@article {pmid41871945,
year = {2026},
author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT},
title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337436},
pmid = {41871945},
issn = {1468-3288},
abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.

OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.

DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.

RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.

CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.},
}

@article {pmid41872229,
year = {2026},
author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q},
title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71095-7},
pmid = {41872229},
issn = {2041-1723},
abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.},
}

@article {pmid41872577,
year = {2026},
author = {Shan, X and Cao, K and Jeckel, H and Alcalde, RE and Trindade, IB and Kwiecinski, JV and Newman, DK},
title = {Drought drives elevated antibiotic resistance across soils.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41872577},
issn = {2058-5276},
support = {2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2209379//National Science Foundation (NSF)/ ; ALTF 191-2023//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.},
}

@article {pmid41872600,
year = {2026},
author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E},
title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41872600},
issn = {1546-170X},
abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.},
}

@article {pmid41872963,
year = {2026},
author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ},
title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00825-5},
pmid = {41872963},
issn = {1757-4749},
support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; },
}

@article {pmid41874180,
year = {2026},
author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV},
title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264825},
doi = {10.1128/spectrum.02648-25},
pmid = {41874180},
issn = {2165-0497},
abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.},
}

@article {pmid41874256,
year = {2026},
author = {Lam, WKJ and Chan, KKP and Wang, G and Lai, CKC and Kang, G and Chan, C and Leung, ACY and Wong, NHL and Tso, CSN and Chow, KM and Ramakrishnan, S and Wong, KT and Lau, CHY and Ng, JKC and Lo, RLP and Yip, WH and Ngai, JCL and To, KW and Tse, IOL and Cheng, SH and Shang, H and Chan, KW and Lai, A and Chan, CML and Lee, VCT and Malki, Y and Choy, LYL and Ma, ML and Zhou, Q and Yu, SCY and Jiang, P and Ko, FWS and Chan, KCA and Hui, DSC and Lee, YCG and Lo, YMD},
title = {Sequencing of Pleural Fluid and Plasma for Tuberculous Pleuritis.},
journal = {NEJM evidence},
volume = {5},
number = {4},
pages = {EVIDoa2500237},
doi = {10.1056/EVIDoa2500237},
pmid = {41874256},
issn = {2766-5526},
mesh = {Humans ; *Tuberculosis, Pleural/diagnosis/microbiology/blood ; Male ; Female ; Middle Aged ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Pleural Effusion/microbiology ; *DNA, Bacterial/analysis ; Prospective Studies ; Sensitivity and Specificity ; Aged ; Adult ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The laboratory diagnosis of tuberculous pleuritis (TBP) is hindered by the paucibacillary nature of Mycobacterium tuberculosis in the pleural space, resulting in low sensitivity of microbiological culture and polymerase chain reaction-based analyses on pleural fluid. The use of metagenomic next-generation sequencing for diagnosing TBP may be limited by the background noise of DNA from nontuberculous mycobacteria.

METHODS: We performed targeted sequencing to analyze M. tuberculosis DNA in paired pleural fluid and plasma from prospectively enrolled consecutive patients with new-onset pleural effusion. We used a bioinformatics alignment algorithm to the M. tuberculosis genome that was masked for regions with high sequence similarity to nontuberculous mycobacteria. Our primary outcome was a comparison of diagnostic sensitivity between M. tuberculosis sequencing as described above and culture using McNemar's test.

RESULTS: Among the included 329 patients with pleural effusion, 34 patients with TBP were identified. Targeted sequencing detected M. tuberculosis DNA fragments in the pleural fluid of all TBP cases (median, 267.6 reads per 10 million [RP10M]; interquartile range [IQR], 30.8-2644.3) but absent in 288 out of 295 (97.6%) non-TBP samples (median, 0 RP10M; IQR, 0-0). Targeted sequencing of pleural fluid achieved a sensitivity of 97.1% for TBP detection at a cutoff of 2 RP10M, in contrast to 47.1% by M. tuberculosis culture (P<0.001, McNemar's test). Sequencing yielded an area-under-the-curve value of 0.9996 (95% confidence interval, 0.9988-1.0000) for differentiating TBP and non-TBP. Plasma analysis by targeted sequencing with the same alignment algorithm reported an area-under-the-curve value of 0.9475 (95% confidence interval, 0.8929-1.0000).

CONCLUSIONS: Targeted sequencing of pleural fluid with selectively masked M. tuberculosis genomic alignment accurately diagnosed TBP and outperformed conventional diagnostic tests. (Supported by InnoHK and the Hong Kong Tuberculosis, Chest and Heart Diseases Association; ClinicalTrials.gov number, NCT05397730.).},
}

Humans
*Tuberculosis, Pleural/diagnosis/microbiology/blood
Male
Female
Middle Aged
*Mycobacterium tuberculosis/genetics/isolation & purification
*Pleural Effusion/microbiology
*DNA, Bacterial/analysis
Prospective Studies
Sensitivity and Specificity
Aged
Adult
High-Throughput Nucleotide Sequencing

@article {pmid41874416,
year = {2026},
author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI},
title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntag057},
pmid = {41874416},
issn = {1469-994X},
abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.

METHODS: We used osmotic minipumps as an application of chronic nicotine for 15 days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24 h and 1 week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.

RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24 h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.

CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.},
}

@article {pmid41874421,
year = {2026},
author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X},
title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag066},
pmid = {41874421},
issn = {1751-7370},
abstract = {The biofilm colonizing plastic debris, termed 'the plastisphere', is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.},
}

@article {pmid41874457,
year = {2026},
author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP},
title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00291.2025},
pmid = {41874457},
issn = {1522-1555},
support = {W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically-active men were randomized to receive 200mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ~2000 kcal/d SED. Multi-omic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.},
}

@article {pmid41874663,
year = {2026},
author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C},
title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02742-1},
pmid = {41874663},
issn = {1432-184X},
support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; },
}

@article {pmid41874734,
year = {2026},
author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM},
title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41874734},
issn = {1573-0972},
}

@article {pmid41874898,
year = {2026},
author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM},
title = {Protective holobiome promotes strawberry tolerance of biotic stresses.},
journal = {Stress biology},
volume = {6},
number = {1},
pages = {},
pmid = {41874898},
issn = {2731-0450},
support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.},
}

@article {pmid41874931,
year = {2026},
author = {Gong, K and Xie, Z and Zhang, P and Xu, J and Huang, J and Li, X and Huang, L},
title = {Limosilactobacillus reuteri LR-99 Modulates Gut Microbiota and Core Symptoms in Children with Autism Spectrum Disorder: A Single-arm Pilot Study.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41874931},
issn = {1867-1314},
support = {3502Z202372073//Xiamen Natural Science Foundation of China/ ; },
}

@article {pmid41875072,
year = {2026},
author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT},
title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70127},
doi = {10.1111/1755-0998.70127},
pmid = {41875072},
issn = {1755-0998},
support = {LP190100555//Australia Research Council Linkage Project/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; },
abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.},
}

*DNA Barcoding, Taxonomic/methods
*DNA Primers/genetics
*DNA, Environmental/genetics
*Electron Transport Complex IV/genetics
Animals
Biodiversity
*Metagenomics/methods

@article {pmid41875156,
year = {2026},
author = {Shen, LQ and Wang, L and Yao, Z and Lin, D and Ye, YQ and Zhang, WR and Ye, M and Sun, MM and Du, S and Wu, D and O'Connor, P and Zhu, D},
title = {Phages drive the dissemination of antibiotic resistance genes by facilitating host adaptation to heavy metal stress.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {13},
pages = {e2535653123},
doi = {10.1073/pnas.2535653123},
pmid = {41875156},
issn = {1091-6490},
support = {22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {*Metals, Heavy/toxicity/metabolism ; *Bacteriophages/genetics/physiology ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Adaptation, Physiological/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/virology/drug effects ; Stress, Physiological ; Genes, Bacterial ; China ; Gene Transfer, Horizontal ; },
abstract = {Heavy metals are increasingly recognized as major drivers of antibiotic resistance gene (ARG) dissemination in soil ecosystems. However, the role of phages in heavy metal-driven ARG dissemination and the underlying mechanisms remain poorly understood. Here, through integrative metagenomic, viromics, and metabolomic analyses of paddy soils across China, we reveal that soil phages promote ARG dissemination under heavy metal stress, likely through two potential mechanisms. First, phage-encoded auxiliary metabolic genes (AMGs) reprogram host metabolism to enhance bacterial survival and adaptation, thereby facilitating the cotransfer of adjacent ARGs and indirectly promoting horizontal dissemination. Second, phage-encoded heavy metal detoxification genes (HDGs) directly mediate metal detoxification, driving the cotransfer of neighboring ARG fragments and inducing lipid peroxidation-associated increases in membrane permeability, which collectively enhance ARG mobilization. We further identify a significant enrichment of lysogenic phages coharboring ARGs with AMGs or HDGs (AMG-ARG and HDG-ARG fragments), underscoring their contribution to ARG dissemination. Phage transplantation experiments confirm that elevated heavy metal stress triggers lysogenic phage-mediated ARG transduction to bacterial hosts. Cumulatively, our experiments highlight the pivotal role of phages in mediating ARG transfer under heavy metal pressure and underscore the necessity of incorporating phage dynamics into ARG risk assessments.},
}

*Metals, Heavy/toxicity/metabolism
*Bacteriophages/genetics/physiology
Soil Microbiology
*Drug Resistance, Microbial/genetics
*Adaptation, Physiological/genetics
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/virology/drug effects
Stress, Physiological
Genes, Bacterial
China
Gene Transfer, Horizontal

@article {pmid41875508,
year = {2026},
author = {Estrada, CSD and de Oliveira, OA and Lopes, TAC and Maria, CRC and Avelino-Alves, D and Lima, M and Vidal, LM and de Siqueira Campos, L and Dias, GM and Thompson, C and Tschoeke, D and Thompson, F},
title = {Rhodolith metagenome diversity shifts across the Great Amazon System.},
journal = {The Science of the total environment},
volume = {1027},
number = {},
pages = {181652},
doi = {10.1016/j.scitotenv.2026.181652},
pmid = {41875508},
issn = {1879-1026},
abstract = {Rhodolith-forming coralline algae in the Great Amazon Reef System (GARS) occur under strong light and redox gradients imposed by the Amazon River plume. We tested whether a conserved microbial and metabolic core persists across sectors while functions reorganize with local conditions. We conducted shotgun metagenomics on rhodolith holobionts collected in the South, Central, and North sectors and profiled taxonomic composition and pathway markers (KEGG/SEED; METABOLIC). Bacteria dominated the holobiont, with Proteobacteria, Chloroflexi, and Bacteroidetes prevailing, and Thaumarchaeota as the main archaeal lineage. Functional profiles showed structured not random variation among sectors. In the South, high water transparency supported oxygenic phototrophy (psa/psb, rbcL/S; phycobiliproteins) and stronger coupling between carbon fixation and respiration. The Central sector displayed a transitional configuration combining oxygenic and anoxygenic phototrophy (pufL/M; bch genes) with co-occurring nitrification-denitrification (amoA, nxrAB, nirK, nosZ), indicating tight NS cycling. The North was enriched in sulfur redox pathways linked to suboxic microzones, with sulfate-reducing and sulfur-oxidizing lineages and contributions from methanogenic archaea. Across sectors, high diversity and functional redundancy likely underpin holobiont persistence in mesophotic settings. Our results indicate a resilient, sector-specific reorganization of rhodolith-associated microbiomes along plume-driven gradients, with implications for biogenic calcification and biogeochemical stability under climate change and ocean acidification scenarios.},
}

@article {pmid41875555,
year = {2026},
author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S},
title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120059},
doi = {10.1016/j.ecoenv.2026.120059},
pmid = {41875555},
issn = {1090-2414},
abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.},
}

@article {pmid41875615,
year = {2026},
author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J},
title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.},
journal = {Marine genomics},
volume = {86},
number = {},
pages = {101245},
doi = {10.1016/j.margen.2026.101245},
pmid = {41875615},
issn = {1876-7478},
abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.},
}

@article {pmid41875710,
year = {2026},
author = {Gadoin, E and Massot, M and Callens, M and Arnout, P and Bedhomme, S and Rajkovic, A},
title = {Shotgun metagenomic profiling reveals a high diversity of taxa and genes within biofilms formed on microplastics incubated in urbanised aquatic ecosystems.},
journal = {Marine pollution bulletin},
volume = {228},
number = {},
pages = {119569},
doi = {10.1016/j.marpolbul.2026.119569},
pmid = {41875710},
issn = {1879-3363},
abstract = {Microplastics (MPs) are ubiquitous in aquatic ecosystems, where they are colonized by microbial communities, called the plastisphere. Of great concern is the detection of potential pathogens and antimicrobial resistance genes (ARG) in the plastisphere, which might be transported across ecosystems through MPs drifting. We used shotgun metagenomic profiling to assess taxa diversity, ARG and virulence genes (VG), within biofilm formed on polypropylene (PP) particles incubated in situ in five locations, following an anthropic gradient around Ostend (Belgium). Our results demonstrated significant variability of the plastisphere across incubation sites, but not between PP and control glass beads. Potential pathogenic bacteria (PPB) represented about 7% of bacterial reads within biofilms and VG were mainly involved in nutrition and adherence. Using dqPCR results to normalize metagenomic reads, we demonstrated a selective enrichment of ARG and VG in biofilms, while these were less abundant but more diverse in surrounding water. These findings highlight the presence of PPB, ARG and VG across all sites, likely driven by anthropogenic pressures. Although no substrate-specific effect was detected, the ability of PP particles to act as microbial reservoirs, coupled with their high mobility, reinforces concerns about their potential role in the transport and dissemination of microbial hazards.},
}

@article {pmid41875745,
year = {2026},
author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J},
title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.},
journal = {Water research},
volume = {297},
number = {},
pages = {125768},
doi = {10.1016/j.watres.2026.125768},
pmid = {41875745},
issn = {1879-2448},
abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.},
}

@article {pmid41875962,
year = {2026},
author = {Rector, A and Karatas, M and Bloemen, M and De Coninck, L and Swinnen, J and Close, L and Thijssen, M and Pourkarim, MR and Matthijnssens, J and Desmet, S and Van Ranst, M and Johnson, MC and Wollants, E},
title = {Airplane wastewater as a gateway for pathogen surveillance wastewater surveillance in airplane.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105930},
doi = {10.1016/j.meegid.2026.105930},
pmid = {41875962},
issn = {1567-7257},
abstract = {BACKGROUND: Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility of using wastewater surveillance from airplanes as a method for monitoring SARS-CoV-2 variants and other pathogens entering Belgium.

METHODS: From January to March 2023, in the wake of the COVID pandemic, 32 wastewater samples were collected at Brussels Airport from direct flights originating in Beijing, China. We applied various qPCR panels and sequencing methods, including hybrid-capture metagenomic sequencing (Twist Bioscience) targeting more than fifteen thousand strains of known human and animal viruses.

RESULTS: Nineteen out of 32 samples tested positive for SARS-CoV-2. Various other pathogens, including enterovirus/rhinovirus, adenovirus, norovirus, adenovirus 40/41, and multiple clinically relevant bacteria, were identified using respiratory and gastrointestinal qPCR panels. In 7 samples, SARS-CoV-2 variants could be determined, belonging to known lineages BA4/BA5, BA4.6/BF7, and XBB. Moreover, hybrid-capture approach allowed us to recover complete genomes of viruses from families Polyomaviridae, Papillomaviridae, Herpesviridae as well as Aichivirus A and Hepatitis B virus.

CONCLUSION: This pilot project demonstrates the feasibility of detecting SARS-CoV-2 and its variants in wastewater of commercial airplanes. This method offers a valuable means of obtaining information from regions with limited SARS-CoV-2 genomic surveillance data. Moreover, using a hybrid-capture approach, a broad range of viruses of concern can be detected. The implementation of this novel screening approach is promising for enhancing traveler-based surveillance.},
}

@article {pmid41876072,
year = {2026},
author = {Shen, Q and Xiong, JQ and Wang, Q and Yang, L and Shen, Z and Lei, Z and Ru, S},
title = {Cyanobacteria-driven morphology and adaptive microbial succession: Resilience mechanisms in algal-bacterial granular sludge under tripartite stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134481},
doi = {10.1016/j.biortech.2026.134481},
pmid = {41876072},
issn = {1873-2976},
abstract = {Algal-bacterial granular sludge (ABGS) is a promising wastewater treatment technology, yet its practical application is constrained by its unknown stability under realistic multi-stressor conditions. This work demonstrated that ABGS could withstand combined low temperature (< 15°C), carbon scarcity, and sulfamethoxazole (SMX) exposure (0-100-1000 μg/L) through the defense strategy that integrated morphological, microbial and metabolic adaptations. Metagenomics revealed a metabolic trade-off, characterized by the downregulation of energy-intensive pathways (e.g., oxidative phosphorylation and TCA cycle), and the upregulation of biosynthetic and stress-responsive pathways (e.g., glyoxylate shunt and amino sugar metabolism), redirecting carbon towards extracellular polymeric substances (EPS) production. This was synergized by the protective cyanobacterial surface barrier and reconfigured protein-rich EPS for SMX sequestration. Microbial community restructuring enhanced functional resilience, as exemplified by the shift from Nitrospira to Candidatus Nitrotoga, which sustained stable nitrification. This coordinated adaptation not only enabled the robust removal of COD (> 90%) and NH4[+]-N (> 97%), but also suppressed the proliferation of antibiotic resistance genes (ARGs) under 100 μg/L SMX stress. These findings position ABGS as self-engineering ecosystems that actively modulate microbial community assembly and metabolic networks to remove nutrients and mitigate the dissemination of ARGs.},
}

@article {pmid41876074,
year = {2026},
author = {Zhang, Y and Wu, J and Yue, C and Wang, X and Qu, Y and Zhang, X and Sun, Y and Liu, Z and Qu, J and Xu, X},
title = {Enhancing anaerobic digestion of agricultural waste via a stable Fe-Emodin-Biochar composite: Kinetic performance, energy recovery, and metabolic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134463},
doi = {10.1016/j.biortech.2026.134463},
pmid = {41876074},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) efficiency is often constrained by energy transfer in interspecies electron transfer. To address this, a cost-effective electron mediator was engineered by immobilizing industrial-grade Emodin onto an Fe-biochar matrix via one-step hydrothermal synthesis. The optimal composite (Fe/Emodin molar ratio 1.5:1) achieved a 43.3 % increase in cumulative methane yield and shortened the lag phase by 38.1 %. According to biochemical tests, the composite reduced energy barriers on the breakdown of volatile fatty acids, as shown by a 2.2-fold rise in ATP levels and increased expression of Coenzyme F420. A community shift marked by the co-enrichment of Methanothrix and syntrophic bacteria was revealed by metagenomic analysis. A change from energetically constrained hydrogen transfer to pathways mediated by the composite was suggested by the abundance of Type IV pili genes and Cytochrome c genes, which suggested the possible activation of direct interspecies electron transfer (DIET). By utilizing low-cost precursors and overcoming the instability of free mediators, this study offers a scalable biotechnological method for agricultural residue valorization. Furthermore, this approach demonstrates economic viability and potential life-cycle sustainability.},
}

@article {pmid41865966,
year = {2026},
author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J},
title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124325},
doi = {10.1016/j.envres.2026.124325},
pmid = {41865966},
issn = {1096-0953},
abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.},
}

@article {pmid41866421,
year = {2026},
author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R},
title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866421},
issn = {1573-0972},
}

@article {pmid41866581,
year = {2026},
author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW},
title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45459-4},
pmid = {41866581},
issn = {2045-2322},
support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; },
}

@article {pmid41867450,
year = {2026},
author = {Jia, C and Liu, X and Liu, W and Yao, X and Chen, X and Zhao, J and Wang, P and Ge, W and Han, Y},
title = {Multi-Omics Reveal the Potential Associations of Streptococcus, 13'-Hydroxy-Alpha-Tocopherol and Glutathione Metabolism in Children with Chronic Rhinosinusitis with Nasal Polyps.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {567582},
pmid = {41867450},
issn = {1178-7031},
abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) in children is a clinically significant inflammatory disorder characterized by persistent symptoms and complex underlying mechanisms. This study used multi-omics approaches to investigate potential microbial and metabolic associations in pediatric CRSwNP.

METHODS: Nasal secretions from 20 children with CRSwNP and 19 healthy controls were analyzed using metagenomics, untargeted metabolomics, and proteomics.

RESULTS: CRSwNP patients showed higher microbial diversity and altered microbial communities, with increased Streptococcus abundance. Metabolomic sequencing revealed that 13'-Hydroxy-alpha-tocopherol was significantly upregulated in the CRSwNP group and exhibited a positive correlation with the abundance of Streptococcus. Proteomic sequencing revealed that proteins involved in glutathione metabolism were significantly downregulated in the CRSwNP group, with GCLM and GGCT showing a significant negative correlation with 13'-Hydroxy-alpha-tocopherol.

CONCLUSION: These associative findings suggest potential links among Streptococcus, 13'-Hydroxy-α-tocopherol, and glutathione metabolism, indicating that oxidative stress-related imbalance may contribute to pediatric CRSwNP. These results provide preliminary evidence that 13'-Hydroxy-α-tocopherol may serve as a potential biomarker for pediatric CRSwNP.},
}

@article {pmid41867493,
year = {2025},
author = {Alali, M and Imani, M},
title = {Bayesian Topology Inference of Regulatory Networks under Partial Observability.},
journal = {Results in control and optimization},
volume = {19},
number = {},
pages = {},
pmid = {41867493},
issn = {2666-7207},
abstract = {Biological systems, such as microbial communities in metagenomics and gene regulatory networks (GRNs) in genomics, are composed of a vast number of interacting components observed through inherently noisy data. These systems play a critical role in understanding fundamental biological processes, including gene regulation, microbial interactions, and cellular dynamics. For example, microbial communities involve complex interactions between microbes, bacteria, genes, and small molecules observed through omics data, while GRNs consist of numerous interacting genes observed via various gene-expression technologies. However, reconstructing the topology of such networks poses significant challenges due to their large scale, high dimensionality, and the presence of noise. Existing inference techniques often struggle with scalability, interpretability, and overfitting, making them unsuitable for analyzing large and complex biological systems. To overcome these challenges, this paper proposes a Bayesian topology optimization framework for efficient and scalable inference of regulatory networks modeled as partially-observed Boolean dynamical systems (POBDS). The method combines the Boolean Kalman Filter (BKF) as an optimal estimator for POBDS, with Bayesian optimization, which employs Gaussian Process regression and a topology-inspired kernel function to model the log-likelihood function. Numerical experiments demonstrate the superior performance of our framework. In the p53-MDM2 network, our method accurately infers topology with 8 and 16 unknown regulations, achieving higher log-likelihood with 100 and 200 evaluations, respectively. For the mammalian cell cycle network with 10 unknown regulations, proposed method identifies the correct topology among 59,049 possibilities with lower error and faster convergence.},
}

@article {pmid41867523,
year = {2026},
author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S},
title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.},
journal = {ACS omega},
volume = {11},
number = {10},
pages = {16913-16921},
pmid = {41867523},
issn = {2470-1343},
abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.},
}

@article {pmid41867691,
year = {2026},
author = {Jiang, D and Wang, Y and Ling, Y and Eremin, SA and Mukhametova, LI and Du, J and Hu, H},
title = {Impacts of high-temperature and humidity transportation on rice quality: an integrated analysis of microbial community succession and flavor compound alterations.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1792369},
pmid = {41867691},
issn = {2296-861X},
abstract = {This study investigated the dynamic changes in rice quality, microbial communities, and volatile compound profiles during simulated summer transportation (35 °C, 70% RH, 15 days). Indica rice samples were systematically collected every 3 days and analyzed using HS-SPME-GC-MS/MS, HS-GC-IMS, and metagenomic sequencing. Prolonged transportation significantly altered the physicochemical properties of the rice. Moisture content plateaued on day 12, while germination rates declined significantly starting from day 6. Furthermore, fatty acid values increased continuously due to accelerated lipid hydrolysis and oxidation. Visible mold growth became evident on day 12, marking a critical tipping point for quality deterioration. The odor activity value (OAV) and relative odor activity value (ROAV) analyses revealed that the decline in unsaturated fatty aldehydes such as (E)-2-nonenal and the significant accumulation of alcohols, ketones, and short-chain esters, including 1-octen-3-ol and ethyl acetate, drove the transition from a "fresh and fatty" aroma to one characterized by moldy, fermented, and pungent notes. Metagenomic analysis demonstrated a profound ecosystem shift from bacterial dominance (Proteobacteria, Actinobacteria) to fungal dominance. Notably, Lichtheimia surged from <0.01% to 23.95%, becoming the dominant genus, while Aspergillus increased from 0.03% to 4.57%. Correlation analysis indicated that while Pseudomonas was associated with elevated fatty acid levels, the flavor shift was primarily linked to microbial succession. These findings provide insights into the synergistic mechanisms of rice spoilage and suggest that specific volatile markers could serve as early warning indicators for quality control in real-world grain logistics.},
}

@article {pmid41867766,
year = {2026},
author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S},
title = {Learning functional groups in complex microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.03.709366},
pmid = {41867766},
issn = {2692-8205},
abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~ 4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.},
}

@article {pmid41867767,
year = {2026},
author = {Nguyen, MH and Schatz, MC},
title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.06.710148},
pmid = {41867767},
issn = {2692-8205},
abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.

RESULTS: We present Perseus , a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.

Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus .

CONTACT: mnguye99@jh.edu , mschatz@cs.jhu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available online.},
}

@article {pmid41868021,
year = {2026},
author = {Zhan, M and Tu, S and Yang, S and Yin, Y and Wang, Z and Zhang, F and Zhang, Y and Wang, Q and Zhao, C and Wang, X and Wang, H and Chen, H},
title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Diagnosing Central Nervous System Infections in Hematopoietic Stem Cell Transplant Recipients: A Retrospective and Prospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {554425},
pmid = {41868021},
issn = {1178-6973},
abstract = {BACKGROUND: Diagnosing central nervous system infections (CNSI) in hematopoietic stem cell transplant (HSCT) recipients remains challenging due to nonspecific presentations and low sensitivity of conventional microbiological methods.

METHODS: This study evaluated the clinical utility of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in 127 HSCT recipients (87 retrospective, 40 prospective) from Peking University People's Hospital. Pathogens detected by mNGS and conventional methods were validated via Sanger sequencing.

RESULTS: mNGS identified 20 pathogen-positive samples (19 confirmed by sequencing), while conventional methods detected none. mNGS demonstrated 82.6% sensitivity and 99.0% specificity for CNSI diagnosis, with sensitivity rising to 100.0% when combined with conventional approaches. Notably, mNGS excelled in detecting viral pathogens, particularly in allogeneic HSCT recipients.

CONCLUSION: Our findings advocate for the integration of mNGS into the diagnostic algorithm for CNSI, especially in immunocompromised hosts. This approach enables earlier and more precise pathogen identification, which has the potential to streamline antimicrobial therapy and improve clinical management. To maximize its benefit and ensure reliable interpretation, mNGS results should be correlated with comprehensive clinical and paraclinical data. Further prospective studies are warranted to validate its impact on therapeutic decision-making and patient prognosis.},
}

@article {pmid41868024,
year = {2026},
author = {Wang, QL and Teng, SN and Zhang, XJ and Guo, YX and Kong, Y and Tian, XH and Zhang, Y},
title = {Fatal Primary Amoebic Meningoencephalitis in Coastal Areas of North China in an Immunocompetent Patient: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {559408},
pmid = {41868024},
issn = {1178-6973},
abstract = {PURPOSE: Primary amoebic meningoencephalitis (PAM) is a rapidly fatal infection caused by Naegleria fowleri (N. fowleri) with a mortality rate exceeding 95%. This study presented the clinical course, diagnosis, treatment, and outcome of a confirmed PAM case in an adult female. Additionally, we analyzed the epidemiology of PAM in China and review the therapeutic regimens of surviving cases worldwide, aiming to enhance disease awareness and improve clinical outcomes.

CASE PRESENTATION: The patient was a 50-year-old immunocompetent woman with a history of hot spring bathing before symptom onset, which was not initially disclosed. Moreover, her early infectious symptoms, particularly fever following a tick bite in an orchard, directed clinical suspicion toward tick-borne disease. Four days later, she was hospitalized with generalized convulsions and coma. Clinical examination suggested a bacterial intracranial infection, and treatment with meropenem and vancomycin was initiated. However, her condition deteriorated rapidly. The presence of N. fowleri was identified by cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and smear. The etiology was clarified only after retrospective confirmation of hot spring contact, which was later confirmed by blood mNGS. Despite intensive therapy with amphotericin B (AmB), the patient unfortunately died. To provide insights into PAM management in China, we also conducted a systematic analysis of 15 domestic cases and 18 global survivors.

CONCLUSION: PAM is characterized by rapid progression, underscoring the importance of early diagnosis. In cases of rapidly advancing meningoencephalitis, clinicians should maintain a high index of suspicion for rare pathogens such as N. fowleri, with thorough and repeated assessment of recent environmental exposures such as hot spring immersion or freshwater swimming. Early application of mNGS is essential for timely pathogen identification. While AmB remains the first-line therapy, its dosing and duration should be tailored to individual patient factors, and combination therapy should be considered to enhance efficacy. Overall, improved clinical vigilance, advanced pathogen diagnostics, and standardized anti-amoebic therapy form the cornerstone of enhancing outcomes in PAM. As the first documented PAM case in Shandong Province, China, this report highlights the need for heightened awareness in coastal regions while contributing valuable epidemiological insights into this devastating disease.},
}

@article {pmid41868028,
year = {2026},
author = {Wang, Z and Ma, R and Ding, Z and Ma, L and Liu, X and Wang, Y},
title = {Brucellosis Complicated by Thyroid Abscess and Life-Threatening Hemophagocytic Syndrome: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {583365},
pmid = {41868028},
issn = {1178-6973},
abstract = {INTRODUCTION: Brucella infections can affect various systems in the body, such as the osteoarticular and genitourinary systems; however, cases involving the thyroid gland are rare. This case report describes the clinical management of a thyroid abscess associated with brucellosis in a farmer.

CASE PRESENTATION: A 67-year-old male farmer presented to Shanxi Bethune Hospital on 17 March 2024 with a chief complaint of "intermittent fever with fatigue for over 3 months and neck swelling and pain for 2 months". Upon admission, his serum Brucella tube agglutination test titre was 1:200, Rose Bengal plate agglutination test was positive, and blood culture was negative for Brucella. Neck computed tomography revealed a low-density nodular shadow in the right thyroid lobe measuring approximately 4.79×4.45 cm. Coffee-coloured pus was aspirated during thyroid puncture. Pathogenic metagenomic next-generation sequencing and pus culture confirmed Brucella infection as the cause of the thyroid abscess. During treatment, the patient developed hemophagocytic syndrome. The patient's condition was controlled with aggressive anti-infective therapy and glucocorticoid treatment. However, because of symptom recurrence, the patient ultimately underwent surgical intervention, comprising partial thyroidectomy, abscess incision and drainage, and thyroid injection, following which he recovered fully.

CONCLUSION: This article reports an extremely rare case of brucellosis leading to a thyroid abscess. Physicians should consider the possibility of brucellosis when encountering patients with thyroid abscesses and be vigilant of other potential complications.},
}

@article {pmid41868358,
year = {2026},
author = {Ribeiro-Junior, MR and Cardwell, KF and Nascimento, D and Espindola, AS and Ramachandran, A and Gupta, SK and Tyungu, D},
title = {Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi[®]).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743643},
pmid = {41868358},
issn = {1664-302X},
abstract = {Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi[®]) software for detection of nine RNA viruses of human and veterinary clinical importance. Species specific signature sequences in the different pathogen genomes were identified, and specific electronic probe sets were curated using the MiFi[®] software. Analytical specificity and sensitivity were evaluated through simulated metagenomes and public sequence databases, respectively. Host-specific internal control probes were designed to ensure diagnostic reliability and quality control. Diagnostic performance was assessed using Oxford Nanopore sequence data from clinical nasal swab samples. In silico validation showed 100% specificity across 83 datasets and limits of detection as low as 0.0010% of total reads (10 reads per 10[6]) for some targets. Internal controls generated stable background signals without interfering with pathogen detection. In vivo testing of 44 clinical samples matched PCR performance for Human respiratory syncytial virus (HRSV), Influenza B virus (IBV), Influenza A virus (IAV), Bovine respiratory syncytial virus (BRSV), and Canine distemper virus (CDV). These findings demonstrate that the MiFi[®] software enables rapid, multiplex, and strain-specific detection of respiratory viruses in metagenomic sequence data without the need for advanced bioinformatics expertise. The approach supports scalable use in clinical laboratories, veterinary diagnostics for surveillance and triage, offering a valuable tool for improving respiratory pathogen detection across diverse settings.},
}

@article {pmid41869352,
year = {2026},
author = {Zhou, YM and Cui, XQ and Zhao, P and Peng, ZG and Guo, N and Sun, HB and Liu, SL},
title = {The species, distribution, resistance of donor-derived pathogens and their impact on solid organ transplant recipients.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1777244},
pmid = {41869352},
issn = {1664-3224},
mesh = {Humans ; Middle Aged ; Male ; Female ; Retrospective Studies ; *Tissue Donors ; Adult ; *Transplant Recipients ; *Liver Transplantation/adverse effects ; *Kidney Transplantation/adverse effects ; Aged ; *Organ Transplantation/adverse effects ; Drug Resistance, Multiple, Bacterial ; Incidence ; Bacteria/isolation & purification/drug effects ; },
abstract = {BACKGROUND: Donor-derived infections (DDIs) have become a significant cause of infection in organ transplant recipients. Elaborating on the species, distribution, and resistance of donor-derived pathogens (DDPs) holds important implications.

METHODS: A retrospective cohort study included 302 deceased donors and their corresponding 464 kidney transplant recipients and 175 liver transplant recipients. We detected DDPs in preservation fluid (PF) using both conventional culture and mNGS, and subsequently analyzed the incidence of DDIs after transplantation.

RESULTS: 89.4% (270/302) of donors had positive cultures. Predominant multidrug-resistant organism included HLAR-Enterococcus, CRAB, CRKP, CRPA, MRS and ESBL-Escherichia coli. Compared with conventional culture, mNGS exhibited superior sensitivity for detecting bacteria and fungus in PF, with shorter turnaround time (p < 0.001). The incidences of DDIs in kidney and liver transplant recipients were 16.6% (77/464) and 19.4% (34/175) respectively. The recipients with DDIs were associated with elevated serum creatinine or total bilirubin levels, increased infection events, higher risks of graft loss, elevated mortality, and longer length of hospital stay (p < 0.05).

CONCLUSIONS: Multidrug-resistant organism are prevalent in deceased donors, with PF contamination primarily originating from donors. Integration of mNGS into donor screening protocols enables timely antimicrobial intervention, potentially improving transplant outcomes.},
}

Humans
Middle Aged
Male
Female
Retrospective Studies
*Tissue Donors
Adult
*Transplant Recipients
*Liver Transplantation/adverse effects
*Kidney Transplantation/adverse effects
Aged
*Organ Transplantation/adverse effects
Drug Resistance, Multiple, Bacterial
Incidence
Bacteria/isolation & purification/drug effects

@article {pmid41869502,
year = {2026},
author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T},
title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.},
journal = {Environmental science and ecotechnology},
volume = {30},
number = {},
pages = {100683},
pmid = {41869502},
issn = {2666-4984},
abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.},
}

@article {pmid41869518,
year = {2026},
author = {Liu, J and Wu, R},
title = {Intraoperative sampling for postoperative metagenomic next-generation sequencing to guide biofilm-targeted therapy for Cutibacterium acnes infective endocarditis complicated by ruptured sinus of Valsalva aneurysm: a case report.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1707117},
pmid = {41869518},
issn = {2297-055X},
abstract = {BACKGROUND: Cutibacterium acnes is an easily overlooked pathogen in infective endocarditis (IE) due to its slow growth, propensity for biofilm formation, and high rate of culture-negative results. When complicated by structural heart disease such as a ruptured sinus of Valsalva aneurysm (RSVA), its indolent course can lead to severe hemodynamic compromise.

CASE SUMMARY: A 35-year-old male with a known ventricular septal defect (VSD) and unruptured aortic sinus aneurysm presented with persistent fever and progressive heart failure (NYHA class IV). Echocardiography revealed a ruptured right coronary sinus of Valsalva aneurysm (RCSVA) into the right ventricular outflow tract (RVOT) with a large vegetation. Blood cultures were negative. After 6 days of ineffective empirical antibiotic therapy, emergency surgery was performed to resect the aneurysm and vegetation and repair the cardiac structures. Intraoperatively, a vegetation sample was collected for metagenomic next-generation sequencing (mNGS). Postoperatively, mNGS identified Cutibacterium acnes with high sequence reads (1,284) and coverage (47.62%), enabling a definitive diagnosis. Pathology confirmed microcolonies and necrotic inflammation. The antibiotic regimen was switched to a regimen with potential activity against biofilms with oral doxycycline and intravenous clindamycin for 6 weeks. The patient's inflammatory markers normalized, and cardiac function recovered to NYHA class I, with no recurrence at 12-month follow-up.

CONCLUSION: This case highlights the diagnostic synergy of intraoperative histopathology and mNGS for pathogen identification, underscores the rationale for biofilm-conscious adjuvant therapy, and reaffirms the crucial role of early surgical debridement and repair in achieving cure.},
}

@article {pmid41869816,
year = {2026},
author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K},
title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0250325},
doi = {10.1128/spectrum.02503-25},
pmid = {41869816},
issn = {2165-0497},
abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.},
}

@article {pmid41869825,
year = {2026},
author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G},
title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261428562},
doi = {10.1177/15578666261428562},
pmid = {41869825},
issn = {1557-8666},
abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.},
}

@article {pmid41869887,
year = {2026},
author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J},
title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e20332},
doi = {10.1002/advs.202520332},
pmid = {41869887},
issn = {2198-3844},
support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; },
abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.},
}

@article {pmid41870053,
year = {2026},
author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S},
title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0147625},
doi = {10.1128/mra.01476-25},
pmid = {41870053},
issn = {2576-098X},
abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.},
}

@article {pmid41870088,
year = {2026},
author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S},
title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0010426},
doi = {10.1128/msystems.00104-26},
pmid = {41870088},
issn = {2379-5077},
abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.},
}

@article {pmid41870133,
year = {2026},
author = {Ni, B and Chen, XP and Lin, D and Yao, Z and Xia, J and Zhang, TL and Zheng, J and Cai, TG and Wang, X and Vollertsen, J and Zhu, D and Zhu, DZ},
title = {Potential Viral Regulation of Sulfur Cycling in Urban Sewer Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15040},
pmid = {41870133},
issn = {1520-5851},
abstract = {Sewer sediments are microbial hotspots for sulfur cycling and sulfide generation, which is the leading cause of sewer corrosion and poses significant economic losses and public safety concerns. However, viruses in sewer sediments remain inadequately explored regarding their characteristics, interactions with their hosts, and ecological regulatory potential for sulfur cycling. In this study, we explored viral characteristics and virus-host interactions in sewer sediments from three distinct types of urban functional areas through metagenomics and viromics. Compared with single-function (commercial and residential) areas, sewer sediments in multifunctional areas contain higher nutrients and nutrient-induced acidification, which can promote host density and drive a shift from lytic to lysogenic infection. This shift may potentially enhance sulfide formation through the insertion of more auxiliary metabolic genes related to sulfate reduction into host genomes. Conversely, a higher viral lytic tendency in single-function area can lyse sulfate-reducing microorganisms, thereby mitigating sulfide formation. Phage transplantation experiments and the high prevalence of key viral hosts across global sewers (76 cities across six countries) demonstrated the high potential of viruses in alleviating sewer corrosion. Our findings reveal the dual role of viruses as metabolic "tuners" in sewer sulfur dynamics, suggesting that comprehensive urban sewer management requires consideration of exploiting viral lysis.},
}

@article {pmid41870192,
year = {2026},
author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM},
title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261433762},
doi = {10.1177/15578100261433762},
pmid = {41870192},
issn = {1557-8100},
abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.},
}

@article {pmid41870201,
year = {2026},
author = {Li, N-P and Gupta, S and Kollipara, SK and Hung, T-H and Rao, GP and Kuo, C-H},
title = {Draft genome sequence of "Candidatus Phytoplasma australasiaticum" strain TBB-AP associated with tomato big bud disease in India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0003326},
doi = {10.1128/mra.00033-26},
pmid = {41870201},
issn = {2576-098X},
abstract = {We report the draft metagenome-assembled genome (MAG) of "Candidatus Phytoplasma australasiaticum" strain TBB-AP, obtained from a symptomatic tomato plant collected in Andhra Pradesh, India. This assembly provides a genomic resource for functional and evolutionary studies of phytoplasmas associated with tomato big bud disease.},
}

@article {pmid41870280,
year = {2026},
author = {Werbowy, O and Håkansson, M and Dorawa, S and Stefańska-Kaźmierczak, A and Svensson, LA and Al-Karadaghi, S and Jurczak-Kurek, A and Kwiatkowska-Semrau, K and Plotka, M and Fridjonsson, OH and Hreggvidsson, GO and Aevarsson, A and Dąbrowski, S and Kaczorowska, AK and Kaczorowski, T},
title = {Structural and functional characterization of a hyperthermostable single-stranded DNA-binding protein from a hot spring metagenome.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {4},
pages = {e70538},
doi = {10.1002/pro.70538},
pmid = {41870280},
issn = {1469-896X},
support = {UMO-2019/34/H/NZ2/00584//National Science Centre (Poland)/ ; 685778//European Union Horizon 2020/ ; },
mesh = {*Hot Springs/microbiology ; *DNA-Binding Proteins/chemistry/genetics/metabolism ; *Metagenome ; Crystallography, X-Ray ; *DNA, Single-Stranded/metabolism/chemistry ; Models, Molecular ; Escherichia coli/genetics/metabolism ; *Bacterial Proteins/chemistry/genetics/metabolism ; Amino Acid Sequence ; Protein Multimerization ; },
abstract = {We present the structural and functional characterization of a single-stranded DNA-binding protein (SSB-M5) identified from a hot spring metagenome in Vatnajökull National Park, Iceland. This small protein (136 aa; 15,695 Da) shares 100% amino acid sequence identity with two previously uncharacterized SSBs from hyperthermophilic Fervidobacterium species. Functional complementation assay demonstrated that SSB-M5 can substitute for Escherichia coli SSB in an ssb[-] mutant strain, confirming its biological activity. A recombinant C-terminally His-tagged SSB-M5 was overproduced, purified to homogeneity, and subjected to structural, biochemical, and biophysical analysis. The crystal structure revealed that SSB-M5 forms a dimer through a crystallographic twofold axis, with each monomer contributing to a large antiparallel β-sheet. The flat surfaces of the β-sheets from the two dimers are packed together via a second crystallographic twofold axis, forming a tetramer that serves as the functional unit of the SSB-M5. Electrophoretic mobility shift assays showed that SSB-M5, after heat treatment up to 100°C, forms stable DNA-protein complexes with the (dT)40 oligo. Quantitative analyses revealed that SSB-M5 binds (dT)70 oligonucleotide with very high affinity (KD = 72 ± 6 pM). Hill analysis indicated cooperative binding, yielding an EC50 of 141 pM and a Hill coefficient of 2. Moreover, inclusion of SSB-M5 in PCR reactions significantly enhanced amplification by eliminating non-specific products. Together, these findings identify SSB-M5 as a hyperthermostable, high-affinity single-stranded DNA-binding protein with potential applications in molecular biology and biotechnology.},
}

*Hot Springs/microbiology
*DNA-Binding Proteins/chemistry/genetics/metabolism
*Metagenome
Crystallography, X-Ray
*DNA, Single-Stranded/metabolism/chemistry
Models, Molecular
Escherichia coli/genetics/metabolism
*Bacterial Proteins/chemistry/genetics/metabolism
Amino Acid Sequence
Protein Multimerization

@article {pmid41871361,
year = {2026},
author = {Lipovac, J and Šikić, M and Vicedomini, R and Križanović, K},
title = {MADRe: Strain-level Metagenomic Classification Through Assembly-Driven Database Reduction.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag030},
pmid = {41871361},
issn = {2047-217X},
abstract = {Strain-level metagenomic classification is essential for understanding microbial diversity and functional potential, yet remains challenging, particularly when sample composition is unknown and reference databases are large and redundant. Here we present MADRe, a modular and scalable pipeline for long-read strain-level metagenomic classification based on Metagenome Assembly-Driven Database Reduction. Beyond system-level integration, MADRe introduces statistical strategies that leverage assembly-derived genomic context to guide database reduction and probabilistic read reassignment. Specifically, it combines long-read metagenome assembly, contig-to-reference reassignment using an expectation-maximization framework for reference reduction, and probabilistic read mapping reassignment on a reduced database to achieve sensitive and precise strain-level classification. We extensively evaluated MADRe on simulated datasets, mock communities, and a real anaerobic digester sludge metagenome. Across diverse similarity and coverage conditions, MADRe consistently improves precision by reducing false-positive strain detections. MADRe's design allows users to apply either the database reduction or read classification step individually. Using only the read classification step shows results on par with other tested tools. MADRe is open source and publicly available at https://github.com/lbcb-sci/MADRe.},
}

@article {pmid41871943,
year = {2026},
author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB},
title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336675},
pmid = {41871943},
issn = {1468-3288},
abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.

OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.

DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.

RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.

CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.},
}

@article {pmid41680704,
year = {2026},
author = {Huang, Y and Huang, X and Wei, X and Yang, X and Su, T and Duan, Q and Wan, J and Sun, Y and Xu, Y},
title = {Characterization of multiple herpes viremia via next-generation sequencing in patients with lower respiratory tract infections: a retrospective cohort study.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {41680704},
issn = {1471-2334},
support = {H-2024060//the Yunnan health training project of high level talents/ ; XDYC-QNRC-2024-448//the Yunnan revitalization talent support program/ ; 202302AA310044-01//Key Projects of Yunnan Province Science and Technology Department/ ; },
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of the substantial morbidity and mortality associated with severe pneumonia. Herpesviruses (HHVs) frequently reactivate during critical illness, but their bronchoalveolar lavage fluid (BALF) coinfection patterns and clinical correlates remain incompletely defined.

METHODS: A retrospective cohort study was conducted among hospitalized adults with suspected LRTIs who underwent BALF next-generation sequencing (NGS) at the Yunnan First People’s Hospital between November 2024 and May 2025. Two analytical workflows were evaluated, namely metagenomic DNA sequencing (mNGS-DNA) and a targeted NGS (tNGS) panel, including 289 and 675 patients, respectively. Participants were subsequently classified into a herpesvirus-detected (HD) group and a non-herpesvirus-detected group (non-HD).

RESULTS: In mNGS-DNA, detection frequencies were EBV 17.30%, CMV 14.88%, HHV-7 9.00%, HSV-1 8.30%, HHV-6 4.15%, and VZV 0.34%, single- and multi-virus positivity were 22.84% and 11.76%. In tNGS, the corresponding values were 17.93%, 12.00%, 7.11%, 10.07%, 2.96%, and 0.30%, single- and multi-virus positivity were 24.44% and 15.11%. HD patients were older and more likely to have severe pneumonia in both cohorts (P < 0.0001). Bacteria were the predominant pathogens in the patients with suspected LRTIs, followed by viruses and fungi. In matched BALF subsets, sequencing outperformed culture for bacterial detection (mNGS-DNA 37.90% vs. 20.56%; tNGS 87.45% vs. 13.45%; all P < 0.001), underscoring the complementary yield over conventional culture methods. HHVs exhibited the highest co-infection rates with pathogens such as Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Candida albicans.

CONCLUSIONS: In BALF from hospitalized LRTI patients, EBV and CMV predominate among herpesviruses, with HHV-7 a frequent coinfection partner. These findings underscore the need for prospective studies to define the prognostic impact of HHV coinfections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12866-x.},
}

@article {pmid41860726,
year = {2026},
author = {Stevens, KA and de Souza, JO and Li, H and Ouro-Djobo, A and Alabi, OJ and Al Rwahnih, M},
title = {Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave.},
journal = {Archives of virology},
volume = {171},
number = {4},
pages = {},
pmid = {41860726},
issn = {1432-8798},
abstract = {UNLABELLED: We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an Agave tequilana leaf sample during a routine metagenomic screening of Agave plants from California. The 16,161 bp genome contains the protein hallmarks of the family Closteroviridae, the HSP70h and the three coat protein homologs (CPh, CP, CPm), along with the open reading frames (ORFs) unique to criniviruses. Two ORFs downstream of the CPm are unique to AaCA. The monopartite nature of the genome was verified by PCR and Sanger sequencing. Phylogenetic analysis of the HSP70h gene clusters AaCA basally with existing criniviruses.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-026-06580-x.},
}

@article {pmid41862850,
year = {2026},
author = {Li, Z and Wu, C and Huang, D and Liang, Y and Zhai, Y and Mai, C and Han, Y and Tang, LA and Wang, W and Ning, C and Tan, W},
title = {Metagenomics reveals pathogenic diversity and temporal dynamics in severe pneumonia among patients in adult intensive care unit.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13107-x},
pmid = {41862850},
issn = {1471-2334},
support = {2021YFC2300101//the National Key Research and Development Program of China/ ; },
}

@article {pmid41863347,
year = {2026},
author = {Lutfi, A and Holstein, T and Andreotti, S and Muth, T},
title = {MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag134},
pmid = {41863347},
issn = {1367-4811},
abstract = {MOTIVATION: A central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include in the protein reference database or to use tailored metagenome-derived databases, which are expensive and error-prone in their generation. A possible strategy to circumvent this database search issue is de novo sequencing, where peptide sequences are directly identified from mass spectra. However, these sequences must still be mapped back to potentially extensive databases. Here, alignment-based approaches enable robust and precise results, with the potential drawback of high memory usage and long run times.

RESULTS: We present MegaPX, a software for rapidly classifying de novo peptide sequences against large protein databases. MegaPX implemented as a C ++-based tool, uses an alignment-free, k-mer approach as a taxonomic classification method with the possibility of generating mutated reference databases for error-tolerant searching. It uses various algorithms, including interleaved Bloom filters, to efficiently compute approximate membership queries, ensuring fast processing times while querying and indexing large databases in a multi-indexing fashion. We demonstrate the potential of MegaPX by analyzing different samples, including metaproteomics, against extensive reference databases, highlighting its use as a fast screening tool.},
}

@article {pmid41863618,
year = {2026},
author = {Majumder, D and Dash, S and Bhattacharya, D and Gill, HS and Raja, V and Dewi, JR and Roy, A and Rajeev, M and Pandit, S and Sharma, S and Dwivedi, SP and Nag, M and Lahiri, D},
title = {Genetically engineered lipases: advances in expression and upscaling for industrial applications.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41863618},
issn = {1432-072X},
}

@article {pmid41863619,
year = {2026},
author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY},
title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41863619},
issn = {1432-072X},
support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*Metagenomics/methods ; *Microbial Consortia ; Biodegradation, Environmental ; *Polyesters/metabolism ; Artificial Intelligence ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics ; },
abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.},
}

*Metagenomics/methods
*Microbial Consortia
Biodegradation, Environmental
*Polyesters/metabolism
Artificial Intelligence
Fungi/metabolism/genetics
Bacteria/metabolism/genetics

@article {pmid41863708,
year = {2026},
author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H},
title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41863708},
issn = {2509-2723},
abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.},
}

@article {pmid41863933,
year = {2026},
author = {Dong, X and Zhu, L and He, Y and Li, C and Wu, R and Li, D},
title = {Microbial degradation of plastics in the environment: Mechanisms, enzymatic pathways, and constraints from laboratory studies to environmental reality.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129422},
doi = {10.1016/j.jenvman.2026.129422},
pmid = {41863933},
issn = {1095-8630},
abstract = {Microplastic (MP) pollution has become a persistent environmental challenge, raising increasing concern due to its global distribution and potential risks to human health. Biological degradation, including microbial and insect mediated processes, represents a promising and environmentally sustainable strategy for mitigating plastic and MP pollution; however, its effectiveness remains highly variable and strongly context dependent. This review systematically summarizes recent advances in microbial degradation of plastic, as well as emerging research on insect mediated plastic biodegradation, focusing on degrading microorganisms, key enzymes, metagenomic discovery, and enzyme engineering strategies. A wide range of bacterial and fungal taxa capable of degrading major plastic polymers, including polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS), polyvinyl chloride (PVC), polyurethane (PU), and polylactic acid (PLA), has been reported. In addition, several insect species capable of ingesting and transforming plastics have been identified as model systems for studying plastic degradation, where mechanical fragmentation, host digestive processes, and gut microbial metabolism jointly contribute to polymer transformation. Among these, PET degrading enzymes, particularly PETase, are the most extensively characterized, benefiting from detailed structural insights and intensive protein engineering efforts that have markedly enhanced catalytic efficiency and thermostability. In contrast, enzymatic mechanisms involved in the biodegradation of polyolefins such as PE and PP remain poorly understood, representing a major knowledge gap. Recent metagenomic approaches have substantially expanded the repertoire of candidate plastic degrading enzymes by accessing uncultured MP associated microbial communities and insect gut microbiomes. Nevertheless, functional validation and evaluation under environmentally relevant conditions remain critical bottlenecks. Moreover, most reported degradation efficiencies are derived from optimized laboratory settings and may substantially overestimate microbial performance under natural environmental constraints, including low temperature, high salinity, nutrient limitation, and mixed polymer substrates. Overall, this review highlights the gap between laboratory based biodegradation studies and real world applications and emphasizes the need for integrated strategies to advance scalable plastic and MP remediation solutions.},
}

@article {pmid41863937,
year = {2026},
author = {Liu, X and Liu, X and Zhu, D and Wang, J and Wang, Z and Liu, W and Zhou, X and Zhou, H and Wu, L},
title = {Harvesting reshapes greenhouse gas exchange in reservoir drawdown soils via soil state control and context-dependent microbial functions.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129375},
doi = {10.1016/j.jenvman.2026.129375},
pmid = {41863937},
issn = {1095-8630},
abstract = {Reservoir drawdown zones, the seasonally exposed and re-flooded margins of reservoirs, are extensive pulsed wetlands that can act as hotspots of greenhouse gas (GHG) exchange. Vegetation harvesting is common in these zones, yet its net climate effect across CO2, CH4, and N2O, and the controls behind it, remain unclear. We compared harvested and unharvested plots across longitudinal river reaches and elevation bands in the drawdown zone of the Three Gorges Reservoir (China). We measured soil-atmosphere fluxes of CO2, CH4, and N2O, together with soil physicochemical properties and metagenome-derived functional markers. Harvesting increased CO2 flux and decreased CH4 flux, while N2O showed no detectable net treatment effect. Across analyses, soil hydrothermal and nutrient conditions were the dominant predictors of flux variation; microbial functional signals added information mainly through soil-dependent interactions. In CO2-equivalent terms, lower CH4 emissions only partly compensated for higher CO2, leaving a net positive effect under both 20- and 100-year horizons. These results underscore that harvest impacts in drawdown soils should be assessed as multi-gas trade-offs and interpreted through soil moisture-redox dynamics.},
}

@article {pmid41863981,
year = {2026},
author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C},
title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106706},
doi = {10.1016/j.psj.2026.106706},
pmid = {41863981},
issn = {1525-3171},
abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.},
}

@article {pmid41864025,
year = {2026},
author = {Yu, H and Zhang, X and Liang, Y and Mu, Q and Shi, X and Deng, Z and Chen, J and Cao, J and Deng, Y and Han, Z and Chen, H and Zhang, C},
title = {Deciphering the environmental fate of halogenated organic compounds in cold seep sediments: Insights from non-targeted analysis and metagenomics across vertical redox gradients.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141804},
doi = {10.1016/j.jhazmat.2026.141804},
pmid = {41864025},
issn = {1873-3336},
abstract = {Halogenated organic compounds (HOCs) are pervasive in marine environments, yet their molecular diversity, vertical distribution, and fate in deep-sea ecosystems remain largely uncharted. Here, we integrated non-targeted analysis, geochemical profiling, and metagenomics to systematically analyze a 500-cm sediment core from the Haima deep-sea cold seep, deciphering these key aspects and their controlling factors. Non-targeted analysis identified 669 HOCs (at molecular formula level), predominantly of marine origin with saturated structures. The highest HOC diversity was found in the oxic/suboxic (OS) zone, where 73.4% of the frequently detected HOCs reached their peak abundance. Concurrently, a marked decrease in organochlorines was observed at the OS-suboxic/anoxic (SA) interface, followed by level stabilization below this transition, suggesting regulation by abrupt redox shifts. Correlation analyses revealed co-regulation of HOC distribution by geochemical (e.g., depth, pH, and SO4[2-]) and microbial (e.g., reductive and hydrolytic dehalogenases) factors. Metagenomics combined with redundancy analysis further demonstrated significant interactions between HOCs and dehalogenating microbial community along the vertical profile. In summary, this study provided an integrated perspective on the biogeochemical cycling of HOCs in the deep-sea cold seep, linking their removal at redox boundaries, long-term burial, and spatial organization to underlying microbial and geochemical drivers.},
}

@article {pmid41864266,
year = {2026},
author = {Wang, X and Wang, Y and Yan, G and Chu, N and Huang, H and Nie, W},
title = {The Clinical Diagnostic Value of Metagenomic Next-Generation Sequencing for Patients with Suspected Nontuberculous Mycobacterial Osteoarticular Infection: A National Multicenter Clinical Cohort.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108578},
doi = {10.1016/j.ijid.2026.108578},
pmid = {41864266},
issn = {1878-3511},
abstract = {OBJECTIVE: This study aimed to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing non-tuberculous mycobacteria (NTM) osteoarticular infection (OAI) and compare it with mycobacteria growth indicator tube (MGIT) culture.

METHODS: This study was conducted on 193 patients with suspected NTM OAI treated from January 2019 to July 2022 at the Beijing Chest Hospital, Capital Medical University, Yantai Qishan Hospital or The Fourth People's Hospital of Nanning who had mNGS assay and MGIT culture results. Clinical comprehensive diagnosis was taken as the "gold standard". We investigated the diagnostic sensitivity, specificity, predictive value, and likelihood ratio of these tests.

RESULTS: Of the 193 patients, 26 (13.47%) were diagnosed with NTM OAI, and 167 (86.53%) had non-NTM OAI. Compared to the MGIT culture results, mNGS showed higher sensitivity (100.0% vs. 7.7%), specificity (99.4% vs. 80.2%), positive predictive value (96.3% vs. 5.7%), negative predictive value (100.0% vs. 84.8%), positive likelihood ratio (167.000 vs. 0.389) and negative likelihood ratio (0.000 vs. 1.150). The area under the curve of the mNGS assay was 0.997 (95% confidence interval, 0.990-1.000).

CONCLUSIONS: The mNGS assay had greater diagnostic accuracy than the MGIT culture in patients with suspected NTM OAI.},
}

@article {pmid41864408,
year = {2026},
author = {Wang, Z and Chen, Z and Zhu, L and Liu, Y and Wen, Q},
title = {Substrate type determines the interplay between metabolic efficiency and microbial stress response in mixed culture PHA production under high salinity.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124330},
doi = {10.1016/j.envres.2026.124330},
pmid = {41864408},
issn = {1096-0953},
abstract = {Polyhydroxyalkanoates (PHAs) from mixed cultures offer a sustainable alternative to plastics, and high salinity presents a promising selective pressure for PHA producers. However, the osmotic stress imposed by high salinity perturbs carbon and energy metabolism, yet how different volatile fatty acid (VFA) substrates influence PHA synthesis efficiency under sustained saline conditions remains poorly understood, particularly regarding carbon flux partitioning and energy trade-offs. This study investigated the effects of single VFA (acetate, propionate, butyrate, and valerate) on the enrichment, PHA accumulation, and metabolic flux of PHA-producing mixed cultures under 1.8% salinity. Butyrate and valerate-fed systems achieved superior PHA accumulation (0.636 ± 0.015 and 0.698 ± 0.005 g PHA/g VSS, respectively) compared to acetate (0.541 ± 0.006 g PHA/g VSS) and propionate (0.382 ± 0.021 g PHA/g VSS). This was due to more direct precursor supply and lower energy demands. Carbon flux analysis confirmed butyrate and valerate directed over 85% of utilized carbon to PHA, whereas propionate diverted more to cell maintenance. Metagenomics revealed that Paracoccus was a versatile salt-tolerant PHA producer across all substrates. Cultures fed with butyrate and valerate also exhibited enhanced respiratory chain activity and higher ATP/NAD(P)H, enabling better salt stress while maximizing PHA synthesis. These findings highlight the critical interplay between VFA type, salt stress, and metabolic trade-offs, providing crucial insights for optimizing high-salinity waste to PHA bioprocesses.},
}

@article {pmid41864933,
year = {2026},
author = {Dai, QB and Lai, LM and Zhu, Q and Yuan, L},
title = {Clinical efficacy of plasma cell-free dna metagenomic next-generation sequencing in diagnosing bloodstream infections.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13134-8},
pmid = {41864933},
issn = {1471-2334},
support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commissio/ ; },
}

@article {pmid41865546,
year = {2026},
author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C},
title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129432},
doi = {10.1016/j.jenvman.2026.129432},
pmid = {41865546},
issn = {1095-8630},
abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.},
}

@article {pmid41865575,
year = {2026},
author = {Xie, H and Zhou, J and Shi, Y},
title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141830},
doi = {10.1016/j.jhazmat.2026.141830},
pmid = {41865575},
issn = {1873-3336},
abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.},
}

@article {pmid41865593,
year = {2026},
author = {Asokan, S and Banerjee, N and Saleem, M and Atiyah, HM and Pandey, RK and Abbas, RK and Yousif, SIA and Radhamanalan, G and Parashar, A and Gowtham, B and Balaji, VK and Jacob, T and Vijayan, S and Rajeswary, D and Atiyah, MM},
title = {Healthcare associated infections (HAI): Insights into epidemiology, microbiology, and diagnostics.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {3},
pages = {117376},
doi = {10.1016/j.diagmicrobio.2026.117376},
pmid = {41865593},
issn = {1879-0070},
abstract = {Healthcare associated infections remain a major global health concern because they increase illness, mortality, hospital stay, and healthcare costs. This review provides an updated synthesis of recent evidence on the epidemiology, microbiology, diagnostics, and prevention of healthcare associated infections. These infections arise from patient susceptibility, invasive procedures, antibiotic overuse, contaminated equipment, and poor infection control practices. Device associated infections such as catheter associated urinary tract infection, central line associated bloodstream infection, ventilator associated pneumonia, and surgical site infection are common and often involve multidrug resistant pathogens. Biofilm formation on devices and hospital surfaces creates persistent reservoirs that promote resistance spread. Advances in automated culture systems, rapid molecular assays, metagenomics, and whole genome sequencing improve detection and surveillance. This article integrates evidence from 2020 to 2025 to provide a multidisciplinary framework for understanding and controlling HAIs.},
}

@article {pmid41865818,
year = {2026},
author = {Wang, J and Sun, Y and Zhang, Y and Guo, Y and Liu, J and Wang, X and Yang, Y and Shi, L},
title = {Mechanisms underlying differences in nitrogen removal characteristics of anammox granular sludge immobilization filler with varying particle sizes: Performance, structure, and nitrogen removal pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134471},
doi = {10.1016/j.biortech.2026.134471},
pmid = {41865818},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process serves as a green, low-carbon, and sustainable wastewater nitrogen removal technology. However, anammox processes based on granular sludge systems face structural instability issues, resulting in the loss of anammox bacteria (AnAOB). In this study, an immobilized filler system for AnAOB based on hydrogel encapsulation was constructed using anammox granular sludge (AnGS) of varying particle sizes (G1: < 0.10 cm, G2: 0.10-0.20 cm, G3: 0.20-0.32 cm, and G4: > 0.32 cm). The differences in nitrogen removal characteristics, microstructures, and pathways of these AnGS immobilized fillers were thoroughly investigated. The large particles (G3 and G4) immobilized fillers showed the best nitrogen removal performance, with total nitrogen removal rates reaching 0.591 kgN·m[-3]·d[-1] and 0.615 kgN·m[-3]·d[-1], respectively. The G2 immobilized filler was more conducive to the self-growth and enrichment of AnAOB, and the absolute abundance and relative abundance of Candidatus Brocadia increased by 23-fold and 9.20-fold, respectively. Conversely, the G1 immobilized filler displayed the poorest nitrogen removal rate due to insufficient microbial growth. The G1-G3 immobilized fillers possessed uniform and dense small pores, whereas the G4 filler featured uniform large pores. Metagenomic analysis confirmed that the abundance of denitrification-related genes in G3 and G4 immobilized fillers was highest, indicating that anammox and denitrification synergistically achieve nitrogen removal, whereas G2 immobilized fillers mainly relied on anammox. This study provides a crucial theoretical basis and technical guidance for optimizing the application of anammox immobilized filler systems.},
}

@article {pmid41865820,
year = {2026},
author = {Luo, Z and Li, W and Zhang, N and Lei, M and Chen, B and Li, Y and Liu, Q and Zhang, M and Lv, S and Cheng, F and Li, J},
title = {A novel continuous-flow three-stage tandem system based on partial nitrification/Anammox granular sludge and partial denitrification-Anammox biofilm (PN/A-PD-A) for advanced nitrogen removal from mature landfill leachate.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134474},
doi = {10.1016/j.biortech.2026.134474},
pmid = {41865820},
issn = {1873-2976},
abstract = {A novel continuous-flow system coupling partial nitrification/Anammox (PN/A), partial denitrification (PD), and Anammox (Amx) biofilm reactors was developed (PN/A-PD-A) to treat mature landfill leachate (MLL). To maximize synergy, the NH4[+]-N removal in the PN/A reactor was regulated based on the NO2[-]-N accumulation ratio (NAR) in the PD stage, ensuring optimal substrate stoichiometry for the final Amx polishing step. Over 174 days of operation, the system achieved a superior total nitrogen removal efficiency (TNRE) of 98.30 ± 0.14% (effluent TN: 21.80 ± 1.71 mg/L). The PN/A granular sludge, enriched with Candidatus_Kuenenia (5.87%) and Nitrosomonas (9.73%), demonstrated high adaptability to MLL characteristics and contributed to 83.51% of the TN removal. In the PD stage, the dominant genus Thauera (43.91%) facilitated efficient NAR (82.86 ± 1.61%) at a limited COD/NO3[-]-N ratio of 2.32 ± 0.02. The Anammox biofilm (Candidatus_Kuenenia, 27.80%) in the Amx reactor contributed to 13.10% of TN removal, ensuring to meet the MLL discharge standard. Kinetic and metagenomic analyses confirmed that distinct shifts from complete to partial nitrification (and denitrification) in enzymes activity and gene abundance under chronic MLL stress underpinned the robust NO2[-]-N accumulation in both PN/A and PD reactors. Notably, compared to conventional nitrification-denitrification process, the PN/A-PD-A system significantly reduced oxygen demand (60.18%), exogenous organic carbon consumption (91.61%), sludge yield (83.72%), and CO2 emission (94.66%), demonstrating a sustainable pathway for low-carbon nitrogen removal from high-strength wastewater.},
}

@article {pmid41865821,
year = {2026},
author = {Wang, X and Liang, BJ and Wu, DN and Zhang, XM and Zhao, HP and Lai, CY},
title = {Efficient anaerobic metformin biodegradation driven by a Cross-Feeding Consortium: Novel Pathways, Enzymes, and toxicity dynamics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134473},
doi = {10.1016/j.biortech.2026.134473},
pmid = {41865821},
issn = {1873-2976},
abstract = {Metformin is one of the most widely prescribed antidiabetic drugs worldwide and is now ubiquitously detected in aquatic environments, yet its anaerobic biodegradation remains largely unexplored and mechanistically unresolved. Here, an anaerobic membrane bioreactor (AnMBR) was operated and near-complete metformin removal (∼98%) at influent concentrations up to 5.3 mg/L was achieved, corresponding to a maximum degradation rate of 7.2 mg/L/d, approximately sixfold higher than previously reported anaerobic systems degrading metformin. High-resolution mass spectrometry identified three concurrent anaerobic metformin transformation pathways. Notably, a previously unreported biological C-N bond cleavage route yielding dimethylguanidine was discovered, expanding the known anaerobic metabolic repertoire of metformin. In silico toxicity prediction revealed a non-monotonic toxicity trajectory during metformin transformation, with transiently elevated toxicity at intermediates (particularly 2,4-AMT) followed by an overall attenuation at the terminal product guanidine. Metagenomic and metatranscriptomic analyses uncovered a cooperative, cross-feeding microbial network dominated by Ignavibacterium album and Denitrolinea symbiosum, and identified HypAB (metformin-to-guanylurea), YafV and AmiA/B/C/E (guanylurea-to-guanidine), and, critically, SpeB as the key enzyme initiating the newly proposed C-N bond cleavage pathway. Molecular dynamics simulations further suggested stable binding of metformin to SpeB with strong affinity, providing mechanistic support for SpeB-mediated initiation of the novel pathway. Overall, this study establishes the first mechanistic framework for anaerobic metformin biodegradation, reveals an unprecedented C-N scission pathway, and demonstrates that high-rate, low-carbon pharmaceutical removal can be achieved through intrinsic microbial metabolism, offering new conceptual and practical foundations for energy-efficient treatment of emerging pharmaceutical contaminants.},
}

@article {pmid41865866,
year = {2026},
author = {Wang, Y and Wang, D and Wang, H},
title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {},
number = {},
pages = {111996},
doi = {10.1016/j.cbpa.2026.111996},
pmid = {41865866},
issn = {1531-4332},
abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.},
}

@article {pmid41784805,
year = {2026},
author = {Shen, J and Gao, J and Gao, L and Yan, D and Wang, Y and Meng, J and Li, H and Chen, D and Wu, J},
title = {Melatonin ameliorates autistic-like behaviors by restoring gut microbiota-derived tryptophan metabolites.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {41784805},
issn = {1420-9071},
support = {2023-MS-310, 2019-BS-098//Natural Science Foundation of Liaoning Province/ ; LJKQZ2021149//Scientific Research Fund of Liaoning Provincial Education Department/ ; },
abstract = {UNLABELLED: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive stereotyped behavior. Disrupted microbiota‒gut‒brain axis (MGBA) signaling contributes to the pathology of ASD and cognitive disability. Melatonin (MT), a naturally occurring compound, has shown potential in ameliorating core symptoms of ASD and mitigating gut microbiota dysbiosis, yet the underlying mechanism is poorly understood. This study aimed to investigate whether exogenous melatonin improves behavioral deficits in valproic acid (VPA)-exposed male offspring rats, and the modulation of gut microbiota-derived tryptophan metabolites. In prenatal VPA-induced model rats, microbial diversity and construction was analyzed through metagenomic sequencing, targeted-metabolomics and transcriptomics were conducted to explore related metabolic pathways and molecular profiles. We identified 7 gut bacterial genus causally associated to ASD: Faecali-bacterium, Lachnospiraceae, Ruminococcaceae, Butyricimonas, and Bacteroides exhibited protection, whereas Erysipelotrichaceae and Clostridia enhanced risk. The exacerbation of Erysipelotrichaceae and Clostridia by VPA versus restoration of Faecalibacterium, Butyricimonas, Bacteroides and Bifidobacterium by melatonin, which are known to participate in tryptophan metabolism. Correspondingly, systemic metabolomics pointed to melatonin’s restoration of tryptophan metabolic disorders (IDO1-kynurenine, TPH1/2-serotonin-melatonin, and Indole-3-propionic acid (IPA)) induced by VPA, paralleled the rectification of microglial reactivity, synaptic proteins, dendritic morphology, and hippocampal neurogenesis. These molecular profiles were further integrated by transcriptomics, highlighted tryptophan-derived neurotransmitters and neuroactive ligand-receptor interaction, contributing to enhanced social and cognitive behaviors under melatonin intervention. Based on multi-omic analysis, our findings underscore key bacteria and metabolites contributing to neurological and immune dysfunction in VPA-exposed rats, providing novel targets for possible therapeutics of melatonin.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06163-8.},
}

@article {pmid41862052,
year = {2026},
author = {Rajalakshmi, SG and Ramesh Babu, K and Viswanathan, P},
title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124336},
doi = {10.1016/j.lfs.2026.124336},
pmid = {41862052},
issn = {1879-0631},
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.

METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.

KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p < 0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.

SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.},
}

@article {pmid41856866,
year = {2026},
author = {Jelen, BI and Baker, BJ},
title = {Mapping environmental microbiomes across an entire country.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.02.013},
pmid = {41856866},
issn = {1878-4380},
abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.},
}

@article {pmid41857415,
year = {2026},
author = {},
title = {Metagenomic surveillance of zoonotic yellow fever and spillover dynamics at a forest-urban interface.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41857415},
issn = {2058-5276},
}

@article {pmid41857851,
year = {2026},
author = {Yu, X and Wen, Z and Zhou, W and Zheng, Y and Chen, J and Xiao, WJ and Lin, S and Liang, H and Duan, X and Wang, W and Wu, H and Chen, X},
title = {Respiratory syndromic disease study in Shanghai community population.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e103001},
doi = {10.1136/bmjopen-2025-103001},
pmid = {41857851},
issn = {2044-6055},
mesh = {Humans ; China/epidemiology ; Male ; Female ; *Respiratory Tract Infections/epidemiology/microbiology ; Adult ; Prospective Studies ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Child, Preschool ; Incidence ; Coinfection/epidemiology ; Urban Population ; Seasons ; },
abstract = {PURPOSE: This prospective community-based cohort study (Acute Respiratory Infection Epidemiological Characteristics Assessment Study (ARI-ECAS)) aims to systematically monitor acute respiratory infection (ARI) incidence, characterise multiple pathogen coinfection patterns and explore microbial landscape dynamics in Shanghai's general population. By integrating syndromic surveillance, molecular diagnostics and metagenomic sequencing, the study seeks to enhance understanding of ARI epidemiology, seasonal variation and host-pathogen interactions to inform predictive modelling and optimise public health interventions in high-density urban environments.

PARTICIPANTS: The study enrolled 15 199 permanent residents from all 16 districts of Shanghai, with baseline oropharyngeal swab samples across five representative districts (Xuhui, Jing'an, Jiading, Songjiang and Fengxian). Inclusion criteria required residency ≥6 months and consent for weekly follow-ups. Exclusion criteria addressed mobility limitations (planned relocation >6 months) and recent ARI history. Participants provided demographic, behavioural and clinical data via the Shanghai Health Cloud platform, with baseline and symptomatic-phase biological samples collected for analysis.

FINDINGS TO DATE: During the initial 8-month surveillance period (May 2024-January 2025), the ARI-ECAS cohort demonstrated critical insights into the epidemiology of acute respiratory infections in Shanghai's urban communities. Among 15 199 participants, 10.96% reported symptomatic episodes, of whom 21.43% experienced recurrent infections. Pathogen detection using targeted next-generation sequencing (tNGS) identified microbial aetiologies in 53.52% of symptomatic cases, revealing a high prevalence of coinfections: 27.96% involved dual pathogens, while 33.01% showed polymicrobial interactions (≥3 pathogens). Notably, 85.09% of symptomatic episodes were self-managed, underscoring a low healthcare-seeking rate (14.91%) consistent with patterns observed in urban China during postpandemic transitions.

FUTURE PLANS: The current phase of data collection will conclude in June 2025; however, syndromic surveillance and tNGS protocols will be sustained to capture multiyear seasonal transmission patterns. To enhance comparative rigour, future protocols will aim to collect samples from participants during asymptomatic periods in the subsequent year to serve as seasonal baseline controls. Building on this foundation, the study will integrate contact behaviour and mobility surveys to quantify parameters critical for understanding pathogen transmission dynamics (eg, household contacts and public transportation usage). Furthermore, pathogen detection and metagenomic data will be combined with transcriptomic and metabolomic profiling in selected cases to model multipathogen interaction networks and delineate host immune response pathways, thereby advancing mechanistic insights into polymicrobial cocirculation.},
}

Humans
China/epidemiology
Male
Female
*Respiratory Tract Infections/epidemiology/microbiology
Adult
Prospective Studies
Middle Aged
Adolescent
Aged
Child
Young Adult
Child, Preschool
Incidence
Coinfection/epidemiology
Urban Population
Seasons

@article {pmid41857857,
year = {2026},
author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G},
title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e115290},
doi = {10.1136/bmjopen-2025-115290},
pmid = {41857857},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; },
abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.

METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

Humans
*Gastrointestinal Microbiome/immunology
Adult
Young Adult
*Brassica
Quality of Life
*Fermented Foods
Adolescent
Randomized Controlled Trials as Topic
*Conjunctivitis, Allergic/immunology/diet therapy
*Rhinitis, Allergic/immunology/diet therapy
Female
Male
Biomarkers

@article {pmid41858204,
year = {2026},
author = {Chen, X and Ji, M and Yan, D and Liu, Y and Chen, Y and Dong, R and Shen, L and Takeuchi, N and Kong, W},
title = {Metabolic capacities and potential microbial interactions in red and green snow of the Antarctic Peninsula.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71089},
pmid = {41858204},
issn = {1469-8137},
support = {32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 72574092//National Natural Science Foundation of China/ ; },
abstract = {Colored (red and green) snow is widespread in Antarctica due to climate warming. This phenomenon reduces snow albedo, accelerates snowmelt, alters microbial functions, and impacts regional geochemical cycles. Diverse microorganisms are associated with this phenomenon, yet their functions remain poorly understood. We employed metagenomic sequencing to reveal the metabolic interactions and functional specialization within microbial communities of colored snow, focusing on carbon, nitrogen, phosphorus, and sulfur metabolism. While broad metabolic profiles were similar between red and green snow, targeted analysis of specific pathways revealed significant enrichment of denitrification and organic-phosphorus mineralization genes in green snow and labile carbon degradation genes in red snow. Betaproteobacteria were dominant drivers of nitrogen, sulfur, and phosphorus transformation, while diverse eukaryotic algae and bacteria were responsible for carbon fixation. Additionally, we recovered 2257 bacteriophages, 529 algal viruses, and 2302 secondary metabolite gene clusters. Specifically, viruses encoded 126 auxiliary metabolic genes that may influence the elemental cycling of hosts, while secondary metabolites, such as pyoverdine, may assist algal iron acquisition. Our findings offer new insights into the metabolic potentials and interactions of microbial communities in Antarctic colored snow, highlighting their potential relevance to snow biogeochemical processes.},
}

@article {pmid41858247,
year = {2026},
author = {Groninga, J and Wittig, L and Bouderka, F and Bornemann, TLV and Lipp, JS and Schubotz, F and Keden, S and Probst, AJ and Hinrichs, KU},
title = {Novel Extended Tetraether Lipids Found in a High-CO2 Geyser.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70286},
doi = {10.1111/1462-2920.70286},
pmid = {41858247},
issn = {1462-2920},
support = {101118631/ERC_/European Research Council/International ; },
mesh = {*Carbon Dioxide/metabolism/analysis ; *Archaea/genetics/metabolism/chemistry ; Germany ; *Groundwater/microbiology ; *Lipids/chemistry ; *Ethers/chemistry ; Metagenome ; *Glyceryl Ethers/chemistry ; },
abstract = {The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.},
}

*Carbon Dioxide/metabolism/analysis
*Archaea/genetics/metabolism/chemistry
Germany
*Groundwater/microbiology
*Lipids/chemistry
*Ethers/chemistry
Metagenome
*Glyceryl Ethers/chemistry

@article {pmid41858251,
year = {2026},
author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L},
title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70131},
doi = {10.1111/1755-0998.70131},
pmid = {41858251},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; },
abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/classification/genetics
*DNA, Environmental/genetics
Quebec
Ecosystem
Fresh Water
Rivers
*Biological Monitoring/methods
Biodiversity
*Environmental Monitoring/methods
*Metagenomics/methods
*Biota

@article {pmid41858257,
year = {2026},
author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF},
title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70128},
doi = {10.1111/1755-0998.70128},
pmid = {41858257},
issn = {1755-0998},
support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Programático FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; },
mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; },
abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.},
}

*Metagenomics/methods
*Diatoms/genetics/classification
Phylogeny
*Computational Biology/methods
*DNA, Environmental/genetics
*Eukaryota/genetics/classification
Metagenome
*Biodiversity
Czech Republic
Fresh Water/microbiology

@article {pmid41858380,
year = {2026},
author = {Beran, P and Rost, M and Beranová, K and Kváč, M and Stehlíková, D and Udoh, OE and Jozová, E and Čurn, V},
title = {genCRC32: collision-free CRC32-based hashing of DNA sequences.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbaf315},
pmid = {41858380},
issn = {2635-0041},
abstract = {MOTIVATION: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Traditional hashing methods often result in collisions, impacting the precision and/or performance of downstream analyses. Thus, it is highly advantageous to have hashing functions that guarantee collision-free mappings for DNA sequences, particularly for k-mers up to length 16, where practical limits for 32-bit hashing are reached. In this study, we evaluate genCRC32 as a hashing primitive, reporting collision behavior, bucket balance, sensitivity to single-base changes, and speed to inform its potential use in downstream tools. Evaluation within specific software tools is outside the scope of this paper and is planned as future work.

RESULTS: We present genCRC32, an innovative hashing method that integrates a straightforward preprocessing step (gen32) with CRC32 hashing, specifically identifying eight CRC32 polynomials that ensure collision-free hashing for all DNA k-mers up to 16 nucleotides in length. Through extensive empirical evaluations, genCRC32 demonstrated zero collisions for these k-mers, achieving a one-to-one mapping without auxiliary data structures. Benchmark tests confirmed minimal computational overhead introduced by preprocessing, maintaining hashing performance comparable to established methods such as MurmurHash3 and xxHash32.

The source code for genCRC32 is publicly available at: https://github.com/berybox/genCRC32. The implementation is provided in Go (version 1.24) and leverages only standard libraries, ensuring portability and ease of integration into existing bioinformatics workflows.},
}

@article {pmid41858392,
year = {2026},
author = {Tu, W and Zeng, P and Wu, Z and Li, Z and Yu, T and Zhang, W and Chen, R and Liang, L},
title = {A case report of brain abscess caused by Nocardia cyriacigeorgica identified by metagenomic next-generation sequencing.},
journal = {World journal of emergency medicine},
volume = {17},
number = {2},
pages = {199-201},
pmid = {41858392},
issn = {1920-8642},
}

@article {pmid41858535,
year = {2026},
author = {Zhang, L and Chen, S and Li, H and Li, L and Liu, H},
title = {Molecular epidemiology and genomic analysis of bulbul coronavirus in Guangdong, China.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1659863},
pmid = {41858535},
issn = {2297-1769},
abstract = {INTRODUCTION: Bulbul coronavirus (BuCoV), a delta coronavirus recently identified in passerine birds, remains poorly characterized regarding its ecology and evolutionary dynamics. This study aimed to determine the prevalence of BuCoV in wild avifauna, clarify its evolutionary relationship with other delta coronaviruses, and identify genetic signatures potentially relevant to host adaptation and cross-species transmission in southern China.

METHODS: From 2023 to 2024, we conducted molecular surveillance across 12 regions in Guangdong Province, China. A total of 2,145 avian fecal samples were collected and screened for BuCoV using real-time quantitative PCR. The complete genomes of representative strains were obtained using next-generation sequencing. Subsequent analyses included phylogenetic reconstruction using maximum likelihood methods, recombination detection using RDP4 and SimPlot, and comparative amino acid analysis.

RESULTS: BuCoV was detected exclusively in Shenzhen (3/168, 1.78%), with all positive samples originating from bulbuls (Pycnonotus spp.). The Shenzhen strain GD2411 exhibited the highest nucleotide identity with BuCoV strains HKU11-796 (97.26%) and HKU11-934 (96.79%), but far lower similarity (78.9%-82.4%) to other delta coronaviruses. Phylogenetic analysis placed GD2411 in a monophyletic clade with HKU11 strains. Recombination analyses revealed mosaic structures within the spike (S) gene, involving multiple coronavirus lineages. Thirty-one amino acid substitutions were detected in the S protein, together with mutations in RdRp, 3CLpro, and nucleocapsid.

DISCUSSION: These findings suggest that BuCoV GD2411 emerged through inter-lineage recombination and is undergoing adaptive evolution, particularly in the spike protein. The detection of BuCoV exclusively in Shenzhen, a critical node in the East Asian-Australasian Flyway, suggests that migratory birds may facilitate viral dissemination. The identified mutations may affect viral replication, host adaptation, or immune evasion. These findings provide essential baseline genomic and epidemiological data critical for understanding BuCoV diversity and assessing potential zoonotic risks in southern China.},
}

@article {pmid41858674,
year = {2026},
author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z},
title = {Microbiome and plant relationship: a symbiosis against phytopathogens.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1722279},
pmid = {41858674},
issn = {1664-462X},
abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.},
}

@article {pmid41859061,
year = {2026},
author = {Wang, Z and Yang, R and Xiao, Y and Huang, B and Yang, Z and Yang, L},
title = {Primary Cutaneous Aspergillosis Due to Aspergillus flavus in an Immunocompetent Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {565781},
pmid = {41859061},
issn = {1178-6973},
abstract = {Invasive aspergillosis is a life-threatening infection caused by Aspergillus species, affecting the lungs, central nervous system, nasal and orbital regions, and skin. Primary cutaneous aspergillosis (PCA) occurs through direct skin inoculation via trauma, burns, or surgical wounds, with Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger as common causative species, and is rare in immunocompetent individuals. We report a case of PCA in a 56-year-old immunocompetent patient with facial and right ankle ulcers, persisting for two years. The patient had no history of diabetes, corticosteroid use, or immunodeficiency. Fungal culture and metagenomic next-generation sequencing (mNGS) confirmed A. flavus infection. Voriconazole therapy, surgical debridement, and specialized wound care led to the gradual healing of the ulcers. This case highlights the importance of early diagnosis and intervention to prevent infection spread and progression to systemic aspergillosis or septic shock.},
}

@article {pmid41859064,
year = {2026},
author = {Gu, P and An, X and Wei, Y and Xu, W and Han, Y and Gao, Q and Liu, S and Bi, Y},
title = {Elusive Diagnosis of Recurrent Subcutaneous Emphysema: Nocardia farcinica Infection in an Immunocompetent Female Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {556094},
pmid = {41859064},
issn = {1178-6973},
abstract = {This case report describes an immunocompetent female with recurrent subcutaneous emphysema and refractory soft tissue infections involving multiple non-contiguous sites-bilateral breasts, chest wall, and upper limb-over seven years, consistent with disseminated nocardiosis. Initial presentations mimicked bacterial mastitis, with localized swelling, erythema, crepitus, and elevated inflammatory markers. Despite repeated incision and drainage procedures, antibiotic therapies, and bilateral mastectomies, symptoms recurred persistently. Conventional microbial cultures repeatedly failed to identify a pathogen, while metagenomic next-generation sequencing (mNGS) of a late-stage chest wall lesion ultimately revealed Nocardia farcinica, an opportunistic actinomycete with a known propensity for systemic dissemination even in immunocompetent hosts. The patient's atypical clinical course-marked by multifocal gas-forming soft tissue necrosis, chronic recurrence, and resistance to empiric treatments-underscores the diagnostic challenges posed by fastidious pathogens like Nocardia. Key lessons include the utility of mNGS in identifying culture-elusive organisms, the importance of considering nocardiosis in refractory subcutaneous infections regardless of immune status, and the necessity of prolonged, targeted antimicrobial regimens (eg, sulfonamides) combined with surgical intervention. This case highlights evolving paradigms in managing complex disseminated infections through advanced genomic diagnostics and multidisciplinary approaches.},
}

@article {pmid41859067,
year = {2026},
author = {Jiang, X and Wu, L and Duan, S and Bian, J and Lv, T and Zheng, L and Zhao, Y and Shen, P and He, J and Chen, Y},
title = {Long-Term Antibiotic-Driven Gut Microbiota Disruption Promotes Toxigenic Clostridioides difficile Proliferation: A Four-Year Retrospective Study of a Single ICU Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {562973},
pmid = {41859067},
issn = {1178-6973},
abstract = {OBJECTIVE: This four-year longitudinal study of a single critically ill patient leverages deep temporal profiling to unravel the dynamic interplay between antibiotic pressure, gut microbiota, and Clostridioides difficile (C. difficile) colonization, providing temporal insights unattainable through cross-sectional designs.

METHODS: We performed a retrospective analysis of one critically ill patient (2015-2019). Sixty-four fecal samples were subjected to toxigenic C. difficile culture and metagenomic sequencing. To isolate short-term effects, we implemented a 7-day retrospective window, categorizing each sample based on antibiotic exposure in the preceding week: no antibiotics, monotherapy, or polypharmacy.

RESULTS: Antibiotic exposure significantly reduced microbial diversity and promoted dysbiosis. Crucially, we identified a transitional C. difficile colonization state (Tcd±) that potentially determines progression to toxigenic (Tcd+) or non-toxigenic (Tcd-) outcomes. Analysis using the 7-day window revealed that intensive antibiotic pressure was strongly associated with successional progression towards toxigenic dominance. Conversely, brief antibiotic-free intervals were linked to partial restoration of microbial network complexity and a competitive landscape favoring non-toxigenic strains.

CONCLUSION: This deep temporal profiling of a single case provides novel, hypothesis-generating insights. The identification of a transitional colonization state and the association between short-term antibiotic pressure and colonization outcomes define critical dynamics for future validation. These findings highlight the potential of longitudinal data to inform precise antibiotic stewardship strategies in high-risk, critically ill populations.},
}

@article {pmid41859237,
year = {2026},
author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H},
title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag011},
pmid = {41859237},
issn = {2730-6151},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.},
}

@article {pmid41859321,
year = {2026},
author = {Salama, RA and Abdel Kader, RG and Wadid, NA},
title = {Artificial intelligence in combating challenges in antimicrobial resistance: a narrative review.},
journal = {Infection prevention in practice},
volume = {8},
number = {2},
pages = {100522},
pmid = {41859321},
issn = {2590-0889},
abstract = {Antimicrobial resistance (AMR) is a major global health challenge that threatens the effective prevention and treatment of infections. It arises from increasing resistance rates, limited diagnostic capacity, inappropriate antimicrobial use, and a declining pipeline of new antibiotics. These challenges highlight the need for innovative approaches to complement existing AMR control strategies. Artificial intelligence (AI) has emerged as a valuable tool to address the complexity and scale of AMR. This narrative review examines how AI can be more effectively integrated into key components of AMR management. By analysing large clinical and laboratory datasets, AI-based surveillance and predictive models enable near real-time monitoring of resistance patterns and early outbreak detection. AI-powered diagnostic tools, including image analysis and genomic methods, improve rapid pathogen identification and prediction of antimicrobial susceptibility. In clinical practice, AI-driven decision support systems strengthen antimicrobial stewardship by optimizing prescribing and monitoring antibiotic use. In addition, deep learning approaches accelerate antimicrobial drug discovery and repurposing, reducing development timelines. AI also enhances the detection and surveillance of resistance genes through genomic and metagenomic analyses across human, animal, and environmental settings. Despite its potential, AI applications in AMR face challenges related to data quality, bias, interoperability, privacy, and clinician adoption. Therefore, AI should be seen as a tool that supports, rather than replaces, existing AMR strategies. When regulated well and integrated within One Health frameworks, AI can strengthen surveillance, improve treatment decisions, and support evidence-based interventions to curb AMR.},
}

@article {pmid41859442,
year = {2026},
author = {Wang, Y and Zhang, L and Huang, W and Wang, N and Sun, M and Wu, L and Wang, W and Shi, C},
title = {Metagenomic analysis of the community structure and functional potential of Tamarix rhizosphere microbiomes along a soil salinity gradient.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1756020},
pmid = {41859442},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil salinization strongly shapes rhizosphere microbial communities and their functional potential in arid ecosystems. Tamarix is a key halophytic shrub in desert saline-alkali environments, yet how its rhizosphere microbiomes respond to natural salinity gradients remains insufficiently understood. Here, we compared community structure, functional potential, and potential salt-adaptation strategies across a soil salinity gradient.

METHODS: Rhizosphere soils of Tamarix were collected from four sites (S1-S4) in Xinjiang, China spanning increasing salinity. Soil physicochemical properties were measured, followed by shotgun metagenomic sequencing. Taxonomic profiles and functional annotations were generated from metagenomic data and compared among salinity groups.

RESULTS: Salinity was associated with clear shifts in community composition. Bacteria dominated at low-to-moderate salinity, whereas archaeal relative abundance increased at higher salinity, with Euryarchaeota becoming dominant in the high-salinity group. Functional profiling indicated that core metabolic pathways remained prevalent along the gradient, suggesting relative stability in overall metabolic capacity. However, higher salinity was accompanied by enrichment of functions linked to genetic information processing (e.g., translation and replication/repair) and ion transport, while lipid metabolism, cell motility, and signal transduction were reduced.

DISCUSSION: Together, these results support a salinity-driven transition in microbial functional strategy from "growth expansion" toward "homeostasis maintenance." Under high salinity, microbes appear to allocate more resources to maintaining cellular integrity and coping with stress, consistent with the observed enrichment of genetic information processing and repair-related functions. Mechanistically, the increased representation of Na[+]/H[+] antiporter systems and V/A-type ATPases in the very high salinity group suggests that energy-dependent ion homeostasis is a prominent adaptation, helping regulate intracellular ion balance and mitigate salt toxicity. In contrast, pathways for compatible solute synthesis (e.g., betaine and ectoine biosynthesis) were relatively reduced, indicating that osmoprotection may rely less on de novo solute production and more on ion regulation and maintenance processes along this gradient. Overall, the metagenomic evidence clarifies how Tamarix rhizosphere microbiomes restructure taxonomically and functionally with increasing salinity and highlights key candidate mechanisms underpinning salt-stress adaptation. These insights provide a microbial basis for understanding plant-microbe interactions in desert saline-alkali soils and may inform ecological restoration and management in salinized regions.},
}

@article {pmid41859445,
year = {2026},
author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W},
title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783810},
pmid = {41859445},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.},
}

@article {pmid41859451,
year = {2026},
author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L},
title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755652},
pmid = {41859451},
issn = {1664-302X},
abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.},
}

@article {pmid41860433,
year = {2026},
author = {Boers, D and Chapleur, O and Andersson, AF and Schnürer, A},
title = {Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag029},
pmid = {41860433},
issn = {1574-6941},
abstract = {Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible; metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesising that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularised regression, which allowed filtering out irrelevant features even with limited sample sizes. Within studies, taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations. When applying trained models to other studies however, while performance was generally poor, functional models more often performed better compared to taxonomic models than the other way around. All in all, our hypothesis that functional metagenomics would outperform taxonomic metagenomics only found limited support.},
}

@article {pmid41860453,
year = {2026},
author = {Shen, S and Zhao, S and He, Z and An, X and Dong, J and Wang, L and Ji, W and Li, A},
title = {The Efflux-Two-Component System (TCS)-Virulence Axis Drives Resistance-Virulence Convergence in Aquatic "Superhost Precursors" under Pollution Stress.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09604},
pmid = {41860453},
issn = {1520-5851},
abstract = {The coexpression of antibiotic resistance and virulence traits in aquatic bacteria represents an emerging ecological and public health threat, yet the mechanisms underlying their coordinated regulation under complex environmental pressures remain unclear. In this work, we integrated metagenomic, proteomic, and metabolomic data sets from surface water samples across the Yangtze River Basin in Jiangsu Province to elucidate the drivers of resistance-virulence convergence under multipollutant stress. Among 392 multidrug-resistant (MDR; resistant to ≥3 antibiotic classes) isolates, approximately 5% were identified as "culturable superhost precursors" exhibiting pandrug-resistant (PDR; resistant to ≥10 antibiotic classes) phenotypes. Multiomics analyses indicated frequent colocalization and synchronous activation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in these environmental reservoirs. Functional assays under subinhibitory antibiotic exposure demonstrated enhanced cytotoxicity and efflux activity, accompanied by the upregulation of tolC and two-component regulators evgA/evgS. Together, these results characterize a putative redox-coupled efflux-two-component system (TCS)-virulence functional axis that synchronizes adaptive gene expression under pollution stress. Crucially, our findings challenge traditional antimicrobial resistance (AMR) surveillance approaches, which rely primarily on static gene abundance metrics, by demonstrating that the dynamic regulatory activation of this axis provides a more sensitive indicator of environmental health risks. Furthermore, tolC and evgA were identified as potential transcript-level biomarkers, providing a proof of concept for environmental antimicrobial resistance early warning tools within the One Health framework.},
}

@article {pmid41860568,
year = {2026},
author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J},
title = {Klebsiella Enrichment Is Associated with Disease Severity in Ulcerative Colitis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag079},
pmid = {41860568},
issn = {1365-2672},
abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.

METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥18 years) from First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.

RESULTS: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, p=0.005); mucosal diversity showed no difference (p=0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, p=0.14; mucosal: 3.40 vs. 3.72, p=0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g., allopurinol, histidine), enriching tyrosine and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g., quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.

CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.},
}

@article {pmid41860897,
year = {2026},
author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S},
title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {3},
pages = {e0014118},
doi = {10.1371/journal.pntd.0014118},
pmid = {41860897},
issn = {1935-2735},
abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.},
}

@article {pmid41861238,
year = {2026},
author = {Yao, ML and Dai, Y and Zhang, W},
title = {Natural Products from the Oral Microbiome.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-050248},
pmid = {41861238},
issn = {1545-4509},
abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.},
}

@article {pmid41861543,
year = {2026},
author = {Mohapatra, RK and Choi, Y},
title = {Exploring multi-omics approaches in anammox-based wastewater treatment processes: A review of recent applications and technological advances.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129342},
doi = {10.1016/j.jenvman.2026.129342},
pmid = {41861543},
issn = {1095-8630},
abstract = {Anaerobic ammonium oxidation (anammox) has arisen as a sustainable and energy-efficient approach for nitrogen removal in wastewater treatment. Recently, the utilization of multi-omics approaches, mainly metagenomics, metatranscriptomics, metaproteomics, and metabolomics has risen to reveal the complexity and functionality of anammox-based systems. These integrated approaches offer a comprehensive investigation of microbial community structure, gene expression, protein function, and metabolite dynamics across diverse operating contexts. Progress in high-throughput sequencing, mass spectrometry, and bioinformatics has facilitated the discovery of novel anammox bacteria, functional genes, and metabolic pathways, resulting in vital processes such as nitrogen cycling, microbial interactions, and system resilience. Metagenomics has shown the taxonomic and functional diversity within anammox consortia, whereas metatranscriptomics and metaproteomics have elucidated active metabolic pathways and functional responses to environmental alterations. Metabolomics has furnished direct evidence of metabolic states and biomarkers for enhancing reactor health and efficacy. Researchers have begun to elucidate the intricate physiological and biochemical mechanisms that govern the stability, recovery, and effectiveness of the anammox process through the integration of multi-omics datasets. This review explores recent technological breakthroughs and cutting-edge applications of multi-omics methods in anammox-based wastewater treatment. The article summarizes the principal research findings presented by numerous researchers, providing significant insights for the strategic design and management of robust and efficient water treatment systems aimed at future environmental sustainability.},
}