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Gut Microbiota in Human Disease and Health

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (30 January 2024) | Viewed by 11875

Special Issue Editor


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Guest Editor
Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro, 6-40126 Bologna, Italy
Interests: human microbiome; gut microbiome; microbial ecology; host–microbiome interactions; probiotics; next-generation sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The gut microbiota represents a key environmental modifier of human health, which can have an impact on the onset and/or progression of gastrointestinal and extraintestinal diseases, as well as on the therapeutic response. However, its drivers of variation, its interactions with the human host and the underlying mechanisms remain incompletely understood. Likewise, there is a paucity of information on the impact of manipulating the gut microbiota for preventive and therapeutic purposes.

This Special Issue aims to expand current knowledge on the role of the gut microbiota in health and disease, including the potential of its modulation in disease prevention and treatment. The use of multi-omics approaches (metagenomics, metatranscriptomics, metabolomics and culturomics) is encouraged, as well as the search for and validation of mechanistic insights. Purely clinical studies are not suitable, but clinical submissions with biomolecular experiments are welcomed.

Dr. Silvia Turroni
Guest Editor

Manuscript Submission Information

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Keywords

  • gut microbiota
  • human disease
  • human health
  • omics
  • microbiota–host interactions
  • microbiota manipulation

Published Papers (4 papers)

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Research

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14 pages, 3643 KiB  
Article
A Comparative Investigation of the Bile Microbiome in Patients with Choledocholithiasis and Cholecystolithiasis through Metagenomic Analysis
by Wonsuk Park and Joonhong Park
Int. J. Mol. Sci. 2024, 25(6), 3297; https://doi.org/10.3390/ijms25063297 - 14 Mar 2024
Viewed by 673
Abstract
While the precise triggers of gallstone formation remain incompletely understood, it is believed to arise from a complex interplay of genetic and environmental factors. The bile microbiome is being increasingly recognized as a possible contributor to the onset of gallstone disease. The primary [...] Read more.
While the precise triggers of gallstone formation remain incompletely understood, it is believed to arise from a complex interplay of genetic and environmental factors. The bile microbiome is being increasingly recognized as a possible contributor to the onset of gallstone disease. The primary objective of this study was to investigate distinctions in the microbial communities within bile specimens from patients with choledocholithiasis (common bile duct stones) and cholecystolithiasis (gallbladder stones). We employed massively parallel sequencing of the 16S rRNA gene to examine the microbial communities within bile samples obtained from 28 patients with choledocholithiasis (group DS) and cholecystolithiasis (group GS). The taxonomic composition of the bile microbial communities displayed significant disparities between the group DS and the group GS. Within the 16 prevalent genera, only Streptococcus, Ralstonia, Lactobacillus, and Enterococcus were predominantly found in the group GS. In contrast, the group DS displayed a more diverse range of genera. The alpha diversity of bile specimens was also notably lower in the group GS compared to the group DS (p = 0.041). Principal coordinate analysis unveiled distinct clustering of bile microbial communities depending on the location of the gallstone. Linear discriminant analysis effect size analysis, with a score threshold of >3 and the Kruskall–Wallis test (α < 0.05), recognized Bacilli and Lactobacillales as potential taxonomic markers for distinguishing patients with cholecystolithiasis limited to the gallbladder. Significant variations were found in the distribution and diversity of bile microbial communities between patients with choledocholithiasis and cholecystolithiasis. This observation suggests that alterations in the bile microbiome may contribute to the development of gallstones in these patients. Full article
(This article belongs to the Special Issue Gut Microbiota in Human Disease and Health)
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25 pages, 6890 KiB  
Article
Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus–Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
by Shen-Yuan Hsieh, George M. Savva, Andrea Telatin, Sumeet K. Tiwari, Mohammad A. Tariq, Fiona Newberry, Katharine A. Seton, Catherine Booth, Amolak S. Bansal, Thomas Wileman, Evelien M. Adriaenssens and Simon R. Carding
Int. J. Mol. Sci. 2023, 24(24), 17267; https://doi.org/10.3390/ijms242417267 - 8 Dec 2023
Viewed by 3298
Abstract
Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small [...] Read more.
Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome. Full article
(This article belongs to the Special Issue Gut Microbiota in Human Disease and Health)
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15 pages, 8876 KiB  
Article
Impact of Ivermectin on the Gut Microbial Ecosystem
by LinShu Liu, Karley K. Mahalak, Jamshed T. Bobokalonov, Adrienne B. Narrowe, Jenni Firrman, Johanna M. S. Lemons, Kyle Bittinger, Weiming Hu, Steven M. Jones and Ahmed M. Moustafa
Int. J. Mol. Sci. 2023, 24(22), 16125; https://doi.org/10.3390/ijms242216125 - 9 Nov 2023
Viewed by 5029
Abstract
Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated [...] Read more.
Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME® (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor’s starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment. Full article
(This article belongs to the Special Issue Gut Microbiota in Human Disease and Health)
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Review

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13 pages, 693 KiB  
Review
Estrobolome and Hepatocellular Adenomas—Connecting the Dots of the Gut Microbial β-Glucuronidase Pathway as a Metabolic Link
by Sandica Bucurica, Mihaela Lupanciuc, Florentina Ionita-Radu, Ion Stefan, Alice Elena Munteanu, Daniela Anghel, Mariana Jinga and Elena Laura Gaman
Int. J. Mol. Sci. 2023, 24(22), 16034; https://doi.org/10.3390/ijms242216034 - 7 Nov 2023
Cited by 1 | Viewed by 1819
Abstract
Hepatocellular adenomas are benign endothelial tumors of the liver, mostly associated with female individual users of estrogen-containing medications. However, the precise factors underlying the selective development of hepatic adenomas in certain females remain elusive. Additionally, the conventional profile of individuals prone to hepatic [...] Read more.
Hepatocellular adenomas are benign endothelial tumors of the liver, mostly associated with female individual users of estrogen-containing medications. However, the precise factors underlying the selective development of hepatic adenomas in certain females remain elusive. Additionally, the conventional profile of individuals prone to hepatic adenoma is changing. Notably, male patients exhibit a higher risk of malignant progression of hepatocellular adenomas, and there are instances where hepatic adenomas have no identifiable cause. In this paper, we theorize the role of the human gastrointestinal microbiota, specifically, of bacterial species producing β-glucuronidase enzymes, in the development of hepatic adenomas through the estrogen recycling pathway. Furthermore, we aim to address some of the existing gaps in our knowledge of pathophysiological pathways which are not yet subject to research or need to be studied further. As microbial β-glucuronidases proteins recycle estrogen and facilitate the conversion of inactive estrogen into its active form, this process results in elevated levels of unbound plasmatic estrogen, leading to extended exposure to estrogen. We suggest that an imbalance in the estrobolome could contribute to sex hormone disease evolution and, consequently, to the advancement of hepatocellular adenomas, which are estrogen related. Full article
(This article belongs to the Special Issue Gut Microbiota in Human Disease and Health)
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