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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: 20 June 2026 | Viewed by 12329

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Special Issue Editor

Prof. Dr. Andreas Burkovski

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Guest Editor

Microbiology Division, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
Interests: corynebacteria; host–pathogen interaction; nitrogen control; regulatory networks; secretome analyses; toxins
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Special Issue Information

Dear Colleagues,

Over recent decades microbiome research has undergone rapid growth, especially due to the development and availability of cost-effective next-generation sequencing techniques. Fascinating insights into the influence of microbial communities on human health have already been made. Nevertheless, our understanding of the various and complex interactions of microbes and humans is still limited. Therefore, it is the dedicated aim of this Special Issue to expand our knowledge on this fascinating field of research and to collect the latest studies on human microbiomes. Research articles, short communications, and reviews dealing with the question of how these microbiomes impact development, health, and disease, as well as studies on the development and application of new tools and approaches to study microbiomes in human health and disease, are welcome.

Prof. Dr. Andreas Burkovski
Guest Editor

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Keywords

microbiome
dysbiosis
commensal bacteria
pathobiont
metabolites
immune modulation
nutrient metabolism
barrier function
health and disease

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Published Papers (7 papers)

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Research

Jump to: Review, Other

19 pages, 1552 KB

Open AccessArticle

Minimal Association Between Immunoglobulin A Coating and Gut Microbiota Alterations Induced by High-Fat Diets with Distinct Fatty Acid Compositions

by Mao Teraoka, Naoki Nishino, Tianyang Wang, Kuiyi Chen and Takeshi Tsuruta

Int. J. Mol. Sci. 2026, 27(6), 2645; https://doi.org/10.3390/ijms27062645 - 13 Mar 2026

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Abstract

High-fat diets (HFDs) containing dietary fats with different fatty acid (FA) compositions alter gut microbiota composition in a fat-source-dependent manner. Immunoglobulin A (IgA) and unabsorbed lipids in the distal gut are potential regulators of the gut microbiota. However, their roles in mediating gut microbiota alterations induced by dietary fats with different FA compositions remain unclear. This study aims to examine the associations of these two factors with fat-source-dependent gut microbiota alterations. BALB/c mice were fed a normal diet, a high-lard diet, a high-olive oil diet, or a high-soybean oil diet for 27 weeks. Fecal samples were collected to assess microbiota composition, the IgA coating index (ICI)—which quantifies the extent of IgA coating on gut microbiota—and fecal fatty acid concentrations. At the phylum level, the concentration of fecal total long-chain fatty acids (LCFAs) was positively correlated with the relative abundance (RA) of Bacillota and negatively correlated with that of Bacteroidota. In addition, a trend toward a positive association between the RA and the ICI was observed for Bacillota but not for Bacteroidota. At the genus level, the RAs of 12 taxa were positively correlated with fecal LCFA concentrations, whereas those of 6 taxa were negatively correlated. Although the RAs of most taxa appeared to be influenced by unabsorbed lipids and additional factors, only four Bacillota genera exhibited a positive correlation between the RA and the ICI. Our observations suggest that IgA coating of the gut microbiota may have a minimal association with fat-source-specific alterations in gut microbiota composition during HFD intake. Full article

(This article belongs to the Special Issue Microbiomes in Human Health and Disease)

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Review

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17 pages, 587 KB

Open AccessReview

Impact of Gut Microbiota on Bone Metabolism—Present Concepts and Therapeutic Implications

by Marta Toboła and Alina Kuryłowicz

Int. J. Mol. Sci. 2026, 27(9), 3865; https://doi.org/10.3390/ijms27093865 (registering DOI) - 27 Apr 2026

Abstract

The gut microbiota plays a multifaceted role in calcium homeostasis and bone metabolism —acting through metabolic, immunological, and hormonal pathways that collectively constitute the gut–bone axis. The microbiota influences calcium bioavailability through several overlapping mechanisms that act in the intestine. Moreover, microbial fermentation products may directly impact the osteoblast–osteoclast interplay and, by modulating immune and endocrine functions, are crucial for bone metabolism. A healthy microbiota supports bone formation; however, intestinal dysbiosis may impair bone structure and function. This narrative review aims to present pathways linking the gut microbiota to bone metabolism, both in health and disease. First, we will discuss the influence of gut microbiota on calcium absorption. We will then outline the role that microbial metabolites, such as bile acids and short-chain fatty acids (SCFAs), play in regulating bone structure and function. In the following section, we will discuss the role of the microbiota in the immunological and hormonal modulation of bone metabolism. Finally, we will discuss how dysbiosis affects bone and how therapeutic interventions, such as probiotics, prebiotics, and postbiotics, may influence bone tissue quality. Full article

(This article belongs to the Special Issue Microbiomes in Human Health and Disease)

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33 pages, 828 KB

Open AccessReview

From Probiotics to Postbiotics—An Update on Their Biotherapeutic Potential and the Emerging Strategies in Human Health

by Nicoleta Maricica Maftei, Lenuța Ambrose, Elena Dogaru, Răducu Răileanu, Oana Laura Mierlan, Octavian Amariței, Ana Ramos-Villarroel, Gabriela Isabela Răuță Verga, Tudor Vladimir Gurău and Gabriela Gurău

Int. J. Mol. Sci. 2026, 27(5), 2218; https://doi.org/10.3390/ijms27052218 - 26 Feb 2026

Viewed by 1488

Abstract

Probiotics and postbiotics have gained increasing attention in microbiome research due to their potential roles in maintaining gut homeostasis and supporting human health. While probiotics are defined as live microorganisms that confer health benefits when administered in adequate amounts, postbiotics represent preparations of inanimate microorganisms and/or their components that also exert biological effects on the host. This narrative review provides an updated overview of the current knowledge on probiotics and postbiotics, with a particular focus on their mechanisms of action, production strategies, and emerging applications in human health. The review discusses key mechanisms through which probiotics and postbiotics interact with the host, including modulation of the gut microbiota, enhancement of epithelial barrier integrity, immune system regulation, metabolic modulation, and systemic signaling pathways. Advances in production technologies, ranging from conventional fermentation to innovative inactivation and stabilization approaches, are also examined, alongside challenges related to yield optimization, stability, safety, and standardization. Although a growing body of evidence suggests potential benefits of probiotics and postbiotics in metabolic, inflammatory, gastrointestinal, and immune-related conditions, much of the available data is derived from preclinical studies or small-scale clinical trials. Consequently, their clinical efficacy, optimal dosing, and long-term safety require further validation. By integrating current findings and highlighting existing gaps in the literature, this review aims to clarify the therapeutic potential of probiotics and postbiotics and to support the development of more robust, evidence-based strategies for their application in functional foods, supplements, and future biotherapeutic interventions. Full article

(This article belongs to the Special Issue Microbiomes in Human Health and Disease)

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13 pages, 560 KB

Open AccessReview

Dopamine and the Gut Microbiota: Interactions Within the Microbiota–Gut–Brain Axis and Therapeutic Perspectives

by Aurelia Cristiana Barbu, Smaranda Stoleru, Aurelian Zugravu, Elena Poenaru, Adrian Dragomir, Mihnea Costescu, Sorina Maria Aurelian, Yara Shhab, Clara Maria Stoleru, Oana Andreia Coman and Ion Fulga

Int. J. Mol. Sci. 2026, 27(1), 271; https://doi.org/10.3390/ijms27010271 - 26 Dec 2025

Cited by 2 | Viewed by 2112

Abstract

The microbiota–gut–brain axis (MGBA) comprises a complex bidirectional communication network integrating neural, immune, metabolic, and endocrine pathways. Dopamine, traditionally viewed as a central neurotransmitter, also plays essential roles in the gastrointestinal (GI) tract, where it regulates motility, secretion, barrier homeostasis, and mucosal immunity. Growing evidence indicates that the gut microbiota significantly contributes to intestinal dopamine metabolism through specialized enzymatic pathways, particularly tyrosine decarboxylase in Enterococcus species and catechol dehydroxylase in Eggerthella species. These microbial reactions compete with host processes, alter dopaminergic tone, and degrade orally administered levodopa (L-DOPA), providing a mechanistic explanation for the variability in treatment response in Parkinson’s disease (PD). Beyond PD, microbially mediated alterations in dopaminergic signaling have been implicated in mood disorders, neurodevelopmental conditions, metabolic dysfunction, and immune-mediated diseases. This review synthesizes current mechanistic and translational evidence on the dopamine–microbiota interface, outlines microbial pathways shaping dopaminergic activity, and highlights therapeutic opportunities including microbiota modulation, dietary strategies, fecal microbiota transplantation, and targeted inhibitors of microbial dopamine metabolism. Understanding this interface offers a foundation for developing personalized approaches in neurogastroenterology and neuromodulatory therapies. Full article

(This article belongs to the Special Issue Microbiomes in Human Health and Disease)

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15 pages, 625 KB

Open AccessReview

Akkermansia muciniphila in Metabolic Disease: Far from Perfect

by Oana Laura Mierlan, Camelia Busila, Octavian Amaritei, Dogaru Elena, Cosmin Raducu Raileanu, Nicoleta-Maricica Maftei, Madalina Nicoleta Matei and Gabriela Gurau

Int. J. Mol. Sci. 2025, 26(23), 11602; https://doi.org/10.3390/ijms262311602 - 29 Nov 2025

Cited by 5 | Viewed by 4258

Abstract

The root of metabolic disease lies in the gastrointestinal tract, where nutrient absorption occurs. Within this environment, a diverse community of microorganisms exerts effects that extend beyond the intestinal barrier. Akkermansia muciniphila (A. muciniphila), one such bacterium, has been associated with enhanced intestinal integrity, reduced intestinal inflammation, weight loss, and improved insulin sensitivity, mediated through mucus fermentation, production of short-chain fatty acids (SCFAs), bacterial proteins, and extracellular vesicles (EVs). Research in this field is promising, yet far from perfect. Its clinical applicability remains limited by factors such as strain variability, scarcity of human intervention studies, and the lack of established causality. While associations have been consistently observed in both rodent and human studies, causality has thus far been demonstrated only in animal models. This issue is of critical importance, as metabolic disease remains highly prevalent, carries systemic consequences, and imposes a substantial burden on healthcare systems, underscoring the urgent need for alternative therapeutic strategies. The aim of this narrative review is to synthesize current knowledge on A. muciniphila and to highlight the key limitations consistently reported in the literature. By addressing these factors, the review seeks to provide realistic perspectives on its therapeutic potential and to outline directions for future research. Full article

(This article belongs to the Special Issue Microbiomes in Human Health and Disease)

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20 pages, 1276 KB

Open AccessReview

The Urinary Microbiota and the Gut–Bladder Axis in Bladder Cancer

by Usman Akhtar Butt and Daniela De Biase

Int. J. Mol. Sci. 2025, 26(21), 10558; https://doi.org/10.3390/ijms262110558 - 30 Oct 2025

Cited by 3 | Viewed by 2475 | Correction

Abstract

The human bladder hosts a resident, low-biomass microbial community (urobiota) that has only become the subject of intense investigation in the last 15 years. The advantages that the urobiota may confer to the bladder, in contrast to the microbiota of other mucosal sites, remain to be elucidated. Alterations in the urobiota have been associated with various pathological urogenital conditions, including urinary tract infections (UTIs) and recurrent UTIs. A potential link between bladder cancer (BC), the ninth most common human cancer by incidence worldwide, and a dysbiotic urobiota is still unclear and represents an emerging field of study. In this review, we focus on recent studies that not only analyzed the urobiota of BC patients using urine specimens to identify biomarkers and microbial signatures of the disease, but also monitored therapeutic responses to therapies. We also discuss novel techniques of culturing, such as culturomics, animal models of BC, and 3D organotypic models. Furthermore, we review studies on the gut–bladder axis which, though still limited, already suggest that diet- and gut-derived bacterial metabolites can influence BC progression and individual responses to therapy. Full article

(This article belongs to the Special Issue Microbiomes in Human Health and Disease)

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