensive reviews in the areas of microbiome characterization, biomarker identification and microbiome-based therapeutic manipulations. Any type of article on host–microbiome crosstalk is welcome.

Dr. Walid Mottawea
Guest Editor

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. Biology 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 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

  • gut microbiome
  • fecal microbiota therapy
  • prebiotics
  • probiotics
  • microbiome therapeutics

Related Special Issue

Published Papers (6 papers)

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Research

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14 pages, 2247 KiB  
Article
Identification of Bioactive Phytochemicals from Six Plants: Mechanistic Insights into the Inhibition of Rumen Protozoa, Ammoniagenesis, and α-Glucosidase
by Aurele Gnetegha Ayemele, Lu Ma, Xiumei Li, Peilong Yang, Jianchu Xu, Zhongtang Yu and Dengpan Bu
Biology 2021, 10(10), 1055; https://doi.org/10.3390/biology10101055 - 18 Oct 2021
Cited by 8 | Viewed by 2395
Abstract
Rumen protozoa prey on feed-degrading bacteria synthesizing microbial protein, lowering nitrogen utilization efficiency in ruminants. In this in vitro study, we evaluated six plants (Adansonia digitata, Flemingia macrophylla, Kalimeris indica,Brassica rapa subsp. chinensis, Portulaca oleracea, and Calotropis gigantea [...] Read more.
Rumen protozoa prey on feed-degrading bacteria synthesizing microbial protein, lowering nitrogen utilization efficiency in ruminants. In this in vitro study, we evaluated six plants (Adansonia digitata, Flemingia macrophylla, Kalimeris indica,Brassica rapa subsp. chinensis, Portulaca oleracea, and Calotropis gigantea) for their potential to inhibit rumen protozoa and identified the phytochemicals potentially responsible for protozoa inhibition. Rumen protozoa were anaerobically cultured in vitro in the presence of each plant at four doses. All of the tested plants reduced total rumen protozoa (p ≤ 0.05), but C. gigantea and B. rapa were the most inhibitory, inhibiting rumen protozoa by 45.6 and 65.7%, respectively, at the dose of 1.1 mg/mL. Scanning electron microscopy revealed a disruption of the extracellular structure of protozoa cells. Only C. gigantea also decreased the wasteful ammoniagenesis (p ≤ 0.05). Moreover, the A. digitata extract inhibited α-glucosidase activity by about 70% at 100 µg/mL. Reversed-phase high-performance liquid chromatography analysis detected quercetin, anthraquinone, 3-hydroxybenzoic acid, astragaloside, and myricetin in the tested plant leaves. These plants may hold potential as feed additives to reduce rumen protozoa and α- glucosidase activity. Future research is needed to identify the specific anti-protozoal compound(s), the effects on the rumen microbiome, and its fermentation characteristics. Full article
(This article belongs to the Special Issue Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications)
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22 pages, 4255 KiB  
Article
Modulation of Stem Cell Progeny by Probiotics during Regeneration of Gastric Mucosal Erosions
by Farah Al-Yassir, Ghalia Khoder, Subi Sugathan, Prashanth Saseedharan, Asma Al Menhali and Sherif M. Karam
Biology 2021, 10(7), 596; https://doi.org/10.3390/biology10070596 - 28 Jun 2021
Cited by 11 | Viewed by 2768
Abstract
Patients with gastric mucosal erosions are predisposed to chronic gastritis, ulcer or even cancer. The repair of mucosal erosions involves several events including proliferation of gastric epithelial stem cells. The aim of this study was to investigate the effects of the probiotic mixture [...] Read more.
Patients with gastric mucosal erosions are predisposed to chronic gastritis, ulcer or even cancer. The repair of mucosal erosions involves several events including proliferation of gastric epithelial stem cells. The aim of this study was to investigate the effects of the probiotic mixture of De Simone Formulation on gastric epithelial stem cell lineages in mouse models of gastric mucosal erosions. Gastric erosions were induced by a single oral gavage of 80% ethanol containing 15 mg/mL acetylsalicylic acid (5 mL/kg) following a daily dose of probiotic mixture (5 mg/day/mouse) for 10 days. In another protocol, erosions were induced by a daily gavage of acetylsalicylic acid (400 mg/kg/day/mouse) for 5 days before or after daily administration of probiotic mixture for 5 days. Control mice received water gavage for 10 days. All mice were injected with bromodeoxyuridine two hours before sacrifice to label S-phase cells. The stomachs of all mice were processed for histological examination, lectin binding, and immunohistochemical analysis. The results reveal that mice that received probiotics before or after the induction of erosion showed a decrease in erosion index with an increase in gastric epithelial stem/progenitor cell proliferation and enhanced production of mucus, trefoil factors, and ghrelin by mucous and enteroendocrine cell lineages. These mice also showed restoration of the amount of H+,K+-ATPase and pepsinogen involved in the production of the harsh acidic environment by parietal and chief cell lineages. In conclusion, this study demonstrates the beneficial effects of probiotics against gastric mucosal erosion and highlights the involvement and modulation of proliferative stem cells and their multiple glandular epithelial cell lineages. Full article
(This article belongs to the Special Issue Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications)
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20 pages, 4407 KiB  
Article
Lactobacillus Sps in Reducing the Risk of Diabetes in High-Fat Diet-Induced Diabetic Mice by Modulating the Gut Microbiome and Inhibiting Key Digestive Enzymes Associated with Diabetes
by Aneela Gulnaz, Jawad Nadeem, Jong-Hun Han, Lee-Ching Lew, Jae-Dong Son, Yong-Ha Park, Irfan A. Rather and Yan-Yan Hor
Biology 2021, 10(4), 348; https://doi.org/10.3390/biology10040348 - 20 Apr 2021
Cited by 17 | Viewed by 3507
Abstract
Obesity caused by a high-fat diet (HFD) affects gut microbiota linked to the risk of type-2 diabetes (T2D). This study evaluates live cells and ethanolic extract (SEL) of Lactobacillus sakei Probio65 and Lactobacillus plantarum Probio-093 as natural anti-diabetic compounds. In-vitro anti-diabetic effects were [...] Read more.
Obesity caused by a high-fat diet (HFD) affects gut microbiota linked to the risk of type-2 diabetes (T2D). This study evaluates live cells and ethanolic extract (SEL) of Lactobacillus sakei Probio65 and Lactobacillus plantarum Probio-093 as natural anti-diabetic compounds. In-vitro anti-diabetic effects were determined based on the inhibition of α-glucosidase and α-amylase enzymes. The SEL of Probio65 and Probio-093 significantly retarded α-glucosidase and α-amylase enzymes (p < 0.05). Live Probio65 and Probio-093 inhibited α-glucosidase and α-amylase, respectively (p < 0.05). In mice fed with a 45% kcal high-fat diet (HFD), the SEL and live cells of both strains reduced body weight significantly compared to HFD control (p < 0.05). Probio-093 also improved blood glucose level compared to control (p < 0.05). The gut microbiota modulatory effects of lactobacilli on HFD-induced diabetic mice were analyzed with qPCR method. The SEL and live cells of both strains reduced phyla Deferribacteres compared to HFD control (p < 0.05). The SEL and live cells of Probio-093 promoted more Actinobacteria (phyla), Bifidobacterium, and Prevotella (genus) compared to control (p < 0.05). Both strains exerted metabolic-modulatory effects, with strain Probio-093 showing more prominent alteration in gut microbiota, substantiating the role of probiotics in gut microbiome modulations and anti-diabetic effect. Both lactobacilli are potential candidates to lessen obesity-linked T2D. Full article
(This article belongs to the Special Issue Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications)
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14 pages, 22535 KiB  
Article
Diversion Colitis: Macro and Microscopic Findings after Probiotics Stimulation
by Ángela Rodríguez-Padilla, Germán Morales-Martín, Rocío Pérez-Quintero, Juan Gómez-Salgado, Ricardo Rada-Morgades and Carlos Ruiz-Frutos
Biology 2021, 10(4), 303; https://doi.org/10.3390/biology10040303 - 06 Apr 2021
Cited by 4 | Viewed by 2797
Abstract
The use of a loop ileostomy as the defunctioning procedure of choice to protect a distal colonic anastomosis causes histological and endoscopic changes in the intestinal mucosal architecture, which have been related to chronic inflammation and changes in the microflora that consequently impact [...] Read more.
The use of a loop ileostomy as the defunctioning procedure of choice to protect a distal colonic anastomosis causes histological and endoscopic changes in the intestinal mucosal architecture, which have been related to chronic inflammation and changes in the microflora that consequently impact the intestinal structure and function following fecal stream diversion. The aim of this study was to evaluate the histological and endoscopic changes on the colonic mucosa in patients with diversion colitis after stimulation of the efferent loop with probiotics prior to closure of the protective ileostomy. A prospective, randomized, double-blind, controlled study was designed. All patients who underwent surgery for colorectal carcinoma with protective ileostomy between January 2017 and December 2018 were included. These patients were pending reconstructive surgery and were diagnosed with endoscopic and histological diversion colitis. Divided into two groups, a group stimulated with probiotics (SG) and a control group (CG). 34 cases and 35 controls were included in the study. Histological and endoscopic changes were evaluated after stimulation, after restorative surgery and during the short-term follow-up after surgery. A decrease in endoscopic pathological findings (mucosal friability, mucous erosions, polyps, edema, erythema and stenosis) and in histological findings (follicular hyperplasia, eosinophils, cryptic abscesses, lymphocyte infiltration, plasma cell infiltration and architecture distortion) was observed in SG. These results were statistically significant with a p < 0.001. The stimulation of the efferent loop of the ileostomy in patients with diversion colitis produced a decrease of the endoscopic and histological severity of colitis in the short term. Full article
(This article belongs to the Special Issue Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications)
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24 pages, 3412 KiB  
Article
Antibiotics Modulate Intestinal Regeneration
by Lymarie M. Díaz-Díaz, Natalia Rosario-Meléndez, Andrea Rodríguez-Villafañe, Yariel Y. Figueroa-Vega, Omar A. Pérez-Villafañe, Angela M. Colón-Cruz, Paola I. Rodríguez-Sánchez, Julio M. Cuevas-Cruz, Sonya J. Malavez-Cajigas, Sergio M. Maldonado-Chaar and José E. García-Arrarás
Biology 2021, 10(3), 236; https://doi.org/10.3390/biology10030236 - 19 Mar 2021
Cited by 6 | Viewed by 3623
Abstract
The increased antibiotics usage in biomedical and agricultural settings has been well documented. Antibiotics have now been shown to exert effects outside their purposive use, including effects on physiological and developmental processes. We explored the effect of various antibiotics on intestinal regeneration in [...] Read more.
The increased antibiotics usage in biomedical and agricultural settings has been well documented. Antibiotics have now been shown to exert effects outside their purposive use, including effects on physiological and developmental processes. We explored the effect of various antibiotics on intestinal regeneration in the sea cucumber Holothuria glaberrima. For this, holothurians were eviscerated and left to regenerate for 10 days in seawater with different penicillin/streptomycin-based cocktails (100 µg/mL PS) including: 100 µg/mL kanamycin (KPS), 5 µg/mL vancomycin (VPS), and 4 µg/mL (E4PS) or 20 µg/mL (E20PS) erythromycin. Immunohistological and histochemical analyses were performed to analyze regenerative processes, including rudiment size, extracellular matrix (ECM) remodeling, cell proliferation, and muscle dedifferentiation. A reduction in muscle dedifferentiation was observed in all antibiotic-treated animals. ECM remodeling was decreased by VPS, E4PS, and E20PS treatments. In addition, organisms subjected to E20PS displayed a significant reduction in the size of their regenerating rudiments while VPS exposure altered cell proliferation. MTT assays were used to discard the possibility that the antibiotics directly affect holothurian metabolic activity while bacterial cultures were used to test antibiotic effects on holothurian enteric microbiota. Our results demonstrate a negative effect on intestinal regeneration and strongly suggest that these effects are due to alterations in the microbial community. Full article
(This article belongs to the Special Issue Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications)
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Review

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25 pages, 1320 KiB  
Review
Changes of Gut-Microbiota-Liver Axis in Hepatitis C Virus Infection
by Mohammed El-Mowafy, Abdelaziz Elgaml, Mohamed El-Mesery, Salma Sultan, Tamer A. E. Ahmed, Ahmed I. Gomaa, Mahmoud Aly and Walid Mottawea
Biology 2021, 10(1), 55; https://doi.org/10.3390/biology10010055 - 13 Jan 2021
Cited by 22 | Viewed by 4067
Abstract
The gut–liver-axis is a bidirectional coordination between the gut, including microbial residents, the gut microbiota, from one side and the liver on the other side. Any disturbance in this crosstalk may lead to a disease status that impacts the functionality of both the [...] Read more.
The gut–liver-axis is a bidirectional coordination between the gut, including microbial residents, the gut microbiota, from one side and the liver on the other side. Any disturbance in this crosstalk may lead to a disease status that impacts the functionality of both the gut and the liver. A major cause of liver disorders is hepatitis C virus (HCV) infection that has been illustrated to be associated with gut microbiota dysbiosis at different stages of the disease progression. This dysbiosis may start a cycle of inflammation and metabolic disturbance that impacts the gut and liver health and contributes to the disease progression. This review discusses the latest literature addressing this interplay between the gut microbiota and the liver in HCV infection from both directions. Additionally, we highlight the contribution of gut microbiota to the metabolism of antivirals used in HCV treatment regimens and the impact of these medications on the microbiota composition. This review sheds light on the potential of the gut microbiota manipulation as an alternative therapeutic approach to control the liver complications post HCV infection. Full article
(This article belongs to the Special Issue Gut Microbiome Manipulation: Focus on Microbiome Characterization, Diagnostics and Therapeutic Indications)
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