Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.7
4.2
Journals
Microorganisms
Special Issues
Gut Microbiome in Homeostasis and Disease, 3rd Edition
share announcement

Gut Microbiome in Homeostasis and Disease, 3rd Edition

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

Deadline for manuscript submissions: 15 January 2026 | Viewed by 3079

Special Issue Editor

Dr. Michael Doulberis

E-Mail Website
Guest Editor
Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001 Aarau, Switzerland
Interests: Helicobacter pylori; IBD; gut dysbiosis; MASLD
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issues “Gut Microbiome in Homeostasis and Disease" and “Gut Microbiome in Homeostasis and Disease, 2nd Edition”. 

There is emerging evidence that the gut microbiome plays a central role in orchestrating homeostasis, and its disturbance, commonly known as dysbiosis, has been linked to numerous pathologies, such as metabolic syndrome, intestinal diseases, and cancer. With this in mind, we invite you to submit original or review articles that cover both clinical and preclinical field of research, illuminating the role of the gut microbiome in shaping immunity and organisms’ pathophysiology. Once we comprehend the complex mechanisms regulating the balance of the gut microbiome and the benefits or detrimental effects of several genera, we will be able to effectively treat patients with chronic and still unsolved diseases. Welcome are, among others, studies on the gut–brain axis, gut–liver axis, fecal microbiota transplantation, probiotics, and commensal and non-commensal microorganisms, including Helicobacter species. These data are hopefully going to lead to new opportunities for the diagnosis, prognosis, and treatment of a plethora of human diseases. 

Dr. Michael Doulberis
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. 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 microbiome
  • dysbiosis
  • gut–brain axis
  • gut–liver axis
  • fecal microbiota transplantation
  • gut probiotics
  • commensal and non-commensal microorganisms
  • Helicobacter

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Related Special Issues

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review, Other

20 pages, 3699 KB  
Article
Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn’s Disease
by Alexei B. Chukhlovin, Oleg V. Goloshchapov, Oksana B. Shchukina, Aleksandra M. Kharitidis, Alexander A. Zhloba, Tatiana F. Subbotina, Aleksey V. Kusakin, Oleg V. Kosarev, Viktoria V. Tsai, Roman S. Kalinin, Yury A. Eismont and Oleg S. Glotov
Microorganisms 2025, 13(10), 2337; https://doi.org/10.3390/microorganisms13102337 - 10 Oct 2025
Viewed by 286
Abstract
Intestinal bacterial dysbiosis develops in a number of immune-mediated disorders. Fecal microbiota transfer (FMT) is considered a potentially efficient tool for restoration of the patient’s gut microbiota. The aim of our study was to trace the time course of dominant bacterial populations and [...] Read more.
Intestinal bacterial dysbiosis develops in a number of immune-mediated disorders. Fecal microbiota transfer (FMT) is considered a potentially efficient tool for restoration of the patient’s gut microbiota. The aim of our study was to trace the time course of dominant bacterial populations and some Enterobacteria phages in patients with GVHD and Crohn’s disease after FMT procedure. Patients and methods: We observed 12 patients with intestinal graft-versus-host disease (GVHD), and 15 persons with Crohn’s disease after massive anti-infectious treatment. FMT was performed by a standard protocol using oral capsules administered for 2 days. Fecal bacteriome was assessed by 16S rRNA sequencing. Viral sequences were identified by NGS with a customized primer set. Plasma citrulline levels were measured in order to assess enterocyte damage in the patients. Results: Complete clinical response to FMT was observed in 5 of 12 GVHD patients and 10 of 15 Crohn’s disease cases. Before FMT, most anaerobic Bacillota were exhausted in both Crohn’s disease patients and GVHD. Following FMT, Akkermansia ratios tended to decrease within 30 days in Crohn’s disease, along with higher Faecalibacteria, Romboutsia, and Dialister ratios than in GVHD, thus suggesting lesser damage to anaerobic microbiota in Crohn’s disease. Increased contents of facultative anaerobes (Enterococcus and E. coli) was detected in GVHD patients after FMT. Fecal virome changes in Crohn’s disease after FMT included early transient decrease in Caudoviricetes with a rise in Lederbergvirus and Eganvirus ratios at later terms. In GVHD patients, reverse correlations were revealed between E. coli and E. coli-hosted Eganvirus species. Intestinal damage assessed by low plasma citrulline levels was associated with fecal Klebsiella expansion, being more pronounced in GVHD than in Crohn’s disease. Clinical response to FMT in GVHD patients correlated with increased plasma citrulline and lower Eganvirus abundance. Future studies will concern specific relations between fecal bacteriome and virome reconstitution following FMT in gut GVHD and other immune-mediated intestinal disorders. Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
►▼ Show Figures

Figure 1

19 pages, 2101 KB  
Article
Infantile Anemia and Iron Treatments Affect the Gut Microbiome of Young Rhesus Monkeys
by Christopher L. Coe, Gabriele R. Lubach, Wellington Z. Amaral, Gregory J. Phillips, Mark Lyte, Michael K. Georgieff, Raghavendra B. Rao and James R. Connor
Microorganisms 2025, 13(10), 2256; https://doi.org/10.3390/microorganisms13102256 - 26 Sep 2025
Viewed by 385
Abstract
The influence of iron deficiency anemia and iron treatments on the gut microbiome was evaluated in young rhesus monkeys. First, the hindgut bacterial profiles of 12 iron-deficient anemic infants were compared to those of 9 iron-sufficient infants at 6 months of age, a [...] Read more.
The influence of iron deficiency anemia and iron treatments on the gut microbiome was evaluated in young rhesus monkeys. First, the hindgut bacterial profiles of 12 iron-deficient anemic infants were compared to those of 9 iron-sufficient infants at 6 months of age, a time when the risk of anemia is high due to rapid growth. After this screening, the anemic monkeys were treated with either parenteral or enteral iron. Seven monkeys were injected intramuscularly with iron dextran, the typical weekly treatment used in veterinary practice. Four other anemic infants were treated with a novel oral supplement daily: yeast genetically modified to express ferritin. Fecal specimens were analyzed using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Bacterial species richness in anemic infants was not different from that of iron-sufficient infants, but beta diversity and LEfSe analyses of bacterial composition indicated that the microbiota profiles were associated with iron status. Both systemic and oral iron increased alpha and beta diversity metrics. The relative abundance of Ruminococcaceae and other Firmicutes shifted in the direction of an iron-sufficient host, but many different bacteria, including Mollicutes, Tenericutes, and Archaea, were also enriched. Collectively, the findings affirm the important influence of the host’s iron status on commensal bacteria in the gut and concur with clinical concerns about the possibility of adverse consequences after iron supplementation in low-resource settings where children may be carriers of iron-responsive bacterial pathogens. Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
►▼ Show Figures

Graphical abstract

18 pages, 3495 KB  
Article
Structural and Functional Differences in the Gut and Lung Microbiota of Pregnant Pomona Leaf-Nosed Bats
by Taif Shah, Qi Liu, Guiyuan Yin, Zahir Shah, Huan Li, Jingyi Wang, Binghui Wang and Xueshan Xia
Microorganisms 2025, 13(8), 1887; https://doi.org/10.3390/microorganisms13081887 - 13 Aug 2025
Viewed by 754
Abstract
Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. [...] Read more.
Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. Of the 350 bats captured using mist nets in Yunnan, nine pregnant Pomona leaf-nosed bats with similar body sizes were chosen. Gut and lung samples were aseptically collected from each bat following cervical dislocation and placed in sterile cryotubes before microbiota investigation. Microbial taxonomic annotation revealed that the phyla Firmicutes and Actinobacteriota were most abundant in the guts of pregnant bats, whereas Proteobacteria and Bacteroidota were abundant in the lungs. Family-level classification revealed that Bacillaceae, Enterobacteriaceae, and Streptococcaceae were more abundant in the guts, whereas Rhizobiaceae and Burkholderiaceae dominated the lungs. Several opportunistic and potentially pathogenic bacterial genera were present at the two body sites. Bacillus, Cronobacter, and Corynebacterium were abundant in the gut, whereas Bartonella, Burkholderia, and Mycoplasma dominated the lungs. Alpha diversity analysis (using Chao1 and Shannon indices) within sample groups examined read depth and species richness, whereas beta diversity using unweighted and weighted UniFrac distance metrics revealed distinct clustering patterns between the two groups. LEfSe analysis revealed significantly enriched bacterial taxa, indicating distinct microbial clusters within the two body sites. The two Random Forest classifiers (MDA and MDG) evaluated the importance of microbial features in the two groups. Comprehensive functional annotation provided insights into the microbiota roles in metabolic activities, human diseases, signal transduction, etc. This study contributes to our understanding of the microbiota structure and functional potential in pregnant wild bats, which may have implications for host physiology, immunity, and the emergence of diseases. Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
►▼ Show Figures

Figure 1

Review

Jump to: Research, Other

21 pages, 509 KB  
Review
Microbial Landscapes of the Gut–Biliary Axis: Implications for Benign and Malignant Biliary Tract Diseases
by David Meacci, Angelo Bruni, Alice Cocquio, Giuseppe Dell’Anna, Francesco Vito Mandarino, Giovanni Marasco, Paolo Cecinato, Giovanni Barbara and Rocco Maurizio Zagari
Microorganisms 2025, 13(9), 1980; https://doi.org/10.3390/microorganisms13091980 - 25 Aug 2025
Viewed by 1043
Abstract
Next-generation sequencing has overturned the dogma of biliary sterility, revealing low-biomass microbiota along the gut–biliary axis with metabolic and immunologic effects. This review synthesizes evidence on composition, function, and routes of colonization across benign and malignant disease. In cholelithiasis, Proteobacteria- and Firmicutes [...] Read more.
Next-generation sequencing has overturned the dogma of biliary sterility, revealing low-biomass microbiota along the gut–biliary axis with metabolic and immunologic effects. This review synthesizes evidence on composition, function, and routes of colonization across benign and malignant disease. In cholelithiasis, Proteobacteria- and Firmicutes-rich consortia provide β-glucuronidase, phospholipase A2, and bile salt hydrolase, driving bile supersaturation, nucleation, and recurrence. In primary sclerosing cholangitis, primary biliary cholangitis, and autoimmune hepatitis, intestinal dysbiosis and disturbed bile acid pools modulate pattern recognition receptors and bile acid signaling (FXR, TGR5), promote Th17 skewing, and injure cholangiocytes; bile frequently shows Enterococcus expansion linked to taurolithocholic acid. Distinct oncobiomes characterize cholangiocarcinoma subtypes; colibactin-positive Escherichia coli and intratumoral Gammaproteobacteria contribute to DNA damage and chemoresistance. In hepatocellular carcinoma, intratumoral microbial signatures correlate with tumor biology and prognosis. We critically appraise key methodological constraints—sampling route and post-sphincterotomy contamination, antibiotic prophylaxis, low biomass, and heterogeneous analytical pipelines—and outline a translational agenda: validated microbial/metabolomic biomarkers from bile, tissue, and stent biofilms; targeted modulation with selective antibiotics, engineered probiotics, fecal microbiota transplantation, and bile acid receptor modulators. Standardized protocols and spatial, multi-omic prospective studies are required to enable risk stratification and microbiota-informed therapeutics. Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
►▼ Show Figures

Figure 1

Other

Jump to: Research, Review

19 pages, 1345 KB  
Systematic Review
Associations Between the Gut Microbiome and Outcomes in Autologous Stem Cell Transplantation: A Systematic Review
by Ema Pitts, Brian Grainger, Dean McKenzie and Salvatore Fiorenza
Microorganisms 2025, 13(10), 2302; https://doi.org/10.3390/microorganisms13102302 - 4 Oct 2025
Viewed by 373
Abstract
Autologous stem cell transplantation (ASCT) is the standard frontline consolidation strategy in fit, eligible patients with chemosensitive multiple myeloma, and it also serves as salvage option in other haematological malignancies, such as diffuse large B cell lymphoma. Moreover, ASCT is known to disrupt [...] Read more.
Autologous stem cell transplantation (ASCT) is the standard frontline consolidation strategy in fit, eligible patients with chemosensitive multiple myeloma, and it also serves as salvage option in other haematological malignancies, such as diffuse large B cell lymphoma. Moreover, ASCT is known to disrupt the gut microbiome (GM), and the impact on clinical outcomes has been understudied. The aim of this review is to examine the associations between the GM and outcomes in patients undergoing ASCT. Using the PRISMA 2020 guidelines for systematic reviews and meta-analyses, a total of 11 articles were included in this review, comprising both observational studies (cohort studies, case–control studies) and interventional trials (randomised controlled trials). Consistent findings included a notable decrease in beneficial bacteria, including Bacteriodetes, Firmicutes and Faecalibacterium prausnitzii, which maintain gut homeostasis and modulate immune responses. Conversely, an increase in pathogenic bacteria, including Escherichia coli, Enterococcus spp. and Klebsiella spp., was observed post-transplantation. This review includes an overview of the GM following ASCT and the techniques commonly used to assess it, and highlights gaps, thereby identifying key areas for future research, although conclusions are limited by variation in sample size and reporting inconsistencies. Understanding the GM’s role in ASCT may lead to interventions that optimise patient outcomes through therapeutic manipulation of the GM. Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop