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Search Results (298)

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22 pages, 1850 KB  
Review
Memory in Misfire: The Gut Microbiome-Trained Immunity Circuit in Inflammatory Bowel Diseases
by Binbin Yang, Jiacheng Wu, Xiaohua Hou, Tao Bai and Shi Liu
Int. J. Mol. Sci. 2025, 26(19), 9663; https://doi.org/10.3390/ijms26199663 - 3 Oct 2025
Abstract
Inflammatory bowel disease (IBD) demonstrates chronic relapsing inflammation extending beyond adaptive immunity dysfunction. “Trained immunity”—the reprogramming of innate immune memory in myeloid cells and hematopoietic progenitors—maintains intestinal inflammation; however, the mechanism by which gut microbiome orchestration determines protective versus pathological outcomes remains unclear. [...] Read more.
Inflammatory bowel disease (IBD) demonstrates chronic relapsing inflammation extending beyond adaptive immunity dysfunction. “Trained immunity”—the reprogramming of innate immune memory in myeloid cells and hematopoietic progenitors—maintains intestinal inflammation; however, the mechanism by which gut microbiome orchestration determines protective versus pathological outcomes remains unclear. Microbial metabolites demonstrate context-dependent dual effects along the gut–bone marrow axis. Short-chain fatty acids typically induce tolerogenic immune memory, whereas metabolites like succinate and polyamines exhibit dual roles: promoting inflammation in certain contexts while enhancing barrier integrity in others, influenced by cell-specific receptors and microenvironmental factors. Interventions include precision probiotics and postbiotics delivering specific metabolites, fecal microbiota transplantation addressing dysbiotic trained immunity, targeted metabolite supplementation, and pharmacologic reprogramming of pathological myeloid training states. Patient stratification based on microbiome composition and host genetics enhances therapeutic precision. Future research requires integration of non-coding RNAs regulating trained immunity, microbiome–immune–neuronal axis interactions, and host genetic variants modulating microbiome–immunity crosstalk. Priorities include developing companion diagnostics, establishing regulatory frameworks for microbiome therapeutics, and defining mechanistic switches for personalized interventions. Full article
(This article belongs to the Section Molecular Immunology)
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27 pages, 930 KB  
Review
Gut Permeability and Microbiota in Parkinson’s Disease: Mechanistic Insights and Experimental Therapeutic Strategies
by Yicheng Liang, Yuhang Zhao, Alessio Fasano and Chien-Wen Su
Int. J. Mol. Sci. 2025, 26(19), 9593; https://doi.org/10.3390/ijms26199593 - 1 Oct 2025
Abstract
Globally, Parkinson’s disease (PD) is the neurodegenerative condition with the most rapidly increasing prevalence, and a growing body of evidence associates its pathology with impairments in the gut–brain axis. Traditionally viewed as a disease marked by the loss of dopaminergic neurons, emerging evidence [...] Read more.
Globally, Parkinson’s disease (PD) is the neurodegenerative condition with the most rapidly increasing prevalence, and a growing body of evidence associates its pathology with impairments in the gut–brain axis. Traditionally viewed as a disease marked by the loss of dopaminergic neurons, emerging evidence emphasizes that chronic neuroinflammation is a driver of neurodegeneration, with gut-originating inflammation playing a crucial role. Increased intestinal permeability, often called “leaky gut,” allows harmful substances, toxins, and misfolded α-synuclein into the systemic circulation, potentially exacerbating neuroinflammation and spreading α-synuclein pathology to the brain through the vagus nerve or compromised blood–brain barrier (BBB). This review synthesizes current insights into the relationship between gut health and PD, emphasizing the importance of gut permeability in disrupting intestinal barrier function. This paper highlights innovative therapeutic approaches, particularly personalized therapies involving gut microbiome engineering, as promising strategies for restoring gut integrity and improving neurological outcomes. Modulating specific gut bacteria to enhance the synthesis of certain metabolites, notably short-chain fatty acids (SCFAs), represents a promising strategy for reducing inflammatory responses and decelerating neurodegeneration in Parkinson’s disease. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
14 pages, 2164 KB  
Article
Triacetin and a Mushroom Blend Restore Butyrate Production by IBS Microbiomes Ex Vivo, Thus Promoting Barrier Integrity
by Pieter Van den Abbeele, Jonas Poppe, Aurélien Baudot and Lam Dai Vu
Int. J. Mol. Sci. 2025, 26(19), 9388; https://doi.org/10.3390/ijms26199388 - 25 Sep 2025
Abstract
Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder, characterized by abdominal pain, altered bowel habits (diarrhea and/or constipation) and a dysbiosis of the gut microbiome. This dysbiosis is difficult to restore via fiber supplementation, which typically promotes gas production, potentially worsening IBS [...] Read more.
Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder, characterized by abdominal pain, altered bowel habits (diarrhea and/or constipation) and a dysbiosis of the gut microbiome. This dysbiosis is difficult to restore via fiber supplementation, which typically promotes gas production, potentially worsening IBS symptoms. We therefore studied how two novel products, triacetin (TA; REBiome™) and a mushroom blend (MB; Hōlistiq™), modulate the microbiome of IBS subjects (n = 8) using the ex vivo SIFR® (Systemic Intestinal Fermentation Research) technology combined with a co-culture of epithelial/immune (Caco-2/THP-1) cells. First, the IBS microbiomes revealed large interpersonal variability and an IBS-associated dysbiosis. TA increased the beneficial metabolites acetate and butyrate (~Anaerobutyricum soehngenii, Mediterraneibacter_A butyricigenes, Faecalibacterium prausnitzii). Moreover, MB stimulated a wide range of gut microbes and additionally promoted propionate. Despite more strongly increasing total short-chain fatty acid (SCFA) levels, TA induced significantly less gas production than MB. Mechanistically, acetate with TA was derived from hydrolysis, a process that indeed does not induce gas production. Notably, both TA and MB enhanced gut barrier integrity (transepithelial electrical TEER), which is related to lower symptom severity in IBS patients. Overall, our findings highlight the product-specific microbiome modulation and potential of MB, TA or combinations thereof as dietary interventions for managing IBS symptom severity. Full article
(This article belongs to the Collection Feature Papers in Bioactives and Nutraceuticals)
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52 pages, 1456 KB  
Review
The Gut Microbiome in Enteric Viral Infections: Underlying Mechanisms and Therapeutic Approaches
by Alejandro Borrego-Ruiz and Juan J. Borrego
Microorganisms 2025, 13(10), 2247; https://doi.org/10.3390/microorganisms13102247 - 25 Sep 2025
Abstract
Despite growing recognition of the role of the gut microbiome in host health and in modulating pathogen activity, the dynamic and reciprocal relationship between enteric viruses and the gut microbial ecosystem remains insufficiently defined and requires further exploration. This comprehensive review examines the [...] Read more.
Despite growing recognition of the role of the gut microbiome in host health and in modulating pathogen activity, the dynamic and reciprocal relationship between enteric viruses and the gut microbial ecosystem remains insufficiently defined and requires further exploration. This comprehensive review examines the bidirectional interplay between the gut microbiome and enteric viral infections by addressing (i) viruses associated with gastrointestinal alterations, (ii) how enteric viral infections alter the composition and function of the gut microbiome, (iii) how the gut microbiome modulates viral infectivity and host susceptibility, and (iv) current microbial-based approaches for preventing or treating enteric viral infections. Gastrointestinal viral infections induce gut microbiome dysbiosis, marked by reductions in beneficial bacteria and increases in potentially pathogenic populations. Specific gut microorganisms can modulate host susceptibility, with certain bacterial genera increasing or decreasing infection risk and disease severity. Pattern recognition receptors in the intestinal epithelium detect microbial signals and trigger antimicrobial peptides, mucus, and interferon responses to control viral replication while maintaining tolerance to commensal bacteria. The gut microbiome can indirectly facilitate viral infections by creating a tolerogenic environment, suppressing antiviral antibody responses, and modulating interferon signaling, or directly enhance viral replication by stabilizing virions, promoting host cell attachment, and facilitating coinfection and viral recombination. In turn, commensal gut bacteria can inhibit viral entry, enhance host antiviral responses, and strengthen mucosal barrier function, contributing to protection against gastrointestinal viral infections. Probiotics and fecal microbiota transplantation constitute potential microbial-based therapeutics that support antiviral defenses, preserve epithelial integrity, and restore microbial balance. In conclusion, the role of the gut microbiome in modulating enteric viral infections represents a promising area of future investigation. Therefore, integrating microbiome insights with virology and immunology could enable predictive and personalized strategies for prevention and treatment. Full article
(This article belongs to the Special Issue Microbiota and Gastrointestinal Diseases)
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20 pages, 1651 KB  
Review
Emerging Roles of the Gut Microbiome in Musculoskeletal Injury and Repair
by Joseph L. Roberts and Connor C. Park
Microorganisms 2025, 13(9), 2193; https://doi.org/10.3390/microorganisms13092193 - 19 Sep 2025
Viewed by 368
Abstract
Over the past decade, significant attention has been directed toward understanding the role of the gut microbiome in health and disease. The gut microbiota, comprising a complex and diverse community of microorganisms, has been linked to numerous conditions, including metabolic disorders, gastrointestinal diseases, [...] Read more.
Over the past decade, significant attention has been directed toward understanding the role of the gut microbiome in health and disease. The gut microbiota, comprising a complex and diverse community of microorganisms, has been linked to numerous conditions, including metabolic disorders, gastrointestinal diseases, and inflammatory or autoimmune conditions. Recently, a growing body of evidence has revealed a compelling relationship between gut microbiota composition and musculoskeletal injury recovery, highlighting its potential as a novel therapeutic target. Musculoskeletal injuries, including fractures, post-traumatic osteoarthritis, and tendon or ligament injuries, commonly lead to changes in the community structure of the gut microbiota, intestinal permeability, and systemic inflammation, processes known to negatively influence tissue repair. Preclinical studies demonstrate that microbiota-targeted interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, effectively restore gut barrier integrity, modulate inflammation, and normalize gut-derived metabolite profiles. Despite these promising findings, critical gaps remain in translating these effects into clinical practice, particularly regarding the mechanisms linking specific microbiota changes to improved musculoskeletal healing outcomes. Future research incorporating rigorous clinical trials, multi-omics analyses, and advanced predictive tools, including artificial intelligence and microbiome-informed digital twins, is urgently needed to fully harness the therapeutic potential of microbiome-based interventions in musculoskeletal injury recovery. This narrative review provides insights into our evolving understanding of the relationship between the gut microbiota and musculoskeletal injury and explores the potential of gut microbiota-targeted therapies for improved healing outcomes. Full article
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14 pages, 2248 KB  
Article
Region-Specific Gut Microbiome Variation Between Changle Geese and Yellow-Feathered Broilers: Correlations with Growth and Intestinal Development
by Dingcheng Ye, Jianxing Qiu, Zitao Fan, Luwei Zhu, Chengyong Lv and Pingting Guo
Microorganisms 2025, 13(9), 2145; https://doi.org/10.3390/microorganisms13092145 - 13 Sep 2025
Viewed by 350
Abstract
This study comparatively analyzed the spatial heterogeneity of the gut microbiome across gastrointestinal segments in Changle geese versus yellow-feathered broilers to discover their links with growth and intestinal development. Twelve 63-day-old male yellow-feathered broilers and twelve 70-day-old male Changle geese were selected. Body [...] Read more.
This study comparatively analyzed the spatial heterogeneity of the gut microbiome across gastrointestinal segments in Changle geese versus yellow-feathered broilers to discover their links with growth and intestinal development. Twelve 63-day-old male yellow-feathered broilers and twelve 70-day-old male Changle geese were selected. Body weight (BW), slaughter weight (SW), absolute lengths of the small intestine (LSI) and cecum (LC), and their relative lengths normalized to body size (RLSI/RLC) were measured. Additionally, 16S rDNA sequencing of crop, proventriculus, gizzard, jejunum, cecum, and rectum microbiota was conducted to assess microbial diversity, composition, and its correlation with phenotypes. Results demonstrated higher BW, SW, LSI, LC and lower RLSI and RLC in geese versus broilers (p < 0.001). Alpha diversity analysis revealed lower microbial richness and diversity in broilers across most gastrointestinal segments (p < 0.05), while beta diversity analysis confirmed distinct community structures between two species (p = 0.001). Firmicutes dominated broiler gut microbiota (94.49%), whereas geese exhibited greater phylum-level diversity (p < 0.05). Random forestry analysis identified Top 15 core Amplicon Sequencing Variants in both the cecum and rectum, with ASV12260 (unclassified Lachnospiraceae) and ASV12412 (uncultured Faecalibacterium sp.) as key biomarkers. Correlation analyses found 21 phenotype-related ASVs (p < 0.05). Specially, two Lactobacillus ingluviei strains showed negatively correlated with LSI and RLSI in the chicken foregut (p < 0.05). And two Gallibacterium anatis strains were associated with RLSI, with one strain also showing an inverse correlation with LSI in the goose foregut (p < 0.05). Interestingly, one Peptococcus strain was negatively correlated with BW and SW, while the other was inversely associated with LC and RLC in the goose hindgut (p < 0.05). These findings provide insights into species-specific distribution patterns of gut microbiota across poultry species and their correlation with growth performance and intestinal development, developing a theoretical foundation for advancing avian digestive physiology research and optimizing feeding strategies. Full article
(This article belongs to the Section Veterinary Microbiology)
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25 pages, 957 KB  
Review
The Role of Probiotics in Healing Burns and Skin Wounds; An Integrative Approach in the Context of Regenerative Medicine
by Lenuta Ambrose, Ciprian Adrian Dinu, Gabriela Gurau, Nicoleta-Maricica Maftei, Madalina Nicoleta Matei, Maria-Andrada Hincu, Marius Radu and Mihaela-Cezarina Mehedinti
Life 2025, 15(9), 1434; https://doi.org/10.3390/life15091434 - 12 Sep 2025
Cited by 1 | Viewed by 679
Abstract
In the context of thermal injury, local tissue integrity and systemic homeostasis are compromised, often resulting in delayed healing, infections, and disturbances of the skin and intestinal microbial balance. Despite several reviews addressing probiotics in wound healing, none has specifically focused on their [...] Read more.
In the context of thermal injury, local tissue integrity and systemic homeostasis are compromised, often resulting in delayed healing, infections, and disturbances of the skin and intestinal microbial balance. Despite several reviews addressing probiotics in wound healing, none has specifically focused on their role in thermal injuries and burn-associated pathophysiology. This review uniquely integrates evidence on the gut–skin axis, postbiotic innovations, and regenerative perspectives tailored to burn care. We conducted a critical synthesis of recent preclinical and clinical trials evaluating the use of probiotics and their derivatives to promote tissue regeneration following burn injury. Previous reviews have addressed probiotics in general wound repair, but the present synthesis advances the field by bridging mechanistic insights (immune modulation, angiogenesis, microbiome restoration) with translational evidence in burn patients, offering a framework for personalized regenerative approaches. Based on a structured review of the literature—including in vitro models, animal experiments, and randomized trials with topical, enteral, and systemic administration of probiotic—we identified four main mechanisms of action: modulation of the immune response by balancing cytokines and polarization of T lymphocytes; stimulation of tissue repair by increasing the proliferation of keratinocytes and fibroblasts, increased collagen synthesis, and induction of angiogenesis; direct antimicrobial activity against biofilms and multiresistant pathogens; and the restoration of eubiosis with the improvement of the function of epithelial barriers. While these findings endorse the adjunctive use of probiotics in burn management, large multicenter trials are required to standardize strains, dosages, and formulations before their routine clinical adoption. Full article
(This article belongs to the Section Medical Research)
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16 pages, 1894 KB  
Article
Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data
by Clarissa Reginato Taufer, Juliana da Silva and Pabulo Henrique Rampelotto
Microorganisms 2025, 13(9), 2061; https://doi.org/10.3390/microorganisms13092061 - 4 Sep 2025
Viewed by 511
Abstract
The gut microbiome has emerged as a potential modulator of COVID-19 severity, and there is particular interest in the Lachnospiraceae family due to its role in maintaining gut homeostasis. This study presents a comprehensive meta-analysis of microbiome datasets from multiple investigations focused on [...] Read more.
The gut microbiome has emerged as a potential modulator of COVID-19 severity, and there is particular interest in the Lachnospiraceae family due to its role in maintaining gut homeostasis. This study presents a comprehensive meta-analysis of microbiome datasets from multiple investigations focused on gut microbiota across various stages of COVID-19. We used a standardized bioinformatics pipeline based on Mothur v.1.47.0 and the SILVA v.138 reference database to analyze 16S rRNA gene sequencing data targeting the V3-V4 regions. Our findings reveal consistent patterns of depletion in key Lachnospiraceae genera, particularly Lachnospira and Roseburia, correlating with increased COVID-19 severity. Complex patterns were observed for Blautia and Coprococcus, suggesting strain-specific responses to disease states. In addition, several unclassified Lachnospiraceae taxa showed differential abundance across severity levels, indicating the need for further characterization of these potentially important bacteria. These results provide robust evidence for the association between specific Lachnospiraceae genera and COVID-19 severity. The observed microbial shifts suggest potential mechanisms by which gut dysbiosis may contribute to COVID-19 pathogenesis, including reduced production of beneficial metabolites and compromised intestinal barrier function. These findings highlight the potential of Lachnospiraceae genera as biomarkers for COVID-19 severity and suggest avenues for developing targeted probiotic interventions in COVID-19 management. Full article
(This article belongs to the Collection Microbiomes in Health and Disease)
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17 pages, 422 KB  
Review
Gut Microbiome and Intestinal Colonization with Multidrug-Resistant Strains of Enterobacterales: An Interplay Between Microbial Communities
by Béla Kocsis, Dóra Szabó and László Sipos
Antibiotics 2025, 14(9), 890; https://doi.org/10.3390/antibiotics14090890 - 3 Sep 2025
Viewed by 611
Abstract
Background: The intestinal tract is a host to a high number of diverse bacteria, and the presence of multidrug-resistant (MDR) Enterobacterales strains acts as a reservoir and a source of infection. The interactions between the intestinal microbiome and colonizer Enterobacterales strains influence [...] Read more.
Background: The intestinal tract is a host to a high number of diverse bacteria, and the presence of multidrug-resistant (MDR) Enterobacterales strains acts as a reservoir and a source of infection. The interactions between the intestinal microbiome and colonizer Enterobacterales strains influence long-lasting colonization. Aims: In this narrative review, we summarize available data about the intestinal colonization of MDR Enterobacterales strains and correlations between colonization and the intestinal microbiome. Results: Several endogenous and exogenous factors influence the intestinal colonization of MDR Enterobacterales strains. On the gut microbiome level, the intestinal microbial community is composed of the Lachnospiraceae family (e.g., Lachnoclostridium, Agathobacter, Roseburia, Tyzzerella), which indicates a protective role against colonizer MDR Enterobacterales strains; by contrast, a high abundance of Enterobacterales correlates with the colonization of MDR Enterobacterales strains. In specific patient groups, striking differences in microbiome composition can be detected. Among hematopoietic stem-cell-transplanted patients colonized by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, a greater abundance of Bifidobacterium, Blautia, Clostridium, Coprococcus, L-Ruminococcus, Mogibacteriaceae, Peptostreptococceae and Oscillospira was observed compared to patients not colonized by ESBL-producing strains, who had a greater abundance of Actinomycetales. In liver transplant patients, a reduction in the alpha-diversity of the intestinal microbiome in fecal samples correlates with the carriage of MDR Enterobacterales. Conclusions: Intestinal colonization with MDR Enterobacterales is a multifactorial process that involves the MDR strain (e.g., its plasmids, fimbria), host and mucosal factors (e.g., IgA and defensin) and exogenous factors (e.g., use of antibiotics, hospitalization). On the gut microbiome level, the Lachnospiraceae family is dominant among intestines not colonized by MDR strains, but a high abundance of Enterobacterales was correlated with colonization with MDR Enterobacterales strains. Full article
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21 pages, 4193 KB  
Article
Comparison of Bacterial Community in the Jejunum, Ileum and Cecum of Suckling Lambs During Different Growth Stages
by Mengrong Su, Chunmei Du, Wenjie Zhang, Jie Liao, Tao Li, Shangquan Gan and Jian Ma
Microorganisms 2025, 13(9), 2024; https://doi.org/10.3390/microorganisms13092024 - 29 Aug 2025
Viewed by 437
Abstract
Given that suckling lambs with immature rumen development rely on intestinal microbiota for nutrient utilization, investigating the composition and functional characteristics of their intestinal microbiota is therefore of paramount importance. In this study, 16S rRNA gene amplicon sequencing technology was adopted to characterize [...] Read more.
Given that suckling lambs with immature rumen development rely on intestinal microbiota for nutrient utilization, investigating the composition and functional characteristics of their intestinal microbiota is therefore of paramount importance. In this study, 16S rRNA gene amplicon sequencing technology was adopted to characterize and analyze the diversity and composition of the jejunum, ileum and cecum bacterial communities of lambs at 0, 7 and 28 days of age, and to predict the functions of the bacterial communities. The α-diversity analysis results revealed that in the jejunum of lambs, the Chao1, PD, Simpson and Shannon indexes differed significantly among the three age groups (p < 0.05). In the ileum, Shannon and Simpson indexes of the 0-days-of-age group were slightly lower than those of the 7 (8.84% and 12.66% reductions, respectively) and 28-days-of-age groups (19.34% and 15.85% reductions, respectively) (0.05 < p < 0.10). In the cecum, Simpson and Shannon indexes differed significantly (p < 0.05) among the three age groups. At the phylum level, Firmicutes (64.68%) and Proteobacteria (21.76%) dominated the bacterial communities across all intestinal segments, with a total of 42 phyla detected. At the genus level, 19 dominant genera were identified in the jejunum. Except for Bifidobacterium, which showed no significant age-related variation (p > 0.05), the relative abundance of the remaining 18 genera changed significantly with age (p < 0.05). In the ileum, compared with the 0-days-of-age group, the Lactobacillus abundance was significantly higher in the 7- and 28-days-of-age groups (p < 0.05), while the Escherichia-Shigella, Mannheimia and Enterobacter abundances were significantly reduced (p < 0.05). In the cecum, the genera, including Blautia, Sellimonas and Ruminococcaceae UCG-014, exhibited significant age-related differences (p < 0.05), whereas other genera showed no significant variation (p > 0.05). Collectively, the bacterial community α-diversity, compositional structure and specific genus abundance in the jejunum, ileum and cecum of lambs demonstrated pronounced age-dependent variation and intestinal segment specificity patterns. This study provides a foundation for a deeper understanding of the succession patterns of the early digestive tract microbiota in lambs, and is conducive to the development of early nutrition strategies based on precise regulation of the microbiome. Full article
(This article belongs to the Section Gut Microbiota)
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12 pages, 1231 KB  
Article
Leptin, Nesfatin-1, Glucagon-like Peptide 1, and Short-Chain Fatty Acids in Colon Cancer and Inflammatory Bowel Disease
by Tamás Ilyés, Paul Grama, Simona R. Gheorghe, Vlad Anton, Ciprian N. Silaghi and Alexandra M. Crăciun
Gastroenterol. Insights 2025, 16(3), 32; https://doi.org/10.3390/gastroent16030032 - 27 Aug 2025
Viewed by 472
Abstract
Background: Short-chain fatty acids (SCFAs) are produced by the colon microbiome and bind to specific G-protein coupled receptors GPR 41 and GPR 43. Leptin and glucagon-like peptide 1 (GLP-1) are produced mainly in the intestinal lumen as a result of SCFAs binding to [...] Read more.
Background: Short-chain fatty acids (SCFAs) are produced by the colon microbiome and bind to specific G-protein coupled receptors GPR 41 and GPR 43. Leptin and glucagon-like peptide 1 (GLP-1) are produced mainly in the intestinal lumen as a result of SCFAs binding to their receptors at this level. Inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) and ulcerative colitis (UC), and their major complication, colorectal cancer (CRC), can disturb the dynamics of the colonic microenvironment thus influencing SCFAs production and effects. Our study aimed to investigate serum levels of SCFAs and SCFAs-mediated production of circulating leptin, GLP-1, and Nesfatin-1 in patients with IBD and CRC. Methods: A total of 88 subjects (29 with CRC, 29 with IBD, and 30 controls) were included in this pilot study. Serum SCFAs, leptin, Nesfatin-1, and GLP-1 levels were analyzed. Results: Nesfatin-1 levels were significantly higher in CRC patients (p < 0.05) compared to IBD and controls. Leptin levels were positively correlated with Nesfatin-1 levels in CRC, IBD, and control groups (CRC: R2 = 0.6585, p < 0.01; IBD: R2 = 0.2984, p < 0.01; Control: R2 = 0.2087, p < 0.05). Serum SCFAs levels were negatively correlated with GLP-1 levels in CRC and IBD (CRC: R2 = 0.3324, p < 0.01; IBD: R2 = 0.1756, p < 0.05) and negatively correlated with Nesfatin-1 levels in CRC (R2 = 0.2375, p < 0.05). Conclusions: These findings suggest that alterations in gut microenvironment may influence systemic metabolic regulators involved in appetite control and inflammation, potentially influencing IBD and CRC pathogenesis. This is the first study to evaluate the relationships between Nesfatin-1, leptin, GLP-1, and SCFAs in CRC and IBD patients; further research is needed to clarify their mechanistic links and therapeutic potential. Full article
(This article belongs to the Section Gastrointestinal Disease)
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34 pages, 1413 KB  
Review
Resistant Starch and Microbiota-Derived Secondary Metabolites: A Focus on Postbiotic Pathways in Gut Health and Irritable Bowel Syndrome
by Eniko Kovacs, Katalin Szabo, Rodica-Anita Varvara, Alina Uifãlean, Angela Cozma, Romana Vulturar, Adela Viviana Sitar-Taut, Rosita Gabbianelli, Mari C. W. Myhrstad, Vibeke H. Telle-Hansen, Olga Hilda Orãșan, Adriana Fodor, Ramona Suharoschi and Simona-Codruţa Hegheș
Int. J. Mol. Sci. 2025, 26(16), 7753; https://doi.org/10.3390/ijms26167753 - 11 Aug 2025
Cited by 2 | Viewed by 2526
Abstract
Resistant starch (RS) is emerging as a multifunctional dietary component and delivery platform for microbiota-accessible carbohydrates. Upon fermentation by gut microbiota, particularly in the colon, RS generates a wide spectrum of postbiotic compounds—including short-chain fatty acids (SCFAs), indoles, bile acid derivatives, and neuroactive [...] Read more.
Resistant starch (RS) is emerging as a multifunctional dietary component and delivery platform for microbiota-accessible carbohydrates. Upon fermentation by gut microbiota, particularly in the colon, RS generates a wide spectrum of postbiotic compounds—including short-chain fatty acids (SCFAs), indoles, bile acid derivatives, and neuroactive amines such as GABA and serotonin precursors. These metabolites modulate gut–brain signaling, immune responses, and intestinal barrier integrity, which are critical pathways in the pathophysiology of irritable bowel syndrome (IBS). This review synthesizes current knowledge on RS structure, classification, and fermentation dynamics, with a special focus on RS3 due to its practical dietary relevance and strong microbiota-modulatory effects. We highlight emerging evidence from clinical studies supporting RS-mediated improvements in IBS symptoms, microbial diversity, and inflammation. Importantly, RS acts as a smart colonic delivery system by escaping enzymatic digestion in the small intestine and reaching the colon intact, where it serves as a targeted substrate for microbial fermentation into bioactive metabolites. This host–microbiota interplay underpins the development of personalized, microbiome-informed nutrition interventions tailored to specific IBS subtypes. Future directions include omics-based stratification, optimized RS formulations, and predictive algorithms for individualized responses. This review aims to clarify the mechanistic links between RS fermentation and postbiotic production, highlighting its therapeutic potential in IBS management. Full article
(This article belongs to the Special Issue Bioactive Compound Delivery Systems and Microbiome Interactions)
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26 pages, 13311 KB  
Article
A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment
by Jingli Yuan, Zewen Sun, Ruiping Sun, Jun Wang, Chengfeng Wu, Baozhen Liu, Xinyuan Zhao, Qiang Li, Jianguo Zhao and Keqi Cai
Biology 2025, 14(8), 980; https://doi.org/10.3390/biology14080980 - 1 Aug 2025
Viewed by 492
Abstract
The gut microbiota of macaques, highly homologous to humans in biological characteristics and metabolic functions, serves as an ideal model for studying the mechanisms of human intestinal diseases and therapeutic approaches. A comprehensive characterization of the macaque gut microbiota provides unique insights into [...] Read more.
The gut microbiota of macaques, highly homologous to humans in biological characteristics and metabolic functions, serves as an ideal model for studying the mechanisms of human intestinal diseases and therapeutic approaches. A comprehensive characterization of the macaque gut microbiota provides unique insights into human health and disease. This study employs metagenomic sequencing to assess the gut microbiota of wild M. mulatta brevicaudus across various ages, sexes, and physiological states. The results revealed that the dominant bacterial species in various age groups included Segatella copri and Bifidobacterium adolescentis. The predominant bacterial species in various sexes included Alistipes senegalensis and Parabacteroides (specifically Parabacteroides merdae, Parabacteroides johnsonii, and Parabacteroides sp. CT06). The dominant species during lactation and non-lactation periods were identified as Alistipes indistinctus and Capnocytophaga haemolytica. Functional analysis revealed significant enrichment in pathways such as global and overview maps, carbohydrate metabolism and amino acid metabolism. This study enhances our understanding of how age, sex, and physiological states shape the gut microbiota in M. mulatta brevicaudus, offering a foundation for future research on (1) host–microbiome interactions in primate evolution, and (2) translational applications in human health, such as microbiome-based therapies for metabolic or immune-related disorders. Full article
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20 pages, 3217 KB  
Article
Microbiome of the Proximal Small Intestine in Patients with Acute Pancreatitis
by Vladimir V. Kiselev, Stanislav I. Koshechkin, Alexey V. Kurenkov, Vera E. Odintsova, Maria S. Zhigalova, Alekxandr V. Tyakht, Sergey S. Petrikov, Petr A. Yartsev and Ilya V. Dmitriev
Diagnostics 2025, 15(15), 1911; https://doi.org/10.3390/diagnostics15151911 - 30 Jul 2025
Viewed by 692
Abstract
Currently, due to the complexity of obtaining samples, specific features of laboratory processing and analysis of the results, there is a lack of data on the microbial signature of the small intestine in healthy and diseased states of the upper gastrointestinal tract. Objective: [...] Read more.
Currently, due to the complexity of obtaining samples, specific features of laboratory processing and analysis of the results, there is a lack of data on the microbial signature of the small intestine in healthy and diseased states of the upper gastrointestinal tract. Objective: To investigate the characteristics of the small intestinal microbiome in acute pancreatitis of varying severity and to identify correlations with clinical factors. Methods: This study included 30 patients with acute pancreatitis of varying severity treated between 1 January 2019 and 31 December 2021. The composition of the microbiota was analyzed by metagenomic sequencing of the 16S rRNA gene from jejunal samples. Results: The mortality rate in the study group was 23.3%. The small intestinal microbiome was dominated by Streptococcus (median relative abundance 19.2%, interquartile range 6.4–35.1%), Veillonella (3.4%; 0.6–7%), Granulicatella (2.7%; 0.6–5%), Fusobacterium (2.2%; 0.3–5.9%), Prevotella (1.5%; 0.3–8%), Haemophilus (0.9%; 0.2–10%), Gemella (0.8%; 0.2–4.3%), and Lactobacillus (0.2%; 0.1–0.9%). More severe disease was associated with decreased abundance of Neisseria mucosa, Parvimonas micra, and Megasphaera micronuciformis. In contrast, the relative abundance of the genera Streptococcus (species S. rubneri/parasanguinis/australis), Actinomyces, and several genera within the family Enterobacteriaceae was higher in these patients. Conclusions: The state of the microbiota has important prognostic value and correlates with the duration from the onset of the pain syndrome to the time of receiving qualified care in the hospital. Full article
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17 pages, 2295 KB  
Article
BDE-47 Disrupts Gut Microbiota and Exacerbates Prediabetic Conditions in Mice: Therapeutic Potential of Grape Exosomes and Antioxidants
by Zaoling Liu, Fang Cao, Aerna Qiayimaerdan, Nilupaer Aisikaer, Zulipiya Zunong, Xiaodie Ma and Yale Yu
Toxics 2025, 13(8), 640; https://doi.org/10.3390/toxics13080640 - 29 Jul 2025
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Abstract
Background: BDE-47, a pervasive environmental pollutant detected in >90% of human serum samples, is increasingly linked to metabolic disorders. This study investigates the specific impact of BDE-47 exposure on the gut microbiota in prediabetic mice and evaluates the efficacy of therapeutic interventions [...] Read more.
Background: BDE-47, a pervasive environmental pollutant detected in >90% of human serum samples, is increasingly linked to metabolic disorders. This study investigates the specific impact of BDE-47 exposure on the gut microbiota in prediabetic mice and evaluates the efficacy of therapeutic interventions in mitigating these effects. Objectives: To determine whether BDE-47 exposure induces diabetogenic dysbiosis in prediabetic mice and to assess whether dietary interventions, such as grape exosomes and an antioxidant cocktail, can restore a healthy microbiota composition and mitigate diabetes risk. Methods: In this study, a prediabetic mouse model was established in 54 male SPF-grade C57BL/6J mice through a combination of high-sugar and high-fat diet feeding with streptozotocin injection. Oral glucose tolerance tests (OGTT) were conducted on day 7 and day 21 post-modeling to assess the establishment of the model. The criteria for successful model induction were defined as fasting blood glucose levels below 7.8 mmol/L and 2 h postprandial glucose levels between 7.8 and 11.1 mmol/L. Following confirmation of model success, a 3 × 3 factorial design was applied to allocate the experimental animals into groups based on two independent factors: BDE-47 exposure and exosome intervention. The BDE-47 exposure factor consisted of three dose levels—none, high-dose, and medium-dose—while the exosome intervention factor included three modalities—none, Antioxidant Nutrients Intervention, and Grape Exosomes Intervention. Fresh fecal samples were collected from mice two days prior to sacrifice. Cecal contents and segments of the small intestine were collected and transferred into 1.5 mL cryotubes. All sequences were clustered into operational taxonomic units (OTUs) based on defined similarity thresholds. To compare means across multiple groups, a two-way analysis of variance (ANOVA) was employed. The significance level was predefined at α = 0.05, and p-values < 0.05 were considered statistically significant. Bar charts and line graphs were generated using GraphPad Prism version 9.0 software, while statistical analyses were performed using SPSS version 20.0 software. Results: The results of 16S rDNA sequencing analysis of the microbiome showed that there was no difference in the α diversity of the intestinal microbiota in each group of mice (p > 0.05), but there was a difference in the Beta diversity (p < 0.05). At the gate level, the abundances of Proteobacteria, Campylobacterota, Desulfobacterota, and Fusobacteriota in the medium-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Patellar bacteria was lower than that of the model control group (p < 0.05). The abundances of Proteobacteria and Campylobacterota in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Planctomycetota and Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Campylobacterota in the grape exosome group was higher than that of the model control group (p < 0.05). The abundance of Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Firmicutes and Fusobacteriota in the antioxidant nutrient group was higher than that of the model control group (p < 0.05). However, the abundance of Verrucomicrobiota and Patescibacteria was lower than that of the model control group (p < 0.05). At the genus level, the abundances of Bacteroides and unclassified Lachnospiraceae in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Lachnospiraceae NK4A136_group and Lactobacillus was lower than that of the model control group (p < 0.05). The abundance of Veillonella and Helicobacter in the medium-dose BDE-7 group was higher than that in the model control group (p < 0.05), while the abundance of Lactobacillus was lower (p < 0.05). The abundance of genera such as Lentilactobacillus and Faecalibacterium in the grape exosome group was higher than that in the model control group (p < 0.05). The abundance of Alloprevotella and Bacteroides was lower than that of the model control group (p < 0.05). In the antioxidant nutrient group, the abundance of Lachnospiraceae and Hydrogenophaga was higher than that in the model control group (p < 0.05). However, the abundance of Akkermansia and Coriobacteriaceae UCG-002 was significantly lower than that of the model control group (p < 0.05). Conclusions: BDE-47 induces diabetogenic dysbiosis in prediabetic mice, which is reversible by dietary interventions. These findings suggest that microbiota-targeted strategies may effectively mitigate the diabetes risk associated with environmental pollutant exposure. Future studies should further explore the mechanisms underlying these microbiota changes and the long-term health benefits of such interventions. Full article
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