Search Results (6,530)

Anemia represents one of the most frequent systemic complications of inflammatory bowel disease (IBD), with a consistently higher prevalence reported in patients with Crohn’s disease (CD) compared with ulcerative colitis (UC). While chronic inflammation, impaired iron absorption, and intestinal blood loss are recognized contributors, microbiome-mediated mechanisms influencing host iron availability remain insufficiently explored. Emerging evidence indicates that CD-associated dysbiosis is characterized by an increased abundance of siderophore-producing bacteria, particularly members of the Enterobacteriaceae family. Because siderophores are high-affinity iron-chelating molecules capable of competing with host iron acquisition systems and partially escaping lipocalin-2-mediated sequestration, their expansion may contribute to reduced luminal iron bioavailability. In this systematic review, we analyzed comparative microbiome studies published between 2016 and 2026 that directly evaluated microbial differences between CD and UC. CD microbiota consistently demonstrated enrichment in siderophore-associated taxa relative to UC. Based on these findings, we propose that microbiome-driven iron competition may represent an additional mechanistic contributor to the increased prevalence and persistence of anemia observed in CD. Although direct in vivo quantification of siderophore activity in IBD remains limited, the convergence of ecological, functional, and strain-level microbiome evidence supports a biologically plausible interaction between microbial iron-scavenging strategies and host iron metabolism. Full article

Plastics and microplastics are widespread in the environment, yet knowledge about their impact on agricultural soils, including their microbiological properties, remains limited. Therefore, this study addressed the research question regarding the impact of secondary microplastics, biodegradable poly(lactic acid) (PLA) mulch film, and low-density polyethylene (LDPE) film on the abundance, structure, and functions of soil bacteria, with particular emphasis on the presence of bacterial pathogens. PLA and LDPE were applied to the soil at a dose of 4 g kg⁻¹ d.m. of soil. The aim of the experiment was to evaluate and compare the effectiveness of soil bioaugmentation with the Pseudomonas umsongensis strain and its biostimulation with humic acids in mitigating the negative effects of microplastics. The response of culturable bacteria revealed high sensitivity of organotrophic bacteria to both microplastics, with a stronger inhibitory effect from PLA, as well as stimulation of actinomycetes. 16S rRNA gene amplicon sequencing indicated that the materials differentially influenced the bacterial response. PLA most strongly stimulated Actinobacteriota and favored the dominance of Bacillus and Limnochorda, whereas LDPE promoted the growth of Actinobacteriota and Chloroflexota as well as genera KD4-96 and 1921-2. Both microplastics were colonized by potential pathogens, including Bacillus, Mycobacterium, Ralstonia, and Cupriavidus. PLA additionally stimulated the proliferation of Leifsonia sp. and Curtobacterium sp., while both PLA and LDPE reduced the abundance of Enterobacter sp. and Herbaspirillum sp. Bioaugmentation using the Pseudomonas umsongensis strain was more effective in restoring the balance of the soil microbiome than biostimulation with humic acids. The results indicate that microbial preparations based on Pseudomonas umsongensis may serve as an important tool in restoring the balance of soil exposed to microplastics. Full article

Background & Aims: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease frequently requiring liver transplantation (LTx). The gut–liver axis, host genetics, and microbial dysbiosis are thought to contribute to disease progression and post-transplant outcomes. The FUT2 rs601338 polymorphism influences mucosal fucosylation, host–microbial interactions, and susceptibility to infection. This study aimed to investigate the association between FUT2 genotype, colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in a retrospective single-center PSC cohort. Methods: This retrospective cohort study included PSC patients who underwent LTx at Erasmus MC University Medical Center (Rotterdam, The Netherlands) between 1987 and 2015. Pre-transplant archival formalin-fixed paraffin-embedded (FFPE) colonic biopsy specimens were available for microbiome analysis. Of 169 transplanted patients, FFPE tissue was available for 98 individuals, and FUT2 rs601338 genotyping was successfully performed in 87 patients. Patients were classified as FUT2 non-secretors (AA, n = 28) and secretors (GA/GG, n = 59). Post-transplant bacteremia was assessed based on clinically indicated blood cultures during follow-up. Colonic mucosal microbiome composition was analyzed using 16S rRNA gene sequencing. Results: FUT2 non-secretors showed a distinct colonic mucosal microbiome profile compared with secretors, characterized by differential abundance of selected taxa within Proteobacteria, Firmicutes, and Bacteroidetes. Post-transplant bacteremia occurred in 30 patients and was more frequent among non-secretors (43%) compared with secretors (15%). Both FUT2 non-secretor status and post-transplant bacteremia were associated with reduced all-cause post-transplant survival in Kaplan–Meier analysis and remained associated with mortality in multivariable regression models. Specific microbial taxa were also showed associations with bacteremia, mortality, and established prognostic scores, including the Amsterdam–Oxford Model and Mayo Risk Score. Conclusions: FUT2 genotype is associated with alterations in colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in PSC patients undergoing liver transplantation. These findings suggest a potential interplay between host genetics, intestinal microbiota, and infectious complications after transplantation. Given the retrospective design, limited sample size, and use of archival FFPE tissue, all findings should be interpreted as exploratory and hypothesis-generating. Prospective multicenter studies using standardized sampling and high-resolution metagenomic approaches are warranted for validation. Full article

Disentangling the combined effects of heat and ash in natural forest fires is challenging, hindering understanding of soil microbial post-fire responses. A 90-day simulated fire experiment with 16S rRNA sequencing monitored bacterial communities and functional potential in topsoil (0–10 cm) and subsoil (10–20 cm) under seven treatments: blank control/BC, dry ash/DA, wet ash/WA, low-intensity heating/LH, high-intensity heating/HH, charcoal smoldering combustion/CSC, and Fire, with samples collected every ten days. Results: (1) α diversity declined mainly in the topsoil, with reductions of 12.04–19.82% for Shannon, 1.23–2.86% for Simpson, and 16.03–31.34% for the Chao index. Subsoil only declined under CSC. (2) Both heating and ash treatments increased the relative abundance of low-abundance and endemic taxa. Heating significantly enriched thermotolerant, xerotolerant, and oligotrophic taxa, such as Ramlibacter. (3) Topsoil heating treatments separated from BC (p ≤ 0.01), ash clustered with BC; pH and water content drove differentiation (p ≤ 0.05). (4) Topsoil predicted function potential showed early suppression (0–20 d), mid recovery (30–60 d), and late enhancement (70–90 d) for most treatments, except WA with sustained suppression. Heat determines disturbance depth and initial bacterial loss, while ash reshapes soil properties to influence community reassembly, acting as sequential but distinct environmental filters, providing a framework for post-fire bacterial community reorganization. Full article

As a precious indigenous goose resource in China, the Zhedong white goose occupies an essential position in the domestic goose industry. However, this breed spontaneously enters a prolonged non-laying period of over two months per year, which greatly limits egg production capacity and restricts the economic development of the goose industry. Herein, this study systematically compared serum physiological indices and serum and fecal metabolome, as well as fecal microbial communities, between laying and non-laying Zhedong white geese, aiming to reveal the key regulatory mechanisms underlying reproductive stage transition. Physiological analyses indicated that non-laying geese had higher serum levels of GnRH, PRL, APOA, and T-AOC, whereas the concentrations of LH, E₂, TNF-α, IL-1, and calcium were significantly reduced; FSH, PROG, and BA levels showed no significant differences between the two groups. Metabolomic analysis identified 277 upregulated and 403 downregulated DAMs in feces, and 386 DAMs in serum. The shared enriched pathways across serum and fecal samples encompassed arginine biosynthesis, histidine metabolism, and pantothenate and CoA biosynthesis, as well as steroid hormone biosynthesis. A total of 120 DAMs overlapped in two specimens, and the non-laying geese presented pronounced depletion of tryptophan-derived metabolites and steroid hormone-related metabolites. Metagenomic results showed no significant difference in gut microbial alpha diversity between groups, while their microbial community structures were clearly differentiated. A total of 774 upregulated and 854 downregulated microbial species were screened in non-laying geese, and these differential microbes were primarily enriched in pathways associated with reproductive hormone signaling, steroid biosynthesis and energy metabolism. Multi-omics correlation analysis verified close associations between differential microbes and reproductive-related metabolites. Certain probiotic strains, including Pediococcus pentosaceus and Lactococcus raffinolactis, were positively correlated with steroid hormones and tryptophan metabolites, and their abundances declined obviously in the non-laying stage. Collectively, this study elaborates the holistic changes in serum biochemistry, gut metabolome and microbiome in geese at different reproductive stages. The dysregulation of amino acid and steroid hormone metabolism, combined with the loss of beneficial intestinal microbes, jointly induces the non-laying phenotype. This study provides new perspectives for understanding the gut–reproductive axis and supplies promising biomarkers to improve the laying performance of geese. Full article

Liangshan Yanying chicken is a valuable plateau-adapted indigenous poultry breed in China. The poultry cecum modulates nutrient metabolism, gut microbial colonization and intestinal immune barrier establishment, while the molecular mechanisms driving its age-dependent development during the brooding stage remain unclear. Here, integrated transcriptomic and metabolomic profiling coupled with bioinformatics correlation analysis were conducted on cecal samples collected from chickens at post-hatching days 1, 14 and 28. Significant temporal changes were observed in cecal gene expression and metabolite abundance, and day 14 was identified as a critical window for cecal functional maturation and microbial colonization. In total, 2424 metabolites were annotated, including 600 differentially accumulated metabolites. The cecum exhibited phase-specific metabolic patterns: endogenous energy metabolism dominated at 1–14 d, while lipid biosynthesis prevailed at 14–28 d. The intestinal IgA immune network was verified as the core pathway maintaining cecal immune homeostasis in young chicks. Multi-omics conjoint analysis yielded 53 overlapping KEGG pathways, 14 core pathways, 3 pivotal metabolites and 5 hub genes, based on which three interactive regulatory networks were constructed. Transcriptomic data were validated via qRT-PCR. This study reveals cecal metabolic remodeling and regulatory characteristics during the brooding period, supplementing gut developmental research on plateau indigenous chickens. Notably, these results reflect age-related cecal developmental changes rather than breed-specific high-altitude adaptation mechanisms. Further independent verification is required for metabolomic data and predicted regulatory networks. This finding provides a theoretical basis for scientific breeding and feeding management of Liangshan Yanying chickens. Full article

Grain for Green, as an important ecological restoration method, profoundly affects soil nitrogen (N) cycling by altering the soil physicochemical properties and microbial community. Soil nitrogen mineralization is a key process in the terrestrial N cycle. However, the dynamics and underlying driving mechanisms of soil N mineralization rate (Rmin) that respond to afforestation remain unclear. In this study, we selected a typical afforestation sequence in Northeast China, including farmland (F), 21-year-old larch plantation (L21), 42-year-old larch plantation (L42), and natural larch forest (NL). The soil Rmin, associated soil physicochemical properties, and microbial community characteristics were determined to explore the effects of afforestation on soil Rmin and its potential mechanisms of action. The results suggested that soil Rmin was ranked in the order of L42 (0.41 mg kg⁻¹ d⁻¹) > F (0.39 mg kg⁻¹ d⁻¹) > L21 (0.23 mg kg⁻¹ d⁻¹) (p < 0.05) along the afforestation sequence, with no significant difference between L42 and F. Compared to the L42, the NL exhibited significantly lower soil Rmin (0.23 mg kg⁻¹ d⁻¹) (p < 0.05). The changes in soil Rmin during the afforestation were significantly positively related to soil total N (TN) and organic carbon (SOC) concentrations, but significantly negatively related to pH (p < 0.05). Furthermore, the abundances of Proteobacteria and Acidobacteria (bacteria) and Ascomycota (fungi) were also closely correlated with soil Rmin. Structural equation modeling (SEM) analysis further indicated that the afforestation mainly regulated soil Rmin by altering soil temperature (ST) and NH₄⁺-N content. Meanwhile, soil NH₄⁺-N content could also exert a significantly positive effect on soil Rmin by influencing the microbial community. In conclusion, afforestation effectively altered soil Rmin, which was even higher in the plantation than in natural forests. This finding further enhances our understanding of forest restoration and land management practices on soil N cycling in temperate regions. Full article

Background: Childhood obesity is increasingly associated with gut microbiome dysbiosis. This systematic review (PROSPERO CRD420251131354) evaluates evidence from studies published between 2020 and 2026 assessing how nutritional and lifestyle interventions influence gut microbiota in children with obesity. Methods: A systematic search of PubMed, EMBASE and EBSCO identified 21 interventional studies involving children aged 5–18 years with obesity, with the last search conducted in April 2026. Interventions comprised prebiotics, probiotics, synbiotics, postbiotics, high-fiber diets, calorie-restricted dietary approaches, and lifestyle modifications such as physical activity. Microbiome outcomes were analyzed using 16S rRNA sequencing, quantitative real-time polymerase chain reaction (qPCR), or metagenomics. Risk of bias was evaluated using the RoB 2 and ROBINS-I (version 2) tools. Due to substantial heterogeneity in study design, participant characteristics, intervention types, and analytical methods, a meta-analysis was not feasible. Results: Across 21 studies, nutritional interventions included measurable but heterogeneous alterations in gut microbiome composition. Inulin supplementation was associated with a significant increase in alpha diversity and with higher relative abundances of Bifidobacterium, Blautia, Megasphaera, Subdoligranulum, and Eubacterium coprostanoligenes. Synbiotic supplementation increased Prevotella and Dialister and reduced the Firmicutes/Bacteroidetes ratio. High-fiber dietary interventions increased Faecalibacterium, Bifidobacterium, and Clostridium, while reducing Bacteroides, and were associated with shifts in metabolic pathways related to carbohydrate, lipid, and nucleotide metabolism. Calorie-restricted diets and combined diet–exercise interventions increased beneficial taxa such as Akkermansia muciniphila, improved microbial diversity, and correlated with favorable metabolic and anthropometric outcomes. Overall, nutritional and lifestyle interventions in pediatric obesity were associated with taxon-specific and context-dependent microbiome changes, rather than uniform restructuring. Conclusions: Nutritional interventions can modulate gut microbiota diversity, composition, and predicted function in pediatric obesity; however, the observed effects vary substantially across studies. The limited number of trials, small sample sizes, and methodological heterogeneity underscore the need for larger, standardized studies to better define clinical and therapeutic implications. Full article

Background/Objectives: Malnutrition and diabetes mellitus (DM) have been linked to gut microbial perturbations, yet data are scarce for the aging population, especially in a nursing-home setting. As this group is generally at risk for malnutrition, we aimed to investigate the link between DM and gut microbial patterns in interaction with nutritional risk status in nursing-home residents. Methods: Stool samples were collected from 173 nursing-home residents (77.5% female, mean age 86 years) and were analyzed via 16S rRNA sequencing. Furthermore, the Geriatric Nutritional Risk Index (GNRI) was assessed and data on comorbidity status, anthropometric measurements, and medication were acquired. Results: Fifty-one residents had DM (mean HbA1c 6%). There were no DM-related differences in alpha diversity (observed richness: p = 0.733; Shannon index: p = 0.747). PERMANOVA revealed slight differences in beta diversity according to GNRI (R² = 0.009, p = 0.032), but no significant differences when adding DM status. Differential abundance analysis showed Clostridium_Clostridiaceae, Haemophilus, Actinomycetaceae and Micrococcaceae as significantly decreased with DM, independent of age, sex, and BMI. No interaction between DM and the GNRI in microbial diversity or composition was found. Conclusions: We report malnutrition-related differences in beta diversity and diabetes-related microbial taxa differences in nursing-home residents. DM status did not influence the relationship between the GNRI and gut microbiota in this population. Full article

The intricate interaction of a host’s microbiome, the microbiomes of other hosts, and environmental microbial populations significantly impacts host health, given the essential physiological functions the microbiome performs within the organism. The oral microbiome of domesticated animals is also influenced by a variety of host and environmental factors. This study investigated the characteristics of the oral microbiome of dogs and cats under comparable and disparate living conditions, emphasizing the description of diversity patterns, taxonomic composition, and predicted functional profiles. Oral buccal swabs were collected from four groups of companion animals (n = 5 per group): dogs housed alone in single-pet households (Group A), dogs cohabiting with cats in multi-pet households (Group B), cats cohabiting with dogs from the same households (Group C), and cats housed alone in single-pet households (Group D). The cohabiting groups were derived from five multi-pet households, with one dog and one cat sampled from each household. Amplicon sequence variations (ASVs) were used for downstream analysis after 16S rRNA gene sequencing. Rarefaction curve behavior indicated proper sequencing depth. Alpha diversity varied by group (Shannon index, p = 0.045), with Groups C and D having larger diversity. A Beta diversity study revealed community composition differences (Bray–Curtis dissimilarity, R² = 0.257, p = 0.001), with some overlap between groupings. In all samples, Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota dominated the microbiome. The relative abundance of Fusobacterium, Porphyromonas, and Pasteurella varied across groups. Core microbiome analysis identified limited overlap of core ASVs between groups, with most taxa being group-specific. Functional prediction using PICRUSt2 suggested differences in predicted metabolic and cellular pathways. Overall, these exploratory findings suggest that the oral microbiome of companion animals may be influenced by host species and cohabitation conditions. Although limited by the small sample size, the study provides preliminary insights into microbial diversity, community structure, and predicted functional profiles that may inform future One Health-oriented investigations. Full article

The objective of this study was to evaluate the effects of partially replacing wheat bran with poplar wood composite fiber (PWCF) on growth performance, immune status, apparent total tract digestibility (ATTD), and gut microbial composition in growing pigs. A total of 140 healthy crossbred (Duroc × Landrace × Yorkshire) growing pigs with an initial body weight of 47.25 ± 0.49 kg were randomly assigned to two dietary treatments, with five replicates per treatment and fourteen pigs per replicate. The control (CT) group was fed a corn–soybean meal-based diet containing wheat bran and rice bran meal, whereas the experimental group received the same diet in which 2% wheat bran was replaced by PWCF. The experiment lasted for 60 days. Compared with the CT group, replacing wheat bran with PWCF did not affect body weight, average daily feed intake, feed conversion ratio, or average daily gain on days 30 or 60 (p > 0.05). In addition, no negative effects were observed on ATTD of nutrients and serum immunoglobulin A (IgA), IgG, and IgM levels at either time point, indicating that PWCF can serve as a suitable partial substitute for wheat bran in growing pig diets. However, it could regulate nitrogen metabolism by reducing blood urea nitrogen (BUN) concentration and the BUN/creatinine ratio, as well as decreasing total free amino acids in serum (p < 0.05). In addition, the antioxidant capacity can be transiently improved by increasing catalase activity. Gut microbiota analysis showed that the replacement significantly increased the relative abundances of Treponema, the Lachnospiraceae_XPB1014_group and Prevotellaceae_UCG-001 (p < 0.05). These changes suggest that PWCF modulates gut microbiota and enriches fiber-degrading bacterial populations. Overall, substituting wheat bran with PWCF did not impair growth performance, immunity, or digestibility, while altering microbial community composition. These findings support the potential application of PWCF as an alternative fiber source, contributing to greater diversity in feed formulation. Full article

The Loess Hilly Region of northern Shaanxi is one of the most erosion-prone areas in the world due to its porous, erodible loess, steep slopes, and seasonal rainfall. To address this, conversion of sloping farmland to terraces has been extensively conducted across China’s loess regions, as terracing can reduce soil and water loss and enhance soil fertility. However, disturbance of soil layers during terracing can also lead to short-term decline in farmland productivity. This study investigates the effects of terracing operations at two sites of different ground substrate configurations in the Loess Hilly Region. Utilizing geochemical and molecular biological analysis methods, we examined the changes in the physicochemical and microbial properties of the ground substrate after terracing, using adjacent sloping farmlands as control sites. The results show that when the ground substrate configuration remained intact, terracing increased the average water content (from 8.44% to 14.34%) and soil organic carbon (from 2.74 g/kg to 5.76 g/kg) by 70% and 110%, respectively, and increased soil microbial α-diversity by 90%. The microbial community structure was also enhanced with an increase in relative abundance of soil- and plant-benefiting genera such as Streptomyces and Nocardioides, thereby promoting plant growth. Conversely, when the ground substrate configuration was altered, terracing led to a decrease in soil nutrient and moisture content, which was detrimental to crop growth. Therefore, maintaining the integrity of the ground substrate configuration is crucial during the terracing process to achieve optimal soil and water conservation outcomes. Full article

The management of livestock manure is associated with substantial ammonia (NH₃) emissions and the accumulation of emerging contaminants, including antibiotics, antibiotic resistance genes (ARGs), and microplastics, posing risks to environmental quality and public health. Biochar has emerged as a promising strategy for mitigating gaseous emissions and reducing contaminant mobility during manure storage and composting processes. This review synthesizes recent research on the application of biochar in livestock manure management systems, focusing on NH₃ emissions, antibiotic degradation, ARG reduction, and microplastic removal. Particular attention is given to the effectiveness of biochar in mitigating pollutants during manure storage, housing operations, and composting processes. Across the literature, reported NH₃ mitigation efficiencies vary widely, from negligible effects to reductions exceeding 90–97%, depending on feedstock type, pyrolysis conditions, particle size, and application strategy. Biochar also promotes antibiotic degradation and ARG mitigation, with reductions of up to 98% reported in composting systems. Emerging evidence further suggests that biochar can reduce microplastics by approximately 15–64% in sludge composting. Plant-derived and chemically modified biochars generally outperform manure-derived biochars due to higher surface area, cation exchange capacity, and greater abundance of functional groups. The review highlights that activation treatments, co-composting strategies, and microbial interactions are key factors controlling pollutant mitigation efficiency. Despite promising outcomes, large-scale application remains limited by economic constraints, variability in biochar properties, and the lack of long-term field-scale validation. Future research should prioritize standardized production protocols, field implementation studies, and integrated environmental and economic assessments to support the practical adoption of biochar in sustainable livestock waste management systems. Full article

Common bean (Phaseolus vulgaris L.) is a strategic crop whose sustainable production depends on symbiosis with nitrogen-fixing bacteria. However, the composition and functional potential of the nodule microbiome in varieties adapted to semi-arid regions, such as northern Mexico, remain poorly documented. Therefore, this study evaluated the influence of host genotype on nodule-associated bacterial communities in three improved varieties (Pinto Bravo, NOD1, and Jamapa) under conventional management, using high-throughput sequencing of the V3–V4 regions of the 16S rRNA gene. Alpha and beta diversity analyses showed no significant differences among varieties, indicating a similar nodular microbiome regardless of genotype. At the phylum level, Proteobacteria and Bacteroidota predominated, suggesting a conserved microbial core. At the genus level, Rhizobium was the most abundant taxon, while non-rhizobial genera such as Acinetobacter and the JC017 lineage were also detected. Functional prediction using PICRUSt2 revealed conserved metabolic profiles, with dominant pathways associated with amino acid biosynthesis, carbon metabolism, aerobic respiration, and fatty acid biosynthesis, indicating metabolic redundancy linked to tolerance to osmotic, thermal, and oxidative stress. The results suggest that under semi-arid conditions, the symbiotic interaction is governed by mechanisms at the host species level (P. vulgaris), which ensure the recruitment of a functional core microbiome, whereas intraspecific variation among improved varieties may influence the recruitment of specific accessory taxa. Full article

Background: The upper gastrointestinal (GI) tract is a complex environment characterized by sharp physicochemical gradients. While the oral microbiome is a major source of microbial seeding for downstream organs, it remains unclear how these communities correlate and diverge across different anatomical sites. This study provides a high-resolution re-analysis of a comprehensive multi-site dataset to delineate the microbial architecture and ecological signatures along the oral–upper GI axis. Method: Human oral, esophageal, gastric mucosal, and gastric juice microbiome sequencing data were retrieved from the publicly available National Center for Biotechnology Information (NCBI) BioProject PRJNA1049979 database. Using these publicly available 16S rRNA sequencing data, we performed an integrated ecological analysis. Microbial diversity, taxonomic composition, and niche-specific community structures were evaluated using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and R-based tools, including linear discriminant analysis effect size (LEfSe) and phylogenetic mapping. Results: The esophageal microbiome showed significantly greater richness and evenness than the oral cavity and stomach. Beta diversity analysis demonstrated clear compositional separation between oral and downstream upper GI communities, whereas gastric samples, particularly gastric juice, showed greater heterogeneity. Although major phyla were shared across sites, their relative abundances differed markedly. Oral samples were enriched with periodontal-associated taxa, including Porphyromonas, Prevotella, Alloprevotella, and Fusobacterium. In contrast, gastric mucosal samples were enriched with Akkermansia muciniphila and Helicobacter pylori, whereas gastric juice was characterized by Sarcina ventriculi, Fusobacterium periodonticum, and Clostridium perfringens. These findings indicate both taxonomic continuity and pronounced site-specific ecological divergence along the oral–upper GI axis. Conclusion: The oral cavity, esophagus, stomach, and gastric juice share a common microbial framework but exhibit distinct community restructuring driven by local environmental selection. This study provides a detailed ecological view of the oral–upper GI microbiome and highlights the importance of site-specific microbial organization in upper GI health and disease. Full article