This study aimed to compare the Helicobacter pylori (H. pylori) eradication efficacy, safety, patient compliance, and short-term effects on the gut microbiota of vonoprazan-based potassium-competitive acid blocker (P-CAB) dual therapy and esomeprazole-based proton pump inhibitor (PPI) dual therapy. A total of 110 H. pylori-positive patients were enrolled and non-randomly assigned to the P-CAB group (n = 50, vonoprazan 20 mg bid + amoxicillin 750 mg qid) or the PPI group (n = 60, esomeprazole 20 mg qid + amoxicillin 750 mg qid). Twenty-two H. pylori-negative individuals served as healthy controls (HC). Eradication was assessed by the ¹³C-urea breath test four weeks after treatment. Fecal samples were collected at baseline (week 0), after eradication (week 2), and at confirmation (week 6) for 16 S rRNA gene sequencing to analyze gut microbiota diversity, composition, and functional changes. The P-CAB group showed a higher eradication rate than the PPI group across all analysis sets, reaching statistical significance only in the per-protocol analysis (97.73
Clostridioides difficile infection (CDI) is an urgent threat in the United States (US). The severity of the disease is strongly correlated with intestinal inflammation. Biomarkers of intestinal inflammation can be detected in fecal specimens. The aim of this study was to investigate whether fecal S100 calcium-binding protein B (S100B) is associated with poor CDI outcomes. Fecal samples from patients diagnosed with CDI were collected from April 2021 to February 2022. Levels of S100B and other known biomarkers for intestinal inflammation (myeloperoxidase-MPO, lipocalin-2-Lcn2, calprotectin-S100A8/A9, IL-6, and brain-derived neurotrophic factor-BDNF) were measured in fecal specimens by ELISA. C. difficile isolates from matched fecal specimens were tested for the binary toxin genes (cdtA/cdtB) by qPCR. The majority of patients were female (59.06
The human microbiome, particularly the gut microbiome, plays a critical role in host immunity, metabolism, and barrier function. Emerging evidence suggests that persistent alterations in microbiome composition—termed dysbiosis—may contribute to the development and symptom persistence of Long COVID. To map the available literature on microbiome dysbiosis in relation to Long COVID, identify key microbial alterations, associated symptoms, and evaluate potential microbiome-targeted interventions. The scoping review followed Joanna Briggs Institute (JBI) methodological guidance and was reported according to PRISMA-ScR. A comprehensive search of PubMed, Scopus, Web of Science, and Cochrane Library databases was conducted for studies published from January 2000 to May 2025. Eligible studies included human subjects with a clinical diagnosis of Long COVID and microbiome-related outcomes. Data was charted using a standardized form and synthesized narratively and descriptively. A total of 62 sources were included, most of which were narrative, conceptual, or descriptive in nature. The available literature most frequently discussed gut microbiome dysbiosis in relation to Long COVID, including reduced abundance of beneficial taxa such as Faecalibacterium prausnitzii and Bifidobacterium adolescentis, and increased abundance of opportunistic or pro-inflammatory taxa such as Ruminococcus gnavus and Clostridium innocuum. Reported or proposed associations involved fatigue, gastrointestinal symptoms, neuropsychiatric manifestations, and immune dysregulation. Evidence from respiratory and oral microbiomes was more limited. Microbiome-targeted interventions, including probiotics, prebiotics, synbiotics, diet, and fecal microbiota transplantation (FMT), were mainly proposed or discussed, with limited direct interventional evidence. Current evidence suggests that microbiome alterations may be associated with Long COVID, but the available literature remains largely descriptive, observational, and hypothesis-generating. Further longitudinal and interventional studies are needed to clarify causality and determine whether microbiome-targeted strategies have therapeutic value.
The gut virome remains one of the least resolved components of the human microbiome, limiting interpretation of how viral communities shape intestinal injury and recovery. Hematopoietic stem cell transplantation (HSCT), particularly in the allogeneic setting, offers an informative human model of gut virome instability because conditioning-related epithelial injury, profound immune depletion, delayed immune reconstitution, antimicrobial and antiviral pressure, and graft-versus-host disease (GvHD) converge over a short time window to destabilize the intestinal ecosystem. In this context, the gut virome is best understood not only as a reservoir of reactivating pathogens, but as a clinically informative ecological layer linking mucosal vulnerability, bacterial network instability, metabolite loss, infection risk, and post-transplant recovery. Emerging human studies show that post-transplant virome signals are dynamic, individualized, and compartment-dependent. Longitudinal stool profiling has revealed viral blooms, enrichment of persistent DNA viruses, reduced phage richness, and cross-kingdom ecological disruption in association with enteric GvHD. Targeted enteric viral studies and biopsy-based analyses further indicate that stool, blood, and tissue viral signals are not clinically interchangeable, and that broader virologic interrogation may uncover intestinal viral activity not captured by routine plasma surveillance alone. Multi-omics evidence now extends this view by linking bacteriophage-associated bacterial consortia to protective intestinal metabolites and outcome-related ecological states. These advances shift the field from single-virus interpretation toward a cross-kingdom model of injury and recovery. The next step is to convert association-rich viromics into longitudinal, compartment-aware, and intervention-linked frameworks that can support ecological risk stratification and more precise supportive care in HSCT.
Lancefieldella parvula (previously known as Atopobium parvulum) has been associated with inflammatory bowel disease (IBD); however, prior in vivo studies relied on an oral-derived reference strain rather than intestinal clinical isolates, limiting interpretation of its role in gut inflammation. To address this gap, we isolated a clinical strain of L. parvula (designated L. parvula TI19E08) from a mucosal luminal aspirate of an ulcerative colitis (UC) participant. We developed a strain-specific quantitative PCR assay to quantify its abundance across anatomical sites in treatment-naïve pediatric IBD participant (UC and Crohn’s disease (CD)) and examined its relationship with site-specific endoscopic inflammation severity. We demonstrated that the relative abundance of L. parvula TI19E08 increased with increasing local inflammation severity. In UC, both strain-specific and total L. parvula levels were strongly correlated with inflammation severity, particularly in the proximal colon. In CD patients, strain-level associations were most pronounced in the terminal ileum, which is consistent with the disease distribution. This study characterizes an intestinal L. parvula isolate and demonstrates that strain-level expansion correlates with disease severity across IBD subtypes and anatomical regions. These findings identify L. parvula TI19E08 as a candidate mucosal marker of inflammation severity in IBD patients.
Multidrug resistance in Helicobacter pylori has reached alarming levels, compromising standard eradication therapies worldwide. This narrative review examines the interaction between efflux pumps and biofilm formation as key factors driving multidrug resistance (MDR) in this pathogen. A systematic search of databases (PubMed, ResearchGate, Google Scholar, Web of Science, and Scopus) was conducted to identify relevant literature, and findings were synthesized narratively. Efflux pumps belonging to resistance–nodulation–division (RND), the major facilitator superfamily (MFS), the ATP-binding cassette (ABC) superfamily, the multidrug and toxic compound extrusion (MATE) family, and the small multidrug resistance (SMR) family actively expel antibiotics and reduce intracellular drug concentrations. Concurrently, biofilms create a protective matrix that restricts drug penetration and harbors persister cells. Emerging evidence indicates that efflux pumps not only confer resistance but also support biofilm architecture, stress adaptation, and bacterial survival in the gastric environment. Based on the recent in vitro, in vivo, and clinical studies, we explore key molecular mechanisms, including efflux gene upregulation during biofilm development and regulatory control by SpoT-mediated stringent responses. We also discuss therapeutic strategies targeting this interaction, such as efflux pump inhibitors, biofilm disruptors, natural compounds, and nanoparticle-based delivery systems. Understanding this dynamic collaboration is essential for developing novel strategies to revitalize the eradication of H. pylori and reduce associated disease burdens.
Bifidobacteria are the initial colonizers of the human gastrointestinal tract. Due to an obligate anaerobic character, the isolation and culture of Bifidobacterium spp. is challenging. This bottleneck has led to studies being focused on metagenomic analysis rather than genome sequencing of Bifidobacterium spp. from pure cultures. Our metadata analysis revealed paucity of Bifidobacterium genomes reported from the Indian subcontinent. In this report, we describe the selective isolation and whole genome sequencing (WGS) of Bifidobacterium crudilactis from a pure culture of dairy origin from India. The WGS by Oxford Nanopore long-read sequencing of genomic DNA of B. crudilactis isolate NASR_001 revealed a single circular chromosome of 2,347,652 bp with a GC content of 57.5
Considerable evidence has accumulated over the past two decades demonstrating that Escherichia coli, specifically adherent-invasive E. coli, contributes to the pathogenesis of Crohn’s disease. Adherent-invasive E. coli can adhere to and invade intestinal epithelial cells, survive, and replicate within macrophages, thereby enabling a key mechanism that induces chronic inflammation. Despite extensive knowledge of the molecular interactions between adherent-invasive E. coli and the host from these studies, translating this knowledge into targeted therapy remains limited.In this review, we summarize current and proposed treatments to prevent or eliminate adherent-invasive E. coli colonization. We provide a theoretical framework that categorizes these strategies into four main pillars: direct pathogen targeting (e.g., antibiotics, phage therapy), blockade of bacterial virulence factors (e.g., anti-adhesive compounds, QseC inhibitors), host-mediated clearance (e.g., autophagy inducers), and ecological intervention/restoration (e.g., fecal microbiota transplantation, Probiotic, Prebiotic and Probiotics). Finally, we discuss new modalities, including predatory bacteria, siderophore immunization, and other approaches. This review identifies the latest weapons against adherent-invasive E. coli, synthesizes experimental and clinical evidence to provide a comprehensive view of this evolving therapeutic arsenal, and offers ideas for future treatment of Crohn’s disease.
Gut microbiota dysbiosis is increasingly viewed as a disruption of microbial metabolic functions rather than only a shift in microbial composition. Microbiota-derived metabolites not only shape microbial ecology but also directly influence surrounding host tissues by modulating epithelial cell signaling, inflammation, and tumor-associated processes. Among dysbiosis-associated microbes, Fusobacterium is consistently enriched in colorectal cancer (CRC) and contributes to tumor progression, yet the ecological factors regulating its expansion and interaction with host tissues remain unclear. Here, we investigated how microbiome-derived metabolite environments associated with healthy and dysbiotic microbial communities influence Fusobacterium fitness and colorectal epithelial cell behavior. CRC-associated dysbiosis was generated using an orthotopic murine CRC model combined with antibiotic-induced microbiota perturbation. Gut microbial communities were profiled using 16 S rRNA gene sequencing. Metabolite-enriched supernatants derived from healthy gut microbiota, oral microbiota, dysbiotic microbiota and probiotic cultures were evaluated for their effects on CRC-associated bacteria and Fusobacterium sp. growth, adhesion and invasion. These metabolite supernatants were applied to colorectal cancer cells and their effects on viability (MTT assay), migration (scratch assay), apoptosis (Annexin V-FITC flow cytometry), and inflammatory signaling (Western blot analysis of inflammatory markers) were evaluated. CRC-associated dysbiosis showed reduced microbial diversity with enrichment of opportunistic taxa including Fusobacterium and depletion of beneficial commensals such as Lactobacillus and Bifidobacterium. Metabolite-enriched supernatants from healthy gut and oral microbiota suppressed Fusobacterium growth by 55–65
To investigate the clinical characteristics of invasive non-typhoidal Salmonella (iNTS) infection in children and systematically analyze associated factors. Clinical data, including epidemiological information, demographic characteristics, clinical manifestations, laboratory test results, bacterial strain characteristics, and antimicrobial susceptibility profiles, were collected from pediatric patients hospitalized with non-typhoidal Salmonella (NTS) infection at Fujian Maternal and Child Health Hospital or Fujian Children’s Hospital from January 2013 to December 2022. Patients were categorized into iNTS and non-iNTS infection groups based on bacterial culture sources. Univariate comparisons explored clinical features associated with iNTS infection. Multivariate logistic regression and receiver operating characteristic (ROC) curve analyses identified associated factors for iNTS infection. Subgroup analysis was performed by age stratification (infants: <1 year, toddlers: 1–<3 years, and older children: ≥3 years). A total of 314 children with NTS infection were included, of whom 38 (38/314, 12.1
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. 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. 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.
Acute Lymphoblastic Leukemia (ALL) is an aggressive malignancy of lymphoid progenitors, and remains the most commonly diagnosed hematological cancer in the pediatric population. Although 5-year overall survival rates now exceed 90
BackgroundIncreasing evidence highlights the critical role of gut microbiota diversity in maintaining systemic homeostasis; however, the mechanisms by which microbiota-derived metabolites regulate host targets remain incompletely understood. Intervertebral disc degeneration (IDD) is strongly associated with chronic inflammation and metabolic dysregulation. This study employed a network pharmacology approach to elucidate metabolite-target interactions underlying the gut-disc axis.MethodsGut microbiota-derived metabolites were retrieved from the gutMGene database, and their potential targets were predicted using the Similarity Ensemble Approach and SwissTargetPrediction. IDD-related genes were collected from GeneCards and OMIM databases. Overlapping targets were identified to construct a protein-protein interaction (PPI) network and screen core genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using R software. A gut microbiota-metabolites-targets (G-M-T) network was established, followed by molecular docking to assess metabolite-target binding affinities.ResultsTwenty-two overlapping targets were identified, among which nine key candidates were initially screened. Network analysis revealed IL6, TLR4, CXCL8, and JUN as core targets due to their high connectivity. Enrichment analyses indicated that these targets were mainly involved in inflammatory responses, oxidative stress, apoptosis, extracellular matrix metabolism, and IL-17- and lipid-related pathways. The G-M-T network highlighted butyrate, propionate, acetate, succinate, trimethylamine oxide, and 3-indolepropionic acid as core metabolites. Molecular docking suggested favorable binding affinities, with 3-indolepropionic acid exhibiting the strongest interactions.ConclusionGut microbiota-derived metabolites, particularly 3-indolepropionic acid, may modulate IDD progression by targeting IL6, TLR4, CXCL8, and JUN through inflammation- and lipid-related pathways, providing mechanistic insights into the gut-disc axis.
Candida albicans (C. albicans) is among the most common opportunistic fungal pathogens and causes superficial infections and life-threatening invasive candidiasis in immunocompromised individuals. In recent years, C. albicans has become resistant to a wide range of clinical drugs, and the identification of effective antifungal drugs is an extremely urgent medical need. Acetylshikonin (ASK) is a naphthoquinone compound extracted from Lithospermum erythrorhizon that exhibits potent antibacterial activity. However, its efficacy against C. albicans and antimicrobial mechanisms, especially against drug-resistant C. albicans, are unclear. The antifungal activity of ASK was evaluated based on minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) measured in vitro and in mouse models of vulvovaginal candidiasis and oropharyngeal candidiasis to assess its efficacy in vivo. Mechanistic investigations included assessments of cell membrane and cell wall damage, adhesion ability, oxidative stress evaluation, protein expression, and target identification (including RT‒qPCR, molecular docking, and related methods). The main active ingredient from Lithospermum erythrorhizon that targets C. albicans was identified as ASK. It exhibits significant activity against drug-resistant fungi both in vitro and in vivo. Moreover, ASK can reduce the adhesion of C. albicans and damage to cell membrane and cell wall and induce apoptosis-like cell death-like cell death. In addition, ASK may directly bind to Malate Synthase 1 (Mls1) and effectively downregulate its expression and inhibit the glyoxylate cycle, leading to the generation and accumulation of large amounts of ROS, and damage to DNA to achieve its antifungal effects. ASK can treatment drug-resistant C. albicans infections, its mechanism of action is related to the inhibition of Mls1.
Asymptomatic Entamoeba histolytica (Eh) carriage is a major transmission reservoir, yet how the gut ecosystem—particularly microbiota-derived metabolites such as secondary bile acids—supports persistent colonization remains unclear. We investigated whether gut microbiome–metabolite features are associated with Eh carriage and could influence parasite phenotypes We integrated shotgun metagenomics from a prospectively screened outpatient cohort (n=36) with functional in vitro assays. An ordinal stepwise model across detection states (Eh−, Eh_qPCR, Eh_Cyst) was used to identify candidate microbial features, followed by bile-acid exposure assays and transcriptomic profiling to evaluate impacts on parasite fitness and metronidazole susceptibility in vitro Microbiome profiling suggested taxon-specific shifts rather than wholesale dysbiosis. Community-level beta diversity showed no significant separation, whereas genus richness was higher in Eh_Cyst (unadjusted p=0.046). Multivariable modeling yielded concordant directional but non-significant trends (all q>0.9), highlighting Firmicutes genera including Coprococcus, Ruminococcus, and Catenibacterium as candidate taxa. We then evaluated deoxycholic acid (DCA), a microbiota-modified secondary bile acid. In vitro, 100 μM DCA extended Eh survival under nutrient-limited conditions and reduced metronidazole susceptibility after pretreatment. Transcriptomic profiling showed that DCA induced a distinct response, including an 8.34-fold induction of the ABC transporter P-glycoprotein-2 and upregulation of lipid remodeling and stress-response genes, supporting a bile acid–driven adaptive program consistent with intestinal persistence Our findings suggest that secondary bile acids, exemplified by DCA, can reprogram Eh gene expression and attenuate metronidazole susceptibility in vitro. In the context of cyst-associated microbiome signatures, this supports the plausibility of a microbiome–bile acid–parasite axis that may promote persistence in asymptomatic carriers and could influence treatment efficacy
Ulcerative colitis (UC) is associated with gut microbiota alterations, but the role of the fungal microbiota remains underexplored. We conducted a prospective study quantifying absolute bacterial and fungal abundance in faecal samples from UC patients with varying disease activity. We amplified the ITS2 sequence (fungi) and 16 S rRNA gene (bacteria) in three groups of patients: UC long remission (UClr); UC short remission (UCsr) and UC flare (UCfl). Two faecal samples from UClr and UCsr, and one sample from UCfl group (at flare-onset) were collected. Eighty-seven patients were included: 29 UClr, 20 UCsr, and 38 UCfl. Across all patients, fungal ITS2 gene copies were markedly lower than bacterial 16 S rRNA copies (median 9.27E + 05 vs. 4.28E + 11 copies/g), with a fungal-to-bacterial ratio of 1:461,000. Fungal abundance was significantly higher in UCfl than in UClr (p = 0.0026), but not UCsr. The ITS2/16S ratio was also elevated in UCfl versus both remission groups (p < 0.01). Over time, fungal abundance showed greater variability than bacterial abundance, with a modest but significant decrease in the ITS2/16S ratio at 8 weeks (p = 0.029). While bacterial loads remained stable across disease states, fungal abundance and the fungal-to-bacterial ratio were higher during UC flares. These findings describe an association between fungal dynamics and disease activity in UC and support further investigation of inter-kingdom microbial relationships in this context.
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea in hospitalized patients and is classified as an urgent public health threat. Current therapies, while effective, are limited by antibiotic-induced dysbiosis, treatment failure, and high recurrence rates, underscoring the need for novel therapeutics. Carbadox (CRX), an antibacterial growth promoter, has recently been identified as a potential anti-C. difficile inhibitor. This study aimed to comprehensively evaluate the anti-C. difficile activity, mechanism of action, and in vivo efficacy of CRX. CRX activity was assessed against a diverse panel of clinical C. difficile isolates using MIC determination, time-kill kinetics, and post-antibiotic effect assays. Its effects on toxin production were evaluated at subinhibitory concentrations, while post-germination vegetative growth was assessed under germination-permissive conditions at bactericidal concentrations. Mechanistic studies included macromolecular synthesis assays, reactive oxygen species (ROS) quantification, and antioxidant rescue experiments. Potential drug interactions were tested in combination assays with standard-of-care agents. Finally, the efficacy of CRX was examined in both acute and recurrent C. difficile infection (CDI) mouse models. CRX demonstrated potent in vitro activity, inhibiting 50
Amebiasis, which is caused by Entamoeba histolytica, is prevalent worldwide. Clinical presentation varies from asymptomatic infection to life-threatening extraintestinal disease, and the clinical form can change within one infectious episode. It is also known that periodical animal passages are required for maintaining virulence of E. histolytica in vivo model, such as a hamster liver abscess or murine colitis model. However, it remains uncertain whether or for how long virulence induced by environmental stimuli persists during in vitro passage at the clonal level. We generated clones from a hamster liver-passaged E. histolytica strain and periodically checked their liver abscess-forming capability during subsequent in vitro passages. We obtained three clones (ALA-1, ALA-5, and ALA-6) that were highly virulent (abscess weight accounting for > 30
Campylobacter species are among the leading causes of bacterial gastroenteritis worldwide, with poultry recognized as a major reservoir for several life-threatening foodborne and zoonotic infections. The overuse and possible misuse of antimicrobials in the livestock sector in different countries of the world have contributed to the emergence of multidrug-resistant Campylobacter jejuni strains with significant public health concerns. To better understand the evolution, host adaptation, and antimicrobial resistance (AMR) of C. jejuni, we performed a global comparative genomic analysis of 1,125 high-quality genomes from human and chicken hosts, including five newly sequenced isolates representing broiler chicken samples. Pangenome analysis of 1,125 C. jejuni genomes identified 4,489 orthologous gene clusters, of which 1,360 constitute the conserved core genome. The findings indicate a weakly open pangenome approaching saturation, suggesting limited gene acquisition. Phylogenomic analysis revealed three major clades with limited geographic clustering, consistent with global dissemination and evolutionary divergence. Human isolates were distributed across all clades, whereas chicken isolates were primarily restricted to clade one. Sequence typing identified 290 STs across 30 clonal complexes, with ST-48 enriched in chickens while ST-50 predominated in humans, reflecting potential host adaptation and epidemiological structuring. All five in-house isolates were multidrug-resistant, producing extended-spectrum β-lactamases (ESBLs) that conferred β-lactam resistance. Additionally, three isolates exhibited resistance to macrolides and tetracycline, further underscoring their broad resistance phenotype. Genome-wide AMR profiling of 1,125 C. jejuni isolates identified 31 well-characterized resistance genes, including those encoding RND and MATE efflux systems, penicillin-binding proteins, and metallo- and serine-beta-lactamase families, underscoring their intrinsic role in the core resistome. The most common resistance mutations were gyrA p.T86I (60.3
Helicobacter pylori is the principal infectious driver of chronic gastritis, a precursor to several gastric lesions. Data on tissue-based prevalence and associated histopathology in Uganda remain limited. H. pylori affect over half the global population, leading to chronic gastritis and subsequent complications with increased risk of gastric cancer in about 1–3
