@article {pmid41554738,
year = {2026},
author = {Zheng, J and Zhang, C and Xiang, S and Li, M and Wang, H and Shi, K and Tondrob, D and Han, Y},
title = {Integrated metabolomics and metagenomics uncover pathogenic mechanisms of Fusarium wilt and faba bean defense responses.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00673-8},
pmid = {41554738},
issn = {2396-8370},
support = {31901929//National Natural Science Foundation of China/ ; cstc2021jcyj-msxmX1021//Natural Science Foundation of Chongqing Municipality/ ; },
abstract = {Fusarium wilt diseases pose a huge threat to faba bean (Vicia faba L.) production globally, with significant outbreaks in Chongqing, China. Symptomatic plants showed wilting leaves and rotten roots, ultimately perishing in the advanced stage. Morphological features, multilocus phylogenetic analyses, and pathogenicity tests demonstrated that the primary causal agent was Fusarium oxysporum. Untargeted metabolomics of faba beans revealed substantial metabolic differences in the infected faba bean roots. Plants responded to fungal biotic stress by reprogramming key metabolic pathways, including alanine, aspartate, and glutamate metabolism, the citrate cycle, arginine biosynthesis, and jasmonic acid metabolism, which collectively underscore activated defense responses. Metagenome sequencing showed that Fusarium wilt significantly reshaped the structure of the rhizosphere microbiota and affected the abundance of genes encoding element cycling in soil. This work elucidates the pathogenic mechanisms of F. oxysporum by integrating pathogen identification, host metabolism, and microbiome ecology. Our findings offer biomarkers for disease diagnosis and targets for biocontrol, advancing sustainable management of Fusarium wilt diseases in legumes.},
}

@article {pmid41552949,
year = {2026},
author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B},
title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70124},
pmid = {41552949},
issn = {1529-8817},
support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; },
abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.},
}

@article {pmid41552936,
year = {2026},
author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y},
title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04604a},
pmid = {41552936},
issn = {2042-650X},
abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.},
}

@article {pmid41552860,
year = {2026},
author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A},
title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70102},
pmid = {41552860},
issn = {1755-0998},
support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; },
mesh = {*DNA, Environmental/isolation & purification/genetics ; *Biodiversity ; *Deoxyribonucleases/metabolism ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/classification/genetics ; Rivers/chemistry ; *Metagenomics/methods ; },
abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.},
}

*DNA, Environmental/isolation & purification/genetics
*Biodiversity
*Deoxyribonucleases/metabolism
*DNA Barcoding, Taxonomic/methods
Animals
*Fishes/classification/genetics
Rivers/chemistry
*Metagenomics/methods

@article {pmid41552431,
year = {2026},
author = {Buonaccorsi, A and McMullen, BN and Builder, B and Drummond, K and Halteman, S and See, JC and Thomas, E and Viands, A and Worley, S and Wright, JR and Keeney, J and Lamendella, R},
title = {Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101305},
pmid = {41552431},
issn = {2352-7714},
abstract = {The rise in tick populations across the United States has contributed to a surge in tick-borne diseases, with Pennsylvania ranking among the highest in reported cases. To better understand local pathogen prevalence and microbial community structure, an integrative study of ticks collected from ten recreational trails in Huntingdon County, Pennsylvania during the summer of 2023 was conducted. A total of 96 ticks were sampled, with 33 PCR-positive specimens selected for shotgun metagenomic sequencing. Pathogen screening via qPCR detected Borreliella burgdorferi, Borrelia miyamotoi, Babesia spp., and Anaplasma phagocytophilum. Shotgun metagenomics revealed a broader diversity of tick-borne pathogens, including Rickettsia and Ehrlichia spp., and demonstrated increased sensitivity by detecting low-abundance pathogens in samples that were PCR-negative. Co-infections were common, and multivariate statistical analysis identified significant associations between environmental variables (e.g., humidity, time of day, land cover) and microbial diversity and predicted gene function. Notably, diversity was higher in ticks collected during early afternoon and from northern sites. Co-occurrence network analysis showed Rickettsia as a central taxon with multiple significant positive associations with other microbes while other pathogens were largely absent or peripheral. These findings underscore the enhanced resolution of metagenomic approaches for pathogen detection and the value of combining molecular surveillance with ecological metadata. Our study provides critical insights into local tick microbiomes and pathogen prevalence, which may inform public health interventions and vector management strategies in central Pennsylvania.},
}

@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}

*Metagenomics/methods
*Software
Workflow
*Computational Biology/methods
Microbiota

@article {pmid41551812,
year = {2026},
author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Zhang, Z and Xie, F and Ai, L},
title = {Docynia delavayi polyphenols enhance short-chain fatty acid synthesis via the chlorogenic acid-caffeic acid-protocatechuic acid pathway: insights from in vitro digestion-fermentation.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103416},
pmid = {41551812},
issn = {2590-1575},
abstract = {Docynia delavayi fruit polyphenols (DDP) demonstrate potential for enhancing short-chain fatty acid (SCFA) synthesis; however, underlying mechanisms remain poorly understood. This study utilized an in vitro digestion-fermentation model combined with multi-omics analyses to explore these mechanisms. The in vitro model revealed notable alterations in both 1,1'-diphenyl-2-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical-scavenging capacities, as well as in total phenolic and flavonoid content, accompanied by increased production of acetic, propionic, and butyric acids. Metagenomic indicated that DDP stimulated Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Bifidobacterium longum, and Bifidobacterium bifidum growth. Metabolomics demonstrated enrichment of SCFA-associated metabolic pathways, including propanoate and butyrate metabolism, and identified caffeic acid and protocatechuic acid as primary bioactive metabolites produced from DDP. Multi-omics analysis suggested that DDP modulated gut microbiota by enriching the chlorogenic acid-caffeic acid-protocatechuic acid metabolic pathway (r > 0.95, p < 0.01), ultimately boosting SCFA biosynthesis. This study offers new insights into the mechanisms by which polyphenols regulate health.},
}

@article {pmid41551788,
year = {2026},
author = {Song, Q and Li, J and Liu, Y and Li, W and Li, M and Zhang, B and Guo, B},
title = {Metagenomics and volatile metabolomics reveal microbial succession and its correlations with fruity flavor volatile compounds during Mianhua industrial processing.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103446},
pmid = {41551788},
issn = {2590-1575},
abstract = {Mianhua, a traditional fermentation-type staple food popular in northern China, undergoes dynamic microbial and volatile compound changes during industrial processing. 848 volatile compounds were identified using volatile metabolomics dominated by esters (18.51 %), notably hexanoic acid ethyl ester and octanoic acid ethyl ester, which confer fruity flavors. Metagenomics analysis revealed Proteus (25.93 %), Fructilactobacillus (16.63 %), Lactobacillus (10.16 %) and Companilactobacillus (7.14 %) as dominant genera. Mixing with traditional starters was critical for flavor development, driven by microbial succession and synergistic interactions between Lactobacillaceae (e.g., Fructilactobacillus sanfranciscensis and Lactobacillus helveticus) and Kazachstania during fermentation. Notably, F. sanfranciscensis and L. helveticus were significantly correlated with the formation of key esters with fruity characteristics, elucidating their roles in substrate conversion via carbohydrate metabolism and the esterification pathways. This study clarifies the microbial contributions to fruity flavor and provides insights into volatile-microbiota correlations, laying a foundation for future flavor-oriented research and industrial applications of microbiota regulation in Mianhua production.},
}

@article {pmid41551588,
year = {2026},
author = {Arnold, CB and Kelder, A and Woltemate, S and Geffers, R and von Felde, A and Knudsen, KEB and Visscher, C and Vital, M},
title = {Uncovering differences in rye and wheat degradation by human gut microbiota applying a quantitative multi-metaOmics in vitro approach.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100532},
pmid = {41551588},
issn = {2666-5174},
abstract = {While wheat is the most common grain used in bread-making worldwide, rye is popular in many European countries too. Rye is associated with several health benefits, which is attributed to its comparatively higher dietary fiber content (primarily fructans and arabinoxylans) that promote production of short chain fatty acids (SCFA) by gut microbiota, in particular butyrate. Intervention studies revealed bacterial alterations upon rye administration, however, the detailed mechanisms involved in its degradation are not understood. We grew fecal communities (n = 20) on pre-digested rye and wheat, respectively, demonstrating that rye was yielding higher cell and SCFA concentrations in almost all samples along with distinct abundances of many taxa. A multi metaOmics (metagenomics/metatranscriptomics) approach (n = 5 donors) showed higher bacterial growth rates for most taxa on rye compared to wheat. The higher growth rate of rye was accompanied by increased expression of genes involved in growth and energy generation suggesting higher carbon substrate accessibility. The carbohydrate active enzyme repertoire was greatly distinct between communities growing on the two substrates with several specific glycoside hydrolases increasingly expressed in rye containing cultures. Agathobacter faecis was revealed as the key butyrogenic species for rye degradation and its expression pattern based on metagenome assembled genomes showed adaptation to growth on rye via expression of genes involved in arabinoxylan degradation and fructose (major monomer of fructans) uptake. Our study verifies higher SCFA production from rye over wheat and gives detailed insights into molecular mechanisms involved. It suggests that the observed health benefits of rye are mediated by gut microbiota.},
}

@article {pmid41551583,
year = {2026},
author = {Chen, T and Huang, R and Huang, Y and Wang, J and Wang, Z and Zhang, X},
title = {Shared signatures of alcohol-associated dysbiosis in humans and non-human primates.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100534},
pmid = {41551583},
issn = {2666-5174},
abstract = {Alcohol use disorder (AUD) is a chronic brain disease with limited therapeutic options. Increasing evidence suggests that the gut microbiome contributes to AUD via the microbiome-gut-brain axis. Here, we conducted a cross-species investigation of gut microbiota alterations in patients with clinically diagnosed AUD and in non-human primates (NHPs) subjected to long-term alcohol (ethanol) self-administration, using metagenomic sequencing. Both cohorts showed reduced microbial diversity and conserved dysbiosis, with consistent depletion of Verrucomicrobia, Actinobacteria, Faecalibacterium, Akkermansia, Intestinibacter, Phascolarctobacterium, and Ruminococcus, alongside increased Blautia and Coprococcus. These microbial shifts correlated with liver function indices, notably positive associations between Ruminococcus and bilirubin levels in both species, suggesting a potential role in liver injury. Functional analyses revealed conserved microbial adaptations, including upregulated DNA repair pathways, fermentative energy metabolism, and downregulated glutamate/glutamine biosynthesis. Together, these results identify evolutionarily conserved microbial and metabolic alterations linking alcohol consumption, gut dysbiosis, and hepatic dysfunction. Our cross-species evidence highlights the gut microbiome as a potential biomarker and therapeutic target for AUD.},
}

@article {pmid41551517,
year = {2025},
author = {Wang, Y and Zhang, X},
title = {Rapid diagnosis of Lemierre's syndrome by metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1730031},
pmid = {41551517},
issn = {2296-858X},
abstract = {Lemierre's syndrome, also known as postopharyngeal septicaemia or necrobacillosis, is a rare, fatal opportunistic infection, often caused by Fusobacterium necrophorum invading the throat. Bacterial culture is a conventional method to establish a diagnosis, but is time-consuming and insensitive in some cases. Metagenomic next-generation sequencing (mNGS), as an emerging technique, has become an important supplementary detection method for infectious diseases. It greatly favors the rapid, precise diagnosis and treatment of Lemierre's syndrome through accurately obtaining etiological information. We reported a case of Lemierre's syndrome that was rapidly and accurately diagnosed by mNGS.},
}

@article {pmid41551358,
year = {2026},
author = {Wu, X and Yin, Y and Guo, Y and Sun, L and Shi, Q and Ji, T and Wang, H},
title = {A case of atypical cat scratch disease with bone and joint infection diagnosed through clinical metagenomics.},
journal = {IDCases},
volume = {43},
number = {},
pages = {e02482},
pmid = {41551358},
issn = {2214-2509},
abstract = {Cat scratch disease (CSD) is a common zoonotic infection caused by Bartonella henselae (B. henselae) and typically presents with fever and regional lymphadenopathy. However, skeletal involvement, including osteomyelitis and arthritis, is rare. We report a 28-year-old immunocompetent female who presented with a five‑month history of persistent right knee swelling without fever or lymphadenopathy. She had previously undergone distal femoral tumor resection with prosthetic joint replacement, and this episode of chronic knee swelling together with the imaging findings was highly suggestive of prosthetic joint infection. Approximately one month before the onset of knee swelling, she had sustained a scratch from a cat. Conventional microbiological tests, including joint effusion and drainage fluid cultures, were negative. Metagenomic next‑generation sequencing (mNGS) of joint effusion identified B. henselae with 27 specific sequence reads, 0.1 % genome coverage and an RPM ratio of 1.9. This result was subsequently confirmed by a quantitative PCR assay targeting the nuoG gene. The patient underwent surgical debridement followed by oral minocycline and rifampin for 8 weeks, resulting in marked clinical improvement. This case underscores that B. henselae infection should be considered in culture‑negative bone and joint, particularly prosthetic joint, infections with a history of cat exposure, and that mNGS can provide valuable etiological evidence in atypical CSD.},
}

@article {pmid41551289,
year = {2025},
author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP},
title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {},
pmid = {41551289},
issn = {2993-3935},
support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R35 GM155168/GM/NIGMS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK122042/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; },
abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.},
}

@article {pmid41551178,
year = {2026},
author = {Esposito, A and Valentino, V and Tagliamonte, S and Sequino, G and Vitaglione, P and Ercolini, D and De Filippis, F},
title = {Development of a synbiotic dietary supplement containing potential Next Generation Probiotics for modulation of the gut microbiome and metabolome.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101289},
pmid = {41551178},
issn = {2665-9271},
abstract = {The term Next Generation Probiotics (NGPs) refers to microbial strains positively impacting on human health, but do not belong to common probiotic species (e.g., lactic acid bacteria, LAB). We characterized genomically and phenotypically 14 strains isolated from the gut microbiome of healthy individuals, to evaluate their ability to produce urolithins, equol and short-chain fatty acids (SCFA). The 4 most promising strains (namely Bacteroides uniformis A4, Bacteroides thetaiotaomicron A14, unclassified Bacteroidaceae A26 and unclassified Lachnospiraceae A49) were used for the production of a synbiotic formulation, containing the strains and the precursors of health-promoting molecules. This dietary supplement was administered for 2 weeks to a continuous mucosal-Simulator of the Human Intestinal Microbial Ecosystem (mSHIME) model inoculated with a faecal sample from a low fiber-consuming donor. We performed Shotgun Metagenome Sequencing on a total of 204 samples collected from lumen and mucosa compartments, and determined the concentration of SCFA, equol and urolithin. Our results highlighted that the potential NGP strains contained in the supplement persisted in the gut ecosystem during 2 weeks of washout (Wilcoxon's rank sum test, p-value <0.05). In addition, the treatment led to an enrichment in beneficial taxa and to an increase in the production of SCFAs (p-value <0.05). This study demonstrated that feeding the gut microbiota with NGPs and dietary prebiotics can modulate both the gut microbiome and metabolome, suggesting a potential beneficial impact on human health. However, further in vivo studies are needed to confirm these results.},
}

@article {pmid41551170,
year = {2026},
author = {Chang, CC and Pak, J and Bae, S and Kim, GD and Son, HS},
title = {Impact of low aging temperature on the microbial and metabolic dynamics of rice wine during long-term storage.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101294},
pmid = {41551170},
issn = {2665-9271},
abstract = {This study investigated the effects of aging temperature and microbial inoculation on the physicochemical, microbiological, and metabolic properties of Korean rice wine (makgeolli) during long-term storage. Samples were aged at three different temperatures (4 °C, -1 °C, and -5 °C) for 180 days and were inoculated with Lactiplantibacillus plantarum or Saccharomyces cerevisiae to examine their respective influences on metabolite shifts during cold storage. Microbial communities were analyzed using amplicon (16S rRNA) and shotgun metagenomic sequencing, and metabolite profiles were determined by GC-MS to provide an integrative understanding of microbial and metabolic stability during long-term cold storage. Lower aging temperatures reduced fluctuations in metabolic and microbial activities, particularly among LAB, thereby contributing to a more stable physicochemical profile and extended shelf life. During rice wine aging, LAB exerted a more pronounced effect on metabolite dynamics than yeast, particularly for pyruvate, γ-aminobutyric acid, and lactic acid, underscoring their role in the aging process. Additionally, sub-zero aging temperatures preserved the initial microbial composition, limited enzymatic degradation, and stabilized organic acid profiles, reflecting enhanced chemical stability of the product during aging. While such chemical stability may have implications for sensory outcomes, this remains a hypothesis that requires direct sensory evaluation in future studies. Overall, the findings suggest that controlled storage temperatures and targeted microbial inoculation can improve the chemical and microbiological stability of rice wine during long-term storage.},
}

@article {pmid41551013,
year = {2025},
author = {Wang, C and Chang, K and Chen, M and Zou, X and Ni, Y and Zhang, Q and Zhao, L and Xing, B and Guo, L and Chen, W and Cao, B},
title = {Enrichment of the commensal microbiome in the lower respiratory tract is associated with improved outcomes following lung transplantation.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {3},
number = {4},
pages = {308-318},
pmid = {41551013},
issn = {2772-5588},
abstract = {BACKGROUND: Alterations in the respiratory microbiome are common following lung transplantation; however, the complex relationship between microbial composition and posttransplant clinical outcomes remains insufficiently characterized. This study aimed to delineate microbial signatures within the lower respiratory tract and to elucidate their associations with posttransplant outcomes in lung transplant recipients (LTRs).

METHODS: Metagenomic sequencing was performed on 138 bronchoalveolar lavage fluid (BALF) samples collected in 2023 from patients who had undergone lung transplantation between 2017 and 2023 at the China-Japan Friendship Hospital. Lung function indices, hematologic parameters, and serum cytokine levels were assessed, and patients were prospectively followed to record adverse clinical events.

RESULTS: The lung microbiome of stable LTRs formed four distinct clusters, exhibiting marked heterogeneity in both α- and β-diversity. The most prevalent cluster, enriched with oral-origin commensals, such as Neisseria subflava (N. subflava), Prevotella melaninogenica, and Streptococcus mitis (S. mitis), demonstrated the highest microbial diversity, and was associated with the lowest C-reactive protein levels, fewest adverse events, and the longest complication-free postoperative duration. In contrast, a virus-enriched cluster characterized by reduced diversity and high abundance of Torque teno virus and Cytomegalovirus human betaherpesvirus 5 was associated with poorer outcomes. BALF samples from infected LTRs exhibited more severe dysbiosis than those from immunocompetent individuals, with reduced diversity and pathogen dominance. Concurrent infections aggravated antibody-mediated rejection-related lung function decline, indicating complex microbiome-immune interactions. Integrative modeling of microbiome, hematologic, and pulmonary function data yielded superior diagnostic performance for infection detection (area under the receiver operating characteristic curve = 0.93).

CONCLUSION: The composition of the lung microbiome may serve as a prognostic biomarker for clinical outcomes after lung transplantation. The presence of diverse, commensal-dominated communities was associated with improved outcomes, whereas viral enrichment correlated with adverse events. These findings underscore the clinical importance of microbiome monitoring in posttransplant management and suggest that targeted modulation of microbial communities could improve long-term graft stability and patient prognosis.},
}

@article {pmid41550607,
year = {2025},
author = {Zhang, W and Zhang, L and Liu, H},
title = {Correction: Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1760028},
doi = {10.3389/fped.2025.1760028},
pmid = {41550607},
issn = {2296-2360},
abstract = {[This corrects the article DOI: 10.3389/fped.2025.1594899.].},
}

@article {pmid41550372,
year = {2025},
author = {Tenea, GN and Jarrin-V, P and Lin, L},
title = {Editorial: Trigger the microbiome changes in foods via metagenomic technologies: from diagnostic to potential changes in product safety or quality risk profiles.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1766291},
doi = {10.3389/fbioe.2025.1766291},
pmid = {41550372},
issn = {2296-4185},
}

@article {pmid41549319,
year = {2026},
author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Chen, J and Fang, H},
title = {The impact of the timing of mNGS-guided antibiotic adjustment on clinical outcomes in ICU patients with severe community-acquired pneumonia: a retrospective study.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12941-026-00848-5},
pmid = {41549319},
issn = {1476-0711},
support = {No. 2023KY1296//Zhejiang Provincial Department of Health/ ; No. 2022K71//the Quzhou Bureau of Science and Technology/ ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of intensive care unit (ICU) admission and mortality. Prompt pathogen identification and timely administration of appropriate antimicrobial therapy are essential for improving patient outcomes. Although metagenomic next-generation sequencing (mNGS) enables rapid pathogen detection, the prognostic impact of the timing of mNGS-guided antibiotic adjustment remains unclear.

METHODS: We conducted a multicenter retrospective study of ICU patients diagnosed with SCAP who underwent both bronchoalveolar lavage fluid (BALF) mNGS and conventional microbiological tests (CMTs). Patients were categorized into early (≤ 72 h) and late (> 72 h) antibiotic adjustment groups based on the interval from ICU admission to the time of antibiotic adjustment guided by mNGS results. Subgroup analyses were performed according to immune status.

RESULTS: In our study, mNGS significantly outperformed conventional microbiological tests (CMTs) in pathogen detection (92.70% vs. 57.18%, P < 0.001), with a particularly higher yield for mixed infections (51.63% vs. 19.14%, P < 0.001). Early mNGS-guided antibiotic adjustment was associated with a significantly reduced 28-day mortality compared to late adjustment (41.98% vs. 53.76%, P = 0.037). Furthermore, multivariate logistic regression analysis confirmed early adjustment as an independent protective factor for 28-day mortality (adjusted OR = 0.44, 95% CI: 0.23-0.83, P = 0.011). In the immunocompromised subgroup, early mNGS-guided adjustment was associated with significantly lower 28-day mortality than late adjustment (39.29% vs. 60.00%, P = 0.029), with a significant interaction observed between timing and immune status (P = 0.042).

CONCLUSION: Early mNGS-guided antibiotic adjustment is associated with improved survival among ICU patients with SCAP. This benefit is more pronounced in immunocompromised patients, underscoring the importance of early mNGS application to guide antimicrobial decision-making in this vulnerable population.},
}

@article {pmid41549294,
year = {2026},
author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC},
title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {139},
pmid = {41549294},
issn = {1432-0991},
mesh = {*Lakes/virology ; *Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; India ; Phylogeny ; Ecosystem ; Biodiversity ; Fresh Water/virology ; Bacteriophages/genetics/classification/isolation & purification ; },
abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.},
}

*Lakes/virology
*Metagenomics
*Viruses/genetics/classification/isolation & purification
*Virome
Genome, Viral
India
Phylogeny
Ecosystem
Biodiversity
Fresh Water/virology
Bacteriophages/genetics/classification/isolation & purification

@article {pmid41549250,
year = {2026},
author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J},
title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04582-8},
pmid = {41549250},
issn = {1471-230X},
support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; },
}

@article {pmid41548675,
year = {2026},
author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A},
title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: comparative performance of endogenous vs. exogenous consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134038},
doi = {10.1016/j.biortech.2026.134038},
pmid = {41548675},
issn = {1873-2976},
abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.},
}

@article {pmid41548597,
year = {2026},
author = {Zhao, M and Yu, X and Zhao, M and Zhang, G},
title = {Structured framework for the application of metagenomic next-generation sequencing in the whole-process management of lower respiratory tract infections.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102910},
doi = {10.1016/j.jiac.2026.102910},
pmid = {41548597},
issn = {1437-7780},
abstract = {OBJECTIVES: This study aims to assess the impact of metagenomic next-generation sequencing (mNGS) on optimizing diagnostic-therapeutic pathways for lower respiratory tract infections (LRTIs).

METHODS: This retrospective observational study analyzed 42 consecutive LRTI patients at Jiading Branch of Shanghai General Hospital (June 2023-October 2024). Comprehensive clinical data were evaluated including demographic features, laboratory result, radiological findings, mNGS interpretation, treatment modifications, and outcomes.

RESULTS: The mNGS detected pathogens in 37/42 patients (88.1%), despite the fact that 38 patients (90.5%) had received ineffective empirical antibiotic therapy prior to mNGS testing. More than half the patients(22/42, 52.4%) had comorbidities and about half the cases were within the normal range in the level of inflammatory biomarker. Pathognomonic CT features suggesting specific pathogens were observed in 33.3% (14/42) of cases. With regard to the interpretation of mNGS reports combaining the clinical characteristics, the results were consistent with the final diagnosis in 30 (30/42, 71.4%) patients. Crucially, 92.9% (39/42) underwent treatment modifications: 66.7% (28/42) transitioned to targeted/narrower-spectrum antibiotics and 26.2% (11/42) discontinued antimicrobial therapy following infection exclusion. Patients receiving targeted regimens demonstrated universal clinical improvement with radiological resolution, particularly in complex infections.

CONCLUSION: While mNGS provides robust pathogen detection, its clinical application requires integration with multidimensional patient data. The standardized protocol proposed in this study has the potential to enhances diagnostic efficiency and resource utilization in LRTI management.},
}

@article {pmid41548304,
year = {2026},
author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T},
title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141134},
doi = {10.1016/j.jhazmat.2026.141134},
pmid = {41548304},
issn = {1873-3336},
abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.},
}

@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-025-01699-2},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}

@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41547817,
year = {2026},
author = {Xiao, Y and Tang, Y and Yan, Y and Cheng, Q and Chen, X and Wang, L and Li, X},
title = {Targeted next-generation sequencing has comparable clinical value to metagenomic NGS for pulmonary infections in hematological malignancy patients: a real-world propensity score-matched study.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03893-0},
pmid = {41547817},
issn = {2047-783X},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is widely recognized in immunocompromised populations due to its unbiased ability to identify pathogens, while targeted next-generation sequencing (tNGS) combines PCR amplification with high-throughput sequencing technology, with advantages of lower costs and shorter turnaround times. However, it remains unclear whether tNGS can be applied in the same way as mNGS for immunodeficient patients with hematologic malignances (HM).

METHODS: This retrospective study analyzed clinical data from 245 HM patients suspected of pneumonia between April 2019 and April 2024. Bronchoalveolar lavage fluid (BALF) samples were tested using either tNGS or mNGS. Propensity score matching (PSM) (1:1) balanced the groups.

RESULTS: tNGS and mNGS showed comparable sensitivity, specificity, and accuracy for pathogen detection (97.3% vs 94.2%, 26.3% vs 26.1%, 82.6% vs 77.2%; all P > 0.05), with similar accuracy across immunodeficiency states (severe immunodeficiency: 80.0% vs 81.8%; non-severe immunodeficiency: 64.7% vs 86.7%; both P > 0.05). For non-severe pneumonia, tNGS was comparable to mNGS (accuracy: 77.9% vs 86.3%, P > 0.05), but mNGS was significantly superior in severe cases (accuracy: 50.0% vs 100.0%, P = 0.002). Both groups improved rate of correct antibiotic use (tNGS: 50.9% to 84.3%; mNGS: 57.1% to 77.8%, P < 0.01) and reduced overuse rates (tNGS: 25.9% to 2.8%; mNGS: 4.8% to 25.4%; P < 0.01), with no difference in chemotherapy intervals (37.5 ± 22.9 days vs 41.0 ± 38.4 days; P = 0.89).

CONCLUSION: In HM patients suspected of pulmonary infection, BALF-tNGS showed comparable diagnostic efficacy as BALF-mNGS, with similar clinical value across varying immunodeficiency states. tNGS is a viable alternative for non-severe pneumonia, while mNGS is superior in severe cases. Collectively, the findings of this study highlight tNGS as an alternative diagnostic approach for HM patients.},
}

@article {pmid41547254,
year = {2026},
author = {Li, C and Liu, Z and Zhao, N and Pan, H and Wang, H and Zhang, Y},
title = {Hidden oral-joint-lung axis: Porphyromonas gingivalis Infection promotes the EMyT of RA-ILD by inhibiting the JUN-regulated palmitoylation balance.},
journal = {International immunopharmacology},
volume = {172},
number = {},
pages = {116210},
doi = {10.1016/j.intimp.2026.116210},
pmid = {41547254},
issn = {1878-1705},
abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a major cause of mortality among patients with rheumatoid arthritis (RA), yet the pathological mechanism linking joint and lung involvement remains poorly understood. The pathogenic role of Porphyromonas gingivalis (P.g) in RA has been established. This study investigated how P.g infection drives RA-ILD through palmitoylation-mediated epithelial-myofibroblast transition (EMyT), thereby uncovering a mechanistic basis for the oral-joint-lung connection.

METHODS: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and 16S rRNA sequencing of fecal samples from patients with RA-ILD were analyzed to assess the association between P.g and RA-ILD. A collagen-induced arthritis (CIA) mouse model and human lung epithelial cell lines (A549 and BEAS-2B) infected with P.g were established. Palmitoylation dynamics, EMyT marker expression, and the function of the hub gene JUN were evaluated using immunopathology, qPCR, western blotting (WB), single-cell sequencing, and molecular docking. Mechanistic studies employed the JUN activator c2-ceramide, the JUN inhibitor pterostilbene, and the palmitoylation inhibitor 2-BP to determine how P.g regulates palmitoylation in promoting RA-ILD.

RESULTS: Both mNGS and 16S rRNA analyses revealed a strong association between Porphyromonas spp. infection and RA/RA-ILD. P.g infection significantly increased EMyT marker expression (collagen I, fibronectin, and vimentin) in vitro and induced pulmonary fibrosis in CIA-ILD mice, with palmitoylation playing a central role. Mechanistically, JUN was identified as a key regulator of palmitoylation. P.g suppressed JUN level, activated ZDHHC3, and inhibited PPT1, leading to palmitoylation imbalance. Activation of JUN by c2-ceramide, combined with inhibition of palmitoylation by 2-BP, effectively suppressed EMyT progression in RA-ILD.

CONCLUSION: This study identifies a novel "oral-joint-lung axis" in which P.g infection promotes EMyT and fibrosis in RA-ILD by disrupting JUN-regulated palmitoylation homeostasis. Modulation of this axis provides a promising therapeutic strategy for RA-ILD.},
}

@article {pmid41547203,
year = {2026},
author = {Zhi, C and Wang, D and He, B and Hou, G and Gao, M and Mu, H and Wei, R and Wu, X and Bai, J and Jiao, Y and Hu, X},
title = {Metabolic coupling of arsenic, carbon, nitrogen, sulfur and iron in high-salinity groundwater in the Yellow River Delta: Insights from metagenomic analyses.},
journal = {Water research},
volume = {292},
number = {},
pages = {125368},
doi = {10.1016/j.watres.2026.125368},
pmid = {41547203},
issn = {1879-2448},
abstract = {Arsenic (As) mobilization in deltaic aquifers is regulated by tightly linked C-N-S-Fe-As biogeochemical processes, yet the influence of salinity on these interactions remains poorly resolved. Here, we investigated high-salinity groundwater from the Yellow River Delta, where total dissolved solids range from 1 to 35 g/L and As concentrations reach 303 μg/L. By integrating metagenomic sequencing, metagenome-assembled genomes (MAGs), and nitrogen and sulfur isotopic measurements, we characterized how salinity and redox gradients restructure microbial functional potential and regulate As cycling. Functional-gene profiles show a transition from nitrate- and Fe(III)-coupled metabolisms in low-salinity groundwater to sulfate- and sulfite-driven anaerobic pathways under high-salinity conditions, consistent with δ[15]N-NH4[+], δ[15]N-NO3[-], and δ[34]S-SO4[2-] signatures. Genome-resolved analyses further reveal that Pseudomonadota and Desulfobacterota dominate carbon oxidation, nitrogen and iron reduction, and sulfur-intermediate reduction, while Muiribacteriota and Planctomycetota specialize in sulfite reduction and anammox/Feammox, respectively. Together, these results show that microbial communities reorganize along the salinity gradient, with arsenic mobilization associated with nitrogen- and iron-coupled reductive processes in low-salinity groundwater and with sulfur-driven reduction under high-salinity conditions. By linking microbial metabolic interactions to salinity-related redox environments, this study provides a process-based basis for anticipating how arsenic mobility may change as coastal aquifers undergo salinization.},
}

@article {pmid41547150,
year = {2026},
author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W},
title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111622},
doi = {10.1016/j.ijfoodmicro.2026.111622},
pmid = {41547150},
issn = {1879-3460},
abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.},
}

@article {pmid41546704,
year = {2026},
author = {Ramadoss, R and Siddique, A and Rashid, N and Liberski, AR and Vincent, AS and Mackey, HR},
title = {Effects of nitrogen and phosphorous concentrations on PHA synthesis by PNSB enriched phototrophic mixed microbial culture.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41546704},
issn = {1615-7605},
support = {NPRP11-S-0110-180245//Qatar National Research Fund/ ; },
abstract = {Global economic burden due to plastic pollution is estimated to be over $3 trillion annually. Bioplastics derived from bacteria-synthesized biopolymers like polyhydroxyalkanoates (PHAs), are a remarkably versatile sustainable alternative. Research on optimal growth-conditions for microbial PHA-synthesis fed-on sustainable substrates, particularly by phototrophic-mixed-cultures (PMC) enriched with purple non-sulphur bacteria (PNSB) is essential. This study intends to understand the effect of nitrogen and phosphorus concentrations on PHA-production by PMC grown using fuel synthesis wastewater (FSW) (organic by-product of Fischer-Tropsch process) as substrate. Stoichiometric quantification and 16 S metagenomic sequencing followed by statistical and bioinformatic analysis were done. High PHA-production (65-82% of biomass) is observed to be induced by Low-Nitrogen conditions enriching Rhodopseudomonas, Paludibacter and Pleomorphomonas and a Low-Phosphorus condition enriching Rhodopseudomonas, Rhodoplanes and Lentimicrobium. Analysis of metabolic-potential revealed 16 enzymes (of 8 different PHA-synthesis-pathways) inherent within the genomes of bacteria enriched by these culture conditions. This study identifies optimal nitrogen and phosphorus concentrations and the corresponding microbial-composition of FSW substrate-grown PMC-system to maximize PHA-production in a laboratory-scale bioprocess.},
}

@article {pmid41546695,
year = {2026},
author = {Zhang, T and Liu, H and Huang, Z and He, Z and Fan, Y and Liu, F and Su, E and Ming, Y and Zhu, W and Wang, C and Yu, X and Niu, M and Wu, K and Sun, X and Yang, Y and He, Z and Yan, Q},
title = {Microbially Driven Organic Carbon Degradation and Nutrient Cycling during Macroalgal Decomposition.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09758},
pmid = {41546695},
issn = {1520-5851},
abstract = {The release of labile organic carbon (OC) and nutrients during seasonal macroalgal blooms can undermine blue carbon sequestration in coastal ecosystems. Although marine microorganisms mediate OC degradation during macroalgal decay, the underlying mechanisms remain poorly defined. This study employed an integrated multiomics approach (amplicon sequencing, metagenomics, and metatranscriptomics) to investigate microbial regulation of OC degradation and coupled nutrient cycling in coastal sediments with and without decomposing Sargassaceae. Total carbon in sediments increased by over 33% in the Sargassaceae area. Microbial α-diversity in the Sargassaceae area decreased significantly (p < 0.05), while processes linked to OC degradation, carbohydrate metabolism, nitrate (NO3[-]) reduction, inorganic phosphorus utilization, and sulfur metabolism were significantly upregulated (p < 0.05). Accordingly, gene expression and extracellular hydrolase activities targeting key biopolymers (i.e., cellulose, hemicellulose, starch, and chitin) were significantly upregulated (p < 0.05) in the area with Sargassaceae. Metabolism reconstruction of metagenome-assembled genomes identified Vibrio, Pseudoalteromonas, Alteromonas, and Exiguobacterium_A as primary OC degraders, with genomic capacities enriched in NO3[-] reduction and assimilatory sulfate reduction. Key environmental drivers─including the C/N ratio, dissolved organic carbon, total dissolved nitrogen (DON), and NO3[-]─shaped microbial metabolic activities during macroalgal decomposition. Our finding demonstrates that microbially driven OC degradation is a pivotal process coupled with nutrients cycling, advancing the mechanistic understanding of microbial carbon processing and its biogeochemical linkages during macroalgal decomposition in coastal ecosystems.},
}

@article {pmid41546513,
year = {2026},
author = {Yang, YY and Bueno de Mesquita, CP and Lawrence, CR and Weyman, PD and Dores, D and Timmermann, T and Fierer, N and Fuenzalida-Meriz, GA},
title = {Synergistic Effects of a Microbial Amendment and Crushed Basalt: Soil Geochemical and Microbial Responses.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70705},
pmid = {41546513},
issn = {1365-2486},
support = {//Andes Ag, Inc./ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacillus subtilis/physiology/metabolism ; *Silicates/chemistry/metabolism ; Carbon Dioxide/metabolism ; Glycine max ; },
abstract = {Over geologic timescales, the natural weathering of silicate minerals in soils and regolith regulates atmospheric CO2. Although this process is slow relative to anthropogenic emissions, several strategies have been proposed to accelerate this process for climate mitigation. These include the application of finely-ground silicate rock to increase mineral surface area (enhanced weathering, EW) and the use of microbes that catalyze mineral dissolution and CO2 biomineralization (microbial carbon dioxide mineralization, MCM). While both approaches show promise, their combined application has rarely been tested. Here, we examined how soil chemistry and bacterial communities respond to a basalt feedstock rich in silicate minerals, a Bacillus subtilis strain (MP1) previously shown to enhance weathering, and their combination. In a 91-day soybean mesocosm experiment with slightly acidic soil (pH 6.6), MP1 persisted where applied, indicating successful inoculation via seed treatment. Basalt amendments had the strongest effect on soil bacterial community composition, whereas inoculation with MP1 exerted a smaller but detectable influence. Biogeochemical indices of weathering indicated that co-application of basalt and MP1 enhanced carbonate alkalinity beyond basalt alone. Soil carbonate alkalinity increased with MP1 treatment both with and without basalt, while soil pH and cation exchange capacity (CEC) increased with basalt in both MP1 and non-MP1 treatments. Total carbon was highest in the combined MP1 + basalt treatment, suggesting that MP1 may mitigate short-term organic carbon losses associated with basalt-driven priming. Overall, these results provide new insights into interactions between biological and mineral-based carbon dioxide removal (CDR) strategies, suggesting that co-application of MP1 with basalt in slightly acidic soil may enhance carbonate alkalinity while reducing organic carbon losses relative to basalt alone. Thus, pairing B. subtilis MP1 with enhanced weathering deployments emerges as a promising strategy to improve CDR efficiency.},
}

*Soil Microbiology
*Soil/chemistry
*Bacillus subtilis/physiology/metabolism
*Silicates/chemistry/metabolism
Carbon Dioxide/metabolism
Glycine max

@article {pmid41546385,
year = {2026},
author = {Chang, H and Qin, X},
title = {Red Complex Bacteria as a Hidden Cause of Chronic Lung Abscess: A Case Report.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e949102},
doi = {10.12659/AJCR.949102},
pmid = {41546385},
issn = {1941-5923},
mesh = {Humans ; *Lung Abscess/microbiology/diagnostic imaging/diagnosis/drug therapy ; Chronic Disease ; Male ; *Chronic Periodontitis/complications/microbiology ; Tomography, X-Ray Computed ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Hemoptysis/etiology ; },
abstract = {BACKGROUND Common oral pathogens such as Treponema denticola, Porphyromonas gingivalis, and Tannerella forsythia, which form biofilms in the periodontal pockets, are classified together as Red Complex bacteria in Socransky's subgingival cluster model and are key pathogenic bacteria in periodontitis. Oral pathogens play a critical role in pulmonary infections, particularly in the pathogenesis of lung abscesses. Lung abscesses caused by Red Complex bacteria have rarely been described; to our knowledge, few cases have been reported to date. CASE REPORT We present the first documented case of chronic lung abscess caused by Red Complex bacteria, with recurrent hemoptysis as the main symptom. The patient had chronic periodontitis and uncontrolled diabetes, and exhibited an indolent clinical course with consistently negative bacterial cultures. Chest computed tomography (CT) demonstrated a thick-walled cavity with minimal liquefactive changes in the right upper lobe. Red Complex bacteria in the bronchoalveolar lavage fluid and the lung tissue were identified by metagenomics next-generation sequencing (mNGS). The patient underwent intravenous penicillin therapy. The hemoptysis resolved completely coupled with improvement in clinical status and inflammatory markers. The chest CT demonstrated near-complete resolution of the lung abscess during follow-up. CONCLUSIONS Red Complex bacteria are rare pathogens in patients with periodontitis who develop culture-negative chronic lung abscesses accompanied by recurrent hemoptysis. This case report highlights this rare etiology and reveals a critical diagnostic limitation, as routine cultures frequently fail to detect these fastidious organisms. The incorporation of mNGS into the diagnostic algorithm for such cases can facilitate a definitive diagnosis and guide precise antimicrobial therapy.},
}

Humans
*Lung Abscess/microbiology/diagnostic imaging/diagnosis/drug therapy
Chronic Disease
Male
*Chronic Periodontitis/complications/microbiology
Tomography, X-Ray Computed
Middle Aged
Anti-Bacterial Agents/therapeutic use
Hemoptysis/etiology

@article {pmid41545847,
year = {2026},
author = {Xu, Z and Gao, L and Chen, Z and Tang, L and Wang, Y},
title = {Metagenomic next-generation sequencing for the diagnosis and evaluation of pediatric pleural effusion: a case series.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04117-1},
pmid = {41545847},
issn = {1471-2466},
support = {2023C03009//the "Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
}

@article {pmid41545588,
year = {2026},
author = {Buddle, S and Brown, LK and Morfopoulou, S and Torres Montaguth, OE and Scoto, M and Herder, V and Dhawan, A and Brown, JR and Atkinson, L and Kopec, A and Davis, D and Storey, N and Campos, L and Sebire, N and Macpherson, H and Lee, J and Orton, R and Baranello, G and Asamaphan, P and Ilia, G and Karda, R and Belfield, H and , and Counsell, J and Waddington, SN and Thomson, EC and Muntoni, F and Breuer, J},
title = {Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41545588},
issn = {1546-170X},
abstract = {Adeno-associated viruses (AAVs) are common vectors in gene therapy but can frequently cause liver complications in patients. The mechanisms underlying AAV-related liver toxicity remain poorly understood, posing challenges for effective prevention and intervention. Here we conducted a case study of a child with spinal muscular atrophy type 1 experiencing substantial hepatitis after receiving onasemnogene abeparvovec, undertaking long- and short-read metagenomic sequencing of liver tissue. We identified manufacturing plasmid sequences with complex structures and recombination. Vector genomes had extensive disruption and concatemerization as well as numerous vector-human fusion junctions. We also identified human betaherpesvirus 6B in the liver. Further work and investigation of more patients is needed to establish whether the presence of manufacturing plasmid sequences or helper viruses contribute to the formation of these complex concatemeric DNA structures in the liver, and whether these are a factor in the development of liver toxicity after AAV gene therapy.},
}

@article {pmid41545429,
year = {2026},
author = {Maharaj, SD and Nkuna, R and Matambo, TS},
title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35157-6},
pmid = {41545429},
issn = {2045-2322},
abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.},
}

@article {pmid41544986,
year = {2026},
author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z},
title = {Rumen fermentation, microbial flora, and their metabolite interaction patterns: A comparison between non-pregnant and gestational Ashidan yaks.},
journal = {Genomics},
volume = {},
number = {},
pages = {111205},
doi = {10.1016/j.ygeno.2026.111205},
pmid = {41544986},
issn = {1089-8646},
abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.},
}

@article {pmid41544844,
year = {2026},
author = {Wei, Y and Hu, Y and Shi, Q and Su, N and Chen, X and Chong, L and Cui, X},
title = {Successful Treatment of Probable Disseminated Mucormycosis Using Liposomal Amphotericin B and Isavuconazole in Myelodysplastic Syndrome: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108394},
doi = {10.1016/j.ijid.2026.108394},
pmid = {41544844},
issn = {1878-3511},
abstract = {BACKGROUND: Mucormycosis is a rare, aggressive, and life-threatening fungal infection that predominantly affects immunocompromised individuals and is associated with a high mortality rate.

CASE PRESENTATION: We treated a 72-year-old woman with myelodysplastic syndrome (MDS) who developed disseminated mucormycosis involving the lungs, skin, and central nervous system (CNS). Diagnosis was supported by metagenomic next-generation sequencing (mNGS), and she received combination antifungal therapy with liposomal amphotericin B and isavuconazole. Her clinical status stabilized after 4 weeks of treatment. She later died approximately 2 weeks after discharge because of carbapenem-resistant Pseudomonas aeruginosa bacteremia.

CONCLUSIONS: Our case highlights the importance of prompt diagnosis and timely initiation of therapy for mucormycosis and indicates that combination antifungal therapy may be an effective approach to managing severe disseminated mucormycosis in immunocompromised patients.},
}

@article {pmid41544592,
year = {2026},
author = {Zheng, Z and Lyu, H and Li, Z and Tang, J and He, J},
title = {Unraveling water depth dependent microplastic aging driven by functional microbial community interaction in a real urban river.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141133},
doi = {10.1016/j.jhazmat.2026.141133},
pmid = {41544592},
issn = {1873-3336},
abstract = {Microplastic (MPs) biofilms are dynamic microhabitats that regulate substance transformation processes. However, the influence of natural urban water depth gradients on the biofilm functions and subsequent aging of MPs remains poorly understood. Herein, we characterized the aging process of MPs in different depths of a real urban river, and the biofilm driven aging mechanism was illustrated. Surface characterization of the MPs showed an increase in oxygen-containing functional groups (CO, C-O) and O/C in polylactic acid (PLA) during aging, which indicated oxidation and hydrolysis reactions, especially at 2.0 m deep water depth. In polyvinyl chloride (PVC) MPs, carbonyl index (CI) was 2 times higher at 2.0 m as compared to 0.1 m water depth and lower chlorine content was found, indicating higher oxidative degradation and dechlorination processes in deeper water. Moreover, biofilms may regulate the synergism between oxygenase and hydrolases in PLA biofilms and oxygenase and dehalogenase in PVC biofilms. Microorganisms with both denitrification and MPs degradation functions, such as Acidovorax, Comamonas, Dechloromonas, were enriched in MPs biofilm. In addition, a positive correlation was found between MPs degradation genes (TGL2, katG, ncd2) and denitrification genes (napA, nirS, norB) in PLA biofilms at deeper water depth, suggesting a potential effect of denitrification functions on MPs aging (45 d incubation). This research challenges the conventional thoughts of higher MPs aging in shallow water, emphasizing the significant role of moderate depth gradients water in regulating the ecological function of microplastic biofilm, which is essential for evaluating the fate of MPs in real urban rivers.},
}

@article {pmid41544536,
year = {2026},
author = {Chen, R and Li, Z and Li, D and Mao, X and Xu, Z},
title = {Clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in the etiological diagnosis of community-acquired pneumonia in children.},
journal = {International journal of medical microbiology : IJMM},
volume = {322},
number = {},
pages = {151701},
doi = {10.1016/j.ijmm.2026.151701},
pmid = {41544536},
issn = {1618-0607},
abstract = {CAP is a major cause of pediatric hospitalization on a global scale, particularly in developing countries where the morbidity and mortality rates remain high. The etiological diagnosis of CAP in children is challenging, particularly for children with severe and high-risk conditions, such as immunodeficiency. This is primarily due to the nonspecific distribution of the causative agent and the limitations of traditional detection methods. As an emerging molecular diagnostic technology, BALF mNGS has been shown to detect the nucleic acid sequences of bacterial, viral, fungal, and atypical pathogens directly from clinical samples. This is attributed to the technology's unbiased, high throughput, and high sensitivity, which significantly improves the detection rate of pathogens. Furthermore, BALF mNGS also improves the detection of mixed infections. This capacity for precise analysis is of significant value, as it facilitates the identification of drug-resistant genes and rare pathogens. Consequently, this enhanced diagnostic capability provides a reliable foundation for the precise treatment of childhood CAP. Nevertheless, its clinical application continues to encounter challenges, including high cost, invasive sampling methods, complex data analysis processes, and insufficient standardization of pre-analytical sample processing. The technical principles, clinical value and optimization strategies of BALF mNGS are systematically reviewed in this paper, with the aim of providing a reference for improving the pathogenetic diagnosis of CAP in children.},
}

@article {pmid41544440,
year = {2026},
author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X},
title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106373},
doi = {10.1016/j.psj.2026.106373},
pmid = {41544440},
issn = {1525-3171},
abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.},
}

@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}

Animals
Male
*Lactiplantibacillus plantarum/physiology
*Probiotics/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects/physiology
Mice, Inbred C57BL
*Liver Diseases, Alcoholic/therapy/microbiology
Liver/metabolism
Mice
Dysbiosis
NF-E2-Related Factor 2/metabolism/genetics
Oxidative Stress
Bile Acids and Salts/metabolism
Disease Models, Animal

@article {pmid41543271,
year = {2026},
author = {Yamazaki, K and Yamaguchi, T and Yokoyama, Y and Tonosaki, Y and Kursanbaeva, K and Motooka, D and Akeda, Y and Kashimoto, T},
title = {Nutrient acquisition drives Edwardsiella tarda pathogenesis in necrotizing soft tissue infection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0165725},
doi = {10.1128/msystems.01657-25},
pmid = {41543271},
issn = {2379-5077},
abstract = {Necrotizing soft tissue infections (NSTIs) are rapidly progressive and life-threatening diseases caused by diverse bacterial pathogens. While classical virulence factors, such as toxins and secretion systems, have been extensively characterized, the role of metabolic fitness in supporting bacterial survival within the nutrient-restricted host environment remains underexplored. Edwardsiella tarda, a human-pathogenic bacterium implicated in NSTIs, represents an emerging model for studying non-canonical pathogenic strategies. Here, we employed transposon-directed insertion site sequencing (TraDIS) to identify genes critical for E. tarda survival in a murine soft tissue infection model. A genome-wide screen revealed 41 genes significantly depleted during the infection, including those involved in iron and zinc acquisition (fetB, zupT), vitamin biosynthesis (pdxK, cobA), and polyamine metabolism (speB). Functional assays using defined minimal media demonstrated that supplementation with vitamin B6 or putrescine enhanced bacterial growth, validating their contribution to fitness under nutrient-limited conditions. Our findings indicate that E. tarda pathogenesis is driven not solely by classical virulence factors but also by its ability to acquire essential nutrients and adapt metabolically to host-imposed nutritional stress. This study provides the first genome-wide fitness map for E. tarda during soft tissue infection and reveals new targets for therapeutic intervention that disrupt nutrient acquisition systems. These results also emphasize the broader relevance of metabolic adaptation as a determinant of virulence in invasive bacterial infections.IMPORTANCENecrotizing soft tissue infections (NSTIs) are severe, rapidly progressing bacterial infections with high morbidity and mortality. Although classical virulence factors such as toxins have been widely studied, much less is known about how pathogens adapt metabolically to survive within the nutrient-restricted environment in host tissues. This study uses Edwardsiella tarda, an emerging NSTI pathogen, as a model to identify genes required for in vivo fitness using transposon insertion sequencing. By revealing the critical roles of nutrient acquisition and metabolic adaptation, rather than toxin production alone, this work challenges conventional paradigms of bacterial virulence. Our findings suggest that targeting bacterial nutrient acquisition pathways may offer a novel therapeutic approach to control invasive infections. Furthermore, this study provides the first genome-wide fitness map of E. tarda during soft tissue infection, offering a valuable resource for future research into polymicrobial wound infections and host-pathogen nutrient competition.},
}

@article {pmid41543249,
year = {2026},
author = {Beals, DG and Carper, DL and Hochanadel, LH and Jawdy, SS and Klingeman, DM and Piatkowski, BT and Weston, DJ and Doktycz, MJ and Pelletier, DA},
title = {Genomic signatures in Variovorax enabling colonization of the Populus endosphere.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160525},
doi = {10.1128/msystems.01605-25},
pmid = {41543249},
issn = {2379-5077},
abstract = {Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.IMPORTANCEPlants often depend on diverse microbial partners to support their growth, resilience, and adaptation to changing environments. Among these microbes, some bacteria inhabit the rhizosphere (the narrow zone around roots where microbes interact with the plant) while others are able to enter and persist within root tissues. The traits that distinguish these two lifestyles remain poorly understood. In this study, we examined a group of related Variovorax strains from poplar tree root microbiomes to ask why some rhizosphere-associated strains also become successful endosphere colonizers. We found that strains appear to succeed through different strategies: some may benefit from rapid growth on plant-derived carbon sources, while others may rely on stress tolerance or fine-tuned regulation. These results suggest that there is no single path from the rhizosphere into the root interior, but rather multiple strategies shaped by the host environment. Understanding this diversity can inform efforts to design resilient plant-microbe communities.},
}

@article {pmid41543189,
year = {2026},
author = {Hasan, GM and Mohammad, T and Zaidi, S and Shamsi, A and Sohal, SS and Hassan, MI},
title = {<p>Klebsiella pneumoniae and pyogenic liver abscess: Emerging clinical threats, virulence mechanisms and therapeutic strategies (Review)</p>.},
journal = {Molecular medicine reports},
volume = {33},
number = {3},
pages = {},
doi = {10.3892/mmr.2026.13800},
pmid = {41543189},
issn = {1791-3004},
mesh = {Humans ; *Klebsiella pneumoniae/pathogenicity/drug effects/genetics ; *Liver Abscess, Pyogenic/microbiology/drug therapy/diagnosis/epidemiology/therapy ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Klebsiella Infections/drug therapy/microbiology/epidemiology/diagnosis ; Virulence ; Drug Resistance, Multiple, Bacterial ; Animals ; },
abstract = {

Klebsiella pneumoniae has emerged as a leading cause of pyogenic liver abscess (PLA), driven by hypervirulent and multidrug‑resistant (MDR) strains that pose major diagnostic and therapeutic challenges. This organism exhibits extensive capsular diversity (K1‑K80), with serotypes K1, K2, K5, K20, K54 and K57 being the most associated with invasive infections and severe clinical outcomes. Increasing convergence between hypervirulence and MDR determinants threatens effective management worldwide. Pharmacological and safety limitations of current antibiotics, including nephrotoxicity of colistin, hepatotoxicity of tigecycline and poor drug penetration into abscess cavities, further complicate treatment and encourage exploration of non‑traditional strategies such as anti‑virulence or immunomodulatory approaches. Recent advancements in rapid diagnostic tools such as metagenomic sequencing, MALDI‑TOF and point‑of‑care PCR assays offer promising prospects for early detection and antimicrobial optimization. Pharmacokinetic challenges at the abscess site and the emergence of hybrid hvKp‑MDR strains emphasize the urgency of precision‑guided therapy and robust global surveillance. K. pneumoniae‑associated PLA thus represents an evolving global health threat and understanding serotype diversity, antibiotic limitations and diagnostic innovations is essential for developing more effective preventive and therapeutic strategies. The present review provides current insights into the epidemiology, pathogenesis and therapeutic challenges of K. pneumoniae‑associated PLA, while highlighting translational opportunities and research priorities to counter the escalating dual threat of hypervirulence and resistance.

Humans
*Klebsiella pneumoniae/pathogenicity/drug effects/genetics
*Liver Abscess, Pyogenic/microbiology/drug therapy/diagnosis/epidemiology/therapy
Anti-Bacterial Agents/therapeutic use/pharmacology
*Klebsiella Infections/drug therapy/microbiology/epidemiology/diagnosis
Virulence
Drug Resistance, Multiple, Bacterial
Animals

@article {pmid41542367,
year = {2026},
author = {Sladký, O and Veselý, P and Břinda, K},
title = {FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT).},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbaf290},
pmid = {41542367},
issn = {2635-0041},
abstract = {MOTIVATION: The growing volumes and heterogeneity of genomic data call for scalable and versatile k-mer-set indexes. However, state-of-the-art indexes such as SBWT and SSHash depend on long non-branching paths in de Bruijn graphs, which limits their efficiency for small k, sampled data, or high-diversity settings.

RESULTS: We introduce FMSI, a superstring-based index for arbitrary k-mer sets that supports efficient membership and compressed dictionary queries with strong theoretical guarantees. FMSI builds on recent advances in k-mer superstrings and uses the Masked Burrows-Wheeler Transform, a novel extension of the classical Burrows-Wheeler Transform that incorporates position masking. Across a range of k values and dataset types-including genomic, pangenomic, and metagenomic-FMSI consistently achieves superior query space efficiency, using up to 2-3× less memory than state-of-the-art methods, while maintaining competitive query times. Only a space-optimized version of SBWT can match the FMSI's footprint in some cases, but then FMSI is 2-3× faster. Our results establish superstring-based indexing as a robust, scalable, and versatile framework for arbitrary k-mer sets across diverse bioinformatics applications.

FMSI is developed in C++ and released under the MIT license, with source code provided at https://github.com/OndrejSladky/fmsi and an installable package available through Bioconda. The datasets used in the experiments are deposited at Zenodo (https://doi.org/10.5281/zenodo.14722244).},
}

@article {pmid41542089,
year = {2025},
author = {Zhang, D and Hu, J and Gu, B and Cao, B and Lu, J and Chen, Q and Wang, L and Pei, G and Liu, ZX and Cheng, MG and Gao, S and Li, X},
title = {BodyMeta: A comprehensive database for microbes under various pathological and physiological conditions.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {3685-3692},
pmid = {41542089},
issn = {2001-0370},
abstract = {Microorganisms residing in the gut and other anatomical sites exhibit substantial alterations under both physiological and pathological conditions, which are intricately linked to human health. Consequently, the establishment of a comprehensive metagenomic database encompassing diverse body sites under both pathological and physiological conditions is highly important. In this study, we developed BodyMeta (Body Metagenome Database), an upgraded version of the gutMEGA (gut Metagenome Atlas database), and we expanded the included studies considerably from 182 to 1261. These studies were classified into two categories: 600 literature-based studies without raw data (comprising 107 whole-genome sequencing and 493 16S amplicon sequencing studies) and 661 studies containing 663 raw datasets. We systematically categorized 1842 conditions derived from the 1261 studies into 966 pathological and 879 physiological conditions spanning 31 body sites, with the pathological conditions organized according to MeSH (Medical Subject Headings) terms. We comprehensively annotated the microbial contents, diversities, biomarkers and functional differences of the curated raw 16S amplicon sequencing data. In total, 59010 microbial taxa from literature sources and 40657 from raw datasets were mapped to the NCBI Taxonomy database. Additionally, related information about literature and experiments were compiled within BodyMeta. Collectively, the BodyMeta database provides a comprehensive resource for metagenomic investigations related to both physiological and pathological conditions, which can be freely accessed at https://bodymeta.omicsbio.info/.},
}

@article {pmid41542073,
year = {2025},
author = {Kapoor, S and Mehta, P and Patial, V and Pandey, R and Padwad, YS},
title = {Phloretin-induced modulation in gut microbiome, mitigates colonic inflammation and alleviates colitis-associated colorectal cancer in mice.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {2730-2746},
pmid = {41542073},
issn = {2001-0370},
abstract = {Colitis associated colorectal cancer (CAC) is the fourth common cancer known to cause significant mortalities worldwide. Phloretin is a dihydrochalcone naturally found in apple, pear and strawberry. It exhibited different biological activities, namely anti-inflammatory, anticancer and anti-microbial. In the present study, the role of phloretin towards alleviating colonic inflammation and regulating gut microbiota was explored. The treatment of phloretin led to the reduction in the intestinal inflammation and maintained colon length-weight ratio by decreasing the total number of tumor nodules. We registered reduction in the colonic inflammatory cytokines levels namely TNFα, IL1β, IFNγ, and IL6 as well as expression of HSP90, Cox2, and Src found decreased. Results highlighted the restoration in the levels of tight junction proteins and the expression of Muc2 and Muc3. Further, role of phloretin in inducing apoptosis of tumor cells and the deregulation β-catenin pathway was studied. The histopathological analysis revealed normal colonic structure by decreasing leukocyte infiltration, as well as, circumvention in the reduction of the numbers of goblet cell, crypt abscess and ulceration in phloretin and 5-ASA (5-aminosalicylic acid) treated animals, compared to the diseased group. Metagenomic analysis of the gut microbiome in CAC mice revealed that phloretin significantly increased the abundance of Lactobacillus species, which exert probiotic effects and inhibit synchronous colon tumor growth by modulating β-catenin signaling. The increased abundance of L. reuteri and L. murinus was associated with regulated cellular proliferation, reduced TNF-α production, and decreased expression of COX-2, cyclin D1, and Bcl-2. In conclusion, the results obtained signify the nutraceutical potential of phloretin in restoring the intestinal barrier, maintaining the beneficial gut microbial population, and amelioration of CAC in mice.},
}

@article {pmid41541500,
year = {2025},
author = {Broedlow, CA and Swanson, E and Cherenack, EM and Basting, C and Nogueira, NF and France, M and Yue, P and Chakrawarti, A and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Ravel, J and Fein, LA and Holm, J and Alcaide, ML and Klatt, NR},
title = {Common cervicovaginal sequencing methods result in discordant molecular diagnoses of bacterial vaginosis and reveal strain level effects of Gardnerella vaginalis.},
journal = {npj women's health},
volume = {3},
number = {},
pages = {},
pmid = {41541500},
issn = {2948-1716},
support = {P30 AI073961/AI/NIAID NIH HHS/United States ; R01 AI138718/AI/NIAID NIH HHS/United States ; },
abstract = {Bacterial vaginosis (BV) is associated with HIV transmission and pre-term birth, yet the etiology of BV remains unknown. Our analysis addressed that knowledge gap by comparing diagnostic techniques and using Bayesian inference to find species-specific associations with clinical indicators. We also assessed the effect of sequencing methodology on the results of molecular BV profiling. We observed significant differences in microbial diversity within BV-associated CSTs based on clinical diagnosis. CST assignments were substantially influenced by sequencing methodology, with concordance between methods as low as 59% for metatranscriptomic and metataxonomic-based CST assignment. We also found that Gardnerella has a strain-dependent association with individual Amsel's criteria, and that Dialister micraerophilus and Parvimonas micra are positively associated with Amsel's criteria while Lactobacillus is negatively associated. These results highlight the challenge of characterizing a condition without a single etiological agent, reinforcing the need for more granular diagnoses and treatments that are sensitive to BV variability.},
}

@article {pmid41541065,
year = {2025},
author = {Zhang, X and Liu, C and Han, Y and She, J and Wu, W and Wang, L and Song, J and Gao, GF and Xu, Z and Liang, H and Liu, J},
title = {Sustained circulation of Aedes albopictus-derived novel almendraviruses in the urban parks.},
journal = {Biosafety and health},
volume = {7},
number = {6},
pages = {369-376},
pmid = {41541065},
issn = {2590-0536},
abstract = {The Rhabdoviridae family comprises a diverse range of negative-sense single-stranded ribonucleic acid (RNA) viruses, including significant human and mammalian viruses transmitted by various arthropod species. Herein, using Aedes albopictus (Ae. albopictus) samples collected in two urban parks during 2023 and 2024, through metagenomics sequencing, 16 sequences were identified as putative novel viruses, showing closest homology to insect-specific viruses, mycoviruses, or plant-associated viruses. Notably, two novel viruses, Aedes albopictus almendravirus GCCDC15 (Aealb-AlmV GCCDC15) and Aedes albopictus almendravirus GCCDC16 (Aealb-AlmV GCCDC16) were identified and successfully isolated. Both of these viruses belong to the genus Almendravirus within the Rhabdoviridae family. Phylogenetic analysis revealed that Aealb-AlmV GCCDC15 and GCCDC16 are distantly related to Coot Bay virus (the United States of America, 2013) and Menghai rhabdovirus (Yunnan Province, China, 2017). The genetic distances between these two viruses and their most similar viruses are marked by 59.85 % and 87.20 % of amino acid identity in the L protein, respectively, supporting their classification as two new species in the Rhabdoviridae family. Cytopathic effects and rod-like virions were observed in mosquito cells (C6/36) after inoculating with supernatants from the Ae. albopictus samples. To investigate the natural distribution and persistence of the novel almendraviruses, we conducted a specific reverse transcription-polymerase chain reaction (RT-PCR) screening of Ae. albopictus mosquitoes collected from two urban parks across different time points. The assays confirmed the presence of both Aealb-AlmV GCCDC15 and GCCDC16 in mosquito populations. Critically, these viruses were detected repeatedly over successive sampling periods and in mosquitoes from geographically distinct sites within the urban environment. In summary, our study delineates the virome characteristics of Aedes mosquitoes in the urban ecosystem and successfully isolated two novel rhabdoviruses. The recurrent detection provides clear evidence for the sustained circulation of Ae. albopictus-derived almendraviruses in urban parks, highlighting their ongoing transmission and establishment in these habitats.},
}

@article {pmid41540749,
year = {2026},
author = {Kong, L and Xu, H and Wang, Y and Tao, Y and Xiao, P and Wang, Z and Zhang, M and Zheng, X and Zhang, C and Cui, S and Xu, T and Pang, Z and Wang, A and Ren, N and Zheng, C},
title = {Single-Cell Profiling Reveals Hidden Drivers of Sediment Phosphorus Release.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15684},
pmid = {41540749},
issn = {1520-5851},
abstract = {As external phosphorus inputs are progressively brought under control, microbe-mediated release of legacy phosphorus from sediments to the overlying waters has become a primary contributor to persistent eutrophication and recurrent algal blooms in global freshwater ecosystems. However, inherent challenges exist in capturing the in situ metabolic activity of phosphorus-solubilizing bacteria (PSB) due to intrinsic cultivation biases and the disconnect between bulk metagenomic profiles and the functions of viable cells. Furthermore, a lack of research into the coupling the phenotypic activity and adaptive genetic strategies of PSB in heterogeneous sedimentary environments has led to limited understanding of the mechanisms underlying endogenous phosphorus release. Here, using single-cell Raman spectroscopy coupled with deuterium oxide labeling (Raman-D2O), distinct in situ phosphorus-solubilizing activities of PSB inhabiting eutrophic, mesotrophic, and oligotrophic sediments were quantified. Inorganic PSB dominated in all sediment types but exhibited the highest activity in nutrient-rich eutrophic sites. Their activities correlated strongly with phosphorus speciation and release fluxes at the sediment-water interface of their habits. In contrast, organic PSB prevailed in oligotrophic sediments. Raman-activated cell sorting conbined with metagenomic sequencing uncovered that low-abundance taxa (e.g., Bacillus and Acinetobacter) acted as disproportionate drivers of phosphorus mobilization. PSB from eutrophic sediments were enriched in genes encoding phosphatases and organic acid hydrolysis pathways, whereas their oligotrophic counterparts favored genes related to high-affinity transporters and polyphosphate storage. These findings elucidate how nutrient regimes shape PSB metabolic traits, advancing mechanistic insights into microbial phosphorus dynamics in aquatic ecosystems and providing a theoretical basis for optimizing lake management strategies to mitigate endogenous pollutant-driven eutrophication risks.},
}

@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04699-6},
pmid = {41540332},
issn = {1471-2180},
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

@article {pmid41540059,
year = {2026},
author = {St John, E and Reysenbach, AL},
title = {Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06612-w},
pmid = {41540059},
issn = {2052-4463},
support = {DEB-2409507//National Science Foundation/ ; },
abstract = {Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993-2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.},
}

@article {pmid41539958,
year = {2026},
author = {Chen, D and Luo, LL and Yang, M and Wang, Y and Zhang, HY and Liu, ZQ and Qiao, LN},
title = {[Clinical characteristics of Pneumocystis jirovecii pneumonia in non-human immunodeficiency virus infected children].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {64},
number = {2},
pages = {204-209},
doi = {10.3760/cma.j.cn112140-20250811-00740},
pmid = {41539958},
issn = {0578-1310},
support = {2021YFC2701704//National Key Research and Development Program of China/ ; },
abstract = {Objective: To analyze the clinical characteristics of Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV) infected children, aiming to provide a basis for early diagnosis, timely treatment, and improved prognosis. Methods: A single-center retrospective case series study was conducted to analyze the general information, laboratory indicators, imaging features, treatment, and outcomes of 59 pediatric patients with non-HIV-infected PJP admitted to the Department of Pediatrics, West China Second Hospital, Sichuan University, from February 2022 to June 2025.These patients were categorized into two groups based on the presence or absence of underlying diseases.Comparative analysis was performed to assess differences in hospitalization duration, intensive care unit (ICU) admission rate, mechanical ventilation rate, mortality, and other relevant aspects between the 2 groups.The rank sum test, χ[2] test, or Fisher's exact test was employed for intergroup comparisons. Results: The age at presentation of 59 patients: 0.5 (0.3, 2.5) years, including 40 males and 19 females. Among the underlying diseases, there were 12 cases (20%) of primary immunodeficiency, 4 cases (11%) each of autoimmune diseases, hematologic malignancies, and organ transplantation 30 cases (51%) had received treatment with glucocorticoids and immunosuppressants before diagnosis. The main clinical symptoms were cough in 57 cases (97%), dyspnea in 51 cases (86%) and, fever in 35 cases (59%). The peripheral white blood cell count was 9.2 (6.3, 13.9)×10[9]/L, with neutrophils 4.4 (1.8, 7.4)×10[9]/L and lymphocytes 3.4 (2.0, 6.1)×10[9]/L. C-reactive protein (CRP) 1.4 (0.5, 11.6) mg/L, procalcitonin 0.2 (0.1, 0.6) μg/L, the lactate dehydrogenase was (582±49) U/L. Fifty-three percent (16/30) of fungal G-test results were positive, 27% (11/41) of the children had CD4[+] T-cell counts <0.5×10[9]/L, and 32% (13/41) had CD4[+]/CD8[+] ratios <1.0.The main imaging findings included consolidation or patchy opacities in 48 cases (81%), diffuse ground-glass opacities in 29 cases (49%), and decreased transparency in 20 cases (34%). Pneumocystis was detected via metagenomic next-generation sequencing (mNGS) in all cases. Co-infections were present in 57 cases (97%). Among the 59 pediatric patients, 34 cases (58%) were treated with trimethoprim-sulfamethoxazole monotherapy, 19 cases (32%) received combination therapy with micafungin, and 7 cases (12%) received combination therapy with clindamycin. Fifty-three cases (90%) required varying degrees of respiratory support. Concurrent glucocorticoid therapy was administered in 70% (41/59) of cases at anti-PJP treatment initiation. Fifty-five cases (93%) improved, and 4 cases (7%) died.There were 36 cases in the group with underlying diseases and 23 cases in the group without underlying diseases. No statistically significant differences were observed between the two groups in terms of length of hospital stay, ICU admission rate and length of ICU stay, mechanical ventilation rate, or mortality rate (all P>0.05). Conclusions: Non-HIV-infected children with PJP tend to occur in infants under 3 years old. It is often complicated by underlying diseases such as immunodeficiency, with most patients having a history of glucocorticoid or immunosuppressant use. Clinical manifestations and imaging findings lack specificity, and mNGS facilitates early diagnosis. The core treatment is trimethoprim-sulfamethoxazole, most children require respiratory support, and combination with low-dose glucocorticoids may improve prognosis.},
}

@article {pmid41539854,
year = {2026},
author = {Choi, S and Kwon, H and Kim, WK and Ko, G},
title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510017},
doi = {10.4014/jmb.2510.10017},
pmid = {41539854},
issn = {1738-8872},
mesh = {*Clostridium Infections/microbiology/therapy/prevention & control ; Animals ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; *Clostridioides difficile ; Disease Models, Animal ; Feces/microbiology ; Metagenomics ; },
abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.},
}

*Clostridium Infections/microbiology/therapy/prevention & control
Animals
*Clostridium/physiology/genetics
Gastrointestinal Microbiome
Mice
*Clostridioides difficile
Disease Models, Animal
Feces/microbiology
Metagenomics

@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