Search Results (167)

The earliest gut and nasal bacterial community profiles after birth remain incompletely characterized, particularly when both sites are examined in parallel. We aimed to characterize these profiles according to delivery mode within the first 48 h of life in a Mexican cohort. Meconium and nasal wash samples from 60 neonates (30 vaginal and 30 cesarean deliveries) were analyzed by V3–V4 16S rRNA gene amplicon sequencing on an Illumina MiSeq platform, followed by QIIME 2 processing. All 60 meconium samples yielded analyzable 16S rRNA profiles. Nasal washes yielded analyzable profiles in 10/30 vaginally delivered and 12/30 cesarean-delivered neonates (p = 0.79). No statistically significant differences in alpha diversity were detected by delivery mode in gut samples (observed ASVs, p = 0.842; Shannon index, p = 0.183; Pielou’s evenness, p = 0.121; Faith’s phylogenetic diversity, p = 0.574) or nasal samples (p = 0.356, 0.947, 0.644, and 0.114, respectively). In unadjusted PERMANOVA comparisons, gut community structure differed by delivery mode for Bray–Curtis (p = 0.001), weighted UniFrac (p = 0.021), and unweighted UniFrac (p = 0.013) distances, whereas nasal comparisons were not statistically significant. Traditional ANCOM identified Staphylococcus as the feature with the highest W statistic in cesarean-delivered neonates (W = 65). Descriptive phylum-level profiles were examined across maternal urinary tract infection, premature rupture of membranes, maternal comorbidities, maternal BMI, hours since birth, and recorded antibiotic exposure; these comparisons were not multivariable and cannot exclude residual confounding. Delivery mode was associated with differences in early gut bacterial community structure in this cohort. Nasal findings were inconclusive because only 22 washes yielded analyzable 16S rRNA profiles and the workflow was not optimized to quantify ultra-low-biomass bacterial DNA. These cross-sectional data do not establish persistence, causality, or the timing at which nasal communities become stable. Full article

Broodiness is a natural behavior whereby female birds stop laying eggs to sit on and hatch them. This behavior is regulated through genetic, hormonal, and environmental factors. The Taihe Black-Boned Silky Fowl (TBSF), a Chinese traditional domestic breed, exhibits a strong brooding tendency; however, the molecular mechanisms underlying this trait remain unclear. In this study, we performed an integrated multi-omics analysis to characterize differences between two groups of TBSF hens: 8 individuals undergoing 30 days of active brooding (BR30) and 8 individuals in the normal laying egg stage (NB), selected from a total group of 230 hens. We combined 16S rRNA sequencing, untargeted metabolomics, and hepatic transcriptome sequencing, with statistical analyses including QIIME 1.9.1, OPLS-DA (VIP > 1), Student’s t-test (p ≤ 0.05), and DESeq2 (|log₂FC| ≥ 1, FDR < 0.05) for differentially expressed genes (DEGs), respectively, and Pearson’s correlation analysis for multi-omics integration. Phenotypically, brooder hens showed significantly reduced feed intake, body weight, and main digestive tissue indices, alongside altered liver and blood biochemical parameters. Hepatic transcriptome analysis identified 1582 DEGs between groups, enriched in pathways related to fatty acid oxidation and the amino acid degradation pathway. In addition, 16S rRNA sequencing revealed distinct gut microbial community structures: the NB group was enriched in Bacilliota and Pseudomonadota, while the BR30 group was enriched in Spirochaetota and Synergistota. Metabolomic profiling identified a total of 143 differential metabolites, which were enriched in lipid and amino acid metabolites, including alpha-linolenic acid and pyruvate metabolites. Multi-omics correlation analysis revealed tight associations between gut microbial taxa, circulating metabolites, and hepatic gene expression. Specifically, beneficial lipid metabolites, including phospholipids, lysophosphatidylcholines, and sphingomyelins, were positively correlated with Synergistes and the Christensenellaceae R-7, as well as with key hepatic lipid metabolism genes FABP1, LPL, and FADS2. In summary, this study reveals that the gut–liver axis plays a critical part in the modulation of energy metabolism during broodiness, and further highlights new insights into metabolic targets that could optimize reproductive behavior and enhance poultry production. Full article

Intestinal microbiome dysbiosis has been associated with transplant-related mortality and graft-versus-host disease in allo-HSCT patients. We assessed how pre-transplant antibiotic and antineoplastic exposures, together with multidrug-resistant colonization, are associated with baseline gut microbiome diversity at allo-HSCT. We conducted a prospective, single-center cohort study at Fundeni Clinical Institute (Bucharest, Romania) between August 2024 and June 2025, enrolling 52 allo-HSCT recipients and 27 healthy controls. Fecal samples were collected before conditioning. Gut microbiome composition was assessed via 16S rRNA gene sequencing and analyzed using QIIME2 and R. Associations were evaluated using Wilcoxon test, multivariable linear regression, and PERMANOVA. Shannon diversity was significantly lower in patients (median 4.71, IQR 3.97–5.44) than in healthy controls (median 6.09, IQR 5.87–6.28; p < 0.001). In bivariate analyses, carbapenem (p adj = 0.02) and oxazolidinone exposure (p adj = 0.005) were associated with reduced diversity, while immunotherapy was associated with higher diversity (p adj = 0.042). Broad-spectrum penicillin (p adj = 0.062) and ESBL colonization (p adj = 0.066) did not reach significance. In the multivariable antibiotic model, although the overall model was statistically significant (model p = 0.039), no individual antibiotic class remained significantly associated with Shannon diversity after adjustment for co-exposures. Beta diversity differed modestly with carbapenem exposure (R² = 0.033, p = 0.019). Pre-transplant antibiotic exposures were associated with lower gut microbiome diversity at allo-HSCT admission, with patterns consistent with a cumulative rather than a class-specific association. These findings support antibiotic stewardship in pre-transplant care. Full article

Background: Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide despite advances in diagnosis and treatment. Increasing evidence suggests that alterations in the lung microbiome may contribute to NSCLC development and progression; however, findings remain inconsistent due to heterogeneous biological materials and methodological differences among studies. Therefore, this study aimed to characterize the lung tissue microbiome in NSCLC using a paired tissue-based approach. Methods: Thirty-two patients with NSCLC were enrolled. For each patient, two samples were collected: primary tumor tissue and matched macroscopically unchanged adjacent lung tissue. The V3-V4 region of the 16S rRNA gene was amplified and sequenced, followed by bioinformatic analysis using the QIIME2 pipeline. Results: Tumor tissues demonstrated lower alpha (Shannon H = 9.60, q = 0.001) and beta (Jaccard pseudo-F = 1.26, q = 0.015) diversity compared with adjacent controls, indicating reduced microbial complexity within the tumor microenvironment. Escherichia-Shigella was the most abundant detected genus (~12%) in both groups, although without a statistically significant difference. Analysis of microbiome variation in relation to spatial distance between sampled tissues revealed a strong trend toward significance (p = 0.07) with a substantial effect size (R² = 0.207). Conclusions: The observed microbiome alterations in NSCLC were more evident at the ecological level than in overall taxonomic composition, supporting a model of microbial community simplification rather than complete compositional replacement. Our findings also suggest that tumor-adjacent lung tissue may not represent a fully neutral control due to the local field effect. The relatively high abundance of Escherichia-Shigella indicates that this taxon may warrant further investigation in NSCLC microbiome studies. Full article

Geographic and ecological variations are frequently associated with differences in the microbiota of arthropod vectors, with potential implications for pathogen transmission and public health. This study characterized and compared the bacterial microbiota associated with the brown dog tick (Rhipicephalus sanguineus) across three ecologically contrasting regions of Mexico: Cancun (Quintana Roo), Comarca Lagunera (Durango–Coahuila), and Hermosillo (Sonora). Non-engorged ticks collected from stray dogs were analyzed using 16S rRNA gene (V3–V4) sequencing. Amplicon sequence variants (ASVs) generated in QIIME2 were used for taxonomic, diversity, and predictive functional analyses. Proteobacteria dominated all samples, with Coxiella-like bacteria tentatively assigned as Coxiella mudrowiae identified as a dominant taxon across all localities. Significant geographic differences were observed in alpha and beta diversity, with Comarca Lagunera showing the highest diversity and Hermosillo the lowest. Sequences tentatively assigned to Rickettsia rickettsii were detected exclusively in two pools from Hermosillo. Functional predictions revealed a conserved metabolic repertoire alongside geographic variation in pathway abundance. Overall, the results support the existence of a stable symbiotic component accompanied by a geographically variable bacterial fraction associated with ecologically contrasting regions. These findings highlight the importance of geographic context in shaping tick-associated bacterial communities. Full article

To perform the first concurrent characterization of gut and respiratory microbiome profiles in colorectal cancer patients from Western Siberia, Russia. We analyzed synchronous fecal and sputum samples from 40 treatment-naive colorectal cancer patients and 45 healthy controls using 16S rRNA gene (V3-V4) sequencing and QIIME 2-based bioinformatic workflows. While alpha-diversity indices did not differ significantly between groups, beta-diversity analysis revealed substantial compositional differences for both ecosystems. Colorectal cancer patients exhibited gut enrichment of Proteobacteria, Fusobacteria, Fusobacterium, Odoribacter, Lachnospiraceae_UCG-010, Erysipelatoclostridium, Parvimonas, Finegoldia, Clostridium and Bacteroides (Bacteroides fragilis), alongside sputum enrichment of phyla Bacteroidetes and Actinobacteria, as well as genera Neisseria, Prevotella, Lactobacillus, Rothia, Nocardia, Leptotrichia, Campylobacter, and Helicobacter. Stage-associated shifts included elevated Akkermansia in gut microbiomes of patients with advanced-stage disease and higher Campylobacter in early-stage sputum. These findings identify distinct gut–respiratory dysbiotic signatures in a previously understudied population. Our results underscore the potential of dual-compartment microbiome profiling for developing non-invasive biomarkers and require validation in larger, multicenter cohorts to elucidate mechanistic links between respiratory dysbiosis and colorectal carcinogenesis. 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

Background: Rosacea is a chronic inflammatory dermatosis with emerging links to the gut–skin axis, yet integrative data connecting fecal microbiota with metabolic and immune parameters remain scarce. Methods: Within a cohort of Croatian women (N = 300, aged 30–35), participants with self-reported physician-diagnosed rosacea (n = 19) were compared to controls (n = 281). Assessments included validated questionnaires, anthropometrics, fasting blood parameters, and fecal 16S rRNA gene sequencing (QIIME2). Taxonomic profiling at four levels (899 features) used Mann–Whitney U tests with per-level Benjamini–Hochberg FDR correction. This study follows STROBE and STORMS guidelines. Results: On the host side, rosacea was nominally associated with higher BMI (p = 0.037), poorer sleep quality (p = 0.038), elevated monocytes (p = 0.031), and higher HOMA-B (p = 0.013); these comparisons were not corrected for multiple testing. Fecal 16S rRNA analysis (rosacea n = 18, controls n = 265) identified 15 nominally significant genera, including depleted Bifidobacterium (p = 0.007), Roseburia (p = 0.033), and enriched Anaerostignum (p < 0.001). However, no taxon survived FDR correction at any taxonomic level (lowest q = 0.165), and the total number of nominally significant features (48/899, 5.3%) did not exceed chance expectation (binomial p = 0.340). All key taxa remained nominally significant after BMI adjustment. An exploratory Random Forest classifier (five genera + HOMA-B + cortisol) achieved LOOCV AUC = 0.785, but feature selection on the training data limits interpretation. Conclusions: In this narrowly age-defined female cohort, host-side metabolic and immune differences reached nominal significance without multiple-testing correction. Fecal microbiota differences were exclusively exploratory: no taxon survived FDR correction, and the overall signal did not exceed chance expectation. The pattern of findings is compatible with—but does not constitute evidence for—a gut–skin axis contribution to rosacea. Confirmation in adequately powered cohorts with clinical rosacea verification, comprehensive confounder capture, and pre-registered analyses is required before any mechanistic or clinical conclusions can be drawn. Full article

Background: Agaro-oligosaccharides (AOS) have been shown to modulate the gut microbiota in in vitro and animal studies; however, human evidence remains scarce. Methods: Herein, we conducted a four-week open-label, single-arm, non-randomized pilot trial in 18 healthy Japanese adults to examine the association of AOS intake at 200 mg/day with gut microbiota composition and bowel condition. Fecal samples collected before and after the intervention were analyzed using QIIME2-based 16S rRNA sequencing, and bowel condition was assessed with the Bristol Stool Form Scale. This study was registered in the UMIN Clinical Trials Registry (UMIN000056992). Results: AOS intake was not associated with significant changes in bowel condition. Gut microbiota analysis showed no significant alterations in overall community structure but revealed taxon-specific trends in the relative abundance of several bacterial taxa. Notably, nominal changes were observed in the abundance of the Ruminococcus gnavus group and Bacteroides uniformis after the intervention. In addition, quantitative PCR analysis showed an increase in 3,6-anhydro-L-galactose cycloisomerase (ACI) gene abundance after the intervention. Conclusions: These findings suggest that, in this exploratory pilot study, AOS intake was associated with a taxon-specific pattern in the gut microbiota. Further randomized controlled studies are needed to clarify the microbiota-related effects of AOS in humans. Full article

Increasing consumer demand for natural and safe food products has led to the exploration of biocontrol alternatives to chemical preservatives, especially in the cured meat industry. The yeast Debaryomyces hansenii has emerged as a promising biocontrol candidate due to its antagonistic properties against spoilage fungi. This study assessed the impact of D. hansenii inoculation on the fungal community structure of Iberian cured pork loin using high-throughput sequencing of the ITS1 region. Ion Torrent ITS1 amplicon sequencing, QIIME2/DADA2 pipeline, and ALDEx2 differential abundance analysis were applied to this study. Pork loin samples inoculated with D. hansenii were compared to non-inoculated controls to evaluate changes in the fungal microbiome. Inoculation resulted in a marked decrease in fungal diversity and evenness, indicating strong competition by D. hansenii against native fungal populations. This effect was reflected in a significant reduction in alpha diversity in inoculated samples (Shannon, p = 0.0042; Pielou p = 0.0075; Gini–Simpson, p = 0.0081). Notably, genera associated with spoilage and mycotoxin production, particularly Aspergillus and Penicillium, were significantly reduced in inoculated samples. Simultaneously, D. hansenii became dominant, reducing other yeasts and filamentous fungi. These findings highlight the powerful competitive and biocontrol potential of D. hansenii, demonstrating its ability to improve microbial safety by potentially reducing mycotoxin-associated risks through the suppression of toxigenic genera. This is the first study to characterise the fungal community of Iberian pork loin using metabarcoding under D. hansenii inoculation. The findings confirm that the inoculation of D. hansenii can substantially reduce fungal contamination risks. Overall, the results contribute valuable insights into microbial interactions during meat curing and underscore the practical benefits of targeted starter cultures for enhancing food safety and quality. Full article

Background: Metabolic syndrome (MetS) is a cluster of cardiometabolic abnormalities linked to increased risk of type 2 diabetes and cardiovascular disease. Emerging evidence implicates gut microbiota dysbiosis in MetS pathophysiology; however, human clinical data on seaweed-based dietary interventions remain scarce. Methods: Twenty-four older women were stratified into a MetS group (n = 13) and a control group (n = 11) per NCEP-ATP III criteria with Korean-specific waist circumference cutoffs. All participants consumed 4 g of dried laver (Porphyra tenera) per day for 12 weeks. Fecal DNA was subjected to 16S rRNA gene amplicon sequencing (V4 region; Illumina iSeq 100). Bioinformatic processing used QIIME2 and MicrobiomeAnalyst; alpha diversity was quantified by Chao1 and Fisher indices; beta diversity by Bray–Curtis, Jensen–Shannon, and UniFrac metrics; and differential abundance by LEfSe. Results: The Firmicutes/Bacteroidetes ratio declined 0.81-fold in the control group and 0.54-fold in the MetS group. Alpha diversity (Chao1 and Fisher indices) increased significantly in both groups (p < 0.001 and p < 0.05, respectively). Unweighted UniFrac distance showed significant compositional differences (R² = 0.141, p = 0.001). LEfSe identified four FDR-significant genera: CAG_873 in the control group and Muribaculaceae, Paraprevotella, and Tyzzerella in the MetS group. Conclusions: Twelve-week dried laver supplementation produced measurable shifts in gut microbial diversity and community composition in older women, with potentially greater responsiveness in those with MetS. These preliminary findings justify adequately powered randomized controlled trials to evaluate laver as a gut-microbiome-targeted dietary strategy for MetS. Full article

Background/Objectives: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Emerging evidence highlights the role of the gut microbiota in the development and progression of CRC. Microbial dysbiosis is hypothesized to contribute to chronic inflammation through a variety of mechanisms, such as the production of free radicals, which induce mutagenesis and immune dysregulation in the host, ultimately leading to diseases such as cancer. Methods: Tumor tissue samples or healthy mucosa tissue were collected for bacterial DNA extraction. The V3–V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Bioinformatics analysis was performed with QIIME2, including quality control, DADA2 denoising, alpha and beta diversity calculation, and taxonomic classification using the SILVA database. Results: Differences in microbial composition were observed between groups. The healthy controls exhibited high relative abundances of beneficial genera such as Faecalibacterium, Bacteroides, and Asteroleplasma, whereas the patients with CRC showed enrichment of atypical genera including Novosphingobium, Bradyrhizobium, and Undibacterium. Alpha diversity was lower in the CRC group, and clear clustering by group was observed in the beta diversity analysis. LEfSe analysis identified potential bacterial biomarkers associated with CRC at both the species and genus levels. Conclusions: The findings of this study support the hypothesis that colorectal cancer is associated with distinct alterations in gut microbiota composition, such as an increase in the Novosphingobium genus and a decrease in the Bacteroides genus. An exploratory description of these microbial profiles may aid in the development of microbiome-based diagnostic and therapeutic strategies and contribute to current knowledge of the role of the gut microbiota in CRC in southern Peru. Full article

Previously, the role of decreased biodiversity of gut microbiota in polycystic ovary syndrome (PCOS) was demonstrated, but the objective criteria for assessing the representation of microorganisms associated with hyperandrogenemia (HA) were limited. A total of 175 premenopausal women (26 women with PCOS and HA and 149 women without HA, including 19 healthy controls) were recruited during the Eastern Siberia PCOS Epidemiology and Phenotype (ESPEP) Study (2016–2019). Methods included a questionnaire survey, clinical examination, pelvic U/S, blood and feces sampling. Gut microbiome was analyzed by high-throughput sequencing of the V1–V3 of the variable regions of the 16S rRNA gene (Illumina MiSeq, San Diego, CA, USA). Amplicon libraries of 16S rDNA were processed using the QIIME2 bioinformatics pipeline. All data were analyzed using R 3.6.3. The gut microbiocenosis in women with HA was characterized by a higher representation of Lactobacillus and a lower prevalence of the Clostridia class. For Faecalibacterium, Christensenellaceae_R-7_group, and [Eubacterium] eligens group the cut-off values of their relative presence, associated with HA, were estimated as: ≤0.043%, ≤0.039%, and ≤0.02%, respectively. Conclusions: Women with PCOS-associated HA demonstrate a lower prevalence, predominantly, of Clostridia class gut microorganisms, compared with those without any forms of HA. The study presents the quantitative criteria for assessing the representation of gut microorganisms, negatively associated with hyperandrogenic phenotypes of PCOS. The threshold values proposed may be useful to justify the administration of probiotics in PCOS patients with HA. Full article

Ash dieback, caused by the fungus Hymenoscyphus fraxineus, continues to threaten European ash (Fraxinus excelsior), yet the contribution of the leaf microbiome to disease severity remains poorly understood. We surveyed 133 ash trees across nine sites in Northern Ireland, using canopy cover as a proxy for health, and characterised leaf-associated microbial communities using Pacific Biosciences (PacBio) long-read amplicon sequencing (full-length 16S and ITS) and QIIME2-based workflows. Many trees exhibited partial tolerance to ash dieback, with most maintaining stable canopy cover year-on-year, while fewer trees show a decline and a smaller portion showing improvement. Microbial communities were largely stable irrespective of ash health with little difference in alpha diversity (Shannon) or beta diversity (Bray–Curtis PERMANOVA) for either bacteria or fungi. Differential abundance and correlation analyses showed that H. fraxineus was, as expected, negatively associated with canopy cover. Only one fungal species, Papiliotrema flavescens, demonstrated a strong positive association with healthier trees, consistent with previous findings. These results indicate that Northern Ireland hosts a reservoir of ash trees displaying tolerance to ash dieback. While the leaf microbiome does not appear to drive this tolerance at the community level, one fungus, P. flavescens, was correlated with healthier ash. Full article

Hospital environments host diverse microbial communities that may contribute to nosocomial infections. Moisture-retaining surfaces such as cleaning sponges and faucet edges represent high-contact, under-investigated hygiene hotspots, particularly in wards caring for immunocompromised patients. Environmental samples were collected from cleaning sponges (n = 14) and faucet edges (n = 4) across multiple hospital rooms of a paediatric haematology–oncology unit, with domestic physician sponges as controls (n = 3). DNA was extracted and sequenced targeting the V3–V4 and V7–V9 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. Taxonomic composition and alpha/beta diversity were assessed using QIIME 2 and R. Sponge samples were dominated by Moraxellaceae, particularly Acinetobacter and Enhydrobacter, and showed significantly lower alpha diversity than faucet samples (Shannon index: Kruskal–Wallis H = 8.4, p = 0.01; Faith’s phylogenetic diversity: H = 9.17, p = 0.01). Faucet samples were enriched in human-associated genera including Staphylococcus, Streptococcus, and Chryseobacterium. Statistically significant beta-diversity differences were detected between sponge and faucet communities by PERMANOVA based on Bray–Curtis dissimilarity (p = 0.01), whereas no significant clustering by room or floor location was observed (p = 0.29). Potentially pathogenic taxa including Aeromonas, Pseudomonas, and Enterobacteriaceae were identified across both surface types. Domestic control sponges showed distinct microbiome profiles from hospital samples. Microbial communities differ significantly between hospital sponges and faucets, with surface type rather than location as the primary determinant of community structure. The presence of opportunistic pathogens on both surface types highlights the importance of enhanced hygiene protocols, inclusion of faucet edges and sink drains in routine decontamination schedules, and regular microbiological surveillance in clinical settings caring for immunocompromised patients. Full article