Gut Pathogens最新文献

{"title":"Enteric opportunistic infections in patients with inflammatory bowel disease receiving biologic therapies: a retrospective cohort study.","authors":"Ting-Chieh Huang, Tony Kou, Chia-Jung Kuo, Cheng-Hsun Chiu, Tai-Di Chen, Chien-Ming Chen, Jen-Wei Chou, Tien-Yu Huang, Chen-Wang Chang, Cheng-Tang Chiu, Ming-Yao Su, Yu-Bin Pan, Puo-Hsien Le","doi":"10.1186/s13099-025-00793-2","DOIUrl":"10.1186/s13099-025-00793-2","url":null,"abstract":"<p><strong>Background: </strong>Biologic therapy has improved outcomes in inflammatory bowel disease (IBD) but may predispose patients to enteric opportunistic infections. Asian data comparing infection risk across biologic classes remain scarce. We therefore assessed the incidence of Clostridioides difficile infection (CDI), Clostridium innocuum (CI) infection, and cytomegalovirus (CMV) colitis in IBD patients treated with Vedolizumab (VDZ), anti-tumor necrosis factor agents (anti-TNF), or Ustekinumab (UST).</p><p><strong>Methods: </strong>This single‑center, retrospective cohort study included IBD patients who initiated VDZ, anti‑TNF (infliximab or adalimumab) or UST at Chang Gung IBD Center between January 2017 and December 2024. Opportunistic infection was defined as: (i) toxin‑gene PCR-positive CDI, (ii) CI isolated in stool/colonic culture, or (iii) CMV‑positive immunohistochemistry on intestinal biopsy. Incidence rates were expressed per 100 patient‑years. Infection‑free survival was compared with Kaplan-Meier analysis and log‑rank testing. Multivariable logistic regression identified independent predictors of CDI.</p><p><strong>Results: </strong>A total of 614 patients (377 Crohn's disease; 237 ulcerative colitis) contributed 941 patient‑years of follow‑up. The incidences per 100 patient-years were 3.51 for CDI, 0.85 for CI, and 3.30 for CMV colitis. CDI and CI risks were comparable across VDZ, anti‑TNF and UST cohorts. CMV colitis was significantly more common with anti‑TNF therapy (5.9%) than with VDZ (3.4%) or UST (0.5%) (p = 0.020). Independent predictors of CDI were an acute IBD flare (odds ratio [OR] 3.64; 95% confidence interval 1.91-6.91), concurrent CMV colitis (OR 6.34; 95% confidence interval 2.03-19.8) and CI infection (OR 7.79; 95% confidence interval 1.40-43.3).</p><p><strong>Conclusion: </strong>VDZ and UST were not associated with excess CDI, CI or CMV risk, whereas anti‑TNF therapy conferred a higher burden of CMV colitis. Heightened infection surveillance is warranted during acute flares and refractory disease courses.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"7"},"PeriodicalIF":4.0,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The microbiological and clinical characteristics of 1,204 human cases of Aliarcobacter spp. infections that occurred in France between 2002 and 2024.","authors":"Marine Jauvain, Lucie Bruhl, Astrid Ducournau, Johanna Aptel, Moeava Martin, Philippe Lehours","doi":"10.1186/s13099-025-00790-5","DOIUrl":"10.1186/s13099-025-00790-5","url":null,"abstract":"<p><p>Aliarcobacter spp. bacteria are human enteropathogens, as are Campylobacter spp. However, the epidemiology of the former infections is not well described. Here, we present microbiological and clinical data on 1,204 Aliarcobacter spp. infections that occurred in France between 2002 and 2024. Aliarcobacter butzleri was the principal species identified, followed by A. cryaerophilus. Aliarcobacter spp. infections affected patients principally over 60 years of age, mostly men, particularly during autumn. Analysis of 253 clinical information sheets highlighted both diarrhea and abdominal pain that were only rarely associated with fever or blood in the stool. Many isolates of both main species were resistant to group A penicillins and ciprofloxacin.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"5"},"PeriodicalIF":4.0,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12781572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota and host transcriptome interactions reveal diagnostic biomarkers in MASLD-associated hepatocellular carcinoma.","authors":"Thananya Jinato, Jakkrit Khamjerm, Satjapot Manprasong, Nutta Iadsee, Pisit Tangkijvanich, Intawat Nookaew, Natthaya Chuaypen","doi":"10.1186/s13099-025-00782-5","DOIUrl":"10.1186/s13099-025-00782-5","url":null,"abstract":"<p><strong>Background: </strong>Alterations in the gut microbiome via the gut-liver axis are closely linked to metabolic dysfunction-associated steatotic liver disease (MASLD) and may contribute to hepatocellular carcinoma (HCC) development. However, the interplay between the gut microbiome and host gene expression in MASLD and HCC remains poorly understood.</p><p><strong>Methods: </strong>We analyzed the gut microbiome from fecal samples and host transcriptomic profiles from peripheral blood mononuclear cells (PBMCs) in healthy controls and MASLD patients without HCC (mild fibrosis F01 and significant fibrosis F234) and with HCC.</p><p><strong>Results: </strong>Integrated analysis identified 260 differentially expressed genes (DEGs) and 29 bacterial taxa differentiating MASLD without HCC from MASLD-HCC. Subgroup analysis revealed seven bacterial genera associated with 84 host genes. Notably, Veillonella correlated with regulating synaptic membrane exocytosis 3 (RIMS3), collagen type X alpha 1 (COL10A1), and enabled homolog (ENAH). Real-time PCR validation confirmed COL10A1 as a significant diagnostic biomarker for distinguishing MASLD from MASLD-HCC (AUC = 0.835). Combining COL10A1, and AFP, or Veillonella with AFP, significantly improved differentiation between MASLD and MASLD-HCC, particularly in early-stage fibrosis (F01) (AUC = 0.941 and 0.996, respectively).</p><p><strong>Conclusions: </strong>Gut microbiome-host gene interactions appear to play a significant role in MASLD-related HCC progression. Specific bacterial genera and host gene expression profiles may serve as early diagnostic markers for MASLD-HCC.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"107"},"PeriodicalIF":4.0,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12723900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145767914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synergistic potentiation of antibiotics by chamomile phytochemicals against multidrug-resistant Helicobacter pylori.","authors":"Menna M M Mohammed Ali, Hala Mohamed Abu Shady, Sayed M M, Hayam A E Sayed","doi":"10.1186/s13099-025-00777-2","DOIUrl":"10.1186/s13099-025-00777-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Helicobacter pylori is a significant global health issue, infecting nearly half of the population. Increasing antibiotic resistance leads to treatment failures. This study examined the antibacterial effects of chamomile ethanolic extract, both alone and combined with standard antibiotics, as a potential approach to fighting antibiotic-resistant H. pylori strains.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Thirty antral gastric biopsies were collected from patients undergoing diagnostic upper endoscopy at El-Demerdash Hospital in Cairo, Egypt. H. pylori isolates were identified by rapid urease test (RUT), cultured, and tested for antimicrobial susceptibility to clarithromycin (CLR, 15 µg), metronidazole (MET, 5 µg), amoxicillin (AX, 25 µg), tetracycline (TE, 30 µg), rifampicin (RA, 30 µg), and levofloxacin (LEV, 5 µg). The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined. The antibacterial activity of chamomile ethanolic extract was tested alone and in combination with these antibiotics. Phytochemical profiling was conducted using FT-IR and GC-MS. The identified compounds were analyzed through molecular docking against ten H. pylori targets: lipoprotein 20 (LPP20, HP1456), aspartate α-decarboxylase (ADC), S-ribosylhomocysteinase (LuxS), GTP cyclohydrolase II (GCH II), cytotoxin-associated gene A (CagA), sialic acid-binding adhesin (SabA), blood group antigen-binding adhesin (BabA), vacuolating cytotoxin A (VacA), and fructose-1,6-bisphosphate aldolase (FBA), using AutoDock Vina 1.5.7.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;All thirty biopsies tested positive for RUT, although only 20 yielded successful cultures. The chamomile ethanolic extract demonstrated anti-H. pylori activity against all 20 isolates, with MIC values ranging from 1.562 to 6.25 mg/mL and MBC values from 3.12 to 12.5 mg/mL. When combined with antibiotics, the extract altered their antibacterial activity, primarily producing synergistic effects, while a few combinations exhibited antagonistic effects. Notably, in cases where antibiotics alone had limited activity, adding chamomile extract significantly enhanced effectiveness, increasing inhibition zones by 2.2-fold for tetracycline, 2.1-fold for rifampicin, and 1.7-2.3-fold for levofloxacin. FT-IR analysis confirmed the chemical safety of the extract, while GC-MS profiling identified 38 constituents, including 14 compounds with known antimicrobial properties. Molecular docking revealed strong binding affinities of eight bioactive compounds toward H. pylori target proteins. Additionally, Lipinski's Rule of Five and ADMET profiling indicated these compounds possess favorable drug-like properties, including safety and oral bioavailability.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Chamomile ethanolic extract shows promising anti-H. pylori activity and can enhance the effectiveness of standard antibiotics, indicating its potential as a complementary treatment to combat antibio","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"105"},"PeriodicalIF":4.0,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12703921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145756202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correlation between the antibiotic resistance and virulence determinants of vancomycin-resistant enterococci: paradoxical involvement of vanA in phenotypic resistance to teicoplanin.","authors":"Rana M Amr, Amr S Bishr, Khaled M Aboshanab, Nadia A Hassouna","doi":"10.1186/s13099-025-00776-3","DOIUrl":"10.1186/s13099-025-00776-3","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance, particularly in clinical Enterococcus isolates, poses a serious global health threat because of difficult-to-treat nosocomial infections. The emergence of vancomycin-resistant enterococci (VRE), mediated by VanA or VanB operons, has significantly limited treatment options. This study aimed at identifying antibiotic resistance and virulence genes in enterococci and exploring potential correlations between these genetic traits.</p><p><strong>Methods: </strong>A total of 100 suspected enterococci were gathered from two hospitals and identified through phenotypic methods and the VITEK 2 Compact system. The Kirby-Bauer disk diffusion and MIC by microbroth dilution methods were employed for antimicrobial susceptibility. The gelatinase production and biofilm were evaluated phenotypically, while the presence of vancomycin resistance (vanA, vanB) and virulence (esp, gelE, hyl) genes was confirmed by PCR and sequenced for genetic characterization.</p><p><strong>Results: </strong>Sixty-five Enterococcus isolates were characterized, with E. faecium (50.7%) and E. faecalis (41.5%) being the predominant species. Linezolid, teicoplanin, and chloramphenicol still retain good activity with 6.15%, 10.7%, and 29.2% resistance, respectively. About 40% of isolates were VRE, and all harbored the vanA gene. Biofilm formation and gelatinase production were most prevalent in E. faecium and E. faecalis, indicating enhanced virulence. Sequencing confirmed the chromosomal location and identity of the resistance and virulence genes, supporting their accurate detection and distribution among different Enterococcus species. Statistical analysis revealed that both esp and gelE genes were significantly associated with biofilm formation and gelatinase activity; however, esp showed a positive correlation with vanA and vancomycin resistance, while gelE demonstrated a negative correlation. Even though vanA is typically linked to high levels of resistance to both teicoplanin and vancomycin, only seven out of the twenty-six isolates that were vanA-positive showed phenotypic resistance to teicoplanin.</p><p><strong>Conclusion: </strong>Enterococcus faecium and E. faecalis were identified as predominant multidrug-resistant species carrying multiple virulence determinants, with esp and gelE strongly linked to biofilm formation and gelatinase activity. Linezolid, teicoplanin, and chloramphenicol remained the most effective agents. Our findings demonstrate the coexistence of resistance and virulence traits, along with unexpected genotype-phenotype variations, underscoring the need for integrated molecular and phenotypic approaches in surveillance and clinical management.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"110"},"PeriodicalIF":4.0,"publicationDate":"2025-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12744406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145756177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the intricate link between gut microbiota dysbiosis and the aging process: implications for age-related diseases.","authors":"Hanin M Abahussin, Maryam S Alotaibi, Othman A Alhazzaa, Aminah G Alotaibi, Sarah M Alsaab, Nora A Aljawini, Abdullah O Alawad","doi":"10.1186/s13099-025-00788-z","DOIUrl":"10.1186/s13099-025-00788-z","url":null,"abstract":"<p><p>Aging is a complex process marked by the gradual accumulation of impairments in molecules and tissues, leading to frailty and dysfunction. This decline is a significant risk factor for many debilitating conditions. Recently, gut microbiota dysbiosis has been identified as one of the hallmarks of aging. This review sheds light on the role of gut microbiota dysbiosis in accelerating aging and its relation to age-associated diseases, including neurodegenerative disorders, cardiovascular diseases, cancer and diabetes. Emerging research demonstrates a strong link between the gut microbiome and the aging process, although the underlying mechanisms remain under investigation. Animal studies suggest that targeting the gut microbiome may offer a promising approach to mitigate aging and related diseases. However, further human studies are needed to confirm these findings.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"3"},"PeriodicalIF":4.0,"publicationDate":"2025-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12777186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145756259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactobacillus probiotics potential in Blastocystis infection: in vitro and in vivo studies.","authors":"Mona Gamal Baz Mohamed, Ibrahim A Aboul Asaad, Dareen Abd Elaziz Mohamed Ali, Dalia Abdelmageed Ahmad Elmehy, Sarah M Abdo","doi":"10.1186/s13099-025-00765-6","DOIUrl":"10.1186/s13099-025-00765-6","url":null,"abstract":"<p><p>Blastocystis is a widespread intestinal parasite with debated pathogenicity. Blastocystis infection often persists despite metronidazole therapy, highlighting the need for adjunctive strategies. This study evaluated the therapeutic efficacy of metronidazole, Lactobacillus probiotics, and their combination against Blastocystis infection using in vitro and in vivo models. In vitro cultures of Blastocystis were treated with metronidazole (10 µg/mL), probiotics (10⁸ CFU/mL), or both. Viability and parasite counts were assessed at 24 and 48-hours post-treatment. In vivo, infected mice received metronidazole (20 mg/kg), probiotics (10⁹ CFU/day), or both for 7 days. Parasitological, histopathological, immunohistochemical, and cytokine evaluations were conducted. At 48 h in vitro, metronidazole reduced Blastocystis count by 88.6% and viability by 91.3%; probiotics reduced count by 87.2% and viability by 90.6%. The combination achieved 94.8% and 96.8% reductions, respectively (p < 0.001). In vivo, stool cysts decreased by 86% (metronidazole), 84% (probiotics), and 98.5% (combined). Intestinal cysts decreased by 85.1%, 82.9%, and 98.5%, respectively. Histological improvements and restoration of IgA-secreting cells were most prominent in the combined group. Pro-inflammatory cytokines (IL-1β, IL-6, IFN-γ) decreased most with combination therapy-by 66.9%, 57.8%, and 60.1%, respectively-compared to untreated controls (p < 0.001). These findings indicate that probiotics enhance the efficacy of metronidazole, supporting their role as a promising adjunctive therapy for Blastocystis infection. The combined treatment yielded the most profound parasitological, immunological, and histological improvements, supporting its potential as a superior therapeutic strategy.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"108"},"PeriodicalIF":4.0,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12739847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotyping and molecular profiling of intestinal microsporidiosis and cryptosporidiosis in HIV-infected patients in Alborz Province, Iran.","authors":"Benyamin Djawadi, Nazila Parvizi, Hossein Vazini, Milad Badri, Aida Vafae Eslahi, Ioannis Adamopoulos, Mahendra Pal, Majid Pirestani","doi":"10.1186/s13099-025-00785-2","DOIUrl":"10.1186/s13099-025-00785-2","url":null,"abstract":"<p><strong>Background: </strong>Cryptosporidium and Microsporidia are major opportunistic pathogens in individuals with HIV, frequently causing gastrointestinal manifestations. Molecular identification of these parasites provides crucial insights into their transmission dynamics, clinical relevance, and zoonotic potential.</p><p><strong>Methods: </strong>This cross-sectional study investigated 275 HIV-infected patients in Alborz Province, Iran (2018-2020). Stool samples were examined using Ziehl-Neelsen and modified trichrome staining, followed by PCR amplification and sequencing of the 18 S rRNA and GP60 genes for Cryptosporidium spp., and the ITS region for Enterocytozoon bieneusi and Encephalitozoon intestinalis. Associations between parasitic infections and demographic/clinical variables were analyzed using univariate and multivariable methods.</p><p><strong>Results: </strong>Molecular analysis identified Cryptosporidium spp. in 7.6% and Microsporidia in 9.1% of patients, including E. bieneusi (6.5%), E. intestinalis (2.5%), and mixed infections (1.8%). Subtyping revealed that C. parvum (5.8%) predominantly belonged to subtype family IId (IIdA20G1, IIdA19G1), while C. hominis (1.8%) was IdA15G1. E. bieneusi genotypes D, Peru6, and J were detected-genotype J being reported for the first time in Iranian HIV-positive patients. Infections were significantly associated with clinical symptoms including chronic diarrhea, abdominal pain, vomiting, and fever. The highest rates of infection were found among patients with CD4 + counts < 200 cells/µL, no history of ART, animal contact, and use of well water.</p><p><strong>Conclusions: </strong>This study highlights the clinical and epidemiological significance of Cryptosporidium, E. bieneusi, and E. intestinalis in HIV-infected individuals. The identification of zoonotic genotypes and their association with gastrointestinal symptoms and immunosuppression emphasizes the need for routine molecular screening, targeted public health interventions, and adoption of One Health strategies to control transmission.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"106"},"PeriodicalIF":4.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12723857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145722374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning approach and internet of things technologies to unravel the complex interaction between microbiome-metabolome in inflammatory bowel disease: a new frontier in precision medicine.","authors":"Orazio Palmieri, Anna Lucia Cannarozzi, Anna Latiano, Luca Massimino, Fabrizio Bossa, Matteo Riva, Federica Ungaro, Maria Guerra, Anna Laura Pia Di Brina, Sonia Carparelli, Gionata Fiorino, Francesco Perri, Silvio Danese","doi":"10.1186/s13099-025-00758-5","DOIUrl":"10.1186/s13099-025-00758-5","url":null,"abstract":"<p><p>Inflammatory bowel diseases (IBD) are chronic, relapsing inflammatory disorders with ulcerative colitis (UC) and Crohns disease (CD) representing the two major phenotypes. While these conditions share common features, they exhibit distinct clinical presentations, disease behaviors, and pathogenetic mechanisms, highlighting the complexity of IBD. The global incidence and prevalence of IBD have risen dramatically in recent decades, probably linked to environmental changes such as dietary habits, urbanization, and reduced microbial exposure during early life, highlighting the interplay between environmental and genetic factors in disease pathogenesis. However, genetic factors alone cannot fully explain disease onset, emphasizing the critical role of environmental and microbial influences. Dysbiosis, characterized by reduced microbial diversity, loss of beneficial commensals, and an overabundance of pathogenic taxa, has emerged as a hallmark of IBD. Recent research has increasingly focused on the functional consequences of dysbiosis, its impact on microbial metabolites and pathways that contribute to chronic inflammation and disease progression. Understanding the functional implications of multi-omics changes, rather than simply cataloguing compositional changes, is now a priority in IBD research. Using artificial intelligence to combine data from noninvasive multi-omics technologies offers a significant opportunity to explore interactions among individual omics. It could represent a shift in IBD research by showing the complex mechanisms behind disease. This approach may revolutionize diagnostics and treatments, improving the quality of life for patients through precision medicine. This review aims to provide a comprehensive assessment of current progress. It highlights critical challenges and suggests possible future directions.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"102"},"PeriodicalIF":4.0,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12696923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota and intestinal polyps: a systematic review and meta-analysis based on 16S rRNA gene sequencing.","authors":"Qian Wu, Siyu Lu, Lizhong Wang, Xiaoli Liao, Dangheng Wei","doi":"10.1186/s13099-025-00784-3","DOIUrl":"10.1186/s13099-025-00784-3","url":null,"abstract":"<p><strong>Aim: </strong>Colorectal polyps serve as precursors to colorectal cancer and pose a growing public health challenge with their increasing incidence. The potential role of gut microbiota (GM) dysbiosis in colorectal polyp pathogenesis has garnered attention, yet existing evidence remains inconsistent. This study aimed to compare gut microbiota differences between colorectal polyp patients and healthy controls using systematic review and meta-analysis using 16S rRNA sequencing data.</p><p><strong>Materials and methods: </strong>Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic search was performed across multiple databases (PubMed, Web of Science, Embase, Cochrane Library) up to April 2025. Only studies comparing gut microbiota profiles between colorectal polyp patients and healthy controls were included. Data was independently screened and extracted by two reviewers, and study quality was assessed using the Newcastle-Ottawa Scale. Meta-analyses were conducted with R (version 4.4.1) and Stata (version 18.0), with heterogeneity assessed via the I² statistic and publication bias through funnel plots, Egger's test, Begg's test, and sensitivity analyses.Logit transformation was applied to enhance the accuracy and reproducibility of the analysis. Additionally, KEGG pathway data was utilized to explore the distinct metabolic pathway patterns between polyp patients and healthy controls.</p><p><strong>Key findings: </strong>Systematic review and meta-analysis were performed by synthesizing 11 independent 16S rRNA-sequenced studies. Our analysis revealed that patients with colorectal polyps exhibited significantly reduced GM diversity, decreased Firmicutes abundance, and increased Fusobacteria abundance. KEGG pathway analysis indicated enrichment of the TCA cycle in polyp patients and more active amino acid metabolism in healthy controls.</p><p><strong>Significance: </strong>Patients with colorectal polyps have distinct gut microbiota characteristics and specific metabolic shifts. These findings may facilitate the discovery of non-invasive biomarkers, guide personalized prevention strategies, and improve risk stratification for early intervention.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"104"},"PeriodicalIF":4.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12699881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}