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Molecular Progression of Gut Microbiota
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Molecular Progression of Gut Microbiota

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 18027

Special Issue Editor

Dr. Emina Pustijanac

E-Mail Website
Guest Editor
Faculty of Natural Sciences, Juraj Dobrila University of Pula, 52100 Pula, Croatia
Interests: microbiology; virology; molecular biology

Special Issue Information

Dear Colleagues,

The gut microbiota, a diverse community of microorganisms in the human intestinal tract, is essential for preserving human health, contributing to various physiological functions and acting as a metabolic organ. Recent technological advancements have allowed us to identify and quantify these microbiota components, collectively called the microbiome. Techniques such as whole-genome sequencing and metagenomics/metabolomics reveal differences in gut microflora between healthy and diseased states; however, due to various external and internal factors, like genetic, dietary, and environmental factors, a one-size-fits-all “healthy” gut microbiome is impossible to define at a population level. Despite this, specific combinations of microbial species are consistently linked to certain conditions, diseases, and geographical regions.

The aim of this Special Issue is to explore the latest technologies in the analysis of the molecular gut microbiota. It seeks to investigate the significance of the normal gut microbiota's role and composition in maintaining intestinal balance. Additionally, it underscores the variations in microbial communities among individuals and their connections to intestinal dysbiosis and various diseases. Ultimately, the goal of this Special Issue is to endeavor to provide answers and potential solutions to address a very important question: how can we optimize disease management and restore a healthy state?

Dr. Emina Pustijanac
Guest Editor

Manuscript Submission Information

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Keywords

  • gut microbiota
  • microbiome
  • differences in gut microflora
  • molecular techniques
  • gut microbiota’s role and composition
  • healthy state
  • dysbiosis

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Published Papers (7 papers)

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Research

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12 pages, 1344 KiB  
Article
Investigating the Immunomodulatory Impact of Fecal Bacterial Membrane Vesicles and Their IgA Coating Patterns in Crohn’s Disease Patients
by Nader Kameli, Heike E. F. Becker, Daisy M. Jonkers, John Penders, Paul Savelkoul and Frank Stassen
Int. J. Mol. Sci. 2024, 25(23), 13194; https://doi.org/10.3390/ijms252313194 - 8 Dec 2024
Viewed by 1248
Abstract
The human intestinal tract contains trillions of bacteria that coexist in a symbiotic relationship with human cells. Imbalances in this interaction can lead to disorders such as Crohn’s disease (CD). Bacteria membrane vesicles (MVs), which are released by almost all bacteria, have been [...] Read more.
The human intestinal tract contains trillions of bacteria that coexist in a symbiotic relationship with human cells. Imbalances in this interaction can lead to disorders such as Crohn’s disease (CD). Bacteria membrane vesicles (MVs), which are released by almost all bacteria, have been demonstrated to play a crucial role in bacteria–host interactions. In this study, we assessed the physical characterizations, immunomodulatory effects, and IgA interactions of MVs derived from fecal samples of CD patients and healthy controls (HCs). MVs were isolated from the frozen fecal samples using a combination of ultrafiltration and size-exclusion chromatography. Using nanoparticle tracking analysis, we found that the MVs of the CD patients showed a significantly lower concentration compared to those of the HCs. Cryo-transmission electron microscopy revealed the larger size of the MVs in active CD (Ac-CD) compared to the MVs of remission CD (Re-CD) and HCs. Differentiated monocyte THP-1 cells released more TNF-a when exposed to MVs from the HCs compared to the CD patients. On the other hand, the MVs from the HCs and Re-CD patients but not the Ac-CD patients induced more anti-inflammatory IL-10. Intriguingly, bead-based flow cytometry analysis showed that the MVs of the HCs and Re-CD patients were more coated with IgA compared to those of the Ac-CD patients. These results suggest the potential role of MVs in the immunomodulatory impact on the pathophysiology of CD. Moreover, IgA seems to regulate these effects by direct binding, which was not the case for the Ac-CD patients. Finally, the IgA coating patterns of the MVs could be used as an additional disease biomarker, as they can clearly identify the exacerbation status of CD. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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20 pages, 3569 KiB  
Article
Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes
by Ricardo Domingo-Bretón, Federico Moroni, Socorro Toxqui-Rodríguez, Álvaro Belenguer, M. Carla Piazzon, Jaume Pérez-Sánchez and Fernando Naya-Català
Int. J. Mol. Sci. 2024, 25(23), 12603; https://doi.org/10.3390/ijms252312603 - 23 Nov 2024
Viewed by 2102
Abstract
Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all the experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into the use of different library preparation methods (standard-RAP and native barcoding-LIG), [...] Read more.
Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all the experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into the use of different library preparation methods (standard-RAP and native barcoding-LIG), primers (V3–V4, V1–V3, and V1–V9), and basecalling models (fast-FAST, high-HAC, and super-accuracy-SUP) implemented in ONT to elucidate the microbiota associated with the aquatic environment and farmed fish, including faeces, skin, and intestinal mucus. Microbial DNA from water and faeces samples could be amplified regardless of the library–primer strategy, but only with LIG and V1–V3/V1–V9 primers in the case of skin and intestine mucus. Low taxonomic assignment levels were favoured by the use of full-length V1–V9 primers, though in silico hybridisation revealed a lower number of potential matching sequences in the SILVA database, especially evident with the increase in Actinobacteriota in real datasets. SUP execution allowed for a higher median Phred quality (24) than FAST (11) and HAC (17), but its execution time (6–8 h) was higher in comparison to the other models (0.6–7 h). Altogether, we optimised the use of ONT for water- and fish-related microbial analyses, validating, for the first time, the use of the LIG strategy. We consider that LIG–V1–V9-HAC is the optimal time/cost-effective option to amplify the microbial DNA from environmental samples. However, the use of V1–V3 could help to maximise the dataset microbiome diversity, representing an alternative when long amplicon sequences become compromised by microbial DNA quality and/or high host DNA loads interfere with the PCR amplification/sequencing procedures, especially in the case of gut mucus. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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13 pages, 2267 KiB  
Article
Impacts of Different Perinatal Factors on Faecal Immune Compounds in Infants: Determination of Normal Values
by Marta Suárez, Gonzalo Solís, Laura Mantecón, Miguel Gueimonde and Silvia Arboleya
Int. J. Mol. Sci. 2024, 25(19), 10675; https://doi.org/10.3390/ijms251910675 - 3 Oct 2024
Viewed by 1172
Abstract
The gut microbiota is a key and primary stimulus for the development of a host’s immune system. The early establishment of the gut microbiota is affected by several perinatal factors but little is known about their influence on shaping normal immune development and, [...] Read more.
The gut microbiota is a key and primary stimulus for the development of a host’s immune system. The early establishment of the gut microbiota is affected by several perinatal factors but little is known about their influence on shaping normal immune development and, consequently, on the programming of future health. The analysis of different immune compounds is well-documented in serum samples; however, their presence in faecal samples has not been studied, and this information could be valuable in early life. In this context, the authors of this study aimed to both describe the immunological faecal profile of a cohort of one-month-old infants and describe the impact of different perinatal factors, exploring possible associations between immune compounds and gut microbiota in faecal samples. Clear differences in immune profile were observed between full-term and premature infants. Breastfeeding increases IgG2, IgG4, and IgA; in addition, male babies showed some increased Igs, among other observations. Overall, the findings of this study reinforce the hypothesis that microorganisms and immune compounds interact with each other in the early neonatal gut and that understanding these interactions in depth will help us comprehend the influence of the gut microbiota on short- and long-term infant health outcomes. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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16 pages, 4910 KiB  
Article
Escherichia coli Activate Extraintestinal Antibody Response and Provide Anti-Infective Immunity
by Xiang Liu, Xuanxian Peng and Hui Li
Int. J. Mol. Sci. 2024, 25(13), 7450; https://doi.org/10.3390/ijms25137450 - 7 Jul 2024
Cited by 1 | Viewed by 1752
Abstract
The effects of intestinal microflora on extraintestinal immune response by intestinal cytokines and metabolites have been documented, but whether intestinal microbes stimulate serum antibody generation is unknown. Here, serum antibodies against 69 outer membrane proteins of Escherichia coli, a dominant bacterium in [...] Read more.
The effects of intestinal microflora on extraintestinal immune response by intestinal cytokines and metabolites have been documented, but whether intestinal microbes stimulate serum antibody generation is unknown. Here, serum antibodies against 69 outer membrane proteins of Escherichia coli, a dominant bacterium in the human intestine, are detected in 141 healthy individuals of varying ages. Antibodies against E. coli outer membrane proteins are determined in all serum samples tested, and frequencies of antibodies to five outer membrane proteins (OmpA, OmpX, TsX, HlpA, and FepA) are close to 100%. Serum antibodies against E. coli outer membrane proteins are further validated by Western blot and bacterial pull-down. Moreover, the present study shows that OstA, HlpA, Tsx, NlpB, OmpC, YfcU, and OmpA provide specific immune protection against pathogenic E. coli, while HlpA and OmpA also exhibit cross-protection against Staphylococcus aureus infection. These finding indicate that intestinal E. coli activate extraintestinal antibody responses and provide anti-infective immunity. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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Review

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22 pages, 3749 KiB  
Review
Microbiota and Inflammatory Markers: A Review of Their Interplay, Clinical Implications, and Metabolic Disorders
by Emiliano Peña-Durán, Jesús Jonathan García-Galindo, Luis Daniel López-Murillo, Alfredo Huerta-Huerta, Luis Ricardo Balleza-Alejandri, Alberto Beltrán-Ramírez, Elsa Janneth Anaya-Ambriz and Daniel Osmar Suárez-Rico
Int. J. Mol. Sci. 2025, 26(4), 1773; https://doi.org/10.3390/ijms26041773 - 19 Feb 2025
Viewed by 3650
Abstract
The human microbiota, a complex ecosystem of microorganisms, plays a pivotal role in regulating host immunity and metabolism. This review investigates the interplay between microbiota and inflammatory markers, emphasizing their impact on metabolic and autoimmune disorders. Key inflammatory biomarkers, such as C-reactive protein [...] Read more.
The human microbiota, a complex ecosystem of microorganisms, plays a pivotal role in regulating host immunity and metabolism. This review investigates the interplay between microbiota and inflammatory markers, emphasizing their impact on metabolic and autoimmune disorders. Key inflammatory biomarkers, such as C-reactive protein (CRP), interleukin-6 (IL-6), lipopolysaccharides (LPS), zonulin (ZO-1), and netrin-1 (Ntn1), are discussed in the context of intestinal barrier integrity and chronic inflammation. Dysbiosis, characterized by alterations in microbial composition and function, directly modulates the levels and activity of these biomarkers, exacerbating inflammatory responses and compromising epithelial barriers. The disruption of microbiota is further correlated with increased intestinal permeability and chronic inflammation, serving as a precursor to conditions like type 2 diabetes (T2D), obesity, and non-alcoholic fatty liver disease. Additionally, this review examines therapeutic strategies, including probiotics and prebiotics, designed to restore microbial balance, mitigate inflammation, and enhance metabolic homeostasis. Emerging evidence positions microbiota-targeted interventions as critical components in the advancement of precision medicine, offering promising avenues for diagnosing and treating inflammatory and metabolic disorders. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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16 pages, 1035 KiB  
Review
Study of Microbiota Associated to Early Tumors Can Shed Light on Colon Carcinogenesis
by Anna Aspesi, Marta La Vecchia, Gloria Sala, Emilia Ghelardi and Irma Dianzani
Int. J. Mol. Sci. 2024, 25(24), 13308; https://doi.org/10.3390/ijms252413308 - 11 Dec 2024
Cited by 1 | Viewed by 1239
Abstract
An increasingly important role for gut microbiota in the initiation and progression of colorectal cancer (CRC) has been described. Even in the early stages of transformation, i.e., colorectal adenomas, changes in gut microbiota composition have been observed, and several bacterial species, such as [...] Read more.
An increasingly important role for gut microbiota in the initiation and progression of colorectal cancer (CRC) has been described. Even in the early stages of transformation, i.e., colorectal adenomas, changes in gut microbiota composition have been observed, and several bacterial species, such as pks+ Escherichia coli and enterotoxigenic Bacteroides fragilis, have been proposed to drive colon tumorigenesis. In recent years, several strategies have been developed to study mucosa-associated microbiota (MAM), which is more closely associated with CRC development than lumen-associated microbiota (LAM) derived from fecal samples. This review summarizes the state of the art about the oncogenic actions of gut bacteria and compares the different sampling strategies to collect intestinal microbiota (feces, biopsies, swabs, brushes, and washing aspirates). In particular, this article recapitulates the current knowledge on MAM in colorectal adenomas and serrated polyps, since studying the intestinal microbiota associated with early-stage tumors can elucidate the molecular mechanisms underpinning CRC carcinogenesis. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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20 pages, 2625 KiB  
Review
Intestinal Microbiota Interventions to Enhance Athletic Performance—A Review
by Bharati Kadamb Patel, Kadamb Haribhai Patel, Chuen Neng Lee and Shabbir Moochhala
Int. J. Mol. Sci. 2024, 25(18), 10076; https://doi.org/10.3390/ijms251810076 - 19 Sep 2024
Cited by 3 | Viewed by 5620
Abstract
Recent years have witnessed an uptick in research highlighting the gut microbiota’s role as a primary determinant of athletes’ health, which has piqued interest in the hypothesis that it correlates with athletes’ physical performance. Athletes’ physical performances could be impacted by the metabolic [...] Read more.
Recent years have witnessed an uptick in research highlighting the gut microbiota’s role as a primary determinant of athletes’ health, which has piqued interest in the hypothesis that it correlates with athletes’ physical performance. Athletes’ physical performances could be impacted by the metabolic activity of the assortment of microbes found in their gut. Intestinal microbiota impacts multiple facets of an athlete’s physiology, including immune response, gut membrane integrity, macro- and micronutrient absorption, muscle endurance, and the gut–brain axis. Several physiological variables govern the gut microbiota; hence, an intricately tailored and complex framework must be implemented to comprehend the performance–microbiota interaction. Emerging evidence underscores the intricate relationship between the gut microbiome and physical fitness, revealing that athletes who engage in regular physical activity exhibit a richer diversity of gut microbes, particularly within the Firmicutes phylum, e.g., Ruminococcaceae genera, compared to their sedentary counterparts. In elite sport, it is challenging to implement an unconventional strategy whilst simultaneously aiding an athlete to accomplish feasible, balanced development. This review compiles the research on the effects of gut microbiota modulation on performance in sports and illustrates how different supplementation strategies for gut microbiota have the ability to improve athletic performance by enhancing physical capacities. In addition to promoting athletes’ overall health, this study evaluates the existing literature in an effort to shed light on how interventions involving the gut microbiota can dramatically improve performance on the field. The findings should inform both theoretical and practical developments in the fields of sports nutrition and training. Full article
(This article belongs to the Special Issue Molecular Progression of Gut Microbiota)
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