Search Results (9,874)

Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease. Full article

Lutein is a dietary xanthophyll carotenoid with recognized antioxidant and immunomodulatory potential, yet the molecular basis underlying its nutritional effects in laying hens remains insufficiently understood. Here, liver transcriptomic profiling and 16S rRNA sequencing were combined to investigate the response of laying hens to dietary lutein supplementation. A total of 951 differentially expressed genes were identified in the liver, indicating marked transcriptional remodeling after lutein supplementation. Functional enrichment, gene set enrichment, and weighted gene co-expression network analyses consistently showed that these changes were mainly associated with metabolic regulation, redox/stress adaptation, and immune-related communication. In parallel, lutein supplementation changed cecal microbial community structure and shifted specific microbial biomarkers. Integrated correlation analyses further identified candidate host–microbiota association patterns, including a KLF2/FOXO3/Faecalibacterium axis and a KLF2/IL8L2/Prevotellaceae_Ga6A1_group axis. Overall, dietary lutein was associated with coordinated changes in the hepatic transcriptional profile and cecal microbial community structure, which converged on these two functional directions. These findings provide new insight into the nutritional effects of lutein in laying hens and identify candidate pathways and microbial nodes for future functional validation in poultry feeding systems. Full article

This study systematically compared the structural, functional, pathogenic, and assembly-mechanism characteristics of bacterial communities between urban and rural rivers across China, based on integrated water quality data from 421 sampling sites and 16S rRNA gene sequences from 475 sampling sites. The results revealed that urban rivers had significantly higher nutrient concentrations and bacterial α-diversity, along with lower β-diversity. Urban rivers were enriched with organic matter-degrading phyla such as Chloroflexi and Acidobacteriota and might exhibit more complex co-occurrence networks (average degree: 85.41). In contrast, rural rivers were enriched with phyla including Firmicutes and Cyanobacteria, as well as genera such as Exiguobacterium and Limnohabitans, and might display higher network modularity (modularity: 0.59) and greater spatial heterogeneity in community composition. Functional prediction indicated stronger carbon-cycling potential in urban rivers, whereas nitrogen-cycling functions did not differ between the two river types. Regarding pathogen composition, urban rivers contained a higher number of pathogen species than rural rivers. It was suggested that stochastic processes dominated community assembly in both systems; however, heterogeneous selection contributed more strongly in urban rivers (14.7%). Overall, this work elucidated systematic differences in bacterial community structure, function, pathogen profile, and assembly mechanisms between urban and rural rivers, offering a scientific foundation for differentiated watershed management. Full article

Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna’s microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns. Full article

The effects of pre-harvest application of Bacillus velezensis LYB73 on rhizosphere soil properties, microbial communities, fruit quality, and flavor-related traits in different peach cultivars are still not well understood. In this study, three peach cultivars, “Jinxia” (JX), “Wanhujing” (WHJ), and “Youpantao” (YPT), were subjected to B. velezensis LYB73 treatment or a sterile-water control under field conditions. Rhizosphere bacterial (16S rRNA) and fungal (ITS) communities were analyzed by high-throughput sequencing. Soil physicochemical properties, fruit nutritional and functional components, antioxidant capacity, and electronic sensory traits were also evaluated. The application of LYB73 was associated with lower rhizosphere soil pH (5.52–6.82) and changes in several soil nutrient-related parameters. Microbial community analyses indicated that LYB73 treatment was accompanied by shifts in the composition of rhizosphere bacterial and fungal communities. For example, the relative abundance of Pseudomonadota increased in the JX treatment group, while Ascomycota was enriched in the JX and YPT treatment groups. At the genus level, taxa such as Gemmatimonas, Saitozyma, and Cephalotrichum showed increased relative abundance in some treated groups. Compared with the control, LYB73-treated fruits generally showed higher levels of reducing sugars, titratable acids, amino acids, total phenols, total flavonoids, and antioxidant capacity. The magnitude of these responses varied among cultivars: JX showed larger increases in total phenols, total flavonoids, and DPPH scavenging activity, WHJ showed a greater increase in amino acids and ABTS scavenging activity, and YPT showed the largest increase in superoxide anion scavenging activity. Electronic sensory analysis further suggested that LYB73 treatment affected taste and aroma-related traits, although the responses differed among cultivars. Correlation analysis showed that several dominant microbial genera were significantly associated with soil properties, fruit quality indices, and sensory indicators. Overall, these results suggest that pre-harvest application of B. velezensis LYB73 may influence rhizosphere microecology and fruit quality in a cultivar-dependent manner, providing preliminary support for its potential use in peach production. Full article

Currently, the most commonly used methods for detecting Mycoplasma are the culture method and the indicator cell culture method. However, both approaches exhibit low sensitivity and are incapable of detecting low-concentration contamination. In addition, the detection period may extend up to 28 days, which is unsuitable for rapid screening and may delay timely contamination control measures. To address these limitations, a Mycoplasma detection method based on nucleic acid amplification technology (NAT) was developed following a comparative analysis of gene sequences from various Mycoplasma species. The method was validated with respect to its detection performance and its applicability to biological product samples. DNA was extracted from Mycoplasma-contaminated samples using a magnetic bead-based nucleic acid extraction method. Universal primers were designed based on the highly conserved 16S rRNA gene sequence of Mycoplasma, and amplification was performed using multiplex quantitative PCR (qPCR) with fluorescent probes. The limit of detection (LOD) was established based on statistics of 24 replicates. Method specificity and robustness were evaluated according to the guidelines set by the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH Q2), while sample applicability was assessed in accordance with the European Pharmacopoeia (EP) <2.6.7>. The NAT-based Mycoplasma detection method enabled rapid, qualitative identification of Mycoplasma contamination. The validated LOD was 10 CFU/mL, and the method met predefined requirements for sensitivity, specificity, and robustness. To assess applicability, real biological product samples, including monoclonal antibodies, antibody fusion proteins, bispecific antibodies, and trispecific antibodies, were spiked with 10 CFU/mL of standard Mycoplasma strains. All spiked samples tested positive. These findings confirm that the NAT-based Mycoplasma detection method is suitable for process control and product release testing in the production of biological products. Full article

Acaryochloris marina is a distinctive cyanobacterium that uses chlorophyll d as its primary photosynthetic pigment and possesses two major light-harvesting systems: membrane-integral chlorophyll-binding Pcb/CBP complexes and water-soluble phycobiliproteins. How these antenna systems respond at the transcriptome level to contrasting light environments remains incompletely characterized. Here, we re-analyzed a publicly available RNA-seq dataset for A. marina MBIC11017 (NCBI BioProject PRJNA1130970), comparing cells grown under low-irradiance far-red light (LL-FR; 1.5–2 µmol photons m⁻² s⁻¹, 710-nm peak) and high-irradiance white light (HL-WL; 30–35 µmol photons m⁻² s⁻¹). Because light quality and irradiance both differ in this experimental design, the two effects cannot be separated; all transcriptional changes are therefore interpreted as responses to the combined LL-FR versus HL-WL contrast rather than to far-red wavelength alone. Of 8439 expressed genes, 1810 (21.4%) were significantly differentially expressed (adjusted p < 0.05). Using GFF-verified locus tags which corrected mis-annotations propagated in earlier analyses, the PS-I core gene set showed a mean log₂ fold-change of +1.96 (3.9-fold; 11/11 loci significant), whereas the PS-II core gene set showed a mean log₂ fold-change of +1.10 (2.1-fold; 12/20 loci significant). Light-harvesting genes showed the strongest response: 17/18 phycobiliprotein-pathway genes in KEGG amr00196 were upregulated, together with multiple putative Pcb/CBP loci (mean antenna log₂FC = +3.51; 11.4-fold). Weighted gene co-expression network analysis placed the antenna-associate genes examined here within a module positively correlated with the LL-FR condition (r = 0.802, p = 0.017), and STRING analysis supported an enriched network of predicted or known protein associations (1115 nodes, 4763 edges; PPI enrichment p < 1.0 × 10⁻¹⁶). Recent matched-irradiance experiments indicate that, at equal photon flux, far-red wavelengths reduce phycobilisome content relative to white light. The transcriptional pattern reported here is therefore most parsimoniously interpreted as predominantly a low-irradiance response, with possible wavelength-associated CA5 contributions that cannot be isolated in the present design. Overall, the analysis reveals coordinated transcript-level changes across plasmid-encoded reacquired phycobiliprotein genes, chromosomal Pcb/CBP loci, chlorophyll biosynthesis genes, and photosystem core genes, consistent with coordinated regulation of light-harvesting components in A. marina. Full article

Background: Neuroinflammation and gut–brain axis (GBX) dysregulation are key pathological drivers of stress-related neuropsychiatric disorders. Zhi-Zi-Chi Decoction (ZZCD), a classic Traditional Chinese Medicine (TCM) formula, has been clinically used to alleviate mental disturbances via the TCM principle of “clearing heat and relieving restlessness.” Still, its modern neuroprotective mechanisms, especially its links to gut microbiota and central signaling pathways, remain incompletely elucidated. Purpose: This study aimed to systematically investigate the therapeutic effects of ZZCD on chronic restraint stress (CRS)-induced neurodysfunction in mice and clarify its mechanisms from the perspectives of TCM theory, material basis, gut microbiota–metabolite axis, and central signaling pathways. Method: CRS mice were treated with ZZCD or protocatechuic acid. Behavioral tests evaluated depression- and anxiety-like behaviors. UHPLC-Q-TOF/MS identified ZZCD’s chemical constituents; 16S rRNA sequencing and untargeted metabolomics analyzed gut microbiota and metabolite changes. Western blot, immunofluorescence, and proteomics examined neuroinflammation, microglial polarization, and signaling pathway activity (PI3K/Akt/mTOR, AMPK). Results: ZZCD reversed CRS-induced depression- and anxiety-like behaviors and suppressed neuroinflammation. Mechanistically, UHPLC-Q-TOF/MS identified 424 ZZCD constituents, with prenol lipids, organooxygen compounds, and flavonoids as the most abundant. ZZCD reversed CRS-induced imbalance in gut microbiota, reducing pro-inflammatory Prevotella and enriching beneficial Lactobacillus, and mediated the enrichment of the prebiotic metabolite PCA in colonic and serum samples, which crossed the blood–brain barrier (BBB) to exert neuroprotection. Additionally, ZZCD and PCA normalized the PI3K/Akt/mTOR pathway and activated AMPK, promoting M2 microglial polarization and restoring synaptic plasticity. Conclusions: ZZCD exerts antidepressant effects by a gut-microbiota-dependent modulation of PCA-PI3K/Akt/mTOR and AMPK dual axes that converts microglia from M1 to M2, providing ethnopharmacological evidence and a mechanistic rationale for its clinical application in major depressive disorder. Full article

Coccotorus beijingensis is a typical gall-inducing insect whose larvae complete their development within enclosed galls, providing a unique model for investigating host–microbe symbiosis. This study aimed to characterize the dynamic succession of the symbiotic microbiota in C. beijingensis across the larval stage (April–August) and pupal stage (September). Using high-throughput 16S rRNA gene sequencing, we performed a systematic analysis of monthly collected samples spanning the larval and pupal stages. The results revealed significant temporal variation in the structure of the larval microbial community. Bacillota and Bacteroidota were the dominant bacterial phyla throughout development. Although non-core bacterial groups, such as Pseudomonadota, showed pronounced seasonal fluctuations, no clear microbial reset was observed during metamorphosis. Exploratory PICRUSt2-based functional prediction suggested that the predicted metabolic potential of the microbiota may vary across development, with pathways related to carbohydrate metabolism, amino acid metabolism, and energy metabolism showing higher predicted representation during the middle larval stages. Overall, this study demonstrates that, within the confined gall microhabitat, larval development and seasonal dynamics jointly drive the temporal restructuring and functional adaptation of the microbial community. These findings provide new insights into the symbiotic mechanisms of holometabolous insects and their associated microbiota. Full article

Accurate detection and monitoring of antimicrobial resistance (AMR) in Helicobacter pylori mainly rely on phenotypic methods and culture, which can sometimes fail when bacterial load is low or after recent treatment. We investigated whether gastric biopsies classified as H. pylori-negative by standard diagnostic techniques still contain detectable bacterial DNA, including regions linked to AMR, and assessed whether selected DNA fragments can mediate allelic exchange in vitro. Gastric biopsies from 46 dyspeptic patients in the Democratic Republic of the Congo (including 23 phenotypically positive and 23 phenotypically negative individuals) were analyzed using long-read amplicon sequencing of seven resistance-associated loci, selective whole-genome amplification (sWGA) followed by long-read sequencing of H. pylori-enriched reads, and a proof-of-concept natural transformation assay. Phenotypically negative biopsies exhibited significantly lower sequencing depth across multiple loci (including 23S rRNA, gyrA, gyrB, and pbp1A; p = 0.003–0.014), indicating a reduced H. pylori DNA burden. However, AMR-associated mutations linked to various antibiotic classes were found in both groups. sWGA enabled recovery of fragmentary H. pylori sequence data from phenotypically negative samples, including reads that map to resistance- and virulence-associated genes. In vitro, 23S rRNA A2143G amplicons from both phenotypically positive and negative biopsies produced clarithromycin-resistant transformants in strain 26695. These findings indicate that phenotypically negative gastric biopsies might contain low-abundance and fragmentary H. pylori DNA. Although certain DNA fragments can mediate allelic exchange under controlled in vitro conditions, these results do not confirm bacterial viability, active infection, or clinically relevant in vivo resistance transfer. Therefore, they should be interpreted with caution in molecular AMR surveillance and detection contexts. Full article

Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID-19 syndrome (LC) show substantial clinical overlap, but direct comparative microbiome studies remain limited. Methods: In this cross-sectional study, we compared the fecal gut microbiome of patients with ME/CFS, LC, and healthy controls (HC) within a unified analytical framework using 16S rRNA profiling, differential abundance testing, and multivariate modeling. We also examined associations between microbiome variation and questionnaire-derived symptom-domain scores. Results: Alpha-diversity did not differ significantly among groups, whereas beta-diversity analyses showed small but significant disease-associated community differences with broad overlap between cohorts. Differential abundance analysis identified stronger signals in disease-versus-control contrasts than in the direct ME/CFS vs. LC contrast. Both ME/CFS and LC shared enrichment of Sutterella and depletion of Terrisporobacter and Lachnospiraceae relative to HC. Predicted functional profiling showed shared disease-versus-control changes in pathways related to anaerobic acetate/H₂ carbon flow, inositol/polyol degradation, phosphonate/C1-related metabolism, and lysine-derived fermentation. Regression analyses showed the strongest microbiome associations with fatigue-related and physiosomatic domains, while affective, cognitive, and gastrointestinal outcomes showed weaker signals. Conclusions: Overall, these findings support the presence of overlapping but non-identical gut microbiome alterations in ME/CFS and LC. The results provide a basis for future longitudinal and multi-omics studies aimed at clarifying the stability, functional relevance, and clinical utility of these microbial patterns. Full article

Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness driven by elevated intraocular pressure from compromised aqueous outflow. While genome-wide association studies have identified numerous risk loci, specific candidate proteins and their cellular mechanisms remain elusive. We employed a multi-omics framework integrating UK Biobank plasma proteomics (N = 53,022) and large-scale POAG GWAS summary statistics. We performed a Proteome-Wide Association Study, Mendelian Randomization, and Bayesian colocalization to infer causality. Identified candidates were mapped to human and mouse ocular scRNA-seq atlases to characterize cell-type specificity, followed by druggability assessments. We prioritized five putative causal proteins, with SEL1L and TFPI demonstrating the strongest evidence. Cross-species scRNA-seq revealed that SEL1L and SERPINF1 are robustly expressed in the trabecular meshwork (TM), particularly the juxtacanalicular tissue, implicating them in outflow resistance. Conversely, TFPI and SLC9A3R2 localize to Schlemm’s canal endothelium, suggesting a role in modulating barrier function. Pathway analyses highlighted endoplasmic reticulum protein processing and coagulation cascades. This study maps putative causal POAG proteins to conventional outflow pathway cells, highlighting SEL1L as a novel target for TM homeostasis and TFPI for drug repurposing, thereby providing data-driven hypotheses to facilitate precision glaucoma therapeutics. Full article

The weaning-to-estrus interval (WEI) is an important indicator of sow reproductive performance, yet the mechanisms underlying post-weaning anestrus in Tibetan sows remain unclear. In this study, multiparous Tibetan sows were classified into an estrus group (FQ) and an anestrus group (WQ) based on estrus status after weaning. Serum reproductive hormones, hematological parameters, gut microbiota (16S rRNA sequencing), and fecal metabolites (untargeted metabolomics) were analyzed. Compared with the FQ group, the WQ group showed significantly lower estradiol (E₂) and higher progesterone (P) levels (p < 0.01), along with a decreased proportion of neutrophils and an increased proportion of lymphocytes (p < 0.05). No significant differences in alpha diversity were observed, whereas PLS-DA revealed differences in microbial community structures between groups. LEfSe analysis indicated that Methanobrevibacter and Acinetobacter were enriched in the FQ group, whereas Muribaculaceae and Prevotella were enriched in the WQ group. Differential metabolites were mainly involved in amino acid and lipid metabolism and enriched in pathways related to steroid hormone biosynthesis, oocyte maturation, and tryptophan metabolism. These findings suggest that post-weaning anestrus may be associated with endocrine imbalances, immune changes, and gut microbiota–metabolite interactions. They may provide a basis for future studies in Tibetan pig breeding and genetic improvement. Full article

With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation. Full article

Background: Uterine sarcomas are rare, heterogeneous malignancies with distinct pathological behaviors. This study aimed to identify clinicopathological characteristics, prognostic risk factors, and potential therapeutic targets to enhance clinical management. Methods: A retrospective analysis was conducted on 148 patients with uterine sarcoma treated at Peking University People’s Hospital between 1996 and 2025. Clinical outcomes, pathological subtypes, and immunohistochemical profiles were assessed. Additionally, bioinformatics analyses from RNA bulk sequencing of GEO datasets (GSE87581, GSE85383, GSE222045 and GSE64763) were performed to elucidate molecular characteristics across subtypes. Results: The most prevalent subtypes were uterine leiomyosarcoma (uLMS; 38.5%) and low-grade endometrial stromal sarcoma (LG-ESS; 29.7%). The 5-year recurrence rate was 50.5%, with frequent metastases to the pelvis and lungs. LG-ESS demonstrated the most favorable 5-year survival rate (90.3%), significantly higher than that of uLMS (61.8%) and undifferentiated uterine sarcoma (50.0%). Multivariate analysis identified histological subtype, stage, and coagulative necrosis as independent prognostic factors for overall and progression-free survival. Transcriptomic profiling revealed immunosuppression (CSF1R/CSF3R expression) in high-grade ESS, while uLMS exhibited activation of cell cycle and homologous recombination pathways. Conclusions: Histological subtype, stage, and coagulative necrosis were critical prognostic factors in uterine sarcoma. The findings suggest that vigilant pulmonary surveillance and further investigation into tailored therapeutic strategies may be warranted-including endocrine therapy for hormone-receptor-positive tumors, immunotherapy for high-grade ESS, and PARP inhibitors for uLMS. However, these hypotheses require thorough preclinical and clinical validation. Additionally, caution should be exercised to avoid overtreatment of chemotherapy in early-stage uLMS. Full article