@article {pmid41695450,
year = {2026},
author = {Rusiñol, M and Martínez-Puchol, S and Ribeiro, D and Verdaguer, J and Torrejón-Llorens, O and Itarte, M and Estarlich-Landajo, I and Mejías-Molina, C and Juliachs-Torroella, G and Girones, R and Ramírez, GA and Baliellas, J and Bofill-Mas, S and Fernández-Cassi, X},
title = {Livestock aggregated samples for monitoring viruses infecting animals and potentially zoonotic viral pathogens.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101340},
pmid = {41695450},
issn = {2352-7714},
abstract = {Active surveillance of livestock pathogens is essential to prevent animal health losses and zoonotic spillover. This study evaluted aggregated environmental sampling as a non-invasive approach for monitoring swine- and cattle-associated viruses across farms and slaughterhouses, bridging the gap between agricultural biosecurity and public health. Over eleven months, 105 samples, including swine slurry, cattle manure, farm air, and slaughterhouse wastewater, were collected and analyzed using pathogen-specific (RT) qPCR and targeted viral metagenomics. Seasonal and sample patterns were evident, with higher detection of rotavirus A (RoV-A) and bovine coronavirus (BCoV) in slurry and wastewater during winter, and porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) sporadicly in slaughterhouse wastewater. Farm slurry or manure were optimal for enteric viruses such as RoV-A or hepatitis E virus (HEV), and farm air proved valuable for respiratory viruses like BCoV. Targeted sequencing identified a broader viral community, revealing up to 80% of total detected viral species in slaughterhouse wastewater alone. Frequent detection of porcine bocavirus, circoviruses and astrovirus, alongside zoonotic viruses such as HEV and porcine bufavirus (PBuV), underscored the environmental transmission risk at the human-animal interface. Sequencing also uncovered viruses of unclear pathogenicity, including kobuvirus and copiparvovirus, underscoring the complexity of the livestock virome and the potential for emerging viral threats. Slaughterhouse wastewater consistently captured the highest viral richness, integrating inputs from multiple farms and regions, while farm air samples yielded lower diversity but detected respiratory (astrovirus, caliciviruses) and persistent viruses (papillomaviruses, polyomaviruses). Aggregated sampling proved particularly efficient in swine systems, while cattle surveillance may require adapted strategies due to lower stocking densities and greater ventilation. This work demonstrates the novelty and value of aggregated environmental samples, collected at different points in the production chain, as strategic One Health sentinels. This scalable, practical approach supports early warning and control of animal and zoonotic diseases, directly contributing to One Health surveillance.},
}

@article {pmid41695017,
year = {2026},
author = {Galdamez, IA and Jimenez, K and Cira, M and Osborn, K and Ayad, M and Lee, CM and Patel, K and Galdamez, BA and Sloan, A and Shenkiryk, A and Cason, T and Gomez, NA and Phillips, M and Rosado, S and Rosado, A and Mishra, DR and Cherrington, EA and Griffin, R and Jay, JA},
title = {Evaluating Antibiotic Resistance in Urban Rivers and Coral Reefs of Belize: Evidence for Hotspots and a Potential Screening Tool.},
journal = {GeoHealth},
volume = {10},
number = {2},
pages = {e2025GH001427},
pmid = {41695017},
issn = {2471-1403},
abstract = {Antibiotic resistance is a significant threat to global public health and can disproportionately affect low- and middle- income countries (LMICs). There is a lack of studies focusing on antibiotic resistance in coral reef regions and environmental reservoirs in Central America. This study followed modified World Health Organization (WHO)'s Global Tricycle Surveillance protocols for the environmental sector to address these gaps. Water samples were collected from key areas in the lower Belize River, including above and below the Belize City, an open fish market, and sewage lagoon outfall, and coral reefs. Water samples underwent qPCR analysis for a suite of antibiotic resistance gene classes (sul1, sul2, ermF, tetA, and blaSHV), intI1, and 16S rRNA. Additionally, a subset of samples were tested for extended-spectrum β-lactamase (ESBL) E. coli and underwent shotgun sequencing. Results show that antibiotic resistance genes (ARGs) were highest and most diverse near Belize City, particularly near the treatment lagoons and open fish market. The coral reef regions had lower levels of antibiotic resistance though not void of their presence. This study is an application of a modified Global Tricycle Surveillance protocol integrated with qPCR- and metagenomics-based characterization of environmental antibiotic resistance in understudied areas. Notably, data from this study indicated that ESBL-E. coli could potentially be used as a screening tool for environmental antibiotic resistance, as it was only present at sites that had the highest levels of ARGs.},
}

@article {pmid41694529,
year = {2026},
author = {Vivarelli, S and De Francesco, C and Paba, E and Giambò, F and Fenga, C},
title = {The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1746385},
pmid = {41694529},
issn = {2296-2565},
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Occupational Exposure ; One Health ; },
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, driven by the extensive use of antibiotics in both human medicine and livestock production. In the context of the One Health framework, this review investigates the role of the gut microbiome and resistome, which represents the collection of antimicrobial resistance genes (ARGs), within livestock and among occupationally exposed workers. Intensive farming practices often involve routine, subtherapeutic antibiotic use, fostering antibiotic-resistant bacteria (ARB) in the gastrointestinal tract of animals. These ARB and ARGs are excreted into the environment, contributing to resistance spread through mobile genetic elements. From a Planetary Health perspective, this environmental dissemination reflects how human-driven livestock practices can perturb ecosystems, creating global health risks that link animal, human, and environmental well-being. Human exposure, particularly among farm workers and veterinarians, raises significant concerns about zoonotic transmission of pathogens and, potentially, ARB. Novel advances in metagenomic and metatranscriptomic technologies enhanced our understanding of gut microbial communities and their resistomes, revealing overlaps in ARG profiles between animals and livestock workers. These technologies also support the development of novel microbiome-targeted strategies, including prebiotics, probiotics, food supplementation and workplace-improvement strategies, aimed at reducing antimicrobial use and restoring healthy microbiome balance. The review also highlights the importance of integrated surveillance and cross-sectoral collaboration to monitor and control AMR transmission. Understanding the ecological dynamics of the gut resistome in livestock systems is essential for designing effective interventions that safeguard both animal and human health.},
}

Animals
*Livestock/microbiology
Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Occupational Exposure
One Health

@article {pmid41694517,
year = {2026},
author = {Song, Z and Huang, Y and Gu, Y and Che, L and Zhang, K and Liu, Q and Guan, Q and Sui, L},
title = {Correction: Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1788645},
doi = {10.3389/fpubh.2026.1788645},
pmid = {41694517},
issn = {2296-2565},
abstract = {[This corrects the article DOI: 10.3389/fpubh.2025.1756127.].},
}

@article {pmid41694508,
year = {2026},
author = {Scaglione, G and Mastroianni, N and Rizzo, A and Palomba, E and Carcione, D and Brigante, G and Principe, L and Colaneri, M and Gori, A and Borgonovo, F},
title = {Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1757161},
pmid = {41694508},
issn = {2296-2565},
mesh = {Humans ; *Artificial Intelligence ; *Whole Genome Sequencing/methods ; Machine Learning ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance (AMR) represents an escalating global health threat, demanding diagnostic strategies capable of rapid, accurate, and comprehensive pathogen characterization. Genomic sequencing has transformed our ability to elucidate resistance mechanisms and track their evolution, yet its routine clinical adoption remains limited by cost, workflow constraints, and extended turnaround times. This narrative review examines how artificial intelligence (AI) and machine learning (ML) can enhance and operationalize sequencing-based diagnostics across the clinical microbiology continuum. We summarize current AI applications in whole-genome sequencing for AMR prediction, pan-genome feature extraction, and multicenter model generalizability, including emerging approaches such as federated learning. We then explore AI-driven metagenomic analytics for pathogen detection, resistome profiling, outbreak investigation, and prognostic modeling. Complementary non-genomic technologies, Raman spectroscopy and MALDI-TOF MS, are also evaluated for their potential to deliver rapid resistance profiling when integrated with ML. Finally, we discuss practical barriers, including cost, dataset standardization, interpretability, and regulatory challenges, while outlining future directions toward scalable, explainable, and equitable AI-guided diagnostics. Integrating AI with genomic and rapid phenotypic tools offers a pathway to real-time surveillance, optimized antimicrobial stewardship, and strengthened preparedness against emerging infectious threats.},
}

Humans
*Artificial Intelligence
*Whole Genome Sequencing/methods
Machine Learning
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid41694087,
year = {2026},
author = {Hu, Q and Sardi, MI and Naqvi, SA and Paton, ND and Hackenhaar, L and Pluk, P and de Laat, J and Chakrabarti, A and Khafipour, E},
title = {Effects of processed soybean meal on growth performance and gut microbiome composition in pigs in regular nursery and enterotoxigenic Escherichia coli challenged conditions.},
journal = {Translational animal science},
volume = {10},
number = {},
pages = {txag004},
pmid = {41694087},
issn = {2573-2102},
abstract = {Hydrothermal-mechanical (HTM) processing of soybean meal (SBM) has been shown to enhance intestinal health and growth in post-weaning pig compared to conventional SBM. It was hypothesized that HTM processing improves protein utilization, particularly under enterotoxigenic Escherichia coli (ETEC) challenge, resulting in better growth and a more resilient hindgut microbiome. A total of 268 weaned pigs (6.82 ± 0.85 kg body weight) were allotted to regular nursery (5 pigs/pen, 10-11 pens/treatment) or ETEC challenge (3 pigs/pen, 12 pens/treatment) and fed one of three isocaloric diets with equal standardized ileal digestible lysine: SBM, HTM SBM, or enzyme-treated (Enz Trt) SBM. Test soy products replaced SBM in a wheat-barley-SBM base diet for the first 3 wk, followed by a common diet for 3 wk. On d 14 post-weaning, ileal digesta and feces were collected for crude protein (CP) digestibility, short-chain fatty acid (SCFA), and microbiome analysis. Growth performance, digestibility, and SCFA data were analyzed using general linear models and microbiome data from Nanopore shotgun sequencing were center-log-ratio transformed for statistical analysis in R. No diet × challenge interaction was observed on ADG, ADFI or BW. Pigs in regular nursery conditions had higher ADG (P < 0.01) and ADFI (P < 0.05) than ETEC challenged pigs during d 0-7. HTM SBM and Enz Trt SBM improved ADG (P < 0.05) with similar ADFI compared to SBM across conditions. From d 7-12, pigs fed HTM SBM or Enz Trt SBM had greater ADG (P < 0.05) and ADFI (P < 0.01) than SBM-fed pigs. BW remained lower (P < 0.05) in SBM-fed pigs from d 12-21 and during the final 3 wk. Under regular nursery conditions, HTM SBM improved apparent total tract digestibility of CP (P < 0.01) compared SBM, but with no difference from Enz Trt SBM. Microbiome composition was affected by diet (P < 0.01) and ETEC challenge (P < 0.01). HTM SBM and Enz Trt SBM tended to increase α-diversity (P = 0.10) of the microbiome compared to SBM, with no difference between the two treatments. HTM SBM and Enz Trt SBM increased abundance of species positively correlated with growth and beneficial SCFA, such as caproate (P < 0.05) and valerate (P < 0.05). In conclusion, HTM SBM and Enz Trt improved ADFI, ADG resulting higher BW and promoted beneficial microbes linked to performance in nursery pigs under both regular nursery and ETEC-challenged conditions.},
}

@article {pmid41693971,
year = {2026},
author = {Xu, T and Hou, WX and Yang, ST and Shao, YP and Wang, J and Han, TT and Li, JN},
title = {Danggui-Baishao herb pair protects against dextran sulfate sodium-induced colitis by modulating the Wnt/β-catenin pathway.},
journal = {World journal of gastroenterology},
volume = {32},
number = {5},
pages = {113024},
pmid = {41693971},
issn = {2219-2840},
mesh = {Animals ; Dextran Sulfate/toxicity ; *Wnt Signaling Pathway/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Disease Models, Animal ; Mice ; Humans ; Molecular Docking Simulation ; *Colitis/chemically induced/drug therapy/pathology/prevention & control ; Colon/pathology/drug effects ; Male ; beta Catenin/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Intestinal Mucosa/drug effects/pathology ; Glucosides/pharmacology ; Metabolomics ; Pyrimidinones ; Bridged Bicyclo Compounds, Heterocyclic ; },
abstract = {BACKGROUND: The Danggui-Baishao herb pair is the foundation of a traditional Chinese medicine formula known as Shaoyao decoction, which is widely used in the treatment of colitis.

AIM: To uncover the mechanisms underlying the anti-colitis effects of the Danggui-Baishao herb pair.

METHODS: The chemical composition of the herb pair was characterized by high performance liquid chromatography-quadrupole/time of flight mass spectrometry analysis. A mouse model of colitis was induced by administering 2.5% dextran sulfate sodium. The therapeutic effects of the herb pair were evaluated based on body weight changes, colon length, histopathological, intestinal inflammation, and barrier function. To investigate the underlying mechanisms, RNA sequencing, metabolomics, 16S rRNA sequencing, metagenomics, and the β-catenin inhibitor ICG-001 were utilized. Furthermore, molecular docking and dextran sulfate sodium-treated HCT 116 cells were conducted to explore the protective mechanisms of benzoylpaeoniflorin.

RESULTS: The herb pair improved body weight, colon length, intestinal inflammation, and barrier function. Additionally, the herb pair upregulated the expression of intestinal stem cells marker leucine-rich repeat-containing G-protein coupled receptor 5 and proliferation-related proteins. RNA sequencing analysis showed that the herb pair activated the Wnt/β-catenin signaling pathway. Metabolomic analysis revealed changes in bile acids composition. Through 16S rRNA and metagenomic sequencing, it was observed that the herb pair modulated the gut microbiota, with an enrichment of probiotics and a depletion of pathogenic bacteria. Following intraperitoneal injection of antagonist ICG-001, the therapeutic efficacy was diminished. Molecular docking showed that benzoylpaeoniflorin can bind to β-catenin. Furthermore, benzoylpaeoniflorin can activated the Wnt/β-catenin signaling pathway and the therapeutic efficacy was also diminished by the ICG-001 in vitro.

CONCLUSION: The herb pair effectively reduces colonic inflammation and maintains the integrity of the intestinal barrier. Moreover, the anti-colitis efficacy of the herb pair is closely associated with activation of the Wnt/β-catenin pathway.},
}

Animals
Dextran Sulfate/toxicity
*Wnt Signaling Pathway/drug effects
*Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry
Disease Models, Animal
Mice
Humans
Molecular Docking Simulation
*Colitis/chemically induced/drug therapy/pathology/prevention & control
Colon/pathology/drug effects
Male
beta Catenin/metabolism
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Intestinal Mucosa/drug effects/pathology
Glucosides/pharmacology
Metabolomics
Pyrimidinones
Bridged Bicyclo Compounds, Heterocyclic

@article {pmid41693862,
year = {2025},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1726935},
pmid = {41693862},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology ; Mycobacterium tuberculosis/genetics ; Male ; Female ; Gene Expression Profiling ; Biomarkers/analysis ; Metagenomics ; Prospective Studies ; Middle Aged ; Adult ; Microbiota ; Transcriptome ; Bacteriophages/genetics ; Lung/microbiology ; },
abstract = {BACKGROUND: Drug-resistant tuberculosis (DR-TB) undermines global TB control, yet how resistant Mycobacterium tuberculosis strains interact with the lung microbiome, phage communities, and local host immunity remains poorly defined.

METHODS: In a prospective cohort of 130 pulmonary TB patients (49 DR-TB, 81 drug-susceptible TB [DS-TB] patients), bronchoalveolar lavage fluid (BALF) was subjected to paired metagenomic and transcriptomic profiling. Microbial and bacteriophage community structures were assessed by diversity metrics and differential abundance testing, whereas host responses were characterized by gene expression, pathway enrichment, and immune cell deconvolution. A Random Forest model was trained to evaluate the diagnostic potential of host transcriptional signatures.

RESULTS: DR-TB airways presented distinct microbial beta diversity, with enrichment of Streptococcus spp. and streptococcal-targeting phages (e.g., Javan variants, phi-Ssu5SJ28rum). Transcriptomic analysis revealed 494 differentially expressed genes, which were associated with increased oxidative phosphorylation, suppressed ion channel and transporter activity, and enrichment of extracellular matrix remodeling pathways. Immune profiling demonstrated a significant reduction in γδ T cells in DR-TB patients (P = 0.0059). An 8-gene host-derived signature (ARHGEF5, PTGES3L, GAL3ST1, RANBP17, ACTA2_AS1, CBY3, MAMSTR, and LOC102031319) discriminated DR-TB from DS-TB with high accuracy (AUC = 0.837).

CONCLUSION: This dual-omics study defines the airway niche of DR-TB as a convergence of microbial dysbiosis, phage imbalance, and host immune-metabolic dysfunction. By uncovering DR-TB-specific microbial and transcriptional signatures, and deriving a predictive host-based classifier, our findings provide mechanistic insights and highlight novel opportunities for microbiome- and host-directed interventions in drug-resistant tuberculosis.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology
Mycobacterium tuberculosis/genetics
Male
Female
Gene Expression Profiling
Biomarkers/analysis
Metagenomics
Prospective Studies
Middle Aged
Adult
Microbiota
Transcriptome
Bacteriophages/genetics
Lung/microbiology

@article {pmid41693402,
year = {2026},
author = {Parveen, S and Shafi, Z and Shahid, M and Iqbal, MZ and Naznine, F and Ansari, MI},
title = {Omics-Driven Insights Into Soil Microbial Diversity and Phytopathogen Interactions for Sustainable Agriculture and Food Security.},
journal = {Journal of basic microbiology},
volume = {66},
number = {2},
pages = {e70155},
doi = {10.1002/jobm.70155},
pmid = {41693402},
issn = {1521-4028},
support = {//The authors are thankful for the support received from the Department of Science and Technology-Funds for Improvement of Science and Technology Infrastructure (DST-FIST), with grant acknowledgment and sanction number (SR/FST/LS-1/2017/13(C)). The authors express their deep gratitude to Integral University, Lucknow-226026, India, for their generous support of this work and for providing the manuscript communication number (IU/R&D/2025-MCN0003515)./ ; //Department of Science and Technology-Funds/ ; },
mesh = {*Soil Microbiology ; *Food Security ; *Agriculture/methods ; Biodiversity ; Metabolomics/methods ; Crops, Agricultural/microbiology/growth & development ; Proteomics ; Metagenomics ; Microbiota ; Plant Diseases/microbiology ; Bacteria/genetics/metabolism ; Ecosystem ; },
abstract = {Soil microbial diversity plays a pivotal role in sustainable agriculture by regulating nutrient cycling, organic matter turnover, and natural suppression of phytopathogens, thereby supporting crop productivity and ecosystem resilience. However, intensive agricultural practices and environmental stressors have led to a decline in soil biodiversity, compromising soil functionality and food security. Recent advances in omics technologies-including metagenomics, transcriptomics, proteomics, and metabolomics offer powerful tools to unravel the complexity, of soil microbial communities and their interactions with plants and pathogens. These integrated approaches provide high-resolution insights into microbial structure, functional dynamics, metabolic pathways, and the mechanisms underpinning plant-microbe-pathogen interactions. Furthermore, omics-driven understanding supports the development of sustainable strategies such as organic farming, conservation practices, and microbial bioinoculants, which restore microbial diversity, enhance nutrient use efficiency, reduce chemical inputs, and mitigate disease pressure. By linking soil health to crop nutritional quality and broader food system sustainability, this review highlights the potential of omics-guided approaches to optimize soil microbial ecosystems for resilient agriculture and global food security.},
}

*Soil Microbiology
*Food Security
*Agriculture/methods
Biodiversity
Metabolomics/methods
Crops, Agricultural/microbiology/growth & development
Proteomics
Metagenomics
Microbiota
Plant Diseases/microbiology
Bacteria/genetics/metabolism
Ecosystem

@article {pmid41693232,
year = {2026},
author = {Morsli, M and Magnan, C and Salipante, F and Dubois, A and Schuldiner, S and Cellier, N and Sotto, A and Lavigne, JP and Dunyach-Remy, C},
title = {Enhancing diabetic foot osteomyelitis diagnosis with metagenomics next-generation sequencing, proof of concept.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {},
number = {},
pages = {e70235},
doi = {10.1111/dme.70235},
pmid = {41693232},
issn = {1464-5491},
abstract = {Diabetic foot osteomyelitis (DFOM) is a serious medical condition that necessitates robust diagnostic tools for effective clinical management. Conventional diagnostic methods for DFOM rely heavily on bacterial culture, which is time-consuming and may fail to capture the full microbial diversity present in infections. This pilot study explored the utility of metagenomics next-generation sequencing (mNGS) as a complementary diagnostic tool for DFOM. We retrospectively analysed ten bone biopsies from nine diabetic persons using both routine microbiological culture and mNGS. Routine culture identified 11 bacterial species across seven biopsies, while mNGS detected 84 species, including all those found by culture. High microbial diversity (Shannon index = 1.10) was associated with severe osteomyelitis, leading to amputation in three of seven DFOM cases. Interestingly, one culture-negative biopsy revealed high bacterial diversity by mNGS and progressed to a severe infection within 7 days. mNGS also identified resistance genes, providing additional insights for targeted therapy. Integrating mNGS into routine clinical microbiology may serve as a complementary method to conventional diagnostics, particularly for distinguishing infection from colonization and predicting clinical outcomes. However, challenges such as human DNA contamination and limited sequencing depth must be addressed to optimize its clinical application. These findings support the integration of mNGS into diagnostic workflows for bone biopsies for improved management of DFOM.},
}

@article {pmid41692940,
year = {2026},
author = {Le, B and Jia, L and Pang, T and Han, S and Duan, Y and Zhao, XM},
title = {A review of computational approaches for metagenomics by long-read sequencing.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41692940},
issn = {1869-1889},
abstract = {The metagenomic next-generation sequencing (mNGS), also known as short-read sequencing (SRS), is widely used to explore microbial composition and function. However, short reads, due to their difficulty in crossing repetitive regions, can lead to fragmented assemblies, hampering the comprehensive characterization of microbial genomes. In contrast, long-read sequencing (LRS) technologies, such as those from Pacific Biosciences (PacBio) and Oxford Nanopore, can span these complex repetitive regions and reconstruct continuous genomes, which enables high-resolution taxonomic classification and the precise recovery of essential genetic elements. This review provides a systematic overview of the computational approaches for long-read metagenomics, highlighting the progress in taxonomic profiling strategies, assembly and binning methods, and the detection of genetic elements. Furthermore, the review discusses the application of LRS in detecting structural variations (SVs), identifying methylation patterns, and characterizing strains. By combining advanced technologies and computational improvements, this review indicates the transformative potential of LRS in enhancing our understanding of microbial diversity, functions, and interactions within microbial communities.},
}

@article {pmid41692795,
year = {2026},
author = {Vega, L and Birchenall-Jiménez, CI and Aponte, A and Durán, D and López, C and Moreno-Matson, MC and Perilla, C and Pinilla, D and Rodríguez-Leguizamón, G and Sánchez, E and Santana, A and Herrera, G and Ramírez, JD and Muñoz, M},
title = {Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00809-5},
pmid = {41692795},
issn = {1757-4749},
abstract = {BACKGROUND: Diarrhea remains a major cause of morbidity worldwide, particularly in low- and middle-income countries. Hospital environments impose strong selective pressures on the gut microbiome through antimicrobial exposure, invasive procedures, and pathogen transmission, yet differences between hospital-onset and community-onset diarrhea remain poorly characterized at the microbiome level. This study aimed to compare the taxonomic and functional profiles of the gut microbiome in hospitalized (Hosp) and emergency room (ER) patients with diarrhea using shotgun metagenomics.

RESULTS: Fecal samples from 41 patients (Hosp = 24; ER = 17) attending the Hospital Universitario Mayor-Méderi (Bogotá, Colombia) were analyzed. The gut microbiomes were dominated by Enterobacteriaceae, particularly Klebsiella pneumoniae and Escherichia coli, together with abundant bacteriophages from the families Myoviridae, Siphoviridae, Podoviridae, and crAss-like phages. Phages predicted to infect Escherichia and Klebsiella were significantly depleted in Hosp patients (p < 0.05). Read-based functional profiling revealed the presence of virulence factors associated with K. pneumoniae capsule biosynthesis, secretion systems, and toxins from Clostridioides difficile and Clostridium perfringens. In parallel, Hosp patients showed a higher diversity of antimicrobial resistance markers, with a marked increase in glycopeptide resistance determinants. A total of 492 high-quality metagenome-assembled genomes were reconstructed, including multiple diarrhea-associated taxa. Hosp patients exclusively harbored genomes of K. pneumoniae, Enterococcus faecium, and most reconstructed Clostridium species (C. symbiosum, C. saccharolyticum_A, C. innocuum, C. scindens, C. leptum, and Clostridium sp000435835). In contrast, ER patients harbored genomes classified as Escherichia coli, Escherichia flexneri, and Enterococcus faecalis. Genomes associated with hospitalization carried higher loads of antimicrobial resistance markers (e.g., oqxA and aac(6')-Ii) and virulence factors (e.g., iutA and traT), whereas ER genomes, particularly E. coli and E. flexneri, encoded diverse aminoglycoside resistance and adhesion traits.

CONCLUSIONS: Hospital-onset diarrhea was associated with distinct microbiome features, including differences in phage-bacteria dynamics involving key diarrhea-associated taxa, as well as a higher abundance of virulence factors and antimicrobial resistance markers. These findings underscore the potential value of shotgun metagenomics as a complementary approach for infection surveillance and the development of precision diagnostic strategies in hospital settings.},
}

@article {pmid41691988,
year = {2026},
author = {Pan, Y and Zong, G and Liu, M and Wang, Z and Zhu, H and Wei, Z and Shan, Y and Lu, Y},
title = {Restoring gut microbiota homeostasis to ameliorate colitis via Huangqin decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {153},
number = {},
pages = {157929},
doi = {10.1016/j.phymed.2026.157929},
pmid = {41691988},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory gut disorder involving dysregulated host-microbiota interactions. Huangqin decoction (HQD) is an herbal formula with known anti-inflammatory and microbiota-modulating effects, but its protective mechanism in ulcerative colitis remains unclear.

PURPOSE: To investigate whether HQD ameliorates colitis by rebalancing gut microbiota homeostasis and to elucidate the underlying immunological and regenerative mechanisms involved.

METHODS: A DSS-induced colitis mouse model was used to evaluate the effects of HQD. Colitis severity and inflammation were evaluated by the clinical disease index, histological analysis, and cytokine levels, and the gut microbiota profiles were analyzed via metagenomic sequencing. We used mechanistic assays to evaluate the effects of specific bacterial strains on intestinal organoids and neutrophil NETosis.

RESULTS: HQD significantly alleviated colitis symptoms and inflammation. It remodelled the gut microbiota, suppressing Desulfovibrionaceae while enriching Lachnospiraceae. This microbiota shift drove reduced NETosis and activated Wnt/β-catenin signaling to enhance intestinal stem cell (ISC) proliferation, thereby promoting mucosal repair. In organoid cultures, Lachnospiraceae promoted organoid growth, whereas Desulfovibrionaceae caused epithelial damage and, independently, triggered NETosis in immune contexts. Notably, administration of the Lachnospiraceae bacterium ameliorated colitis and increased colonic Wnt/β-catenin signaling, confirming its regenerative role.

CONCLUSION: HQD ameliorates colitis by rebalancing the gut microbiota, thereby suppressing harmful inflammation and promoting epithelial regeneration. These findings provide mechanistic support for HQD as a microbiota-mediated therapeutic strategy in colitis.},
}

@article {pmid41691957,
year = {2026},
author = {Jiang, W and Pu, J and Wang, F and Yan, J and Yang, Q and Yang, S and Bian, D},
title = {Study on the degradation performance and toxicity reduction mechanism of electroplating wash wastewater by a hydrolysis-acidification-MPR synergistic system.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128990},
doi = {10.1016/j.jenvman.2026.128990},
pmid = {41691957},
issn = {1095-8630},
abstract = {This study focuses on high-strength, low-biodegradability electroplating wash wastewater (COD ≥20,000 mg/L, BOD5/COD ≤0.1). A laboratory-scale hydrolysis-acidification (HA)-micro-pressure internal circulation multiphase reactor (MPR) combined treatment process was constructed. In the HA stage, wastewater biodegradability was significantly improved, with the BOD5/COD ratio being increased from 0.03 to 0.31. The MPR stage then further deepened degradation, enabling the system to maintain a COD removal rate above 97% during stable operation, linear alkylbenzene sulfonate (LAS) and TN removal rates were achieved at over 99% and 96.8%, respectively. Vibrio fischeri luminescence inhibition was reduced from >95% in the influent to approximately 65% in the HA effluent and <10% in the MPR effluent. GC-MS analysis revealed that the HA stage cleaved high-molecular-weight pollutants such as long-chain alkanes and esters into mid- and small-molecule products (e.g., 3-methylcyclohexanone and 2,5-dimethylnonane), while the MPR stage further converted these intermediates into low-toxicity small molecules (e.g., trimethylsilanol and hexamethylcyclotrisiloxane). Metagenomic analysis showed that facultative anaerobic fermenters (Aminivibrio, Alcaligenes) were enriched in the HA stage, whereas aerobic bacteria (Pseudomonas, Brevundimonas) predominated in the MPR stage. Key functional genes (alkB, cyp450, gpmB) were significantly enriched during the stable period, promoting carbon metabolism and stress resistance. This study elucidated that the HA-MPR synergistic system achieved efficient and stable degradation and toxicity mitigation of electroplating wash wastewater through a multi-stage cooperative mechanism of acidification cleavage and aerobic deep mineralization, providing theoretical and technical support for the engineering application of this process.},
}

@article {pmid41691930,
year = {2026},
author = {Liu, Q and Chen, S and Wang, Y and Wang, S and Zhou, R and Kou, G},
title = {Prunus persica (L.) Batsch root enriched Pseudomonas for enhanced saline-alkali tolerance by inducing fatty acid and flavonoid biosynthesis.},
journal = {Plant physiology and biochemistry : PPB},
volume = {232},
number = {},
pages = {111134},
doi = {10.1016/j.plaphy.2026.111134},
pmid = {41691930},
issn = {1873-2690},
abstract = {Peach (Prunus persica (L.) Batsch) is one of the most widely cultivated economic fruit crops worldwide. However, saline-alkali stress poses substantial challenges to its cultivation and production. This study investigated the synergistic response of peach roots and their rhizosphere microbiota to saline-alkali stress. We examined alterations in the rhizosphere bacterial community and its functional characteristics under such stress using 16S rRNA and metagenomic sequencing. The results indicated a significant enrichment of the genus Pseudomonas in the rhizosphere, accompanied by enhanced functional potential related to cell motility, biofilm formation, and signal transduction. Nine Pseudomonas strains were isolated from the stressed rhizosphere, all of which exhibited plant growth-promoting (PGP) traits in vitro, among which strains R8 showed the most comprehensive PGP profile and most significantly enhanced plant growth in pot experiments. Physiological and transcriptomic analyses demonstrated that R8 inoculation upregulates key genes involved in fatty acid (e.g., FAD, KCS, PAS) and flavonoid biosynthesis (e.g., CHS, CHI, F3H, FLS). This transcriptional reprogramming enhanced membrane stability (increased proline content) and antioxidant capacity (higher flavonoid levels), leading to systemic improvement in saline-alkali tolerance. This study reveals the adaptive strategy of peach to saline-alkali stress mediated by rhizobacteria and highlights the potential of R8 as a microbial inoculant for sustainable cultivation.},
}

@article {pmid41691882,
year = {2026},
author = {Xie, Y and Xu, Y and Ma, C and Chen, L and Cai, Y and Wu, S and Fan, Y and Zhang, C and Tian, Y and Tian, Y and Zhang, Y and Li, X and He, D},
title = {Cerebral sparganosis caused by spirometra sp.: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {1},
pages = {117311},
doi = {10.1016/j.diagmicrobio.2026.117311},
pmid = {41691882},
issn = {1879-0070},
abstract = {Cerebral sparganosis is a rare parasitic infection caused by plerocercoid larvae of the genus Spirometra. Due to its nonspecific clinical manifestations, diagnosis remains challenging in clinical practice. Here, we report a case of a 72-year-old female who presented with intermittent fever and migratory intracranial mass lesions over a seven-year period, accompanied by progressive cognitive decline and right homonymous hemianopia. Metagenomic next-generation sequencing (mNGS) analysis of cerebrospinal fluid identified Spirometra sp. The diagnosis was further confirmed through brain lesion biopsy and tissue mNGS analysis. Following treatment with praziquantel and albendazole, the patient showed clinical improvement with no evidence of recurrence during 1-year follow-up. This case report highlights the diagnostic value of mNGS in identifying rare parasitic infections, particularly in cases of cerebral sparganosis where clinical presentation may be non-specific.},
}

@article {pmid41691872,
year = {2026},
author = {Zhang, XR and Hou, J and Rong, Z and Wu, YH and Cui, HL},
title = {Haladaptatus marinus sp. nov., Haladaptatus rarus sp. nov., Haladaptatus ordinarius sp. nov., and Halomicrococcus pelagicus sp. nov., halophilic archaea from diverse coastal tidal flats.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126698},
doi = {10.1016/j.syapm.2026.126698},
pmid = {41691872},
issn = {1618-0984},
abstract = {Six novel halophilic archaeal strains, DFWS20[T], NG-SE-30[T], NG-WS-4[T], HHT-WS-8, NG-SE-24[T], and SG-WS-1, were isolated from different coastal regions of China. Metagenome and amplicon analyses showed that the abundance of archaea in the corresponding samples was very low. Strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 were found to cluster with current Haladaptatus species, while strains NG-SE-24[T] and SG-WS-1 with those of Halomicrococcus based on 16S rRNA and rpoB' gene phylogenies. The overall-genome related indexes (OGRIs), average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values, between strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], HHT-WS-8, and Haladaptatus species were 77.0-83.1%, 22.2-28.3%, and 74.7-84.8%, while those between strains NG-SE-24[T], SG-WS-1, and Halomicrococcus species were 79.6-94.9%, 26.0-63.9%, and 76.5-94.1%, respectively. These values were lower than the threshold of species classification. In contrast, the OGRIs between strains NG-WS-4[T] and HHT-WS-8, as well as those between strains NG-SE-24[T] and SG-WS-1, were above the threshold of species classification. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, and antibiotic sensitivity, were determined in these six strains and the existing species of the corresponding genera. The most abundant pathways in the genera Haladaptatus and Halomicrococcus were related to carbohydrate metabolism and amino acid metabolism. Based on the natural habitat analysis of the 16S rRNA genes of the strains, their target sequences were primarily found in habitats such as aquatic, soil, sediments, plant, and marine environments. The major polar lipids of strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and sulfated mannosyl glucosyl diether (S-DGD-1), while those of strains NG-SE-24[T] and SG-WS-1 were PG, PGP-Me, S-DGD-1, and galactosyl mannosyl glucosyl diether (TGD-2). Based on these polyphasic classification, strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 represent three novel species of the genus Haladaptatus while NG-SE-24[T] and SG-WS-1 represent a novel species of the genus Halomicrococcus.},
}

@article {pmid41691815,
year = {2026},
author = {Xia, J and Han, J and Hong, L and Qiu, YY and Xie, Y and Xu, H and Zhang, L and Jiang, F},
title = {Resilient sulfur-driven treatment of real acid mine drainage enabled by reorganization of core sulfidogenic microorganisms.},
journal = {Water research},
volume = {294},
number = {},
pages = {125521},
doi = {10.1016/j.watres.2026.125521},
pmid = {41691815},
issn = {1879-2448},
abstract = {Elemental sulfur-driven sulfidogenic processes offer a promising alternative to conventional sulfate reduction for acid mine drainage (AMD) treatment, with advantages in lower operation cost induced by lower organic demand. However, their long-term performance and microbial stability under real AMD conditions, where high acidity and metal concentrations impose strong environmental stress, remain poorly understood. Here, we operated a laboratory-scale sulfur-driven bioreactor for 258 days to evaluate the long-term sulfide production, metal removal efficiency, and microbial succession when treating real AMD. The system maintained stable sulfide production (68.3 ± 12.1 mg S/L-h) under acidic conditions (pH 4.1 ± 0.2) with a carbon-to-sulfur ratio (∼0.23, mg TOC per mg sulfide) consistent with the theoretical value for sulfur reduction. Over 99.9% of Zn[2+], Cu[2+], Ni[2+], Cd[2+], and Co[2+] in AMD were effectively removed via in-situ precipitation with biogenic sulfide. Even exposed to high metal concentrations (e.g., ∼400 mg/L Zn[2+], ∼51 mg/L Cu[2+]), the sulfidogenic bacteria exhibited strong resilience and robustness. Microbial analyses revealed a substantial shift from diverse fermenters under synthetic wastewater to specialized, metal-tolerant sulfur reducers (e.g., Desulfurella, Athalassotoga) under AMD conditions. Metagenome-assembled genomes of these taxa revealed distinct metabolic strategies, including sulfur respiration, acid resistance, and metal detoxification, supporting their dominance under metal-rich and low-pH environments. Notably, the community exhibited strong structural resilience to both long-term metal exposure and acute metal shocks, maintaining sulfidogenic functionality through internal community reorganization rather than taxonomic turnover. These findings demonstrated the feasibility, robustness, and ecological adaptability of sulfur-driven sulfidogenic systems for cost-effective treatment of real-world AMD.},
}

@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}

@article {pmid41691450,
year = {2026},
author = {Chen, S and Gu, Y and Bahadur, A and Liu, E and Wu, T and Zhu, X and Zou, Y and Liang, H and Wei, P and Wu, L and Wu, Q and Yang, P and Yu, H and Yang, Y},
title = {Divergent Responses of Bacterial Communities to Permafrost Degradation and Their Associations With Carbon Across Vertical Profiles.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e10516},
doi = {10.1002/advs.202510516},
pmid = {41691450},
issn = {2198-3844},
support = {2022YFF0801903//National Key R&D Program of China/ ; xbzg-zdsys-202214//"Light of the West" Cross-team Project of the Chinese Academy of Sciences/ ; U23A2062//National Natural Science Foundation of China/ ; U24A20586//National Natural Science Foundation of China/ ; 23ZDFA017//Science and Technology Program of Gansu Province/ ; CSFSE-FX-2505//Freedom Project of the State Key Laboratory of Cryospheric Science and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, CAS/ ; },
abstract = {Permafrost degradation poses a significant threat to the organic carbon (C) pool primarily through regulating microorganisms. However, microbial responses and their associations with C loss across vertical profiles remain unclear. Here, we use metagenomic sequencing to investigate bacterial communities in 125 samples from five 15 m-depth permafrost cores, spanning from the active layer to the permafrost layer along a degradation gradient on the Qinghai-Tibet Plateau. We find that α-diversity decreases, while stochastic processes and community stability increase from the active layer to the permafrost layer. Along permafrost degradation, these community attributes follow similar variations within the active layer but remain constant within the permafrost layer. The relative abundance and interaction of core taxa play important roles in maintaining community stability in the active and permafrost layers, respectively. As permafrost degrades, the negative relationships between community stability and C storage become more intense, especially in the active layer. These findings demonstrate that degradation induces microbial responses that potentially amplify C release, supporting a positive feedback loop to climate warming. Our work provides novel insights into the vertical heterogeneity of this mechanism and is crucial for modeling future permafrost C dynamics.},
}

@article {pmid41691253,
year = {2026},
author = {Daryani, NE and Jazayeri, SM and Izadi, N and Ahmadi, H and Baghi, HB and Shirmohammadi, M and Sabbaghian, M and Shekarchi, AA and Marvi, SS and Azadi, A and Poortahmasebi, V},
title = {Characterizing the gut virome in ulcerative colitis and crohn's disease: signatures of disease severity.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03091-8},
pmid = {41691253},
issn = {1743-422X},
support = {979157//National Institute for Medical Research Development/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic disorder marked by intestinal inflammation and immune dysregulation. While bacterial dysbiosis has been widely investigated, the gut virome remains less explored. Altered viral communities, particularly bacteriophages, may destabilize microbial balance and amplify host inflammation.

METHODS: To characterize virome alterations, we conducted a cross-sectional observational study in Tabriz, Iran, involving fifty participants divided into five groups: mild UC, severe UC, mild CD, severe CD, and healthy controls. Stool samples were processed for viral nucleic acid extraction and analyzed using metagenomic next-generation sequencing. Bioinformatics pipelines included diversity assessment, taxonomic profiling, functional annotation, and discriminant analysis (LEfSe). Predictive modeling was performed with random forest classifiers.

RESULTS: Virome richness and diversity were reduced in severe UC and CD compared with controls, whereas mild cases showed values closer to healthy individuals. Taxonomic profiling revealed depletion of crAss-like phages and microviridae in IBD, along with enrichment of Caudovirales families such as siphoviridae and myoviridae. Among eukaryotic viruses, anelloviridae were prominent in severe IBD, and herpesviridae were enriched specifically in severe UC. Functional annotation highlighted enrichment of structural and lytic phage proteins in severe groups, whereas lysogeny-associated domains were more abundant in healthy controls. Random forest models based on viral features achieved appropriate accuracy, with an AUC of 0.89 for distinguishing IBD from controls and 0.83 for classifying mild versus severe disease.

CONCLUSION: Thus, IBD is associated with reduced virome diversity, loss of core protective phages, and selective enrichment of bacteriophages and eukaryotic viruses. These findings suggest that virome features may have potential as biomarkers for non-invasive diagnosis and severity stratification in IBD, requiring validation in larger and longitudinal cohorts.},
}

@article {pmid41691172,
year = {2026},
author = {Motta, H and Perin, APA and Rosin, GF and Reuwsaat, JCV and Mocelin, I and Lopes, FC and Mayer, FQ and de Medeiros, VP and Brum, IS and Baethgen, LF and Gregianini, TS and Staats, CC and Vainstein, MH and Kmetzsch, L},
title = {SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04828-9},
pmid = {41691172},
issn = {1471-2180},
support = {405934/2022-0//Instituto Nacional de Ciência e Tecnologia (INCT FUNVIR)/ ; 408717/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/2551-0000396-6//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; },
}

@article {pmid41691170,
year = {2026},
author = {Zhou, W and Zou, X and Li, J and Alhaskawi, A and Abdalbary, SA and Lu, H},
title = {Chronic osteomyelitis of the right thumb caused by Actinomyces radingae and Finegoldia magna: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12860-3},
pmid = {41691170},
issn = {1471-2334},
abstract = {BACKGROUND: Osteomyelitis of the hand is relatively uncommon and often results from penetrating trauma or postoperative infection. Rare pathogens such as Actinomyces radingae and Finegoldia magna pose diagnostic and therapeutic challenges due to their slow growth, frequent involvement in polymicrobial infections, and limited antibiotic susceptibility data.

CASE PRESENTATION: A 66-year-old male sustained a crush injury being caught in a door to his right thumb over two years prior, leading to repeated episodes of redness, swelling, pain, and restricted motion. Despite undergoing surgical intervention three months earlier at another hospital, his symptoms persisted. Radiography revealed cortical irregularity and surrounding soft tissue swelling of the distal phalanx. Magnetic resonance imaging revealed bone marrow edema of the distal phalanx and adjacent soft tissue inflammation, raising suspicion for underlying osteomyelitis in the appropriate clinical context. Laboratory markers of infection were within normal limits. The patient underwent surgery including necrotic bone removal, extensor tendon reconstruction with muscle transposition, and nail bed debridement. Intraoperative findings included purulent drainage, nail deformity, and tendon necrosis. Metagenomic next-generation sequencing (mNGS)of bone tissue identified Actinomyces radingae (8,019 reads) and Finegoldia magna (4,223 reads). Based on the chronic clinical course, imaging findings, intraoperative evidence of necrotic bone, and pathogen identification by metagenomic next-generation sequencing, a diagnosis of chronic osteomyelitis of the distal phalanx was established. Postoperatively, the patient received ertapenem (1 g QD) with good clinical response.

CONCLUSION: This case highlights the importance of considering uncommon pathogens in chronic post-traumatic hand infections and demonstrates the utility of mNGS in identifying atypical bacteria, enabling targeted therapy and improved outcomes.},
}

@article {pmid41690672,
year = {2026},
author = {Zhang, Y and Bai, Y and Ni, J and Shi, J and Zhang, Y and Bell-Sakyi, L and Wu, X and He, C and Deng, F and Yin, F and Shen, S and Fang, Y},
title = {Evidence of human exposure to tick-borne viruses based on viromes of ticks and presence of specific antibodies among patients in Hainan Island, Southern China.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.02.008},
pmid = {41690672},
issn = {1995-820X},
abstract = {Hainan Island, located in the South China Sea, is known as an area with diseases related to Rickettsia spp. or spirochete infection; however, the potential threat there from infection with tick-borne viruses (TBVs) remains obscure. In the present study, the dominant tick species, including Rhipicephalus sanguineus and Rhipicephalus microplus, were collected in Hainan Island, and tick viromes were investigated by metagenomic sequencing. In total, 27 viral species were identified belonging to the families Orthomyxoviridae, Flaviviridae, Nairoviridae, Phenuiviridae, Totiviridae, Chuviridae, Rhabdoviridae, and Parvoviridae, amongst which one novel virus and 13 new strains were discovered. Subsequently, individual ticks were screened for seven TBVs, Huanggang Rhabd tick virus 1 (HRTV1), Lihan tick virus (LHTV), Mivirus (MIV), Guangdong tick quaranjavirus (GTQV), Wenchang Ephemerovirus (WEPMV), Jingmen tick virus (JMTV), and brown dog tick phlebovirus (BDPTV), resulting in high prevalence rates of 16.97%, 9.59%, 10.33%, 7.38%, 7.01%, 6.27%, and 3.69%, respectively. While co-infection with multiple viruses was more frequent in R. sanguineus, R. microplus ticks generally had higher viral loads. Four febrile patients showed antibody responses to three TBVs, one each to LHTV and JMTV, and two to GTQV; the patient with antibodies to JMTV also showed neutralizing activity against this virus. This study promoted our understanding of the diversity and complexity of the TBV community in Hainan Island. The results provide serological evidence that human exposure to TBVs like JMTV may have occurred in Hainan, raising concern about potential risks from TBVs and the need to perform further surveys of TBVs among ticks, animals and humans.},
}

@article {pmid41690272,
year = {2026},
author = {Bao, M and Liu, X and Chang, N and Wang, M and Zuo, S and Yin, G and Li, W and Zhang, S and Zhang, Y and Shen, W},
title = {Seasonal variation and co-occurrence of metal resistance and virulence genes in landfill leachate pathogens: Implications for environmental risk management.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141460},
doi = {10.1016/j.jhazmat.2026.141460},
pmid = {41690272},
issn = {1873-3336},
abstract = {The co-dissemination of metal resistance genes (MRGs) and virulence factor genes (VFGs) in landfill leachate pathogens poses a significant yet underquantified public health risk. To address this gap, this study used metagenomic analysis to assess MRG/VFG occurrence and removal efficiency, and proposed a novel metal resistance index (MRI)-virulence risk index (RVI) framework to quantify microbial risks across raw, ultrafiltered, reverse-osmosis-treated leachate and adjacent groundwater in Hohhot, China. Metagenomic analyses identified 175 MRGs and 1024 VFGs, highlighting significant co-occurrence patterns (Spearman R > 0.6, P < 0.05) among dominant pathogens, including Pseudomonas aeruginosa and Escherichia coli. The results of PCoA analysis showed that the leachate treatment process could significantly change the spectrum of virulence gene and heavy metal resistance gene in the leachate. Linear regression analysis (all P < 0.001) revealed significant positive correlations between treated leachate and groundwater microbial VFGs/MRGs across seasons. Summer showed the strongest associations (R[2]: 0.733-0.892), followed by moderate correlations in spring (R[2]: 0.364-0.698) and autumn (R[2]: 0.349-0.642), with spatial heterogeneity in BG3 and marked seasonal impacts overall. MRI, RVI, and the MRI/RVI ratio increased sequentially after treated, indicating that high-risk microbial traits persist post-treatment. Importantly, this elevated MRI/RVI ratio is attributable to the relative proportional increase of high-risk genes rather than an absolute rise in their abundance. Our results demonstrate the leachate treatment partially mitigates heavy metal resistance/virulence loads but fails to eliminate all high-risk genes, revealing seasonal MRG-VFG co-enrichment and treatment efficacy. The MRI-RVI framework guides leachate management optimization for environmental and public health.},
}

@article {pmid41690221,
year = {2026},
author = {Jiang, Y and Shu, W and Wan, J and Yan, J and Liu, Q and Jiang, Y},
title = {Impacts of co-exposure to nanoplastics and ofloxacin on marine planktonic microbial communities and DMSP dynamics.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107908},
doi = {10.1016/j.marenvres.2026.107908},
pmid = {41690221},
issn = {1879-0291},
abstract = {Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound in marine food webs and the main precursor of the climate-active gas dimethyl sulfide (DMS), yet its water-column cycling under the joint influence of emerging pollutants remains poorly constrained. A 19-day microcosm experiment was conducted to examine the long-term effects of single and combined exposure to nanoplastics (NPs) and the antibiotic ofloxacin on planktonic microbial communities and DMSP cycling in coastal seawater. Combined exposure induced much stronger inhibitory effects than either single pollutant, markedly weakening the late-phase biomass recovery observed under the antibiotic-only treatment. DMSP dynamics exhibited a biphasic disruption pattern: an initial transient accumulation was followed by persistently low concentrations later in the experiment, coinciding with pronounced declines in microeukaryotic and total biomass. Combined metagenomic and flow cytometric analyses revealed a "functional decoupling" scenario, in which the surviving community displayed elevated relative abundances of DMSP biosynthesis- and degradation-related genes, while the sharp reduction in microeukaryotic biomass and overall community size constrained the maintenance and renewal of the water-column DMSP pool. Co-occurrence network analysis further showed that co-exposure simplified the microbial network from a more distributed, complex structure to a highly centralized one, with fewer nodes and keystone taxa and decreased robustness indices along the pollution gradient. Together, these findings indicate that the co-occurrence of nanoplastics and antibiotics can disturb DMSP-related functions by eroding community structural stability and functional redundancy, providing experimental evidence for the vulnerability of coastal DMSP cycling to mixed-pollutant stress.},
}

@article {pmid41689625,
year = {2026},
author = {Hayashi, T and Iida, N and Yasuda, K and Yoshio, T and Terashima, T and Takatori, H and Moriyama, H and Takeshita, Y and Takamura, T and Yamashita, T},
title = {Escherichia coli as a gut microbial marker of obesity and its reduction following bariatric treatment.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {41689625},
issn = {1435-5922},
support = {19K17394//Japan Society for the Promotion of Science/ ; 23K15036//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Alterations in the gut microbiota have been implicated in obesity-related metabolic disorders; however, the disease-relevant microbial features that link gut dysbiosis to metabolic risk remain incompletely defined. In particular, whether quantitative expansion or strain-level divergence of specific taxa underlie metabolic dysfunction is unclear.

METHODS: We performed cross-sectional and longitudinal metagenomic analyses of fecal samples from 19 patients with severe obesity undergoing bariatric intervention and 30 healthy donors. Whole-genome shotgun sequencing was combined with quantitative PCR to assess both relative and absolute bacterial abundance. Cultured Escherichia coli isolates were further examined by whole-genome sequencing to evaluate strain-level diversity. Associations between microbial features and metabolic parameters were analyzed.

RESULTS: The gut microbiota of patients with severe obesity was taxonomically and functionally distinct from that of healthy donors. Among altered taxa, E. coli was significantly enriched in obesity and showed a consistent and marked reduction at 6 months post-intervention, irrespective of procedure type. Absolute E. coli abundance quantified by qPCR decreased significantly following intervention. In contrast, whole-genome analysis revealed no clear genotypic clustering of E. coli strains by host phenotype. Notably, E. coli abundance correlated positively with HbA1c and systolic blood pressure and negatively with serum albumin levels, whereas global microbial diversity and KEGG-based metabolic pathways showed limited longitudinal change.

CONCLUSIONS: Quantitative expansion of gut E. coli, rather than strain-specific genomic divergence, is associated with metabolic risk in severe obesity and is consistently reduced at 6 months after bariatric intervention. These findings suggest that microbial load-dependent effects of E. coli may be associated with obesity-related metabolic dysfunction and represent a potential biomarker. This exploratory, single-center study is hypothesis-generating and warrants further validation in larger, multi-center cohorts as well as interventional studies using preclinical animal models.},
}

@article {pmid41689511,
year = {2026},
author = {Xu, R and Mayer, MJ and Philo, M and Gall, GL and Mulaw, G and Ponsero, A and Narbad, A},
title = {Combining Lactiplantibacillus plantarum and Bifidobacterium adolescentis can improve GABA production in faecal fermentations.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag047},
pmid = {41689511},
issn = {1365-2672},
abstract = {AIMS: This project aimed to investigate production of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) from potential probiotic strains. We studied production in co-cultures and faecal fermentations and examined the effect of selected strains on the faecal microbiome composition and metabolome in vitro.

METHODS AND RESULTS: Strains of intestinally-derived Bifidobacterium adolescentis and Lactiplantibacillus plantarum from fermented cereals were grown singly, in co-culture and in faecal fermentations designed to simulate colonic conditions.Isolates synthesised varing amounts of GABA in vitro; GABA production could be increased by co-culture, lactic acid or reduced pH but was decreased in the presence of high buffering. In faecal fermentations, selected strains inoculated singly or in combination persisted over 24 hours and increased the GABA concentration without causing major disruptions in the microbiome or metabolome. B. adolescentis supplementation increased short chain fatty acids acetate and propionate and L. plantarum was associated with increased succinate levels, while all treatments exhibited a reduction in Escherichia compared to the controls.

CONCLUSIONS: GABA production from these lactic acid bacteria is strain-specific and the combination of these two species shows potential for future next-generation probiotic development.},
}

@article {pmid41688638,
year = {2026},
author = {Dekkers, KF and Pertiwi, K and Baldanzi, G and Lundmark, P and Hammar, U and Moksnes, MR and Coward, E and Nethander, M and Salih, GA and Miari, M and Nguyen, D and Sayols-Baixeras, S and Eklund, AC and Holm, JB and Nielsen, HB and Volpiano, CG and Méric, G and Thangam, M and Hakaste, L and Tuomi, T and Ahlqvist, E and Smith, CA and Allen, M and Reimann, F and Gribble, FM and Ohlsson, C and Hveem, K and Melander, O and Nilsson, PM and Engström, G and Smith, JG and Michaëlsson, K and Ärnlöv, J and Orho-Melander, M and Fall, T},
title = {Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {41688638},
issn = {1546-1718},
support = {2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2020-02191//Vetenskapsrådet (Swedish Research Council)/ ; 2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; 521-2013-2756//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01236//Vetenskapsrådet (Swedish Research Council)/ ; 2021-02273//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01291//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01015, 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784, 2018-02837, EXODIAB 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20200173//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2022-0344//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2020-0711//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//Lars Erik Lundbergs Stiftelse för Forskning och Utbildning (Lundberg Foundation for Research and Education)/ ; CKFUU-1025348, 987986, 976460, 963488, 936407, 695401, and 797891//Centrum fÖr Klinisk Forskning Dalarna (Center for Clinical Research Dalarna)/ ; },
abstract = {Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 × 10[-11]) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.},
}

@article {pmid41688119,
year = {2026},
author = {Akpulu, CP and Maikudi Sada, H and Ahmed, H and Idris, HB and Yakubu, R and Aminu, A and Iregbu, K and Oduwo, J and Owinoh, E and Lankapalli, AK and De Nies, L and Achi, CR and Thomson, K and Stracy, M and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Nigeria (INBUGS-NG).},
journal = {BMJ open},
volume = {16},
number = {2},
pages = {e111007},
doi = {10.1136/bmjopen-2025-111007},
pmid = {41688119},
issn = {2044-6055},
mesh = {Humans ; Nigeria ; *Gastrointestinal Microbiome ; Female ; Infant ; *Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; Male ; Infant, Newborn ; Longitudinal Studies ; Feces/microbiology ; Adult ; Breast Feeding/statistics & numerical data ; Milk, Human/microbiology ; Delivery, Obstetric ; Pregnancy ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Nigeria (INBUGS-NG) investigates how delivery mode, antibiotic exposure, feeding practices and environmental factors shape gut microbiome development and acquisition of antibiotic resistance genes (ARGs) during the first year of life in northern Nigeria.

PARTICIPANTS: Between February and July 2024, 90 mother-infant dyads were enrolled at a tertiary hospital in Kano city, Nigeria. This was a prospective longitudinal cohort with follow-ups at 10 scheduled time points: days 0, 1, 3, 5, 7, 14, 28, 90, 180 and 365. We also intensified stool sampling after infant antibiotic administration, enabling dense early-life sampling. To date, the cohort has contributed 480 infant stool samples, 232 maternal rectal swabs, 254 breast milk samples and 806 environmental samples (total 1772). In parallel, socio-demographic, clinical and cultural data were collected using Research Electronic Data Capture (REDCap) and household visit diaries.

FINDINGS TO DATE: Baseline data show that 84/90 mothers (93.3%) received postpartum antibiotics, and 26/90 infants (28.9%) received antibiotics within the first 3 months of life. Only 8% of infants were exclusively breastfed, with early water supplementation common. Caesarean deliveries accounted for 25% of births, and the mean gestational age was 38.5 weeks. Across the cohort, high retention was achieved, and the study has generated a unique long-read metagenomic resource from an African infant population, with analyses ongoing.

FUTURE PLANS: Shotgun long-read metagenomic sequencing (Oxford Nanopore) will enable strain-level and plasmid-level profiling of microbial communities and ARGs. Planned analyses include associations between early-life exposures and resistome dynamics, as well as cross-cohort comparisons with a parallel study in Pakistan. Follow-up will continue through 12 months.},
}

Humans
Nigeria
*Gastrointestinal Microbiome
Female
Infant
*Anti-Bacterial Agents/therapeutic use
Prospective Studies
Male
Infant, Newborn
Longitudinal Studies
Feces/microbiology
Adult
Breast Feeding/statistics & numerical data
Milk, Human/microbiology
Delivery, Obstetric
Pregnancy

@article {pmid41687886,
year = {2026},
author = {Jin, B and Yan, Y and Bai, Z and He, H and Du, J and Xu, Y and Ma, C and Wang, L and Ji, J},
title = {Metagenomics reveals the mechanisms of endogenous partial denitrification (EPD) driven by different valence iron states:Nitrite accumulation, microbial adaptation, functional gene and metabolic pathways.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134209},
doi = {10.1016/j.biortech.2026.134209},
pmid = {41687886},
issn = {1873-2976},
abstract = {To enhance the performance of endogenous partial denitrification (EPD) systems, different iron valence states (nano-zero-valent iron (nZVI), Fe(II), and Fe(III)) were introduced, and their effects on microbial communities and metabolic pathways were investigated using metagenomics. The results indicated that iron supplementation significantly improved the removal of COD, NO3[-]-N, and PO4[3-]-P, as well as NO2[-]-N accumulation. Notably, Fe(III) proved most effective, achieving a NO2[-]-N accumulation of 27.7 ± 3.7 mg/L and a PO4[3-]-P removal efficiency of 64.7 ± 7.5%, whereas excessive Fe(II) and Fe(III) (40 mg/L) inhibited NO2[-]-N accumulation. While the overall microbial community structure remained stable, iron addition enriched specific denitrifying and phosphorus-accumulating genera such as Candidatus Competibacteraceae (1.36%, 2.40%, 2.30%), Candidatus Competibacter (0.40%, 0.65%, 0.62%), and Thauera (3.02%, 1.76%, 3.00%). nZVI promoted carbon utilization and denitrification gene expression, enhanced the including endogenous carbon transformation and nitrogen metabolism. In contrast, Fe(II) and Fe(III) enhanced NO2[-]-N accumulation by suppressing key genes (nirS/nirK, norB, nosZ) and shifted phosphorus metabolism toward chemical removal as the dominant pathway. Exogenous iron optimizes the performance of the EPD system by downregulating iron metabolism genes (afuA, fbpA, and afu) to mitigate iron toxicity stress. These findings provide theoretical support for optimizing EPD systems and improving nutrient removal in wastewater treatment.},
}

@article {pmid41687847,
year = {2026},
author = {Wang, N and Kang, Z and Wang, X and Zhang, Y and Li, X and Sun, Y and Xi, J and Shen, L},
title = {Sewage-sludge-derived biostimulant enables fertilizer reduction while maintaining rice yield through microbiome-mediated nutrient cycling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124020},
doi = {10.1016/j.envres.2026.124020},
pmid = {41687847},
issn = {1096-0953},
abstract = {Modern agriculture relies heavily on chemical fertilizers to sustain high yields, yet excessive inputs contribute to soil acidification, water eutrophication, greenhouse gas emissions, and biodiversity loss. Sewage-sludge-derived biostimulants (SS-BS) may help reduce fertilizer dependency while sustaining crop performance through plant-soil-microbiome interactions. Here, we evaluated SS-BS in a paddy rice field trial conducted during a single growing season (2024) under conventional management. Three fertilization regimes were compared: low-fertilizer control (CK), conventional fertilization (FP), and reduced mineral fertilization supplemented with SS-BS (BS). Across the 2024 season, rice yield and key yield components in BS were comparable to, or approached, those in FP with reduced mineral fertilizer input. Shotgun metagenomic profiling indicated that BS was associated with shifts in microbial functional pathways related to nitrogen, phosphorus, and potassium cycling, and with changes in the relative abundance of taxa linked to nutrient transformation processes. Partial least squares path modeling (PLS-PM) further suggested that microbial functional attributes were associated with the relationships among fertilization regime, soil properties, and yield outcomes. Collectively, these results from a single-season field experiment indicate that SS-BS has the potential to support fertilizer-reduction strategies in rice systems and motivate multi-season validation of its agronomic performance and microbiome- associated effects.},
}

@article {pmid41648108,
year = {2026},
author = {Martinez, NAP and Arnaldi, MR and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in a Drosophila Autism-like Model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41648108},
issn = {2692-8205},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that has no cure and is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B or KDM5C are found in patients with intellectual disability and ASD. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5 [LOF]) ASD-like model revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.

METHODS: Here, we evaluated multiple microbiota-based interventions, including probiotic supplementation with Lactiplantibacillus plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in Kdm5 [LOF] flies. Gut bacterial abundance was quantified using colony-forming unit (CFU) assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.

RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5 [LOF] and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5 [LOF] flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5 [LOF] mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5 [LOF] recipient flies.

CONCLUSIONS: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships relevant to ASD and for evaluating targeted probiotic and microbiota-transfer strategies.},
}

@article {pmid41687784,
year = {2026},
author = {Thriene, K and Stanislas, V and Huang, KD and Strowig, T and Michels, KB},
title = {Impact of Yogurt and Rolled Oats Consumption on the Gut Microbiome: A Randomized Crossover Study displaying Individual Responses and General Resilience.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101408},
doi = {10.1016/j.tjnut.2026.101408},
pmid = {41687784},
issn = {1541-6100},
abstract = {BACKGROUND: Yogurt and rolled oats are commonly linked to gut health through pro- and prebiotic effects, but these benefits remain understudied, especially in healthy individuals eating a regular diet.

OBJECTIVE: This study primarily aimed to investigate the effects of daily yogurt and rolled-oats consumption on gut microbial composition. Secondary outcomes included stool metabolites and blood-based health markers.

METHODS: In this randomized, open-label, two-period crossover trial, 110 healthy participants were randomly assigned to one of two sequences: 250 g of yogurt daily followed by 250 g of yogurt with 50 g of rolled oats, or the reverse with a washout period in between. Stool and blood samples were collected at baseline and post-intervention. Metagenomic sequencing and metabolomic analysis were conducted on stool samples, while health markers related to metabolic control, inflammation, immune response, oxidative stress, and gut permeability were assessed in the participants' blood.

RESULTS: Of the 119 randomized participants, 110 completed the study (53 yogurt first, 57 yogurt and rolled oat first). Yogurt consumption transiently increased yogurt-associated bacteria, with Streptococcus thermophilus rising from absent to 0.97% (95% CI 0.71-1.26) in the yogurt intervention and 0.79% (0.58-1.03) in the yogurt with oats intervention. In a small Prevotella-predominant subgroup (n = 8), adding rolled oats increased microbial evenness (q < 0.001) and reduced inter-individual divergence (q < 0.05), suggesting a temporary slight homogenization. No additional effects on fecal short-chain fatty acids (SCFAs) concentrations or human health markers were identified. Functional metagenomic changes were mainly driven by yogurt-derived bacterial enrichment.

CONCLUSION: A healthy gut microbiota is largely stable and resilient to short-term diet changes, yet individual differences in small changes highlight the importance of personalized dietary recommendations.

CLINICAL TRIAL REGISTRATION: German register for clinical studies, identifier: DRKS00023146 https://drks.de/search/en/trial/DRKS00023146/details.},
}

@article {pmid41687589,
year = {2026},
author = {Luo, S and Tang, C and Shan, Y and Wan, C and Mo, Y and Huang, Y and Wu, R and Yu, F and Li, Y},
title = {Phosphate-solubilizing bacteria enhance cadmium phytoremediation by Solanum nigrum L. through improved phosphorus availability and cycling in contaminated soil.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141422},
doi = {10.1016/j.jhazmat.2026.141422},
pmid = {41687589},
issn = {1873-3336},
abstract = {Phosphate-solubilizing bacteria (PSB)-assisted phytoremediation has been recognized as an effective strategy for remediating cadmium (Cd)-contaminated soils, yet species-specific physiological and ecological traits among hyperaccumulators result in distinct Cd uptake mechanisms. Although the pivotal role of phosphorus (P) cycling in promoting Cd uptake is established, its mechanistic linkage with PSB-mediated phytoremediation remains poorly understood. This study employed Enterobacter sp. FM-1 and the Cd hyperaccumulator Solanum nigrum L. (S. nigrum L.) to elucidate how PSB regulate Cd accumulation through P cycling. Enterobacter inoculation significantly decreased soil pH and increased bioavailable Cd by 43.4 %-104.3 % relative to the control. The pH-driven mineralization of organic P was the primary process enhancing soil available P (AP), which rose by 12.1-32.2 %. Soil AP content was positively correlated with Cd concentrations in S. nigrum tissues, indicating a close association between enhanced phosphorus availability and plant Cd accumulation, accompanied by strengthened antioxidant defense related responses. Furthermore, PSB inoculation elevated phytochelatin levels via P-starvation response pathways, mitigating oxidative stress. Enhanced polyphosphate synthesis and phosphatase activity further promoted plant growth and P turnover. Metagenomic analysis revealed that Proteobacteria were the predominant carriers of P-cycling genes in the S. nigrum L. rhizosphere. Overall, Enterobacter sp. inoculation reshaped rhizosphere microbial communities, increased P bioavailability and improved Cd tolerance. These findings provide mechanistic insight into the coupling between microbial P activation and Cd uptake, offering a sustainable, microbially driven strategy for Cd-contaminated soil phytoremediation.},
}

@article {pmid41687586,
year = {2026},
author = {Xu, L and Xu, W and Yang, Y and Wu, J and Su, X and Dong, F and Xiao, X and Chen, C and Zheng, X and Sun, F},
title = {Single-stage bioreactor integrating anammox and sulfur-driven autotrophic denitrification for nitrogen removal from landfill leachate.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141444},
doi = {10.1016/j.jhazmat.2026.141444},
pmid = {41687586},
issn = {1873-3336},
abstract = {An integrated anaerobic ammonium oxidation-sulfur autotrophic denitrification (Anammox-SAD) bioreactor was developed for nitrogen removal from real landfill leachate without external organic carbon. The system was operated continuously for 105 days under stepwise-decreasing hydraulic retention time (HRT), with a stable influent NO2[-]-N/NH4[+]-N ratio of 1.2-1.5 provided by partial nitrification. The anammox zone maintained robust performance, yielding average effluent NH4[+]-N, NO2[-]-N and NO3[-]-N of 18 ± 5, 6 ± 9, and 110 ± 16 mg/L, respectively. At an HRT as low as 0.5 d, the maximum nitrogen removal rate reached 2.04 kg N/(m[3] d). Despite influent fluctuations (total nitrogen of 600-840 mg/L), the integrated reactor achieved a stable total nitrogen removal of 85-89 %. The downstream SAD zone effectively polished anammox-derived nitrate, reducing NO3[-]-N from 80-150 to 35-60 mg/L. Sulfur oxidation was confirmed by elevated sulfate concentrations, while anammox-associated alkalinity generation provided intrinsic pH buffering, sustaining favorable conditions for SAD. Metagenomic analyses revealed coordinated nitrogen-sulfur metabolic networks, showing that shortening HRT enhanced microbial diversity and functional redundancy but revealed kinetic limitations in substrate reduction. Overall, the integrated anammox-SAD system provides a robust and low-carbon strategy for treating high-strength landfill leachate.},
}

@article {pmid41687578,
year = {2026},
author = {Zhou, Q and Liang, H and Huang, J and Klümper, U and Fang, P and Yu, Z and Wang, Y and Berendonk, TU and Lin, L and Li, X and Li, B},
title = {Impact of sulfonamides on microbial community and antibiotic resistome profiles in anaerobic digestion of swine wastewater.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141426},
doi = {10.1016/j.jhazmat.2026.141426},
pmid = {41687578},
issn = {1873-3336},
abstract = {Residual antibiotics in swine wastewater promote the proliferation of the antibiotic resistome, posing significant threats to environmental and human health. Although anaerobic digestion (AD) is widely applied for treating swine wastewater, the effects of antibiotics on the microbial community and resistome during AD remain unclear. This study employed amplicon and metagenomic sequencing, combined with long- and short-read hybrid assembly, to comprehensively investigate the impact of sulfonamides on the microbiome and resistome during AD. Enterococcus, a genus capable of utilizing exogenous folate, was identified as the dominant genus under sulfonamide stress. A total of 24 antibiotic resistance gene (ARG) types and 440 subtypes were identified. Sulfonamide stress selectively enriched sulfonamide resistance genes, with no notable co-selective effects on ARGs for other antibiotic classes. Short-term exposure significantly enriched sul2 (3.8-fold) and sul3 (4.0-fold), while long-term exposure enriched sul1 (1.6-fold). Sulfonamides especially promoted the proliferation of sulfonamide resistance genes on both mobilizable and non-mobilizable plasmids. The co-occurrence of multiple categories of mobile genetic elements and ARGs on contigs was inferred to play a critical role in driving ARG dissemination. Whereas a strain belonging to Enterococcus_I emerged as the dominant resistant bacterium in the AD system, a particular multidrug-resistance risk was identified for a strain belonging to the Filifactoraceae family. This work provides a new perspective on the impact of antibiotics on microbial community and antibiotic resistome composition and dynamics during the AD treatment process of swine wastewater.},
}

@article {pmid41687577,
year = {2026},
author = {Feng, Y and Zhang, X and Lai, S and Chen, F and Hu, J and Li, M and Sun, W},
title = {Nontarget screening uncovers the overlooked impact of antibiotic transformation products on riverine resistomes.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141425},
doi = {10.1016/j.jhazmat.2026.141425},
pmid = {41687577},
issn = {1873-3336},
abstract = {Antibiotics, their transformation products (TPs), and antibiotic resistance genes (ARGs) pose a major environmental threat, yet the influence of TPs on ARGs remains poorly understood. This study combined target, suspect and nontarget analysis via high-resolution mass spectrometry with metagenomic analysis to systematically profile the occurrence of antibiotics, TPs, and ARGs in an urban river. A total of 32 parent antibiotics and 49 TPs were identified, with concentrations ranging from 0.002193 ng/L and not detected145 ng/L, respectively. TPs accounted for a substantial portion of total antibiotic loads (41.3 % in spring and 31.9 % in summer). Metagenomic sequencing revealed 1599 ARG subtypes conferring resistance to 28 classes of antibiotics. TPs can drive antimicrobial resistance directly by exerting selective pressure through their residual antibacterial activity, and indirectly through reverting to parent compounds, thereby reintroducing bioactive antibiotics into the environment. Therefore, the inclusion of TPs improved ARG-antibiotic correlations. Multivariate analyses revealed that TPs exerted comparable or greater influence on ARG profiles than parent antibiotics. Specific TPs, particularly β-lactams, macrolides, and quinolones, significantly affected the abundance of multiple ARGs, underscoring their substantial and non-negligible impact. This study highlights the previously underestimated role of antibiotic TPs in shaping ARG profiles and calls for an urgent update of risk assessment frameworks to incorporate TPs for comprehensive environmental and public health evaluation.},
}

@article {pmid41687496,
year = {2026},
author = {Shyam, S and Sarma, H},
title = {Microbial community shifts and nutrient alteration in rice rhizospheres induced by Fe functionalized magnetic nanocarbon derived from rice husk.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128840},
doi = {10.1016/j.jenvman.2026.128840},
pmid = {41687496},
issn = {1095-8630},
abstract = {Soil fertility degradation and low nutrient-use efficiency remain major constraints in sustainable rice cultivation, especially in acidic soils. Biochar-based nanocomposites have emerged as advanced tools to improve nutrient bioavailability and soil health. This study examines the influence of rice husk biochar (HB) and its Fe-functionalized nanoscale variant, magnetic nanocarbon husk biochar (MNHB), on soil physicochemical properties, early growth of Oryza sativa (rice), and rhizosphere microbial dynamics. MNHB exhibited a fixed carbon content of 49.6%, ash content of 17.4%, and strong thermal stability above 400 °C. Dynamic light scattering and zeta potential analyses confirmed nanoscale particle size (<100 nm) with a surface charge of -25 mV, indicating good colloidal stability. FE-SEM imaging verified nanoscale morphology (81.58 ± 17.22 nm). Application of MNHB (5%) significantly enhanced root length (15.7 ± 0.49 cm), shoot length (46.41 ± 1.89 cm), and biomass (48.9% above Control, 25.3% above HB; p < 0.05). Soil pH, electrical conductivity, organic carbon, and macronutrients (N, P, K) increased substantially, demonstrating improved nutrient cycling and bioavailability. Metagenomic sequencing revealed reduced microbial alpha diversity but a marked community shift favoring Pseudomonadota (∼20% increase) and enrichment of beneficial genera such as Streptomyces, Micromonospora, and Neurospora tetrasperma. This work lies in establishing that Fe-functionalization in biochar nanosystems not only enhances nutrient transformation and uptake efficiency but also selectively restructures the rhizosphere microbiome, thereby coupling nutrient enrichment with microbial modulation for sustainable soil fertility restoration and crop productivity improvement.},
}

@article {pmid41687486,
year = {2026},
author = {Wang, H and Tian, Z and Jiang, Q and Feng, L and Tian, Z and Cheng, J and Jiang, S and Li, B},
title = {Enhancing sulfide-based denitrification under dual high-salinity and sulfide stress: Metabolic adaptation via compatible solutes in functional microbes.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128858},
doi = {10.1016/j.jenvman.2026.128858},
pmid = {41687486},
issn = {1095-8630},
abstract = {This study demonstrated enhanced sulfur autotrophic denitrification (SAD) under dual high-salinity (3% Na2SO4) and sulfide (142.5 mg L[-1] S[2-]) stress using biostimulants. Screening of ten biostimulants (1 mg L[-1]) revealed compatible solutes (glycine betaine, trehalose, and mannitol) as optimal enhancers. At a higher level of 100 mg L[-1], the addition of all compatible solutes significantly boosted TN removal rates >3-fold, with mannitol achieving the highest (9.38 mg L[-1] h[-1]) (p < 0.05). Short term of dosage tests further showed better TN removal at higher trehalose/mannitol concentrations (10-100 mg L[-1]), while glycine betaine peaked at 50 mg L[-1]. Furthermore, metagenomic analysis revealed potential mechanisms for resisting the dual stress of high salinity and sulfide. Those mechanisms act through osmotic protection (via specific transporter genes and elevated extracellular polymeric substances), carbon provision boosting TN removal via heterotrophic denitrification (nirS), and enzymatic antioxidant defense (SOD1/NQO1). The addition of exogenous compatible solutes critically mitigates dual stress from high salinity and sulfide toxicity, demonstrating significant potential for SAD system enhancement.},
}

@article {pmid41687314,
year = {2026},
author = {He, J and Duan, Y and Yang, S and Toldrá, F and Zheng, J and Du, M and Wang, L and Ndraha, N and Wang, S and Chen, J},
title = {Insights into the mechanism of nutty aroma formation by Staphylococcus saprophyticus in fermented sausages.},
journal = {International journal of food microbiology},
volume = {451},
number = {},
pages = {111669},
doi = {10.1016/j.ijfoodmicro.2026.111669},
pmid = {41687314},
issn = {1879-3460},
abstract = {To achieve a starter culture with the ability of improving nutty aroma in the formulation of fermented sausage, this study evaluated sixteen staphylococci strains first, then demonstrated the function of the strain in sausage fermentation using volatolomics and metagenomics. Within sixteen tested strains, S. saprophyticus 108 presented superior safety and technological properties and produced the highest amounts of 3-methylbutanal. With spontaneously fermented sausage as control, S108 group distinctly enhanced the production of 3-methylbutanal, 3-methylbutanoic acid and its ethyl ester, and nutty note of S108 group was obviously perceivable. The relative abundance of S. saprophyticus in both control and S108 groups increased throughout the fermentation process and such increase was more dramatic in S108 group. Although the differences in the number of functional genes predicted by control and S108 group in CAZy, eggNOG, and KEGG databases were comparatively small, the contribution of S. saprophyticus to major nutrient metabolisms was the main difference. Both S. saprophyticus and L. mesenteroides were annotated with predominant abundances in main metabolic pathways, while S. saprophyticus abundance involved in the metabolic pathways was higher in S108 group than in control. Specifically, branched-chain amino acid degradation, phenylalanine metabolism, glycolysis, pyruvate metabolism, butanoate and propanoate metabolism, glycerolipid and glycerophospholipid metabolism were mainly driven by S. saprophyticus, linked to the higher generation of volatile compounds in S108 group compared to control. The results provided scientific support for developing a functional starter culture through clarifying the mechanism of nutty aroma formation by S. saprophyticus in the production of fermented sausages.},
}

@article {pmid41687166,
year = {2026},
author = {Wang, P and Wang, J and Zhang, P and Jiao, Z and Bai, X and Zhao, Z and Fan, J and Zhang, S and Zhao, B and Ren, X and Dou, H and Bai, W},
title = {Temperature-dependent effects of lanthanum-modified bentonite on sediment nitrogen removal processes and the underlying microbial mechanisms.},
journal = {Water research},
volume = {294},
number = {},
pages = {125514},
doi = {10.1016/j.watres.2026.125514},
pmid = {41687166},
issn = {1879-2448},
abstract = {Lanthanum-modified bentonite (LMB) is widely used for phosphorus control in eutrophic lakes, but its effects on sediment nitrogen removal remains unclear. This study investigated the effects of LMB on denitrification and anammox, and underlying microbial mechanisms, under different dissolved oxygen (DO) and temperature (T) conditions using isotope tracing and metagenomics. The results demonstrated that the influence of LMB on sediment nitrogen removal was highly temperature-dependent. At 15 °C, LMB significantly enhanced both processes: denitrification increased by an average of 67.75 % under aerobic conditions, while anammox increased by 163.52 % and 93.47 % under aerobic and anaerobic conditions, respectively. Conversely, at 30 °C, LMB inhibited both processes. The denitrification decreased by average reductions of 57.36 % and 79.46 %, and anammox decreased by 32.51 % and 54.46 % under aerobic and anaerobic conditions, respectively. Microbial results revealed that LMB regulated denitrification in a temperature-dependent manner by modulating the key functional gene nosZ. In contrast, LMB generally suppressed anammox genes (hzsA, hzsB, and hdh), particularly under anaerobic conditions. Redundancy analysis (RDA) and structural equation modeling (SEM) identified pH, moisture content (MC), electrical conductivity (EC), total carbon (TC), total nitrogen (TN), NO3[-]-N, and NH4[+]-N as the key environmental factors driving variations in functional gene abundances. Our findings reveal that the temperature-dependent effects are primarily driven by the regulation of the nosZ gene and synergistic interactions among key physicochemical factors. Therefore, for remediating of eutrophic lakes with severe nitrogen pollution, the addition of LMB should be strategically adjusted to low-temperature seasons to maximize its ecological benefits in promoting nitrogen removal.},
}

@article {pmid41687083,
year = {2026},
author = {Olaniyi, KS and Moodley, J and Moodley, R and Mackraj, I},
title = {Assessment of human placental microbial signatures in pre-eclampsia using shotgun metagenomics.},
journal = {Canadian journal of physiology and pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjpp-2025-0274},
pmid = {41687083},
issn = {1205-7541},
abstract = {This study evaluated the presence of bacterial species in the placenta of women with pre-eclampsia and compared with that of normotensive women. One hundred and twenty participants, comprising 60 pre-eclamptic (30 early- and late-onset, respectively) and 60 age-matched normotensive women (30 early and late-gestation normotensive, respectively) were recruited. After informed consent was obtained, the placenta were obtained through caesarean section with sterile and standardized clinical procedures. DNA was extracted from each tissue, and the samples were pooled into six libraries and sequenced on Illumina NextSeq500 using a shotgun metagenomic approach. Bioinformatics was used to analyse the reads with the implementation of Kraken2/MetaPhlAn classification methods and complemented by multi-layered contamination assessment strategy that included frequency-based decontam filtering. Most reads were classified as belonging to the phyla Cutibacterium acnes, Staphylococcus epidermidis, and various Bradyrhizobium species. PE samples showed notable Corynebacterium tuberculostearicum and Pseudomonas species, while Bradyrhizobium and Cutibacterium acnes dominated normotensive samples. Further analysis showed no significant difference between bacterial species of pre-eclamptic and normotensive placental samples. The results show very low levels of bacteria in the placental samples. In addition, a little difference was observed between the bacterial compositions of pre-eclamptic and age-matched normotensive placental tissues, but not statistically significant.},
}

@article {pmid41686700,
year = {2026},
author = {Ierardi, RA and Ericsson, AC and Lahmers, KK and Shen, Z and Raghavan, RK},
title = {Detection of Anaplasma marginale (Rickettsiales: Anaplasmataceae) in host-seeking adult Dermacentor variabilis (Acari: Ixodidae) on cattle pastures, Missouri, United States.},
journal = {Journal of medical entomology},
volume = {63},
number = {1},
pages = {},
doi = {10.1093/jme/tjag014},
pmid = {41686700},
issn = {1938-2928},
support = {00081722//Taylor Geospatial Institute/ ; 7003929 and 7006485//USDA National Institute of Food and Agriculture, Animal Health projects/ ; //University of Missouri College of Veterinary Medicine Veterinary Research Scholars Program/ ; 58-2090-2-020//USDA Agricultural Research Service/ ; },
mesh = {Animals ; *Anaplasma marginale/isolation & purification ; Missouri ; *Dermacentor/microbiology ; Male ; Cattle ; Cattle Diseases/microbiology ; Anaplasmosis ; },
abstract = {Bovine anaplasmosis is an economically important and globally distributed disease of cattle caused by a rickettsia, Anaplasma marginale Theiler, which infects bovine red blood cells. In the United States, A. marginale is transmitted by adult male Dermacentor spp. ticks. Our objectives were to estimate the prevalence of A. marginale among host-seeking D. variabilis Say males and describe tick activity on beef cow-calf grazing operations in Missouri. Ticks were collected by dragging a total of 348 750-meter transects on 5 field sites from May 2022 to August 2024. In total, 29,132 ticks were collected: 27,502 Amblyomma americanum Linnaeus, 1,504 D. variabilis, 101 Haemaphysalis longicornis Neumann, and 25 individuals of uncommonly encountered species. A total of 692 adult male D. variabilis were divided into 154 pools of ≤5 ticks/pool for analysis. Anaplasma marginale was detected by quantitative polymerase chain reaction (qPCR) in 1 pool of 5 adult males (0.6%). Illumina sequencing detected an Anaplasma bovis (Donatien and Lestoquard 1936)-like sequence in 38 pools (24.7%). The endosymbionts Francisella spp. and Rickettsia spp. were detected in 100% and 32.5% of pools, respectively. To the best of our knowledge, this is the first study to detect A. marginale in host-seeking D. variabilis collected in the field. Our findings also represent the first reports of H. longicornis, an invasive species, in 4 Missouri counties.},
}

Animals
*Anaplasma marginale/isolation & purification
Missouri
*Dermacentor/microbiology
Male
Cattle
Cattle Diseases/microbiology
Anaplasmosis

@article {pmid41686580,
year = {2026},
author = {Zhang, H},
title = {Diagnostic value of mNGS in patients with suspected tumor: An observational study.},
journal = {Medicine},
volume = {105},
number = {7},
pages = {e47379},
doi = {10.1097/MD.0000000000047379},
pmid = {41686580},
issn = {1536-5964},
mesh = {Humans ; *DNA Copy Number Variations ; Female ; Male ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Neoplasms/genetics/diagnosis ; Adult ; Aged ; *Metagenomics/methods ; Chromosome Aberrations ; *Infections/diagnosis/genetics ; },
abstract = {Some patients suspected of infection may have potential causes, such as tumors, but conventional examination methods are negative. Copy number variation (CNV) analysis based on metagenomics next generation sequencing (mNGS) can simultaneously detect pathogenic microorganisms and tumors signals. Patients with suspected infection in our department were retrospectively analyzed, and mNGS and chromosomal CNV analysis were performed simultaneously. A total of 9 patients with positive tumor signal were included in the study. This study was divided into 2 parts: in the first part, patients suspected of infection were finally diagnosed with a tumor by CNV assisted analysis; in the second part, the accuracy of this analysis was verified again by patients with a history of cancer. Three of five patients without a history of tumor were diagnosed with hematological malignancy. All patients with active tumor had obvious abnormal CNV signals. The chromosomal abnormalities mainly included multiple chromosome duplication and deletion, arm level duplication and deletion, and chromosome aneuploidy. mNGS-based CNV analysis had clinical value for patients with underlying tumor.},
}

Humans
*DNA Copy Number Variations
Female
Male
Retrospective Studies
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Neoplasms/genetics/diagnosis
Adult
Aged
*Metagenomics/methods
Chromosome Aberrations
*Infections/diagnosis/genetics

@article {pmid41686420,
year = {2026},
author = {Senthilkumar, K and Muthiah, P},
title = {A Comprehensive Review of Kombucha Fermentation and Probiotic Functional Mechanisms: Microbial Dynamics, Bioactive Compounds and Health Effects.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41686420},
issn = {1867-1314},
abstract = {The rising demand for health-promoting beverages, kombucha presents significant opportunities for scientific innovation and commercial growth. Symbiotic culture of bacteria and yeast (SCOBY), which includes acetic acid bacteria (AAB), lactic acid bacteria (LAB), and several yeast species, plays a major role in kombucha fermentation. During fermentation, kombucha produces bioactive compounds mainly catechins, theaflavins, tannins, and organic acids that enhance health efficacy and probiotic properties, supporting gut health and non-communicable disease prevention. The present study emphasizes, nutritional qualities of kombucha through different Komagataeibacter starter cultures and alternative substrates such as herbal infusions and fruit extracts. This review also highlights the role of AAB, LAB, and Yeast in the production mechanism of the kombucha beverage by the different microbial strains of microbial species and the fibril network of bacterial cellulose. This study further explains the bioactivities in the human body, especially mechanisms of action in the intestine through fundamental signaling pathways such as PIK3-AKT, MAPK, NFκB, PPARγ, and JAK-STAT. Therapeutic efficacy of kombucha, including various substrate-based antioxidants, antimicrobials, synergistic impact, delivery mechanism of anticancer, anti-diabetic insulin, and glycaemic responses, regulations of inflammatory markers (ILs) in anti-obese properties, has also been reviewed. Further, it is necessary to develop the advanced kombucha beverage qualities through metagenomics, metabolomics. Future studies should address these research gaps to ensure controlled microbial and probiotic stability, validate metabolites availability, and explore innovative applications for improved functionality and shelf-life.},
}

@article {pmid41686173,
year = {2026},
author = {Yang, Z and Zhang, F and Li, H and Liu, B and Liu, P and Wu, Z and Li, Y and Miao, J and Li, X and Liang, H and Zhong, Y and Xiao, L and Zou, Y and He, N and Li, S},
title = {Gut Commensal Phocaeicola vulgatus AF107-22 Alleviates Obesity-Induced Metabolic Syndrome via Promoting Gut Microbiota-Derived Spermidine Synthesis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14443},
pmid = {41686173},
issn = {1520-5118},
abstract = {Obesity-induced metabolic syndrome (MetS) is a prevalent metabolic disorder, and therapeutic strategies targeting the gut microbiota hold considerable promise. Phocaeicola vulgatus (P. vulgatus) is a gut commensal bacterium that plays an important role in modulating the composition and metabolism of gut microbiota. This study demonstrated that the abundance of P. vulgatus is significantly negatively correlated to obesity-induced MetS and complications in human metagenomic data. Oral gavage of P. vulgatus significantly ameliorated high-fat-diet (HFD)-induced MetS symptoms in mice, reducing body weight, systemic inflammation, and hepatic steatosis. Furthermore, multiomics analyses indicated that P. vulgatus treatment significantly enhanced the production of gut microbiota-derived spermidine and spermine. Subsequently, population-based analysis confirmed a strong negative correlation between plasma spermidine levels and MetS progression, supporting that such parameters may serve as potential biomarkers for MetS. This study reveals a potential mechanism, bridging commensal probiotic and spermidine metabolism, with implications for treating obesity-induced MetS.},
}

@article {pmid41685655,
year = {2026},
author = {Zhai, Y and Wang, X and Deng, X and Li, X and Hu, B and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M},
title = {Sequential Oxidizing-Reducing Degradation of Organic Micropollutants in Simulated Riverbank Filtration.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18277},
pmid = {41685655},
issn = {1520-5851},
abstract = {Riverbank filtration is a nature-based water treatment strategy known for its effective removal of organic micropollutants. Yet, the mechanisms governing their biodegradation, especially the role of redox transitions in mediating biotransformation, remain insufficiently understood. Here, we integrate metagenomic profiling with chemical analytics in a 10 m simulated riverbank filtration system to demonstrate how sequential oxidizing-reducing degradation enhances organic micropollutant transformation. Oxygen stratification structured distinct microbial and enzymatic pathways: oxidizing zones (>+200 mV redox potential) facilitated cytochrome P450-mediated oxidation (oxidizing condition, OXD), while subsequent redox shifts to reducing conditions (←400 mV, sequential oxidizing-reducing (SOR) conditions) activated reductive transformations (e.g., via nitronate monooxygenase and aldehyde dehydrogenase) and conjugation pathways. These SOR conditions significantly enhanced the removal of recalcitrant compounds, including irbesartan (+25.3%), benzotriazole (13.4%), and gabapentin (+9.7%). Metagenomic analysis revealed redox-driven microbial specialization, with Pseudomonadota and Nitrospirota dominating in oxidizing zones and reducing microzones enriched in pathways associated with nitrotoluene and ethylbenzene degradation, providing genomic evidence for sequential organic micropollutant breakdown. These findings establish a mechanistic framework for harnessing oxidizing-reducing microbial partnerships to amplify organic micropollutant removal in nature-based water treatment systems, which can be used for riverbank filtration site selection and well field construction and optimization.},
}

@article {pmid41685543,
year = {2026},
author = {Mwakibete, L and Hoarau, AOG and Ahyong, V and Waltari, E and Bender, SJ and Davison, S and Niedringhaus, KD and Gibison, ML and Gagne, RB and Miller, EA and Murphy, LA and Kistler, AL and Tato, CM},
title = {Discovery of a novel bandavirus using metagenomic sequencing in a retrospective analysis of an unresolved 2020 mortality event involving wild black vultures in the northeastern United States.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {10406387261418632},
doi = {10.1177/10406387261418632},
pmid = {41685543},
issn = {1943-4936},
abstract = {Investigations of wildlife diseases and mortality events can sometimes lead to inconclusive results because of limitations in testing combined with an ever-increasing number of emerging viruses. The use of tools such as unbiased metagenomic next-generation sequencing (mNGS) can facilitate the identification of causative agents when conventional investigation methods fail. We performed a retrospective mNGS analysis on RNA isolated from postmortem samples collected during a mortality event in free-ranging, wild black vultures (Coragyps atratus) that occurred in eastern Pennsylvania and western New Jersey in 2020. We describe the discovery and identification of a novel species of bandavirus (family Phenuiviridae) in case specimens from this die-off, as well as some of the associated pathology findings. The Bandavirus genus comprises tickborne viral species that have been reported across 5 continents. These viruses have been implicated in outbreaks in a variety of mammalian hosts, including humans, and in avian species, making them important potential sources of zoonotic spillover events. Genomic and phylogenetic analyses of the bandavirus that we detected indicate that its closest relative is Hunter Island virus, a bandavirus previously implicated in albatross mortality events off the coast of Tasmania, Australia. Follow-up PCR testing of samples from 16 additional vultures from the same cohort indicate that this new bandavirus was the likely cause of death.},
}

@article {pmid41685410,
year = {2026},
author = {Brandão-Dias, PFP and Guri, G and Shaffer, MR and Allan, EA and Kelly, RP},
title = {Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70104},
pmid = {41685410},
issn = {1755-0998},
support = {N00014-22-1-2719//Office of Naval Research/ ; },
mesh = {*Haplotypes ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Genetics, Population/methods ; Computer Simulation ; },
abstract = {Environmental DNA (eDNA) provides powerful insights into species presence and community composition but remains limited in its capacity to infer species abundance or population structure. Here, we show that the deviation between within-sample haplotype frequencies and the overall population-level haplotype frequencies can be used to estimate the number of individual contributors to a given sample. We first establish the theoretical framework for approximating population haplotype frequencies directly from eDNA data, enabling application even in the absence of tissue-derived references. Building on this foundation, we introduce a maximum likelihood estimator to infer the number of contributors and assess its performance through simulations spanning a range of haplotype frequency distributions and noise scenarios. These approaches assume that all samples are drawn from a single, panmictic population. We find that accurate estimates are attainable when haplotypes are sufficiently variable, population frequencies are well-characterised, and samples are large enough to capture frequency deviations. By bridging population genetic theory and eDNA, our method complements existing molecular approaches and offers a novel path towards quantifying abundance from eDNA metabarcoding data.},
}

*Haplotypes
*DNA, Environmental/genetics
*Metagenomics/methods
*Genetics, Population/methods
Computer Simulation

@article {pmid41684896,
year = {2025},
author = {Das, R and Malard, L and Pearce, DA and Convey, P and Rahlff, J},
title = {Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1726848},
pmid = {41684896},
issn = {1664-302X},
abstract = {Studying airborne viruses in remote environments like the sub-Antarctic island of South Georgia offers key insights into viral ecology, diversity, and their role in shaping ecosystems through microbial and nutrient interactions. We analyzed airborne viral community composition at two sites in South Georgia. Sampling took place using multiple methodologies, with the data produced subjected to viral metagenomics. The Coriolis μ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were only obtained from the coastal location, indicating that location influences airborne viral diversity. Protein-based clustering of 39 viral operational taxonomic units (vOTUs) revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the airborne viral community. Protein homologs related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed across major oceans, suggesting their potential role in supporting the resilience of marine microorganisms under changing climate conditions. Some vOTUs had protein similarities to viruses infecting extremophiles, indicating viral adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems. It underscores the need for continued monitoring to assess how these communities respond to shifting atmospheric and ecological conditions.},
}

@article {pmid41684743,
year = {2025},
author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Garrido, G and Lázaro-Martínez, JL},
title = {Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1729196},
pmid = {41684743},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology/complications ; *Osteomyelitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Biofilms/growth & development ; Male ; Middle Aged ; Female ; Hispanic or Latino ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Chile ; Microbiota/genetics ; Metagenomics ; DNA, Bacterial/genetics ; Adult ; Bone and Bones/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics ; White ; },
abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of diabetes and a leading cause of lower-limb amputations. Conventional culture-based diagnostics often underestimate the microbial diversity of infected bone tissue. This study represents the first characterization of both total and ribosomally active bone microbiota in Hispanic patients with DFO using high-throughput 16S rRNA gene sequencing. The work aims to contribute to the inclusion of underrepresented populations in microbiome research and informing molecular-based antimicrobial strategies.

METHODS: Bone specimens (n = 13) were collected from seven Chilean patients with histologically confirmed DFO. Samples were analyzed using conventional aerobic culture and 16S rRNA gene sequencing from both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the total bacterial community and the ribosomally active fraction. In three patients, samples were stratified by bone depth (superficial/top, middle and bottom). Microbial diversity and relative abundance were assessed across patients and bone layers.

RESULTS: Acute osteomyelitis was the predominant histopathological pattern. Culture yielded 19 bacterial isolates, 95% of which were Gram-negative bacilli. Sequencing identified 3,412 operational taxonomic units (OTUs), with Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Enterobacteriaceae and Enterococcaceae were the most ribosomally active families. Microbial community composition varied substantially among patients and across bone depths. Staphylococcus aureus was infrequent (5% of culture isolates; ~1% of sequence reads), whereas low-abundance but ribosomally active taxa, such as Corynebacteriaceae, were consistently detected across all layers.

DISCUSSION: This combined metagenomic and ribosomal transcript analysis reveals a polymicrobial, patient-specific bone microbiota in Chilean patients with DFO, highlighting potentially active bacteria frequently overlooked by standard diagnostic methods. These findings underscore the value of integrating molecular approaches into clinical workflows to improve pathogen detection and support more personalized antimicrobial strategies, while also helping to address gaps in microbiome research among underrepresented populations.},
}

Humans
*Diabetic Foot/microbiology/complications
*Osteomyelitis/microbiology
RNA, Ribosomal, 16S/genetics
*Biofilms/growth & development
Male
Middle Aged
Female
Hispanic or Latino
*Bacteria/classification/genetics/isolation & purification
Aged
Chile
Microbiota/genetics
Metagenomics
DNA, Bacterial/genetics
Adult
Bone and Bones/microbiology
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
DNA, Ribosomal/genetics
White

@article {pmid41684676,
year = {2026},
author = {Chukwujindu, C and Kolton, M and Fasakin, O and Pathak, A and Seaman, J and Chauhan, A},
title = {Microbial community structure and functional potential in a long-term uranium-nickel contaminated ecosystem.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741152},
pmid = {41684676},
issn = {1664-302X},
abstract = {This study examined the microbial community structure, functional potential, and resistance determinants in uranium (U)- and nickel (Ni)-contaminated soils from the Savannah River Site (SRS), a former nuclear materials production and waste collection facility operated by the U. S. Department of Energy (DOE). Soil cores were collected from the Steed Pond area, where long-term discharge of acidic wastewater resulted in spatially variable contamination levels. Concentrations of U and Ni in the collected samples ranged from 0.22-10.44 g kg[-1] and 0.79-2.28 g kg[-1], respectively. Shotgun metagenomic and high-throughput quantitative PCR (HT-qPCR) analyses revealed bacterial communities dominated by Pseudomonadota, Actinomycetota, and Acidobacteriota, with enrichment of taxa affiliated with genera known to include diazotrophic members (e.g., Bradyrhizobium and Burkholderia), alongside increased abundance of nitrogen fixation-related functional genes. Carbon and nitrogen cycle genes were generally well represented across samples, with selective shifts observed in acetate assimilation genes (acsA/acsE) and comparatively low abundance of hydrazine oxidoreductase (hzo), indicating pathway-specific variation rather than broad metabolic suppression. A total of 117 resistance-associated genes were identified, comprising 93 antibiotic-resistance genes (ARGs), 3 metal-resistance genes (MRGs), and 21 mobile genetic elements (MGEs). Strong positive correlations among ARGs, MRGs, and MGEs indicate co-selection and horizontal gene transfer, forming a genetically mobile resistome. Collectively, these findings demonstrate that long-term U-Ni contamination selects for metabolically versatile, diazotroph-enriched, and genetically mobile microbiomes. Such communities exhibit both resistance proliferation and bioremediation potential, providing key insights into microbial adaptation and ecosystem recovery in legacy nuclear-contaminated soils.},
}

@article {pmid41684459,
year = {2026},
author = {Sgarabotto, E and Zadra, N and Tyrell, JA and Rossi, C and Hewson, I and Searle, JB and Hauffe, HC},
title = {Virome analysis reveals ORF7 sequences of type 2 porcine respiratory and reproductive syndrome virus (PRRSV) for the first time in a rodent host (Microtus pennsylvanicus).},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101345},
pmid = {41684459},
issn = {2352-7714},
abstract = {The lung virome of meadow vole (Microtus pennsylvanicus) from six neighbouring locations in New York State, USA was investigated using metagenomics to determine the circulation of potentially zoonotic viruses in a common wild rodent. This study provides the first evidence of the occurrence of Type 2 Porcine Respiratory and Reproductive Syndrome Virus (PRRSV2) in a rodent, or indeed in any species apart from wild and domestic pigs (Sus scrofa). PRRSV has the highest economic impact on the pig husbandry industry of any pathogen, but up to now, farm-to-farm transmission of this virus has been assumed to be associated with movement of and contact with infected pigs and fomites. Our results showing the natural occurrence of this virus in potential transmission hosts other than wild or domestic pigs challenge this scenario. Phylogenetic analysis of assembled partial genomes from four of our pooled samples and all other nucleocapsid protein (ORF7) sequences available in Genbank showed that the sequences recovered from meadow voles unambiguously clustered within the PRRSV2 clade together with sequences derived from wild and domestic pigs. Historical research suggests that spillover from voles to domestic pigs may be the most parsimonious explanation for these results; however, we cannot rule out the reverse: that the source of PRRSV2 in these wild voles derives from pigs. From a One Health perspective, our results reinforce the importance of characterizing wildlife viromes to survey possible sources of zoonotic pathogens, which is vital for making evidence-based decisions regarding potential threats to the health of humans, livestock and wild fauna.},
}

@article {pmid41684123,
year = {2026},
author = {Cheng, R and Deng, Z and Lin, F and Zhang, B and Liang, J and Lu, M},
title = {Clinical, laboratory, and radiological features of community-acquired pneumonia due to Chlamydia psittaci and Legionella pneumophila confirmed using next-generation sequencing.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2627122},
doi = {10.1080/07853890.2026.2627122},
pmid = {41684123},
issn = {1365-2060},
mesh = {Humans ; Male ; *Chlamydophila psittaci/genetics/isolation & purification ; Female ; *Community-Acquired Infections/microbiology/drug therapy/diagnosis ; Retrospective Studies ; Middle Aged ; High-Throughput Nucleotide Sequencing ; *Legionella pneumophila/genetics/isolation & purification ; Aged ; Anti-Bacterial Agents/therapeutic use ; *Legionnaires' Disease/drug therapy/diagnosis/microbiology ; *Psittacosis/drug therapy/diagnosis/microbiology ; Adult ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND AND OBJECTIVE: Chlamydia psittaci and Legionella pneumophila are common atypical pathogens that cause severe community-acquired pneumonia (CAP). This study aimed to compare the clinical features and outcomes of Chlamydia psittaci pneumonia (CPP) and Legionella pneumophila pneumonia (LPP) identified using next-generation sequencing (NGS) for accurate identification.

METHODS: This retrospective study included 68 patients with CPP and 42 patients with LPP. All cases were confirmed by metagenomic or targeted next-generation sequencing (mNGS/tNGS) of bronchoalveolar lavage fluid, serum, or sputum samples.

RESULTS: Patients with LPP had a higher prevalence of diabetes and were predominantly male. Poultry contact was common in CPP (64.7% vs. 14.3%), whereas recent travel was associated with LPP (47.6% vs. 2.9%). LPP presented with increased extrapulmonary symptoms. Inflammatory marker levels were higher in LPP, including leukocytosis, neutrophilia, C-reactive protein, and procalcitonin (all p < 0.05). Organ dysfunction was more frequent in LPP, with higher creatinine levels. Patients with LPP had more severe hypoxemia, required more respiratory support, and had higher intensive care admission rates. Targeted therapy guided by NGS was effective, with no significant differences in mortality or hospital stay between the two groups.

CONCLUSION: LPP demonstrated greater initial clinical and laboratory severity compared to CPP. Under NGS-guided targeted therapy, both groups achieved comparable outcomes. The observational finding that both pathogens respond to azithromycin and cause severe disease when left undetected underscore the value of guideline-recommended β-lactams/macrolide combination therapy in CAP settings, particularly where these intracellular pathogens remain undiagnosed without NGS.},
}

Humans
Male
*Chlamydophila psittaci/genetics/isolation & purification
Female
*Community-Acquired Infections/microbiology/drug therapy/diagnosis
Retrospective Studies
Middle Aged
High-Throughput Nucleotide Sequencing
*Legionella pneumophila/genetics/isolation & purification
Aged
Anti-Bacterial Agents/therapeutic use
*Legionnaires' Disease/drug therapy/diagnosis/microbiology
*Psittacosis/drug therapy/diagnosis/microbiology
Adult
*Pneumonia, Bacterial/microbiology/drug therapy/diagnosis
Community-Acquired Pneumonia

@article {pmid41683346,
year = {2026},
author = {Fathima, S and Kilgore, PE and Sarkar, T and Sharma, N and Nguyen, HH},
title = {Muno-IgY Supplementation Improves Respiratory Health, Immune Response, and Exercise-Induced Physiological Stress in Healthy Adults: A Randomized Controlled Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683346},
issn = {2072-6643},
mesh = {Humans ; Pilot Projects ; Male ; Adult ; Female ; *Dietary Supplements ; Double-Blind Method ; *Exercise/physiology ; *Respiratory Tract Infections/prevention & control/immunology/epidemiology ; Gastrointestinal Microbiome/drug effects ; *Stress, Physiological/drug effects ; *Immunoglobulins/administration & dosage/pharmacology ; Biomarkers/blood ; Young Adult ; Middle Aged ; },
abstract = {BACKGROUND/OBJECTIVES: Upper respiratory tract infections (URTIs) and exercise-induced immune perturbations are common in adults and may adversely affect quality of life, productivity, and physical performance. Immunoglobulin Y (IgY), a food-derived antibody with broad antimicrobial activity, has demonstrated immunomodulatory potential in preclinical and limited clinical studies. This study evaluated the effects of a multi-pathogen-specific IgY supplement (Muno-IgY) on respiratory health, immune and inflammatory markers, exercise-induced physiological stress, and gut microbiome composition in healthy adults.

METHODS: In this 12-week, double-blind, placebo-controlled trial, 28 healthy adults with a history of URTI were randomly allocated to receive Muno-IgY or placebo and URTI incidence, duration, and severity were recorded daily. Serum immune and inflammatory biomarkers were assessed longitudinally and in response to a standardized exercise challenge. Gut microbiome composition was analyzed using shotgun metagenomic sequencing at baseline and week 12. Safety and tolerability were assessed throughout the study.

RESULTS: URTI incidence was lower in the Muno-IgY group compared with placebo (14.3% vs. 35.7%), with shorter average duration and fewer missed workdays, though differences were not statistically significant (p > 0.05). Following an acute exercise challenge, Muno-IgY supplementation resulted in a significant increase in serum IgA at 24 h post-exercise (p = 0.022) and a significantly greater reduction in lactate dehydrogenase at 1 h post-exercise compared with placebo (p < 0.0001). Exploratory gut microbiome analyses suggested favorable directional shifts, though these changes were not statistically tested.

CONCLUSIONS: In this exploratory pilot study, Muno-IgY supplementation was safe and associated with significant improvements in selected markers of exercise-induced immune response and muscle damage. Numerical trends in URTI incidence and gut microbiome composition were observed but were not statistically significant. These findings are hypothesis-generating and support further evaluation of Muno-IgY in larger, adequately powered clinical trials.},
}

Humans
Pilot Projects
Male
Adult
Female
*Dietary Supplements
Double-Blind Method
*Exercise/physiology
*Respiratory Tract Infections/prevention & control/immunology/epidemiology
Gastrointestinal Microbiome/drug effects
*Stress, Physiological/drug effects
*Immunoglobulins/administration & dosage/pharmacology
Biomarkers/blood
Young Adult
Middle Aged

@article {pmid41683205,
year = {2026},
author = {Yu, W and Tang, K and An, R and Ma, S and Tan, H and Chen, M},
title = {Study on Association Between Gut Microbiota, Serum Metabolism and Gestational Diabetes Mellitus Based on Metagenomic and Metabolomics Analysis.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683205},
issn = {2072-6643},
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology/blood/metabolism ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Case-Control Studies ; Adult ; *Metabolomics/methods ; *Metagenomics ; Feces/microbiology ; Pregnancy Trimester, First ; },
abstract = {Background/Objectives: This study aimed to explore the association between maternal gut microbiota and metabolic profiles in the first trimester and the subsequent risk of gestational diabetes mellitus (GDM), as well as to characterize association patterns linking gut microbiota, serum metabolites, and metabolic traits. Methods: A nested case-control study was conducted among women with GDM (n = 47) and those without GDM (n = 94). Metagenomic sequencing was applied to analyze fecal microbiota, and liquid chromatography-mass spectrometry (LC-MS) was used for non-targeted plasma metabolomics. Differential microbiota and metabolites between groups were identified, and correlation analyses were conducted to assess their associations with clinical indicators. Results: Women who later developed GDM showed lower alpha diversity and higher beta diversity. Eleven differential species were identified, with Collinsella aerofaciens and Clostridium bartlettii enriched in GDM, while nine species such as Alistipes putredinis and Bacteroidales bacterium ph8 were enriched in controls. Sixty-four plasma metabolites differed between groups, including increased glycerol-3-phosphate, aromatic amino acids, and glycerophosphocholine, and decreased cysteine, tryptophan, niacinamide, and stearic acid. Correlation analyses revealed significant relationships between Alistipes putredinis, Eubacterium eligens, and Bacteroidales bacterium ph8 with metabolic and clinical indicators (e.g., TG, TC, LDL). Conclusions: In this nested case-control study, women who later developed GDM exhibited reduced gut microbial diversity and altered metabolic profiles during the first trimester of pregnancy. Several microbial taxa and microbiota-metabolite associations were observed in relation to subsequent GDM status, highlighting early-pregnancy microbial and metabolic features that may be relevant to GDM-related metabolic changes.},
}

Humans
Female
*Diabetes, Gestational/microbiology/blood/metabolism
Pregnancy
*Gastrointestinal Microbiome/physiology
Case-Control Studies
Adult
*Metabolomics/methods
*Metagenomics
Feces/microbiology
Pregnancy Trimester, First

@article {pmid41683069,
year = {2026},
author = {Betoret, E and Jiménez-Hernández, N and Duarte, S and Artacho, A and Bueno, A and Cruz, I and Betoret, N and Gosalbes, MJ},
title = {Persimmon Powder from Discarded Fruits as a Potential Prebiotic to Modulate Gut Microbiota in Postmenopausal Women.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683069},
issn = {2304-8158},
support = {AGROALNEXT/2022/039//European Union Next Generation (PRTR-C17.I1)/ ; CIAICO/2022/27//Generalitat Valenciana/ ; },
abstract = {Faced with the challenge of reducing food waste, transforming discarded fruit into functional ingredients useful for the food industry is a valuable solution. Ingredients from fruit such as persimmons, which are rich in indigestible carbohydrates and bioactive compounds with antiradical capacity, could positively impact on the health of certain population groups due to their potential prebiotic effect. This study aimed to select the most suitable drying conditions and milling intensity for obtaining powdered persimmon ingredients with a prebiotic-like effects observed in vitro for postmenopausal women, and to evaluate this effect by considering the stimulation of health-promoting bacterial growth and short-chain fatty acids (SCFAs) production. First, the effect of the drying method (hot air drying at 60 and 70 °C, and freeze-drying) and grinding intensity on antiradical capacity, particle size, and the release of bioactive antiradical components into the intestinal lumen after an in vitro gastrointestinal digestion was determined. Next, the effect of these conditions on the microbiota composition of postmenopausal women was preliminary assessed in a batch colonic fermentation experiment for 24 h. The results showed that the ingredient dried with air at 70 °C had the highest phenol and flavonoid content, suffered the least degradation during in vitro gastrointestinal digestion and promoted the differential growth of fiber-degrader genera. Consequently, this was the ingredient selected as the most suitable. Lastly, the impact of this ingredient on the microbiota composition of 4 postmenopausal women has been evaluated in a long-term study using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) coupled to high throughput sequencing. The growth stimulation of health-associated bacteria, such as Akkermansia muciniphila, Faecalibacterium prausnitzii or Phascolarctobacterium faecium, and the promotion of beneficial metabolic pathways, such as the sugar uptake-specific phosphotransferase system, sugar metabolism and propionate and isobutyrate production, were detected along 14 days of persimmon powder supplementation. A holistic framework for promoting human health while advancing environmental sustainability is represented by the combination of sustainable by-product valorization and microbiota-targeted functional food development.},
}

@article {pmid41681750,
year = {2026},
author = {Liepina, EE and Sivina, E and Jurkane, L and Daneberga, Z},
title = {Baseline Gut Microbiome and Metabolite Profiles Associate with Treatment Response in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {3},
pages = {},
pmid = {41681750},
issn = {2075-4418},
abstract = {Background/Objectives: Response to neoadjuvant chemotherapy (NAC) varies substantially among breast cancer patients and is only partially explained by tumor-intrinsic factors. The gut microbiome has emerged as a potential modulator of chemotherapy efficacy, yet its role in breast cancer remains underexplored. This study aimed to characterize gut microbial composition, functional potential, and microbially derived metabolites in breast cancer patients undergoing NAC. Methods: baseline stool samples from 39 chemotherapy-naïve breast cancer patients undergoing NAC were analyzed using shotgun metagenomic sequencing and targeted metabolomics. Patients were stratified by pathological complete response (pCR, n = 17; no pCR, n = 22). Microbial taxonomic and functional profiles, short-chain fatty acids (SCFAs) and bile acids were assessed, with subgroup analysis performed in triple-negative breast cancer (TNBC). Results: Patients achieving pCR exhibited significantly higher baseline microbial richness compared to non-responders (p = 0.040). Differential abundance analysis revealed enrichment of Dialister, Kineothrix, and Jutongia in responders, whereas Rothia, Leuconostoc, Klebsiella, Jingyaoa, Cuneatibacter, Youxingia, and Bittarella were enriched in non-responders. SCFAs (acetate, propionate and butyrate) positively correlated with microbial glucose catabolic pathways, while caproate was negatively associated with multiple amino acid, lipid, vitamin, and cell wall biosynthesis pathways, including peptidoglycan maturation. Metabolomic analysis identified higher deoxycholic acid (DCA) levels in non-responders and increased C6 levels in responders, although these associations did not remain significant after multiple testing correction. Similar trends were observed in the TNBC subgroup (n = 15). Conclusions: Baseline gut microbiome diversity, taxonomic composition, and functional metabolic potential are associated with response to neoadjuvant chemotherapy in breast cancer, supporting the gut microbiome and its produced metabolites as a potential biomarker of treatment efficacy.},
}

@article {pmid41681414,
year = {2026},
author = {Mohammed, EAH and Fehér, M and Bársony, P and Teye-Gaga, C and Czeglédi, L and Freytag, C and Váradi, A and Ahmed, AEM and Pál, K},
title = {Growth Performance, Gut Integrity and Intestinal Microbiome Responses of Juvenile Common Carp (Cyprinus carpio L.) to Probiotic and Prebiotic Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
pmid = {41681414},
issn = {2076-2615},
abstract = {The aim of this study was to examine the impact of the probiotics Saccharomyces cerevisiae (SC) and Pediococcus acidilactici (PA), as well as the prebiotic yeast cell wall extract (Cyberlindnera jadinii and S. cerevisiae) (YP), on the growth parameters, intestinal histomorphology, liver and gills normality, and gut microbiome of common carp (Cyprinus carpio L.). These feed supplements were subjected to a 60-day experimental period, during which 120 fish (26.4 ± 5.2 g) were distributed into four groups, with each group comprising 30 fish. The feed supplements were administered at a rate of 1 g/kg of body weight. Before the trial, the fish were acclimatized for two weeks, then injected with Passive Integrated Transponder (PIT) tags. The results showed that none of the feed supplements exhibited a significant effect (p > 0.05) on growth indices. In contrast, the villi length, villi width, muscular thickness, and crypt depth in the anterior, mid, and posterior intestine of the SC group exhibited significant (p < 0.05) improvements compared to the other groups. No alteration or abnormal growth were noticed in the gills and livers. The most dominant microbe genera in all groups, with abundances greater than 60% of the total, were Cetobacterium and Aeromonas. However, Polynucleobacter, Nordella, Mycoplasma, Romboutsia, and Staphylococcus species were present at lower abundances. The presence of Actinobacteria has been observed only in the intestine of fish that have been fed a diet supplemented with PA. It can be concluded that the tested probiotics and the yeast cell wall prebiotic have the potential to produce a remarkable improvement in intestinal morphology and a considerable change in the gut microbiome without notable effect on growth, livers, or gills of common carp.},
}

@article {pmid41681117,
year = {2026},
author = {Maiakovska, O and Link, L and Zayas, M and Sano, Y and Koay, TW and Rapti, K and Liu, J and Bubeck, F and Xu, M and Baumgartl, C and Wiedtke, E and Krämer, C and Naber, L and Grimm, D},
title = {Metagenomic Reconstruction of Adeno-Associated Virus Genomes.},
journal = {Human gene therapy},
volume = {},
number = {},
pages = {10430342261419534},
doi = {10.1177/10430342261419534},
pmid = {41681117},
issn = {1557-7422},
abstract = {The exponential expansion of metagenomic data obtained through high-throughput sequencing technologies has surpassed the petabyte-scale threshold, resulting in an unprecedented abundance of data now enabling the in silico discovery of previously unknown viral and bacterial species. Here, we demonstrate the power and promise of mining sequencing data to uncover natural adeno-associated virus (AAV) cap(sid) genes, with the synergistic aims to expand our repertoire of templates for vector development and to enhance our understanding of the AAV space and of virus evolution across species. Specifically, we harnessed the Serratus Explorer to identify 29 AAV variant genomes from publicly accessible raw metagenomic data generated from birds, nonhuman primates, or human samples, of which 16 were classified as high-quality based on the high coverage of their cap region. To this end, we devised a comprehensive computational pipeline comprising (i) reference candidate selection, (ii) prealigned data acquisition, (iii) variant calling and frequency estimation, (iv) consensus calling, (v) variant resolution, (vi) phylogenetic analysis, and (vii) protein structure analysis steps. Eight representative cap genes from four different host organism species were synthesized and used to produce so-called metAAV vectors, which exhibited intriguing and biomedically relevant properties including partial escape from neutralizing anti-AAV antibodies and muscle tropism combined with robust liver detargeting in systemically injected mice. We concurrently pursued a conventional, reference-independent metagenome-based genome assembly, which also successfully reconstructed AAV cap genes but solely for abundant variants. Together with the fact that this traditional reference-independent method necessitates substantial computational resources and misses to accurately resolve multiple closely related variants, this highlights the assets and superiority of our original consensus-based reconstruction pipeline for fundamental virus research and for future gene therapy vector bioengineering.},
}

@article {pmid41680679,
year = {2026},
author = {Wang, P and Tian, B and Tian, C and Shan, C and Huang, R and Zhang, Q},
title = {Clinical characteristics and prognosis of patients with Chlamydia psittaci pneumonia identified by metagenomic next-generation sequencing.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12822-9},
pmid = {41680679},
issn = {1471-2334},
support = {2024GSPKY23//Jiangsu Province High-Level Hospital Construction Funds of Zhongda Hospital, School of Medicine, Southeast University/ ; },
abstract = {BACKGROUND: Few studies comprehensively reported the clinical characteristics, prognosis, and factors associated with severe disease in patients with confirmed Chlamydia psittaci pneumonia identified by metagenomic next-generation sequencing (mNGS).

METHODS: This retrospective study included 63 patients with Chlamydia psittaci pneumonia diagnosed by mNGS. The clinical characteristics and prognosis were analyzed. Cox regression was used to identified factors associated with severe cases.

RESULTS: A total of 63 patients were confirmed with detected Chlamydia psittaci DNA by mNGS in the bronchoalveolar lavage fluid or blood. A total of 16 (25.4%) patients had severe disease. The overall in-hospital mortality was 4.7% (3/63), with a rate of 18.7% (3/16) in the severe group. 90.4% (57/63) of patients were older than 50 years. 21 (33.3%) patients had poultry/bird exposure. The most common symptoms included fever (100%), cough (63.5%) and fatigue (63.5%). All patients showed lung consolidation (100%) on chest CT, with air bronchograms (96.8%) and pleural effusion (41.3%). In the multivariable Cox regression, the levels of hs-CRP (P = 0.003), creatinine (P = 0.002), and presence of bilateral lung infection (P = 0.003) were independent factors associated with severe pneumonia.

CONCLUSION: Psittacosis pneumonia predominantly affects middle-aged and elderly adults. Elevated levels of hs-CRP and creatinine, the presence of bilateral lung involvement associated with progression to severe disease. Psittacosis-induced severe pneumonia is associated with high mortality.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid41680629,
year = {2026},
author = {Selhorst, P and Van Vyve, E and Falconi-Agapito, F and Mariën, J and Ariën, KK},
title = {Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {188},
pmid = {41680629},
issn = {1471-2164},
support = {U01AI151378/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Metagenomic sequencing for pathogen detection has traditionally suffered from low sensitivity due to the overwhelming presence of host nucleic acids. Commercial host-depletion kits are often prohibitively expensive and limited to specific species, hindering adoption in resource-limited settings, where the burden of zoonotic diseases is highest. To address this, we optimized and combined Sequence-Independent Single Primer Amplification (SISPA) with Depletion of Abundant Sequences by Hybridization (DASH), establishing a low-cost metagenomic protocol on the Oxford Nanopore sequencing platform. Our approach can be adapted to any species to detect microbial RNAs in serum samples at PCR-range sensitivity, outperforming existing methods in the field.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12268-4.},
}

@article {pmid41559772,
year = {2026},
author = {Gómez-Martínez, S and Pérez-Pérez, L and Ucero-Carrretón, A and López-García, Á and Galisteo, C and Carvajal, A and Argüello, H},
title = {Exploring the potential for competitive exclusion of commensal probiotic candidates against the insidious swine pathogen Brachyspira hyodysenteriae.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {19},
pmid = {41559772},
issn = {2524-4671},
support = {EDU/1868/2022//Junta de Castilla y León/ ; EDU 1009/2024//Junta de Castilla y León/ ; CNS2022-136066//Junta de Castilla y León/ ; PRE-2020-093762//Ministerio de Ciencia e Innovación/ ; Predoc grant 2025//Universidad de León/ ; },
abstract = {BACKGROUND: Research into animal microbiota reveals the intricate relationships between commensal bacteria and enteric pathogens. Metagenomics and culturomics offer novel opportunities in probiotic research, which is particularly interesting for diseases where treatment alternatives are limited, such as swine dysentery (SD), which is caused by Brachyspira hyodysenteriae (B. hyo). This study evaluates the potential ability of a collection of 28 isolates from species of interest to outcompete the anaerobic pathogen B. hyo by an array of in vitro assays designed to characterize their competitive exclusion capacity in co-cultures, alongside assessing the antimicrobial activity of the isolates cell-free supernatants (CFS) and the mechanisms by which they inhibit B. hyo growth.

RESULTS: 20 of the 28 isolates tested were able to reduce the growth of B. hyo by more than one log10 bacteria/mL after 96 h of co-culture, with different inhibitory dynamics observed. Notably, Intestinibaculum porci (J1/23 CM6), Dorea longicatena (J1/23 YB16), Bifidobacterium thermoacidophilum (J1/23 YB69), Mobilitalea sibirica (J1/23 YB21), Clostridium butyricum (CECT 361), and Parabacteroides goldsteinii (DSMZ 29187) reduced B. hyo growth in more than 2 log10 units (bacteria/mL). The anti-B. hyo activity of the tested CFS demonstrated that the mechanisms involved went beyond nutrient competition, with a CFS concentration-dependent reduction. CFS from 11 isolates achieved a reduction of over 2 log10 bacteria/mL, with C. butyricum and Paraprevotella clara (DSMZ 19731) CFS standing out with values of 2–3 log10 bacteria/mL. A pH-dependent effect was disclosed for part of the isolates tested, while C. butyricum, Limosilactobacillus mucosae, B. thermoacidophilum and Lactiplantibacillus plantarum maintained part of their anti-B. hyo activity at fixed pH (7.0). A combined analysis of the short chain fatty acid profile and pH on B. hyo growth inhibition revealed differences between isolates, with similar effect for CFS of isolates with similar production of lactic and acetic acids and no clear effect of the pH.

CONCLUSIONS: This study demonstrates the potential of pig gut commensals to outcompete B. hyo and discloses part of the mechanisms involved in the growth inhibition, providing a foundation into future research in competitive exclusion as strategy to control SD.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00511-y.},
}

@article {pmid41680579,
year = {2026},
author = {López-Guzmán, SF and Sánchez-Jasso, DE and Hernández-Sánchez, J and Oviedo, N and Bermudez-Cruz, RM},
title = {Molecular Characterization of the Murine Catsper4 Promoter and its Regulation by CREMτ.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {41680579},
issn = {1933-7205},
support = {IMSS R-2023-785-056//Instituto Mexicano del Seguro Social/ ; },
abstract = {Cation channel sperm-associated protein 4 (CATSPER4) is a subunit of the sperm-specific cation/calcium channel, CatSper, located in the principal piece of the sperm flagellum. It is expressed during the late stages of spermatogenesis, and disruption of the gene encoding this protein leads to male infertility. Mutations in Catsper4 are linked to asthenozoospermia. However, the molecular mechanisms regulating Catsper4 expression remain unclear. Here, we present a detailed molecular characterization of the Catsper4 promoter in mice, focusing on the role of the cAMP-responsive element modulator isoform τ (CREMτ) in its transcriptional regulation. Analysis of publicly available metagenomic chromatin immunoprecipitation-sequencing (ChIP-seq) data revealed the presence of activation histone marks-H3K4me3, H3K4me1, and H3K27ac-within a region corresponding to the 631 bp predicted promoter, suggesting an active promoter region. Although the predicted Catsper4 promoter showed minimal activity, a 65 bp deletion at the 3'-end of the promoter significantly enhanced the transcription. Moreover, removal of the 239 bp in the 5'-flanking region also increased the transcriptional activity, indicating that the core promoter region spans the region from - 99 to + 63 bp relative to the transcription start site (TSS). Notably, a cAMP-responsive element was predicted at + 91, a relevant site in the regulation of other Catsper family genes. To explore its function, we mutated this site and overexpressed CREMτ. Electrophoretic mobility shift assays (EMSA) and ChIP assays confirmed that CREMτ binds to the murine Catsper4 promoter both in vitro and in vivo. This study provides the first functional analysis of the Catsper4 promoter, shedding light on the mechanisms regulating its expression and highlighting the key role of CREMτ in this process.},
}

@article {pmid41680567,
year = {2026},
author = {Chen, L and Hong, C and Xie, Y},
title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.},
journal = {Aging clinical and experimental research},
volume = {38},
number = {1},
pages = {76},
pmid = {41680567},
issn = {1720-8319},
mesh = {Humans ; *Sarcopenia/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; Aged ; Muscle Strength ; },
abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.},
}

Humans
*Sarcopenia/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
Probiotics/therapeutic use
Aged
Muscle Strength

@article {pmid41680318,
year = {2026},
author = {Choudhary, S and Kanaujia, R and Bahadur, R and Angrup, A},
title = {The role of metagenomic next-generation sequencing in spinal infections: a systematic review and meta-analysis.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41680318},
issn = {1432-0932},
}

@article {pmid41680314,
year = {2026},
author = {Alrasheed, AS and Zawawi, AM and Alsulami, LM and Alghirash, FA and Alsalmi, SO and Alhalal, IA},
title = {Clinical utility of metagenomic next-generation sequencing in diagnosing spinal infections: a systematic review and meta-analysis.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41680314},
issn = {1432-0932},
}

@article {pmid41679837,
year = {2026},
author = {Sacco, O and Johansen, EL and Tian, Y and Holck, J and Kirkensgaard, JJK and Blennow, A and De Lise, F and Shaikh-Ibrahim, A and Moracci, M and Curci, N and Svensson, B and Cobucci-Ponzano, B and Wang, Y},
title = {Biochemical characterisation of the 4-α-glucanotransferase from the hyperthermophilic archaeon Pyrobaculum arsenaticum and its formation of high-amylose resistant starch.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124919},
doi = {10.1016/j.carbpol.2026.124919},
pmid = {41679837},
issn = {1879-1344},
mesh = {*Glycogen Debranching Enzyme System/metabolism/chemistry ; *Amylose/chemistry/metabolism ; *Pyrobaculum/enzymology ; *Starch/chemistry ; Hot Temperature ; Hydrolysis ; Hydrogen-Ion Concentration ; },
abstract = {High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85 °C, pH 5.5; Naples, Italy), showed highest activity at 100 °C and pH 5.5, and specific activity of maltotriose disproportionation at 75 °C of 1170 U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75 °C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.},
}

*Glycogen Debranching Enzyme System/metabolism/chemistry
*Amylose/chemistry/metabolism
*Pyrobaculum/enzymology
*Starch/chemistry
Hot Temperature
Hydrolysis
Hydrogen-Ion Concentration

@article {pmid41679819,
year = {2026},
author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M},
title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124886},
doi = {10.1016/j.carbpol.2026.124886},
pmid = {41679819},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation & purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.},
}

*Gastrointestinal Microbiome/drug effects
*Galactans/chemistry/pharmacology/isolation & purification
Fermentation
*Agaricales/chemistry
Molecular Docking Simulation
Fatty Acids, Volatile/metabolism
Prebiotics

@article {pmid41679750,
year = {2026},
author = {Lamont, RF and Jørgensen, JS},
title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.70173},
pmid = {41679750},
issn = {1471-0528},
abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.

METHODOLOGY: A narrative review.

RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.},
}

@article {pmid41679688,
year = {2026},
author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM},
title = {Modulation of Host Proteostasis by Prevotella corporis via Induction of the Heat Shock Response.},
journal = {Cell stress & chaperones},
volume = {},
number = {},
pages = {100150},
doi = {10.1016/j.cstres.2026.100150},
pmid = {41679688},
issn = {1466-1268},
abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, but the mechanisms by which commensal microbes confer proteoprotection remain largely unexplored. We have previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to P. corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ1-42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.},
}

@article {pmid41679496,
year = {2026},
author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y},
title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123973},
doi = {10.1016/j.envres.2026.123973},
pmid = {41679496},
issn = {1096-0953},
abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.},
}

@article {pmid41679417,
year = {2026},
author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J},
title = {Female reproductive microbiome in fertility care.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2026.02.015},
pmid = {41679417},
issn = {1556-5653},
abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. While conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads versus relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches based on clinical context and discuss emerging technologies, including multi-omics integration for implementing microbiome assessment in fertility care.},
}

@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}

@article {pmid41678593,
year = {2026},
author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH},
title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.},
journal = {Circulation research},
volume = {138},
number = {4},
pages = {e326978},
doi = {10.1161/CIRCRESAHA.125.326978},
pmid = {41678593},
issn = {1524-4571},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; },
abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Myocardium/metabolism/pathology
*Regeneration
*Heart/physiology

@article {pmid41678126,
year = {2026},
author = {Yao, Y and Lai, Y and Wu, Q and Xu, W},
title = {Targeted next-generation sequencing improves diagnosis and antimicrobial stewardship in Chlamydia psittaci pneumonia.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41678126},
issn = {1435-4373},
support = {20231001//Changning District Medical Key Specialty/ ; 20231001//Changning District Medical Key Specialty/ ; },
abstract = {UNLABELLED: PURPOSE : Chlamydia psittaci pneumonia (CPP) remains underdiagnosed due to nonspecific clinical manifestations. This study assessed the clinical utility of targeted next-generation sequencing (tNGS) in optimizing CPP diagnosis and antimicrobial stewardship, with a focus on empirical quinolone efficacy.

METHODS: We conducted a retrospective cohort study of 35 CPP patients (November 2022-October 2023) diagnosed by tNGS of respiratory specimens (8 sputum/27 bronchoalveolar lavage fluid [BALF]). Data included epidemiological history, laboratory findings, imaging features, therapeutic interventions, and clinical outcomes. Statistical comparisons between severe and non-severe CPP were performed using Student's t-test and Mann-Whitney U tests.

RESULTS: Median diagnostic delay post-admission was 4 days (IQR:3-5). Fever predominated as initial presentation (97.1%), with 45.7% reporting avian contact. Leukocyte counts were normal/mildly elevated,, yet neutrophil ratio (83.86 ± 6.17%) and D-dimer (1.31 ± 0.86 mg/L) were notably increased. All patients showed elevated CRP (175.52 ± 87.62 mg/L) and ESR (70.00 ± 22.62 mm/h). Severe CPP cases (n = 8) exhibited higher CRP (p = 0.041) and procalcitonin (p = 0.013) than non-severe cases. Common comorbidities included hepatic dysfunction (68.6%) and pleural effusion (34.3%). Polymicrobial co-infections occurred more frequently in severe CPP cases than in non-severe cases (OR = 21.07, 95% CI:1.11-402.30). tNGS-guided diagnosis prompted antibiotic adjustment in 60.0% of patients (21/35) to targeted quinolone, tetracycline, or combination therapy. Clinical recovery was achieved in 97.1%, with 2.9% mortality.

CONCLUSIONS: tNGS enhances early CPP diagnosis and targeted antimicrobial adjustment. Quinolones demonstrate high efficacy as empirical treatment. The strong association between severe CPP and polymicrobial co-infections necessitates comprehensive pathogen screening. Study limitations include a single-center design and a small sample size, warranting validation through prospective multicenter studies.},
}

@article {pmid41678125,
year = {2026},
author = {Hou, Y and Sun, H and Meng, S and Xu, W and Yu, Y and Wang, W and Liu, D and Jia, H and Wang, Y and Chu, H and Sun, Z},
title = {Deciphering the different Mycobacterium avium complex infections of HIV and non-HIV patients by bacterial GWAS and immune cells flow cytometry.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41678125},
issn = {1435-4373},
support = {82272347//National Natural Science Foundation of China/ ; 2022-1G-2161//Capital Health Research and Development of Special Fund/ ; },
abstract = {PURPOSE: Pulmonary diseases caused by Mycobacterium avium complex (MAC) show species-specific epidemiology: M. avium predominates in HIV-positive patients, while M. intracellulare mainly affects immunocompetent hosts. This study aimed to elucidate the bacterial and host mechanisms underlying these differences.

METHODS: We integrated clinical metagenomic next-generation sequencing (mNGS), k-mer-based bacterial genome-wide association study (GWAS) of clinical isolates, peripheral blood immunophenotyping of 175 patients, and mouse infection models with or without CD4 depletion.

RESULTS: K-mer GWAS identified lipid metabolism and transport genes (notably mce) enriched in isolates from hosts with different HIV statuses. Immunophenotyping showed that in HIV-negative patients, M. intracellulare infection elicited higher NKT cell frequencies than M. avium, a difference absent in HIV-positive hosts. In mice, anti-CD4[-]/M. intracellulare infection showed steadily increasing bacterial burden with time (ρ = 0.824), whereas M. avium exhibited no such trend. Early after infection (weeks 1-2), anti-CD4[-]/M. avium group had higher bacterial burden and NKT levels than anti-CD4[-]/M. intracellulare, but by week 4 the pattern reversed (all p < 0.05). CD4 depletion eliminated species-specific differences in NKT activation, and at both weeks 2 (p < 0.05) and 4 post-infection (p > 0.05), the anti-CD4[+]/M. avium groups carried a higher bacterial burden than the anti-CD4[+]/M. intracellulare groups.

CONCLUSION: MAC species exhibit fundamentally divergent infection dynamics driven by differential NKT cell activation, likely shaped by species-specific lipid antigens. This lipid-NKT axis explains contrasting clinical patterns of M. avium and M. intracellulare and highlights a potential target for host-directed interventions.},
}

@article {pmid41677732,
year = {2026},
author = {Dos Santos, LCRM and de Almeida, JDR and de Sousa, NSO and Fernandes, FDS and Ennes, JFV and Frickmann, H and de Souza, JVB and de Souza, ÉS},
title = {Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677732},
issn = {2079-7737},
support = {EDITAL N. 020/2024 - PRODUTIVIDADE EM CT&I//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; CNPq/MCTI Universal Call No. 10/2023//National Council for Scientific and Technological Development/ ; },
abstract = {The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches-culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses-discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota.},
}

@article {pmid41677194,
year = {2026},
author = {Simm, NM and Williams, GM and Fowler, S and Barlow, K and Carter, B and Talley, NJ and Keely, S and Duncanson, K and Hoedt, EC},
title = {A Scoping Review of Methods Used to Investigate Relationships between Dietary Intake and the Gastrointestinal Microbiome.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf306},
pmid = {41677194},
issn = {1753-4887},
support = {//Australian Government Research Training Program Scholarship/ ; //Australian NSW Health Round 5 Early-Mid Career Grant/ ; },
abstract = {The gastrointestinal (GI) microbiome is intrinsically linked to human health and disease, with dietary intake being a major modifiable variable contributing to microbial colonization and fermentation. Diet-microbiome studies are heterogeneous in the methods used to assess and record dietary intake, to sequence the microbiome data, and to analyze associations. To capture the extent of these inconsistencies, we performed a systematic scoping review to synthesize the information on methods used to assess and compare relationships between diet and the GI microbiome in human studies. Our search identified papers with metrics of both dietary intake and the GI microbiome (using either 16S rRNA or metagenomic shotgun sequencing) and specific diet-microbiome associative analysis. The databases searched were MEDLINE, EMBASE, CINAHL, Cochrane, and Google Scholar, and the search produced 22, 228 unique records after de-duplication. After full-text screening, 1,262 articles were selected for full extraction. A subset of 295 studies captured whole dietary intake and investigated associations with the GI microbiome. This subset assessed diet using 84 different food frequency questionnaires, 12 alternative surveys, and 4 types of diet recalls or diaries ranging from 1 to 14 days. Fifty-five percent (n = 163) of studies investigated habitual dietary intake, 35% (n = 101) investigated recent dietary intake, and 10% (n = 30) used methods to assess both. Eighty-one percent of studies employed 16S rRNA sequencing, with wide variation in extraction, sequencing, pre-processing, and annotation methods. Gaps in the reporting of the methods for each step of the sequencing and analysis process were evident, limiting future comparison of study outcomes. Microbiome-specific statistical methods were used in 11% of the subset-predominantly correlational methods that are not recommended for microbiome data. In conclusion, this review revealed extensive inconsistencies within the exploratory diet-microbiome studies, despite the existence of recommendations to assist researchers. Collaborative efforts to develop consensus in methods and reporting are needed to substantially progress the obtaining of high-quality evidence and meta-analysis in the diet-microbiome research field.},
}

@article {pmid41676497,
year = {2026},
author = {Lindstedt, K and Wheelock, A and Samutela, M and Kabir, W and Chasaya, M and Namuziya, N and Marsden, EJ and Kapasa, M and Mumba, C and Mulenga, B and Nkole, L and Pieciak, R and Mudenda, V and Chikoti, C and Ngoma, B and Chimoga, C and Chirwa, S and Pemba, L and Nzara, D and Lungu, J and Forman, L and Simulundu, E and MacLeod, W and Moyo, C and Somwe, SW and Holt, KE and Sundsfjord, A and Gill, CJ},
title = {Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.703236},
pmid = {41676497},
issn = {2692-8205},
abstract = {UNLABELLED: Klebsiella pneumoniae (Kp) is a leading cause of neonatal and infant deaths in sub-Saharan Africa and frequently associated with antimicrobial resistance. Previously, we identified Kp as a major cause of fatal community-associated lower respiratory infections among infants and children under five years in Lusaka, Zambia, using postmortem tissue sampling and pathogen specific multiplex qPCR. In this follow-up study, we employed a novel culture-independent RNA-probe hybridization-capture metagenomic sequencing approach, targeting Kp pan-genome core and accessory genes, to perform in-depth genomic analysis of Kp from eleven post-mortem lung biopsy samples from seven of these children. Analysis detected Kp in all cases except one, which identified Klebsiella quasipneumoniae subspecies similipneumoniae . Core-genome multi-locus sequence typing (cgMLST) revealed six clonal groups (CG607, CG1123, CG10072, CG280, CG3648, and CG10344) belonging to five sublineages (SL607, SL17, SL280, SL37, and SL10072), with perfect concordance between paired samples from the same case. Two infants sampled the same month harbored SL607 lineages sharing 621 out of 629 cgMLST alleles, suggesting clonal spread. Kp capsule (K) loci were detected in all but one case and included potential vaccine targets KL25, KL23, and KL122. Antimicrobial resistance genes were widespread among samples, particularly encoding resistance toward aminoglycosides, β-lactams, sulphonamides, tetracyclines, and trimethoprim. Extended spectrum β-lactamases were identified in four cases, three of which were bla CTX-M-15 . The acquired Kp sideophore yersiniabactin (lineage ybt14) was identified in both cases associated with SL607, and the acquired siderophore aerobactin (lineage iuc5) was identified in one of these, suggesting possible convergence of antimicrobial resistance and hypervirulence. The detection of Kp with extensive antimicrobial resistance causing fatal community acquired pneumonia signals a deeply concerning epidemiologic shift from a largely nosocomial pathogen. This calls for urgent epidemiological investigations to better understand the burden, transmission dynamics, antimicrobial resistances, and potential vaccine targets for Kp in other community settings across sub-Saharan Africa.

AUTHOR SUMMARY: Klebsiella pneumoniae is a major cause of infections and death among newborns and young children, particularly in low-income countries, where it is frequently resistant to antibiotics. While well-known as a hospital-associated pathogen, we previously showed K. pneumoniae is also a leading cause of fatal community lung infections among infants and children in Lusaka, Zambia. In this follow-on analysis, we performed deeper genetic analysis of K. pneumoniae detected from the cluster of community pneumonia deaths using lung tissue samples from seven of these children. Since traditional bacterial cultures were unavailable, we instead used a novel approach that enriched and sequenced specific regions of the K. pneumoniae genome directly from the biopsy samples without culturing bacterial isolates. We identified five different K. pneumoniae genetic subtypes, known as sublineages. Two sublineages, which came from children sampled the same month, were highly similar, suggesting clonal spread. Multiple acquired antimicrobial resistance genes were detected across all sublineages. Acquired virulence factors, which may cause more aggressive infections, were also detected in two cases. We also identified capsule types previously suggested as potential vaccine targets. This study underscores the urgent need to better understand and address the emerging burden of antibiotic-resistant K. pneumoniae pneumonia and other invasive infections among infants and children in community settings in sub-Saharan Africa.},
}

@article {pmid41676450,
year = {2025},
author = {Zhang, L and Liu, Y and Wang, S and Ching, JY and Tam, WH and Leung, TF and Leung, TY and Chan, PKS and Mak, JWY and Cheung, CP and Tun, HM and Chang, EB and DeLeon, O and Huang, Q and Chen, X and Huo, H and Miao, Y and Cheong, PK and Ip, KL and Yeung, YL and Chang, MK and Lyu, C and Yang, H and Li, B and Fan, Y and Sun, Y and Jiang, S and Ng, SC and Chan, FKL},
title = {MOMMY study profile: An integrative early-life multi-omics cohort in China.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70068},
pmid = {41676450},
issn = {2996-9514},
abstract = {Large-scale, prospective birth cohorts capturing the complex interplay between the gut microbiome, host biology, and environmental exposures are crucial to understanding early-life health but remain scarce, particularly within Asian populations. To address this gap, we established the MOMMY cohort (The MOther-infant Microbiota transmission and its link to long terM health of babY), a large, prospective birth cohort uniquely designed to investigate maternal-paternal-infant microbiota transmission and its impact on child health within the understudied Chinese population. MOMMY aims to recruit 20,000 families from three geographically and economically diverse regions across China. This cohort prospectively follows pregnant mothers, fathers, and their infants, with children up to 7 years of age. Since September 2019, we have systematically collected a comprehensive repository of longitudinal biospecimens-including maternal and infant stool, breast milk, cord blood, and parental blood-stored in an accredited biobank. This is complemented by extensive data on environmental exposures, diet, and health outcomes gathered through validated questionnaires and physician assessments. The MOMMY cohort's unique value lies in its unprecedented scale, geographic diversity, and its integrative multi-omics design, which will combine metagenomic, metabolomic, immunologic, and epigenetic data. By creating this unique resource, MOMMY will elucidate how early-life microbial and molecular trajectories, shaped by genetic and environmental factors, influence child development and disease risk, thereby filling a critical gap in global microbiome research.},
}

@article {pmid41676447,
year = {2025},
author = {Deng, F and Han, Y and Li, M and Peng, Y and Chai, J and Yang, G and Li, Y and Zhao, J},
title = {HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70041},
pmid = {41676447},
issn = {2996-9514},
abstract = {Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively compares PacBio High-Fidelity (HiFi) sequencing-based metagenome-assembled genomes (MAGs) against Illumina MAGs, Oxford Nanopore Technologies (ONT) MAGs, and isolate whole-genome sequencing genomes from the same sample. HiFi sequencing yielded 31 high-quality MAGs, including 10 complete circular genomes. HiFi MAGs demonstrated significantly higher completeness, continuity, and lower contamination than Illumina or ONT MAGs (p-adj < 0.05). Crucially, HiFi MAGs exhibited closer genomic proximity to corresponding isolates at both single-nucleotide polymorphism and gene presence/absence levels. This benchmarking establishes HiFi as a robust approach for generating MAGs rivaling isolated genome quality, providing critical insights for accurate microbial genomic studies.},
}

@article {pmid41676442,
year = {2025},
author = {Chaboy-Cansado, R and Talavera-Marcos, S and Gallego-Simón, R and Cobeta, P and Roscales, G and Rastrojo, A and de Cárcer, DA},
title = {Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70037},
pmid = {41676442},
issn = {2996-9514},
abstract = {Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research.},
}

@article {pmid41676438,
year = {2025},
author = {Liu, Y and Ise, Y and Takami, H and Urakawa, R and Tateno, R and Toyoda, A and Ohte, N and Shi, W and Jiang, L and Isobe, K},
title = {Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70054},
pmid = {41676438},
issn = {2996-9514},
abstract = {Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene- or taxon-specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium-related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and [[15]]N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation-that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower-pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher-pH range but diminished within the lower-pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher-pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower-pH soils were enriched in stress-adaptive functions, which promoted ammonium retention and limited N transformations-thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium-related N cycling processes across forests under varying environmental conditions.},
}

@article {pmid41676216,
year = {2026},
author = {Dang, Y and Deng, Z and Wang, K and Luo, J and Wang, C and Long, F and Kong, J},
title = {Cystic fibrosis complicated by allergic bronchopulmonary aspergillosis in a Chinese adolescent: a case report and literature review.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {43},
pmid = {41676216},
issn = {2523-1995},
abstract = {BACKGROUND: Cystic fibrosis (CF) predisposes patients to allergic bronchopulmonary aspergillosis (ABPA). The objective of this study is to enhance the recognition of CF-related ABPA (CF-ABPA) in adolescents through a detailed case study. A multidisciplinary management approach is essential. Early diagnosis and intervention could substantially improve outcomes, warranting further longitudinal research on optimized treatment protocols.

CASE DESCRIPTION: A 15-year-old patient presenting with persistent respiratory symptoms underwent a series of diagnostic tests, including serum immunoglobulin E (IgE) testing, chest computed tomography (CT), bronchoscopy, bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), and whole-exome sequencing to identify CFTR mutations. The diagnostic findings revealed markedly elevated serum IgE levels (2,359.0 IU/mL), the presence of bronchiectasis with mucus plugging on CT imaging, and mNGS detection of Aspergillus fumigatus with an abundance of 97.28%. The diagnosis of CF-ABPA was confirmed by identification of a pathogenic CFTR mutation. Later antifungal therapy and corticosteroids produced notable clinical improvement.

CONCLUSIONS: CF was under-recognized historically, but this case shows that it is a clinically important cause of bronchiectasis and ABPA in Chinese adolescents. The identification of Aspergillus was accurate with the mNGS. Genetic test confirmed that the subject is a CF patient with compound heterozygous mutations in CFTR gene. The finding urges the clinician to have a high index of suspicion for the CF-ABPA in those with asthma-like refractory symptoms with structural lung disease. When diagnosed early and accurately, antifungal therapy and inhaled corticosteroids can be administered timely. The patient experienced a notable improvement both clinically and radiologically, as well as functionally. The future work should promote awareness of this clinical entity and systematic screening of similar patients in China. Further multicenter studies are necessary to formulate diagnostic and therapeutic guides for CF-ABPA in Asia.},
}

@article {pmid41676189,
year = {2026},
author = {Zhang, G and Fang, X and Yang, H and Zhu, Y},
title = {Severe empyema caused by mixed oral anaerobic bacterial infection: a case report.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {28},
pmid = {41676189},
issn = {2523-1995},
abstract = {BACKGROUND: Empyema is a life-threatening pleural infection that can result from various bacterial sources. While oral anaerobic bacteria are recognized as potential pathogens, severe empyema caused by mixed oral anaerobic bacterial infection remains clinically rare. Recent advances in metagenomic next-generation sequencing (NGS) have improved the etiological diagnosis of complex infections. This case demonstrates the clinical significance of NGS technology and oral health in preventing systemic infections.

CASE DESCRIPTION: An 80-year-old male with poor oral hygiene and multiple dental caries presented with acute onset of left-sided chest pain, chills, and fever. Physical examination revealed diminished breath sounds over the left lung. Imaging studies confirmed left-sided empyema. Pleural fluid NGS identified mixed oral anaerobic bacteria including Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Finegoldia magna. The patient underwent thoracoscopic empyema debridement, with postoperative tissue pathology showing suppurative inflammation with fibrinous necrosis. Surgically excised tissue NGS additionally detected Finegoldia magna along with Epstein-Barr virus and human herpesvirus 6. Following targeted anti-infective therapy with meropenem and metronidazole, the patient recovered successfully.

CONCLUSIONS: This case highlights the critical role of NGS technology in identifying mixed oral anaerobic pathogens and guiding precision-targeted treatment of empyema. The atypical presentation of empyema caused by oral anaerobic bacteria warrants early surgical intervention combined with appropriate antimicrobial therapy. Our findings emphasize the importance of oral health maintenance in preventing life-threatening systemic infections and broaden our understanding of oral-systemic disease relationships.},
}

@article {pmid41676099,
year = {2026},
author = {Zheng, H and QuBie, X and Wang, J and Liu, P and Zhang, W},
title = {Clinical features and chest CT findings of Chlamydia pneumoniae pneumonia.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1717744},
pmid = {41676099},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aimed to investigate the clinical features and chest computed tomography (CT) findings in 42 patients with Chlamydia pneumoniae pneumonia, as confirmed by metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective analysis of clinical data and chest CT findings (both at disease onset and within 1 month thereafter) in 42 patients diagnosed with Chlamydia pneumoniae pneumonia by mNGS at our hospital between August 2022 and August 2025.

RESULTS: Of the 42 patients, 25 (59.5%) presented with fever, 26 (61.9%) with sore throat, 30 (71.4%) with cough, 27 (64.3%) with expectoration, 11 (26.2%) with myalgia, 10 (23.8%) with general fatigue, and 10 (23.8%) with neurological symptoms such as headache and dizziness. Laboratory tests revealed that 12 patients (28.6%) showed a mild increase in white blood cell count, 10 (23.8%) had elevated neutrophil counts, 21 (50.0%) exhibited elevated C-reactive protein (CRP) levels, and 6 (14.3%) had CRP levels exceeding 100 mg/L. In the early stage, chest CT demonstrated a lobular pneumonia pattern in 16 patients (55.2%), involvement of a single lung lobe in 20 (69.0%), predominant lower-lung distribution in 19 (65.5%), and a nodular-patchy pattern in 8 patients (27.6%) with a nodular-patchy pattern. The main accompanying features included a halo sign in 25 patients (86.2%), centrilobular nodules in 23 (79.3%), and bronchial wall thickening in 20 (69.0%). In the mid-to-late stage, chest CT revealed a lobular pneumonia pattern in 23 patients (76.7%), single-lobe involvement in 23 (76.7%), and predominant lower-lung distribution in 20 (66.7%). The major concomitant features were a halo sign in 21 patients (70.0%), centrilobular nodules in 20 (66.7%), and bronchial wall thickening in 24 (80.0%).

CONCLUSION: Chest CT findings of Chlamydia pneumoniae pneumonia are predominantly characterized by a lobular pneumonia pattern, lower-lobe distribution, and associated features such as bronchial wall thickening, centrilobular nodules, and a peripheral halo sign. Certain imaging differences exist between early and middle-to-late stages, with the nodular-patchy pattern potentially representing an ultra-early imaging marker, which may provide clues for early clinical intervention.},
}

@article {pmid41676059,
year = {2026},
author = {Li, X and Yi, H and Wu, G and He, A and Li, R and Long, Y and Lin, C and Jiang, Z},
title = {Neutrophil CD64 index for rapid diagnosis of Pneumocystis jirovecii pneumonia in malignancy patients requiring mechanical ventilation: a retrospective analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1706786},
pmid = {41676059},
issn = {1664-302X},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) incidence and associated mortality have risen significantly in non-HIV immunocompromised patients, highlighting the urgent need for rapid, non-invasive diagnostics. Current methods face limitations including invasiveness, prolonged processing, or inadequate specificity. The neutrophil CD64 (nCD64) index emerges as a promising novel biomarker. Here, we conducted this study to evaluate the diagnostic performance of nCD64 index for PJP and further assess the predictive value of its longitudinal changes for 28-day mortality.

METHODS: This retrospective cohort study (July 2022-March 2025) analyzed mechanically ventilated malignancy patients with unexplained diffuse pulmonary infiltrates at a tertiary intensive care unit (ICU). PJP diagnosis required predefined clinical, radiological, and bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF mNGS) criteria. The nCD64 index was measured via flow cytometry at ICU admission and serially after ≥3 days of anti-PJP therapy. Diagnostic performance for PJP and prognostic value for 28-day mortality were assessed.

RESULTS: Among 28 PJP and 38 non-PJP patients, nCD64 index was significantly higher in PJP (13.33 vs. 2.84, p < 0.001). Receiver operating characteristic (ROC) curve analysis showed an area under the curve (AUC) of 0.846 (95% CI: 0.736-0.932) for PJP diagnosis, with sensitivity 89.3% and specificity 71.1% at cutoff ≥7. Multivariate analysis confirmed nCD64 index as an independent PJP predictor (OR = 1.097, 95% CI: 1.026-1.173; p = 0.007). Post-therapy nCD64 index elevation predicted 28-day mortality with high sensitivity (81.8%) and specificity (86.7%).

CONCLUSION: The nCD64 index functions as a dual-purpose biomarker for malignancy patients with respiratory failure requiring mechanical ventilation: it provides a rapid, non-invasive diagnostic tool for PJP and dynamically stratifies mortality risk. Moreover, dynamic tracking offers a real-time window into treatment response, guiding therapeutic decisions.},
}

@article {pmid41675707,
year = {2025},
author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L},
title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e62},
pmid = {41675707},
issn = {2996-9514},
abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.},
}

@article {pmid41675165,
year = {2025},
author = {Liu, S and Ye, Y and Guo, B and Hu, Y and Jiang, K and Liang, C and Xia, S and Wang, H},
title = {ViOTUcluster: A high-speed, All-in-one pipeline for viromic analysis of metagenomic data.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70023},
pmid = {41675165},
issn = {2996-9514},
abstract = {ViOTUcluster is a user-friendly, high-speed, accurate, All-in-one solution that streamlines the entire viromic analysis workflow-from raw reads to the generation of viral operational taxonomic units tables, as well as other key viromic analysis tasks.},
}

@article {pmid41675153,
year = {2025},
author = {Ye, L and Hu, Q and Zang, T and Wang, Y and Heng, H and Chan, EWC and Chen, S},
title = {Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70004},
pmid = {41675153},
issn = {2996-9514},
abstract = {The pork microbiome was investigated using an integrated approach combining isolation and metagenomic sequencing methods to comprehensively analyze the pathogens and resistome on pork surfaces. The study revealed a large number and diversity of pathogens and resistance genes, potentially originating from air, transportation, water, or cross-contamination. These findings underscore the importance of implementing multifaceted food surveillance strategies to monitor and mitigate these risks effectively.},
}

@article {pmid41675151,
year = {2025},
author = {Skoog, EJ and Kebabonye, K and Klempay, B and Gondwe, M and Makati, K and Babayani, N and Jongman, M and Bowman, J and Aluwihare, L},
title = {Viral metagenomics of Okavango Delta water pans reveal novel insights into wildlife disease potential.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70018},
pmid = {41675151},
issn = {2996-9514},
abstract = {Botswana's Seronga region saw a mass elephant die-off potentially linked to water sources. This study analyzes Okavango Delta metagenomes, uncovering a diversity of viruses and harmful pathogens. Findings highlight the importance of understanding viral ecology in these waters and support One Health's objective in protecting human, animal, and ecosystem health.},
}

@article {pmid41675149,
year = {2025},
author = {Shen, H and Du, C and Jiang, S and Dong, W and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Native synthetic microbial communities enhance zha-chili by boosting the fermentation capacity of indigenous microorganisms.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70009},
pmid = {41675149},
issn = {2996-9514},
abstract = {Fermented foods are a crucial part of the global diet, accounting for one-third of global food intake. Traditional fermented foods often rely on natural fermentation, leading to safety risks. The construction of synthetic microbial communities (SynComs) tailored for fermented foods is a key strategy to solve these issues. Here, we designed and constructed SynComs consisting of two bacterial and three fungal species, utilizing the study model of zha-chili. Using various high-throughput sequencing technologies, the dynamic alternations of microorganisms during the fermentation process were investigated, and the impact of SynComs on the fermentation process was evaluated. SynComs reduced fermentation time by approximately 15 d, increased flavor yields (8% for ethyl lactate and ethyl acetate), and greatly improved the quality of the zha-chili. Meanwhile, SynComs altered the succession of the fungal community so that Pichia became the dominant microorganism throughout the fermentation process, and the pattern of fungal community succession was brought closer to the null model. Metagenomic annotation results showed notable changes in functional genes, especially in glycoside hydrolases family. SynComs enhanced the positive correlations between indigenous microorganisms and flavor compounds while increasing other community microorganisms' contribution to flavor production. These findings provide a new approach to improve the quality of zha-chili and other traditional fermented foods through natural fermentations. We proposed that SynComs enhanced fermented foods by boosting the fermentation capacity of indigenous microorganisms.},
}

@article {pmid41674905,
year = {2025},
author = {Díaz-Santiago, E and Sadio, TD and Diéme, JS and Hurtado-Martínez, M and Kindler, C and Manrique, E and Pugnaire, FI},
title = {Soil microbial communities in contrasting environments show a common core of species linked to Maytenus senegalensis shrubs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699694},
pmid = {41674905},
issn = {1664-302X},
abstract = {INTRODUCTION: The existence of a core microbiota specific to a plant species, or the set of microorganisms shared by all plant individuals of the species, is of utmost importance because of its many conceptual and practical consequences. The core microbiota is assumed to gather the most ecologically and functionally relevant microorganisms associated to a plant in a given environment, presumably establishing positive feedbacks that support its persistence and performance in a plant community.

METHODS: We tested the existence of a potential core microbiota in Maytenus senegalensis shrubs in two contrasted, distant ecosystems; a dry environment (Almeria, Spain) and a relatively wetter ecosystem (Dakar, Senegal).

RESULTS: Soil microbial community structure widely differed between sites influenced by soil and climate. However, a subset of microbial phylotypes appeared consistently associated to all M. senegalensis plants across our two disparate ecosystems while they were absent in the surrounding soil, suggesting the presence of a core microbiota in M. senegalensis.

DISCUSSION: Microbiota had an effect on germination that differed between sites, perhaps due to climatic constrains. We show that the assembly of understory microbial communities depends on the plant's sorting effect on the surrounding soil microbiota, plus some other taxa likely transferred by seeds; this assembly mechanism is relevant for the coevolution of plants and microorganisms, and critical for potential community responses to environmental changes.},
}

@article {pmid41674903,
year = {2025},
author = {Ding, Z and Ren, K and Xu, Y and Feng, T and Cui, K and Liu, Q and Liao, C},
title = {Disease-driven restructuring of the gut microbiome underlies inflammatory bowel disease dysbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1744574},
pmid = {41674903},
issn = {1664-302X},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent intestinal disorder with rising global incidence, yet its complex pathogenesis remains poorly understood, underscoring the need to clarify the microbial mechanisms underlying intestinal inflammation. IBD is associated with a profound imbalance of the gut microbial ecosystem. However, the ecological and functional remodeling of the gut microbiota during IBD progression remains unclear. This study used metagenomic sequencing to investigate microbial composition, functional capacity, and ecological interactions in the gut microbiota of IBD patients compared with healthy individuals.

RESULTS: The IBD group exhibited significantly reduced microbial diversity and a distinct community structure compared with healthy controls. Pro-inflammatory genera such as g_Fusobacterium (p < 0.001) and g_Morganella (p < 0.001) were enriched, whereas short-chain fatty acid producing bacteria, including g_Ruminococcus (p < 0.0001) and g_Agathobacter (p < 0.0001), were markedly depleted. Functional annotation revealed decreased abundance of carbohydrate-active enzymes (GH3, GH44, GH53, and GH77; all p < 0.05) associated with polysaccharide degradation, together with enrichment of pathways related to immune activation and inflammation, such as the JAK-STAT and chemokine signaling pathways (p < 0.05). Co-occurrence network analysis further showed that IBD-associated microbes formed positively correlated clusters dominated by inflammatory taxa, whereas healthy microbiota were organized around SCFA-producing commensals.

CONCLUSION: Compared with healthy individuals, the gut microbiota of IBD patients undergoes functional reprogramming characterized by loss of metabolic versatility and enrichment of inflammation-related pathways. These findings provide new insights into the ecological and metabolic mechanisms through which the gut microbiota contribute to intestinal inflammation and disease progression.},
}

@article {pmid41674838,
year = {2026},
author = {Berta, J and Rowe, L and Garry, B},
title = {Catching the Mardi Gras fever: Quantifying the impact of mass gathering tourism on local bacterial prevalence and community diversity in municipal wastewater.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8681977/v1},
pmid = {41674838},
issn = {2693-5015},
abstract = {We employed 16S metagenomic analysis to measure the impact of Mardi Gras tourism on the bacterial ecology found in New Orleans' municipal wastewater. Throughout the peak of the 2023 Carnivale season, species turnover was significantly higher in New Orleans than it was in our control site. Alpha diversity metrics peaked 2-to-3 weeks after Mardi Gras Day, increasing between 65% and 1967% over Carnivale. We also found that human pathogens and microbiota had significantly stronger, more positive correlations with the rise in Mardi Gras tourism than did environmental control species. These changes in wastewater abundance for two species - S. enterica and E. coli - mirrored the concurrent clinical isolate data from the same region for Salmonella spp. and STEC. We also found that multiple alpha and beta diversity measures correlated strongly with increases in tourism during the peak of Carnivale season.},
}

@article {pmid41674736,
year = {2026},
author = {Mukenschnabl, K and Humpel, O and Abdalla, TE and Wood, E},
title = {An Unusual Case of Unexplained Infertility: Co-colonization of the Uterus and Seminal Fluid.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e101251},
pmid = {41674736},
issn = {2168-8184},
abstract = {Chronic endometritis (CE) is defined as a persistent, mild inflammation of the endometrium induced by intrauterine bacterial infection. CE has been associated with infertility in patients with recurrent in vitro fertilization (IVF) failure. We report an unusual case of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility. A 35-year-old woman presented to the office for infertility evaluation after 16 months of inability to conceive naturally using ovulation kits. Initial workup revealed adequate ovarian reserve with an anti-Müllerian hormone (AMH) level of 4.8 ng/mL, tubal patency on hysterosalpingogram, and normal semen analysis. The patient and her partner failed to conceive following three cycles of ovulation induction with intrauterine insemination (IUI). In preparation for IVF, an endometrial biopsy (EMB) was performed, and five CD138+ plasma cells per 10 high-power fields suggested CE. The patient underwent antibiotic therapy, yet EMB remained positive. At this time, the partner's semen culture was positive for Enterococcus faecalis and Escherichia coli. Endometrial microbiome metagenomic analysis (EMMA) and analysis of infectious chronic endometritis (ALICE) demonstrated co-colonization with the same bacteria seen on her partner's semen culture. Both the patient and her partner required multiple rounds of antibiotic therapy before successful conception via IVF. This case demonstrates an unusual occurrence of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility, suggesting a potential pathway for CE development from bacteriospermia. The patient's EMMA/ALICE tests and the partner's semen cultures revealed the presence of the same bacteria. While current literature does not identify the development of CE from the bacteria in a partner's semen, there is an association between bacteria in semen and infertility. In couples with unexplained infertility, thorough evaluation for CE with EMB and EMMA/ALICE can be performed in conjunction with a semen culture on the partner to explore potential co-colonization and guide dual-partner treatment.},
}

@article {pmid41674628,
year = {2026},
author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA},
title = {Plant-based whole-food diets are feasible during autologous stem cell transplantation and are associated with dose-dependent microbiome modulation: Results from a pilot clinical trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.26345403},
pmid = {41674628},
abstract = {Plant-based dietary strategies may offer a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked to infectious complications and inferior survival. We conducted a single-arm study to test the feasibility and biological activity of a high-fiber, plant-based, whole-food meal delivery intervention during the peri-transplant period. Adults with multiple myeloma (n = 22) received fully prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting consumption of nutrient-dense, high-fiber foods despite transplant-related symptoms that often limit oral intake. The primary endpoints were feasibility and tolerability, defined by successful enrollment, adherence to study procedures, and patient-reported intake of study meals; diet was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming at least some proportion of delivered meals and with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. Larger randomized trials are warranted to determine whether microbiome-targeted nutrition can reduce transplant-related toxicities, enhance immune recovery, and improve disease control in multiple myeloma. The trial is registered at ClinicalTrials.gov (NCT06559709).},
}

@article {pmid41674603,
year = {2026},
author = {Agudelo, C and Nsereko, M and Ainebyona, A and Andama, A and Castro, R and Leung, SRM and Nakafeero, J and Nannyonga, G and Nolan, K and Teran, L and Wambi, P and Young, MG and Kato-Maeda, M and Cattamanchi, A and Jaganath, D and Wobudeya, E and Wolf, AR},
title = {Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.29.26345155},
pmid = {41674603},
abstract = {BACKGROUND: Stool-based molecular tests are a noninvasive option for pediatric tuberculosis (TB) diagnosis, but have lower sensitivity compared to sputum-based tests. Untargeted metagenomic sequencing (mNGS) on stool could improve sensitivity and identify new gene targets for molecular testing.

METHODS: We performed shotgun mNGS on DNA isolated from stool samples of children undergoing assessment for pulmonary TB in Uganda. We defined the performance of mNGS to identify Mycobacterium tuberculosis (Mtb) against a microbiological reference standard (MRS, TB if sputum Xpert Ultra or culture positive) and a composite reference standard (TB if confirmed or unconfirmed TB). We also compared accuracy of mNGS against the stool-based Xpert Ultra test. Finally, we identified enriched genomic loci among Mtb classified reads.

RESULTS: We analyzed 176 stool samples of children with a median age of 3.6 years (IQR, 1-6 years). !"#$%&'(')*(+,-. (')*(&*%&$'$/$'$*&(01(234-(5$')(60&$'$/*(78(9*1$%*9(as ≥ 1, 2, or 5 sequence fragments were 35.5% (95% CI 19%:;;<=.(>;?@<(AB>< : 45%), and 19.4% (13%-25%) respectively, and specificities 92.64% (87%-96%), 97% (93%-99%), and 99.3% (96%-100%). Stool Xpert Ultra had similar sensitivity (22.6%) to stool mNGS considering all samples tested. In a head-to-head comparison, stool mNGS had lower sensitivity than stool Xpert Ultra (38.5% vs. 53.8%, difference -15.3%, 95% CI 14-68 to 25-81). mNGS utilized rRNA, virulence proteins and membrane proteins not targeted in current PCR-based platforms.

CONCLUSIONS: Metagenomic sequencing of stool DNA did not increase sensitivity of TB detection, but identified novel targets for molecular testing that may support development of more sensitive tests.},
}