Gut Pathogens最新文献

{"title":"Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services.","authors":"Laura Vega, Claudia Inés Birchenall-Jiménez, Anghy Aponte, Daniela Durán, Camila López, María C Moreno-Matson, Camila Perilla, Darío Pinilla, Giovanni Rodríguez-Leguizamón, Erika Sánchez, Aldair Santana, Giovanny Herrera, Juan David Ramírez, Marina Muñoz","doi":"10.1186/s13099-026-00809-5","DOIUrl":"10.1186/s13099-026-00809-5","url":null,"abstract":"<p><strong>Background: </strong>Diarrhea remains a major cause of morbidity worldwide, particularly in low- and middle-income countries. Hospital environments impose strong selective pressures on the gut microbiome through antimicrobial exposure, invasive procedures, and pathogen transmission, yet differences between hospital-onset and community-onset diarrhea remain poorly characterized at the microbiome level. This study aimed to compare the taxonomic and functional profiles of the gut microbiome in hospitalized (Hosp) and emergency room (ER) patients with diarrhea using shotgun metagenomics.</p><p><strong>Results: </strong>Fecal samples from 41 patients (Hosp = 24; ER = 17) attending the Hospital Universitario Mayor-Méderi (Bogotá, Colombia) were analyzed. The gut microbiomes were dominated by Enterobacteriaceae, particularly Klebsiella pneumoniae and Escherichia coli, together with abundant bacteriophages from the families Myoviridae, Siphoviridae, Podoviridae, and crAss-like phages. Phages predicted to infect Escherichia and Klebsiella were significantly depleted in Hosp patients (p < 0.05). Read-based functional profiling revealed the presence of virulence factors associated with K. pneumoniae capsule biosynthesis, secretion systems, and toxins from Clostridioides difficile and Clostridium perfringens. In parallel, Hosp patients showed a higher diversity of antimicrobial resistance markers, with a marked increase in glycopeptide resistance determinants. A total of 492 high-quality metagenome-assembled genomes were reconstructed, including multiple diarrhea-associated taxa. Hosp patients exclusively harbored genomes of K. pneumoniae, Enterococcus faecium, and most reconstructed Clostridium species (C. symbiosum, C. saccharolyticum_A, C. innocuum, C. scindens, C. leptum, and Clostridium sp000435835). In contrast, ER patients harbored genomes classified as Escherichia coli, Escherichia flexneri, and Enterococcus faecalis. Genomes associated with hospitalization carried higher loads of antimicrobial resistance markers (e.g., oqxA and aac(6')-Ii) and virulence factors (e.g., iutA and traT), whereas ER genomes, particularly E. coli and E. flexneri, encoded diverse aminoglycoside resistance and adhesion traits.</p><p><strong>Conclusions: </strong>Hospital-onset diarrhea was associated with distinct microbiome features, including differences in phage-bacteria dynamics involving key diarrhea-associated taxa, as well as a higher abundance of virulence factors and antimicrobial resistance markers. These findings underscore the potential value of shotgun metagenomics as a complementary approach for infection surveillance and the development of precision diagnostic strategies in hospital settings.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12980963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201486","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":"Maternal separation during breastfeeding as a risk factor for developing giardiasis: evaluation in a rodent model.","authors":"M F Gerena-Cruz, I M Guatibonza-Arévalo, G Garcia-Laguna, R Guerrero-Lozano, Z Dueñas","doi":"10.1186/s13099-025-00720-5","DOIUrl":"https://doi.org/10.1186/s13099-025-00720-5","url":null,"abstract":"<p><strong>Background: </strong>Giardia lamblia is a globally prevalent gastrointestinal parasite. Breastfeeding provides protective effects against infections, but the impact of early life stress, such as maternal separation, on G. lamblia infection remains unclear. This study examines how Maternal Separation During Breastfeeding (MSDB) affects G. lamblia infection in Wistar rats.</p><p><strong>Results: </strong>In a Wistar rat model, MSDB led to a significant increase in G. lamblia cyst shedding, with early effects more evident in males and delayed effects in females. Additionally, infected MSDB rats showed elevated eosinophil infiltration in the intestinal mucosa-consistent with heightened immune response-along with altered villus/crypt ratios in non-infected separated animals, particularly in males.</p><p><strong>Conclusions: </strong>Our findings demonstrate that maternal separation during breastfeeding intensifies the severity of G. lamblia infection. This suggests that early-life maternal interactions may play a protective role in host resistance specifically against G. lamblia, highlighting the relevance of early-life conditions in shaping outcomes of giardiasis.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146197643","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":"Shigella flexneri 1c bacteremia in a child: a case report.","authors":"Mehrzad Sadredinamin, Zohreh Ghalavand, Maryam Rostamyan, Raana Kazemzadeh Anari, Seyyed Mohammadreza Hosseini Imeni, Bahram Nikmanesh","doi":"10.1186/s13099-026-00804-w","DOIUrl":"10.1186/s13099-026-00804-w","url":null,"abstract":"<p><strong>Background: </strong>Shigellosis is a significant public health issue in developing countries, particularly affecting young children under the age of five. While it primarily causes gastrointestinal infections, there are rare complications, such as bacteremia, that mainly occur in young children. We present a case of dysentery caused by Shigella flexneri serotype 1c, followed by bacteremia.</p><p><strong>Case presentation: </strong>A 13-month-old Afghan child presented with fever, dysentery, distended abdomen, mild tenderness, and dehydration. He did not respond to empirical treatment with ceftriaxone. However, he was successfully treated with a combination of gentamicin and ciprofloxacin. This is the first report of a patient in Iran who was positive for S. flexneri serotype 1c and harbored the ipaB, ipaC, ipaD, ipaH, ipgD, virA, and sen virulence factors.</p><p><strong>Conclusions: </strong>This case alerts clinicians to consider the possibility of Shigella bacteremia in young children. Early and accurate diagnosis can improve management and prognosis to reduce the risk of fatality outcomes. Additionally, it emphasizes the need to characterize the role of Shigella spp. virulence genes in causing bacteremia.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12961823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146197641","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":"A sixteen-month monitoring of human enteric viruses associated with acute gastroenteritis in Senegal.","authors":"Ousmane Kébé, Bissoume Sambe Ba, Fatou Diène Thiaw, Cheikh Fall, Mamadou Aliou Barry, Landry Gérard Boussiengui, Jean Pierre Diallo, NDack Ndiaye, El Hadji Mamadou Ndiaye, Amadou Alpha Sall, Boly Diop, Yakhya Dièye, Ousmane Faye, Martin Faye","doi":"10.1186/s13099-026-00806-8","DOIUrl":"10.1186/s13099-026-00806-8","url":null,"abstract":"<p><strong>Background: </strong>Human enteric viruses are common pathogens that can cause acute gastroenteritis (AGE). The largest proportion of morbidity and mortality occurs in developing countries. This study aimed to assess the prevalence of enteric viruses causing AGE and genotype rotavirus A and norovirus positive specimens collected between September 2020 and December 2021 in Senegal.</p><p><strong>Methods: </strong>Overall, 417 patients of all ages with AGE were enrolled in this study. Specimens were screened for enteric viruses using the Allplex™ GI-Virus Assay or singleplex RT-qPCR. Samples positive for rotavirus A or norovirus were genotyped using an amplicon-based method with nanopore sequencing. Data were analysed using the R statistical software.</p><p><strong>Results: </strong>Of the 417 patients screened, 37,6% tested positive for at least one enteric virus and 30 (7.2%) patients had mixed infections. Norovirus (n = 58; 13.9%) was most frequently detected, followed by enterovirus (n = 49; 11.8%), rotavirus A (n = 23; 5.5%), adenovirus (n = 22; 5.3%), sapovirus (n = 18;4,3%), astrovirus (n = 15;3.6%) and Aichivirus (n = 3; 0.7%). However, the prevalence of rotavirus A was higher in the border regions (15.9% in Matam and 14.3% in Kédougou), highlighting the need to strengthen surveillance and research programs on rotavirus A in Senegal to better support the national vaccine program. The most common rotavirus A genotype was G12[P8] (47.8%) belonging to the lineage III and grouping with strains from other African countries. GII.4 Sydney 2012 [P31] (47.6%) was the predominant norovirus genotype in our study, followed by GII.16[PNA7] (28.6%), GII.6[P7] (14.3%), GII.2[P16] (4.8%) and GII.13[P16] (4.8%). Vomiting was significantly associated with rotavirus A infection while norovirus and enterovirus were the most common viral pathogens detected in patients with AGE.</p><p><strong>Conclusion: </strong>Our findings provide new insights into the epidemiology of enteric viruses in Senegal. However, integrating these data with information on bacterial etiologies would allow for a more comprehensive assessment of the burden of AGE in Senegal.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13088851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146178554","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":"Feco-prevalence and risk factors of Helicobacter pylori infection among adults with dyspepsia in Mogadishu, Somalia: a cross-sectional study.","authors":"Mohamed Yusuf Abdi, Rowdo Mohamed Mohamud, Salma Yusuf Abdullahi","doi":"10.1186/s13099-026-00807-7","DOIUrl":"10.1186/s13099-026-00807-7","url":null,"abstract":"<p><strong>Background: </strong>Helicobacter pylori is one of the most prevalent bacterial infections in humans, affecting more than half of the global population. It is a major contributor to gastric disorders among patients attending gastroenterology clinics. Therefore, this study aimed to evaluate the fecal prevalence and associated factors of Helicobacter pylori infection in adult patients with dyspepsia in Mogadishu, Somalia.</p><p><strong>Methods: </strong>A cross-sectional investigation was conducted at Shaafi Hospital between February and June 2025, encompassing 385 adult patients with dyspepsia. Researchers employed structured questionnaires to collect sociodemographic data and Helicobacter pylori infection-associated factors. Helicobacter pylori fecal antigen was detected in stool samples using lateral flow immunochromatographic assay. Binary and multiple logistic regression analyses were performed to identify the factors involved. A statistical association between variables was recognized when the p-value was below 0.05, ensuring a 95% confidence level.</p><p><strong>Results: </strong>Out of 385 adult patients with dyspepsia examined, 40% (n = 154) tested positive for Helicobacter pylori infection. Bivariate analysis revealed several factors linked to the infection: residing with children or elderly individuals (OR = 0.447, p = 0.014), consuming unwashed fruits or vegetables (OR = 1.658, p = 0.017), and eating white meat (OR = 1.986, p = 0.001). However, in the multivariate analysis, only two factors remained significant: living with children or elderly people was associated with a reduced likelihood of infection (AOR = 0.471, p = 0.015), whereas consumption of white meat was associated with a higher risk of infection (AOR = 1.699, p = 0.019). Other factors, such as hygiene habits, income, education, and smoking, did not show statistically significant associations.</p><p><strong>Conclusion: </strong>This study found a notable prevalence of Helicobacter pylori infection among adults with dyspepsia. Consumption of white meat was associated with an increased risk of infection, whereas living with children or elderly individuals appeared to provide some protection. These findings highlight the need for targeted public health strategies and suggest the need for further investigation into dietary and household factors that may influence Helicobacter pylori transmission.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12983509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146149533","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":"Tropical sprue: a narrative review of a neglected malabsorption syndrome.","authors":"Esteban Ortiz-Prado, Jorge Vasconez-Gonzalez, Melissa Villavicencio-Gomezjurado, Camila Salazar-Santoliva, José G Prieto-Marin, Karen Villarreal-Burbano, Isaac A Suárez-Sangucho, Ana Paula Bastidas, Emilia Puente-Villamarín, María Paz Cadena, Juan S Izquierdo-Condoy","doi":"10.1186/s13099-026-00803-x","DOIUrl":"10.1186/s13099-026-00803-x","url":null,"abstract":"<p><p>Tropical sprue, a rare malabsorption syndrome, remains a significant yet underrecognized gastrointestinal disorder endemic to tropical regions, including South and Southeast Asia (e.g., India, Pakistan) and Caribbean islands (e.g., Puerto Rico, the Dominican Republic, Haiti). Its etiology remains uncertain, but mounting evidence supports an infectious origin, with bacterial overgrowth involving pathogens such as Alcaligenes, Klebsiella, and Enterobacter species frequently implicated. The disease causes profound intestinal alterations that impair the absorption of vitamin B12, fat-soluble vitamins (A, D, E, and K), and minerals such as calcium and magnesium, frequently resulting in chronic diarrhea and severe nutritional deficiencies. Histologically, villous atrophy of the jejunal and ileal mucosa is a hallmark feature. This narrative review synthesizes current knowledge on the epidemiology, etiology, intestinal pathophysiology, and histopathology of tropical sprue, while highlighting diagnostic challenges and the urgent need for further research to elucidate its pathogenesis and improve clinical management in endemic settings.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"15"},"PeriodicalIF":4.0,"publicationDate":"2026-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142282","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":"Clinical impact of high-dose esomeprazole-amoxicillin dual therapy as rescue treatment for Helicobacter pylori infection: a meta-analysis of randomized controlled trials.","authors":"Iftikhar Khan, Muhammad Ansab, Amna Nadeem, Fatima Aslam, Hooria Aiman Shadab, Fnu Sawaira, Ehsanullah Alokozay, Faisal Naseer, Hira Hameed, Mohamed Fawzi Hemida, Mahnoor Asghar Keen, Saad Khan, Soban Ali Qasim, Amanullah, Kiran Inam","doi":"10.1186/s13099-026-00802-y","DOIUrl":"https://doi.org/10.1186/s13099-026-00802-y","url":null,"abstract":"<p><strong>Background: </strong>Helicobacter pylori infection, linked to peptic ulcer disease and gastric cancer, faces declining eradication rates due to antibiotic resistance. High-dose esomeprazole-amoxicillin dual therapy (HDDT) is a promising rescue regimen, but its efficacy and safety compared to standard therapies remain unclear.</p><p><strong>Methods: </strong>This systematic review and meta-analysis, adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines, included four randomized controlled trials (n = 1,230) that compared HDDT with standard regimens. PubMed, Embase, and Cochrane CENTRAL were searched through April 2025. Outcomes included eradication rates, compliance, and adverse events. A meta-analysis was conducted using the inverse variance method, with heterogeneity assessed via I² statistics.</p><p><strong>Results: </strong>HDDT showed no significant difference in eradication rates (RR = 0.98, 95% CI: 0.89-1.08, P = 0.6438) or compliance (RR = 1.04, 95% CI: 0.97 to 1.12, P = 0.2522) compared to standard therapies. However, HDDT significantly reduced overall adverse events (RR = 0.28, 95% CI: 0.18-0.44, P < 0.0001), including nausea, headache, fatigue, dysgeusia, bloating, and abdominal pain. No significant differences were observed for serious adverse events, diarrhea, dizziness, decreased appetite, constipation, or skin rash. Heterogeneity varied across the outcomes.</p><p><strong>Conclusion: </strong>HDDT is as effective as standard regimens for H. pylori rescue treatment, with a superior safety profile, supporting its use in patients with prior treatment failures.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142350","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":"Species-level dynamics of gastric microbiome after Helicobacter pylori eradication in high-risk Mongolian population.","authors":"Namsrai Renchinsengee, Saruuljavkhlan Batsaikhan, Ayush Khangai, Gantuya Boldbaatar, Bayasgalan Luvsandagva, Aigul Lazatkhan, Davaadorj Duger, Oyuntsetseg Khasag, Takashi Matsumoto, Yoshio Yamaoka","doi":"10.1186/s13099-026-00805-9","DOIUrl":"10.1186/s13099-026-00805-9","url":null,"abstract":"<p><strong>Background: </strong>Species-level resolution is essential to understand gastric microbiome recovery after Helicobacter pylori eradication, yet short-read 16 S rRNA approaches often obscure clinically relevant changes.</p><p><strong>Methods: </strong>Gastric biopsies from 121 adults in Bayan-Ölgii, Mongolia (71 H. pylori-positive, 50 H. pylori-negative) were analyzed, including nine paired pre- and post-eradication gastric biopsy samples collected six months apart, enabling exploratory longitudinal analysis. Full-length 16 S rRNA (V1-V9) sequencing was performed using the Oxford Nanopore platform with EMU taxonomic assignment (SILVA v138.1/NCBI RefSeq). Ecological changes were evaluated using diversity indices, principal coordinates analysis (PCoA) with PERMANOVA, and differential abundance testing (DESeq2, FDR < 0.05). Eradication therapy (esomeprazole-bismuth-doxycycline-levofloxacin) achieved success in 54 of 57 H. pylori-positive patients (94.7%).</p><p><strong>Results: </strong>H. pylori-positive microbiomes were dominated by H. pylori (91.8% ± 3.9%) and exhibited markedly reduced diversity (Shannon = 0.44 ± 0.11) compared with H. pylori-negative samples (2.08 ± 0.25; p < 0.001). Six months after eradication, diversity increased significantly (2.17 ± 0.20; p = 0.0001), with enrichment of oral commensals including Streptococcus mitis (↑ 11.9×), Neisseria elongata (↑ 13.7×), and Prevotella melaninogenica (↑ 13.0×). However, post-eradication profiles at six months remained distinct from H. pylori-negative communities (PERMANOVA R² = 0.12; p = 0.02). In total, 174 amplicon sequence variants changed significantly, including persistence of Fusobacterium nucleatum.</p><p><strong>Conclusions: </strong>Nanopore full-length 16 S sequencing reveals fine-scale, clinically relevant shifts that are masked by partial-gene assays. Eradication rapidly restores microbial diversity, but at six months, is associated with a novel ecological equilibrium rather than complete normalization. This species-resolved approach offers a practical framework for post-eradication microbiome monitoring and may inform strategies to reduce residual gastric cancer risk in high-burden populations.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":"14"},"PeriodicalIF":4.0,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137534","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 microbiome-based strategies for HIV prevention and therapy, current challenges and future prospects.","authors":"Akmal Zubair, Abdullah M Alkahtani, Muhammad Yaqoob Shahani, Naila Afghan","doi":"10.1186/s13099-026-00800-0","DOIUrl":"10.1186/s13099-026-00800-0","url":null,"abstract":"<p><p>The gut microbiome has become a primary controller of host immunity as well as the pathogenesis of human immunodeficiency virus (HIV) infection. Commensal microbes in healthy persons keep the intestinal and other body barriers intact and regulate mucosal and systemic immune responses and generate metabolites, including short-chain fatty acids and indole derivatives that suppress inflammation and stimulate epithelial healing. These functions are impaired by HIV infection via depletion of gut CD4 + T cells, damage caused to epithelium, microbial translocation, and microbiota disruption. In this review article, we summarize recent studies suggesting that a balanced microbiome can mitigate HIV susceptibility and progression by preserving mucosal defenses, limiting systemic immune activation, and generating antiviral compounds. Other interventions, including probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation (FMT), have been trialed with mixed outcomes in most cases, showing small but significant changes in the gut microbial composition and/or inflammatory markers. Current evidence highlights the potential of microbiome-targeted strategies to support HIV management; however, substantial gaps remain. Future research should focus on defining protective microbial signatures, developing next-generation live biotherapeutics, exploring metabolite-based therapies, and conducting large, mechanistically driven clinical trials. Harnessing the microbiome's protective functions could offer novel approaches to reducing HIV transmission, mitigating inflammation, and improving immune reconstitution in infected individuals.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"18 1","pages":"11"},"PeriodicalIF":4.0,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12874720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146124842","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":"Broad-spectrum antibiotic treatment reshapes the gut microbiome, resistome, and colonization potential of opportunistic pathogens: a metagenomics study.","authors":"Abiye Tigabu, Polly H M Leung","doi":"10.1186/s13099-026-00795-8","DOIUrl":"10.1186/s13099-026-00795-8","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The gut microbiota (GM) harbors diverse antibiotic resistance genes (ARGs), which are primarily disseminated through horizontal gene transfer (HGT), contributing to the emergence and spread of multidrug-resistant (MDR) pathogens. Broad-spectrum antibiotics are commonly used to treat a wide range of bacterial infections; however, they also exert collateral effects on non-target microbes. A comprehensive understanding of the impact of broad-spectrum antibiotic treatment on GM composition and the resistome is essential for the effective management of dysbiosis-related complications.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Twenty-one fecal samples were collected from randomly selected study participants. Metagenomic sequencing was performed using the Illumina NovaSeq 6000 platform. FastQC v0.12.1, Trimmomatic v0.39, and Bowtie2 were used for quality control, removal of low-quality reads and adapter sequences, and host DNA removal, respectively. Metagenome assembly, gene prediction, and taxonomic annotation were conducted using MEGAHIT v1.2.9, MetaGeneMark-2, and the NCBI non-redundant protein database (nr), respectively. Resistome profiling was performed using the Comprehensive Antibiotic Resistance Database (CARD) v3.3.4. Functional annotation of protein-coding genes was carried out against the KEGG v112.0, eggNOG v5.0, and CAZy databases.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;An enrichment of the phylum Bacillota and a depletion of Bacteroidota were observed in fecal samples from antibiotic-treated patients. Specifically, the genus Enterococcus and Streptococcus were the most prominent genera in antibiotic-treated patients, whereas Prevotella, Bacteroides, and Faecalibacterium were more abundant in healthy controls. Notably, the opportunistic pathogen E. faecium was elevated in antibiotic-treated patients. In longitudinal patients receiving augmentin treatment, the genera Escherichia and Enterococcus predominated, with E. coli and E. faecium showing increased prevalence compared with baseline in the first and second longitudinal patients, respectively. Antimicrobial resistance genes associated with antibiotic target alteration and protection were strongly linked to Bacillota, whereas efflux pump-mediated resistance mechanisms were positively associated with Bacteroidota and Pseudomonadota. The genes tetM, tet45, vanHM, vanYM, and vanRM were enriched in antibiotic-treated patients, whereas tetQ, tetW, cfxA6, adeF, vanTG, vanYB, and vanWI were more abundant in controls. Furthermore, pmrF, vanM, and cfxA were identified as principal biomarker genes in the first, second, and third augmentin-treated longitudinal patients, respectively.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Dysbiosis of the gut microbiota and alterations in the resistome were detected in antibiotic-treated patients. Notably, the opportunistic pathogens E. faecium and E. coli were enriched in antibiotic-treated individuals, suggesting that broad-spectrum antibiotic therapy","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12950245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146062451","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}