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Microorganisms
Special Issues
Gut Microbiota and Human Health: From Mechanisms to Therapeutic Frontiers
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Gut Microbiota and Human Health: From Mechanisms to Therapeutic Frontiers

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

Deadline for manuscript submissions: 31 May 2026 | Viewed by 2618

Special Issue Editor

Prof. Dr. Jun-Hyung Cho

E-Mail Website
Guest Editor
Digestive Disease Center, Soonchunhyang University Hospital, 59, Daesagwan-ro, Yongsan-gu, Seoul 04401, Republic of Korea
Interests: gastrointestinal tract; Helicobacter pylori
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, advances in microbiome research have fundamentally reshaped our understanding of the gut microbiota as a central regulator of health and disease. Gut microbial composition and function are increasingly recognized as key determinants of host immunity, metabolism, neurological function, and cancer susceptibility. Despite rapid progress, the field still faces critical gaps in mechanistic insight, biomarker discovery, and clinical translation. The forthcoming Special Issue aims to provide a forward-looking platform for cutting-edge research and comprehensive reviews on the role of gut microbiota across health and disease. We seek contributions that move beyond descriptive studies to mechanistic, functional, and translational insights. We also encourage interdisciplinary work that integrates microbiology, immunology, oncology, nutrition, computational biology, and clinical sciences.

Prof. Dr. Jun-Hyung Cho
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 250 words) can be sent to the Editorial Office for assessment.

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. Microorganisms 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 microbiota
  • host–microbe interaction
  • Helicobacter pylori
  • microbiome metabolites
  • gut–brain axis
  • probiotics and prebiotics
  • fecal microbiota transplantation

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Published Papers (3 papers)

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Research

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14 pages, 514 KB  
Article
High Levels of Helicobacter pylori Antimicrobial Resistance in Ireland—A Multicentre Study
by Thomas J. Butler, Stephen Molloy, Atiyekeogbebe Douglas, Denise Brennan, Rebecca FitzGerald, Conor Costigan, Vikrant Parihar, Kevin Van Der Merwe, Serhiy Semenov, Donal Tighe, Sharon Hough, David Kevans, Colm O’Morain, Deirdre McNamara and Sinéad Marian Smith
Microorganisms 2026, 14(3), 704; https://doi.org/10.3390/microorganisms14030704 - 21 Mar 2026
Viewed by 446
Abstract
Resistance surveillance programmes are essential for choosing the most appropriate eradication therapy for the stomach pathogen Helicobacter pylori. This study aimed to determine H. pylori antimicrobial resistance rates in Ireland. H. pylori was cultured from patients attending four gastroenterology clinics from 2018 [...] Read more.
Resistance surveillance programmes are essential for choosing the most appropriate eradication therapy for the stomach pathogen Helicobacter pylori. This study aimed to determine H. pylori antimicrobial resistance rates in Ireland. H. pylori was cultured from patients attending four gastroenterology clinics from 2018 to 2023. Antimicrobial susceptibility testing (AST) was performed using Etests for metronidazole, clarithromycin, levofloxacin, amoxicillin, tetracycline and rifampicin and resistance classified using EUCAST guidelines. Resistance rates were compared between H. pylori treatment-naïve and previously treated patients (primary and secondary resistance, respectively). Samples from 138 culture-positive patients (mean age 49.4 ± 15.7 years, 47.1% female) were analysed. A total of 28.7% of isolates from treatment-naïve patients were susceptible to all antimicrobials tested. Primary resistance rates to metronidazole, clarithromycin, levofloxacin, amoxicillin, tetracycline and rifampicin were 44.3%, 36.5%, 18.3%, 14.6%, 9.6% and 9.6%, respectively. Primary dual resistance to clarithromycin and metronidazole was 22.6% and primary multidrug resistance was 13.0%. Secondary resistance rates were significantly higher than primary resistance rates for clarithromycin, metronidazole, dual resistance to clarithromycin and either amoxicillin, metronidazole or levofloxacin, and multidrug resistance. Female sex and older age were associated with increased risk of resistance. H. pylori resistance rates were high in our cohort. Clarithromycin-based triple therapy should no longer be used in Ireland in the absence of pre-treatment AST. Resistance to amoxicillin, tetracycline and rifampicin should be monitored closely. Full article
(This article belongs to the Special Issue Gut Microbiota and Human Health: From Mechanisms to Therapeutic Frontiers)
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19 pages, 3810 KB  
Article
Deciphering the Post-Operative Dynamics of Opportunistic Gut Microbiota in Colorectal Cancer Patients
by Mutebi John Kenneth, Chuan-Yin Fang, Chin-Chia Wu, Ming-Chih Hsieh, Ming-Liang Lai and Bing-Mu Hsu
Microorganisms 2025, 13(12), 2818; https://doi.org/10.3390/microorganisms13122818 - 11 Dec 2025
Viewed by 594
Abstract
Recent studies indicate that opportunistic gut bacteria contribute to the recurrence and chemoresistance in colorectal cancer (CRC); however, their fate after surgical resection remains poorly understood. This study investigated the longitudinal changes in these bacteria and assessed their potential persistence following CRC surgery. [...] Read more.
Recent studies indicate that opportunistic gut bacteria contribute to the recurrence and chemoresistance in colorectal cancer (CRC); however, their fate after surgical resection remains poorly understood. This study investigated the longitudinal changes in these bacteria and assessed their potential persistence following CRC surgery. Forty fecal samples were collected from ten CRC patients at four timepoints: (1) pre-surgery (S); (2) one week (S1); (3) one month (S2); and (4) three months (S3) post-surgery. Fifteen other fecal samples were collected from healthy individuals as our study controls. Microbial profiling was performed using 16S rRNA gene sequencing, and quantitative PCR was applied to assess the changes in three opportunistic bacteria associated with CRC-associated. Our study revealed that Escherichia coli was significantly enriched in pre-surgical samples (S), while Enterococcus faecalis was predominant in the samples collected one-week after surgery (S1). All the assessed species showed a gradual post-surgical decline in relative abundance, suggesting they do not persist after resection. Additionally, there was a significant increase in relative abundance of beneficial bacterial signatures, including Akkermansia muciniphila, Bacteroides uniformis, Parabacteroides merdae, and Phascolarctobacterium faecium post-surgery, which implies a potential dysbiosis restoration. Our findings suggest that surgical resection gradually reduces the burden of opportunistic gut microbiota, thus gradually lowering the risk of recurrence and chemoresistance. Additionally, it may facilitate the restoration of beneficial taxa. Future studies should include extended follow-up periods to validate our findings and their correlation with clinical outcomes. Full article
(This article belongs to the Special Issue Gut Microbiota and Human Health: From Mechanisms to Therapeutic Frontiers)
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Review

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29 pages, 2272 KB  
Review
The Dual Role of Gut Microbiota and Their Metabolites in Hepatocellular Carcinoma: A Context-Dependent Framework
by Shuyu Zuo, Junhui Ma, Xue Li, Zhengyang Fan, Xiao Li, Yingen Luo and Lei Su
Microorganisms 2026, 14(1), 73; https://doi.org/10.3390/microorganisms14010073 - 29 Dec 2025
Cited by 1 | Viewed by 1238
Abstract
Hepatocellular carcinoma (HCC) is a global health threat, and gut microbiota play a pivotal role in its pathogenesis through the gut–liver axis. However, the literature contains divergent or opposing findings: key microbial metabolites, such as secondary bile acids and indole derivatives, exhibit potent [...] Read more.
Hepatocellular carcinoma (HCC) is a global health threat, and gut microbiota play a pivotal role in its pathogenesis through the gut–liver axis. However, the literature contains divergent or opposing findings: key microbial metabolites, such as secondary bile acids and indole derivatives, exhibit potent pro- and anti-tumorigenic activities across different studies, hindering a unified understanding of their veritable roles. To resolve this ambiguity, this review proposes a unifying “context dependency” framework. We posit that the functions of gut microbiota and their metabolites are not fixed but are dynamically determined by the host’s physiological and pathological “context,” defined here as the integrated dynamic background shaped by local metabolite concentrations, host immune status, specific receptor expression, and tumor microenvironment (TME) features. This framework is systematically substantiated through an analysis of the dichotomous effects of major microbial metabolites, including bile acids (BAs), short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), and indole derivatives. We further elucidate that the key “contextual factors” governing these functional outcomes include the TME, host immune status, metabolite concentration gradients, and the activation patterns of specific signaling pathways (e.g., farnesoid X receptor/takeda G protein-coupled receptor 5, aryl hydrocarbon receptor). This novel framework not only provides a theoretical foundation for integrating existing paradoxical findings but also paves the way for the future development of context-specific precision diagnostic biomarkers and targeted microbial intervention therapies for HCC. Full article
(This article belongs to the Special Issue Gut Microbiota and Human Health: From Mechanisms to Therapeutic Frontiers)
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