@article {pmid42324848,
year = {2026},
author = {Santos-Perdomo, I and Salces-Castellano, A and Moraza, ML and Mateos, E and Muñoz-Barrera, A and González-Montelongo, R and Suárez, D and Vega-Pita, N and Falcón-López, L and Lorenzo-Salazar, JM and Flores, C and Arribas, P and Andújar, C},
title = {Integrating Megabarcoding and Metabarcoding to Unlock Diversity and Distribution Data Shortfalls in Dark Taxa.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70166},
doi = {10.1111/1755-0998.70166},
pmid = {42324848},
issn = {1755-0998},
support = {CGL2015-74178-JIN//Agencia Estatal de Investigación/ ; PID2021-126883NA-I00//Agencia Estatal de Investigación/ ; PID2022-143291NB-I00//Agencia Estatal de Investigación/ ; RYC2020-029196-I//Agencia Estatal de Investigación/ ; RYC2021-034291-I//Agencia Estatal de Investigación/ ; TESIS2022010039//Agencia Canaria de Investigación, Innovación y Sociedad de la Información/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; Spain ; Phylogeography ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; *Metagenomics/methods ; Soil ; },
abstract = {Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Biodiversity
Spain
Phylogeography
High-Throughput Nucleotide Sequencing/methods
Genetic Variation
*Metagenomics/methods
Soil

@article {pmid42325417,
year = {2026},
author = {Zhang, X and Yang, X and Hu, J and Zhang, W and Shen, W},
title = {Treatment of brain abscess rupturing into ventricle: a case report and literature review.},
journal = {Frontiers in surgery},
volume = {13},
number = {},
pages = {1782105},
pmid = {42325417},
issn = {2296-875X},
abstract = {Brain abscess is a focal intraparenchymal infection. Brain abscess breaking into ventricles is a potentially fatal complication of brain abscess, which can lead to sudden deterioration of neurological function. Its incidence rate is 0.3%-35.0%, and the mortality rate is 84.0%-100.0%. This paper reports a case of a 50-year-old male patient who had previously undergone intracranial hematoma evacuation and skull fixation for traumatic brain injury. He was admitted to the hospital with dizziness for 20 days and bradyphrenia for 4 days. After admission, enhanced computerized tomography(CT) and magnetic resonance imaging(MRI) indicated a left frontal lobe brain abscess. During empirical treatment with ceftriaxone and metronidazole, the abscess ruptured into the ventricle, leading to ventriculitis. Bilateral external ventricular drainage (EVD) combined with ventricular lavage was performed using stereotactic technology. Metagenomic next-generation sequencing (mNGS) of the pus identified the infecting bacteria as Parvimonas micra and Fusobacterium. According to clinical guidelines, the anti-infective regimen was adjusted, short-term low-dose methylprednisolone was used, and combined with hyperbaric oxygen therapy. The patient recovered and was discharged. This paper emphasizes that timely identification of brain abscess rupture leading to ventriculitis, adoption of bilateral external ventricular drainage combined with ventricular lavage, determination of abscess pathogens using mNGS technology, and selection of sensitive antibacterial drugs can improve the cure rate of ventriculitis.},
}

@article {pmid42325651,
year = {2026},
author = {Mourad, A and Lupu, DS and Richey, M and Steven, P and Fowler, VG and Perkins, B and Holland, TL and Bergin, SP},
title = {Timing of Bronchoscopy and Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Host Pneumonia.},
journal = {Open forum infectious diseases},
volume = {13},
number = {6},
pages = {ofag361},
pmid = {42325651},
issn = {2328-8957},
abstract = {BACKGROUND: Immunocompromised patients are at high risk of pneumonia, with associated poor outcomes. Rapid microbiologic diagnosis is crucial, yet diagnostic yields vary widely. We evaluated the variability in diagnostic yield of usual care testing and plasma microbial cell-free DNA (mcfDNA) sequencing in the prospective observational Pneumonia in the Immunocompromised-Use of the Karius Test for the Detection of Undiagnosed Pathogens (PICKUP) study, specifically focusing on timing of testing relative to the onset of pneumonia.

METHODS: In this exploratory analysis, patient characteristics, variability in diagnostic yield, and the timing of bronchoscopy and mcfDNA sequencing from date of first abnormal imaging associated with suspected pneumonia were evaluated across enrolling sites.

RESULTS: A total of 222 patients from 10 enrolling sites were analyzed. Usual care diagnostic yield varied across sites (range, 7.7%-57.7%). Patient characteristics did not differ between sites, and median time from abnormal imaging to bronchoscopy was not different across sites (3 days [IQR, 3]). Diagnostic yield of bronchoscopy was significantly higher when performed ≤3 days (early) from abnormal imaging (38.5% [52/135]) versus >3 days (delayed) (21.8% [19/87]) (difference, 16.7% [95% CI, 2.5%-28.3%]; P = .009). Adding mcfDNA sequencing to usual care testing increased overall diagnostic yield by 7.9% for patients undergoing early bronchoscopy, and by 16.3% for delayed bronchoscopy.

CONCLUSIONS: Early bronchoscopy enhances diagnostic yield in immunocompromised patients with suspected pneumonia. Irrespective of timing, plasma mcfDNA sequencing increases overall diagnostic yield in this clinical scenario. These findings underscore the importance of prompt diagnostic strategies in this patient population.},
}

@article {pmid42325854,
year = {2025},
author = {Fan, L and Guan, J and Feng, L and Wang, Y and Zeng, H and Zhu, Y and Li, H and Chen, Q and Li, L and Qian, J and Liu, L and Li, Y},
title = {A patient with long-term diabetes dies following infection with Francisella novicida in Guangdong province, China: a case report.},
journal = {Infectious diseases & immunity},
volume = {5},
number = {1},
pages = {68-71},
pmid = {42325854},
issn = {2693-8839},
abstract = {The rarity of Francisella novicida infection in humans is well-known, and the F. novicida cases occur in immunocompromised patients or those with underlying health problems. Herein, we report the case of a patient with long-term diabetes who died following F. novicida infection that caused multiple organ failure, although F. novicida was effectively eliminated using antimicrobial therapy. Microbiological confirmation of F. novicida infection relies on metagenomic next-generation sequencing (mNGS) and pdpD-2 gene-specific identification. This study highlights the importance of early pathogen diagnosis in severely infected patients, particularly in cases of F. novicida, and indicates that mNGS is a useful tool for early diagnosis.},
}

@article {pmid42326050,
year = {2026},
author = {He, F and Yang, Y and Ma, D and Liu, P},
title = {Disseminated Cryptococcosis in a Non-HIV Patient: Diagnostic Value of Integrating mNGS, Culture, and Antigen Testing.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {597466},
pmid = {42326050},
issn = {1178-6973},
abstract = {Cryptococcus neoformans is an opportunistic fungal pathogen most commonly observed in individuals with human immunodeficiency virus (HIV) infection. Disseminated infections involving multiple organs, such as lungs, bloodstream, urinary tract, pleural cavity and central nervous system, are uncommon in patients without HIV. This work describes the case of a 72-year-old man who developed high fever and increased inflammatory markers after coronary artery bypass surgery. C. neoformans (8 sequence reads) was initially detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and was subsequently isolated from blood, urine and pleural effusion culture. Additionally, the cerebrospinal fluid tested positive for cryptococcal capsular polysaccharide antigen (CrAg), confirming disseminated infection involving multiple anatomical sites. The patient received liposomal amphotericin B combined with flucytosine antifungal treatment, which led to improvement in inflammatory parameters; however, the patient developed secondary multiorgan failure due to the severity of the illness. After 98 days of hospitalization, the patient was eventually discharged. This case highlights the diagnostic challenges of disseminated cryptococcosis in non-HIV hosts, particularly when involving atypical sites such as the urinary tract and pleural cavity. The integration of conventional microbiological methods, CrAg testing, and mNGS facilitated early diagnosis and enabled timely, standardized antifungal therapy.},
}

@article {pmid42326398,
year = {2026},
author = {Zhao, S and Peng, S and Li, H and Yang, G and Gao, X and Xu, K and Shi, L and Yu, H and Qiao, S},
title = {An approach for diagnosis of diarrhea in neonatal piglets based on the core gut microbiota and machine learning.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852304},
pmid = {42326398},
issn = {1664-302X},
abstract = {Diarrheal diseases, such as yellow dysentery and white dysentery caused by pathogens or viruses, in newborn piglets lead to substantial economic losses in the swine industry worldwide. Gut microbiota dysbiosis is frequently observed in diarrheic piglets and is thought to play a role in disease pathogenesis, although causal relationships remain to be established. However, developing reliable microbiome-based diagnostic tools still poses a significant challenge. This study aimed to develop a diagnostic model for piglet diarrhea by integrating core microbiota analysis with machine learning. Fecal samples from diarrheic and healthy piglets were subjected to metagenomic sequencing to characterize archaeal, bacterial, and fungal communities. We identified diarrhea-associated bacterial biomarkers via LEfSe, DESeq2, and microbial cooccurrence network analysis. These microbial features were used to construct and compare multiple machine learning classifiers. Our results revealed significant disparities in the structure and diversity of the gut microbiota between diarrheic and healthy piglets, with the bacterial community showing the most notable changes. Among the models developed, the decision tree classifier based on bacterial genus-level features achieved the highest prediction accuracy of 91.18%. Furthermore, a simplified model utilizing a panel of 18 core bacterial genera also demonstrated high efficacy, with a support vector machine model achieving 88.24% accuracy. In independent validation using our internal dataset, the random forest model exhibited the best generalizability and stability. This study establishes a robust, microbiota-based diagnostic model for diarrhea in neonatal piglets, highlighting the potential of machine learning in leveraging microbiome data for disease classification and health management in livestock production.},
}

@article {pmid42326408,
year = {2026},
author = {Cha, J and Yang, J and Zhang, Z and Qian, L and Yang, F and Li, S and Li, J and Jian, Z and Cheng, W},
title = {Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807081},
pmid = {42326408},
issn = {1664-302X},
abstract = {INTRODUCTION: The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses.

METHODOLOGY: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds.

RESULTS: The results showed no significant differences between the two breeds in core phylum composition or overall microbial diversity. A total of 146 bacterial genera were identified with significant differences at the genus level. Functional analysis revealed that the gut microbiota of Yunnan ponies was significantly enriched in pathways related to carbohydrate metabolism and pectin degradation, which are involved in basic energy acquisition. In contrast, Dutch warmblood horses were more enriched in host immune interaction pathways such as Toll-like receptor signaling. Analysis of ARGs indicated that while there was no difference in the overall diversity of ARGs between the two groups. Their association networks with specific bacterial hosts were markedly distinct, and the dominant ARG subtypes differed.

DISCUSSION: This study provides a descriptive characterization of the gut microbiome of Yunnan ponies, offering baseline data for future research on the conservation of this genetic resource and its health management in breeding.},
}

@article {pmid42326413,
year = {2026},
author = {Peng, C and Delle Grazie, G and Ghanbari, M and May, A and Abeel, T},
title = {Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1702973},
pmid = {42326413},
issn = {1664-302X},
abstract = {BACKGROUND: Efforts to replace antibiotic growth promoters (AGPs) in livestock are often hindered by a limited mechanistic understanding of how sub-therapeutic antibiotic doses enhance animal growth. Since AGP concentrations are typically too low to directly suppress pathogens, their effects on the gut microbiome, particularly its ecological dynamics, warrant closer investigation. A critical but underexplored dimension is how these additives influence the structure and stability of microbial communities as interconnected ecosystems.

METHODS: We conducted a comparative network-based analysis to examine the effects of zinc-bactracin, a commonly used AGP, and Digestarom[®], an alternative phytogenic feed additive (PFA) on cecal microbiome dynamics in broiler chickens. Using metagenomic data from a repeated cross-sectional randomized controlled trial of 96 broiler chickens assigned to three dietary groups: Basal (Control), AGP and PFA, we constructed microbial co-occurrence networks using Spearman's correlation for birds raised on basal, AGP-, or PFA-supplemented diets at key developmental stages (Day 3, 14, 21, and 35). We assessed changes in network topology, modular organization and node centrality. We evaluated whether the network-prioritized keystone taxa could discriminate among diets using a Random Forest classifier.

RESULTS: Compared to the Control group, both AGP and PFA treatments induced consistent shifts in network topology, including reduced connectivity, increased modularity, increased percentage of positive interactions, enhanced mucosa connectivity, and improved structural robustness over experiment time. Overall, these treatment-induced changes were more pronounced under AGP than under PFA. Despite these changes, we identified conserved subgraphs with stable interconnections across diets and time points during the experiment. The node centrality analysis revealed condition-specific keystone taxa, but Linear Discriminant Analysis (LDA) and Random Forest (RF) struggled to accurately differentiate between diets using their abundance, particularly between PFA and the two other groups.

CONCLUSION: Our findings reveal that feed additives can reshape gut microbial dynamics without producing marked compositional shifts. The consistent network-level changes observed for both AGP and PFA highlight the value of ecological network analysis in uncovering microbial community responses. These insights improve our understanding of cecal microbiome responses in chickens, highlight potential modes of action of AGPs, and offer a comparative framework for assessing the microbial impacts of alternative feed additives.},
}

@article {pmid42326425,
year = {2026},
author = {Wang, X and Yang, N and Hu, Y and Wang, X and Wu, Y and Zhang, A and Wang, Y},
title = {Vegetation restoration restructures soil sulfur allocation and sulfur-cycling functional potential in the Mu Us Sandy Land.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1845938},
pmid = {42326425},
issn = {1664-302X},
abstract = {Vegetation restoration in semi-arid sandy ecosystems can alter soil sulfur cycling not only through changes in sulfur stocks, but also through shifts in the partitioning between organic sulfur and sulfate and their microbial regulation. Here, we investigated soil sulfur pool allocation and sulfur-cycling functional potential along a five-stage vegetation restoration gradient in the Mu Us Sandy Land by integrating sulfur fraction measurements with metagenomic analyses. Vegetation restoration markedly reshaped the soil physicochemical and microbial context, as reflected by lower pH and higher TN, microbial biomass carbon, and enzyme activity in restored soils. In contrast, sulfur pools responded asynchronously: total sulfur and organic sulfur declined substantially from bare sandy land to restored vegetation types, whereas sulfate showed a weaker and comparatively more stable response. At the functional level, dominant sulfur-cycling genes were generally more abundant in bare sandy land, declined across restored vegetation types, and showed only partial recovery in forestland, indicating that restoration reorganized sulfur-cycling functional composition rather than uniformly enhancing sulfur-cycling potential. Taxonomically, dominant sulfur-cycling genes were consistently affiliated mainly with Actinomycetota and Pseudomonadota, but restored vegetation types exhibited more partitioned host compositions, with greater contributions from Acidobacteriota, Chloroflexota, and, for some genes, Thermoproteota. MAG-based analyses further showed that key sulfur-cycling genes were phylogenetically widespread but unevenly distributed across specific host lineages. Co-variation and Mantel analyses showed that sulfur-cycling genes formed coordinated functional modules and were most strongly associated with soil sulfur pools and fractions. Overall, vegetation restoration in the Mu Us Sandy Land primarily reshaped sulfur allocation and sulfur-cycling functional potential rather than promoting simple sulfur accumulation. These findings highlight that sulfur recovery in sandy drylands is better characterized by pool reallocation and functional reorganization.},
}

@article {pmid42326426,
year = {2026},
author = {Nelon, JN and Eltaher, SS and Abdelhamid, AG},
title = {Shotgun metagenomic and phenotypic characterization of indigenous lactic acid bacteria from raw milk artisanal cheeses: metagenomic functional insight and starter culture traits.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820264},
pmid = {42326426},
issn = {1664-302X},
abstract = {The diversity of commercial starter cultures of lactic acid bacteria (LAB) used in fermented dairy products is limited. This has created strong demand to discover novel starter culture strains to develop unique products with appealing sensory characteristics. The current study used an integrated shotgun metagenomic and culture-based pipeline to (a) define taxonomic composition and functional potential of selected artisanal raw milk cheese microbiomes and (b) isolate and evaluate native LAB strains as potential starter cultures. Five artisanal cheeses (brie, bleu, plain gouda, mustard seed gouda, and nettle gouda) were analyzed. Shotgun metagenomics profiled the cheese microbiomes and revealed a high abundance of Lactococcus cremoris and Lactococcus lactis in gouda cheeses, whereas brie cheese contained high abundances of L. lactis and Streptococcus thermophilus. Functional profiling of metagenome-assembled genomes recovered from cheese microbiomes identified abundant pathways linked to carbon utilization, energy metabolism, and organic nitrogen metabolism. In parallel, 12 LAB isolates were recovered from all cheeses, of which five strains were classified taxonomically as L. lactis using whole genome sequencing. These five L. lactis strains displayed desirable milk and cream fermentation properties, achieving coagulation within 6 h, with final pH values of 4.5. The resulting fermented products contained 2.9%-4.2% protein content, displayed a relative increase in long-chain fatty acids, and a relative decrease in short-chain fatty acids compared to unfermented controls. The current study links cheese metagenome functional potential to dairy adaptation and identifies indigenous L. lactis strains as promising candidates for novel starter cultures in fermented dairy products.},
}

@article {pmid42326431,
year = {2026},
author = {Mei, X and Wu, W and Fang, N and Guo, Y and Dai, X},
title = {Sludge compost: a double-edged sword for depleted soil restoration revealed by integrated multi-omics analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1731456},
pmid = {42326431},
issn = {1664-302X},
abstract = {The prospective use of sludge compost for restoring depleted soils requires balancing its agronomic benefits against potential ecological risks. This study employed an integrated metagenomic and metabolomic approach to evaluate the dose-dependent effects of sludge compost on soil properties, maize growth, and rhizosphere microbial communities. Results showed that moderate compost application (≤15% w/w) enhanced soil nutrient availability, promoted root development, and enriched beneficial microbial taxa (Streptomyces, Mesorhizobium, Flavisolibacter), while upregulating plant stress-response metabolites (terpenoids, flavonoids). Conversely, excessive application (>20%) induced salinity stress, impaired root growth, and altered the microbial community, favoring thermophilic and xenobiotic-metabolizing taxa. Critically, high application rates led to the accumulation of residual pharmaceuticals (anti-neoplastic and anti-epileptic agents) and pesticides (insecticides and rodenticides), which correlated with the enrichment of microbial pathways associated with human diseases, highlighting a significant ecological risk. In addition, root integrity was the primary determinant of a sustainable plant-microbe feedback loop. These findings underscore the necessity for tailored application strategies to harness the soil-restorative potential of sludge compost while mitigating contaminant-driven risks, providing a framework for its safe use in sustainable agriculture.},
}

@article {pmid42326513,
year = {2026},
author = {Knight, R and Khatib, L and Patel, L and MahmoudianDehkordi, S and Labus, J and Agongo, J and Borkowski, K and Ambre, M and Brydges, C and Schimmel, L and Blach, C and Consortium, AGMP and Karu, N and Taylor, M and Diaz, E and Brosch, J and Bendlin, B and Swerdlow, R and Henderson, V and Chen, D and Saykin, A and Craft, S and Brewer, J and Wisniewski, T and Roberson, E and Dorrestein, PC and Kaddurah-Daouk, R},
title = {Interconnected influences of diet, gut microbiome, and metabolome on cognition across three metabolomics platforms.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9917711/v1},
pmid = {42326513},
issn = {2693-5015},
abstract = {Cognitive impairment is increasing with global aging, yet mechanisms linking diet, the gut microbiome, and metabolism to cognitive function remain unclear. To investigate a diet-microbiome-metabolome axis associated with cognition, we integrated fecal metagenomics, diet, and multi-platform plasma metabolomics in 505 older adults from four ADRCs. Several microbes broadly associated with circulating metabolites were also linked to multiple measures of cognitive performance. These taxa exhibited coordinated metabolic signatures, with cognition-positive microbes associated with antioxidant, lipid, and microbial-host co-metabolites, and microbes negatively associated with cognition were linked to inflammatory and aromatic amino acid-derived metabolites. Dietary patterns, particularly the Healthy Eating Index Greens and Beans component, were associated with microbial composition and metabolomic structure. Mediation analyses supported a diet-microbe-metabolite-cognition pathway, while metabolites remained associated with cognition after accounting for microbial features. These findings highlight the metabolome as a central integrator of diet, microbial activity, and cognitive function.},
}

@article {pmid42326540,
year = {2026},
author = {Yang, J and Nie, D and Zhang, Y and Li, C},
title = {Exploratory Pilot Multi-Omics Profiling of Gut Microbiota and Metabolic Features in Patients with Prolactinoma.},
journal = {Cancer management and research},
volume = {18},
number = {},
pages = {608026},
pmid = {42326540},
issn = {1179-1322},
abstract = {BACKGROUND: Growing evidence suggests a potential role of the gut microbiota in pituitary neuroendocrine tumors (PitNETs). This exploratory study focused on prolactinoma, the most prevalent PitNET subtype, to preliminarily characterize gut microbial and metabolic features associated with the disease.

MATERIALS AND METHODS: Fecal samples were collected from five patients with hyperprolactinemic prolactinoma and five patients with nonfunctioning (NF) PitNETs. Exploratory metagenomic and metabolomic analyses were performed to profile gut microbiota composition and metabolic alterations.

RESULTS: Compared with NF PitNET controls, prolactinoma patients showed distinct trends in gut microbial composition, including increased abundances of Bacteroides and Eubacterium and decreased abundances of Blautia and Clostridium. Metabolomic profiling identified differential metabolic features, including elevated fatty acid esters of hydroxy fatty acids (FAHFAs) and palmitoleic acid, which were mainly associated with glucose and lipid metabolism pathways.

CONCLUSION: This pilot multi-omics analysis provides preliminary evidence of altered gut microbiome-metabolite profiles in prolactinoma. These findings are hypothesis-generating and may support further investigation of gut-pituitary axis interactions in larger, well-powered cohorts.},
}

@article {pmid42326568,
year = {2026},
author = {Stacul, A and Valido, E and Nyfeler, N and Bertolo, A and Zeh, RM and Fontana, AO and Pannek, J and Krebs, J and Leichtle, A and Glisic, M and Stoyanov, J},
title = {Precision Rehabilitation in Spinal Cord Injury: A Systematic Review of Omics Applications for Intervention Monitoring in Spinal Cord Injury.},
journal = {Archives of rehabilitation research and clinical translation},
volume = {8},
number = {2},
pages = {100598},
pmid = {42326568},
issn = {2590-1095},
abstract = {OBJECTIVE: To systematically evaluate the application and utility of omics technologies, high-throughput methods measuring the complete or targeted set of molecules inside a biological system at a certain timepoint, in monitoring and optimizing rehabilitation interventions in traumatic spinal cord injury.

DATA SOURCES: Embase, Medline/Ovid, and Web of Science were searched from inception to November 27, 2024.

STUDY SELECTION: Eligible studies included adults (≥18 years) with spinal cord injury undergoing rehabilitation interventions assessed using omics technologies (genomics, epigenomics, transcriptomics, proteomics, metabolomics, or metagenomics).

DATA EXTRACTION: Following PRISMA guidelines, independent screening, data extraction, and risk of bias (RoB) assessment (National Institutes of Health Quality Assessment Tools) were performed by 2 investigators. Based on RoB assessment, studies were classified from level 1 (most reliable) to level 4 (least reliable).

DATA SYNTHESIS: Twenty-three trials were included: 8 randomized controlled trials, 5 non-randomized controlled trials, and 10 pre-post trials. Twenty-two studies (96%) exhibit a moderate RoB due to small sample size and heterogeneity. Omics technologies were primarily applied to exercise and electrical muscle stimulation interventions (65%), followed by hormonal and cellular therapies (22%), and diet (13%). Transcriptomic analyses revealed consistent molecular adaptations, including increased mitochondrial biogenesis (proliferator-activated receptor gamma coactivator 1-alpha) and reduced muscle atrophy gene expression (myostatin), correlating with enhanced insulin sensitivity and improved aerobic capacity. Metagenomics consistently identified microbiome shifts, such as decreased inflammatory taxa and increased beneficial taxa, associated with improved metabolic profiles and bowel function. Proteomics and metabolomics highlighted systemic changes related to neurorecovery, immune modulation, and sperm motility, linking molecular signatures directly to clinical outcomes.

CONCLUSIONS: Omics technologies enable early identification of molecular alterations. However, given small sample sizes and heterogeneity of the current studies, these findings should be interpreted with caution. Gradual integration of omics, particularly epigenomics which may capture long-term, injury-related changes holds promise for developing personalized rehabilitation protocols and monitoring clinical progression in spinal cord injury.},
}

@article {pmid42326740,
year = {2026},
author = {Avina-Bravo, EG and García-Lorenzo, I and Alfaro-Ponce, M and Breton-Deval, L},
title = {Machine learning-based classification of COVID-19 severity using respiratory microbiome profiles from shotgun metagenomic sequencing.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1801685},
pmid = {42326740},
issn = {2673-7647},
abstract = {Accurate clinical triage is critical for optimizing decision-making and resource allocation during infectious disease outbreaks such as COVID-19. In this study, we present an AI-driven decision-support tool for the triage of COVID-19 patients based on respiratory microbiome profiles derived from shotgun metagenomic sequencing. We analyzed 477 shotgun respiratory metagenomes from three independent public cohorts and generated genus-level taxonomic profiles, which were integrated with minimal clinical metadata (age, sex, and antibiotic exposure) to train supervised machine-learning models, including Random Forest, Support Vector Machine, and XGBoost. Model performance was evaluated using standard classification metrics, cross-validation, and particle swarm optimization for hyperparameter tuning. Across cohorts, we observed a consistent transition from microbiomes dominated by commensal taxa to dysbiotic states enriched in opportunistic and clinically relevant genera, particularly Acinetobacter and Staphylococcus, in severe and deceased patients. Among the evaluated models, XGBoost consistently achieved the best performance, reaching up to 96.1% accuracy, 97.6% F1-score, and 98.2% ROC-AUC in individual cohorts. When trained on the integrated dataset, XGBoost maintained robust performance (95.1% accuracy, 97.2% F1-score, 94.3% ROC-AUC) and demonstrated greater stability and lower variance compared to alternative models. Feature-importance analyses identified a compact and interpretable set of recurrent microbial predictors, and reduced-feature models retained substantial discriminative power when augmented with key clinical variables. These results support the respiratory microbiome as a valuable source of information for outcome-oriented clinical triage and position microbiome-informed machine learning as a scalable and interpretable decision-support approach for managing COVID-19 and future infectious disease scenarios.},
}

@article {pmid42326837,
year = {2026},
author = {Virwani, PD and Qian, G and Cheung, CN and Pijarnvanit, TKKTS and Hsu, MSS and Chow, YH and Tang, LK and Tse, YH and Xian, JW and Lam, SS and Lee, CPI and Lo, CCW and Liu, RKC and Ho, TL and Chow, BY and Leung, KS and Lo, EKK and Yuen, MF and Leung, SY and Hung, IF and Louie, JCY and Teo, KC and El-Nezami, H and Ho, JWK and Lau, KK},
title = {Associations between gut microbiome and 24-hour blood pressure variability: a cross-sectional study highlighting sex differences and potential therapeutic targets.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e9},
pmid = {42326837},
issn = {2632-2897},
abstract = {Blood pressure (BP) variability is an independent risk factor for cardiovascular disease. Gut microbiome (GM) regulates BP, but its association with BP variability remains unclear. We examined the association of GM, determined by stool shotgun metagenomic sequencing, with 24-hour BP average real variability (ARV) assessed by ambulatory BP monitoring in 235 community-dwelling adults from Hong Kong (111 men and 124 women, mean age 54 ± 6 years) using covariate-adjusted statistical models. The GM alpha diversity was negatively associated with systolic BP (SBP) ARV in the full cohort, driven by women. In men, beta diversity of both GM species and function was associated with SBP ARV, while Bacteroides nordii and the steroid hormone biosynthesis pathway had a positive association with SBP ARV. Bacteroides nordii emerged as the key species driving the significant positive association of steroid hormone biosynthesis and other pro-pathogenic pathways with SBP ARV, including lipopolysaccharide biosynthesis, phenylalanine, and sulfur metabolism in men, warranting further investigation for its causal role. We demonstrated distinct signatures of GM dysbiosis, composition, and function with minimal overlap between men and women with increased 24-hour SBP variability. Our work suggests that sex differences should be an important consideration in mechanistic and therapeutic investigations of GM-mediated BP variability.},
}

@article {pmid42327082,
year = {2026},
author = {Loya, O and Villarreal, ES and Carneiro, A and Agarwal, S and Fraidenburg, D and Sun, J and de Jesus Perez, V and Lahm, T and Oliveira, SD},
title = {Sex-linked Lung Estrobolome May Contribute to Pulmonary Hypertension Penetrance of Bmpr2 R899X Mutation via an ET-1 [high] Endoregulatory Macrophage Phenotype.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.08.729693},
pmid = {42327082},
issn = {2692-8205},
abstract = {Mutations in the bone morphogenetic protein receptor 2 (BMPR2) are a major genetic driver of pulmonary arterial hypertension (PAH), yet their penetrance is strikingly sex-biased: females are disproportionately affected, while males experience poorer outcomes. While hormonal and chromosomal factors have been implicated, the biological basis for this disparity remains not fully understood. Here, we investigated the role of the lung microbiome in sex-linked PAH pathogenesis. We hypothesized that increased BMPR2 mutation penetrance in females is partly driven by the accumulation of potent vasoactive molecules, such as endothelin-1 (ET-1), in response to lung microbiome dysbiosis. Using humanized Bmpr2 [+/R899X] mice, we integrate lung metagenomics with basic functional immune profiling to show that females develop a distinct microbiome profile, characterized by increased microbial-derived lipopolysaccharide (LPS), potentially fueling the pathogenic effects of the estrogen metabolite 16α-hydroxyestrone (16α-OHE). These signals converge on macrophages, where co-exposure led to a hyperactivated state characterized by enhanced phagocytosis and ET-1 secretion. Tissue-level analyses confirmed immune cell infiltration and spatial association with elevated ET-1, providing evidence that these factors may contribute to the onset of sex-linked PAH. Taken together, these findings identify a previously unrecognized microbiome-estrogen-immune axis that amplifies BMPR2 dysfunction and provides a mechanistic basis for female-biased disease penetrance.},
}

@article {pmid42327127,
year = {2026},
author = {Troman, L and Kim, J and Rose, JJA and Johnson, M and Banfield, JF and Petrovski, S and Ghosal, D},
title = {A Novel Pilus System in Candidate Phyla Radiation Bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.03.709456},
pmid = {42327127},
issn = {2692-8205},
abstract = {The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15-50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primarily identified through metagenomic approaches. Candidatus Mycosynbacter amalyticus is a parasitic CPR bacterium that specifically targets Gordonia amarae , an actinobacterium with a hydrophobic, mycolic acid-rich cell envelope. Previous cryo-electron tomography indicated that Ca . M. amalyticus assembles thin extracellular filaments that are important for host interaction, yet their molecular identity remains unknown. Here, we applied single-particle cryo-electron microscopy to determine high-resolution structures of these filaments (2.8 and 3.6 Å), enabling the unambiguous identification of two previously uncharacterized pilins from the experimental density maps. These pilins, designated PamA and PamB, assemble into unique helical filaments distinct from all previously characterized filaments in both domain architecture and assembly mechanism. Despite low sequence identity, both PamA and PamB share conserved structural principles, including Ig-like folds and donor-strand exchange-mediated assembly. Phylogenetic analysis indicates that Pam pilins are exclusive to CPR bacteria, with homologues distributed predominantly across the classes Saccharimonadia and Microgenomatia. Analysis of the conserved pam operon identifies putative chaperones (PamC and PamD) and assembly factors structurally homologous to chaperone-usher pili components, suggesting an analogous but distinct assembly pathway. These findings expand the known diversity of bacterial pilus systems and demonstrate the power of structural approaches for characterizing uncharacterized proteins encoded within CPR genomes.},
}

@article {pmid42327471,
year = {2026},
author = {Li, YM and He, FF and Donge-Liu, and Bin-Xu, and Shuyi-Li, },
title = {Multi-Omic Profiling of Gut Microbiota and Fecal Metabolites in Patients With Polycystic Ovary Syndrome: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {9},
number = {6},
pages = {e72593},
pmid = {42327471},
issn = {2398-8835},
abstract = {BACKGROUND AND AIM: Intestinal flora composition in polycystic ovary syndrome (PCOS) varies, and the relationship between intestinal flora, fecal metabolites, clinical characteristics, and PCOS pathogenesis remains unclear. This study aimed to elucidate the gut microbiota characteristics of patients with PCOS, focusing on changes in normal-weight individuals, to provide new insights into its pathogenesis.

METHODS: We combined 16S rRNA gene sequencing re-analysis with metagenomics and metabolomics to investigate gut microbiota and fecal metabolome alterations in PCOS. We re-analyzed our previous data on normal-weight women with PCOS (PCOS, n = 24; healthy controls [HC], n = 12) and the public databases (PCOS, n = 98; HC, n = 71) to further investigate the structure and function of the PCOS intestinal flora. Subsequently, from our previous study samples, we selected 10 patients residing in the Kaifu district, and their fecal samples (normal-weight PCOS group, n = 6; HC group, n = 4) were analyzed using metagenomic sequencing and non-targeted fecal metabolomics. Finally, the correlations among intestinal flora, fecal metabolites, and clinical indicators were evaluated.

RESULTS: Based on the 16S rRNA data reanalysis, there were no significant differences in beta and alpha diversity between PCOS and normal controls. However, the PCOS group displayed a significantly higher relative abundance of Ruminococcus, Lachnospiraceae, and Escherichia-Shigella (p < 0.05) but a significantly lower relative abundance of Prevotella (p < 0.05) compared with the HC group. Subsequent metagenomics and metabolomics analyses revealed functional alterations, particularly in pathways related to secondary bile acid and lipid metabolism. Furthermore, Ruminococcus and Roseburia were positively correlated with Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) and negatively correlated with high-density lipoprotein (HDL) in patients with normal-weight PCOS.

CONCLUSIONS: This study highlights gut microbial dysbiosis as a key feature of PCOS. Reanalysis of 16S rRNA data revealed specific taxonomic shifts without altering overall diversity, notably an enrichment of Ruminococcus and a depletion of Prevotella. Furthermore, our metagenomics study identified functional reprogramming in pathways related to secondary bile acid and lipid metabolism. Crucially, even in normal-weight PCOS patients, these microbial alterations significantly correlated with adverse metabolic profiles (heightened insulin resistance and lower HDL levels), highlighting the microbiome as a potential therapeutic target.

ETHICAL REVIEW NO: CHiECRT1900028223.},
}

@article {pmid42327525,
year = {2026},
author = {Maity, H and Hiwale, K and Meshram, S and Shishodiya, M and Pratyeke Maraskolhe, D and Narang, P},
title = {Zoonotic Nontuberculous Mycobacteria: Transmission Pathways, Laboratory Diagnosis, Detection Methodologies, and One Health Priorities.},
journal = {Infectious diseases & clinical microbiology},
volume = {8},
number = {3},
pages = {232-252},
pmid = {42327525},
issn = {2667-646X},
abstract = {Nontuberculous mycobacteria (NTM) are an ecologically diverse group of environmental mycobacteria that are increasingly recognized as an important cause of human and animal disease. While most infections arise from environmental exposure, evidence from outbreak reports and genomic epidemiology suggests animal- associated and device-associated transmission pathways that intersect with human occupational and clinical risk. This review synthesizes current knowledge on zoonotic and animal-associated NTM, including recent taxonomy updates driven by genomic approaches, major reservoirs (including aquaculture, livestock, wildlife, and engineered water systems), as well as clinical and veterinary manifestations, and operational laboratory approaches for detection and characterization. We present a tiered diagnostic framework, ranging from microscopy and culture to targeted polymerase chain reaction (PCR), whole-genome sequencing, and emerging metagenomic and artificial intelligence (AI)-based pipelines, and we discuss biosafety considerations, reporting standards, and One Health surveillance priorities. Key research gaps include distinguishing true animal-to-human transmission from shared-source exposure, harmonizing One Health metadata and antimicrobial resistance (AMR) surveillance, and validating climate-sensitive predictive models. We propose practical, resource-adaptive recommendations for surveillance, laboratory workflows, and outbreak response. A coordinated global investment in integrated One Health genomic surveillance, harmonized metadata standards, and capacity building is urgently required to detect, attribute, and mitigate zoonotic NTM threats.},
}

@article {pmid42327630,
year = {2026},
author = {Katarzyna, BS and Danuta, CL and Wiktoria, K and Małgorzata, T and Natalia, K and Dominika, MM and Karina, R and Joanna, P and Karina, K and Barbara, G and Danuta, LK and Helena, G and Wiśniewska, M and Karolina, SŻ and Stachowska, E},
title = {The impact of freeze-dried food on gut microbiota composition: a preliminary study.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101470},
pmid = {42327630},
issn = {2665-9271},
abstract = {Freeze-dried food is widely used during space expeditions or flights. However, evidence on how this affects the gut microbiota is limited. This study aimed to assess changes in the composition of gut microbiota in volunteers subjected to a 14-day stay in a controlled space-analogue habitat. Five adults provided stool samples at baseline and after two weeks. Meals were freeze-dried and standardized for portion size and composition. Meals were served according to a daily schedule with no additional snacks allowed. Coffee and tea were permitted. Compliance was monitored by returning and verifying the packaging. Bacterial community profiles were assessed using shallow shotgun metagenomics and analyzed using paired statistical methods, including alpha diversity indices and beta diversity ordination with permutation-based testing. Differential abundance analyses were performed to identify taxa showing trends toward change during the intervention. Overall gut bacterial diversity and community structure were essentially stable over 14 days among all participants. No statistically significant changes in alpha diversity were observed, and global beta diversity patterns did not indicate a consistent separation of the entire community between baseline and day 14. Exploratory analyses suggested small changes within individuals in the relative abundance of selected taxa; however, inter-individual variability prevailed, and the small sample size limited statistical power. It appears that a diet consisting entirely of freeze-dried foods, consumed for 14 days, did not significantly affect the overall diversity of the gut microbiota or the structure of its communities. However, these studies are preliminary in nature and provide hypotheses for use in larger, controlled studies aimed at elucidating the microbiome's response to dietary regimens based on freeze-dried products.},
}

@article {pmid42328576,
year = {2026},
author = {Wu, Y and Gao, Y and Fang, Z and Huang, W and Guo, F},
title = {Time-dependent microbiology of peripancreatic drainage fluid in severe acute pancreatitis: a prospective real-world observational study using metagenomic sequencing and culture.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1795250},
pmid = {42328576},
issn = {2296-858X},
abstract = {OBJECTIVE: The microbiological characteristics of peripancreatic collections in severe acute pancreatitis (SAP) evolve over time, yet prospective data linking pathogen detection to disease timing and first intervention remain limited.

METHODS: This prospective single-center observational study enrolled 20 patients with SAP undergoing first-time percutaneous catheter drainage (PCD) for suspected infected pancreatic necrosis (IPN). Peripancreatic drainage fluid samples were simultaneously analyzed by conventional microbiological culture and metagenomic next-generation sequencing (mNGS). Microbiological positivity rates were compared according to time from disease onset (≤14 vs. >14 days).

RESULTS: Overall, mNGS was positive in 9/20 cases (45.0%) and conventional culture in 6/20 cases (30.0%). When stratified by time from disease onset, microbiological positivity was low within 14 days (mNGS: 1/7, 14.3%; culture: 1/7, 14.3%), but increased in patients undergoing drainage beyond 14 days (mNGS: 8/13, 61.5%; culture: 5/13, 38.5%). mNGS identified a broader spectrum of pathogens, particularly polymicrobial, anaerobic, and fungal organisms. Enterococcus species and Klebsiella pneumoniae were the most frequently detected pathogens.

CONCLUSION: In this prospective observational cohort, peripancreatic collections were predominantly culture- and mNGS-negative during the early phase of SAP, supporting the concept that early necrosis is commonly sterile. In later stages, mNGS provides complementary microbiological information beyond conventional culture. These findings offer descriptive real-world evidence on the time-dependent microbiology of suspected IPN and may inform future studies on optimized diagnostic and antimicrobial strategies.},
}

@article {pmid42328632,
year = {2026},
author = {Alnasser, SM and Ravikumar, S and Jayaraman, S and Selvaraj, D and Gunasekaran, V},
title = {Modulatory effect of porous silicon water-formulated catechin on gut microbiome in chronic unpredictable mild stress-induced dementia in a rat model.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1778580},
pmid = {42328632},
issn = {1663-9812},
abstract = {Stress-induced dysbiosis exacerbates mental health by modulating the nervous system and gut permeability. In this study, we investigate the therapeutic potential of porous silicon water-mixed catechin in alleviating chronic stress-induced dementia in rats. In a 28-day study, chronic unpredictable mild stress (CUMS)-induced rats were treated with Lactobacillus acidophilus (2.5 × 10^9 CFU, p.o), porous silicon water (7 mg/kg, p.o), catechin (30 mg/kg, p.o), and porous silicon water-mixed catechin (PSC) (7 mg and 30 mg/kg, p.o). The effect of porous silicon water-mixed catechin was evaluated through behavioral studies, plasma acetylcholinesterase activity, plasma glutamate, brain reactive oxygen species (ROS), brain endogenous anti-oxidant enzymes, metagenomics analysis, and histological examination of the prefrontal cortex and hippocampus. Administration of PSC significantly improved spatial learning and memory by reducing escape latency time and increased exploratory behavior in the open platform. PSC significantly inhibited acetylcholinesterase enzyme activity and restored endogenous antioxidants such as superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GSH) while reducing lipid peroxidation (LPO) compared to the CUMS group. In addition, PSC decreased the brain ROS levels, as determined by a fluorescence assay, and reduced plasma glutamate levels. 16S rRNA V3-V4 metagenomic analysis revealed a significant increase in microbial diversity (Shannon index: 7.52), microbial richness (Chao1 index: 1059.41), β-diversity index, and overall taxonomic abundance in treated rats. CUMS-induced morphological alterations in the hippocampus and prefrontal cortex were significantly improved following PSC administration. In the present study, Pearson correlation coefficient (r) demonstrates an association between gut microbial abundance and AChE activity. Hence, it has been concluded that PSC treatment may significantly modulate the gut microbiome and improve cognition in chronic unpredictable mild stress-induced dementia.},
}

@article {pmid42328867,
year = {2026},
author = {Wang, Y and Sheng, P and Wang, S and Zhong, X and Cao, H and Li, D and Yan, J and Yang, J and Wang, Y and Peng, J and Sun, F and Wang, S and Feng, Y and Sun, J and Zhang, F},
title = {Gut microbiota translocation contributes to early islet apoptosis in streptozotocin-induced diabetes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0017226},
doi = {10.1128/msystems.00172-26},
pmid = {42328867},
issn = {2379-5077},
abstract = {Dysbiosis of the gut microbiota and impaired intestinal barrier are associated with diabetes development. The translocation of gut microbiota induced by streptozotocin (STZ) has been confirmed to damage pancreatic islets. However, it remains uncertain whether dysregulated gut microbiota plays an essential role in the translocation leading to pancreatic injury. In specific pathogen-free (SPF) and germ-free (GF) mice treated with STZ, we measured glucose metabolism levels, pancreatic islet damage, intestinal barrier integrity, and bacterial content in the pancreas to investigate the role of gut microbiota translocation in diabetes development. Shotgun metagenomic sequencing was used to analyze the impact of STZ on gut microbiota structure and function. Fecal microbiota transplantation was performed to explore if gut microbiota translocation depends on STZ-induced structural dysregulation. STZ induced intestinal damage in SPF mice, resulting in gut microbiota translocation to the pancreas, pancreatic apoptosis, and dysregulated glucose metabolism. Despite inherent intestinal barrier damage, absence of pancreatic apoptosis in GF mice further indicates that gut microbiota translocation is an essential prerequisite for STZ-induced pancreatic islet apoptosis. STZ significantly altered mouse gut microbiota composition and function. Transplantation of fecal microbiota from STZ-treated or saline-treated mice into STZ-induced GF mice also resulted in microbial translocation and pancreas apoptosis. Apoptosis of β cells in STZ-treated mice results from gut microbiota translocating to the pancreas through impaired intestinal barrier caused by STZ treatment independent of alterations in the gut microbial community.IMPORTANCEIn our study, the apoptosis of β cells in STZ-treated mice is the result of the translocation of gut microbiota to the pancreas through the impaired intestinal barrier induced by STZ, independent of alterations in the gut microbiota. These findings proposed the potential role of compounds in impairing the intestinal barrier integrity, promoting microbiota migration and finally damaging pancreatic islets.},
}

@article {pmid42328985,
year = {2026},
author = {Pallotti, S and Nigro, ME and Albini, E and Russo, E and Carpi, FM and Falconi, M and Torbidoni-Baldassari, B and Giuliodori, AM and Petrelli, D and Beccacece, L and Pezzotti, G and Magistrali, CF and Massacci, FR and Napolioni, V},
title = {Long-read metagenomics reveals stable resistome and microbiome in treated Italian slaughterhouse wastewater: a preliminary study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156226},
doi = {10.1128/spectrum.01562-26},
pmid = {42328985},
issn = {2165-0497},
abstract = {Antimicrobial resistance (AMR) poses a major threat to global health, and food production environments are increasingly recognized as potential reservoirs and dissemination points for resistant bacteria and antimicrobial resistance genes (ARGs). Slaughterhouse wastewater contains complex microbial communities originating from multiple animal sources and processing activities, yet the effectiveness of current treatment processes in mitigating microbiological and resistome-associated risks remains poorly understood. In this study, we applied high-throughput long-read metagenomic sequencing to characterize microbial community composition and resistome profiles in wastewater samples collected before and after physicochemical treatment from four Italian slaughterhouses. Taxonomic profiling revealed a diverse microbiome dominated by Bacillota and Pseudomonadota, along with DNA assigned to potentially clinically relevant taxa, including members of the ESKAPE group. Resistome analysis identified 96 ARGs conferring resistance to 16 antimicrobial classes. Comparative analyses of pre- and post-treatment samples showed no significant changes in microbial community structure, alpha- and beta-diversity metrics, or ARG profiles. These findings indicate that the applied coagulation-flocculation-based treatment has limited effects on the relative composition of the wastewater microbiome and resistome, as detected by shotgun metagenomics. Our results suggest that slaughterhouse wastewater may act as a persistent environmental reservoir of antimicrobial resistance determinants and highlight the need for enhanced treatment strategies and resistome-oriented surveillance within a One Health framework. Given the limited sample size and the preliminary nature of this investigation, these findings should be interpreted as exploratory and hypothesis-generating, rather than broadly generalizable.IMPORTANCEAntimicrobial resistance is a growing global health concern that extends beyond clinical settings into agricultural and environmental systems. Slaughterhouses represent critical interfaces where microbial communities from livestock, processing environments, and wastewater converge, creating opportunities for the persistence and dissemination of antimicrobial resistance genes. Despite the widespread use of physicochemical treatments to reduce organic load and suspended solids in slaughterhouse wastewater, their impact on microbial communities and resistome remains poorly characterized. By applying long-read metagenomic sequencing, this study provides a comprehensive characterization of the microbiome and resistome in slaughterhouse wastewater before and after treatment. Our findings show that commonly applied coagulation-flocculation treatments do not substantially alter the relative structure of microbial communities or the diversity of resistance genes. These results highlight the potential role of slaughterhouse wastewater as an environmental reservoir for antimicrobial resistance and emphasize the need for improved treatment technologies and systematic surveillance strategies to mitigate the environmental dissemination of resistance determinants in line with the One Health approach.},
}

@article {pmid42329047,
year = {2026},
author = {Villanelo, SAR and Vestergaard, SZ and Liu, L and Yang, Y and Pedersen, IS and Nielsen, PH and Dueholm, MKD},
title = {Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0147726},
doi = {10.1128/spectrum.01477-26},
pmid = {42329047},
issn = {2165-0497},
abstract = {The microbial communities in activated sludge (AS) drive pollutant degradation and nutrient transformation into biomass and gaseous products, while also enabling resource recovery processes. In these systems, microorganisms grow as flocs, whose aggregation properties are essential for retaining active biomass while producing a clarified effluent. Understanding the microbial composition of AS and the functions of individual taxa is crucial for improving wastewater treatment practices and developing new treatment technologies. Although DNA-based studies have identified abundant taxa and inferred their metabolic roles, many of these organisms remain uncultured, limiting experimental validation of genome-based predictions. Here, we investigated whether antibiotics can transiently reduce community complexity and alleviate competitive exclusion during cultivation, thereby facilitating isolation of previously uncultured activated sludge bacteria. Dispersed single cells from AS were cultivated on agarose plates containing filter-sterilized AS fluid and 1 of 11 antibiotics at three concentrations. Full-length 16S rRNA gene amplicon sequencing indicated that antibiotics reduced microbial diversity and altered community composition in an antibiotic- and concentration-dependent manner. Two antibiotic conditions were selected for pure-culture isolation, resulting in 74 isolates that represented 28 different species based on genomic average nucleotide identity. These include 13 putatively novel species based on GTDB classification, and 19 species belonging to nine globally abundant AS core genera. Although several isolates belonged to genera with cultured representatives, they likely represent distinct species with potentially different ecological functions and physiological traits. These findings demonstrate that antibiotics can function as ecological selectors during cultivation and aid the targeted isolation of ecosystem-relevant activated sludge bacteria.IMPORTANCEBiological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.},
}

@article {pmid42329229,
year = {2026},
author = {Yao, C and Wang, Y and Zhou, J and Liu, B and Qi, L and Wang, B and Chen, F and Hou, L and Liu, M and Zheng, Y},
title = {Acidification Dominates over Hypoxia in Controlling Estuarine Nitrogen Removal Dynamics under Coupled Stressors.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02533},
pmid = {42329229},
issn = {1520-5851},
abstract = {As critical transitional zones between land and sea, estuaries are confronting the dual threats of increasing acidification and hypoxia driven by human activities and climate change. However, the combined effects of these stressors on estuarine nitrogen removal processes remain poorly understood. In this study, using stable-isotope tracing and molecular techniques in the Yangtze estuary, we found that hypoxia promoted N removal, yet concurrent acidification can override this effect, leading to net inhibition and a consequent reduction in estuarine nitrogen removal capacity. However, in seasonally hypoxic zones, these combined stressors generally enhanced nitrogen removal rates (by up to 34.4%), which suggests a degree of resilience under such perturbations. Nevertheless, the concurrent acidification-hypoxia in seasonally hypoxic areas stimulated N2O emissions (8.5-44.4%), which may intensify climate forcing and thereby further exacerbate these environmental stressors. Metagenomic and quantitative PCR analyses corroborated these response patterns, revealing coordinated changes in the abundance and expression of key nitrogen-removal genes, as well as divergent microbial response strategies and niche differentiation under acidification-hypoxia stress. This study elucidates the previously overlooked interactive effects of acidification and hypoxia on estuarine nitrogen removal, providing a mechanistic basis for refining biogeochemical models to improve the reliability of simulations under multiple stressors.},
}

@article {pmid42329244,
year = {2026},
author = {Gallichan, S and Mäklin, T and Picton-Barlow, E and McKeown, C and Forrest, S and Corander, J and Moore, M and Feasey, NA and Heinz, E and Graf, FE and Lewis, JM},
title = {A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producing Escherichia coli using post-enrichment metagenomics.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001757},
pmid = {42329244},
issn = {2057-5858},
mesh = {*Escherichia coli/genetics/enzymology/isolation & purification ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Polymorphism, Single Nucleotide ; Humans ; Escherichia coli Infections/microbiology/transmission ; Feces/microbiology ; Genome, Bacterial ; Whole Genome Sequencing ; Metagenome ; },
abstract = {Inferring transmission relies on accurately distinguishing between isolates from the same source and those from different sources, and high-quality genomic data are frequently used to model transmission scenarios. The post-enrichment metagenome sequencing (pe-MGS) method uses a sequencing approach to analyse the diversity of a target pathogen enriched by pre-culturing and has been effectively used to analyse the transmission of nosocomial infections. However, a direct comparison of single nucleotide variant (SNV) call accuracy, cost and feasibility between single-colony whole-genome sequence (sc-WGS) data and pe-MGS for an antimicrobial resistant bacteria of clinical importance, extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC), is required for implementation in large-scale clinical studies. A spiked stool sample and rectal swabs from six study participants were pre-enriched in buffered peptone water and cultured on MacConkey agar with 1 mg l[-1] cefotaxime. Seven single colonies were picked, and the remaining biomass of all colonies was collected from each plate, sequenced and analysed using the mSWEEP/mGEMS pipeline. We created a custom SNV calling workflow that allows heterozygous SNVs in a bacterial population and found that the choice of reference changed the number of measurable SNV distances between the sc-WGS and pe-MGS. Using our custom workflow with a core-gene reference captured 99% of all the SNV calls from multiple sc-WGS data in the pe-MGS data of the same culture. The plate sweep method offers a feasible, cost-effective alternative to multiple single colony picks for describing within-host ESBL-EC diversity. The workflow we developed allows for effective SNV calling from pe-MGS data that were comparable to SNV calls from multiple sc-WGS data from the same sample.},
}

*Escherichia coli/genetics/enzymology/isolation & purification
*beta-Lactamases/genetics/metabolism
*Metagenomics/methods
*Polymorphism, Single Nucleotide
Humans
Escherichia coli Infections/microbiology/transmission
Feces/microbiology
Genome, Bacterial
Whole Genome Sequencing
Metagenome

@article {pmid42330062,
year = {2026},
author = {Mason, CJ and Weaver, M and Kissinger, KR and Johnson, MA and Copeland, DC and Anderson, KE and Geib, SM},
title = {Applying PCR cycle autonormalization to PacBio full-length 16S rRNA library preparations: impacts on error rates and sequence distributions.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0029526},
doi = {10.1128/msphere.00295-26},
pmid = {42330062},
issn = {2379-5042},
abstract = {The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, errors introduced during library preparation remain a major limitation, particularly during PCR amplification of full-length amplicons, where error accumulation may be elevated due to longer sequence lengths. These challenges are amplified when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated PCR cycle autonormalization for PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional fixed-cycle PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Under the workflow tested here, autonormalized libraries generally retained a high proportion of sequences following denoising and chimera removal, exhibited low residual error rates (<0.005%), and yielded relatively even read distributions across heterogeneous sample inputs. Overamplified reactions (30 cycles) showed elevated residual error rates and greater sequence loss, particularly in samples with higher microbial biodiversity, whereas low-cycle libraries produced more variable read output among specimens. Importantly, the PCR protocol had relatively minor effects on overall community composition compared with specimen type. These results support PCR cycle autonormalization as a useful workflow strategy for heterogeneous full-length 16S library preparation, while also highlighting the importance of library design, pooling strategy, and downstream processing in shaping technical outcomes.IMPORTANCEAmplicon-based sequencing of the 16S rRNA gene is a foundational tool in microbiome research, yet PCR amplification remains a major source of library-preparation error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can underamplify low-biomass samples or overamplify high-titer samples, increasing artifacts and sequence loss during downstream processing. Here, we show that PCR cycle autonormalization can be integrated into a PacBio full-length 16S rRNA workflow and, under the conditions tested, provides low residual error rates and relatively even sample representation across heterogeneous inputs. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale library preparation applications handling diverse specimen types.},
}

@article {pmid42330763,
year = {2026},
author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH},
title = {Dietary polyphenols from shredded, steam-exploded pine particles mitigate the adverse effects of heat stress in broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107298},
doi = {10.1016/j.psj.2026.107298},
pmid = {42330763},
issn = {1525-3171},
abstract = {The current study investigated the impact of supplementing polyphenols extracted from shredded, steam-exploded pine particles (PSPP) on the performance, gene expression, and gut metagenome of broilers exposed to cyclic heat stress (CHS). A total of 216 chickens were distributed into a 2 (temperature) by 3 (diets) design, with each treatment consisting of six replicates of six chickens. Specifically, chickens were fed diets containing 0% PSPP, 0.5% PSPP, and 1% PSPP and exposed to two temperature conditions: CHS (31°C) and Thermoneutral (NT, 21°C). The CHS was conducted for 6 hours every day for 7 consecutive days. Final body weight, average daily gain, and average daily feed intake (ADFI) were decreased, while feed conversion ratio and rectal temperature were increased in heat-exposed chickens. Dietary PSPP supplementation enhanced ADFI. The weight of the liver, bursa, and length of the jejunum and ileum were decreased in heat-exposed chickens. Plasma cholesterol was increased, and triglycerides were decreased in heat-exposed chickens. After heat exposure, gene expression of ZO1, ZO2, GLP2, NOX1, SOD, GPX, HSP70, HSP90, NRF2, TLR2, and TLR4 increased in the jejunum. GLP2 gene expression was similar in 1%PSPP exposed to HS in comparison to the entire NT-exposed chickens. Concerning microbiota analysis, alpha diversity indices, such as Shannon and Gini-Simpson, were increased following CHS exposure. Beta diversity, measured through unweighted and weighted UniFrac distances, showed temperature, dose, and interaction effects. The relative abundance of the phylum Candidatus Melainabacteria was increased, while Tenericutes populations were decreased in heat-exposed chickens. Furthermore, a total of thirty genera were identified as microbial biomarkers of CHS. Interestingly, the relative abundance of five pathogenic bacterial genera was found to be decreased in the 0.5%PSPP treatment. Overall, CHS negatively influences growth performance, modulates the expression of the gut antioxidant-related genes, and favors the colonization of pathogenic bacteria. However, 0.5% PSPP may mitigate CHS by reducing pathogen colonization in the gut of broilers.},
}

@article {pmid42330797,
year = {2026},
author = {Gebert, JT and Huleatt, EM and Scribano, FJ and Eledge, MR and Dorn, LE and Hasmi, SK and Hyser, JM},
title = {High-throughput quantitation of pathogen-induced calcium signals captured through live-cell fluorescence microscopy.},
journal = {Cell calcium},
volume = {136},
number = {},
pages = {103160},
doi = {10.1016/j.ceca.2026.103160},
pmid = {42330797},
issn = {1532-1991},
abstract = {Many intracellular pathogens manipulate host cell calcium to facilitate their survival and replication. Live-cell microscopy using fluorescent calcium indicators has become an indispensable tool for characterizing the mechanisms underlying both homeostatic and pathogen-induced cellular calcium dynamics, but such imaging must be coupled with robust quantitative analysis. Further, calcium imaging is most powerful when paired with reductive studies targeting calcium-modulating proteins. The lack of specific inhibitors or agonists to directly target most pathogen-induced calcium signals precludes many of the approaches that have allowed for robust characterization of major eukaryotic cell calcium signaling mechanisms, such as ER Ca[2+] release by inositol triphosphate receptors. Given this, we sought to develop quantitative imaging pipelines tailored for the characterization of pathogen-induced calcium signals. Using rotavirus as a prototypical calcium-modulating pathogen, we developed and optimized a suite of computational tools for automated quantitation of both intra- and inter-cellular calcium signals detected via live-cell imaging of infected epithelial monolayers expressing genetically encoded calcium indicators. Using recombinant strains of rotavirus that express fluorescent markers, we developed a system that allows for automated detection of rotavirus-infected cells and normalization of signals to infectivity. All tools were built in ImageJ, making them freely available and adaptable across operating systems and microscope setups. These tools required minimal active time from the user and allowed for the extraction of signal parameters previously unquantifiable, increasing the speed and breadth of characterization.},
}

@article {pmid42330834,
year = {2026},
author = {Cabrera, C and Carrión, N and Mateo, D and Heredia, L and Pino, M and Galvez, S and Forcadell-Ferreres, E and Vicens, P and Torrente, M},
title = {Shotgun metagenomic profiling of the gut microbiota in Parkinson's disease dementia and dementia with Lewy bodies.},
journal = {Parkinsonism & related disorders},
volume = {149},
number = {},
pages = {108400},
doi = {10.1016/j.parkreldis.2026.108400},
pmid = {42330834},
issn = {1873-5126},
abstract = {BACKGROUND: Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are related α-synucleinopathies that share Lewy pathology, but they differ clinically. Increasing evidence links gut microbiota (GMB) dysbiosis and microbially derived metabolites to Parkinsonian disorders yet reported associations remain heterogeneous across cohorts and the Lewy body dementia syndromes are comparatively under characterized. This study integrated clinical characterization and GMB profiling in Parkinson's disease dementia (PDD), DLB, and healthy controls (HC) to identify shared and syndrome specific features, and to relate these patterns to cognitive, neuropsychiatric, and functional outcomes.

METHODS: The present cross-sectional case-control study in Spain included 76 adults aged 60 to 85 years (HC = 38, PDD = 27, DLB = 11). Stool samples underwent shotgun metagenomic sequencing, with species-level taxonomic profiling using Kraken2. Community diversity was assessed using observed species and Chao1 richness, Shannon alpha diversity, and Bray-Curtis dissimilarity for beta diversity. LEfSe and multivariate linear modeling with MaAsLin2 were performed to identify GMB species associated with PDD and DLB and their clinical correlates.

RESULTS: PDD showed higher richness compared with HC. Shannon alpha diversity did not differ between groups. Bray-Curtis differed by separation of HC from both PDD and DLB, with no significant difference between Lewy body dementia syndromes. LEfSe identified 19 significantly differential taxa. Furthermore, several taxa showed significant multivariable associations with clinical outcomes.

CONCLUSIONS: PDD and DLB shared a broadly similar GMB alteration away from HC, with multivariable associations between several taxa and clinical outcomes. Longitudinal and functional studies are needed to clarify causality and biomarker potential.},
}

@article {pmid42330882,
year = {2026},
author = {Li, X and Wang, W and Liu, Y and Xu, Z and Wang, M and Zhao, J and Hua, Y},
title = {Role of nitrate-dependent Fe(II)-oxidizing bacteria in coupling nitrogen and phosphorus cycling in nearshore sediments of shallow lakes.},
journal = {Water research},
volume = {304},
number = {},
pages = {126323},
doi = {10.1016/j.watres.2026.126323},
pmid = {42330882},
issn = {1879-2448},
abstract = {The nearshore shallow-water zones of lakes serve as critical interfaces for the interception and transformation of land-derived nitrogen and phosphorus pollutants. Nitrate-dependent Fe(II)-oxidizing bacteria (NDFOB) may promote the formation of Fe(III) (hydr)oxides through nitrate reduction and Fe(II) oxidation, thereby potentially enhancing the adsorption of phosphorus in pore water and coupling of nitrogen removal and phosphorus immobilization; however, their ecological role in shallow lakes remains poorly understood. This study focused on six shallow lakes, analyzing the relationships between most probable number (MPN) counts of NDFOB, nitrogen, iron, and phosphorus contents, and using metagenomic techniques to explore their associations with functional genes involved in nitrogen, iron, and phosphorus cycling. The results showed that the number and spatial distribution of NDFOB were associated with lake trophic status. In moderately eutrophic lakes, elevated nitrogen loads were correlated with NDFOB enrichment possibly due to the provision of abundant electron acceptors (NO3[-]) for nitrate-dependent Fe(II) oxidation, and NDFOB number was positively correlated with nitrogen concentrations and negatively correlated with phosphorus content in pore water. Meanwhile, it was also associated with relative abundances of iron reduction-related genes and the presence of iron oxidation-associated genes. Network analysis further provided statistical clues for putative functional links between the ferrous iron oxidation process linked to NDFOB genera (e.g., Aquabacterium) and iron reduction, denitrification, and organic phosphorus mineralization. This study highlights the potential role of NDFOB in intercepting nitrogen and phosphorus within nearshore sediments and provides a microbial perspective for mitigating the risk of internal phosphorus release in shallow lakes.},
}

@article {pmid42330901,
year = {2026},
author = {Barbe, V and Saint-Picq, C and Odobel, C and Hingant, M and Pujo-Pay, M and Cruaud, C and Petit, JL and Fischer, C and Boulard, Y and Cébron, A and Ter Halle, A and Eyheraguibel, B and Lemechko, P and Bruzaud, S and Ghiglione, JF},
title = {Unveiling plastic biodegradation pathways through [13]C-DNA stable isotope probing and metagenomics.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142755},
doi = {10.1016/j.jhazmat.2026.142755},
pmid = {42330901},
issn = {1873-3336},
abstract = {Polyhydroxyalkanoates (PHAs) are promising biobased and biodegradable alternatives to conventional plastics, yet their degradation mechanisms and the diversity of microorganisms involved remain poorly characterized in marine ecosystems. Here, we used [13]C-labeled poly(3-hydroxybutyrate) (PHB) and combined DNA-stable isotope probing (DNA-SIP) with metagenomic to identify and functionally characterize active PHB-degrading bacteria in seawater. We identified three metagenome-assembled genomes (MAGs) affiliated with the genus Agarilytica that exhibited an exceptional expansion of preficted extracellular short-chain-length PHA depolymerase genes (ephaZscl) with up to 14 copies per genome, far exceeding the one-to-two copies typically reported. Comparative genomic and structural analyses revealed gene duplication and fusion events, given rise to tandem or chimeric depolymerases that may enhance catalytic diversity and substrate accessibility. Three-dimensional structural modeling confirmed that these fusion proteins retained functional catalytic domains with potential cooperative or independent activity. Such genomic redundancy and structural diversification likely confer an adaptive advantage for PHB biodegradation in marine environment. Collectively, our findings provide new insights into the ecological and evolutionary strategies of marine PHB degraders and highlight the power of DNA-SIP metagenomic for elucidating active plastic biodegradation pathways under natural conditions.},
}

@article {pmid42331262,
year = {2026},
author = {He, G and Guo, X and Lu, W and Zou, Y and Zheng, J and Han, X and Hong, Y and Wei, R},
title = {Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.},
journal = {Genomics},
volume = {},
number = {},
pages = {111282},
doi = {10.1016/j.ygeno.2026.111282},
pmid = {42331262},
issn = {1089-8646},
abstract = {OBJECTIVE: External auditory canal cholesteatoma (EACC), a rare destructive benign lesion, causes significant hearing loss, recurrent infections, and impaired quality of life. We characterized its microbial profiles to explore associations with disease progression.

METHODS: Cholesteatoma tissues from surgically treated EACC patients (2021-2022) underwent metagenomic sequencing (Illumina MiSeq). Taxonomic composition, functional genes, and antimicrobial resistance (AMR) profiles were systematically analyzed.

RESULTS: We identified 4377 core genes revealing abundance correlations. Dominant taxa included Firmicutes (42.1%), Proteobacteria (28.6%), and Actinobacteria (19.3%), with enriched Staphylococcus (32.4%) and Corynebacterium (21.7%). Hierarchical clustering and PCA/NMDS confirmed significant taxonomic divergence. AMR profiling detected multidrug-resistant genotypes (e.g., blaTEM, mecA).

CONCLUSION: This study defines EACC's microbial complexity and its pathogenic role, advocating microbiome-targeted strategies to mitigate infections.},
}

@article {pmid42331273,
year = {2026},
author = {Chen, D and Wang, Y and Cao, A and Hou, Y and Kong, F and Shi, J and Wang, S},
title = {Manganese-based activated carbon composites promote nitrogen removal in low temperature constructed wetlands via enhanced extracellular electron transfer.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125092},
doi = {10.1016/j.envres.2026.125092},
pmid = {42331273},
issn = {1096-0953},
abstract = {Constructed wetlands (CWs) provide cost effective, nature based wastewater treatment but suffer performance losses at low temperatures. We tested granular activated carbon-supported manganese composites (MnX-GAC; X = Fe or Zn) positioned within CWs to enhance microbial extracellular electron transfer (EET). MnX-GAC increased electron acceptors/donors, strengthened EET activity, and improved nitrogen removal while mitigating temperature impacts. At 15°C, the MnX-GAC system (CW6) raised ammonium (NH4[+]-N) removal by 31.0% versus CW1. Although CW6 generated more CO2 due to intensified carbon mineralization, it effectively suppressed the emissions of potent greenhouse gases (N2O and CH4) and achieved the lowest GWP per unit of nitrogen removed of 4.53 mg CO2-eq/mg N. Metagenomics showed the enrichment of key functional taxa (e.g., Chloroflexota, Thermodesulfobacteriota, and Bacteroidota) and the upregulation of nitrogen metabolism genes and carbon metabolism genes, alongside increases in electron-transport chain and mediator genes, collectively facilitated electron production and utilization. These changes indicate that MnX-GAC enhances EET mediated pathways to sustain nitrogen removal under low temperature. Overall, MnX-GAC offers a practical strategy to overcome low-temperature limitations in CWs, delivering higher nitrogen removal and lower life-cycle climate impacts.},
}

@article {pmid42331805,
year = {2026},
author = {Shan, Z and Chen, Y and Chen, F and Zhang, Y and Chen, H and Wang, Z and Wang, X and Zhong, J and Wong, IN and Chen, J and Li, X and Lin, Z and Purcell, R and Guo, Y and Li, X and Li, X},
title = {Dietary yacon concentrate reshapes microbial-metabolite crosstalk to inhibit colorectal cancer.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00931-3},
pmid = {42331805},
issn = {2396-8370},
support = {82203520//National Natural Science Foundation of China/ ; 82203264//National Natural Science Foundation of China/ ; SHAX-LC-202332//Shanghai Anti-Cancer Association "Soar" Program/ ; },
abstract = {Yacon concentrate, which is rich in fructan, phenolic compounds, and flavonoids, exhibits notable nutritional and antioxidant properties. This study explored the potential of New Zealand yacon concentrate to modulate the gut microbiota and host metabolism, alleviate inflammation, and enhance antitumor immunity. The anti-inflammatory and antitumor effects of yacon concentrate were evaluated in mouse models of dextran sulfate sodium (DSS)-induced colitis and colorectal cancer (CRC). Ex vivo gut chemostat model experiments were performed to assess the impact of yacon concentrate on human gut microbiota remodeling. The gut microbiota composition was then analyzed via metagenomic sequencing, and metabolomic profiling was conducted to identify the key bioactive metabolites. Yacon concentrate significantly ameliorated DSS-induced colitis by reducing weight loss, lowering the disease activity index scores, and alleviating colonic shortening in mice. In CRC models, yacon concentrate markedly suppressed tumor growth, reduced tumor incidence, and decreased tumor burden. Microbiota derived from the chemostat after yacon supplementation not only enriched beneficial bacteria and inhibited the growth of immunotherapy-resistant bacteria but also enhanced energy and short-chain fatty acid metabolism. Moreover, transplantation of this microbiota into mice significantly improved the tumor microenvironment and inhibited tumor growth. Collectively, these findings indicate that yacon concentrate is associated with changes in the gut microbiota and metabolomic profiles, supporting a potential link between yacon intake and modulation of the gut microbiota-metabolome axis. These observations provide a rationale for further mechanistic and interventional studies evaluating yacon concentrate as a dietary strategy for colitis prevention and CRC prevention, and as an adjunctive treatment.},
}