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Microorganisms
Special Issues
Gut Microbiome in Homeostasis and Disease, 3rd Edition
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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 112

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

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Published Papers (1 paper)

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Research

18 pages, 3495 KiB  
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
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)
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