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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: 20 July 2026 | Viewed by 22203

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Prof. Dr. Tihamer Molnar

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Department of Anaesthesiology and Intensive Care, Medical School, University of Pecs, 7624 Pecs, Hungary
Interests: neurocritical care; stroke; subracahnoid bleeding; biomarkers; personalized medicine; outcome
Special Issues, Collections and Topics in MDPI journals

Dr. Zoltán Péterfi

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Guest Editor

Medical School, University of Pécs, 7622 Pécs, Hungary
Interests: fecal microbiota; inflammatory bowel disease; personalized medicine

Special Issue Information

Dear Colleagues,

The human microbiome has a great impact on our health throughout our lives. The human gut microbiota is the primary source of human microbial populations, contributing considerably to both positive and negative outcomes. The impact of gut microbial population has been studied intensively over the last two decades. The gut microbiota of healthy individuals differs from that of those affected by disease and the deviation in the composition can lead to different disorders. The dysbiosis of the microbiota with respect to different life-threatening diseases such as cancer, cardiovascular disease, bowel inflammatory disease and difficult-to-treat bacterial infections is of great interest. Studies support not only the discovery and understanding of the link between certain diseases and the microbiome, but also the possibility of modifying it through dietary changes, lifestyle changes, the use of special microbe cocktails or fecal microbiota transplantation. Research on the human microbiome and its role in treating diseases is welcomed for publication in this Special Issue.

Prof. Dr. Tihamer Molnar
Dr. Zoltán Péterfi
Guest Editors

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Keywords

microbiome
metagenome
gastrointestinal tract
skin
seminal fluid
lung
saliva
oral mucosa
conjunctiva
dysbiosis
fecal microbiota transplantation

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Published Papers (10 papers)

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Research

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14 pages, 1259 KB

Open AccessArticle

Breast-Cancer-Derived Secretomes from MCF-7 Cells Modulate Bacterial Pathogenic Traits

by Suha M. Mahmood, Huda K. Al-Nasrallah, Alanoud Aldossry, Mysoon M. Al-Ansari and Monther Al-Alwan

Int. J. Mol. Sci. 2026, 27(4), 2073; https://doi.org/10.3390/ijms27042073 - 23 Feb 2026

Viewed by 47

Abstract

Breast cancer is the most frequently diagnosed malignancy among women worldwide, with the luminal A subtype being the most prevalent. Several studies have reported a complex interplay between breast cancer cells and the local microbiome; however, the mechanisms by which tumor cell-secreted factors influence bacterial biological properties remain insufficiently explored. In this study, we established an in vitro model that partially recapitulates the luminal A breast cancer microenvironment by exposing three breast-associated bacterial species, Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, to conditioned media (CM) derived from MCF-7 (tumor) or MCF-10A (non-tumor control) cell lines. A combination of complementary approaches, including ultrastructural morphological assessment, biofilm formation assays, antimicrobial susceptibility testing, and virulence gene abundance profiling by genomic qPCR, was employed to reveal distinct tumor-microbiota interactions. Exposure to MCF-7 CM induced dose-dependent structural alterations in P. aeruginosa and E. faecalis, with pronounced membrane blebbing and structural disruption in E. faecalis. Biofilm formation was differentially modulated in a species- and concentration-dependent manner, with a persistent increase observed in E. coli. Antibiotic susceptibility profiles were selectively altered in E. faecalis, which displayed increased sensitivity to vancomycin, penicillin, and imipenem, along with decreased sensitivity to chloramphenicol. P. aeruginosa exhibited increased sensitivity to imipenem along with reduced sensitivity to meropenem and gentamicin, whereas no significant changes were observed in E. coli. qPCR analyses demonstrated that MCF-7 CM was associated with enrichment of multiple virulence-associated genes (e.g., lasB, exoS, pilB, plcH, fsrC, esp, fimH, and papG), reflecting enhanced pathogenic and adhesive potential. Collectively, these findings suggest that luminal A breast cancer-derived factors can reprogram microbial phenotypes in a species-specific manner, providing mechanistic insight into breast tumor-microbiome crosstalk and a platform to explore microbiome-targeted interventions. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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22 pages, 2526 KB

Open AccessArticle

Untargeted Metabolomics Identifies Faecal Filtrate-Derived Metabolites That Disrupt Clostridioides difficile Metabolism and Confer Gut Barrier Cytoprotection

by Fatimah I. Qassadi, Charlotte Johnson, Karen Robinson, Ruth Griffin, Christos Polytarchou, Dina Kao, Dong-Hyun Kim, Rian L. Griffiths, Zheying Zhu and Tanya M. Monaghan

Int. J. Mol. Sci. 2025, 26(22), 11221; https://doi.org/10.3390/ijms262211221 - 20 Nov 2025

Viewed by 1253

Abstract

Recurrent Clostridioides difficile infection (rCDI) remains a major therapeutic challenge. Although faecal microbiota transplantation (FMT) is highly effective and thought to restore microbial composition and metabolic function, the mechanisms underlying its success are not fully understood. In particular, the contribution of non-bacterial components such as soluble metabolites remains unclear. Therefore, further investigation is needed to identify the mechanistic drivers of FMT efficacy and clarify how non-bacterial factors contribute to therapeutic outcomes. Here, we applied untargeted three-dimensional Orbitrap secondary ion mass spectrometry (3D OrbiSIMS) to profile faecal metabolic reprogramming in rCDI patients pre- and post-FMT, alongside C. difficile cultures exposed to sterile faecal filtrates. FMT induced extensive metabolic shifts, restoring glyoxylate/dicarboxylate and glycerophosphoinositol pathways and normalising disrupted bile acid and amino acid profiles. Faecal filtrate exposure caused strain-specific metabolic disruption in C. difficile, depleting proline, fumarate and succinate while enriching tryptophan. While multiple metabolite classes were profiled, the most significant functional changes were observed in lipids. Lipidomics identified >3.8-fold enrichment of phosphatidylinositol (PI) species, which localised to bacterial membranes and conferred cytoprotection against C. difficile toxins and other epithelial insults. Spatial metabolomics imaging revealed, for the first time, metabolite compartmentalisation within C. difficile, with proline and succinate broadly distributed across the cell surface and fumarate confined to distinct microdomains, highlighting functional heterogeneity in pathogen metabolism. Collectively, these findings demonstrate that soluble metabolites within faecal filtrates mediate pathogen suppression and epithelial barrier protection, establishing metabolite-driven mechanisms underlying FMT efficacy and identifying PI lipids as candidate post-biotic therapeutics for rCDI. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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20 pages, 1893 KB

Open AccessArticle

A Maternal and Postnatal Ad Libitum Propionic Acid-Rich Diet in Mice Alters Intestinal Glia Proliferation and Inflammatory Response: Contrary to Effect in the Brain

by Piotr P. Lagod, Latifa S. Abdelli and Saleh A. Naser

Int. J. Mol. Sci. 2025, 26(19), 9295; https://doi.org/10.3390/ijms26199295 - 23 Sep 2025

Cited by 1 | Viewed by 1062

Abstract

We previously demonstrated that propionic acid (PPA), a common food preservative and a metabolic byproduct of bacteria in dysbiosis (as seen in individuals affected with autism spectrum disorder, ASD), can lead to increased brain astrocyte proliferation and neuroinflammation in mice. We also showed that in vitro treatment of human neural stem cells with PPA increased glial cell vs. neuron differentiation and yielded a marked increase in pro-inflammatory cytokines. In this study, a group of mice (FVB/N-Tg(GFAPGFP)14Mes/J) was exposed in utero through the maternal diet and postnatally ad libitum to a PPA-rich diet, while the control group was fed a normal diet. Intestinal tissue from offspring mice at 1 month (1 M) and 5 months (5 M) were then studied for neurodifferentiation and gastrointestinal (GI) inflammation. There was a significant increase in GFAP (Glial fibrillary acidic protein) expression (1.5427-fold and 1.6097-fold in 1 M and 5 M, respectively) and GFAP protein levels (1.5616-fold and 1.6701-fold in 1 M and 5 M, respectively) in the PPA group mice. It is worth mentioning that the expression level of intestinal astrocyte markers in the PPA group was significantly and multi-fold lower than that in the brain tissue. Contrary to data from brain tissue, the expression of pro-inflammatory cytokines in the PPA group decreased in intestinal tissue at 5 M (IL-6: 0.4403-fold; TNF-α: 0.4007-fold), while IL-10 expression and protein levels increased (1.9360-fold and 1.3428-fold, respectively). The data demonstrates that although there was a significant increase in GFAP in the intestine suggesting gliosis, there was an overall anti-inflammatory cytokine profile. The effect of PPA on intestinal cytokines is most likely in part due to the lower expression of GFAP in the enteric nervous system than the central nervous system (and the lower number of intestinal glia than astrocytes in the brain) and the dominance of intestinal macrophages and other immune cells compared to that in the brain. The overall finding strongly suggests that the PPA-rich diet affects the enteric glia state as shown by an increase in GFAP; however, it maintains the overall anti-inflammatory cytokine profile, possibly due to M2 macrophage polarization. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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19 pages, 5504 KB

Open AccessArticle

The Impact of Bariatric Surgery on Gut Microbiota Composition and Diversity: A Longitudinal Analysis Using 16S rRNA Sequencing

by Radu Petru Soroceanu, Daniel Vasile Timofte, Sergiu Timofeiov, Vlad Ionut Vlasceanu, Madalina Maxim, Ancuta Andreea Miler, Andi Gabriel Iordache, Roxana Moscalu, Mihaela Moscalu, Irina Cezara Văcărean-Trandafir, Roxana-Maria Amărandi, Iuliu Cristian Ivanov and Alin Constantin Pînzariu

Int. J. Mol. Sci. 2025, 26(16), 7933; https://doi.org/10.3390/ijms26167933 - 17 Aug 2025

Cited by 3 | Viewed by 1782

Abstract

Bariatric surgery is considered the most effective treatment for obesity and its associated metabolic disorders, yet the underlying mechanisms are only partially understood. Evidence suggests that the gut microbiota plays an important role in metabolic regulation and can be significantly altered by bariatric and metabolic procedures. This prospective, single-center study aimed to evaluate the dynamic changes in the gut microbiota composition and diversity in obese patients undergoing two types of bariatric surgery: laparoscopic sleeve gastrectomy (LSG) and Roux-en-Y gastric bypass (RYGB). Fecal samples were collected at three time points—before surgery (T0), and at 3 (T3) and 6 months (T6) postoperatively—and analyzed using 16S rRNA gene sequencing targeting the V3–V4 regions with Illumina technology. Significant shifts in microbial diversity and structure were observed over time, indicating a trend toward microbiota normalization post-surgery. Notable changes included a reduction in the Firmicutes/Bacteroidetes ratio and increased relative abundance of Actinobacteria, Proteobacteria, and Verrucomicrobia. These alterations occurred in parallel with improvements in body mass index (BMI) and metabolic parameters. Our findings suggest that bariatric surgery induces favorable and sustained modifications in the gut microbiota, which may contribute to its therapeutic effects in obesity management. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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21 pages, 3038 KB

Open AccessArticle

Exploring the Interplay Between Gut Microbiota and the Melatonergic Pathway in Hormone Receptor-Positive Breast Cancer

by Aurora Laborda-Illanes, Soukaina Boutriq, Lucía Aranega-Martín, Daniel Castellano-Castillo, Lidia Sánchez-Alcoholado, Isaac Plaza-Andrades, Jesús Peralta-Linero, Emilio Alba, José Carlos Fernández-García, Alicia González-González and María Isabel Queipo-Ortuño

Int. J. Mol. Sci. 2025, 26(14), 6801; https://doi.org/10.3390/ijms26146801 - 16 Jul 2025

Viewed by 1975

Abstract

Emerging evidence suggests a bidirectional relationship between gut microbiota, melatonin synthesis, and breast cancer (BC) development in hormone receptor-positive patients (HR+HER2+ and HR+HER2-). This study investigated alterations in gut microbiota composition, the serum serotonin–N-acetylserotonin (NAS)–melatonin axis, fecal short-chain fatty acids (SCFAs) and beta-glucuronidase (βGD) activity, and serum zonulin in HR+ BC patients compared to healthy controls. Blood and fecal samples were analyzed using mass spectrometry for serotonin, NAS, melatonin, and SCFAs; ELISA for AANAT, ASMT, 14-3-3 protein, and zonulin; fluorometric assay for βGD activity; and 16S rRNA sequencing for gut microbiota composition. HR+ BC patients exhibited gut dysbiosis with reduced Bifidobacterium longum and increased Bacteroides eggerthii, alongside elevated fecal βGD activity, SCFA levels (e.g., isovaleric acid), and serum zonulin, indicating increased intestinal permeability. Serum serotonin and N-acetylserotonin (NAS) levels were elevated, while melatonin levels were reduced, with a higher NAS/melatonin ratio in BC patients. AANAT levels were increased, and ASMT levels were decreased, suggesting disrupted melatonin synthesis. Bifidobacterium longum positively correlated with melatonin and negatively with βGD activity, while Bacteroides eggerthii showed a positive correlation with βGD activity. These findings suggested that gut microbiota alterations, disrupted melatonin synthesis, microbial metabolism, and intestinal permeability may contribute to BC pathophysiology. The NAS/melatonin ratio could represent a potential biomarker, necessitating further mechanistic studies to confirm causality and explore therapeutic interventions. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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13 pages, 2585 KB

Open AccessArticle

Effects of Aneurysmal Subarachnoid Hemorrhage in Patients Without In-Hospital Infection on FABP-I, LBP, and sCD-14

by Brigitta Orban, Diana Simon, Szabina Erdo-Bonyar, Timea Berki, Tihamer Molnar, Laszlo Zavori, Attila Schwarcz, Zoltan Peterfi and Peter Csecsei

Int. J. Mol. Sci. 2025, 26(2), 485; https://doi.org/10.3390/ijms26020485 - 8 Jan 2025

Viewed by 1807

Abstract

Aneurysmal subarachnoid hemorrhage (aSAH) is a serious condition complicated by delayed cerebral ischemia (DCI), where inflammation plays a key role. Although altered gut permeability is noted in other conditions, its significance in aSAH remains unclear. Fatty acid-binding protein (FABP-I), lipopolysaccharide-binding protein (LBP), and soluble CD-14 (sCD-14) are established markers of barrier dysfunction. This study investigates gut permeability marker changes in early and late aSAH phases. The study included 177 aSAH patients and 100 controls. Serum samples were collected on days 1 (D1) and 9 (D9) after ictus. FABP-I, LBP, and sCD-14 levels were measured via ELISA, and clinical data were recorded. Outcomes were assessed using the 90-day modified Rankin scale (mRS 0–3 = favorable outcome). Serum FABP-I was significantly lower in aSAH patients (p < 0.05), while LBP and sCD-14 were higher (p < 0.001) compared to controls. FABP-I did not differ between outcome groups, but LBP and sCD-14 were significantly elevated in unfavorable outcomes (p < 0.001). These markers differed in patients without in-hospital infection, with higher levels noted in DCI patients during the later phase (p < 0.05). In aSAH patients without infection, differences in LBP and sCD-14 levels between outcome groups suggest potential endotoxin release from microbial systems, contributing to neuroinflammation and influencing outcomes. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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24 pages, 385 KB

Open AccessReview

The Role of Gut Microbiota in Colorectal Cancer Pathogenesis: A Comprehensive Literature Review

by Dan Nicolae Paduraru, Alexandru Cosmin Palcau, Valeriu Gabi Dinca, Diana Mihaela Ciuc and Alexandru Constantinescu

Int. J. Mol. Sci. 2025, 26(24), 11870; https://doi.org/10.3390/ijms262411870 - 9 Dec 2025

Cited by 1 | Viewed by 1264

Abstract

Colorectal cancer (CRC) represents a significant global health burden, ranking as the third most frequently diagnosed malignancy worldwide. Emerging evidence has established a compelling association between gut microbiota dysbiosis and CRC pathogenesis, revealing complex mechanisms through which specific bacterial communities modulate carcinogenesis. This comprehensive review synthesizes current knowledge on the mechanistic contributions of gut microbiota to CRC development, with particular emphasis on key pathogenic bacteria including Fusobacterium nucleatum, Bacteroides fragilis, and Escherichia coli. We examine the molecular pathways through which these microorganisms promote tumorigenesis, including chronic inflammation induction, immune response modulation, metabolic reprogramming, and direct genotoxic effects. Furthermore, we discuss the therapeutic implications of microbiota-targeted interventions and the potential utility of microbial biomarkers for early CRC detection. Understanding the intricate host–microbiota interactions in CRC pathogenesis may facilitate the development of novel preventive strategies and therapeutic approaches for this devastating disease. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

20 pages, 714 KB

Open AccessReview

The Role of the Gut Microbiome in Type 2 Diabetes Mellitus

by Rahaf Mashal, Amnah Al-Muhanna, Salma Khader, Aiman Khudair, Ahmed Khudair and Alexandra E. Butler

Int. J. Mol. Sci. 2025, 26(23), 11412; https://doi.org/10.3390/ijms262311412 - 26 Nov 2025

Viewed by 2542

Abstract

The gastrointestinal tract in humans hosts trillions of microorganisms, collectively termed the gut microbiota, which perform essential physiological processes and roles, including nutrient metabolism and immunomodulation. Influenced by genetics, age, diet, medication, and the environment, the disruption of this system leads to dysbiosis, which has been linked to a range of diseases, notably type 2 diabetes mellitus (T2DM). As the global prevalence of T2DM continues to trend upwards, research investigating and highlighting the influence the gut microbiome exerts on this disease is warranted. The literature was examined regarding microbial metabolites and metabolic signaling pathways, as well as interventions relating to diet, prebiotics, probiotics, pharmacological agents, and fecal microbiota transplantation (FMT). The gut microbiome, through its effects on insulin resistance, inflammation, bile acid signaling, and glucose–lipid metabolism, impacts the development and progression of T2DM. Furthermore, patients with T2DM have demonstrated reduced microbial diversity, depletion of butyrate-producing bacteria, and an increase in pathogenic species. Interventions including high-fiber diets, metformin, probiotics, and FMT were shown to enrich beneficial microbes and improve metabolic outcomes. Targeted modulation of the microbiome, such as through next-generation probiotics and CRISPR-based therapies, may enhance metabolic control in the context of the future of personalized medicine. This review investigates the intricate relationship between the gut microbiome and T2DM, emphasizing its role in disease pathogenesis, the factors that may impact the microbiome in these patients, as well as therapeutic approaches toward its management. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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22 pages, 945 KB

Open AccessReview

Mapping the Gut Microbiota Composition in the Context of Raltegravir, Dolutegravir, and Bictegravir—A Scoping Review

by Zsófia Gáspár and Botond Lakatos

Int. J. Mol. Sci. 2025, 26(13), 6366; https://doi.org/10.3390/ijms26136366 - 2 Jul 2025

Cited by 1 | Viewed by 1517

Abstract

(1) Background: Second-generation integrase strand transfer inhibitors (INSTIs) are now the preferred first-line therapies for human immunodeficiency virus (HIV). However, concerns regarding their side effects, such as weight gain and metabolic disturbances, have emerged. This scoping review aims to assess the effects of INSTIs on the gut microbiota, with a focus on differences between agents and their clinical implications. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: The majority of available evidence focused on dolutegravir, which demonstrated beneficial effects on microbiota diversity and composition. However, factors such as younger age, lower CD4+ counts, and extreme BMI were associated with proinflammatory changes. Limited data on bictegravir also suggested favorable alterations in the gut microbiota. Raltegravir, a first-generation INSTI, was associated with improvements in alpha diversity and microbial composition, although these changes were not consistently beneficial. Moreover, associated changes in inflammatory and microbial translocation markers suggested unfavorable alterations. (4) Conclusions: Based on the evidence mapped, second-generation INSTIs may generally induce favorable changes in the gut microbiota. However, further research is needed to explore the clinical implications of these microbiota alterations, particularly in specific patient groups. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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34 pages, 2039 KB

Open AccessReview

Gut Microbiota and Cardiovascular Diseases: Unraveling the Role of Dysbiosis and Microbial Metabolites

by Barathan Muttiah and Alfizah Hanafiah

Int. J. Mol. Sci. 2025, 26(9), 4264; https://doi.org/10.3390/ijms26094264 - 30 Apr 2025

Cited by 21 | Viewed by 7782

Abstract

Cardiovascular diseases (CVDs), including heart failure (HF), hypertension, myocardial infarction (MI), and atherosclerosis, are increasingly linked to gut microbiota dysbiosis and its metabolic byproducts. HF, affecting over 64 million individuals globally, is associated with systemic inflammation and gut barrier dysfunction, exacerbating disease progression. Similarly, hypertension and MI correlate with reduced microbial diversity and an abundance of pro-inflammatory bacteria, contributing to vascular inflammation and increased cardiovascular risk. Atherosclerosis is also influenced by gut dysbiosis, with key microbial metabolites such as trimethylamine-N-oxide (TMAO) and short-chain fatty acids (SCFAs) playing crucial roles in disease pathogenesis. Emerging evidence highlights the therapeutic potential of natural compounds, including flavonoids, omega-3 fatty acids, resveratrol, curcumin, and marine-derived bioactives, which modulate the gut microbiota and confer cardioprotective effects. These insights underscore the gut microbiota as a critical regulator of cardiovascular health, suggesting that targeting dysbiosis may offer novel preventive and therapeutic strategies. Further research is needed to elucidate underlying mechanisms and optimize microbiome-based interventions for improved cardiovascular outcomes. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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