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Gut Microbiota in Human Disease and Health
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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 (20 April 2025) | Viewed by 31471

Special Issue Editor

Dr. Silvia Turroni

E-Mail Website
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

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 microbiota
  • human disease
  • human health
  • omics
  • microbiota–host interactions
  • microbiota manipulation

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Published Papers (6 papers)

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Research

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21 pages, 4543 KiB  
Article
Exploring Protein Functions of Gut Bacteriome and Mycobiome in Thai Infants Associated with Atopic Dermatitis Through Metaproteomic and Host Interaction Analysis
by Thanawit Chantanaskul, Preecha Patumcharoenpol, Sittirak Roytrakul, Amornthep Kingkaw and Wanwipa Vongsangnak
Int. J. Mol. Sci. 2024, 25(24), 13533; https://doi.org/10.3390/ijms252413533 - 18 Dec 2024
Viewed by 1283
Abstract
Atopic dermatitis (AD), a prevalent allergic skin condition in children, has been closely associated with imbalances in the gut microbiome. To investigate these microbial alterations and their functional implications, we investigated protein expression, functions and interactions of the gut bacteriome and mycobiome as [...] Read more.
Atopic dermatitis (AD), a prevalent allergic skin condition in children, has been closely associated with imbalances in the gut microbiome. To investigate these microbial alterations and their functional implications, we investigated protein expression, functions and interactions of the gut bacteriome and mycobiome as well as the human proteome in Thai infants with AD using integrative metaproteomic and host interaction analysis. As we observed, probiotic species, such as Lactobacillus acidophilus and Bacteroides salyersiae, were reduced in abundance in the AD group while key pathogenic bacteria and fungi, such as Streptococcus constellatus and Penicillium chrysogenum, increased in abundance. Additionally, the functional analysis of expressed proteins was enriched in response to stress and DNA repair in the bacteriome and ribosome biogenesis-related processes in the mycobiome of the AD group, potentially associated to increased reactive oxygen species (ROS), intestinal inflammation, fungal growth and microbial dysbiosis. Further, a protein–protein interactions (PPIs) network analysis incorporating the human proteome revealed 10 signature proteins related to stress and immune system processes associated with AD. Our findings propose the interactions of the key species and signature protein functions between the gut microbes and the human host in response to AD in Thai infants. To our knowledge, this study serves as the first framework for monitoring bacteriome–mycobiome–human gut studies associated with AD and other allergic diseases in infants. Full article
(This article belongs to the Special Issue Gut Microbiota in Human Disease and Health)
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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
Cited by 1 | Viewed by 1468
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
Cited by 1 | Viewed by 4358
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
Cited by 3 | Viewed by 18915
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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30 pages, 2626 KiB  
Review
Gut Microbiota and Colorectal Cancer: A Balance Between Risk and Protection
by Vlad Alexandru Ionescu, Camelia Cristina Diaconu, Gina Gheorghe, Mara-Madalina Mihai, Carmen Cristina Diaconu, Marinela Bostan and Coralia Bleotu
Int. J. Mol. Sci. 2025, 26(8), 3733; https://doi.org/10.3390/ijms26083733 - 15 Apr 2025
Viewed by 540
Abstract
The gut microbiome, a complex community of microorganisms residing in the intestinal tract, plays a dual role in colorectal cancer (CRC) development, acting both as a contributing risk factor and as a protective element. This review explores the mechanisms by which gut microbiota [...] Read more.
The gut microbiome, a complex community of microorganisms residing in the intestinal tract, plays a dual role in colorectal cancer (CRC) development, acting both as a contributing risk factor and as a protective element. This review explores the mechanisms by which gut microbiota contribute to CRC, emphasizing inflammation, oxidative stress, immune evasion, and the production of genotoxins and microbial metabolites. Fusobacterium nucleatum, Escherichia coli (pks+), and Bacteroides fragilis promote tumorigenesis by inducing chronic inflammation, generating reactive oxygen species, and producing virulence factors that damage host DNA. These microorganisms can also evade the antitumor immune response by suppressing cytotoxic T cell activity and increasing regulatory T cell populations. Additionally, microbial-derived metabolites such as secondary bile acids and trimethylamine-N-oxide (TMAO) have been linked to carcinogenic processes. Conversely, protective microbiota, including Lactobacillus, Bifidobacterium, and Faecalibacterium prausnitzii, contribute to intestinal homeostasis by producing short-chain fatty acids (SCFAs) like butyrate, which exhibit anti-inflammatory and anti-carcinogenic properties. These beneficial microbes enhance gut barrier integrity, modulate immune responses, and inhibit tumor cell proliferation. Understanding the dynamic interplay between pathogenic and protective microbiota is essential for developing microbiome-based interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, to prevent or treat CRC. Future research should focus on identifying microbial biomarkers for early CRC detection and exploring personalized microbiome-targeted therapies. A deeper understanding of host–microbiota interactions may lead to innovative strategies for CRC management and improved patient outcomes. Full article
(This article belongs to the Special Issue Gut Microbiota in Human Disease and Health)
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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 7 | Viewed by 3205
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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