@article {pmid41539847,
year = {2026},
author = {Kong, M and Zhou, W},
title = {Clinical characteristics and outcomes of Rickettsia japonica infection: A retrospective case series of five patients.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {44},
number = {1},
pages = {503047},
doi = {10.1016/j.eimce.2025.503047},
pmid = {41539847},
issn = {2529-993X},
mesh = {Humans ; Retrospective Studies ; Middle Aged ; Male ; Aged ; Female ; *Rickettsia Infections/diagnosis/drug therapy/microbiology ; *Rickettsia/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; },
abstract = {OBJECTIVE: To characterize the clinical manifestations of Rickettsia japonica (R. japonica) infection and to generate evidence facilitating early diagnosis and targeted treatment.

METHODS: We retrospectively reviewed the clinical data of five patients with R. japonica infection who were treated in the Emergency Department, Xiling Campus, Yichang Central People's Hospital, between January 2023 and December 2024.

RESULTS: All patients were residents of Yichang City, Hubei Province, aged 58-70 years, and 80% (4/5) were farmers. The onset of illness occurred exclusively between May and September, and all patients reported a definite history of outdoor exposure. The predominant clinical manifestations were fever, rash, and eschar. Laboratory findings revealed thrombocytopenia, elevated aspartate aminotransferase (AST) and creatine kinase (CK), as well as increased inflammatory markers including C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6). R. japonica nucleic acid was detected in all patients by metagenomic next-generation sequencing (mNGS) of blood samples. Three patients initially received empirical doxycycline therapy, which was subsequently adjusted to a standard regimen after diagnostic confirmation. Defervescence occurred at a median of two days (range, 1-7 days), followed by gradual resolution of rash and alleviation of systemic symptoms. All patients achieved complete clinical recovery and were discharged without complications.

CONCLUSION: This study highlights the importance of heightened clinical awareness of R. japonica infection, emphasizing the integration of epidemiological context with hallmark clinical features - particularly fever, rash, and eschar - during peak transmission seasons in endemic areas. Early recognition allows the timely initiation of doxycycline therapy, which is essential for achieving favorable outcomes. Moreover, metagenomic next-generation sequencing (mNGS) provides the definitive identification of pathogens and guides targeted antimicrobial therapy.},
}

Humans
Retrospective Studies
Middle Aged
Male
Aged
Female
*Rickettsia Infections/diagnosis/drug therapy/microbiology
*Rickettsia/isolation & purification
Anti-Bacterial Agents/therapeutic use
Treatment Outcome

@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}

*Fermentation
*Moringa oleifera/microbiology/chemistry
*Taste
*Plant Leaves/microbiology/chemistry
Gas Chromatography-Mass Spectrometry
Volatile Organic Compounds/analysis
Odorants/analysis
Amino Acids/analysis
*Food Microbiology
Flavoring Agents
*Fermented Foods/microbiology
Bacteria/metabolism/classification/genetics
Microbiota
Metagenomics
Multiomics

@article {pmid41539628,
year = {2026},
author = {Peng, Y and Liu, H and Xing, T and Zhen, F and Wu, D and Sun, Y},
title = {Instability mechanisms of overloaded anaerobic digestion: Insights from volatile fatty acid metabolism.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134006},
doi = {10.1016/j.biortech.2026.134006},
pmid = {41539628},
issn = {1873-2976},
abstract = {To clarify the mechanisms driving process instability under overload stress, a long-term semi-continuous overload instability simulation experiment was conducted. High-throughput sequencing and metagenomics were used to determine the response of the process parameters, community composition, and volatile fatty acid (VFA)-related metabolic functional genes to the organic loading rate (OLR). When the OLR increased to 12.5 kg VS/m[3]/d, the methane yield remained low at 226.40 ± 10.78 mL CH4/g VS. Further increasing the OLR to 20 kg VS/m[3]/d completely destabilized the reactor, resulting in a final methane yield as low as 0.29 mL CH4/g VS, a hydrogen partial pressure as high as 357.37 Pa, and concentrations of butyrate, propionate, and acetate of 4328.49 ± 538.18, 1036.13 ± 75.48, and 9939.67 ± 427.68 mg/L, respectively. Organic overload stress caused reactor instability mainly by blocking VFA metabolism. When the OLR was ≥ 11 kg VS/m[3]/d, the relative abundances of key genes (aceE, buk, ptb, atoD) in the butyrate and propionate metabolic pathways decreased, resulting in the accumulation of butyrate and propionate. Despite a shift in syntrophic acetate oxidation metabolism from the methyl to the carbonyl branch under overload, the latter's recovery was insufficient to compensate for the severe impairment of the methyl branch, ultimately leading to acetate accumulation. VFA accumulation caused severe inhibition of acetogens and some methanogens, while hydrolytic and acidogenic bacteria dominated the microbiome (relative abundance: 94.18 %). As a result, the microbial metabolic balance was broken. Our results provide new insights into the mechanisms driving process instability under overload stress.},
}

@article {pmid41539627,
year = {2026},
author = {Wang, Z and Yang, Y and Qiu, B},
title = {Synergistic improvement of methane production and phosphorus recovery from anaerobic digestion of waste activated sludge by Fe2O3-assisted electroactive microorganisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134004},
doi = {10.1016/j.biortech.2026.134004},
pmid = {41539627},
issn = {1873-2976},
abstract = {Conductive materials and electroactive microorganisms (EAM) are key factors on enhancing methane production in anaerobic digestion of waste actived sludge via the direct interspecies electron transfer (DIET). However, their combined impact on simultaneous methane production and phosphorus recovery remains unclear. The Fe2O3 and EAM were added together to synergistically improve anaerobic processes, resulting in a 1.53-fold increase in methane production and a remarkable 12.03-fold enhancement in phosphorus removal. The co-additon of Fe2O3 and EAM promoted Fe(III/II) redox cycling, increased enzyme activity, and enhanced electron transport system (ETS) functionality while enriching DIET-associated bacteria (e.g., Brooklawnia, Anaerolineae) and methanogens (Methanosarcina). Metagenomic analysis revealed the upregulated genes related to phosphorus and iron metabolism, ETS, and DIET-coupled electron bifurcation. Notably, Fe2O3 may act as an alternative to cytochromes and pili in mediating DIET in electron transfer processes.},
}

@article {pmid41539626,
year = {2026},
author = {Vijande, C and Balboa, S and Lazzari, M and Lema, JM and Pabst, M},
title = {Multi-omics reveals wastewater sludge bacteria with genomic potential to degrade poly(ethylene) terephthalate.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134003},
doi = {10.1016/j.biortech.2026.134003},
pmid = {41539626},
issn = {1873-2976},
abstract = {Plastic pollution is a growing concern, especially poly(ethylene terephthalate) (PET), one of the most produced plastic polymers. Although several microorganisms capable of degrading PET have been identified, little is known about those present in wastewater treatment plants (WWTPs). This study explores their ability to degrade PET and the enzymes involved. Activated sludge from two facilities-one urban WWTP and one industrial WWTP-was cultivated with PET of different crystallinities. The inoculum source primarily determined differences in microbial community composition. Metagenomics revealed more than 300 genes homologous to PET-degrading enzymes in all biofilms; however, metaproteomics confirmed expression of only a few of these enzymes in industrial WWTP-derived biofilms. This inoculum demonstrated the ability to degrade PET breakdown products within 24 h. In addition, FTIR analysis revealed initial signs of surface alteration. In conclusion, this study reveals the presence of microorganisms in industrial wastewater treatment sludge that possess the genetic potential to degrade PET.},
}

@article {pmid41539600,
year = {2026},
author = {Li, W and Guo, H and Wang, Q and Peng, D and Wang, Y and Lu, Z},
title = {Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.022},
pmid = {41539600},
issn = {2090-1224},
abstract = {INTRODUCTION: Taihe Silky Fowl (TSF) has a long growth cycle and slow growth rate, how to effectively improve the growth rate of TSF has become the primary concern for breeders. Currently, extensive research has established the gut microbiota's role in modulating growth rate of commercial chicken breeds, while the specific microbial mechanisms influencing TSF growth rate remain poorly understood.

OBJECTIVES: Therefore, this study aimed to identify growth rate-associated key microbial species in TSF through multi-omics approaches, experimentally validate their growth-promoting roles via controlled interventions, and elucidate the species-metabolite-host interaction mechanisms.

METHODS: Cecal metagenome and metabolome was used to search for differential key microbiota and metabolites of TSF with different growth rate, the whole genome of key microbiota was used to identify the relationship between microbiota and metabolites, and gavage key microbiota to TSF was used to demonstrate the effectiveness of probiotics and preliminarily explore their mechanisms of action.

RESULTS: Cecal metagenome analysis demonstrated a significant enrichment of Phocaeicola vulgatus (P. vulgatus) in high-growth-rate fowls, Erysipelotrichaceae bacterium was significantly enriched in low-growth-rate fowls. The differential metabolites between the two groups were significantly enriched in tryptophan metabolism pathway. Subsequently, gene analysis revealed that P. vulgatus encoded tryptophan biosynthesis genes. In feeding experiment, oral gavage P. vulgatus improved the TSF final body weight, average growth rate and average daily gain, increased cecal P. vulgatus abundance, enriched the metabolites in tryptophan metabolism pathway both in the cecum and serum, and upregulated cecal tissue gene expression in the 'intestinal immune network for IgA production' pathway resulting in the higher secretory IgA (sIgA) concentrations in cecal tissue and luminal content than the control group.

CONCLUSION: P. vulgatus promoted the growth rate of TSF by optimizing the cecal microbiota, elevating cecal tryptophan metabolites and stimulating sIgA production via sIgA gene upregulation in cecal tissues, thereby enhancing host immune modulation. These findings elucidated the microbiota-metabolite-host axis governing TSF growth regulation, providing both mechanistic insights and practical applications for probiotic-based strategies to enhance growth performance and gut health in this valuable poultry breed.},
}

@article {pmid41539598,
year = {2026},
author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H},
title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.027},
pmid = {41539598},
issn = {2090-1224},
abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.},
}

@article {pmid41539568,
year = {2026},
author = {Farhat, I and Kaminski, H and Woerther, PL and Rodriguez, C and Pierre, C and Cheval, J and Korbi, S and Couzi, L and Merville, P and Jambon, F and Moreau, K},
title = {Spiroplasma infection complicated by macrophage activation syndrome and fulminant hepatitis in a kidney transplanted patient.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.01.008},
pmid = {41539568},
issn = {1600-6143},
abstract = {A 65-year-old kidney transplant recipient was admitted with isolated fever. Initial tests revealed pancytopenia and elevated C-reactive protein levels but failed to detect any pathogen. A bone marrow aspirate was performed because of signs suggestive of hemophagocytic lymphohistiocytosis (HLH), but results were negative. The patient subsequently developed fulminant hepatitis. Liver biopsy showed severe acute cytolytic hepatitis with a neutrophil-rich infiltrate, suppurative hepatocytic necrosis, and hemophagocytosis. Etoposide, N-acetylcysteine, and piperacillin-tazobactam were initiated. However, the patient died from hemorrhagic complications of the biopsy. Posthumous shotgun metagenomics (SMg) on liver samples identified Spiroplasma ixodetis.},
}

@article {pmid41539526,
year = {2026},
author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q},
title = {Microbial Taxonomic and Functional Responses to Heavy Metal Gradients in Mining-Impacted Stream Sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123778},
doi = {10.1016/j.envres.2026.123778},
pmid = {41539526},
issn = {1096-0953},
abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1%, 12.4%, and 12.9% of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4%) and Acidithiobacillus (5.0%), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8%) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.},
}

@article {pmid41539415,
year = {2026},
author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL},
title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.},
journal = {Genomics},
volume = {},
number = {},
pages = {111204},
doi = {10.1016/j.ygeno.2026.111204},
pmid = {41539415},
issn = {1089-8646},
abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78,p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.},
}

@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
doi = {10.1016/j.psj.2026.106371},
pmid = {41539238},
issn = {1525-3171},
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}

@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}

@article {pmid41538947,
year = {2026},
author = {Zhang, X and Feng, Y and Jiang, X and Sun, W and Zhang, C and Han, J and Hou, Y and You, X and Zhang, H and Wang, X and Wu, X and Wang, J},
title = {Unveiling hidden risks of chiral fungicide benzovindiflupyr: Stereoselectivity in soil antibiotic resistance gene transmission.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141088},
doi = {10.1016/j.jhazmat.2026.141088},
pmid = {41538947},
issn = {1873-3336},
abstract = {Antibiotic resistance gene (ARG) dissemination is closely associated with modern agricultural practices. However, the stereoselective effects of widely applied chiral pesticides on resistance evolution remain insufficiently investigated. This study systematically explored the differential effects of benzovindiflupyr enantiomers on transmission of ARGs through long-term soil incubation experiments combined with metagenomic and in vitro studies. Results demonstrated that 1S,4R-enantiomer exhibited significantly longer half-life than 1 R,4S-enantiomer. 1 R,4S-enantiomer induced extreme enrichment of a few ARGs. 1S,4R-enantiomer persistently increased abundance of multiple ARGs. Compared with 1 R,4S-enantiomer, 1S,4R-enantiomer more consistently enhanced abundance of mobile genetic elements (MGEs) related to conjugative transfer. Moreover, 1 R,4S-enantiomer primarily enriched specific genera within Pseudomonadota. 1S,4R-enantiomer simultaneously promoted abundance of multiple genera across both Pseudomonadota and Bacteroidota, driving cross-phylum genera to correlate with shared ARGs. Genomic analysis confirmed that Pseudomonadota under 1S,4R-enantiomer treatment carried more ARGs and MGEs. In vitro transformation experiments ultimately validated that 1S,4R-enantiomer significantly enhanced transformation efficiency across multiple ARGs consistently, substantially exceeding 1 R,4S-enantiomer effects. Overall, 1S,4R-enantiomer poses more significant risks for horizontal transfer of ARGs. This study elucidates enantioselective effects of chiral pesticides on transmission of ARGs, providing a foundation for improving chiral agrochemical risk assessment.},
}

@article {pmid41538522,
year = {2026},
author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S},
title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA viromeFIRST REVIEW ROUND - REVIEWERS COMMENTSAUTHORS RESPONSE TO REVIEWERSREVIEWERS COMMENTS.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {120},
number = {},
pages = {e250131},
pmid = {41538522},
issn = {1678-8060},
mesh = {Animals ; *Mosquito Vectors/virology/classification ; *Arboviruses/genetics/isolation & purification ; Colombia ; *Culicidae/virology/classification ; *Virome/genetics ; *RNA, Viral/genetics ; Metagenomics ; Seasons ; Caribbean Region ; *RNA Viruses/genetics/classification ; Arbovirus Infections/transmission ; },
abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.

OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.

METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across Córdoba, Sucre, Bolívar, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50™ platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.

FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.

MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.},
}

Animals
*Mosquito Vectors/virology/classification
*Arboviruses/genetics/isolation & purification
Colombia
*Culicidae/virology/classification
*Virome/genetics
*RNA, Viral/genetics
Metagenomics
Seasons
Caribbean Region
*RNA Viruses/genetics/classification
Arbovirus Infections/transmission

@article {pmid41538320,
year = {2026},
author = {},
title = {Correction to 'MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis'.},
journal = {Nucleic acids research},
volume = {54},
number = {2},
pages = {},
doi = {10.1093/nar/gkag015},
pmid = {41538320},
issn = {1362-4962},
}

@article {pmid41537603,
year = {2026},
author = {Zou, Y and Zhou, J and Zeng, Y and Chen, B and Liu, L and Xu, G},
title = {Mining and engineering of ene-reductases from marine sediment metagenome for prochiral ACE inhibitor synthesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0233325},
doi = {10.1128/aem.02333-25},
pmid = {41537603},
issn = {1098-5336},
abstract = {The development of sustainable biocatalytic processes for pharmaceutical synthesis represents a major goal in green chemistry. Ene-reductases (ERs) are attractive biocatalysts for asymmetric hydrogenation of activated alkenes, yet their industrial application is often constrained by limited substrate scope and stability. In this study, we explored the deep-sea sediment metagenome of the South China Sea and identified 41 putative ER genes, with 22 successfully solubly expressed in Escherichia coli. Biochemical characterization revealed broad substrate specificity, achieving up to 90% conversion for diverse α,β-unsaturated compounds. Notably, three enzymes (S2gene2614772, S2gene1139, and S2gene22028) exhibited exceptional adaptability, maintaining high activity over a wide pH range (5.5-8.5) and at low temperatures (15°C). However, none of the wild-type ERs showed significant activity toward the prochiral substrate 2-oxo-4-phenyl-3-butenoic acid, a key intermediate for angiotensin-converting enzyme inhibitors (ACEIs). Through directed evolution, we obtained a mutant (S2gene22028-G102S) with 30-fold enhanced activity, reaching 90% conversion at 10 mM substrate. Scale-up synthesis (5 mmol substrate) afforded 2-oxo-4-phenylbutyric acid (OPBA) at 11 mg/mL, demonstrating industrial potential. This study highlights marine metagenomes as valuable sources of novel ERs and provides an efficient biocatalytic route to ACEI precursors.IMPORTANCEThe development of sustainable biocatalysts for pharmaceutical synthesis is a pivotal goal in green chemistry. This study leverages the untapped enzymatic diversity of the South China Sea deep-sea sediment metagenome to discover novel ene-reductases (ERs). We not only identified robust ERs with broad substrate promiscuity and exceptional adaptability to low temperature and pH fluctuations but also successfully engineered a variant to overcome the key biocatalytic challenge in the synthesis of 2-oxo-4-phenylbutyric acid (OPBA), a critical precursor to angiotensin-converting enzyme inhibitors. Our work underscores marine metagenomes as a valuable reservoir for discovering industrially relevant biocatalysts and demonstrates the power of combining metagenomic mining with protein engineering to enable greener manufacturing routes for high-value pharmaceuticals.},
}

@article {pmid41537586,
year = {2026},
author = {Belay, KH and Abdelrazek, S and Kaur, S and Mazloom, R and Bily, D and Gyatso, T and Avin, FA and Bonkowski, J and Liyanapathiranage, P and Rodriguez Salamanca, L and Heath, LS and Baysal-Gurel, F and Vinatzer, BA},
title = {Genomic insights into Ceratobasidium sp. associated with vascular streak dieback of woody ornamentals in the United States using a metagenomic sequencing approach.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0252325},
doi = {10.1128/spectrum.02523-25},
pmid = {41537586},
issn = {2165-0497},
abstract = {UNLABELLED: Woody ornamentals are integral to urban landscapes and play important roles in habitat restoration and ecological conservation, yet their national and international trade facilitates the spread of plant diseases with significant ecological and economic consequences. Vascular streak dieback (VSD) recently emerged on woody ornamentals in the United States and was found to be associated with the fungal pathogen Ceratobasidium sp. (Csp), but little is known about its genomic diversity and associated microbial communities. We thus applied metagenomic sequencing to 106 symptomatic samples that had tested positive for Csp and had been collected from 34 woody ornamental species in seven states. Taxonomic profiling identified Csp as the only putative pathogen of which we recovered 17 high-quality draft genomes. Phylogenomic and pangenome analyses revealed that U.S. Csp isolates form a tight genetic cluster, distinct in gene content from C. theobromae, a pathogen of cacao, avocado, and cassava in Southeast Asia. Comparative analyses highlighted gene content differences, including candidate effectors and secondary metabolite clusters, which may underlie host interactions and offer diagnostic targets. These findings provide the first genomic insights into the U.S. Csp population, suggest the recent introduction of a single genetic lineage with a broad host range, and establish a framework for improved detection, monitoring, and management of VSD in woody ornamentals.

IMPORTANCE: Identification of the pathogen that causes an emerging disease, be it of humans, animals, or plants, is a prerequisite to develop effective treatment and/or management practices and to try to control the disease outbreak to prevent further pathogen spread. Vascular streak dieback (VSD) is an emerging disease of ornamental bushes and trees in the United States. Identification of the pathogen has been hindered by the difficulty in growing the fungal pathogen found to be associated with diseased plants in pure culture. Here, we succeeded in sequencing the DNA of the likely pathogen directly from plant tissue or from the fungal mass growing out of collected plant tissue. The sequences were assembled into genomes, which allowed us to precisely identify the pathogen, compare it to related pathogens of other plants, and predict how it causes disease. These results can now be used to inform management and control of VSD.},
}

@article {pmid41537582,
year = {2026},
author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D},
title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084225},
doi = {10.1128/msphere.00842-25},
pmid = {41537582},
issn = {2379-5042},
abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.},
}

@article {pmid41537461,
year = {2026},
author = {Choi, KY and Kang, S and Cook, S and Li, D and Choi, YY and Seo, EH and Han, X and Park, JE and Lee, S and Lee, S and Chung, JY and Chong, A and Choi, SM and Ha, JM and Song, MK and Lee, JS and Choo, IH and Kim, JH and Song, HC and Kim, BC and Kim, H and Farrer, LA and Gim, J and Jun, GR and Lee, KH},
title = {The Gwangju Alzheimer's & Related Dementias (GARD) cohort: Over a decade of Asia's largest longitudinal multimodal study.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e70981},
pmid = {41537461},
issn = {1552-5279},
support = {25-BR-03-05//the KBRI Basic Research Program through the Korea Brain Research Institute, funded by the Ministry of Science and ICT/ ; NRF-2014M3C7A1046041//the Original Technology Research Program for Brain Science of the National Research Foundation funded by the Korean government, MSIT/ ; RS-2024-00407198//Brain Pool program funded by the Ministry of Science and ICT through the National Research Foundation of Korea/ ; 2023-ER1007-01//Korea National Institute of Health research project/ ; //by the Technology Innovation Program (20022810, Development and Demonstration of a Digital System for the evaluation of geriatric Cognitive impairment) funded By the Ministry of Trade, Industry & Energy (MOTIE, Korea)/ ; RS-2024-00433283//the Technology Innovation Program funded by the Ministry of Trade, Industry & Energy, Republic of Korea/ ; HR22C141105//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
mesh = {Humans ; Longitudinal Studies ; Male ; *Alzheimer Disease/epidemiology/diagnostic imaging/genetics/diagnosis ; Female ; Aged ; *Cognitive Dysfunction/epidemiology/diagnostic imaging ; Disease Progression ; Republic of Korea/epidemiology ; Cohort Studies ; Middle Aged ; Biomarkers ; Magnetic Resonance Imaging ; Aged, 80 and over ; Neuroimaging ; Proteomics ; Genomics ; },
abstract = {INTRODUCTION: Alzheimer's disease (AD) is a major public health concern in Korea, with a high prevalence among older adults. A community-based longitudinal study is essential for tracking disease progression, identifying biomarkers, and developing targeted prevention and treatment strategies. The Gwangju Alzheimer's & Related Dementias (GARD) cohort was established to address these needs through a multimodal approach.

METHODS: Participants aged ≥60 years undergo comprehensive clinical evaluations, neuroimaging, and biospecimen collection for multi-omics analyses (genomics, transcriptomics, proteomics, and metagenomics) at baseline and systematic follow-up visits.

RESULTS: From over 17,000 screened individuals, 12,877 were enrolled. Baseline diagnoses include 5,123 cognitively unimpaired (CU), 3,250 mild cognitive impairment (MCI), and 2,125 AD dementia. The resource includes magnetic resonance imaging scans (n = 10,843) and extensive multi-omics data: genomic (n = 10,775), proteomic (n = 116), and microbiome (n = 595).

DISCUSSION: The integrated GARD dataset provides a powerful and scalable resource for identifying novel biomarkers, understanding disease heterogeneity, and advancing precision medicine for AD.

HIGHLIGHTS: Gwangju Alzheimer's & Related Dementias (GARD) is a large-scale, longitudinal, community-based cohort study in South Korea. The study focuses on early detection and monitoring of dementia progression. GARD includes cognitive testing, imaging, biospecimens, and multi-omics data. We aim to identify Korean-specific biomarkers predictive of cognitive decline. Supports East Asian insights and fills gaps in global Alzheimer's research.},
}

Humans
Longitudinal Studies
Male
*Alzheimer Disease/epidemiology/diagnostic imaging/genetics/diagnosis
Female
Aged
*Cognitive Dysfunction/epidemiology/diagnostic imaging
Disease Progression
Republic of Korea/epidemiology
Cohort Studies
Middle Aged
Biomarkers
Magnetic Resonance Imaging
Aged, 80 and over
Neuroimaging
Proteomics
Genomics

@article {pmid41537457,
year = {2026},
author = {Chari, NR and DeAngelis, KM and Aguilar, AA and Chan, ALH and Burgin, GA and Frey, SD and Taylor, BN},
title = {Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag002},
pmid = {41537457},
issn = {1751-7370},
abstract = {Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.},
}

@article {pmid41536238,
year = {2026},
author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C},
title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2607043},
doi = {10.1080/19490976.2025.2607043},
pmid = {41536238},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; Longitudinal Studies ; Adult ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Pregnancy in Obesity/microbiology/metabolism ; Infant ; Male ; Body Mass Index ; Mexico ; },
abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.},
}

Humans
*Milk, Human/chemistry
Female
*Oligosaccharides/analysis/metabolism
*Gastrointestinal Microbiome
Infant, Newborn
Feces/microbiology
Longitudinal Studies
Adult
Pregnancy
*Bacteria/classification/genetics/isolation & purification/metabolism
*Pregnancy in Obesity/microbiology/metabolism
Infant
Male
Body Mass Index
Mexico

@article {pmid41536169,
year = {2026},
author = {Abdulkareem, AA and Gul, SS and Abdulbaqi, HR and Sha, AM and Preshaw, PM},
title = {Assessing Evidence to Include Filifactor alocis as a Novel Candidate in Socransky's Complexes.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {e70018},
doi = {10.1111/omi.70018},
pmid = {41536169},
issn = {2041-1014},
abstract = {Socransky's complexes have identified a range of bacteria as key contributors to the onset and progression of periodontal disease. However, advancements in microbiological detection methods have allowed for exploration of the microbiome in periodontal health/disease in greater detail. In recent years, Filifactor alocis has emerged as a potential periodontal pathogen. Therefore, the aim of this review was to investigate whether this bacterium could be included in Socransky's model by summarizing the available evidence. A comprehensive literature search performed using PubMed, ScienceDirect, and Scopus databases was undertaken. The retrieved articles were filtered according to defined eligibility criteria, which yielded 24 studies. Data were extracted from these observational and clinical studies to synthesize findings. Findings regarding the host immune response were derived from in vitro and experimental animal models and narratively summarized. Observational studies and clinical trials showed heterogeneity and a lack of standardized outcomes. However, the general trend indicated a higher prevalence of F. alocis at diseased sites than at healthy sites. In addition, periodontal treatment was found to significantly reduce F. alocis levels and was associated with improvements in clinical periodontal parameters. Experimental models and in vitro studies showed that F. alocis exhibits a range of virulence attributes and pathogenic behavior similar to that of putative pathogenic periodontal bacteria. The evidence is not sufficient to include F. alocis as a new member of Socransky's model. However, this review suggests that this bacterium has the potential to be included in Socransky's complexes in the future after further research which would require to be highly standardized to enhance comparability and generalizability of findings.},
}

@article {pmid41535941,
year = {2026},
author = {Parida, S and Nandi, D and Verma, D and Yi, M and Yende, A and Queen, J and Gabrielson, KL and Sears, CL and Sharma, D},
title = {A pro-carcinogenic oral microbe internalized by breast cancer cells promotes mammary tumorigenesis.},
journal = {Cell communication and signaling : CCS},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12964-025-02635-9},
pmid = {41535941},
issn = {1478-811X},
support = {90047965//Breast Cancer Research Foundation/ ; BC191572//Congressionally Directed Medical Research Programs/ ; },
abstract = {The intricate relationship between microbiota and breast cancer presents an additional risk factor that can have a profound impact on disease progression. Focusing on dysbiosis, our metagenomic analysis shows overabundance of an oral pathogenic microbe F. nucleatum and co-habitation of associated biofilm forming oral microbes in cancerous breast. Mammary gland colonization with F. nucleatum results in the development of metaplastic lesions accompanied with inflammation, DNA damage and hyper-proliferation in healthy mice. Exhibiting the impact of circulating F. nucleatum introduced via hematogenous route, breast tumor bearing mice show accelerated tumor growth and metastatic progression. Increased proliferation, migration, self-renewal and chemoresistance in breast cancer cells as well as non-tumorigenic breast epithelial cells bearing pathogenic BRCA1 mutation is observed upon F. nucleatum exposure which is internalized by the cells in a Gal-GalNAc dependent manner. Of interest, cells harboring BRCA1 mutations exhibit greater cell surface accumulation of Gal-GalNAc sugar residue. This work sheds light on the oncogenic impact of a pro-carcinogenic oral bacterium, F. nucleatum, on normal mammary epithelium and breast cancer, implicates the impairment of DNA damage and repair pathways as its functional mediators, and proposes the concept of increased vulnerability of BRCA1 mutant breast cancer cells owing to their preferential internalization of F. nucleatum.},
}

@article {pmid41535719,
year = {2026},
author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L},
title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.},
journal = {Cell research},
volume = {},
number = {},
pages = {},
pmid = {41535719},
issn = {1748-7838},
support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.},
}

@article {pmid41535683,
year = {2026},
author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q},
title = {Identification of antimicrobial peptides from ancient gut microbiomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68495-0},
pmid = {41535683},
issn = {2041-1723},
support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science & Technology)/ ; },
abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.},
}

@article {pmid41535304,
year = {2026},
author = {Courtine, D and Lepère, C and Wawrzyniak, I and Moné, A and Billard, H and Colombet, J and Monjot, A and Cruaud, C and Da Silva, C and Aury, JM and Debroas, D and Bronner, G},
title = {A multi-Omic resource for exploring microbial eukaryotes in the meromictic freshwater Lake Pavin.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06573-0},
pmid = {41535304},
issn = {2052-4463},
support = {ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Although recent advances in high-throughput sequencing have greatly expanded our understanding of microbial diversity and function in aquatic ecosystems, progress in studying freshwater microbial eukaryotes has been more limited, mainly due to their large genomes, immense diversity, and largely uncharacterised physiologies. In this work, we present a comprehensive multi-omic dataset, eukaryote-centred, including targeted-metagenomic (18S rDNA V4 and V9), metagenomic, metatranscriptomic and single amplified genomes (SAGs). Both the oxic and anoxic layers of Lake Pavin (France), a permanently stratified freshwater lake, were sampled at four distinct times throughout 2018, by day and night, targeting microbial eukaryotes of two size classes (0.65-10 µm and 10-50 µm). This dataset comprises 106 eukaryotic metagenome-assembled genomes (MAGs), over 9 million unigenes and 11 SAGs, encompassing several under-represented taxa in public databases (e.g. Perkinsea, Chytridiomycota, Cryptista). Altogether, this dataset represents a resource for exploring the functional diversity and spatio-temporal dynamics of microbial eukaryotes.},
}

@article {pmid41535300,
year = {2026},
author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC},
title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00902-8},
pmid = {41535300},
issn = {2055-5008},
support = {NCI202346//New Cornerstone Science Foundation/ ; },
abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.},
}

@article {pmid41535070,
year = {2026},
author = {Zhang, W and Liu, Y and Li, G and Xu, J and Chen, E and Schönhuth, A and Luo, X},
title = {Strain-level metagenomic profiling using pangenome graphs with PanTax.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280858.125},
pmid = {41535070},
issn = {1549-5469},
abstract = {Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, most existing strain-level taxonomic classifiers rely on the sequence representation of multiple linear reference genomes, which fails to capture the sequence correlations among these genomes, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pangenome graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pangenome graphs possess the capability to depict the full range of genetic variability present across multiple evolutionarily or environmentally related genomes. PanTax provides a comprehensive solution to taxonomic classification for strain resolution, compatibility with both short and long reads, and compatibility with single or multiple species. Extensive benchmarking results demonstrate that PanTax drastically outperforms state-of-the-art approaches, primarily evidenced by its significantly higher F1 score at the strain level, while maintaining comparable or better performance in other aspects across various data sets.},
}

@article {pmid41534886,
year = {2026},
author = {Idrees, S and Chen, H and Sadaf, T and Rehman, SF and Johansen, MD and Paudel, KR and Liu, G and Wang, Y and Luecken, MD and Hortle, E and Philp, AS and Budden, KF and O'Rourke, M and Kaiko, GE and Lucas, SEM and Dickinson, JL and Allen, PC and Powell, JE and Zhang, LY and Chambers, DC and Corte, T and Caramori, G and Sauler, M and Wark, PA and Gote-Schniering, J and Lehmann, M and Conlon, TM and Kapellos, TS and Yildirim, AÖ and Faner, R and Dharmage, SC and Wheelock, CE and van den Berge, M and Nawijn, MC and Polverino, F and Belz, GT and Chotirmall, SH and Segal, LN and Faiz, A and Hansbro, PM},
title = {Multi-omics to study chronic respiratory diseases and viral infections.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {35},
number = {179},
pages = {},
doi = {10.1183/16000617.0286-2024},
pmid = {41534886},
issn = {1600-0617},
mesh = {Humans ; Chronic Disease ; *Metabolomics/methods ; *Genomics/methods ; *Proteomics/methods ; *Virus Diseases/genetics/metabolism/diagnosis/virology ; Host-Pathogen Interactions ; Epigenomics ; *Respiratory Tract Infections/genetics/virology/metabolism/diagnosis ; Animals ; Metagenomics ; *Lung/metabolism/virology/physiopathology ; *Respiration Disorders/genetics/metabolism/diagnosis ; Multiomics ; },
abstract = {Despite recent advances, the underlying mechanisms of the development and progression of many chronic respiratory diseases remain to be elucidated. Factors such as heterogeneity and complexity of human diseases and difficulty interpreting large datasets hinder research into chronic respiratory diseases. Omics assesses the changes in specific biological entities, such as mRNA expression, epigenetics/epigenomics, genomics, proteomics, metagenomics and metabolomics, and provides valuable insights into the roles of these processes in chronic respiratory diseases. High-throughput omics at bulk, single-cell and spatial levels empower the exploration of disease-related changes through untargeted data-driven statistical methods. Multi-omics is the exploration and integration of multiple biological processes, which compared to a single-omics, can provide a substantially greater and more holistic overview of the pathogenic mechanisms that underpin complex diseases. Multi-omics analysis can comprehensively characterise the mechanisms that drive chronic respiratory diseases, capturing unique biological signatures and cellular interactions at different omics levels. Use of these methods has begun to identify key factors and biomarkers in chronic respiratory diseases. Here, we review current omics approaches and highlight recent advances in respiratory research achieved using multi-omics and integrative methods. Our review provides a valuable resource for researchers and clinicians in this area.},
}

Humans
Chronic Disease
*Metabolomics/methods
*Genomics/methods
*Proteomics/methods
*Virus Diseases/genetics/metabolism/diagnosis/virology
Host-Pathogen Interactions
Epigenomics
*Respiratory Tract Infections/genetics/virology/metabolism/diagnosis
Animals
Metagenomics
*Lung/metabolism/virology/physiopathology
*Respiration Disorders/genetics/metabolism/diagnosis
Multiomics

@article {pmid41534755,
year = {2026},
author = {Liu, K and Peng, W and Yang, X and Zeng, Y and Liu, Y and Yu, K and Zhu, Y and Gou, H and Li, L and Zhang, C},
title = {Efficacy and Multi-Omics Regulatory Effects of Guilou Tongluo Formula in Patients with Chronic Obstructive Pulmonary Disease Combined with Pulmonary Hypertension: A Prospective, Multicenter, Randomized Controlled Trial.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121204},
doi = {10.1016/j.jep.2026.121204},
pmid = {41534755},
issn = {1872-7573},
abstract = {Pulmonary hypertension (PH) is a serious and common complication in patients with chronic obstructive pulmonary disease (COPD), and this clinical gap has been newly emphasized in the GOLD 2025 guidelines. Guilou Tongluo Formula (GLTLF) is a traditional Chinese herbal prescription widely used in clinical practice for the treatment of COPD combined with PH (COPD-PH). However, there is a lack of high-quality clinical trials to support its efficacy, and the underlying mechanisms of action remain unclear.

AIM OF THE STUDY: This study aims to evaluate the efficacy and safety of GLTLF in the treatment of COPD-PH, and to explore the potential mechanisms underlying its therapeutic effects.

MATERIALS AND METHOD: A total of 104 patients with COPD-PH were randomized to receive either conventional therapy alone (Control group) or in combination with GLTLF (GLTLF group). Clinical efficacy was assessed by changes in traditional Chinese medicine (TCM) syndrome scores, pulmonary artery systolic pressure (PASP), pulmonary function, arterial blood gases, COPD Assessment Test (CAT), modified Medical Research Council (mMRC) grade, WHO functional class (WHO-FC), 6-minute walk distance (6MWD), and laboratory parameters. Potential mechanisms were explored via gut metagenomic and metabolomic analyses.

RESULTS: Clinical efficacy evaluation indicated that the TCM syndrome scores were significantly reduced in both groups post-treatment (P < 0.001). PASP, FEV1, and FEV1/FVC improved significantly in the GLTLF group (P < 0.05), and were superior to the control group post-treatment (P < 0.05). PaO2, PaCO2, BNP, and D-dimer improved after GLTLF intervention (P < 0.05). Both groups had increased 6MWD (P < 0.001), with the GLTLF group performing better (P = 0.006). CAT score, mMRC grade, and WHO FC improved in both groups (P < 0.05), with superior outcomes in the GLTLF group (P < 0.05). Metagenomic sequencing revealed that GLTLF altered the structure and function of the gut microbiota in patients with COPD-PH. Metabolomic analysis identified a total of 87 differential metabolites following GLTLF intervention, which were significantly enriched in 18 metabolic pathways.

CONCLUSION: GLTLF can effectively treat patients with COPD-PH, enhance clinical efficacy, and modulate both metabolic status and gut microbiota composition.},
}

@article {pmid41534666,
year = {2026},
author = {Chang, Y and Qiu, S and Collins, G and Hu, Y and Lee, PH and Zhan, X},
title = {Iron modulation of sulfur-mediated autotrophic denitrification: denitrification efficiency, microbial succession, and metabolic pathways.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {133997},
doi = {10.1016/j.biortech.2026.133997},
pmid = {41534666},
issn = {1873-2976},
abstract = {The application of iron sulfide-mediated autotrophic denitrification is promising for nitrate reduction in carbon-deficient wastewater and polluted groundwater. Previous studies have shown distinct functional microbial communities in different iron sulfide-mediated autotrophic denitrification systems, obscuring how iron modulates their composition and activity. In this study, iron-modulated sulfur autotrophic denitrification efficiency, microbial succession, and key pathways were investigated at different iron levels. Results showed that 1 mM Fe[2+] enhanced denitrification efficiency (91.1 %) and prevented cell encrustation. Metagenomic analysis indicated that phylum Campylobacterota (16.0 %) and genus Sulfurimonas (14.4 %) were enriched under iron-modulated conditions. Iron modulated nitrate reduction by improving the relative abundance of complete denitrification genes (napA, napB, and nosZ) and stimulating sulfur metabolism through the SOX complex pathway (soxZ and soxY). These findings reveal the role of iron in modulating sulfur-mediated autotrophic denitrification and provide new insights into the microbial mechanisms involved in iron-sulfur coupling systems.},
}

@article {pmid41534561,
year = {2026},
author = {Chai, X and Zhang, X and Chen, D and Rong, D},
title = {Whole blood metagenomic next-generation sequencing in the diagnosis of bloodstream infection in patients with hematological diseases.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108375},
doi = {10.1016/j.ijid.2026.108375},
pmid = {41534561},
issn = {1878-3511},
abstract = {OBJECTIVE: To evaluate the value of cell-free DNA (cfDNA) in plasma and genomic DNA (gDNA) in nucleated cell layer of whole blood samples detected by metagenomic next-generation sequencing (mNGS) in the diagnosis of bloodstream infection in patients with hematological diseases.

METHODS: Whole blood samples collected from hematologic patients with suspected bloodstream infections were divided into the plasma and nucleated cell layers. The DNA of plasma and nucleated cell layers was extracted for mNGS. The pathogenic results were compared between whole blood (plasma plus nucleated cell layers) and plasma layer. In addition, the factors influencing the prognosis at discharge were analyzed.

RESULTS: Totally 92 patients were included. The positive rate of mNGS in whole blood was higher than those of the single plasma layer (58.70% vs. 53.26%) and the culture layer (58.70% vs. 17.39%). The consistency of plasma and nucleated cell layers was 57.6%. The proportion of fungi detected in nucleated cell layer was higher than that in plasma layer (30.2% vs. 17.0%). Ten patients had extra pathogens detected in whole blood compared with the single plasma layer, and the positive rate of mNGS increased by 10.87%. gDNA microbe reads and non-host ratios in the extra-detection group were significantly higher than those in the non-extra detection group. cfDNA microbe reads, non-host ratios and microbe percent showed no significant differences between the two groups. The maximum Sequential Organ Failure Assessment (SOFA) score and age in the death group were significantly higher, while cfDNA/gDNA species richness was significantly lower compared with the survival group. The maximum SOFA score and cfDNA Shannon diversity index were found as risk factors for improved prognosis. The maximum SOFA score and cfDNA concentration were combined for the diagnosis of poor prognosis at discharge, with the highest area under the curve of 0.95.

CONCLUSION: Simultaneous metagenomic sequencing of plasma layer and nucleated cell layer contributes to the detection of pathogens in patients with bloodstream infection. cfDNA detection has a certain significance in predicting the prognosis of patients with bloodstream infection.},
}

@article {pmid41534355,
year = {2026},
author = {He, S and Wang, Z and Zhong, Z and Shi, C and Li, D and Yin, F},
title = {Soil salinization alters biogeochemical cycles in agricultural ecosystems by reducing carbon-cycling microorganisms.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119706},
doi = {10.1016/j.ecoenv.2026.119706},
pmid = {41534355},
issn = {1090-2414},
abstract = {Salinity stress can decline crop yield in agricultural systems. Beyond the environmental conditions that drive agricultural plant growth, the diverse roles of microbes represent a critical, often overlooked factor in shaping crop health and productivity. Salinization exerts a profound effect on soil microbial communities, with consequences for biogeochemical cycles. However, the salinity adaptation mechanisms of microorganisms participating in biogeochemical cycles remain incompletely understood, which hold considerable promise for microbial solutions in saline agriculture. In this study, metagenomics-based technology was employed to analyze agricultural soils within a region-scale irrigation area characterized by varying degrees of salinization. According to the results of generalized linear models, bell-shaped trends were observed for the diversity and abundance of biogeochemical cycling genes along the soil salinity gradient, all of which peaked at a salinity of approximately 7.5 ‰. Further comparisons indicated reduced total abundance of all biogeochemical cycling genes in high salinity soils (>7.5 ‰) compared to those in low salinity soils (<7.5 ‰). Furthermore, correlation analysis indicated the coupling of different biogeochemical cycling genes, which were observed to be possessed by similar functional microorganisms, with a predominance of Gammaproteobacteria and Alphaproteobacteria. The presence of elevated salt levels resulted in a decline in the abundance of various microorganisms that play roles in biogeochemical cycling, including members of the Alphaproteobacteria, Actinomycetia, Limnocylindira, and Gemmatimonadetes phyla. Concurrently, there was an enrichment of a limited number of salt-tolerant bacteria, predominantly classified under the Bacteroidia and Bacilli taxonomic groups. The coupling of different biogeochemical cycling genes in some metagenome-assembled genomes (MAGs) was confirmed through metagenomics binning. Three MAGs (strains of Methylophaga, Salinimicrobium, and Sediminibacterium, respectively) with diverse biogeochemical cycling functions were recognized as potential plant-growth-promoting bacteria under salinity stress. These findings contribute to the existing body of knowledge on the salinity adaptability of soil microbial communities and offer guidance for the management of saline agriculture.},
}

@article {pmid41534338,
year = {2025},
author = {Potgieter, S and Oosthuizen-Vosloo, S and Langenfeld, K and Dowdell, KS and Vedrin, M and Lahr, R and Pinto, AJ and Raskin, L},
title = {Biofiltration, seasonality, and distribution system factors influence nitrifier communities in a full-scale chloraminated drinking water system.},
journal = {Water research},
volume = {292},
number = {},
pages = {125288},
doi = {10.1016/j.watres.2025.125288},
pmid = {41534338},
issn = {1879-2448},
abstract = {Nitrification in chloraminated drinking water systems has been widely studied, although limited information is available on the role of biofiltration in shaping the nitrifier communities within drinking water distribution systems (DWDS). Additionally, the co-occurrence of comammox and canonical nitrifiers in drinking water systems remains unclear. This study investigates how biofiltration shapes nitrifier communities in a full-scale drinking water system where chloramine is a secondary disinfectant, and biofilters are backwashed with chloraminated water. Samples were collected monthly for one year from biofilter effluent, finished water, and three DWDS sites with varying water ages, water quality, and nitrite concentrations. Nitrifier abundances were quantified using droplet digital PCR, which showed contrasting temporal trends between the ammonia-oxidizing bacteria amoA gene and both nitrite-oxidizing bacteria 16S rRNA gene and comammox amoB gene abundances. Genome-resolved quantitative metagenomics revealed Nitrosomonas cluster 6a species, canonical Nitrospira species, and Nitrospira-like comammox species as the dominant nitrifiers. The same populations were detected in biofilter effluent and across DWDS sites, indicating that biofilter operation contributed to the persistence of nitrifiers in the DWDS. Further, DWDS site-specific factors, such as water age and disinfectant degradation, influenced the presence and abundance of individual nitrifier populations. These findings advance our understanding of how upstream treatment processes influence microbial community structure and nitrifier persistence in full-scale chloraminated DWDSs, and highlight the importance of considering biofilter operation, alongside disinfection practices, within integrated nitrification control strategies.},
}

@article {pmid41534337,
year = {2026},
author = {Huang, X and Ni, Y and Ma, Z and Xie, Z and Ding, Z and Xu, H and Wei, H and Jin, Q and Zhou, R},
title = {Polymer type and aging drive the selective enrichment of antibiotic resistance genes and pathogens in microplastics biofilms.},
journal = {Water research},
volume = {292},
number = {},
pages = {125364},
doi = {10.1016/j.watres.2026.125364},
pmid = {41534337},
issn = {1879-2448},
abstract = {Microplastics (MPs) biofilms are critical vectors for antibiotic resistance in aquatic environments. In this study, in situ incubation coupled with metagenomic sequencing was employed to investigate microbial colonization patterns, antibiotic resistance gene (ARG) profiles, and mobile genetic element (MGE) dissemination characteristics of biofilms on MPs surfaces of different polymer types and aging states within a unique wetland ecosystem. Results demonstrated that microorganisms preferentially colonized the hydrophobic surface of conventional polypropylene (PP) over biodegradable polylactic acid (PLA). Aging treatments further enhanced MP-microbe interactions. Microbial community analysis revealed selective enrichment of microbial communities in MPs biofilms, including clinically relevant pathogens such as Acinetobacter baumannii. Notably, despite showing lower microbial colonization, PLA enriched a higher abundance of priority antibiotic-resistant pathogens and high-risk ARGs, which further amplified following environmental aging. Co-occurrence network analysis identified seven key MGEs strongly correlated with multiple ARGs and exhibited the highest abundance on PLA-derived biofilms, indicating a high potential for horizontal gene transfer mediating the propagation of antibiotic resistance. Furthermore, Enterobacteriaceae were identified as critical co-hosts of ARGs and MGEs within the plastisphere, potentially playing a central role in maintaining antibiotic resistance. Our findings highlight a significant ecological threat from biodegradable and aged MPs in amplifying antibiotic resistance.},
}

@article {pmid41534271,
year = {2026},
author = {Zhou, W and Duan, C and Xue, M and Li, S and Fan, X and Wu, H},
title = {Diversity and potential environmental risks of DNA viruses on international ships' ballast water at Shanghai port, China.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119198},
doi = {10.1016/j.marpolbul.2025.119198},
pmid = {41534271},
issn = {1879-3363},
abstract = {Over 10 billion tons of ballast water is transferred annually globally, transporting many microorganisms such as bacteria and viruses into new environments and harming local ecology, economy and human health. Numerous studies on bacteria in ballast water have shown its remarkable bacterial diversity and potential risks in recent years. However, the diversity of viruses present in ballast water and their potential environmental implications remain extremely limited in our understanding. In this investigation, we utilized viral metagenomic sequencing to evaluate the viral diversity and distribution in ballast water sourced from five distinct shipping routes that docked at Shanghai Port. Additionally, we compared the distribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) harbored by viruses in ballast water from different routes. The viral diversity and community composition exhibited significant differences in the ballast water samples collected along distinct shipping routes. The virus diversity index varies across different routes, and notably, for the Shannon and Pielou indices, the DJ and GG routes were significantly lower than other routes. Although Caudoviricetes was the dominant viral group, the abundances of Megaviricetes and Faserviricetes were also relatively high, albeit showing variations among different routes. 224 ARGs were identified, including 143 single resistance genes (SARGs) and 81 multiple resistance genes (MARGs), and their distribution varied across different shipping routes. Similarly, certain types of VFs also exhibit differences across various routes, including nutritional/metabolic processes, biofilm formation, and exotoxins. Moreover, the comparison of viral environmental risks showed that ballast water from routes through the Indian Ocean and the South China Sea posed a greater environmental risk. In summary, the results of our research have uncovered the virus diversity and potential risks associated with different routes. This underscores the imperative of implementing targeted management strategies for each individual route.},
}

@article {pmid41533915,
year = {2026},
author = {Pang, J and Wei, Z and Zhang, Z and Xu, X and Peng, Y and Chen, Q and Wei, Y and Liu, J and Zhang, Y and Shi, Q and Wang, Z and Zhang, Y and Chen, K and Zhou, M and Lu, X and Liang, Q},
title = {Genomic Landscape Reveals Correlation of Endosymbiont Ralstonia With Acanthamoeba Keratitis Severity.},
journal = {Investigative ophthalmology & visual science},
volume = {67},
number = {1},
pages = {17},
doi = {10.1167/iovs.67.1.17},
pmid = {41533915},
issn = {1552-5783},
mesh = {Animals ; *Acanthamoeba Keratitis/microbiology/parasitology/diagnosis/genetics ; Mice ; *Acanthamoeba/genetics/microbiology ; *Symbiosis ; *Ralstonia/genetics/physiology ; Humans ; Whole Genome Sequencing ; Disease Models, Animal ; Female ; In Situ Hybridization, Fluorescence ; Microscopy, Electron, Transmission ; Cornea/parasitology/pathology ; Male ; Genome, Bacterial ; Severity of Illness Index ; Genomics ; },
abstract = {PURPOSE: To identify the basic genomic profile of Acanthamoeba, obtain information on Acanthamoeba endosymbionts, and analyze the correlation between these endosymbionts and the prognosis of Acanthamoeba keratitis (AK) patients.

METHODS: Whole-genome sequencing was conducted on 30 cornea-derived Acanthamoeba strains. Pan-genome analysis was performed, and endosymbionts were identified by metagenomic analysis. Gimenez staining, fluorescence in situ hybridization, and transmission electron microscopy were used to prove the existence of endosymbionts. Linear discriminant analysis effect size was used to associate endosymbiont species with AK clinical prognosis. The correlation between the endosymbiont Ralstonia and pathogenicity was experimentally validated by assessing the biological characteristics of Acanthamoeba and by performing clinical and histopathological evaluations in AK mouse models.

RESULTS: Whole genome sequencing revealed that the Acanthamoeba genome size was 37.1-105.0 Mb and GC content was 53.9%-60.5%. Pan-genomic analysis indicated an open state of the Acanthamoeba genome. Metagenomic analysis identified the presence of endosymbionts within Acanthamoeba, notably the endosymbiont Ralstonia, which was associated with poor prognosis at the genus level (P = 0.047). Acanthamoeba harboring the endosymbiont Ralstonia exhibited an increased migration area, enhanced adhesion, and had a more pronounced cytopathic effect. The size of clinical scores and corneal ulcers showed a significant increase in mouse models induced by Acanthamoeba with endosymbiont Ralstonia.

CONCLUSIONS: Whole-genome sequencing highlighted the symbiotic relationship between Acanthamoeba and associated microorganisms. The presence of the endosymbiont Ralstonia influenced the biological characteristics of Acanthamoeba and was correlated with clinical poor prognosis in AK, suggesting its potential as a target for clinical intervention.},
}

Animals
*Acanthamoeba Keratitis/microbiology/parasitology/diagnosis/genetics
Mice
*Acanthamoeba/genetics/microbiology
*Symbiosis
*Ralstonia/genetics/physiology
Humans
Whole Genome Sequencing
Disease Models, Animal
Female
In Situ Hybridization, Fluorescence
Microscopy, Electron, Transmission
Cornea/parasitology/pathology
Male
Genome, Bacterial
Severity of Illness Index
Genomics

@article {pmid41533582,
year = {2026},
author = {Ahrendt, SR and Haridas, S and Stong, S and Salamov, A and Steindorff, A and LaButti, K and Riley, R and Shabalov, I and Lukashin, I and Dusheyko, S and Schulz, F and Romero, MF and Villada, JC and Grigoriev, IV and Mondo, SJ},
title = {Comparative mitogenomics of kingdom Fungi - evolutionary insights and metagenomic applications.},
journal = {Nucleic acids research},
volume = {54},
number = {2},
pages = {},
doi = {10.1093/nar/gkaf1419},
pmid = {41533582},
issn = {1362-4962},
support = {//U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; *Metagenomics/methods ; *Fungi/genetics/classification ; Genome, Fungal ; Phylogeny ; RNA, Transfer/genetics ; Molecular Sequence Annotation ; },
abstract = {Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.},
}

*Genome, Mitochondrial
*Evolution, Molecular
*Metagenomics/methods
*Fungi/genetics/classification
Genome, Fungal
Phylogeny
RNA, Transfer/genetics
Molecular Sequence Annotation

@article {pmid41532487,
year = {2026},
author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK},
title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2026.2614431},
pmid = {41532487},
issn = {1549-7828},
abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.},
}

@article {pmid41532447,
year = {2026},
author = {Ning, W and Hu, G and Yuan, D and Arick, MA and Hsu, CY and Magbanua, ZV and Pechanova, O and Peterson, DG and Dong, Y and Udall, JA and Grover, CE and Wendel, JF},
title = {Comparative Population Genomics of Relictual Caribbean Island Gossypium hirsutum.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70239},
doi = {10.1111/mec.70239},
pmid = {41532447},
issn = {1365-294X},
support = {141589//National Science Foundation Plant Genome Program/ ; 22-605//Cotton Incorporated/ ; 58-6066-0-066//USDA ARS Non-Assistance Cooperative Agreements/ ; 58-6066-0-064//USDA ARS Non-Assistance Cooperative Agreements/ ; //Iowa State University/ ; },
mesh = {*Gossypium/genetics ; *Genetics, Population ; Genetic Variation ; Phylogeny ; Gene Flow ; Genome, Plant ; Puerto Rico ; Guadeloupe ; Metagenomics ; Domestication ; Genomics ; Islands ; },
abstract = {Gossypium hirsutum is the world's most important source of cotton fibre, yet the diversity and population structure of its wild forms remain largely unexplored. The complex domestication history of G. hirsutum combined with reciprocal introgression with a second domesticated species, G. barbadense, has generated a wealth of morphological forms and feral derivatives of both species and their interspecies recombinants, which collectively are scattered across a large geographic range in arid regions of the Caribbean basin. Here we assessed genetic diversity within and among populations from two Caribbean islands, Puerto Rico (n = 43, five sites) and Guadeloupe (n = 25, one site), which contain putative wild or introgressed forms. Using whole-genome resequencing data and a phylogenomic framework derived from a broader genomic survey, we parsed individuals into feral derivatives and truly wild forms. Feral cottons display uneven levels of genetic and morphological resemblance to domesticated cottons, with diverse patterns of genetic variation and heterozygosity. These patterns are inferred to reflect a complex history of interspecific and intraspecific gene flow that is spatially highly variable in its effects. Wild cottons in both Caribbean islands appear to be relatively inbred, especially the Guadeloupe samples. Our results highlight the dynamics of population demographics in relictual wild cottons that experienced profound genetic bottlenecks associated with repeated habitat destruction superimposed on a natural ecogeographical distribution comprising widely scattered populations. These results have implications for conservation and utilisation of wild diversity in G. hirsutum.},
}

*Gossypium/genetics
*Genetics, Population
Genetic Variation
Phylogeny
Gene Flow
Genome, Plant
Puerto Rico
Guadeloupe
Metagenomics
Domestication
Genomics
Islands

@article {pmid41531535,
year = {2025},
author = {Walia, A and Selvarajan, R and Ogola, HJO and Chauhan, R and Bala, J and Verma, SK and Kumar, R},
title = {Genome-resolved analysis of traditional fermented biofertilizers as scalable solutions for soil restoration.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725475},
doi = {10.3389/fmicb.2025.1725475},
pmid = {41531535},
issn = {1664-302X},
abstract = {Soil degradation threatens global food security by eroding nutrient reserves and biological resilience. Microbial solutions that regenerate soil fertility through ecological processes offer a sustainable alternative to chemical intensification, yet lack mechanistic validation linking genomic potential to field performance. Fermented microbial consortia, naturally assembled through traditional practices worldwide, represent promising but underexplored technologies for biological soil restoration. Here, we integrate shotgun metagenomics, metagenome-assembled genome (MAG) reconstruction, and two-season field trials to evaluate Jeevamrit, a cattle-derived fermented biofertilizer widely used across South Asia, as a model system for understanding microbial-mediated soil restoration. Metagenomic profiling revealed that Jeevamrit fermentation of cattle dung and urine produces a functionally rich microbial consortium dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Thirty high-quality MAGs encoded genes for nitrogen fixation (nifHDK), phosphate solubilization (phoA, pstS), potassium transport (trkA, phoR), siderophore biosynthesis, and phytohormone production (trpA, miaB), alongside enriched CAZymes (GH13, PL1) and biosynthetic clusters (NRPS, PKS, terpenes) supporting nutrient turnover and rhizosphere signaling. Field application in severely degraded Himalayan rice soils substantially improved soil health relative to controls: soil organic carbon increased from 0.53%-0.68% to 0.76%-1.04% (up to 96% increase), microbial biomass carbon rose from ~72 mg C kg[-1] to 186-282 mg C kg[-1] (159% increase), available phosphorus increased 39.5%, and grain yield improved 74%, while pH and electrical conductivity remained stable. Principal component analysis confirmed that SOC, microbial biomass, and nutrient availability drove treatment differentiation, corroborating genomic predictions. This genome-to-field framework establishes fermented microbial consortia as multifunctional solutions that restore soil fertility through ecological intensification rather than chemical supplementation. By demonstrating that traditional farmer innovations can be genomically validated and mechanistically understood, this work provides a replicable model for scaling nature-based, low-cost soil restoration technologies to address global agricultural sustainability challenges.},
}

@article {pmid41531093,
year = {2026},
author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W},
title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {650-662},
doi = {10.13227/j.hjkx.202411219},
pmid = {41531093},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Gossypium/growth & development ; Metagenomics ; Soil/chemistry ; Biodegradation, Environmental ; *Agriculture/methods ; Microbiota ; },
abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.},
}

*Soil Microbiology
*Gossypium/growth & development
Metagenomics
Soil/chemistry
Biodegradation, Environmental
*Agriculture/methods
Microbiota

@article {pmid41531057,
year = {2026},
author = {Fan, YT and Chang, S and Wang, ER and Zhu, YY and Wang, SJ and Yin, XY},
title = {[Distribution， Diffusion Regularity， and Influencing Factors of Antibiotic Resistance Genes in the Water Transfer Chain from Luanhe River to Tianjin Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {256-268},
doi = {10.13227/j.hjkx.202410104},
pmid = {41531057},
issn = {0250-3301},
mesh = {Rivers/microbiology ; China ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Water Microbiology ; Environmental Monitoring ; Water Supply ; },
abstract = {Yuqiao Reservoir is an important drinking water source for Tianjin. As the source of the "Water Diversion Project from Luanhe River to Tianjin"， there are more than one hundred types of contamination of antibiotic resistance genes （ARGs） in the Panjiakou and Daheiting Reservoirs. However， the level of ARGs in the upstream water transfer chain of Yuqiao Reservoir （Linhe River， Shahe River， and Lihe River） has not yet been studied. It is necessary to characterize the dynamic mechanism of ARGs in this basin to gain a deeper understanding of water ecosystem security. In this study， metagenomic methods were used to investigate the distribution characteristics of ARGs and mobile genetic elements （MGEs） in the surface water of the water transfer chain from Luanhe River to Tianjin during different periods， combined with the correlation mechanisms among microbial community structure and environmental factors. The results showed that the water transfer chain of the Luan River to Tianjin contained 21 types of ARGs with 1 161 subtypes. The main types of ARGs were multidrug， macrolide-lincosamide-streptogramin b （MLSB）， and tetracycline， with macB and tetA58 being the dominant ARGs. The predominant types of MGEs were integration/excision （IE） and replication/recombination/repair （RRR）. Compared to that during the flood period， there was a significant positive correlation between ARGs and MGEs during the dry period. Correlation analysis indicated that temperature， dissolved oxygen， and nitrate showed significant correlation with various ARGs （P < 0.05）. The abundance of ARGs was more easily affected by multiple environmental factors， but the composition of ARGs showed correlations only with total phosphorus and dissolved total phosphorus. Proteobacteria was the most dominant phylum， and several dominant microbial genera， such as Acidovorax and Rhodoferax， also showed significant correlation with ARGs， especially during the dry period. The co-occurrence network analysis revealed the most significant co-occurrence relationship between ARGs and MGEs， and some microbial genera related to nutrient elements and photosynthesis also showed co-occurrence relationships with major ARGs. This project aims to profoundly understand the biogeochemical cycle mechanisms of ARGs in the upstream water transfer chain of the reservoir， and it can provide a scientific basis for decision-making to control the transmission of resistance genes within the regional basin.},
}

Rivers/microbiology
China
*Drug Resistance, Microbial/genetics
*Metagenomics
*Water Microbiology
Environmental Monitoring
Water Supply

@article {pmid41530917,
year = {2026},
author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF},
title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611544},
doi = {10.1080/19490976.2025.2611544},
pmid = {41530917},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Big Data ; *Software ; Colorectal Neoplasms/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Computational Biology/methods ; Gastrointestinal Microbiome ; Reproducibility of Results ; },
abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.},
}

*Metagenomics/methods
Humans
*Metagenome
*Big Data
*Software
Colorectal Neoplasms/microbiology
*Bacteria/classification/genetics/isolation & purification
*Computational Biology/methods
Gastrointestinal Microbiome
Reproducibility of Results

@article {pmid41530889,
year = {2026},
author = {Bonacolta, AM and Keeling, PJ},
title = {Modern microbialites harbor an undescribed diversity of chromerid algae.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00852-4},
pmid = {41530889},
issn = {2524-6372},
support = {GBMF9201//Gordon and Betty Moore Foundation/ ; },
abstract = {BACKGROUND: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.

RESULTS: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.

CONCLUSIONS: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.},
}

@article {pmid41530817,
year = {2026},
author = {Li, R and Liao, X and Fu, X and Li, X and Liao, X and Cen, S and Zeng, J and Huang, L and Chi, H and Zou, Y},
title = {Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {33},
pmid = {41530817},
issn = {1749-8546},
support = {2022A1515140011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010012//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 20231800936162//Dongguan Science and Technology of Social Development Program/ ; 20221800905632//Dongguan Science and Technology of Social Development Program/ ; },
abstract = {BACKGROUND: Promoting intestinal barrier repair and epithelial regeneration is a core therapeutic objective in managing ulcerative colitis (UC). Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora, and Glycyrrhiza uralensis, is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.

PURPOSE: This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.

METHODS: Mice developed colitis after drinking water with a 3.5% (w/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.

RESULTS: High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.

CONCLUSION: HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel "microbiota-tryptophan metabolism-AhR-ISC differentiation" axis underlying HQD's therapeutic efficacy in UC.},
}

@article {pmid41530663,
year = {2026},
author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX},
title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {40},
pmid = {41530663},
issn = {1471-2164},
support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41530170,
year = {2026},
author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S},
title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {29},
pmid = {41530170},
issn = {2052-4463},
support = {Laboratoire international associé program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; },
abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.},
}

Chile
France
Metagenomics
Ecosystem
*DNA Barcoding, Taxonomic
*Metagenome
Seawater/microbiology
Salinity
Microbiota

@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68255-6},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}

@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}

@article {pmid41529797,
year = {2026},
author = {Cao, X and Zhang, L and Tu, H and Li, T and Wang, G and Xiao, L and Zhang, Y and Liu, P and Li, Y and Li, J and Li, X and Hu, B and Zhang, S and Li, B},
title = {Membrane aerated biofilm reactor for largely enhanced nitrogen removal in low carbon/nitrogen ratio municipal wastewater: integrating nitrification, partial denitrification, and anammox.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133994},
doi = {10.1016/j.biortech.2026.133994},
pmid = {41529797},
issn = {1873-2976},
abstract = {This study first established an integrated nitrification-partial denitrification-anammox (INPDA) process in a single-stage membrane aerated biofilm reactor (MABR) under low dissolved oxygen concentrations (0.12-0.27 mg/L) and low carbon/nitrogen ratios (1.0-3.0), without the need for anaerobic ammonia-oxidizing bacteria (AnAOB) inoculation. The optimal effluent total nitrogen (TN) concentration reached below 5 mg/L, achieving a 92.7% TN removal efficiency. Nitrifiers (including Ellin6067 and Nitrospira) oxidized a portion of ammonium to nitrate, which was subsequently reduced to nitrite by partial denitrifier Thauera utilizing influent organic carbon. Subsequently, AnAOB Candidatus Brocadia converted remaining ammonium and available nitrite into nitrogen. Metagenomics further confirmed a 32.96-fold increase in anammox-associated gene (hdh) abundance during INPDA establishment. Notably, this elevated hdh abundance remained stable even as carbon/nitrogen ratio increased, demonstrating process robustness. This study established a promising single-stage MABR strategy to advance mainstream anammox application.},
}

@article {pmid41529636,
year = {2026},
author = {Díaz-Moreno, N and Lebrero, R and Cantera, S},
title = {Toluene bioconversion into ectoines by halophile mixed microbial cultures.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141045},
doi = {10.1016/j.jhazmat.2026.141045},
pmid = {41529636},
issn = {1873-3336},
abstract = {Toluene, which has been listed in the Pollutant Release and Transfer Register (PRTR) of many countries, is one of the most emitted pollutants to the atmosphere. This study demonstrates for the first time a new perspective in toluene treatment based on its continuous bioconversion into high-value chemicals, specifically ectoine and hydroxyectoine, which hold considerable commercial relevance in the cosmetic industry with market prices reaching 1000 € kg[-1]. Specific ectoine and hydroxyectoine contents of 27.3 mg gTSS[-1] were achieved together with toluene elimination capacities of 7.2 ± 1.9 g m[-3] h[-1] and a maximum biomass concentration of 1.8 g L[-1]. Ectoine synthesis predominated initially, later shifting toward hydroxyectoine, reaching a combined amount of 71.2 mg L[-1] (ectoine:hydroxyectoine 32:68) by the end of the assay. Metagenomic analysis revealed key pathways and taxa involved in toluene degradation and ectoine and hydroxyectoine synthesis. Members of Paenibacillus, Rhodococcus and Microbacterium were identified as possessing the enzymes required for toluene degradation via the TOL pathway, while Gordonia, the most abundant genus, was primarily associated with the degradation of intermediates such as benzoate, muconate, or oxoadipate derivatives and their bioconversion into ectoine. These findings revealed a potential metabolically diverse consortium with functional complementarities, where metabolic synergies overcome species-specific limitations and promote the elimination and subsequent valorization of toluene into high-value products fostering sustainable industrial innovation.},
}

@article {pmid41529631,
year = {2026},
author = {Wang, Y and Qian, Y and Shi, C and Bi, J and Dong, P and Zou, Y and Yang, Y and Tao, Y and Li, H},
title = {Seasonal dynamics and stability of gut antibiotic resistance genes in plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi).},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141112},
doi = {10.1016/j.jhazmat.2026.141112},
pmid = {41529631},
issn = {1873-3336},
abstract = {The extreme ecosystems of the Tibetan Plateau harbor an alarming reservoir of antibiotic resistance genes (ARGs) within wildlife gut microbiomes-an emerging contaminant with significant implications for One Health. However, seasonal dynamics and pathogenic risks of these ARGs remain poorly understood. Through a 2.5-year study comparing the subterranean plateau zokor (Eospalax baileyi) and the surface-dwelling plateau pika (Ochotona curzoniae), we demonstrate how species-specific ecological strategies shape distinct ARG transmission patterns. Our results demonstrated striking eco-evolutionary trade-offs: surface pikas showed 1.3 times higher ARG diversity with strong seasonal variation, influenced by temperature-modulated bacterial community turnover and mobile genetic elements (MGEs). Conversely, subterranean zokors maintained stable, were enriched with high-risk ARGs dominated by mepA and tetO, reflecting their isolated niche. Both species consistently carried pathogenic-ARG complexes (Clostridium-bacA, Staphylococcus-Ermb) across seasons, genders, and ages, indicating established resistance reservoirs in plateau food webs. Metagenomic binning revealed co-transfer potential between ARGs and MGEs. This pioneering longitudinal study exposes a dual pattern: seasonal changes cause temporary turnover of ARGs, which harbor lower resistance risk in surface-dwelling animals, while subterranean hosts retain stable, higher-risk resistance. These findings establish critical baselines for monitoring antimicrobial resistance in vulnerable ecosystems and underscore the need for integrated One Health strategies.},
}

@article {pmid41529629,
year = {2026},
author = {Chen, Z and Zhao, Y and Jin, L and Ma, R and Zhao, H and Ren, H and Huang, H},
title = {Insights into the molecular mechanism driving transformation and detoxification of erythromycin in anoxic biofilters.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141116},
doi = {10.1016/j.jhazmat.2026.141116},
pmid = {41529629},
issn = {1873-3336},
abstract = {Erythromycin (ERY), the most prevalent macrolide antibiotic detected in aquatic environments worldwide, has attracted considerable scientific interest. This concern stems from its persistent environmental presence, largely due to the limited removal efficiency of conventional wastewater treatment processes. Anoxic biofilters were established with two nutritional modes (heterotrophic/autotrophic) and two filter media (bio-ceramic/poly-urethane particle) to reveal the migration and transformation patterns of ERY. Through non-targeted and targeted analysis, 18 transformation products (TPs) were identified, including 11 previously unreported TPs. By integrating metagenomic analysis with molecular docking, key genes, enzymes, and pathways were identified. Linking the molecular mechanism of ERY transformation with toxicity prediction can categorize the toxicity of TPs from high to low into four levels. It is worth noting that the hydrolysis, phosphorylation, and oxidation of hydroxy process is most conducive to reducing the environmental toxicity of ERY. This study elucidated the fate characteristics of ERY in anoxic biofilter at the molecular level. This work provides a theoretical basis for optimizing biofilter operation to mitigate ERY. It also offers insights for developing green, advanced wastewater treatment technologies aimed at ensuring water quality health.},
}

@article {pmid41529435,
year = {2026},
author = {Xiao, Y and Sheng, ZM and Taubenberger, JK},
title = {Precursors to the 1918 pandemic: Finding Rickettsia felis and Mucor co-infection associated with a death in 1912.},
journal = {International journal of paleopathology},
volume = {52},
number = {},
pages = {69-75},
doi = {10.1016/j.ijpp.2026.01.001},
pmid = {41529435},
issn = {1879-9825},
abstract = {OBJECTIVE: To investigate potential molecular evidence of the presence of infuenza A in a patient who died in 1912.

MATERIALS: Two to three paraffin curls from a formalin-fixed paraffin-embedded (FFPE) lung sample from an autopsy case of a one-and-a-half-year-old girl who reportedly died of acute pneumonia at the Royal London Hospital on February 1, 1912.

METHODS: RNA was extracted from the sample. Real-time reverse transcription PCR (RT-PCR) was performed to screen for influenza A virus, followed by total RNA library preparation and high-throughput sequencing on the Illumina NextSeq platform. Bioinformatic analysis was conducted on the obtained reads, which included metagenomic classification and sequence alignment to reference genomes.

RESULTS: Real-time RT-PCR and next-generation sequencing both revealed no evidence of influenza A virus infection. However, metagenomic analysis identified a significant number of reads matching Rickettsia felis, with 233 unique reads specifically aligning to its OmpB gene, and over 4 million fungal reads classified within the Mucor genus, although the exact species could not be determined. These findings provide suggestive molecular evidence of co-infection with R. felis and a Mucor species.

CONCLUSIONS: This study demonstrates the utility of modern molecular techniques in evaluating early diagnoses. Despite records attributing the cause of death to acute pneumonia, no influenza A virus RNA was detected. The identification of R. felis and Mucor sequences suggests that this rare co-infection may have contributed to the infant's death.

SIGNIFICANCE: Retrospective diagnosis is enhanced by the use of modern molecular and bioinformatic techniques. This case study provides important paleopathological insight into the etiology of recorded "acute pneumonia", indicating the presence of pathogens other than influenza A leading up to the 1918 pandemic.

LIMITATIONS: Contamination during autopsy, tissue processing, or storage cannot be ruled out. Due to the lack of remaining material, histopathological confirmation of Mucor or Rickettsia infection was not possible.

Molecular and bioinformatic research into other cases of suspected influenza A.},
}

@article {pmid41529381,
year = {2026},
author = {Haars, J and Cumlin, T and Ladenvall, C and Lennerstrand, J and Kaden, R},
title = {Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel.},
journal = {Virology},
volume = {616},
number = {},
pages = {110789},
doi = {10.1016/j.virol.2026.110789},
pmid = {41529381},
issn = {1096-0341},
abstract = {The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within samples. This study presents a novel protocol called Twist-ONT, integrating Twist CVRP with Oxford Nanopore Technologies (ONT) long-read sequencing. Using clinical nasopharyngeal/throat swab and plasma samples PCR-positive for a variety of different viruses, the protocol's capability for viral species classification was demonstrated. It is also shown how high-quality whole-genome assemblies and consensus sequences can be generated from the sequencing reads of this protocol. This protocol facilitates further studies into the viromes of clinical samples and viral genomics in general using ONT sequencing.},
}

@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}

@article {pmid41528680,
year = {2026},
author = {Wu, C and Zeng, B and Ning, Z and Wang, W and Wang, Y and Zhang, Q and Lu, D},
title = {Cloning and Characterization of a PL6 Alginate Lyase Aly94 from the Marine Bacteria.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41528680},
issn = {1559-0305},
support = {32201039//National Natural Science Foundation of China/ ; ZR2022QC247//Natural Science Foundation of Shandong Province/ ; 2023YX040//Weifang Science and Technology Development Plan Project (Medical Category)/ ; },
abstract = {Microbial alginate lyases are essential biocatalysts for analyzing alginate structure and sustainably producing bioactive alginate oligosaccharides (AOS). In this study, we characterized Aly94, a novel alginate lyase from the polysaccharide lyase family 6 (PL6) family, identified from a marine sediment metagenomic library. Biochemical analyses showed Aly94 exhibits optimal activity at 40 ℃ in 50 mM NaH2PO4-Na2HPO4 buffer (pH 7.0). Adding 20 mM NaCl significantly increases its catalytic efficiency. The enzyme exhibits a strong preference for polyguluronate (polyG) over polymannuronate (polyM), with specific activities of 4.19 U/mg (polyG), 0.25 U/mg (polyM), and 2.45 U/mg (alginate). When degrading substrates-particularly polyG-Aly94 primarily generates trisaccharides. Although Aly94 acts as an endolytic alginate lyase, it also could digest the monosaccharides from small oligosaccharide chains (∆G3, ∆G4). These catalytic properties, combined with its polyG-specific depolymerization, made Aly94 a promising candidate for biotechnological applications requiring controlled alginate saccharification and high-value AOS production.},
}

@article {pmid41528333,
year = {2026},
author = {Velioglu, EM and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, SS},
title = {Corrigendum: Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {75},
number = {1},
pages = {},
doi = {10.1099/jmm.0.002120},
pmid = {41528333},
issn = {1473-5644},
}

@article {pmid41528142,
year = {2026},
author = {Boey, JS and Tee, HS and Waite, DW and Handley, KM},
title = {Genetic mechanisms for estuarine carbohydrate degradation and linked transcriptional activity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0185225},
doi = {10.1128/aem.01852-25},
pmid = {41528142},
issn = {1098-5336},
abstract = {The current understanding of carbohydrate substrate degradation is largely derived from incubation experiments involving specific substrates. In estuaries, carbohydrates are often grouped together with other sources of carbon, for analytical purposes, and measured as total and fractional organic matter. Here, we describe putative carbohydrate degradation at the polysaccharide level by the prokaryotic community in an estuary. Samples were collected along a freshwater-to-marine salinity gradient from both the water column and underlying benthic sediments. Metagenomic and metatranscriptomic data were used to determine carbohydrate-active enzyme (CAZyme)-encoding metagenome-assembled genomes and associated transcriptional activity across the gradient. Previous work demonstrated assimilation of xylan (a component of hemicellulose) in estuaries. We show the genetic mechanisms associated with the degradation of xylan, as well as arabinogalactan (also from hemicellulose), and various other glycans were widespread among estuarine taxa and actively expressed. In addition, results show different carbohydrate degradation strategies between planktonic and benthic organisms. For example, results indicate that sediment communities harbored a greater variety and density of CAZyme-encoding genes and capacity to degrade complex plant biomass (cellulose and hemicellulose) and dedicated more gene transcription overall to CAZymes than planktonic communities. In contrast, planktonic prokaryotes tended to express a greater fraction of their CAZyme-encoding gene repertoires. The transcription of gene clusters associated with degrading beta-1,3-glucans such as laminarin was prevalent in the water column. Microbial activity to degrade alpha-glucans such as glycogen was predicted to be ubiquitous but was greatest in planktonic communities. Taken together, results highlight differences in the capacity of planktonic and benthic communities to degrade carbohydrates, which reflect differences in substrate availability and complexity.IMPORTANCEEstuaries are productive ecosystems that combine various forms of organic carbon from autochthonous (e.g., algal primary producers and mangroves) and allochthonous (e.g., terrestrial plant) sources. The degradation and recycling of this organic carbon is driven by heterotrophic bacteria that are expected to harbor diverse genetic mechanisms for carbohydrate degradation to match the diversity and complexity of organic carbon encountered in the environment. Results here illustrate the diversity of carbohydrate-active enzymes (notably glycosyl hydrolases) encoded by estuarine communities and the different substrate prioritizations of planktonic and benthic communities.},
}

@article {pmid41528122,
year = {2026},
author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW},
title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41528122},
issn = {2057-5858},
mesh = {*Intensive Care Units ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Humans ; Queensland ; *Environmental Monitoring/methods ; Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Metagenomics/methods ; Cross Infection/microbiology ; },
abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.},
}

*Intensive Care Units
*Bacteria/genetics/isolation & purification/classification/drug effects
Humans
Queensland
*Environmental Monitoring/methods
Drug Resistance, Bacterial/genetics
Microbiota/genetics
Metagenomics/methods
Cross Infection/microbiology

@article {pmid41527828,
year = {2026},
author = {Kaur, I and Shaw, B and Multani, A and Malhotra, S and Dong, HV and Lukose, C and Prabaker, K and Saleh, T and Sim, YB and Tymchuk, CN and Uslan, DZ and Zhou, H and Brewer, TF and Yang, S},
title = {Clinical utility of serial plasma cell-free DNA metagenomic next-generation sequencing assays.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1017/ice.2025.10390},
pmid = {41527828},
issn = {1559-6834},
abstract = {This single center retrospective observational study of serial plasma metagenomic next-generation sequencing testing shows that >95% of serial testing was without meaningful clinical impact. Only 5/173 cases were adjudicated as having significant clinical impact.},
}

@article {pmid41527291,
year = {2026},
author = {Chen, W and Guo, R and Zhang, W and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Yan, Q and Kang, J and Yang, J},
title = {Alterations of the gut virome in patients with Parkinson's disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glag001},
pmid = {41527291},
issn = {1758-535X},
abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.},
}

@article {pmid41527156,
year = {2026},
author = {Buffoni, M and Kerkvliet, JJ and Enting, H and Kers, JG and Rogers, M and Visser, JAGM and Paganelli, FL and Willems, RJL and Schürch, AC},
title = {Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {3},
pmid = {41527156},
issn = {2524-4671},
abstract = {BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR) due to their antimicrobial properties and the ability of bacteria to evolve resistance to these drugs. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons.

RESULTS: In this study, we used metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. We also explored the mobile resistome, ARGs located on mobile genetic elements (MGEs) such as plasmids, which are capable of disseminating, investigating ARGs identifying with the potential to disseminate within and beyond farm settings. Our exploratory findings in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identified 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans.

CONCLUSIONS: Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00497-7.},
}

@article {pmid41527141,
year = {2026},
author = {Liu, YY and Xia, F and Yimuran, R and Nuermamaiti, A and Yang, Y and Zhou, JT},
title = {Assessing whether rectal swabs reflect appendiceal microbiota profiles in acute appendicitis: a 16S rRNA-based comparative study.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00794-1},
pmid = {41527141},
issn = {1757-4749},
support = {2023D01A93//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND: Acute appendicitis is associated with characteristic changes in the intestinal microbiota, but direct sampling of appendiceal contents is invasive and cannot be performed in healthy controls. We therefore evaluated whether rectal swabs could partially capture appendiceal microbiome signatures in adults with acute appendicitis.

METHODS: In a prospective cross-sectional study, we enrolled adults with acute appendicitis and healthy volunteers between October 2023 and December 2024. Four types of samples were collected: feces from healthy controls (HC), appendiceal luminal contents from patients with acute appendicitis (AC), intraoperative rectal swabs from patients with acute appendicitis (RS), and initial postoperative feces from patients with acute appendicitis (IF; first stool within 24 h after surgery). 16 S rRNA gene (V3-V4) sequencing was performed, and reads were processed with QIIME2. Alpha and beta diversity, differential taxonomic composition, and PICRUSt2-based functional predictions were compared across matrices. Genus-level and functional concordance between paired AC-RS samples was assessed.

RESULTS: After quality control, 64 AC, 34 RS, 24 IF, and 29 HC samples were included. Phylogenetic diversity (PD whole-tree) was higher in AC and RS than HC, with AC also higher than RS; IF showed lower PD than AC. Bray-Curtis principal coordinate analysis showed AC forming a distinct cluster separated from HC and RS along PC1, whereas IF overlapped with HC and RS. AC, RS, and IF were enriched for Escherichia/Shigella and Fusobacterium and depleted in butyrate-producing genera such as Faecalibacterium compared with HC. In the 21 paired AC-RS cases, genus-level relative abundances and several predicted functional pathways showed concordance, indicating that RS captured many but not all appendiceal dysbiosis features.

CONCLUSIONS: Our findings suggest that intraoperative rectal swabs may partially reflect appendiceal microbiome alterations at the genus and pathway levels and may serve as a minimally invasive adjunct for microbiome profiling in acute appendicitis. However, these associations are inferred from 16 S amplicon data in a modestly sized, antibiotic-exposed cohort and should be validated using shotgun metagenomics in larger, clinically stratified populations.},
}

@article {pmid41527052,
year = {2026},
author = {Zhou, L and Xu, Y and Wang, L and Li, X},
title = {Trichoderma harzianum fungemia following COVID-19-related immune dysregulation in an immunocompetent patient: a case diagnosed by mNGS.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12568-4},
pmid = {41527052},
issn = {1471-2334},
support = {No.2020SCZT062//Jilin Provincial Department of Finance,China/ ; },
}

@article {pmid41527012,
year = {2026},
author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P},
title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.},
journal = {Alzheimer's research & therapy},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13195-025-01941-1},
pmid = {41527012},
issn = {1758-9193},
abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.

METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.

RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.

CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.

TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.},
}

@article {pmid41526953,
year = {2026},
author = {Quijia-Pillajo, J and Naik, S and Chapin, LJ and Owen, JS and Jones, ML},
title = {Calcium phosphate-solubilizing bacteria promote growth and alleviate phosphorus deficiency in French marigold with minimal impact on the rhizosphere microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00844-w},
pmid = {41526953},
issn = {2524-6372},
support = {2021-09976//NIFA Agriculture and Food Research Initiative - Foundational Knowledge of Agricultural Production Systems/ ; },
abstract = {BACKGROUND: Plant roots are surrounded by communities of microbes that influence plant growth, development, and disease resistance. In soilless culture, microbial diversity in root-associated communities primarily originates from the substrate, irrigation water, and applied microbial inoculants. Phosphate solubilizing bacteria (PSB) capable of mobilizing phosphate from insoluble Ca3(PO4)2 were identified from a greenhouse rhizobacteria collection. Plant growth promoting efficacy was investigated at different substrate pH. The influence of the inoculum composition on plant growth responses to the bacteria was also evaluated. Finally, we analyzed the impact of PSB inoculation on microbiome composition and function.

RESULTS: From 1044 isolates in the rhizobacteria collection, 14 solubilized more than 25% of the phosphorus provided in vitro. Only eight bacterial strains resulted in growth promotion benefits in planta when inoculated as a substrate drench onto marigolds grown in a peat-based substrate (pH 7.0) and fertilized with insoluble Ca3(PO4)2. In a follow up experiment, two newly identified (Pantoea sp. C2G6 and Enterobacter soli C4A1) and three previously identified PSB (Pantoea trifolii C2B11, Pantoea formicae C8D10, and Bacillus velezensis) that have demonstrated superior phosphate-mineral solubilization were evaluated. The PSB were tested at a substrate pH of 6.0 and 6.5 using water, 1% glucose, 2% Micromate, or 0.1X Luria-Bertani (LB) broth as inoculant supplements. All five bacteria promoted growth and improved plant health at both pH levels. A greater benefit to marigold growth and health was observed in plants growing at pH 6.5. C2B11, C8D10, C2G6, and B. velezensis treatment resulted in a significant increase in shoot P content. Microbiome diversity and community structure exhibited no significant alterations in response to PSB treatment. Genes enriched in PSB treated rhizospheres were mostly related to colonization, competition, and biofertilization traits.

CONCLUSIONS: PSB isolated from the rhizosphere of floriculture crops grown in soilless substrates promoted growth and enhanced health of marigolds grown under P limitation. They also enhanced growth under optimal or slightly basic pH, but their efficacy was not improved by the inoculant supplements evaluated in this experiment. The native microbial community in peat-based soilless substrate was resilient to PSB inoculation.},
}

@article {pmid41526915,
year = {2026},
author = {Shao, D and Li, Y and Chen, S and Ma, S and Liu, Y and Huang, W and Liu, D and Lyu, Y and Xia, Z and Wang, Y},
title = {Improved RNA-based metagenomic sequencing for rapid pathogen detection in pets.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05174-0},
pmid = {41526915},
issn = {1746-6148},
support = {2022YFD18000400//National Key Research and Development Program of China/ ; PC2023A01002//Pinduoduo-China Agricultural University Research Fund/ ; },
}

@article {pmid41519702,
year = {2026},
author = {Zhang, Y and Tian, J and Xu, Y},
title = {Endogenous endophthalmitis secondary to neisseria meningitidis: a case report.},
journal = {BMC ophthalmology},
volume = {26},
number = {1},
pages = {16},
pmid = {41519702},
issn = {1471-2415},
support = {No.20241205//Medical Science Research Project of Hebei/ ; },
abstract = {BACKGROUND: Bacterial endogenous endophthalmitis (BEE) represents a rare but severe ophthalmological emergency which caused by hematogenous spread of bacterial infection. As its characteristics of insidious onset and rapid progression, BEE may lead to vision loss or even enucleation without immediate treatments. In recent years, with increasing numbers of immunosuppression and prevalence of resistant strains, incidence of BEE has risen, and its diagnosis and treatment face new challenges.

CASE PRESENTATION: A 15-year-old female patient was admitted to department of ophthalmology due to blurred vision and photophobia and lacrimation in the left eye for two days, and was first diagnosed as endophthalmitis and secondary glaucoma. During the diagnosis and treatment process, after smear culture of left chamber and vitreous aspirates, as well as the metagenomic next-generation sequencing (mNGS), final diagnosis of infectious endophthalmitis secondary to Neisseria meningitidis (N. meningitidis) was decided and a targeted treatment plan was developed. After intraocular injection and systemic antibiotic therapy, the patients was discharged after full control of the infection and improved endophthalmitis. Combined with literature review, this study discussed the application value of mNGS in diagnosing endogenous endophthalmitis.

CONCLUSION: mNGS shows significant value in the diagnosis of endogenous endophthalmitis in terms of improving positive rate of pathogen detection in intraocular fluid of infectious endophthalmitis and providing strong support for clinical treatments. The successful treatment of this case further confirms the promise of mNGS in ophthalmic infectious diseases. With the continuous progress of technology, mNGS is expected to be popularized and applied in more medical institutions to benefit more patients.},
}

@article {pmid41526579,
year = {2026},
author = {Fang, H and Pu, M and Jiang, A and Haiti, F and Liu, Y and Ailijiang, N and Mamat, A and Tu, X},
title = {Prevalence of antibiotic resistance gene in different wastewater treatment systems and effluent-irrigated soils through metagenomic analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35758-1},
pmid = {41526579},
issn = {2045-2322},
support = {XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; 51968067//National Natural Science Foundation of China/ ; 2024TSYCCX0014//the "Tianshan Yingcai" Cultivation Program/ ; },
abstract = {Wastewater treatment systems (WWTS) are considered to be the main source of antibiotic resistance genes (ARGs) spreading into the environment. In this study, samples were collected from WWTS influent, biological treatment tank effluent, and recycled water treatment plant (RTP) effluent during summer and winter, followed by metagenomic sequencing. The study investigated the differences in antibiotic resistance gene transfer between two typical wastewater treatment plants (WWTPs) processes and the impact of recycled water irrigation on ARG dissemination in soil. The WWTS (HD and MD) adopting two combined processes of "Adsorption-Biodegradation Process(AB)+ Anaerobic-Anoxic-Oxic Process(AAO)" and "AAO + Membrane Bioreactor(MBR)" as the research objects for the first time.The primary ARGs types identified were multidrug resistance, tetracycline, macrolide, and aminoglycoside resistance genes. The top three ARGs subtypes by relative abundance in the influent, biological treatment tank effluent, and total effluent were msrE, mphE, and ANT(6)-Ia, respectively. Seasonal variations did not significantly influence the distribution of ARGs in the two WWTSs. The AAO and AB processes increase the relative abundance and diversity of ARGs, while ARGs relative abundance decreases after RTP treatment but may proliferate new ARGs subtypes. Additionally, the efficiency of reducing the relative abundance of ARGs in summer is higher than that in winter. The two WWTSs were able to efficiently remove msrE and mphE. The abundance and diversity of ARGs and microorganisms were maximum in soil samples from the RTP. The microbial genera significantly related to ARGs may become its potential host, such as Rhodanobacter had significant correlations with ropB2, carA, and oleB. These results provide new insights into the control of ARGs contamination and focus on the risks associated with irrigated wastewater.},
}

@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00905-5},
pmid = {41526362},
issn = {2055-5008},
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}

@article {pmid41526357,
year = {2026},
author = {Cronin, P and Siegers, JY and Heang, V and Tok, S and Sin, S and Sievers, B and Omondi, V and Nuon, S and Chhel, K and Nouhin, J and Chim, V and Seng, B and Hak, M and San, S and Tum, S and Claes, FF and Firth, C and Su, YCF and Smith, GJD and Karlsson, EA},
title = {Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68245-8},
pmid = {41526357},
issn = {2041-1723},
abstract = {Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose a threat to humans. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission. Traditional sampling strategies are time-consuming, expensive and carry significant biosafety risks. Here, we assess the performance of metagenomics on environmental samples (ES) versus traditional poultry swabs for detecting viral pathogens in two Cambodian LBMs between January 2022 and April 2023. ES, including air (n = 35), cage swabs (n = 17), carcass wash water (n = 17) and drinking water (n = 9) are collected alongside oropharyngeal and cloacal swabs from chickens (n = 30) and ducks (n = 29). ES is sensitive in detecting 40 viruses from pathogen families including Orthomyxoviridae and Coronaviridae. Air samples capture the greatest diversity of poultry viruses. Viral contigs from ES show high sequence identity to poultry swab contigs when aligned to the same gene. We show ES outperforms poultry samples in detecting the highly pathogenic influenza A/H5N1, including clades 2.3.4.4b and 2.3.2.1c, which are found in the environment but are missed by poultry swabs. Our findings show metagenomics on ES replicates traditional surveillance, offering broader coverage and improved pathogen detection. This approach could be pivotal for mitigating zoonotic spillover and enhancing pandemic preparedness.},
}

@article {pmid41525981,
year = {2026},
author = {Yan, Y and Gao, Y and Gao, M and Chen, J and Cui, L and Ma, Y},
title = {Decipherment of dissolved organic matter compositions on waste activated sludge under in situ multi-enzyme pretreatment: novel bioavailability-oriented evaluation framework.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133995},
doi = {10.1016/j.biortech.2026.133995},
pmid = {41525981},
issn = {1873-2976},
abstract = {This study systematically elucidated the dissolved organic matters (DOM) molecular conversion and biological response mechanisms during anaerobic digestion (AD) of waste activated sludge (WAS) under different multi-enzyme pretreatment durations. Fourier transform ion cyclotron resonance mass spectrometry analysis revealed that the biodegradable protein-like and amino sugar-like substances were converted into recalcitrant aromatic nitrogen-containing compounds via hydrolysis, condensation, and cyclization processes as extended pretreatment duration, significantly reducing DOM bioavailability. Metagenomic sequencing further indicated that the DOM deterioration inhibited the enrichment of hydrolytic and acidogenic bacteria, thereby suppressed the acetotrophic methanogenesis and methane production. Based on these insights, a novel DOM bioavailability-oriented evaluation framework was proposed for WAS pretreatment optimization, focusing on three key metrics, including the relative abundance of biodegradable substrates, key microorganisms and functions, and methanogenic pathways. Expectantly this study may provide theoretical and data support for future precise design of enzymatic pretreatment process and high-efficiency AD of WAS.},
}

@article {pmid41525926,
year = {2026},
author = {Sbampato, V and De Marco, G and Tsoupras, A and Khan, A and Beaugé, A and Dayer, R and Tabard-Fougère, A and Ceroni, D},
title = {Next Generation Sequencing for Diagnosing Primary Osteoarticular Infections Compared to Conventional Culture: A Systematic Review and Meta-Analysis.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108380},
doi = {10.1016/j.ijid.2026.108380},
pmid = {41525926},
issn = {1878-3511},
abstract = {BACKGROUND: Osteoarticular infections (OAIs) in children is a significant diagnostic challenge for healthcare professionals. Traditional culture techniques are often time consuming and demonstrated low sensitivity. This systematic review aims to evaluate the diagnostic yield of metagenomic Next Generation Sequencing (mNGS) compared to standard culture for detecting pathogens in OAIs.

METHODS: A systematic review (PROSPERO CRD420251131272) of three databases (2000-2025) was performed. Study quality was assessed using the QUADAS-2 tool. A meta-analysis was performed using a random-effects model to calculate pooled positive detection rate with 95% confidence intervals (95%CI). Heterogeneity was quantified (I[2]), and sensitivity analysis with leave-one-out and subgroups were performed.

FINDINGS: From 35 included studies (>3000 patients), mNGS demonstrated a significantly higher pooled positive detection rate (81%; 95%CI:75 to 85%) than traditional culture (35%; 95%CI:29 to 41%) with high heterogeneity (>80%). mNGS performed consistently in pediatric (79%) and adult (81%) subgroups and was particularly effective for spinal infections (82%).

INTERPRETATION: The mNGS demonstrates a significantly higher diagnostic yield than standard culture for pathogen detection in osteoarticular infections. Its simplicity of execution, its fast-processing methods and high sensitivity, are promising factors that could lead to a more reliable detection of the causative microorganism responsible for an osteoarticular infection.},
}

@article {pmid41525910,
year = {2026},
author = {Fourgeaud, J and Veyrenche, N and Laloum, I and Jais, JP and Roger, C and Rabant, M and Mallet, V and Beaufrère, A and Fontaine, H and Leruez-Ville, M and Durand, F and Anglicheau, D},
title = {Occult rat Hepatitis E Virus Infection as a Cause of Cirrhosis and Post-Transplant Recurrence: Insights into the Role of Metagenomics.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.01.005},
pmid = {41525910},
issn = {1600-6143},
abstract = {We report the case of a kidney transplant recipient (2011) who developed persistent elevation of liver enzymes beginning in 2015. Extensive investigations including standard Hepatitis E virus PCR failed to identify a cause. In 2019, she developed decompensated cirrhosis and underwent liver-kidney transplantation in 2021. Post-transplant, liver function tests remained abnormal. Given suspicion of an unidentified pathogen, metagenomic next-generation sequencing was performed on the graft and identified rat hepatitis E virus. Retrospective testing of native liver and serum samples confirmed infection since 2015. Ribavirin therapy resulted in normalization of liver enzymes and viral clearance.},
}

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
doi = {10.1371/journal.pcbi.1013883},
pmid = {41525322},
issn = {1553-7358},
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

@article {pmid41525137,
year = {2026},
author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW},
title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41525137},
issn = {2057-5858},
mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; Secondary Metabolism/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Genome, Bacterial ; Sequence Analysis, DNA ; },
abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.},
}

*Porifera/microbiology
Animals
*Metagenome
*Microbiota/genetics
Secondary Metabolism/genetics
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
Multigene Family
Genome, Bacterial
Sequence Analysis, DNA

@article {pmid41524947,
year = {2026},
author = {Shafi, Z and Shahid, M and Singh, R},
title = {Food-borne bacterial pathogens: emerging approaches in detection and prevention.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {109},
pmid = {41524947},
issn = {1432-072X},
mesh = {*Food Microbiology/methods ; *Foodborne Diseases/prevention & control/microbiology/diagnosis ; *Bacteria/isolation & purification/genetics/classification/pathogenicity ; Humans ; Food Safety ; Computational Biology/methods ; },
abstract = {Food-borne bacterial pathogens remain a major public health concern, causing extensive illness and economic losses worldwide. Conventional detection methods are often slow and insufficient for identifying viable but non-culturable pathogens. Recent microbiological, biotechnological and bioinformatic advances have markedly improved food safety monitoring. Rapid molecular assays (PCR, qPCR, microarrays), next-generation sequencing, metagenomics, and emerging CRISPR-based diagnostics enable faster and more accurate pathogen detection and outbreak tracing. Bioinformatic tools-including genomic databases, phylogenetics, and machine-learning models-support predictive risk assessment and real-time surveillance. Preventive innovations such as bacteriophages, probiotics, antimicrobial peptides, nanotechnology-based interventions, and engineered microbes provide sustainable alternatives to chemical preservatives. Key challenges include variability across food matrices, biosafety considerations, and limited integration of multi-omics approaches into routine workflows. Overall, these emerging strategies offer improved precision and responsiveness for detecting and preventing food-borne bacterial pathogens.},
}

*Food Microbiology/methods
*Foodborne Diseases/prevention & control/microbiology/diagnosis
*Bacteria/isolation & purification/genetics/classification/pathogenicity
Humans
Food Safety
Computational Biology/methods

@article {pmid41524921,
year = {2026},
author = {Nayab, GE and Ur Rahman, R and Hanan, F and Khan, I and Fahim, M},
title = {Metagenomic Exploration of the Bacteriome Reveals Natural Wolbachia Infections in Yellow Fever Mosquito Aedes aegypti and Asian Tiger Mosquito Aedes albopictus.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {133},
pmid = {41524921},
issn = {1432-0991},
mesh = {Animals ; *Aedes/microbiology/classification ; *Wolbachia/genetics/classification/isolation & purification ; Phylogeny ; Pakistan ; Metagenomics ; *Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; *Microbiota ; *Metagenome ; Electron Transport Complex IV/genetics ; DNA, Bacterial/genetics ; },
abstract = {Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present in various insect genera, including Aedes, has demonstrated promising results globally. In this study we collected Aedes species and investigated its microbiomes with a particular focus on identifying the endosymbiont Wolbachia. Mosquitoes were collected via Gravitraps in the Peshawar region of Pakhtunkhwa province in the northwest of Pakistan. The identity of the mosquitoes was initially confirmed through morphological characters followed by molecular identification using species-specific Cytochrome oxidase I (COI) primers. The DNA from female Ae. aegypti and Ae. albopictus was further subjected to 16 S rRNA sequencing. The hypervariable regions V3/V4 of 16 S rRNA were used for sequencing using the paired-end Illumina MiSeq platform. The phylogenetic analysis of the COI gene in our samples demonstrated similarity to Aedes species previously documented in Pakistan. In comparative analysis of the microbiomes, Ae. albopictus was found to harbor 921 bacterial species, while Ae. aegypti only had 239 species. The metagenomic analysis revealed single-strain Wolbachia pipientis infection in Ae. aegypti, while Ae. albopictus harbored a double-strain infection involving a supergroup A strain (referred to as Wolbachia pipientis in 16 S EzBioCloud database) and a supergroup B strain (referred to as Wolbachia bourtzisii in16S EzBioCloud database).},
}

Animals
*Aedes/microbiology/classification
*Wolbachia/genetics/classification/isolation & purification
Phylogeny
Pakistan
Metagenomics
*Mosquito Vectors/microbiology
RNA, Ribosomal, 16S/genetics
Female
*Microbiota
*Metagenome
Electron Transport Complex IV/genetics
DNA, Bacterial/genetics

@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {41524878},
issn = {1534-4681},
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.

PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.

RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.

CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}

@article {pmid41524860,
year = {2026},
author = {Parab, C and Yadav, KD and Prajapati, V},
title = {Metagenomic Insights into Microbial Community Succession and its Functional Changes during Natural Fermentation of Food Waste.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41524860},
issn = {1559-0291},
abstract = {Food waste is a global concern, necessitating sustainable management strategies. While fermentation offers a promising approach to valorizing food waste, studies about microbial dynamics and functionality assessment of semi-controlled naturally fermented food waste are still seldom. This study employed whole-genome metagenomic sequencing to investigate the microbial succession and functional pathways during natural fermentation of food waste over 15 days. Physicochemical analysis revealed that pH decreased from 5.20 to 4.32 on day 3 and then neutralized. Protein, lipids, and carbohydrate were in the range of 4.03-4.90%, 9.99-17.78%, and 85.44-77.84%, respectively. Taxonomic profiling revealed clear community restructuring from an initially diverse consortium dominated by Enterobacter, Klebsiella, Pseudomonas, and Acinetobacter (collectively > 45% relative abundance at day 0) to a highly specialized lactic acid bacteria (LAB) community (> 80% by day 15). Lactobacillus helveticus and Limosilactobacillus panis emerged as the late-stage co-dominant species, together accounting for 60-75% of the total reads. Functional annotation based on the PFAM, eggNOG, GO, and EC databases revealed a progressive reduction in gene family richness and metabolic breadth, with early samples being enriched in carbohydrate-active enzymes, membrane transporters, and amino acid metabolism pathways. By contrast, late-stage communities were dominated by LAB-associated fermentative functions, including lactate and acetate production, stress-response modules, and transport systems supporting acid tolerance, driven mainly by Lactobacillus, Weissella, Streptococcus, Gluconobacter, Aeromonas, Saccharomyces, Klebsiella, and Cronobacter. These findings provide insights into the microbial dynamics and functional adaptations during natural fermentation of food waste, contributing to the development of optimized waste valorization strategies.},
}

@article {pmid41524778,
year = {2026},
author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK},
title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {105},
pmid = {41524778},
issn = {1432-072X},
support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
}

@article {pmid41524715,
year = {2026},
author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S},
title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41524715},
issn = {2050-084X},
support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; },
mesh = {*Dysbiosis/microbiology ; *Microbial Interactions ; Humans ; *Microbiota ; Metagenomics ; Models, Biological ; },
abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.},
}

*Dysbiosis/microbiology
*Microbial Interactions
Humans
*Microbiota
Metagenomics
Models, Biological

@article {pmid41523444,
year = {2025},
author = {Hofmann, SP and Bieri, U and von Stauffenberg, F and Schneider, S and Singer, G and Greiner, M and Hefermehl, LJ},
title = {Atypical Polypoid Bladder Lesion Mimicking Urothelial Carcinoma in a Young Male: A Case Report About a Possible Autoimmune-Triggered Granulomatous Inflammation With Secondary Colonization.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98879},
pmid = {41523444},
issn = {2168-8184},
abstract = {Gross hematuria is a critical clinical symptom requiring thorough diagnostic evaluation, particularly due to its association with urothelial carcinoma. However, other differential diagnoses must also be considered, including renal carcinoma, infection, urolithiasis, and autoimmune disease. We report the case of a 28-year-old male presenting with gross hematuria, flank pain, and dysuria. Imaging revealed bladder wall thickening and bilateral narrowing of the renal pelvis. Cystoscopy showed a large, polypoid lesion suggestive of urothelial carcinoma. Transurethral resection (TUR-B) was performed; however, histological analysis revealed granulation tissue with inflammatory infiltrates, multinucleated giant cells, and necrosis but no evidence of malignancy. Metagenomic sequencing identified Peptoniphilus sp. SAHP1, Anaerococcus mediterraneensis, and Trichomonas vaginalis, though their pathogenic role remained uncertain. Shortly after, the patient developed systemic inflammatory symptoms, including exanthema and gingivostomatitis. Biopsy of skin lesions showed leukocytoclastic vasculitis, and serologic testing yielded borderline myeloperoxidase-specific antineutrophil cytoplasmic antibody (MPO-ANCA) positivity. Under corticosteroid therapy, all symptoms, including the bladder lesion, regressed completely. This case highlights a rare constellation of findings mimicking urothelial carcinoma, ultimately pointing to a probable autoimmune vasculitic process with possible secondary microbial colonization. It underscores the diagnostic challenges posed by atypical presentations and the need for integrative interpretation of clinical, histological, and molecular findings in complex cases.},
}

@article {pmid41523323,
year = {2026},
author = {Chen, J and Wu, Y and Tang, J and Guo, J and Zhai, Y},
title = {Pertussis is identified among common respiratory diseases: A case report.},
journal = {SAGE open medical case reports},
volume = {14},
number = {},
pages = {2050313X251411124},
pmid = {41523323},
issn = {2050-313X},
abstract = {Pertussis, caused by Bordetella pertussis, is increasingly recognized in adults who often present with atypical symptoms, leading to underdiagnosis. We report a case of a 64-year-old woman with a persistent cough and sore throat initially treated as refractory community-acquired pneumonia. Despite empirical antibiotic therapy, her symptoms persisted. Conventional diagnostic tests, including sputum and bronchoalveolar lavage fluid cultures, were negative. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Bordetella pertussis with high sequence coverage (7497 reads). The patient showed no clinical improvement with azithromycin, prompting a switch to trimethoprim-sulfamethoxazole, after which she improved and was discharged to complete a 14-day course. At 1-month follow-up, she was asymptomatic with resolved radiographic findings. This case highlights that pertussis can mimic refractory pneumonia in adults without typical features such as whooping cough, and underscores the diagnostic value of metagenomic next-generation sequencing when conventional methods fail. Clinicians should consider pertussis in adults with prolonged cough unresponsive to standard community-acquired pneumonia therapy and be aware of potential macrolide resistance, which may necessitate alternative antibiotics like trimethoprim-sulfamethoxazole.},
}

@article {pmid41523242,
year = {2025},
author = {Qi, W and Tian, L and Li, Z and Xu, J and Wang, T},
title = {Pathogen spectrum and management strategies for opportunistic infections in lung cancer in the immunotherapy era: recent advances from fungi to mycobacteria.},
journal = {American journal of cancer research},
volume = {15},
number = {12},
pages = {5140-5167},
pmid = {41523242},
issn = {2156-6976},
abstract = {Lung cancer is one of the most common cancers and the leading cause of cancer death worldwide. Opportunistic infections (OI) are increasingly recognized in this population due to disease-related immune dysfunction and treatment-induced immunosuppression. Compared with the chemotherapy era, the use of immune checkpoint inhibitors and targeted agents has shifted the OI profile. Pneumocystis jirovecii pneumonia (PJP) and invasive pulmonary aspergillosis (IPA) are reported more often in older adults and patients with lymphopenia, while tuberculosis (TB) and nontuberculous mycobacteria (NTM) cluster in those with structural lung disease (e.g., bronchiectasis, cavities) and prolonged immunosuppression. High-risk features include absolute lymphocyte count <500/µL, corticosteroids ≥20 mg prednisone-equivalent for ≥4 weeks, airway obstruction, prior TB, chronic obstructive pulmonary disease/interstitial lung disease (ILD), and recent broad-spectrum antibiotics. Diagnosis should integrate high-resolution computed tomography (HRCT) patterns (e.g., diffuse ground-glass for PJP; nodules with halo sign for IPA), microbiology [bronchoalveolar lavage fluid (BALF) culture/microscopy, galactomannan (GM)/β-D-glucan (BDG)], and metagenomic next-generation sequencing, interpreted against host factors and treatment timeline, while carefully distinguishing immune-related pneumonitis and TKI-associated ILD. Prophylaxis with TMP-SMX is recommended for high-risk patients; voriconazole (or isavuconazole) is first-line for IPA with attention to drug-drug interactions; TB/NTM regimens require coordination with anticancer therapy, especially where rifamycins interact with TKIs. Vaccination (influenza, pneumococcus, zoster) and antimicrobial stewardship are essential. Future work should validate risk scores prospectively and clarify microbiome-immunotherapy-infection relationships.},
}

@article {pmid41523161,
year = {2025},
author = {Sanchez, G and Simakov, O and Nyholm, S and Nishiguchi, M and McFall-Ngai, M and Lami, R and Heath-Heckman, E and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {351},
pmid = {41523161},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Sepioteuthis lessoniana (bigfin reef squid; Mollusca; Cephalopoda; Myopsida; Loliginidae). The genome sequence has a total length of 5,056.23 megabases. Most of the assembly (86.4%) is scaffolded into 44 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 28,970 protein-coding genes.},
}

@article {pmid41522572,
year = {2025},
author = {Pfliegler, WP and Németh, B and Bodnár, V and Pusztahelyi, T and Carbone, I and Pócsi, I},
title = {Global population genomics redefines domestication and clinical diversity in the Aspergillus flavus-oryzae complex.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e172343},
pmid = {41522572},
issn = {2210-6340},
abstract = {Aspergillus flavus is a globally important human pathogen and agricultural contaminant, while its domesticated relative A. oryzae is widely used in food fermentation and biotechnology. Despite their importance, the evolutionary relationship, population structure and domestication history of these fungi remain unresolved. Here, we present the first global population genomic analysis of 639 A. flavus and A. oryzae isolates from clinical, environmental and food-fermentation sources across multiple continents. Our analyses reveal a complex evolutionary landscape comprising well-separated clades interspersed with highly admixed mosaic groups and potential evidence for multiple independent domestication events giving rise to A. oryzae. Clinical A. flavus isolates are distributed across several clades and mosaic groups, some overlapping with fermentation strains, highlighting an apparent role of domestication and admixture in shaping pathogen diversity. These results challenge current species boundaries and provide a framework for understanding evolutionary history, taxonomy and pangenomic architecture in these fungi, with broad implications for pathogenicity, food safety, biocontrol and metagenomic surveillance.},
}

@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}

*Rhizosphere
*Onions/microbiology/growth & development/physiology
*Soil Microbiology
Fertilizers
*Microbiota
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification

@article {pmid41522492,
year = {2026},
author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R},
title = {Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2610588},
pmid = {41522492},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is a known reservoir of antibiotic resistance genes (ARGs), but little is known about their subgingival distribution across health states and regions.

OBJECTIVE: This study aimed to characterize and compare the subgingival resistome and mobile genetic elements (MGEs) in healthy subjects (HS) and periodontitis patients (PP) from Belgium, Chile, Peru and Spain.

DESIGN: Subgingival samples pooled from the deepest site of each quadrant of 40 HS and 40 PP were analyzed via shotgun metagenomic sequencing. After human DNA depletion, the microbial composition was assessed with MetaPhlAn 4.0; ARGs were identified using MEGAHIT and AMRFinderPlus; and MGEs with MGEfinder.

RESULTS: ARG richness was significantly higher in PP (mean 3.98) than in HS (2.15). PP from Peru showed more ARGs than HS from Chile and Spain. In total, 28 ARGs were found, conferring resistance to eight antibiotic classes. β-lactam, tetracycline and aminoglycoside resistance were more abundant in PP. Macrolide resistance was lower in Chilean samples than in Peruvian and Spanish ones. Additionally, 99 MGE-associated genes were detected, with 16 differing by diagnosis and 78 by country.

CONCLUSIONS: Subgingival resistome profiles vary significantly by periodontal status and geography, underscoring the influence of clinical and regional factors on antimicrobial resistance in the oral microbiome.},
}

@article {pmid41521629,
year = {2026},
author = {Shelton, BR and Larrere, J and Yusta Belsham, D and Omacini, M and Argüelles-Moyao, A and Buscardo, E and Alves da Silva, DK and Zhao, X and Nakamura, N and Ángeles-Argáiz, R and Paz, C and Matías-Ferrer, N and Hart, MM},
title = {Fungal ecology in the age of 'omics.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70900},
pmid = {41521629},
issn = {1469-8137},
abstract = {The advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its interactions with the macroscopic world, than ever before. However, fungal studies that use meta'omic technologies have been sparse compared with bacterial and plant-focused studies. In this review, we highlight the ways that meta'omics can help to address pressing questions in belowground plant-fungal ecology, show consistencies that are emerging - and discrepancies that still exist - among analysis pipelines, and advocate for reporting standards that will allow meta'omic research to more fully benefit fungal ecology.},
}

@article {pmid41521588,
year = {2026},
author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I},
title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70117},
doi = {10.1111/jfd.70117},
pmid = {41521588},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.},
}

@article {pmid41521100,
year = {2026},
author = {Zhu, NQ and Zhang, QB and Wang, ZX and Li, RD},
title = {Bacteroides in Bile Detected by Metagenomic Next-Generation Sequencing: Potential Novel Indicator for Early Allograft Dysfunction After Liver Transplantation.},
journal = {Transplantation proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.transproceed.2025.11.001},
pmid = {41521100},
issn = {1873-2623},
abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) is an effective method for the detection of microorganisms. Early allograft dysfunction (EAD) is a common complication after liver transplantation. The association between early postoperative microorganisms in bile and EAD is unclear, so we evaluated the association of microorganisms and other potential risk factors with EAD.

METHODS: A total of 100 patients who underwent orthotopic liver transplantation with biliary T tube placement in Huashan Hospital Fudan University from March 2021 to July 2022 were studied. Clinical data, the occurrence of EAD, and bile microorganisms' information detected by mNGS were collected.

RESULTS: EAD occurred in 22 recipients (22%). Patients with EAD had a longer length of postoperative hospital stay. Bacteroides spp. detected by mNGS in bile was identified as an independent risk factor for EAD. Also, operation time, the MELD score of the recipient, and donor AST level were also independent risk factors for EAD.

CONCLUSION: Bacteroides spp. detected by mNGS in bile after liver transplantation was identified as an independent risk factor for EAD, which may reflect the translocation of intestinal flora into the biliary tract and may serve as a potential early warning indicator of poor quality of the donor liver. Recipients with EAD had longer LOS, which may indicate a poor short-term prognosis.},
}

@article {pmid41519985,
year = {2026},
author = {Bodhe, I and Gokuladoss, V},
title = {Sustainable CO2 valorization for PHB production towards circular economy: metagenomic insights on enriched indigenous microbial cultures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26791-7},
pmid = {41519985},
issn = {2045-2322},
}

@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41519950},
issn = {1530-0447},
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.

METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.

RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.

CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.

IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.},
}

@article {pmid41519314,
year = {2026},
author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K},
title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.},
journal = {Genomics},
volume = {},
number = {},
pages = {111198},
doi = {10.1016/j.ygeno.2026.111198},
pmid = {41519314},
issn = {1089-8646},
abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by circadian rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Circadian rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.

RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.

DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the circadian rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.

CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for circadian rhythm-targeted interventions in metabolic diseases.},
}

@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf283},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}

@article {pmid41518832,
year = {2025},
author = {Hellwig, P and Seick, I and Meinusch, N and Benndorf, D and Wiese, J and Reichl, U and Heyer, R},
title = {Molecular community data meets anaerobic digestion Model 1 (ADM1) - a study about the correlation between metagenome-centric metaproteomics data of a two-step full-scale anaerobic digester and its corresponding mathematical model.},
journal = {Water research},
volume = {292},
number = {},
pages = {125272},
doi = {10.1016/j.watres.2025.125272},
pmid = {41518832},
issn = {1879-2448},
abstract = {Advanced models, such as the Anaerobic Digestion Model No 1 (ADM1), are essential for operating, planning, and optimizing renewable energy production in anaerobic digester plants (AD-P)s. In this study, the ADM1da model was employed to simulate a two-step AD-P in an industrial setting. The ADM1da model is an extended ADM1 model for mixed substrates, accounting for substrate-specific disintegration, temperature effects, biogas-related mass reduction, and mineral solids content. ADM1 models can represent the anaerobic digestion processes, although the biological assumptions are coarse and reflect the knowledge and available tools for microbial communities at the time of development. Meanwhile, metagenome-centric metaproteomics provides deeper insight into the metabolic activities of microbial communities in AD-Ps. Until now, this data has not been integrated with ADM1 models. The objective of this study is to assess the feasibility of incorporating metagenome-centric metaproteome data into the ADM1 model. In a novel approach, 49 high-quality metagenome-assembled genomes (MAGs) with associated protein abundances were systematically classified into the trophic groups defined by the ADM1 model using specifically developed grouping rules. Abundances of MAGs were more variable than the process parameter-dependent dynamics of ADM1. Depending on the grouping rules, 32%-78% of all high-quality MAGs were successfully categorized into ADM1 trophic groups. However, some MAGs, e.g., Methanotrix, were multifunctional (acetoclastic and hydrogenotrophic methanogenesis) and required assignment to multiple groups. Unfortunately, more precise grouping rules resulted in greater discrepancies between metaproteomics data and the model. Additionally, 22% of the MAGs could not be assigned. The metagenome-centric metaproteome data imply that ADM1 probably needs extension to cover the observed microbial function of syntrophic acetate oxidizers, hydrolytic bacteria, lactate- and ethanol-fermenting bacteria, and mortality by phages. It was also observed that changes in process parameters, such as those caused by seasonal feeding, led to significant changes in the protein abundance Integrating metagenome-centric metaproteomic data into ADM1 trophic groups was shown to be feasible.Some trophic groups detected in protein data but not implemented in ADM1 imply the need for data-driven model enhancement and approval. In the future, more accurate models considering molecular data could support a deeper understanding of microbial community dynamics in AD-Ps.},
}

@article {pmid41518812,
year = {2026},
author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Yu, Z and Liu, J},
title = {Urban habitat types modulate soil contamination and bacterial functional traits through antibiotic resistance genes and metal(loid) interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141092},
doi = {10.1016/j.jhazmat.2026.141092},
pmid = {41518812},
issn = {1873-3336},
abstract = {Urban soils are important reservoirs for contaminants, including metal(loid)s and antibiotic resistance genes (ARGs), posing threats to ecosystem function and public health. However, the variation in these contaminants across urban habitat types remains poorly understood. This study integrated shotgun metagenomics, 16S rRNA sequencing, quantitative PCR, and multivariate modeling to investigate the co-distribution of ARGs, metal(loid)s, and bacterial functional traits across six urban habitat types: afforestation areas, croplands, orchards, parks, ruderals, and semi-natural remnants. Our findings revealed habitat-specific contamination patterns, with croplands and orchards showing the highest ARG risks and strong co-selection signals mediated by mobile genetic elements (MGEs) and biocide/metal resistance genes (BMRGs). In contrast, ruderals and remnants exhibited significantly lower ARG abundances (<1.2 × 10[4] copies/g) and metal(loid) concentrations (Cd < 0.05 mg/kg and Pb < 10 mg/kg), as well as nearly 50 % fewer plasmid-associated ARGs, indicating reduced horizontal gene transfer potential. Integrative modeling identified functional genes and BMRGs as the most consistent drivers of MGE dynamics, while MGEs showed limited direct influence on ARGs, suggesting that mobility alone may not explain the spread of resistance in urban soils. Metagenomic analyses linked ARG profiles to disruptions in bacterial functions essential for nutrient cycling and ecosystem services, indicating that resistance risks in urban soils are closely tied to declines in functional capacity. A substantial overlap in ARGs between orchard soils and fruits underscored the potential for soil-to-human transmission. These results provide a cross-habitat framework that links contaminant profiles, resistance mobilization, and functional consequences in urban soils.},
}