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Microorganisms
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Feature Papers in Gut Microbiota Research
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Feature Papers in Gut Microbiota Research

A topical collection in Microorganisms (ISSN 2076-2607). This collection belongs to the section "Gut Microbiota".

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Editor

Dr. Pramod Gopal

E-Mail Website
Collection Editor
1. The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 11600, Palmerston North 4442, New Zealand
2. Riddet Institute, Massey University, Palmerston North, New Zealand
Interests: human gastrointestinal microbiota; food-microbiota; health and disease
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

We are excited to announce our upcoming Topical Collection, titled “Feature Papers in Gut Microbiota Research”, which aims to gather high-quality research and review articles delving into the multifaceted role of the gut microbiota in health, wellness, and disease. We invite submissions that explore various aspects of the gut microbiota, including but not limited to its composition, function, and interactions with the host. We are particularly interested in studies that provide new insights into the mechanisms by which the gut microbiota influences metabolic processes, immune responses, neurological functions, and other physiological effects. Additionally, we welcome research on the impact of diet, probiotics, antibiotics, and other interventions on the gut microbiota. We especially encourage Editorial Board Members of Microorganisms’ Gut Microbiota Section to contribute papers reflecting the latest progress in their area of expertise. We look forward to your innovative and impactful contributions.

Suggested topics for submission include but are not limited to the following:

  • Structure, diversity, and function of the gut microbial community;
  • Gut microbiota and host interactions;
  • Gut–microbiome–brain axis;
  • Gut microbiome and metabolic health;
  • Immune modulation by the gut microbiota;
  • Gut microbiota and neurological impacts;
  • Influence of diet on gut microbiota and physiological consequences;
  • Probiotics and prebiotics effects;
  • Antibiotics and gut microbiota alterations;
  • Gut microbiota in gastrointestinal health;
  • Microbiota and cancer;
  • Gut microbiota in paediatric health and development;
  • Microbiota and healthy ageing;
  • Gut microbiota in women’s health;
  • Gut microbiota and mental health;
  • Fecal microbiota transplantation.

Dr. Pramod Gopal
Collection 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 collection 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 microbiota
  • gut–microbiome–brain axis
  • gut microbiome
  • diet
  • probiotics
  • cancer
  • fecal microbiota
  • health

Published Papers (5 papers)

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2025

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17 pages, 7998 KiB  
Article
The Effect of Apple and Pear Cultivars on In Vitro Fermentation with Human Faecal Microbiota
by Anna M. E. Hoogeveen, Christine A. Butts, Caroline C. Kim, Carel M. H. Jobsis, Shanthi G. Parkar, Halina M. Stoklosinski, Kevin H. Sutton, Patricia Davis, Duncan I. Hedderley, Jason Johnston and Pramod K. Gopal
Microorganisms 2025, 13(8), 1870; https://doi.org/10.3390/microorganisms13081870 - 11 Aug 2025
Viewed by 65
Abstract
Apples and pears are among the most popular and frequently consumed fruits worldwide. The polyphenol and dietary fibre components of these fruits are known to influence the gut microbiota and the subsequent human health outcomes. This study investigated the effects of New Zealand [...] Read more.
Apples and pears are among the most popular and frequently consumed fruits worldwide. The polyphenol and dietary fibre components of these fruits are known to influence the gut microbiota and the subsequent human health outcomes. This study investigated the effects of New Zealand grown apples and pears with differing polyphenol contents on the structure and function of the human gut microbiota. Five apple and two pear cultivars underwent in vitro human digestion and microbial fermentation. Samples taken at 0 and 18 h were analysed for changes in pH, microbial composition, and organic acid production. The change in pH after faecal fermentation was influenced by the type of fruit (apple or pear), with lower pH being observed in the apples. Significant apple or pear cultivar effects were observed for the gut microbiome and organic acid production. The apple cultivar ‘Golden Hornet’ produced the least butyrate and the greatest microbial alpha diversity, while the pear ‘PremP009’ showed greater butyrate production with increases in a butyrogenic species (Acidaminococcus intestini). Further studies are needed to investigate the effect of cultivar and type of fruit on nutrient absorption and microbial fermentation and the impact of these on human health. Full article
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14 pages, 618 KiB  
Review
Management of Neonates in the Special Care Nursery and Its Impact on the Developing Gut Microbiota: A Comprehensive Clinical Review
by Ravisha Srinivasjois, Shripada Rao and Gavin Pereira
Microorganisms 2025, 13(8), 1772; https://doi.org/10.3390/microorganisms13081772 - 29 Jul 2025
Viewed by 484
Abstract
The first few days following the birth are a vulnerable time for the neonate. Sick infants experience various interventions during their stay in the neonatal unit in order to stay alive and grow. Acquisition of gut microbes is critical for the short- and [...] Read more.
The first few days following the birth are a vulnerable time for the neonate. Sick infants experience various interventions during their stay in the neonatal unit in order to stay alive and grow. Acquisition of gut microbes is critical for the short- and long-term health of the neonate. At a time when the gut microbiome is starting to take shape, crucial interventions directed at improving the growth, development and survival of the neonate impact its development. Events prior to and after the birth of the neonate, such as maternal conditions, antibiotic exposure, type of feeds, supplemental probiotics, and neonatal intensive care environment, contribute significantly to shaping the gut microbiome over the first few weeks and maintain its healthy balance crucial for long-term health. In this comprehensive review, we address common interventions the neonate is exposed to in its journey and their impact on gut microbiome, and discuss various interventions that minimize the dysbiosis of the gut. Full article
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14 pages, 760 KiB  
Article
In Vitro Assessment of Biological and Functional Properties of Potential Probiotic Strains Isolated from Commercial and Dairy Sources
by Elmira Kelidkazeran, Meriam Bouri Yildiz and Fikrettin Sahin
Microorganisms 2025, 13(5), 970; https://doi.org/10.3390/microorganisms13050970 - 24 Apr 2025
Viewed by 708
Abstract
Probiotic species have garnered significant attention for their health benefits extending beyond gastrointestinal health. This study investigated the biological and enzymatic functions of selected probiotic species, specifically Lacticaseibacillus rhamnosus (formerly Lactobacillus rhamnosus), Lactiplantibacillus plantarum (formerly Lactobacillus plantarum), Lactobacillus acidophilus, and [...] Read more.
Probiotic species have garnered significant attention for their health benefits extending beyond gastrointestinal health. This study investigated the biological and enzymatic functions of selected probiotic species, specifically Lacticaseibacillus rhamnosus (formerly Lactobacillus rhamnosus), Lactiplantibacillus plantarum (formerly Lactobacillus plantarum), Lactobacillus acidophilus, and Lactobacillus delbrueckii, among others, through in vitro experiments. Enzymatic activities, including hemolytic, lipase, esterase, and protease functions, were evaluated. Antioxidant capacity was assessed using DPPH radical scavenging assays, while antimicrobial efficacy was tested against common pathogenic bacteria. Antibiotic-resistance patterns were analyzed to ascertain their safety for human consumption. Furthermore, simulated digestive fluid tolerance experiments were conducted to evaluate survival in the gastrointestinal tract. The findings indicate that these probiotic strains exhibit diverse functionalities beyond intestinal health, with potential roles in digestion, oxidative stress reduction, and immune support. This study provides valuable insights into the functional diversity of probiotics, suggesting their broader applications in health and nutrition. Future research should focus on in vivo validation, mechanism elucidation, and clinical studies to determine optimal dosages and strain-specific benefits. Full article
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13 pages, 2666 KiB  
Article
Intergenerational Transmission of Gut Microbiome from Infected and Non-Infected Salmonella pullorum Hens
by Qing Niu, Kaixuan Yang, Zhenxiang Zhou, Qizhong Huang and Junliang Wang
Microorganisms 2025, 13(3), 640; https://doi.org/10.3390/microorganisms13030640 - 11 Mar 2025
Viewed by 875
Abstract
Pullorum disease (PD) is one of the common infectious diseases in the poultry industry in the world. Our previous study showed that gut bacterial structure has a significant difference between positive and negative hens. However, the gut bacterial basis of intergenerational transmission of [...] Read more.
Pullorum disease (PD) is one of the common infectious diseases in the poultry industry in the world. Our previous study showed that gut bacterial structure has a significant difference between positive and negative hens. However, the gut bacterial basis of intergenerational transmission of PD continues to elude a scientific explanation. The present study carried out fecal microbiota transplantation (FMT) in chicks of a negative group, then fecal samples of the chicks in the control team (CT), Salmonella pullorum (S. pullorum)-negative transplantation team (PN) and S. pullorum-positive transplantation team (PP) were separately collected to be analyzed for microbial structure and prediction functions. Microbial diversity results revealed that there was a large difference in the gut microbiota of these three groups. Prevotella and Parasutterella with higher abundance in PN (p < 0.05) were transplanted from gut bacteria of S. pullorum-negative hens. Furthermore, the differences of the most major microbial functions (top 100) were similar in hens and chicks, including a pentose phosphate pathway and oxidative phosphorylation. The data provided a reference for exploring the intergenerational transmission and genetic mechanisms of gut microbiota associated with S. pullorum in poultry, as well as a theoretical basis for improving intestinal health through the rational regulation of microbiota-host interactions. Full article
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2024

Jump to: 2025

15 pages, 1872 KiB  
Article
Environmental Changes Driving Shifts in the Structure and Functional Properties of the Symbiotic Microbiota of Daphnia
by Minru You and Wenwu Yang
Microorganisms 2024, 12(12), 2492; https://doi.org/10.3390/microorganisms12122492 - 3 Dec 2024
Viewed by 1141
Abstract
Symbiotic microbiota significantly influence the development, physiology, and behavior of their hosts, and therefore, they are widely studied. However, very few studies have investigated the changes in symbiotic microbiota across generations. Daphnia magna originating from the Qinghai–Tibetan Plateau were cultured through seven generations [...] Read more.
Symbiotic microbiota significantly influence the development, physiology, and behavior of their hosts, and therefore, they are widely studied. However, very few studies have investigated the changes in symbiotic microbiota across generations. Daphnia magna originating from the Qinghai–Tibetan Plateau were cultured through seven generations in our laboratory, and the symbiotic microbiota of D. magna were sequenced using a 16S rRNA amplicon to analyze changes in the structure and functional properties of the symbiotic microbiota of D. magna from a harsh environment to an ideal environment. We detected substantial changes in the symbiotic microbiota of D. magna across generations. For example, the genus Nevskia, a member of the gamma-subclass Proteobacteria, had the highest abundance in the first generation (G1), followed by a decrease in abundance in the fourth (G4) and seventh (G7) generations. The gene functions of the microbiota in different generations of D. magna also changed significantly. The fourth generation was mainly rich in fatty acyl-CoA synthase, acetyl-CoA acyltransferase, phosphoglycerol phosphatase, etc. The seventh generation was mainly rich in osmotic enzyme protein and ATP-binding protein of the ABC transport system. This study confirms that the alterations in the structure and functional properties of the symbiotic microbiota of D. magna under changing environments are typical responses of D. magna to environmental changes. Full article
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