@article {pmid42763741,
year = {2026},
author = {Lian, C and Feng, B and Su, J},
title = {Post-Traumatic Primary Cutaneous Cryptococcosis Presenting as a Chronic Refractory Forearm Ulcer with Polymicrobial Coinfection: An mNGS-Assisted Case Report and Literature Review.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {642965},
pmid = {42763741},
issn = {1178-7015},
abstract = {Primary cutaneous cryptococcosis (PCC) is a rare infection caused by direct inoculation of Cryptococcus through disrupted skin. We report a 52-year-old male farmer with type 2 diabetes but no HIV infection or known major immunosuppressive disease who developed chronic refractory ulcers on the right forearm following suspected insect-bite trauma. Cryptococcus neoformans was isolated from cutaneous specimens. Probe-capture metagenomic next-generation sequencing (MetaCAP) of the ulcer tissue additionally detected C. neoformans at 202 reads per million (RPM), accounting for 91.98% of the fungal sequences, with a reported confidence of 99%. Histopathology demonstrated an infectious granuloma, while bacterial culture identified methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Escherichia coli. Chest computed tomography and cerebrospinal fluid investigations did not support pulmonary or central nervous system cryptococcosis. Liposomal amphotericin B was discontinued because of acute kidney injury, and subsequent fluconazole plus flucytosine treatment resulted in reduced exudation, granulation tissue formation, and partial ulcer healing. PCC should be considered in chronic post-traumatic ulcers, with systematic evaluation for extracutaneous involvement before establishing a primary cutaneous diagnosis.},
}

@article {pmid42763764,
year = {2026},
author = {Ridge, K and Adams, BJ},
title = {annoreport: an interactive tool for metagenome annotation.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag257},
pmid = {42763764},
issn = {2635-0041},
abstract = {SUMMARY: Gene annotation of metagenome-assembled genomes is a critical step in determining the functional potential of microbial communities from environmental samples. However, annotation workflows using tools such as Prokka or Bakta produce per-bin output with 10 to 14 files per bin, making manual review infeasible at scale. Existing tools incompletely aggregate and visualize gene annotation content across an entire metagenomic dataset. Here we present annoreport, a single-script Python tool requiring no external dependencies beyond Python 3.9+ that accepts output from either Prokka or Bakta, automatically detecting the annotation tool used. annoreport produces an interactive web-based report summarizing gene product frequencies, hypothetical protein rates, feature type distributions, and functional gene clustering via UniProt annotation across all bins. Applied to 206 metagenome-assembled genomes from Antarctic soil metagenomes, annoreport identified 603,799 coding sequences with a 47.1% annotation rate and revealed functional categorization in Transport & Membrane, Nucleotide Binding, and DNA Metabolism categories.

Freely available at https://github.com/keplerridge/annoreport under MIT license, via Bioconda (annoreport) and PyPI (annoreport).},
}

@article {pmid42763811,
year = {2026},
author = {Reddy, M and Sze, C and Prokesch, BC and Zimmern, P},
title = {Molecular based diagnostic testing for urinary tract infections: the results remain unclear.},
journal = {World journal of urology},
volume = {44},
number = {1},
pages = {},
pmid = {42763811},
issn = {1433-8726},
mesh = {Humans ; *Urinary Tract Infections/diagnosis/microbiology ; *Molecular Diagnostic Techniques ; },
abstract = {INTRODUCTION: Recent advances have led to a rise in metagenomic and molecular-based testing for more rapid diagnosis of urinary tract infections (UTI). We conducted a contemporary systematic review to understand how these molecular tests affect clinical outcomes.

METHODS: A systematic review was conducted for articles in adults from January 2023 to October 2025 as an update to previous scoping reviews. Cochrane and PRISMA standards were utilized with the following databases: PubMed, OVID, and Embase (PROSPERO number: CRD420251070022). Data was extracted from the selected full-text papers including the type of study (microbiology versus clinical), patient demographics, key findings, and funding source. Excluded studies were abstracts, non-English manuscripts, and those involving only men or children.

RESULTS: The search resulted in 12 full-text articles. Among those, 7 were published in clinical-based journals and 5 were in Microbiology. Two clinical studies were randomized controlled trials (RCTs) which included a total of 773 patients, mostly female and above the age of 65. Compared to a standard urine culture, molecular based testing, specifically with polymerase chain reaction (PCR) testing yielded superior sensitivity despite lack of specificity and guided antibiotic therapy to reduce UTI baseline symptomatology in the short term (i.e. 28 days) in both RCT analyses. Of note, the RCT analyses and several of the prospective studies (5/10) were funded by the companies that developed the molecular tests.

CONCLUSIONS: Based on the increase in publications over the last three years, new industry-funded RCTs, and the limited clinical outcome data reported, this systematic review indicates the urgent need for prospective and multicentric studies to better understand the role of these molecular tests in UTI management.},
}

Humans
*Urinary Tract Infections/diagnosis/microbiology
*Molecular Diagnostic Techniques

@article {pmid42763972,
year = {2026},
author = {Wang, W and Wang, Z and Zhang, L and Zheng, Z and Su, Y and Zhan, M and Xie, B},
title = {Redox homeostasis governs anaerobic microbial stability: mechanistic insights from selective ROS scavenging under microplastic stress.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126935},
doi = {10.1016/j.watres.2026.126935},
pmid = {42763972},
issn = {1879-2448},
abstract = {Redox homeostasis is fundamental to microbial functions in anaerobic ecosystems. Although microplastics (MPs) induce oxidative stress and reactive oxygen species (ROS) accumulation, the regulatory role and reversibility of oxidative stress in microbial functional stability remain unresolved. Here, we employed Cu/Zn-MOF nanozyme for selective ROS scavenging, combined with metagenomics and biochemical analyses, to elucidate how oxidative stress contributes to PS-MPs induced anaerobic microbial dysfunction. EPR spectroscopy revealed that PS-MPs exposure promoted environmentally persistent free radical accumulation in the digestate (4.26 × 10[14] spins/g) and promoted the O2[∙-] generation, resulting in sustained ROS accumulation (> 120% of the control). This oxidative stress impaired microbial viability and reduced cumulative methane production by 22.7% compared to the control (CK). Metagenomic analysis revealed that PS-MPs decreased the relative abundance of key methanogens (Methanothrix sp. and Methanobacterium sp.) and genes associated with Fe-S cluster assembly, antioxidant defense, VFAs conversion, and methanogenesis. ROS regulation by Cu/Zn-MOF (0.25 mg/g-TS) alleviated these metabolic constraints while PS-MPs remained present. Low dose Cu/Zn-MOF was associated with recovery of Fe-S cluster assembly-related functional potential and methanogenesis-related genes, increased the maximum methane production rate from 14.31 to 21.74 mL CH4/g-VS/d, and enhanced methanogen-centered microbial network connectivity. These findings identify oxidative stress as a reversible regulatory node affecting anaerobic microbial stability and highlight targeted redox regulation as a strategy to enhance the resilience of ROS sensitive biological systems.},
}

@article {pmid42764218,
year = {2026},
author = {Huang, QY and Xiang, HR and Tu, HK},
title = {[Current research status of the intratumoral microbiome and evolution of detection technologies].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {9},
pages = {1124-1138},
doi = {10.3760/cma.j.cn112152-20260303-00105},
pmid = {42764218},
issn = {0253-3766},
support = {82574197//National Natural Science Foundation of China/ ; K20230085//Healthy Zhejiang One Million People Cohort/ ; },
mesh = {Humans ; *Microbiota ; *Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metagenomics ; Bacteria/isolation & purification ; },
abstract = {As a core functional component of the tumor microenvironment, the regulatory role of intratumoral microbiome in tumorigenesis and progression has become as a frontier research direction in oncology. Microorganisms such as bacteria, fungi, and viruses participate in the regulation of tumor biological mechanisms through multiple pathways, including metabolite secretion, induction of genomic instability, and remodeling of the immune microenvironment; their species composition and abundance characteristics exhibit distinct cancer-type specificity, and their impact on patient prognosis is highly context-dependent. Current detection systems for the intratumoral microbiome mainly encompass in situ detection technologies, metagenomic sequencing, and computational pathology-driven intelligent detection, each with its own advantages and limitations, among which intelligent detection centered on deep learning is gradually overcoming the technical bottlenecks of identifying low-abundance microbial signals, achieving accurate quantification, and resolving spatial distribution. In the future, with the deep integration of three-dimensional pathological imaging, spatial omics, and multi-modal foundation models, intratumoral microbiome research will advance toward the in-depth development of multi-dimensional data integration, providing innovative ideas and technical pathways for elucidating the regulatory mechanisms between microorganisms and the host and for developing precision diagnostic and treatment strategies based on individual microecological characteristics.},
}

Humans
*Microbiota
*Tumor Microenvironment
*Neoplasms/microbiology/pathology
Metagenomics
Bacteria/isolation & purification

@article {pmid42764265,
year = {2026},
author = {Seok, H},
title = {Redefining post-xenotransplantation surveillance: leveraging metagenomic next-generation sequencing to discriminate true pathogen replication from microchimerism-induced false positives.},
journal = {Clinical transplantation and research},
volume = {},
number = {},
pages = {},
doi = {10.4285/ctr.26.0052},
pmid = {42764265},
issn = {3022-7712},
abstract = {Infection-related risks remain a major concern in xenotransplantation and require continued vigilance as the field progresses toward clinical application. Xenozoonosis is of particular concern, especially in relation to donor-derived porcine viruses such as porcine endogenous retroviruses, porcine cytomegalovirus, porcine lymphotropic herpesviruses, and porcine circoviruses, which are considered significant targets for donor screening and recipient surveillance in clinical xenotransplantation trials. With advances in diagnostic technologies, metagenomic next-generation sequencing may facilitate the detection of unexpected or previously unrecognized pathogens. However, positive molecular findings for donor-derived pathogens should be interpreted cautiously to distinguish microchimerism from true infection in the recipient. Addressing this diagnostic challenge will require complementary assays capable of demonstrating viral integration and replication in recipient-derived human cells, together with expert interpretation by clinicians in the appropriate clinical context. Detailed and tailored surveillance protocols incorporating these advanced methodologies should be developed and validated through well-designed clinical trials, with the resulting evidence guiding their standardization by relevant professional societies and regulatory authorities. These efforts will be essential for the safe and responsible clinical implementation of xenotransplantation.},
}

@article {pmid42764294,
year = {2026},
author = {Liu, H and Qi, Y and Zhang, X and Zhang, T and Zhang, XX and Ma, L},
title = {Systematic citywide analysis reveals ecological connectivity of antimicrobial resistance genes across urban water systems.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42764294},
issn = {2041-1723},
support = {52470217//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Drinking Water/microbiology ; Humans ; Gene Transfer, Horizontal ; *Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Cities ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; Enterobacteriaceae/genetics/drug effects/isolation & purification ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Integrons/genetics ; Bacteria/genetics/drug effects/isolation & purification ; },
abstract = {Antimicrobial resistance (AMR) in drinking water raises public health concerns, while its anthropogenic sources, transmission dynamics, and health risks remain poorly understood, hindering the development of effective strategies to reduce human exposure. Here we conduct a systematic investigation of anthropogenic contributions to AMR across urban water compartments in a megacity, combining metagenomics and culturomics. We identify 1,309 antibiotic resistance genes (ARGs), and tracking their dynamics across microbial communities and fecal Enterobacteriaceae isolates indicates that ecological connectivity establishes a cascading dissemination pathway: wastewater discharge promotes AMR accumulation in natural water bodies, facilitating its persistence in finished drinking water. Critical human-derived ARGs, primarily conferring resistance to beta-lactams and aminoglycosides, are enriched in clinically relevant pathogens. Further analysis reveals synergistic effects of biotic and abiotic drivers, including horizontal gene transfer (HGT), host proliferation, trace metals, disinfectants, and antibiotic residues, acting with connectivity to drive ARG proliferation. Mechanistic insights reveal that integron-mediated HGT captures and rearranges exogenous ARGs, thereby assembling multi-resistant genetic determinants along connected pathways. We establish a risk prioritization framework integrating dynamics, mobility, pathogenicity and clinical relevance to identify high-risk anthropogenic ARGs. These findings elucidate AMR transmission mechanisms via ecological connectivity, informing targeted interventions to disrupt transmission links and mitigate drinking water risks.},
}

*Drinking Water/microbiology
Humans
Gene Transfer, Horizontal
*Water Microbiology
Anti-Bacterial Agents/pharmacology
Cities
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Wastewater/microbiology
Enterobacteriaceae/genetics/drug effects/isolation & purification
Metagenomics
*Drug Resistance, Microbial/genetics
Integrons/genetics
Bacteria/genetics/drug effects/isolation & purification

@article {pmid42764380,
year = {2026},
author = {Li, L and Lei, S and Ngan, C},
title = {Pathogen-oriented mNGS is not equivalent to microbiome profiling: interpreting BALF mNGS diversity in ARDS.},
journal = {Journal of intensive care},
volume = {14},
number = {1},
pages = {},
pmid = {42764380},
issn = {2052-0492},
support = {25LCYJ34//Health Commission of Sichuan Province Medical Science and Technology Program/ ; },
abstract = {Gao et al. provide valuable data-linking bronchoalveolar lavage fluid metagenomic next-generation sequencing with inflammatory subphenotypes of acute respiratory distress syndrome. We highlight three issues relevant to interpretation: an apparent inconsistency concerning exclusion of samples with no micro-organisms detected, use of a pathogen-oriented workflow for community-level ecological inference, and the distinction between detection yield and diagnostic performance without an independent reference standard. Clarification of sample eligibility, sensitivity analysis including technically valid samples reported as negative by sequencing, and confirmation that sequencing and bioinformatic procedures are validated for quantitative microbiome analysis would strengthen interpretation.},
}

@article {pmid42764917,
year = {2026},
author = {Li, B and Yang, Q and Li, M and He, J and Zhang, Z and Wan, X and Mo, Z and Li, R and Li, S and Xu, W and Gu, M and Huang, H and Li, W and Huang, Z and Yang, H and Chen, WH and Liu, Z},
title = {Gut microbiota-derived 5-HTP penetrates the host blood-brain barrier and ameliorates autism symptoms.},
journal = {Acta pharmaceutica Sinica. B},
volume = {16},
number = {9},
pages = {6168-6184},
pmid = {42764917},
issn = {2211-3835},
abstract = {Autism spectrum disorder (ASD), a highly prevalent neurodevelopmental condition, is increasingly recognized for its strong association with the intestinal microbiome. However, the development of gut microbiota-targeted therapies has been impeded by a limited understanding of the molecular mechanisms underlying interactions between commensal bacteria and the host nervous system. In this study, shotgun metagenomic sequencing and UPLC-MS/MS targeted metabolic analyses identified altered tryptophan metabolites in the gut microbiota of both human ASD patients and ASD mouse models. Notably, we demonstrate that commensal bacteria-derived 5-hydroxytryptophan (5-HTP), metabolite of tryptophan, ameliorates anxiety, stereotypical and repetitive behaviors, as well as social deficits in these mouse models. Furthermore, 5-HTP is capable of crossing the blood-brain barrier and inhibits the overexpression of receptor tyrosine kinase (RTK) ligands, thereby suppressing the downstream RTK/MAPK/ERK signaling cascade. This inhibition subsequently normalizes the excessive stabilization of dendritic spines in the hippocampus in MeCP2 mouse. Our research demonstrates that gut microbiota producing 5-HTP improves ASD symptoms in various ASD animal models, elucidates the molecular mechanisms between gut microbiota and the onset and treatment of ASD, and provides a promising therapeutic approach for ameliorating ASD through the expression of neuron-regulated small molecules by gut indigenous bacteria.},
}

@article {pmid42765260,
year = {2026},
author = {Yuan, JY and Wu, YG and Lu, HP and Zhang, P and Yang, YF and Luo, C and Liang, W and Ma, X},
title = {[Effects of Distillery Sewage Sludge on Rhizosphere Soil Quality and Carbon Cycle Functional Genes in Sorghum].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {9},
pages = {6479-6490},
doi = {10.13227/j.hjkx.202507005},
pmid = {42765260},
issn = {0250-3301},
mesh = {*Rhizosphere ; *Sorghum/genetics/growth & development/metabolism ; *Sewage/chemistry ; Soil Microbiology ; *Soil/chemistry ; *Carbon Cycle/genetics ; Nitrogen ; Carbon/metabolism ; },
abstract = {Distillery sewage sludge （DSS）， a typical organic byproduct generated during the production of Chinese Baijiu， has attracted increasing attention for its potential in agricultural resource utilization. However， the ecological effects of different DSS application methods on rhizosphere soil remain unclear. Using brewing sorghum rhizosphere soil as the research object， four application modes （unfertilized control， CK； spherical basal application， BF； spherical lateral application， LF； and powdered mixed application， MF） were comparatively evaluated for their impacts on soil nutrients， enzyme activities， carbon-functional microbial communities， and carbon-cycling functional gene expression. The results showed that， compared with CK， all three DSS treatments （BF， LF， and MF） significantly increased the contents of soil organic matter （SOM）， available nitrogen （AN）， ammonium nitrogen （NH4[+]-N）， and nitrate nitrogen （NO3[-]-N）， with MF achieving the most pronounced effect， raising SOM by 114% （P<0.001）. Meanwhile， DSS application also enhanced soil enzyme activities to varying degrees， with urease （URE） and catalase （CAT） activities increasing by 41.55%-174.47% and 2.83%-30.41%， respectively. Metagenomic analysis revealed that DSS application altered the composition and diversity of carbon-functional microbial communities and elevated the overall expression levels of genes related to carbon degradation， carbon fixation， and methane metabolism. Specifically， MF significantly enhanced the abundance of key genes such as bglX involved in cellulose degradation and those in carbon fixation and degradation pathways， whereas LF promoted the expression of coxL involved in CO oxidation and methane oxidation pathways. Further analysis using a random forest model indicated that soil nitrogen levels and exchangeable Ca and Mg ions under DSS application significantly influenced the expression of carbon cycling functional genes. In conclusion， different DSS application methods regulate the soil nutrient environment and microbial community structure， thereby enhancing the expression of carbon cycling functional genes. Among them， MF was identified as the most effective strategy for improving soil quality and microbial carbon metabolism potential. This study provides theoretical support and mechanistic insight for the efficient utilization of distillery byproducts in circular agriculture and the enhancement of soil ecological functions.},
}

*Rhizosphere
*Sorghum/genetics/growth & development/metabolism
*Sewage/chemistry
Soil Microbiology
*Soil/chemistry
*Carbon Cycle/genetics
Nitrogen
Carbon/metabolism

@article {pmid42765266,
year = {2026},
author = {Wang, DD and Xie, YQ and Huang, YF and Jia, HC},
title = {[Seasonal Response Features of Microbial Community Structure for Nitrogen Transformation in Inland Lakes on the Qinghai-Xizang Plateau].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {9},
pages = {6558-6568},
doi = {10.13227/j.hjkx.202507365},
pmid = {42765266},
issn = {0250-3301},
mesh = {*Lakes/microbiology/chemistry ; *Nitrogen/metabolism/isolation & purification ; Seasons ; China ; *Bacteria/metabolism/classification ; *Water Microbiology ; Ecosystem ; *Microbiota ; },
abstract = {Studying the nitrogen transformation characteristics of microbial communities in the inland lakes of the Qinghai-Xizang Plateau （QXP） is of great significance for a deeper understanding of the nitrogen budget balance and biogeochemical cycling in the regional lake ecosystems. Based on metagenomic sequencing technology， this study constructed a non-redundant gene library of nitrogen-transforming microorganisms and conducted multivariate statistical analysis to explore the characteristics and assembly mechanisms of nitrogen-transforming microbial communities in inland lakes on the QXP. The results indicate： ① Bacteria were the main group of nitrogen transformation microbes in the plateau inland lakes. The dominant bacterial phylum involved in nitrogen conversion both in summer and winter was Pseudomonadota， with an average proportion of 39.35% and 35.09% at different sampling sites in different seasons， respectively. The dominant bacterial genera in summer and winter were Candida_planktophila （the average proportion of different sampling sites was 4.04%） and unclassified_c_Actinomycetes （the average proportion of different sampling sites was 7.91%）. ② Salinity and dissolved oxygen were the most significant environmental factors affecting the microbial community structure of nitrogen transformation in different seasons. There were differences in the process of nitrogen transformation microbial community assembly in different seasons and different sampling lakes. ③ There were differences in the abundance of functional genes of nitrogen transformation microbes in different seasons， and denitrification was the most widely involved process of microbial communities in the plateau inland lakes in different seasons. The environmental factors driving the abundance of nitrogen transformation genes in different seasons were altitude， water temperature， total dissolved solids， and salinity. Overall， there was significant spatiotemporal heterogeneity in the assembly process of nitrogen transformation microbial communities in the plateau inland lakes. The results of this study can provide data support for the understanding of nitrogen-transforming microbes in the plateau inland lake ecosystem and provide a theoretical basis for lake water ecological management and regional greenhouse gas emissions.},
}

*Lakes/microbiology/chemistry
*Nitrogen/metabolism/isolation & purification
Seasons
China
*Bacteria/metabolism/classification
*Water Microbiology
Ecosystem
*Microbiota

@article {pmid42765534,
year = {2026},
author = {Gabrielli, M and Bredel, A and Paoli, L and Robinson, SL},
title = {Advancing biosynthetic pathway discovery through short-read-directed long-read sequencing.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6np00020g},
pmid = {42765534},
issn = {1460-4752},
abstract = {Time span of literature: 2020-todayMetagenomic methods have rapidly advanced, enabling the identification of biosynthetic pathways directly from complex microbiome data. Short-read sequencing, while accurate and cost-effective, often generates fragmented assemblies that can lead to incomplete biosynthetic gene cluster (BGC) recovery. Although long-read sequencing offers a solution to the fragmentation problems, technical requirements and higher costs have limited its scalability. Here, we examine BGC fragmentation in short-read sequencing data across large databases of metagenome-assembled genomes (MAGs) and estimate the targeted genome contiguity required to recover 'complete' biosynthetic gene clusters. We argue that the increasing availability of MAGs recovered from short-read metagenomes with recent advancements in ultra-low input DNA amplification for high-fidelity PacBio sequencing-now requiring as little as nanograms of DNA-can be used sequentially to boost biosynthetic pathway discovery. We demonstrate how natural products researchers can benefit from using short-read MAG comparisons to guide targeted long-read re-sequencing efforts with low amounts of input DNA and/or limited financial resources. Our analysis provides strategic recommendations for the broader scientific community on how to best leverage the strengths of short- and long-read sequencing data to efficiently allocate resources and accelerate natural product discovery.},
}

@article {pmid42765606,
year = {2026},
author = {Zhang, J and Xu, S and Chen, C and Wang, Z and Du, W and Hong, L and Asiegbu, FO and Wang, K},
title = {Synthetic microbial community promotes seedling growth of Chinese fir via dissolving phosphorus and modifying rhizosphere microbial community.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag135},
pmid = {42765606},
issn = {1758-4469},
abstract = {Phosphorus (P) is an essential nutrient for plant growth, yet its availability in soil is severely constrained by fixation into insoluble forms that plants cannot directly utilize. Although phosphate-solubilizing microorganisms (PSM) represent a promising strategy to mobilize soil P, the functional potential of endophytic PSM and their synthetic consortia in promoting tree growth remains largely underexplored. In this study, endophytic bacteria were isolated from the roots of Chinese fir (Cunninghamia lanceolata). Among them, 42 isolates were screened for phosphate-solubilizing activity on media containing calcium phosphate, iron phosphate, aluminum phosphate, and organic phosphorus. Six strains with strong solubilizing capacity and no antagonistic interactions were selected to construct a synthetic microbial community (SynCom-P6), which was then applied to local soil and Chinese fir seedlings. Soil available P content initially decreased but subsequently increased from day 7 to day 21 after SynCom-P6 inoculation, indicating effective mobilization of insoluble P in soil. Inoculation with SynCom-P6 significantly enhanced root elongation and biomass accumulation, with both root fresh and dry weights showing marked increases compared to the control. Absolute quantification 16S amplicon and metagenomic sequencing revealed that SynCom-P6 reshaped the rhizosphere bacterial community, enriching beneficial genera such as Massilia and Dyadobacter, and altered functional profiles, including upregulation of hormone signaling and nitrogen fixation related genes. These results demonstrated that the synthetic community not only improved soil P availability but also promoted root growth and modified the rhizosphere microbiome in a beneficial direction. Our findings highlight the potential of endophytic phosphate-solubilizing SynCom-P6 as a promising bio-inoculant for sustainable forestry, reducing the need for chemical P fertilizers while enhancing Chinese fir productivity. Future research should focus on field validation and mechanistic exploration of microbial interactions and functional gene expression.},
}

@article {pmid42765688,
year = {2026},
author = {Xu, P and Arévalo-Martínez, DL and Middelboe, M and Pohlmann, M and Bange, HW and Löscher, CR},
title = {Microbial diversity and nitrogen cycling across oxygen gradients in the eastern tropical Pacific during two La Niña years.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0089326},
doi = {10.1128/msystems.00893-26},
pmid = {42765688},
issn = {2379-5077},
abstract = {The rapid expansion of ocean oxygen minimum zones (OMZs) may significantly affect the microbial processes that regulate marine nitrogen cycling. The eastern tropical Pacific (ETP) bears one of the largest perennial OMZs, which is strongly influenced by the recurring El Niño Southern Oscillation (ENSO). However, how microbial diversity and nitrogen cycling respond to oxygen variability under comparable ENSO conditions remains unclear. Here, we applied metagenomics to analyze changes in microbial communities across a dissolved oxygen (DO) gradient from oxic to suboxic conditions in the ETP during the 2022 La Niña event and compared our findings to the Tara Oceans data set from the same region during the 2011 La Niña. In 2022, we observed a decline in microbial alpha diversity and abundance, coupled with an increase in nitrogen metabolism genes as DO decreases. The relative abundance of many dominant microbes shifted at a DO threshold of 80 μmol kg[-1], while dominant nitrogen cycle genes varied under different DO thresholds (120, 20, 5 μmol kg[-1]). Despite the 11-year interval between sampling efforts, microbial alpha diversity was similar between 2011 and 2022. We observed a significant reduction of SAR11 and an increase of Poseidoniia in 2022 compared with 2011. While certain nitrogen cycling genes differed in relative abundance in a depth-dependent manner, overall functional group composition was largely consistent, with spatial variation exceeding interannual differences. Overall, our study presents a comprehensive examination of possible shifts of microbial diversity, community, and their potential for nitrogen cycling under deoxygenation during two La Niña years.IMPORTANCEThe eastern tropical Pacific oxygen minimum zones (OMZs), largely impacted by the natural climate cycle-El Niño-Southern Oscillation, are predicted to continually expand while their core may shrink. While deoxygenation is known to profoundly influence microbial ecosystems, how microbial diversity, composition, and nitrogen cycling would shift across oxic/hypoxic/suboxic gradients, and its association with ENSO dynamics remains poorly understood. We surveyed microbial communities under two La Niña years with an 11-year gap and found that vertical variability is more critical than temporal variations for both microbial diversity and microbe-mediated nitrogen pathways, as only slight differences in microbial diversity and nitrogen cycles were detected between the two studied years despite ENSO dynamics, which might have disrupted the system among the 11 years. Moreover, we identified oxygen thresholds causing dominant microbes and potential nitrogen pathways to shift, thus helping to improve prediction on how various microbes and nitrogen pathways might respond to further deoxygenation.},
}

@article {pmid42765727,
year = {2026},
author = {Karačić, J and Singer, L and Bierbaum, G and Parčina, M and Zilles, J and Palmer, B and Karačić, S},
title = {Dental spittoon biofilms as reservoirs of antimicrobial resistance: a longitudinal multi-omics study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0088326},
doi = {10.1128/spectrum.00883-26},
pmid = {42765727},
issn = {2165-0497},
abstract = {Dental chair spittoons are chronically exposed to saliva, aerosols, intermittent water flow, and chemical disinfectants, yet their biofilm ecology and antimicrobial resistance (AMR) dynamics remain poorly defined. We applied longitudinal 16S rRNA gene sequencing, shotgun metagenomics, and culture-based antimicrobial susceptibility testing to biofilms collected across four dental departments at three time points. Community analyses revealed significant temporal succession and department-specific structuring, indicating the establishment of stable, ecologically differentiated biofilm systems. Null-model analysis (Raup-Crick) indicated that community assembly remained predominantly stochastic, although later sampling periods showed modest evidence of increasing ecological filtering. Shotgun metagenomics identified metabolically versatile communities enriched in disinfectant-tolerant environmental taxa, with resistomes dominated by β-lactamases and aminoglycoside-modifying enzymes. Clinically associated plasmid replicons, including IncFII and Col440I, were detected in metagenomically analyzed samples. Culture-based testing of 162 isolates confirmed that 21.7% expressed phenotypic resistance to at least one antimicrobial agent, including multidrug- and carbapenem-resistant representatives of Pseudomonas and Acinetobacter. Together, these findings position dental spittoons as structured aquatic biofilm ecosystems that maintain viable antimicrobial-resistant populations and clinically relevant plasmid replicons under recurrent disturbance, highlighting their ecological role within the broader built-water resistome.IMPORTANCEBiofilms in healthcare environments can act as reservoirs of antimicrobial resistance, yet some potential niches remain poorly studied. Dental chair spittoons are continuously exposed to oral fluids, aerosols, water flow, disinfectants, and residual antimicrobial compounds, creating conditions that may favor biofilm formation and microbial selection. Despite this unique combination of ecological pressures, the microbial communities inhabiting these systems have received little attention. Using a longitudinal multi-omics approach combined with culture-based phenotypic testing, we show that spittoon biofilms harbor diverse microbial communities enriched in antimicrobial resistance determinants, including multidrug-resistant and carbapenem-resistant bacteria. These findings suggest that dental spittoons may represent previously overlooked reservoirs of antimicrobial resistance within clinical environments.},
}

@article {pmid42765765,
year = {2026},
author = {Benot, AO and Waldschmidt, G and Gilvarg, SC and Legge, EOL and Okyere, IJ and Tiyapun, C and Lucas, SK and Vander Yacht, AL and Goff, JL},
title = {Prescribed burns drive lasting changes in soil nitrogen cycling and microbial function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0085226},
doi = {10.1128/msystems.00852-26},
pmid = {42765765},
issn = {2379-5077},
abstract = {Fire is a major pulse disturbance to soil microbial communities, with broad implications for nutrient cycling; however, regular burning is also a natural and often-essential process maintaining biodiversity in unique and imperiled fire-dependent ecosystems. Prescribed fire is widely used to promote this biodiversity and simultaneously reduce wildfire risk. Although such repeated burning is known to alter surface biodiversity, belowground soil geochemistry, and soil microbial community structure, the functional consequences (i.e., the metabolic capabilities that underlie the ecosystem services soil microorganisms provide) remain underexplored. Here, we examined the effects of 30 years of repeated prescribed fire at the Albany Pine Bush-a fire-dependent, inland pitch pine barren ecosystem of the northeastern United States. Compared with the control stands, we observed that this long-term fire management has led to substantial depletion of inorganic soil nitrogen, specifically nitrate. We found no meaningful differences in the higher-level taxonomic composition of soil prokaryotic or fungal communities; however, analysis of metagenome-assembled genomes assembled from these soils revealed several differentially abundant populations. Furthermore, our metagenomic analysis revealed significant changes in the nitrogen-cycling functional potential, specifically decreased dissimilatory nitrate reduction and denitrification potential in repeatedly burned soils. These functional shifts have important implications for both nutrient cycling and emissions of trace nitrogen gases from these soils. Our results suggest that functionally meaningful changes in the soil microbiome can persist between burn events, even when higher-order community membership appears stable. This may imply that repeated fire can deplete reactive nitrogen emissions from soils by lowering the functional capacity of nitrogen-reducing microbes.IMPORTANCEPrescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how repeated burning influences soil biological properties-including the functional role that soil microorganisms play in nutrient cycling and greenhouse gas production. We addressed this gap by studying soils from the Albany Pine Bush, a rare and endangered ecosystem that has experienced regular prescribed fires for 30 years. Long-term fire management significantly altered soil chemistry, specifically lowering the amount of nitrogen in the soil. In addition, we found that fire management decreased the genetic potential of the soil microbial community to produce nitrogen oxides-potent contributors to climate change. Thus, prescribed fire's contribution to greenhouse gas emissions may involve a complex relationship between direct fire-driven emissions, increased fire resilience of promoted vegetation, and-as suggested by our results-the reduced ability of soil microbes to produce greenhouse gases.},
}

@article {pmid42765791,
year = {2026},
author = {Cheng, Z and Luo, X and Shi, Q and Wei, M and Wei, Y and Xu, X and Zhang, Z and Pang, J and Shen, S and Lu, X and Liu, X and Liang, Q},
title = {A Novel Mycovirus Reprograms the Pathogenic State of Aspergillus flavus in Keratitis.},
journal = {Investigative ophthalmology & visual science},
volume = {67},
number = {11},
pages = {39},
doi = {10.1167/iovs.67.11.39},
pmid = {42765791},
issn = {1552-5783},
mesh = {*Aspergillus flavus/virology/pathogenicity/isolation & purification/genetics ; Animals ; *Eye Infections, Fungal/microbiology/virology ; Mice ; *Keratitis/microbiology/virology ; *Aspergillosis/microbiology/virology ; *Fungal Viruses/genetics/physiology/isolation & purification ; Virulence ; Humans ; Disease Models, Animal ; Phylogeny ; RNA, Viral/genetics ; Female ; },
abstract = {PURPOSE: Fungal keratitis (FK) is a major cause of corneal blindness, with substantial variability in disease severity that cannot be fully explained by host factors. This study investigated whether endogenous mycovirus infection contributes to differences in fungal pathogenicity.

METHODS: Fungal isolates from 38 patients with FK were analyzed by metagenomic sequencing. A novel viral RNA identified in an Aspergillus flavus isolate was characterized by sequence and phylogenetic analyses. Virus-cured strains were generated and compared with virus-infected strains using phenotypic assays, transcriptomic profiling, corneal epithelial adhesion assays, macrophage killing assays, and a murine model of FK.

RESULTS: A previously uncharacterized mycovirus, A flavus narnavirus 3, was identified within the family Narnaviridae. Viral infection impaired fungal growth, conidiation, and stress tolerance and suppressed virulence-associated traits, including sclerotia formation and aflatoxin production. A transcriptomic analysis revealed the disruption of the regulatory networks involved in development, stress responses, and metabolism. Functionally, virus-infected strains showed reduced adhesion to corneal epithelial cells and increased susceptibility to macrophage-mediated clearance. In vivo, A flavus narnavirus 3-positive strains exhibited attenuated virulence, with a lower fungal burden and reduced corneal inflammation.

CONCLUSIONS: Mycovirus infection attenuates A flavus pathogenicity and modulates host responses in FK, suggesting a potential role for viral carriage in the clinical heterogeneity of disease severity.},
}

*Aspergillus flavus/virology/pathogenicity/isolation & purification/genetics
Animals
*Eye Infections, Fungal/microbiology/virology
Mice
*Keratitis/microbiology/virology
*Aspergillosis/microbiology/virology
*Fungal Viruses/genetics/physiology/isolation & purification
Virulence
Humans
Disease Models, Animal
Phylogeny
RNA, Viral/genetics
Female

@article {pmid42765918,
year = {2026},
author = {Gregory, CL and Radja, K and Haak, DC and Bradford, EL and Fell, RD and Walke, JB and Belden, LK},
title = {A metagenomic survey reveals widespread antibiotic resistance genes in honey bee (Apis mellifera) gut bacteria across the United States.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075526},
doi = {10.1128/aem.00755-26},
pmid = {42765918},
issn = {1098-5336},
abstract = {Antibiotic use has contributed to antibiotic resistance genes (ARGs) accumulating in many environments, including host-associated microbiomes. Managed honey bee gut bacteria may accumulate ARGs, as honey bees are sometimes treated with antibiotics and often live in agricultural landscapes contaminated with antibiotics. We describe the occurrence and distribution of ARGs in honey bee bacterial gut symbionts from 13 apiaries in a transect across the USA from Washington to Virginia. Using metagenomic sequencing, we detected 55 unique ARGs conferring resistance to 14 classes of antibiotics. Of these, 11 ARGs encoded multidrug resistance. ARGs varied among sites, and ARG composition in hives shifted across the transect. Among honey bee gut bacterial genera, ARG occurrence varied, with Gilliamella and Frischella containing the highest proportions of ARGs despite their low relative abundance in the gut community, suggesting specific genera may serve as ARG reservoirs. As tetracycline is the most used antibiotic in beekeeping, we compared the frequency and abundance of tetracycline resistance genes across apiaries. All hives contained tetracycline resistance genes, with tetB and tetM present at all apiaries. Based on qPCR, tetB and tetM abundance varied significantly among apiaries. TetB was higher overall and declined in abundance from Washington to Virginia. We demonstrate that honey bee gut bacteria possess a diversity of ARGs, not all of which are consistent with antibiotic use in beekeeping, ARG frequency varies among bacterial genera in the honey bee gut, and certain ARGs are associated with hive geographic location.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) to bacterial pathogens is a critical issue facing global health. Gut bacterial symbionts of managed honey bees make good bioindicators for ARGs because honey bees interact with potential environmental reservoirs of ARGs and are broadly distributed across the USA, including in both urban and rural environments. Based on our transect across the USA, ARGs were diverse and widely distributed among honey bee gut symbionts, although certain bacterial genera had a higher propensity for accumulating ARGs. Tetracycline resistance genes were most common, and varied in occurrence and abundance across the transect. The abundance of tetB, in particular, increased from east to west along the sampled transect. These large-scale patterns of ARG distribution within a widely dispersed host-associated microbiome system provide a foundation from which to examine the underlying factors driving differences in ARG occurrence and abundance.},
}

@article {pmid42765955,
year = {2026},
author = {Xue, R and Li, J and Hu, S and Ding, J and Wang, C and Ke, W and Li, C and Corvini, P and Cui, L},
title = {Microbial physiological trait shifts link heavy metal remediation to enhanced soil carbon storage potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag250},
pmid = {42765955},
issn = {1751-7370},
abstract = {Widespread and chronic heavy metal pollution resulting from industrial activities has compromised the sustainability of soil ecosystems. Increasing and stabilizing soil carbon storage is central to soil development, but how remediation reshapes soil carbon cycling processes during the mitigation of heavy-metal contamination remains unclear. Here, we tracked genome-scale microbial metabolism, community turnover, and phenotype-level physiological responses during a 120-day remediation of heavy metal-contaminated soils with several decades of pollution histories and resolved their dynamic interplay with microbial carbon use efficiency (CUE) and CO2 emissions. We found that heavy-metal stress accelerated microbial respiratory carbon loss from soils, with contaminated soils exhibiting significantly higher cumulative CO2 emissions than both nearby uncontaminated and remediated soils. Metagenomic profiles were enriched in oxidative-stress defense and metal-detoxification functions, consistent with elevated maintenance costs that may contribute to enhanced respiration. In contrast, remediation significantly reduced soil CO2 emissions while increasing microbial growth rate and CUE, indicating a shift toward greater soil carbon storage potential. Raman-based in situ monitoring further showed that biomolecules associated with microbial growth, including phospholipids, nucleic acids, and proteins, increased progressively throughout the remediation process. Structural equation modelling further revealed that microbial physiological traits, particularly metabolic activity and intracellular biomolecular composition, exerted stronger direct effects on CUE than community traits, including community stability and life-history strategy. These results identify microbial physiological traits as a key link between environmental stress and soil carbon cycling. Together, these findings suggest that remediating heavy metal-contaminated soils may represent an underappreciated pathway for enhancing terrestrial carbon sequestration.},
}

@article {pmid42766040,
year = {2026},
author = {Gatto, MC and Cozzolino, F and Vitale, L and Palma Esposito, F and Cicatiello, P and de Pascale, D and Monti, M},
title = {Multi-omics insights into bacterial and fungal bioremediation of Potentially Toxic Elements (PTEs): a critical overview of their applications.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42766040},
issn = {1573-0972},
mesh = {*Biodegradation, Environmental ; Multiomics ; *Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; Proteomics ; Metabolomics ; Genomics ; Metals, Heavy/metabolism ; *Environmental Pollutants/metabolism ; Metalloids/metabolism ; },
abstract = {Potentially toxic elements (PTEs) are persistent contaminants of terrestrial and aquatic ecosystems and heavy metals and metalloids represent a major environmental and health concern. Microbial bioremediation exploits the ability of bacteria, fungi, and microbial communities to modulate PTE fate through processes including biosorption, bioaccumulation, redox transformation, biomineralization, precipitation, chelation, and extracellular sequestration. This review examines the major advances of the last decade in the application of genomics, transcriptomics, proteomics, and metabolomics and their integration, to investigate molecular mechanisms of microbial adaptation to PTE contamination, supporting the selection of suitable microorganisms or microbial communities and the development of more effective bioremediation strategies. Genomic and metagenomic analyses enable the identification of genes and gene families associated with PTE resistance and adaptation, revealing both metal-specific and more general responses according to the presence of operons and/or cluster genes. Transcriptomic and proteomic approaches are applied to validate genetic potentialities, identifying mechanisms and protein mediators for transport, detoxification, redox homeostasis, and metal interactions. Metabolomics complements these approaches by characterizing metabolites involved in microbial responses, including organic acids, siderophores, biosurfactants, and extracellular polymeric substance-associated compounds. The review also discusses the advantages, limitations, and complementarity of the different omics approaches, emphasizing their impact in feasibility to move from ex situ to in situ applications. Finally, the review also addresses how omics layers could be combined across the phases of a real bioremediation project (screening, implementation, monitoring), highlighting integrated multi-omics approaches as powerful tools for developing and optimizing effective bioremediation strategies.},
}

*Biodegradation, Environmental
Multiomics
*Fungi/metabolism/genetics
*Bacteria/metabolism/genetics
Proteomics
Metabolomics
Genomics
Metals, Heavy/metabolism
*Environmental Pollutants/metabolism
Metalloids/metabolism

@article {pmid42766345,
year = {2026},
author = {Ürel, H and Sauerborn, E and Biggel, M and Gebhardt, F and Foster-Nyarko, E and Brugger, SD and White, RT and Heidelbach, S and Albertsen, M and Muchaamba, F and Reska, T and Stevens, MJA and Stephan, R and Fetherston, R and Urban, L},
title = {Nanopore metagenomic sequencing links clinically relevant resistance determinants to pathogens.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001834},
pmid = {42766345},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Humans ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Plasmids/genetics ; beta-Lactamases/genetics ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Bacteria/genetics ; },
abstract = {Culture-independent metagenomics enables the detection of plasmid-encoded antimicrobial resistance (AMR) genes directly from clinical samples; however, the clinical significance of these genes depends on their bacterial host and genomic context, which metagenomics cannot fully infer. Nanopore sequencing technology intrinsically encodes epigenetic modifications such as methylation, which can be leveraged for plasmid-host associations from metagenomic data. Existing methods rely on the recovery of metagenome-assembled genomes (MAGs), which can introduce bias towards abundant taxa and leave clinically relevant, low-abundance pathogens unassociated. To address this limitation, we extended methylation-based plasmid-host association from the MAG level to individual assembly contigs and sequencing reads. The Contig- and Unassembled-read-based Pathogen Identification and Delineation (CUPID) pipeline implements the calculation of contig and read similarity scores, which compare weighted mean methylation rates across motifs genetically shared between any contig or read pair. We validated this approach on a mock metagenomic community composed of ten carbapenem-resistant Enterobacterales isolates, where we achieved 93.8% accuracy at the contig level and 100% at the read level for carbapenemase plasmid-host associations. When applied to metagenomic and quasimetagenomic data of 16 patient rectal swabs collected during routine hospital surveillance, our approach assigned every detected plasmid-encoded carbapenemase to its correct bacterial host at the contig level, using matched culture-based diagnostics and whole-genome sequencing as the ground truth. Read-level analysis identified additional associations that were missed at the contig level, including a multi-host plasmid confirmed by established diagnostics. These findings demonstrate a pathway from rapid AMR gene detection using metagenomics to actionable surveillance for infection prevention, transmission tracing and outbreak investigation.},
}

*Metagenomics/methods
*Nanopore Sequencing/methods
Humans
*Drug Resistance, Bacterial/genetics
Metagenome
Plasmids/genetics
beta-Lactamases/genetics
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Carbapenems/pharmacology
Bacteria/genetics

@article {pmid42766540,
year = {2026},
author = {Long, Y and Lang, J and Wang, L and Guo, J and Jiang, X and Jiang, J},
title = {Ecological risk assessment of migratory bird feces in plateau wetland: Phosphorus speciation, ARGs, and pathogens.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0348709},
doi = {10.1371/journal.pone.0348709},
pmid = {42766540},
issn = {1932-6203},
mesh = {Animals ; *Wetlands ; *Feces/microbiology/chemistry ; *Phosphorus/analysis ; *Birds/microbiology/physiology ; *Animal Migration ; Risk Assessment ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {Plateau wetlands are critical habitats for migratory birds, but the potential ecological risks from the large-scale accumulation of migratory bird feces (MBF) remain poorly understood. This study focused on seven wintering waterbird species, including the Grus nigricollis, Grus grus, Fulica atra, Anas strepera, Anas zonorhyncha, Mareca penelope, and Tadorna ferruginea at Caohai Plateau Wetland, sampling across March 2024, January 2025 and March 2025. The phosphorus (P) speciation, antibiotic resistance genes (ARGs), pathogens, and their interactions were assessed using sequential phosphorus extraction, solution 31P-nuclear magnetic resonance (31P-NMR), and shotgun metagenomic sequencing. Results showed that MBF was enriched in nutrients and heavy metals, with Gruiformes feces containing high total P (0.65% dry weight). Orthophosphate accounted for 90.68% of total P and labile NaHCO3-Po constituted the dominant organic P fraction, collectively indicating strong guanotrophication potential. Metagenomic annotation recovered 231 potential pathogens with Staphylococcus aureus, Salmonella enterica, and Pseudomonas aeruginosa as dominant taxa; 21 ARG classes were identified, dominated by multidrug resistance genes (32.14-39.29%). Heavy metal (Cu, Cd, Zn) selection pressure enriched MGEs in avian gut microbiota, thereby facilitating horizontal transfer of ARGs and virulence factors (VFs) and ultimately driving the enrichment of multi-drug resistant pathogens. The low-temperature plateau environment further extended the environmental persistence of these hazardous biological contaminants. This study provides a synergistic risk network linking nutrient loading, heavy metal pollution, antimicrobial resistance, and pathogenic proliferation in MBF-impacted plateau wetlands, providing scientific support for plateau wetland ecological restoration and targeted public health risk mitigation under the One Health framework.},
}

Animals
*Wetlands
*Feces/microbiology/chemistry
*Phosphorus/analysis
*Birds/microbiology/physiology
*Animal Migration
Risk Assessment
Bacteria/genetics
Drug Resistance, Microbial/genetics

@article {pmid42766649,
year = {2026},
author = {O'Brien, K and Elamaran, A and Dayi, M and Keeling, G and Nevin, WD and Liu, Y and Viney, M and Reynolds, K and Bishop, C and Sripa, B and Woubshete, M and Sachs Nique, P and Wright, R and Younger, J and Hunt, VL},
title = {Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014130},
doi = {10.1371/journal.pntd.0014130},
pmid = {42766649},
issn = {1935-2735},
abstract = {Soil-transmitted helminths (STHs) pose significant challenges to public health in endemic areas, necessitating reliable methods for their detection. Shotgun metagenomics enables simultaneous detection of STHs and microbes in a sample without prior knowledge of what is present. However, validation of shotgun metagenomics with known infection intensity or across different sequencing platforms has not been carried out for eukaryote parasites including STHs, and false positives remain a pervasive issue. We validated shotgun metagenomics as a method of STH detection in faecal samples. Using the Strongyloides ratti laboratory model of a STH infection we investigated how analytical methods (nucleotide-nucleotide matching, nucleotide-protein matching, marker gene detection, mitochondrial mapping), infection intensity (low and standard laboratory doses) and sequencing technology (short-read vs. long-read) affects sensitivity and specificity of detection. S. ratti was accurately detected at a standard laboratory dose, but low intensity infection were more difficult to detect. Only mitochondrial sequence mapping was 100% accurate at identifying S. ratti with no false positives. Overall, short-read outperformed long-read sequencing methods. We applied the same analytical methods to human faecal samples with confirmed infections for at least one of four STHs. Mitochondrial sequence mapping was also the most effective method for detecting STHs in human faecal samples, detecting 100% of Necator americanus and 92% of Ascaris spp. infections, but could not reliably detect STHs where DNA levels are expected to be low or variable. In conclusion, mitochondrial mapping was the most effective method of detection for sensitivity and specificity in both the laboratory system and human faecal samples. Our findings indicate that shotgun metagenomics should be approached cautiously using validated methods, particularly when infection intensity or DNA levels are expected to be low.},
}

@article {pmid42767048,
year = {2026},
author = {Zhao, AY and Chen, L and Zhou, LL and Wang, YC and Zheng, F and Yao, ZY and Zhang, WR and Du, S and Khalid, M and Zhu, D},
title = {Wetland plant rhizospheres as selective hotspots for antibiotic resistance genes under microplastic influence.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143660},
doi = {10.1016/j.jhazmat.2026.143660},
pmid = {42767048},
issn = {1873-3336},
abstract = {Wetland plant rhizospheres are active interfaces where pollutants, microbial hosts, and antibiotic resistance genes (ARGs) interact, but their role in environmental resistomes remains unclear. We collected paired rhizosphere and bulk soils associated with five wetland plant species from urban riverine wetlands and integrated 16S rRNA gene amplicon sequencing, metagenomic annotation, viral sequence profiles, and microplastic measurements. Rhizosphere soils contained higher total bacterial ARG abundance than bulk soils, consistent with selective enrichment of specific ARG subtypes. Enrichment varied among plants, with the Hemerocallis fulva rhizosphere showing the broadest enrichment and containing representative Rank I high-risk ARGs. MAG-based annotations suggested potential associations among ARG-carrying hosts, mobile genetic elements, and host-linked viruses, although these predictions do not demonstrate active transfer. Viral ARG enrichment was more species-specific and occurred mainly in H. fulva, suggesting plant-dependent virus-host associations. Total microplastic abundance was positively associated with bacterial ARG abundance in both compartments, whereas viral ARG abundance showed nonlinear relationships. Associations with selected polymer types, particle-size fractions, and soil variables (pH, TC, TN, TOC, and Cu) differed between bacterial and viral ARGs and between compartments. These findings reveal plant-specific rhizosphere ARG patterns associated with multiple microplastics and soil environmental variables.},
}

@article {pmid42767070,
year = {2026},
author = {Xing, W and Zhou, G and Wang, C and Huangfu, K and Guo, X and Yao, H},
title = {Iron-enhanced rTCA cycle drives synergistic enhancement of inorganic carbon fixation and denitrification.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126936},
doi = {10.1016/j.watres.2026.126936},
pmid = {42767070},
issn = {1879-2448},
abstract = {Iron-carbon autotrophic denitrification has shown potential for nitrogen removal from low-C/N wastewater. However, its application has been limited by slow Fe[0] corrosion, increased alkalization, and insufficient inorganic carbon. CO2 induction represents a promising strategy for overcoming the above limitations. Here, a CO2 enhanced iron-carbon autotrophic denitrification process was established to elucidate how CO2 regulates iron corrosion, carbon metabolism, and denitrification. The results showed that the continuous CO2 supply maintained weakly acidic conditions (pH 6.0-6.5), accelerated Fe[0] corrosion, increased Fe[2+] release, and promoted poorly crystalline iron phases, thus enhancing electron transfer and nitrogen removal. The total nitrogen removal efficiencies increased and reached 97.95 ± 1.57%, with the concentrations decreasing to 0.83 ± 0.62 mg N L[-1] in effluents. Metagenomic and enzymatic analyses revealed that CO2 activated two complementary carbon fixation pathways. Concurrent enrichment of the CBB-associated genes rbcL/rbcS and prk/prkB, together with increased apparent Rubisco activity, supported enhanced CBB-associated CO2 assimilation potential. Under Fe-rich reducing conditions, genes involved in ferredoxin-mediated carboxylation were enriched, potentially supporting the reductive tricarboxylic acid (rTCA) cycle. Fixed inorganic carbon was routed into central carbon metabolism, generating bioavailable intermediates that supported denitrification. Metagenome-assembled genome revealed a denitrifier-centered cooperative network linking carbon fixation, carbon turnover, and nitrate reduction. Collectively, CO2 promoted denitrification by coupling Fe[0] corrosion, dual carbon fixation pathways, carbon turnover, and iron-dependent nitrogen transformation. These findings reveal an underappreciated role of iron-mediated carbon fixation in denitrification and provide a strategy for efficient nitrogen removal from low-C/N wastewater.},
}

@article {pmid42767150,
year = {2026},
author = {Huang, Z and Tian, C and Wang, C and Shen, J and Feng, J and Wang, X},
title = {Divergent dissolved organic matter molecular signatures and microbial functional patterns associated with cyanobacterial and dinoflagellate bloom periods in a plateau lake.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130982},
doi = {10.1016/j.jenvman.2026.130982},
pmid = {42767150},
issn = {1095-8630},
abstract = {Plateau lakes are highly sensitive to algal blooms that increasingly threaten their ecological integrity. This study examined cyanobacterial bloom periods (Pseudanabaena sp.) and dinoflagellate bloom periods (Peridinium sp.) in Lake Erhai, integrating Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with metagenomics to investigate dissolved organic matter (DOM) composition, microbial dynamics, and functional gene abundance. Pseudanabaena sp. bloom periods were associated with higher average molecular weight and elevated carboxyl-rich alicyclic molecules (CRAMs, 28.26%). Peridinium sp. bloom periods were associated with peptide-enriched DOM and elevated unsaturated aliphatic compounds (UACs, 24.15%). Putative CH2-related transformations dominated Pseudanabaena sp. peak bloom (32.93%), consistent with progressive functional group modifications toward operationally aromatic structures. Peridinium sp. showed elevated putative H2-related (30.35%) and O-related transformations (28.31%), coinciding with nitrogen-sulfur synergistic release patterns. Microbial Shannon diversity was higher during Peridinium sp. periods, with Actinomycetota more abundant during Pseudanabaena sp. peak bloom and Pseudomonadota more abundant during Peridinium sp. peak bloom. Enrichment of both Calvin-Benson-Bassham cycle and rTCA cycle genes during Pseudanabaena sp. peak bloom indicated enhanced autotrophic carbon fixation potential, whereas denitrification genes were abundant during Peridinium sp. peak bloom, indicating distinct functional potentials. DOM molecular traits emerged as statistically important predictors of microbial community composition and carbon-nitrogen-sulfur cycling gene abundance. These findings highlight the importance of integrating bloom type and seasonal dynamics when assessing DOM-mediated microbial processes in plateau lake ecosystems.},
}

@article {pmid42767155,
year = {2026},
author = {Xu, P and Li, L and Zhang, Y and Jiang, Q and Zhang, Y and Wu, X and Xu, Y},
title = {Threshold effects of organic amendment on acidic red soil remediation: Community assembly and core microbiome-mediated metabolic coupling.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130999},
doi = {10.1016/j.jenvman.2026.130999},
pmid = {42767155},
issn = {1095-8630},
abstract = {To identify the ecological threshold and microbial mechanisms underlying organic amendment (OA)-mediated remediation of acidic red soils, pak choi was employed as a model plant, and a gradient of digestate-derived OA from 0% to 25% was established. This study integrated soil-plant assessment, community assembly modeling, metagenome-assembled genomes (MAGs), and metabolic network analysis. Both soil functioning and plant growth exhibited nonlinear responses. The optimal OA rate was found to be 15%, which increased the soil quality index and pak choi biomass by 92% and more than 13-fold compared to the control group. In contrast, a 25% OA rate elevated electrical conductivity, induced secondary salinity stress, and reduced productivity and economic returns. Under the 15% OA treatment, the microbial community showed the strongest deviation from neutral community model predictions, indicating that neutral processes had limited explanatory power for community assembly, while deterministic processes associated with altered soil conditions may have played a more important role in community reorganization. Accordingly, core functional MAGs (e.g., MAG302, MAG299, MAG321) were significantly enriched under this treatment, with a total relative abundance 17.3 times that of the control group. These MAGs harbored key genes involved in C, N, P, and S cycling (bglB, atoB, narG, nirK, nosZ, gcd, pst, sqr), suggesting functional complementarity in organic matter degradation, denitrification, phosphorus mobilization, and sulfide oxidation, thereby supporting efficient nutrient turnover and system function. Deviation from this threshold resulted in reduced core MAG enrichment and metabolic network synergy. Overall, this study provides genome-resolved targets for functional strain isolation and synthetic community construction, as well as a mechanistic basis for optimizing OA rates and developing microbiome-based precision remediation strategies.},
}

@article {pmid42767176,
year = {2026},
author = {Delican, D and Kılıçkaya, O and Ozden, O and Ensari, Y},
title = {Novel L-Asparaginases from the human gut microbiome: Genome mining, biochemical characterization, and in vitro anti-leukemic activity.},
journal = {Bioorganic chemistry},
volume = {182},
number = {},
pages = {110550},
doi = {10.1016/j.bioorg.2026.110550},
pmid = {42767176},
issn = {1090-2120},
abstract = {L-asparaginase is essential for acute lymphoblastic leukemia treatment; however, current Escherichia coli and Erwinia chrysanthemi formulations face significant limitations, including immunogenicity, glutaminase-associated toxicity, and short plasma half-life. The human gut microbiome represents an unexplored reservoir of therapeutic enzymes that may offer superior biocompatibility due to host-commensal co-evolution. We employed a systematic genome-mining approach to screen human gut metagenomic data for novel L-asparaginase candidates. Five candidate enzymes from the genera Bacteroides, Ruminococcus, Clostridium, and Prevotella were identified using virtual screening. These enzymes were subsequently codon-optimized and heterologously expressed in E. coli, thereby validating our computational selection strategy. Biochemical characterization revealed optimal activity at alkaline pH (8.0-9.0), robust performance at physiological temperature (37 °C), and excellent storage stability. Ruminococcus_seq7 exhibited exceptional kinetic properties (Km = 0.53 ± 0.19 mM; Vmax = 78.6 ± 5.59 U/mg), whereas Bacteroides_seq104 showed intermediate kinetics (Km = 2.04 ± 0.57 mM; Vmax = 75.4 ± 5.75 U/mg). These lead candidates demonstrated complementary anti-leukemic profiles: Ruminococcus_seq7 showed broad-spectrum activity against T-cell leukemias (IC50: 5.1-8.6 U/mL for Jurkat, MOLT-4, and THP-1), while Bacteroides_seq104 exhibited remarkable potency against THP-1 cells (IC50 = 0.9 U/mL) and successfully overcame resistance in REH cells (IC50 = 36.9 U/mL). Both enzymes maintained >95% viability in healthy HUVEC cells. This study provides proof-of-concept for the discovery of therapeutic enzyme from the human gut microbiome. The identified L-asparaginases exhibited favorable biochemical properties, potent and selective anti-leukemic activity, and enhanced safety profiles. The absence of glutaminase activity and high biocompatibility position these gut microbiome-derived enzymes as promising biotherapeutic scaffolds for next-generation leukemia treatment, pending further optimization of substrate affinity to meet clinical standards.},
}

@article {pmid42762650,
year = {2026},
author = {Liu, L and Wang, L and Ma, S and Liu, R and Xia, X},
title = {Shifts in driver dominance shape divergent ARG prevalence patterns and nonlinear responses across the Yellow River Basin.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143580},
doi = {10.1016/j.jhazmat.2026.143580},
pmid = {42762650},
issn = {1873-3336},
abstract = {The impact of environment and biology on antibiotic resistance genes (ARGs) has been widely documented, but the interaction pathways underlying shifts in ARG prevalence patterns remain unclear. This study employed metagenomic analysis to investigate how environmental and biological factors are associated with divergent spatial prevalence patterns of ARGs in the Yellow River. Then, Copula function, Monte Carlo simulation and generalized additive models (GAM) were further integrated to decipher nonlinear responses in divergent prevalence patterns of ARGs. The results revealed prevalence-dependent associations underlying ARG prevalence patterns: MGE-associated processes showed the strongest association with core ARG abundance, whereas environmental factors were indirectly associated with stochastic ARGs through microbial diversity, with some level-I risk ARGs showing localized accumulation. Nonlinear response analysis further revealed prevalence-dependent associations of ARG abundance with elevation and tnpA gradients. This study reveals previously unrecognized shifts in driver dominance of environmental and biological contributions to ARG prevalence patterns.},
}

@article {pmid42762728,
year = {2026},
author = {Miao, H and Zeng, W and Hao, X and Wang, Y and Peng, Y},
title = {High-efficiency simultaneous ammonia and nitrate removal in iron-sulfur coupled system under carbon limitation: Multi-omics insights into metabolic regulation and microbial interactions.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126930},
doi = {10.1016/j.watres.2026.126930},
pmid = {42762728},
issn = {1879-2448},
abstract = {Iron‑sulfur coupling is a promising process for efficient nitrate removal, but its potential for simultaneous ammonia removal remains poorly recognized. This study established a biofilter (ISBF) using sponge iron and elemental sulfur as mixed fillers. Over 228 days of operation, ISBF achieved excellent nitrate (98.1%) and ammonia (89.7%) removal within 2 h. In-situ batch tests and [15]N isotope tracing revealed synergistic nitrogen removal via autotrophic denitrification (56.6%), Feammox (9.1%), and Anammox (30.9%). X-ray diffraction confirmed FeOOH formation within biofilm, providing highly available substrates for iron metabolism. The analysis of microbial and functional genes revealed that Ca. Brocadia was enriched (3.57% and 26.67% at genomic and transcriptional levels, respectively) with high expression of hzsA (cDNA/DNA: 0.73-0.88). The bottom region of ISBF drove multi-pathway nitrogen removal, and middle/upper zones promoted complete denitrification and sulfate reduction, thereby improving nitrogen loss and reducing sulfate pollution. Batch tests and multi-omics analyses suggested that Ca. Brocadia possessed the potential for dual Feammox-Anammox metabolism, thereby facilitating its enrichment and maintenance of activity under NO2[-]-deficient startup conditions. The Thiobacillus-dominated denitrification consortia exhibited a high narG and low nirKS expression pattern, implying a robust capacity for NO2[-] accumulation and supporting efficient nitrogen removal through anammox metabolism. Additionally, the increased abundance of genes involved in the electron transfer process suggested that ISBF could efficiently regulate multi-pathway synergistic nitrogen removal and ensure functional robustness. Therefore, this study provides novel insights for achieving simultaneous nitrate and ammonia removal under carbon limitation.},
}

@article {pmid42762734,
year = {2026},
author = {Ge, J and Liu, Y and Chen, L and Li, D and Deng, F and Xue, B and Liang, T and Yang, Z and Guo, J and Li, Z},
title = {Triphenyl phosphate (TPHP) stress-induced bacterial community differentiation, succession and energy metabolism inhibition under distinct contamination histories.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126955},
doi = {10.1016/j.watres.2026.126955},
pmid = {42762734},
issn = {1879-2448},
abstract = {Triphenyl phosphate (TPHP), a widely used organophosphate flame retardant, is increasingly detected in wastewater systems, landfill leachate-impacted environments, and receiving waters. However, the responses of microbial communities with different contamination histories to TPHP have remained poorly understood. Here, landfill soil and wastewater bacterial communities were subjected to a gradient of TPHP stress under controlled microcosm conditions to assess community, network, and functional responses. The results demonstrated that microbial responses to TPHP were strongly shaped by environmental history. In the landfill soil community, succession followed a consistent directional pattern, as evidenced by the progressive enrichment of Serratia with increasing TPHP concentration. Additionally, the interaction network remains less disrupted compared to the wastewater community, which loses 95.1 % of nodes at a concentration of 70 mg/L. In contrast, the wastewater bacterial community exhibits more pronounced successional shifts and greater simplification of network nodes in response to TPHP. Integrated metagenomic and metabolomic analyses further revealed that TPHP exposure induced broad metabolic reprogramming, particularly affecting amino acid metabolism, purine metabolism, and energy-related pathways. Although the two bacterial community types displayed distinct adaptive strategies, consistent decreases were observed in genes and metabolites associated with the TCA cycle, ATP synthesis, and nucleotide metabolism under TPHP stress. These findings indicated that TPHP not only disrupted the stability of bacterial functions by altering the structure and interaction networks of bacterial communities, but also likely impaired their energy metabolism, thereby weakening the ability of bacterial communities to cope with environmental stress, mediate nutrient transformations, and degrade pollutants.},
}

@article {pmid42762737,
year = {2026},
author = {Ni, G and Su, Z and Wang, Y and Wang, Z and Wu, M and Hua, Z and Leung, PM and Op den Camp, HJM and Lücker, S and Yuan, Z and Hu, S and Guo, J and Greening, C and Zheng, M},
title = {Physiological adaptations of a minimal bacterial consortium enable robust ammonia oxidation at extremely acidic pH.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126966},
doi = {10.1016/j.watres.2026.126966},
pmid = {42762737},
issn = {1879-2448},
abstract = {Microbial communities can efficiently mediate aerobic ammonia oxidation even at acidic pH. However, little is known about the strategies that enable them to simultaneously mitigate acidic and nitrosative stresses. Here, we integrate genome-resolved meta-omic analyses with chemical measurements to infer the composition, metabolic exchange, and stress adaptations of microbial consortia in three acidic nitrification bioreactors operated between pH 2.0 and 5.0. At pH 5.0, the dominant ammonia-oxidising bacterium (AOB) across all conditions was a novel Nitrosococcaceae species, designated "Candidatus Nitrosoglobus kelleri." It reached a relative abundance of up to 56% and possessed genes for ammonia oxidation, aerobic respiration, and carbon fixation. At pH 2.0, the community was strongly simplified and dominated by "Ca. Nitrosoglobus kelleri" together with Mycobacterium species; genome-resolved and transcriptional evidence suggested potential metabolic linkages related to carbon and nitrogen compound cycling. Both "Ca. Nitrosoglobus kelleri" and Mycobacterium spp. concurrently activate metabolic mechanisms to maintain intracellular pH homeostasis, detoxify reactive nitrogen species, and reinforce their cellular envelopes. Despite inhabiting aerobic bioreactors, consortia members also expressed denitrification genes at high levels, likely to eliminate reactive nitrogen species such as nitrite and nitric oxide produced during incomplete nitrification, with a trade-off in respiratory efficiency. Collectively, these findings provide critical insights into the metabolic adaptations of minimalistic microbial communities at extremely low pH. In addition to enhancing understanding of microbial nitrogen cycling, this work has potential implications for improving wastewater treatment technologies through acidic nitrification processes.},
}

@article {pmid42762951,
year = {2026},
author = {Liang, S and Shao, Y and Qin, H and Li, M and Xu, H and Zhang, J and Sun, Z and Cao, H and Qin, X and Zhang, Z and Yang, W},
title = {A cohort study of physical activity, gut microbiota, serum metabolites, and the risk of steatotic liver disease.},
journal = {Annals of hepatology},
volume = {},
number = {},
pages = {102443},
doi = {10.1016/j.aohep.2026.102443},
pmid = {42762951},
issn = {1665-2681},
abstract = {INTRODUCTION AND OBJECTIVES: Prospective evidence on the association between physical activity (PA) and steatotic liver disease (SLD) risk is limited. Gut microbiota profiles and metabolites associated with PA remain unclear.

PATIENTS AND METHODS: We investigated the association between PA and SLD risk in a cohort of 2,942 free-living adults, where PA and SLD were measured using a validated self-reported questionnaire and transient elastography, respectively. We further identified 1-year gut microbial changes and serum metabolites related to moderate-to-vigorous PA (MVPA), and examined their associations with SLD in a subset of the cohort (n=754), where fecal samples for 16S rRNA sequencing were collected twice (1-year apart), species-level microbial profiles were generated using shotgun metagenomics, targeted metabolomics was performed using baseline serum samples, and PA was assessed by accelerometer.

RESULTS: From 2020 to 2025, 565 SLD cases were newly diagnosed. MVPA levels were inversely associated with SLD risk (HRT3vs.T1=0.78, 95% CI: 0.63-0.98), while sedentary hours were positively associated with SLD (HRT3vs.T1=1.26, 95% CI: 1.00-1.58). Twelve genera showed longitudinal changes in relation to MVPA (pFDR<0.05). Proteus was positively associated with SLD risk (OR=1.32, 95% CI: 1.01-1.72), supported by species-level shotgun metagenomics for Proteus cibarius. L-valine concentrations were inversely correlated with MVPA (β=-0.23, pFDR=0.031), while demonstrating a positive association with SLD risk (OR=1.78, 95% CI: 1.22-2.63). L-valine was also correlated with the MVPA-associated genus Synergistes.

CONCLUSIONS: MVPA is associated with changes in the gut microbiota and microbiota-related metabolites that are linked to a more favorable SLD profile, whereas sedentary behavior is associated with higher SLD risk.},
}

@article {pmid42763279,
year = {2026},
author = {Xiaoyi, Z and Mingjun, G and Diandian, C and Wenshuo, Y and Huiqiong, P and Ying, L and Jiaxuan, L and Leyang, J and Jingrong, C},
title = {Rapid and accurate diagnosis of bloodstream infections: A multiplex real-time PCR assay with selective microbial enrichment for direct whole-blood detection and positive blood culture confirmation.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2026.09.004},
pmid = {42763279},
issn = {1995-9133},
abstract = {BACKGROUND: Bloodstream infections (BSIs) remain a critical clinical challenge with high morbidity and mortality, yet conventional blood culture-based diagnostics delayed timely antimicrobial therapy due to long turnaround times. This study evaluated a rapid BSI diagnostic method combining selective microbial enrichment with multiplex real-time fluorescent polymerase chain reaction (PCR), with a focus on direct whole-blood detection as the primary innovation.

METHODS: The enrichment-PCR assay targets 16 common BSI pathogens. Technical performance was confirmed using 479 Gram-stained positive blood culture bottles (May-October 2025, two centers), with conventional culture + MALDI-TOF MS as the reference standard. Direct whole-blood detection was then prospectively evaluated in 50 patients with suspected BSI, using a composite reference standard of blood culture and metagenomic next-generation sequencing (mNGS). Clinical impact was assessed by analyzing time savings and antimicrobial therapy adjustments.

RESULTS: In positive blood culture bottles, enrichment-PCR generated results in 2 h (vs. 18-24 h for conventional methods), achieving 97.48% overall concordance with reference standards (95% CI: 95.65%-98.56%). In the 50-patient direct whole-blood cohort, enrichment-PCR identified all 14 culture-confirmed cases (100% concordance) and detected 6 additional culture-negative infections that were validated by mNGS. Direct testing reduced the median time to pathogen identification from blood collection to approximately 4 h, compared with a median of 19.6 h to blood culture positivity. Among the 6 culture-negative, PCR-positive cases, early identification led to targeted antimicrobial adjustments in 5 of 6 patients. One false-positive result was observed. The enrichment step reduced Ct values by 3-4 cycles (10-fold sensitivity gain; P < 0.001), achieving a limit of detection of 100 CFU/mL.

CONCLUSION: This enrichment-PCR assay enables rapid, accurate BSI diagnosis, with the direct whole-blood application providing a meaningful clinical time advantage over culture-based methods. Preliminary data suggest potential for detecting culture-negative BSI and guiding early antimicrobial decisions, although validation in larger cohorts is needed.},
}

@article {pmid42763436,
year = {2026},
author = {Alberdi, A and Ramirez, J and Gaun, N and Horisberger, Z and Wang, B and Trivedi, U and Bogri, A},
title = {LMDmapper: an open-source desktop tool for spatial mapping of laser microdissection samples.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {257},
doi = {10.12688/openreseurope.24543.2},
pmid = {42763436},
issn = {2732-5121},
abstract = {Laser microdissection (LMD) enables researchers to isolate targeted microsamples from microscopy slide specimens for downstream molecular analyses. While traditionally employed for isolating eukaryotic cells from complex tissues, LMD is starting to be used for micro-scale spatial microbiome analyses, which require the precise location of the microsamples to be tracked for downstream spatial analyses. To address this need, we present LMDmapper, an open-source desktop application that allows designing, tracking and logging micron-scale spatial microsample data and metadata from LMD sessions. The software parses Leica Database LIF image files (containing stage coordinates), imports laser microdissection CSV exports (containing image pixel coordinates), transforms and maps image pixel coordinates into stage coordinates, and presents the resulting cut points together with user-defined plate layouts and collection metadata. LMDmapper supports a variety of microdissection designs, including multiple slides, specimens, collection plates and plate layouts. The application is implemented in TypeScript using Electron, React, Vite, and fast-xml-parser. LMDmapper outputs include a metadata CSV linking microsample identifiers to plate positions, collection information, image labels, pixel coordinates and stage coordinates, as well as the possibility to create overview images of the specimens, and automatically calculating distances between cutting points and regions of interest. With these capabilities, LMDmapper is intended as a practical bridge between microscope-side laser microdissection records and downstream spatial omics sample tracking.},
}

@article {pmid42763505,
year = {2026},
author = {Xie, S and Wu, L and Liu, Y and Jiang, S and Yang, Y and Peng, Q},
title = {Vision-threatening ocular toxoplasmosis involving the fovea diagnosed by intraocular fluid mNGS: A case report.},
journal = {IDCases},
volume = {46},
number = {},
pages = {e02741},
pmid = {42763505},
issn = {2214-2509},
abstract = {Ocular toxoplasmosis is the most common cause of infectious posterior uveitis worldwide and may lead to irreversible visual impairment when the macula is involved. Definitive diagnosis remains challenging because clinical manifestations overlap with those of other infectious and inflammatory retinal disorders. We report a case of active ocular toxoplasmosis involving the fovea in an immunocompetent 44-year-old man presenting with progressive unilateral visual loss and central scotoma. Ophthalmic examination revealed keratic precipitates, mild vitritis, and a yellow-white inflammatory lesion involving the macular region. Fluorescein angiography demonstrated progressive hyperfluorescent staining, and optical coherence tomography showed a hyperreflective subfoveal lesion. Serological testing was positive for anti-Toxoplasma gondii IgM and IgG antibodies. Intraocular fluid analysis demonstrated positive anti-Toxoplasma IgG, while metagenomic next-generation sequencing (mNGS) directly identified Toxoplasma gondii DNA, providing molecular evidence supporting the diagnosis. The patient denied cat ownership or close feline exposure but reported occasional consumption of raw salmon. Treatment consisted of oral trimethoprim-sulfamethoxazole combined with methylprednisolone and two intravitreal injections of clindamycin plus dexamethasone. Significant regression of the retinal lesion was observed after treatment. This case highlights the diagnostic value of intraocular fluid mNGS in ocular toxoplasmosis and emphasizes the importance of considering ocular toxoplasmosis in patients presenting with posterior uveitis involving the macula, even in the absence of traditional epidemiological risk factors.},
}

@article {pmid42759493,
year = {2026},
author = {Ozaki, S and Watanabe, S and Oshima, T},
title = {Genome Microbiology at 20 Years: Who We Are and Where We Are Going.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsag016},
pmid = {42759493},
issn = {1756-1663},
abstract = {The International Symposium "Microbial Growth and Behavior: From Bench to Nature" was held as part of the annual meeting of the Society for Genome Microbiology, Japan. This session was designed to highlight challenges in modern microbiology: how to connect molecular insights obtained from laboratory model systems with the dynamic and complex responses of microbes in natural environments.},
}

@article {pmid42759762,
year = {2026},
author = {Zhang, Y and Xu, Z and Li, C and Ma, X and Cao, J and Lin, Z and Yang, L and Xu, J and Cui, T and Wang, Y and Gao, L and Nie, J and Yang, Y and Tang, Z and Wu, D and Wu, X},
title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Pulmonary Fungal Infections in Patients with Haematological Diseases: A Multicentre Retrospective Study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109125},
doi = {10.1016/j.ijid.2026.109125},
pmid = {42759762},
issn = {1878-3511},
abstract = {OBJECTIVES: To evaluate the diagnostic value, clinical application and potential utility of metagenomic next-generation sequencing (mNGS) for pulmonary fungal infections (PFI) in patients with haematological diseases.

METHODS: A total of 994 patients with haematological diseases and suspected pulmonary infection were included, comprising 514 bronchoalveolar lavage fluid (BALF)-mNGS and 499 peripheral blood (PB)-mNGS tests. Clinical characteristics, diagnostic performance, false-negative factors, antifungal treatment modification and outcomes were analysed.

RESULTS: Based on the 2020 revised EORTC/ MSGERC criteria, 210 patients were classified as PFI, 156 as possible PFI and 628 as non-PFI. For BALF-mNGS, the diagnostic performance for PFI showed an AUC of 0.731, with a sensitivity of 72% and specificity of 74%. For PB-mNGS, the diagnostic performance for PFI showed an AUC of 0.717, with a sensitivity of 63% and specificity of 80%. Among the 156 patients classified as possible PFI (166 mNGS tests), fungi were detected by 130 tests (78.3%). Azole prophylaxis (OR, 2.42; P=0.038) were associated with false-negative mNGS results, whereas neutropenia was associated with fewer false-negative results (OR, 0.33; P=0.012). After mNGS reporting, antifungal therapy was modified in 312 patients (31.4%).

CONCLUSIONS: mNGS enhances fungal pathogen detection in high-risk haematological patients but should not be used as a standalone diagnostic test.},
}

@article {pmid42759851,
year = {2026},
author = {Khan, W and Lee, JS and Jeon, YJ and Kim, TH and Jang, SA and Kim, ES and Yun, YM},
title = {Magnetite Enhances upflow anaerobic sludge blanket resilience to progressive organic overloading by Preserving granule matrix integrity and redox function.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135845},
doi = {10.1016/j.biortech.2026.135845},
pmid = {42759851},
issn = {1873-2976},
abstract = {Progressive organic overloading can destabilize anaerobic granules and constrain syntrophic conversion in upflow anaerobic sludge blanket (UASB) reactors, yet whether and how magnetite retention within granules contributes to reactor resilience remains unclear. This study examined the structural, redox, and microbial responses of control and magnetite-amended UASB reactors subjected to stepwise increases in organic loading rate (OLR). The control reactor showed pronounced deterioration at 4.0-5.0 g COD/L/d, and its operation was terminated at 6.0 g COD/L/d. In contrast, the magnetite-amended reactor maintained methane yields near 300 mL CH4/g CODadded through 6.0 g COD/L/d and remained operational at 8.0 g COD/L/d. At 6.0 g COD/L/d, total residual organic acids reached 2,675 ± 338 mg COD/L in the control reactor but only 709 ± 35 mg COD/L in the magnetite-amended reactor. Propionate in the magnetite-amended reactor remained below 89 mg COD/L during the higher loading stages. The persistent distribution of Fe-bearing material within the granule matrix, consistent with magnetite retention, coincided with sustained granule size, more coherent EPS-associated spectral responses, a smaller increase in humic- and fulvic-like fluorescence, stronger electrochemical responsiveness, and higher electron transport system activity. Metagenomic profiles further showed that methanogenic taxa and genes related to EPS biosynthesis, redox metabolism, and methanogenesis persisted to higher OLRs in the magnetite-amended reactor. Acetate accumulation at the highest OLR indicated that magnetite delayed rather than prevented the eventual limitation in acetate conversion. These results link granule-associated magnetite retention with maintenance of structural stability, redox activity, and microbial functional potential during progressive organic overload.},
}

@article {pmid42759892,
year = {2026},
author = {Halmi, MFA and Edinur, HA},
title = {Two decades of microbiome forensics: Bibliometric insights into publication trends, applications and methodological advancements.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107716},
doi = {10.1016/j.mimet.2026.107716},
pmid = {42759892},
issn = {1872-8359},
abstract = {Microbiome forensics focuses on complex microbial communities for use as unique identification methods for forensic inferences. They include individual identification, crime scene reconstruction, and estimation of post-mortem intervals. This study adopts a bibliometric approach to assess the global scientific output and knowledge structure of the microbiome forensics, applications and methodological advancement in microbiome forensics. A total of 220 documents spanning two decades (2005 to 2024) were retrieved from the Web of Science Core Collection using related keywords. Of the total number of scientific publications, 6306 citations were found, with an average of 28.66 citations per publication. The United States dominated this domain with the most publications, followed by China, Australia, England, and Germany. Although Michigan State University had the highest number of citations, but the works produced by the Centre National de la Recherche Scientifique in Paris, France, had the highest research impact. Research trend mapping of keyword co-occurrence revealed five major clusters of forensic microbiome research: i. post-mortem interval estimation, ii. human identification, iii. Body fluid identification, iv. geolocation and provenance, and v. computational methods. Subsequent analyses indicated that forensic microbiome research has evolved from the use of culture-based and polymerase chain reaction (PCR) amplification of 16S rRNA for microbial identification before 2017 to the application of next generation sequencing (NGS) coupled with machine learning and bioinformatics from 2018 onwards. The findings of this study may be used to strategically inform knowledge gaps and key areas for future investigations in this field. In addition, building partnerships between forensic societies is needed not only to effectively move the field forward through the development of standardised protocols and quality assurance but also in exchanging expertise with developing countries, where knowledge is urgently needed to resolve crime cases.},
}

@article {pmid42759915,
year = {2026},
author = {Cui, HL and Li, YH and Shi, K and Ren, YJ and Li, BZ and Li, Q and Gao, BY and Kong, DY and Zhang, ZF and Wu, Y and Zhang, K and Ma, Y and Wang, AJ and Liang, B},
title = {Stability-Oriented Chemical-Biological Integration Prioritizes Antimicrobials Linked to Resistome Variation in Landfill Leachates across China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129196},
doi = {10.1016/j.envpol.2026.129196},
pmid = {42759915},
issn = {1873-6424},
abstract = {Landfill leachate contains complex mixtures of antimicrobials and other stressors, making it difficult to identify chemical signals consistently associated with environmental resistomes. We integrated targeted antimicrobial measurements with metagenomic antibiotic resistance gene (ARG) profiles from landfill leachates collected in 17 Chinese cities across 12 provinces. Among 52 detected antimicrobials, 37 had risk quotients (RQs) > 0.1, 25 exceeded 1, and 12 exceeded 10 in at least one site; 296 ARG subtypes were detected. Pairwise and matrix-level analyses showed fragmented antimicrobial-ARG relationships. Using Shannon diversity as a resistome-level endpoint, a stability-oriented multivariable analysis prioritized clinafloxacin, clindamycin hydrochloride, and sulfathiazole. Their bootstrap recurrence frequencies were 0.752, 0.389, and 0.226, respectively, with the same stability hierarchy supported by alternative selection and site-omission analyses; clinafloxacin was also least sensitive to measured antimicrobial covariance. Covariate-adjusted higher-versus-lower exposure contrasts were -0.467, +0.250, and +0.089 Shannon units, respectively, with sulfathiazole showing greater context dependence. Integrating chemical exposure with resistome responses thus complements conventional occurrence- and RQ-based screening by adding a biological-response layer for prioritizing reproducible antimicrobial signals within complex environmental mixtures.},
}

@article {pmid42760068,
year = {2026},
author = {Toufiq, R and Shahid, A and Zahra, R and Lankapalli, AK and Oduwo, J and Owinoh, EO and Aftab, S and Hassan, B and Thomson, K and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e120775},
doi = {10.1136/bmjopen-2026-120775},
pmid = {42760068},
issn = {2044-6055},
mesh = {Humans ; Pakistan ; Female ; Infant ; Longitudinal Studies ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Breast Feeding/statistics & numerical data ; Anti-Bacterial Agents/therapeutic use ; Birth Cohort ; Adult ; Milk, Human/microbiology ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Pakistan (INBUGS-P) was established to characterise the longitudinal development of the infant gut microbiome and resistome during the first year of life in a low- and middle-income country setting. The influence of early-life exposures, including mode of delivery, antibiotic use and infant feeding practices on gut bacterial diversity and antimicrobial resistance gene (ARG) profiles is being evaluated.

PARTICIPANTS: A total of 107 mother-infant pairs were recruited at the Pakistan Institute of Medical Sciences between December 2023 and June 2024. Follow-up was conducted at 10 predefined timepoints from birth to 12 months, during which 921 infant stool samples, 158 maternal rectal swabs, 246 breast milk samples and 2171 environmental swabs were collected. Sociodemographic, clinical, cultural and biological data were collected at enrolment and at each follow-up visit using Research Electronic Data Capture.

FINDINGS TO DATE: Baseline characteristics of 98/107 mother-infant dyads are included in the analysis. The cohort reflects an urban low-income population: median household income was PKR 30,000 per month (approximately US$170 per capita per month). Caesarean section accounted for 55% (54/98) of deliveries; 13.0% of infants were late preterm, and 10.0% had low birth weight (<2500 g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6 months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime.

FUTURE PLAN: Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and ARGs. Subject to funding, hybrid long- and short-read sequencing and extended follow-up to 24 months are planned.},
}

Humans
Pakistan
Female
Infant
Longitudinal Studies
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Breast Feeding/statistics & numerical data
Anti-Bacterial Agents/therapeutic use
Birth Cohort
Adult
Milk, Human/microbiology

@article {pmid42760695,
year = {2026},
author = {He, MH and Chen, XL and Feng, BT},
title = {Coinfection of Pneumocystis jirovecii and Aspergillus fumigatus in the lung: A case report.},
journal = {Medicine},
volume = {105},
number = {38},
pages = {e50705},
doi = {10.1097/MD.0000000000050705},
pmid = {42760695},
issn = {1536-5964},
support = {2025YX098//Weifang Science and Technology Development Program (Medical Category)/ ; },
mesh = {Humans ; Male ; *Pneumocystis carinii/isolation & purification ; Aged ; *Aspergillus fumigatus/isolation & purification ; *Coinfection/drug therapy/microbiology/diagnosis ; Antifungal Agents/therapeutic use ; Voriconazole/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; *Pneumonia, Pneumocystis/drug therapy/diagnosis ; Immunocompromised Host ; Lymphoma, Mantle-Cell/drug therapy ; *Pulmonary Aspergillosis/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {RATIONALE: Coinfection with Pneumocystis jirovecii and Aspergillus fumigatus in immunocompromised patients carries high mortality. More importantly, paradoxical clinical and radiological responses during treatment remain poorly understood.

PATIENT CONCERNS: A 66-year-old male with mantle cell lymphoma who had received prolonged corticosteroid therapy after suspected rituximab-associated lung injury presented with progressive pulmonary symptoms.

DIAGNOSES: Concurrent pulmonary infection with P jirovecii and A fumigatus was confirmed by bronchoalveolar lavage combined with metagenomic next-generation sequencing.

INTERVENTIONS: The patient was treated with trimethoprim-sulfamethoxazole and voriconazole.

OUTCOMES: Clinical symptoms improved markedly; however, chest imaging showed paradoxical progression, possibly reflecting an immune reconstitution inflammatory syndrome-like inflammatory response.

LESSONS: bronchoalveolar lavage combined with metagenomic next-generation sequencing enables rapid diagnosis of concurrent opportunistic pulmonary infections. Paradoxical radiographic worsening despite clinical improvement may suggest an immune reconstitution inflammatory syndrome-like inflammatory response, although persistent or progressive infection cannot be excluded.},
}

Humans
Male
*Pneumocystis carinii/isolation & purification
Aged
*Aspergillus fumigatus/isolation & purification
*Coinfection/drug therapy/microbiology/diagnosis
Antifungal Agents/therapeutic use
Voriconazole/therapeutic use
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
*Pneumonia, Pneumocystis/drug therapy/diagnosis
Immunocompromised Host
Lymphoma, Mantle-Cell/drug therapy
*Pulmonary Aspergillosis/drug therapy
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid42761040,
year = {2026},
author = {Ribeiro, GO and Guimarães, LO and Foro Ramos, EDS and Couto, RDS and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Reginato, SL and Mucci, LF and Bergo, ES and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Leal, É and Kirchgatter, K},
title = {RNA virome comparison between sylvatic and urban-interface mosquitoes from Southeastern Brazil.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1894867},
pmid = {42761040},
issn = {2235-2988},
mesh = {Animals ; Brazil ; *Virome/genetics ; *Culicidae/virology/classification ; *RNA, Viral/genetics ; *Mosquito Vectors/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Forests ; },
abstract = {INTRODUCTION: Mosquitoes (Diptera: Culicidae) are primary vectors of public health pathogens, yet their core viromes remain poorly characterized, particularly in Neotropical sylvatic lineages. This study investigated the RNA virome of multiple mosquito species across urban-to-forest gradients in São Paulo State, Brazil, including neglected sylvatic taxa such as Sabethes, Psorophora, Shannoniana, and Wyeomyia.

METHODS: The RNA virome of multiple mosquito species was investigated across urban-to-forest gradients in São Paulo State, Brazil. Ecological analyses were performed to assess the effects of host taxonomy and environment on virome composition. Network analysis was conducted to investigate virus-host associations and viral sharing across ecological interfaces.

RESULTS: Our analysis identified 919 viral contigs across 217 viral species and 37 distinct families, revealing a substantial fraction of "viral dark matter" with low amino acid identity (median < 40%) in predominantly sylvatic mosquito species. Although viral families containing known arboviruses, such as Flaviviridae, Phenuiviridae, and Peribunyaviridae, were detected, no high-consequence human pathogens were identified within the sensitivity limits of our sampling and sequencing depth. Ecological analyses demonstrated that virome composition was strongly structured by host taxonomy and environment (R[2]=0.570, p=0.001), with host species explaining 32.9% of the unique variance (PERMANOVA, R[2]=0.329, p=0.001), whereas ecotope played a secondary role (R[2]=0.029, p=0.001). Network analysis revealed a highly modular virus-host structure dominated by host-restricted specialists, with a limited number of bridge species facilitating viral sharing across ecological interfaces.

DISCUSSION: These findings indicate that intrinsic mosquito biology is the main driver of viral community structure, while environmental gradients play a secondary role, and highlight the importance of host-associated processes in shaping viral diversity at the Neotropical forest-urban interface.},
}

Animals
Brazil
*Virome/genetics
*Culicidae/virology/classification
*RNA, Viral/genetics
*Mosquito Vectors/virology
*RNA Viruses/genetics/classification/isolation & purification
Forests

@article {pmid42761071,
year = {2026},
author = {Zhou, M and Yasuda, S and Miura, H and Xu, T and Kuroiwa, M and Xu, X and Terada, A},
title = {Electron acceptor-dependent duality of nitrous oxide metabolism in Thiobacillus during sulfur autotrophic denitrification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903473},
pmid = {42761071},
issn = {1664-302X},
abstract = {Sulfur-driven autotrophic denitrification (SADN) is a promising biotechnology for nitrogen removal from low-carbon wastewater; however, nitrous oxide (N2O) emissions remain a significant environmental concern. This study systematically investigated the effects of different nitrogen oxide electron acceptors on denitrification performance, microbial community succession, distribution of the N2O reductase gene nosZ clade, and the ecological functions of Thiobacillus using sequential enrichment cultivation. Among the tested conditions, the nitrate (NO 3 -)-fed system achieved the highest denitrification and sulfur oxidation rates, with the lowest net N2O accumulation, whereas the nitrite (NO 2 -)-fed condition led to severe N2O accumulation due to an imbalance between N2O production and reduction. High-throughput sequencing and quantitative PCR analyses revealed that Thiobacillus became the primary sulfur-oxidizing denitrifier in the presence of NO 3 - , NO 2 - , and nitric oxide, accompanied by substantial enrichment of nirS and clade I nosZ genes. In contrast, N2O-fed conditions promoted a more functionally diverse community enriched with clade II nosZ bacteria, including Azonexus and Dechloromonas. Metagenomic analyses recovered three distinct Thiobacillus metagenome-assembled genomes (MAGs 10, 11, and 25), each with distinct denitrification and sulfur oxidation capacities. MAG 10 contains genes for complete sulfur oxidation and denitrification, including clade I nosZ and nirS genes. Conversely, the nosZ gene was not detected in MAG 11, whereas the norB/norC genes were present, indicating their potential role as an N2O producer. MAG 25 exhibits N2O-responsive functional enrichment upon N2O feeding, reflecting a specialized ecological strategy centered on sulfur oxidation coupled with N2O reduction. Overall, these findings show that electron acceptors play a key role in shaping microbial succession, nosZ clade distribution, and the dual roles of Thiobacillus in N2O cycling depending on conditions. This study provides new insights into microbial ecology and offers potential strategies for mitigating N2O emissions in SADN processes.},
}

@article {pmid42761166,
year = {2026},
author = {Li, M and Zhao, X and Zhang, B and Cao, R and Wang, Z and Huang, Z and Cheng, C and Lu, S and Jiang, X},
title = {Gut microbiome-metabolome signatures of osteosarcopenia in fracture patients in China.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1863988},
doi = {10.3389/fendo.2026.1863988},
pmid = {42761166},
issn = {1664-2392},
mesh = {Humans ; Female ; Male ; Middle Aged ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; *Fractures, Bone/metabolism/microbiology/complications/epidemiology ; Aged ; China/epidemiology ; *Metabolome ; *Sarcopenia/microbiology/metabolism/epidemiology ; Multiomics ; Metabolomics ; Metagenomics ; },
abstract = {BACKGROUND: Osteosarcopenia, defined as the coexistence of low bone mass and sarcopenia, is a disabling musculoskeletal condition, yet its gut microbial and metabolic characteristics in clinical populations remain incompletely understood. Integrative multi-omics approaches may help clarify species-metabolite networks associated with this condition, particularly in fracture patients.

METHODS: In this single-center, prospective cross-sectional study, 69 fracture patients aged ≥50 years were classified into four phenotypes: Normal (n = 18), isolated low bone mass (Bone, n = 18), isolated sarcopenia (Muscle, n = 19), and osteosarcopenia (Both, n = 14). Fecal samples were analyzed using shotgun metagenomics and untargeted metabolomics, yielding paired multi-omics data for 52 participants.

RESULTS: The Bone group had the highest mean age (66.6 ± 9.46 years), whereas the mean ages of the other groups ranged from 60.6 to 61.8 years (overall p = 0.029), while sex, BMI, lifestyle factors, and comorbidities did not differ significantly. Neither α-diversity nor overall β-diversity showed marked differences across phenotypes, suggesting that broad community replacement was not observed. A multi-stage, multi-method strategy yielded a 17-species consensus feature set associated with differences among musculoskeletal phenotypes. Taxonomic patterns were consistent with a candidate fiber/short-chain fatty acid (SCFA)-associated module, whereas exploratory microbe-metabolite correlations suggested a candidate lipid/sterol-associated module. The latter included correlations linking Firmicutes bacterium CAG:24053_14 with putatively annotated cholesterol and N-acylethanolamines.

CONCLUSIONS: Osteosarcopenia in fracture patients was associated with unadjusted differences in selected gut microbial taxa and fecal metabolites within a broadly shared microbial community. These findings are hypothesis-generating and require validation in larger independent cohorts before clinical or biomarker application.},
}

Humans
Female
Male
Middle Aged
Cross-Sectional Studies
*Gastrointestinal Microbiome
Prospective Studies
*Fractures, Bone/metabolism/microbiology/complications/epidemiology
Aged
China/epidemiology
*Metabolome
*Sarcopenia/microbiology/metabolism/epidemiology
Multiomics
Metabolomics
Metagenomics

@article {pmid42761512,
year = {2026},
author = {Fu, L and Wu, Y and Jin, X and Ma, X},
title = {Rewriting the genome: harnessing R2 retrotransposons for precise DNA insertion.},
journal = {Frontiers in genome editing},
volume = {8},
number = {},
pages = {1789016},
doi = {10.3389/fgeed.2026.1789016},
pmid = {42761512},
issn = {2673-3439},
abstract = {CRISPR-based genome editors are fundamentally limited by their requirement for double-strand DNA breaks (DSBs), restricted transgene cargo capacity, and reliance on error-prone endogenous DNA repair mechanisms. Non-long terminal repeat (non-LTR) retrotransposons-especially the site-specific R2 element-offer a mechanistically distinct and potentially safer choice for programmable genomic integration. These elements employ target-primed reverse transcription (TPRT)-an RNA-templated integration mechanism that circumvents DSB formation and supports amplification of self-copy. This review delineates the molecular mechanism of R2 retrotransposons, emphasizing their highly specific integration into the 28 S ribosomal DNA locus-a recognized genomic safe harbor. We describe the functional domains of the R2 protein, including the reverse transcriptase, restriction-like endonuclease, and nucleic acid-binding motifs, and explain how they coordinate to achieve precise DNA cleavage and cDNA synthesis. Recent cryo-electron microscopy (cryo-EM) structures have revealed discrete RNA-protein complex that orchestrate the stepwise progression of TPRT. Informed by these mechanistic insights, researchers have engineered programmable platforms-including PRINT and STITCHR-that enable RNA-directed transgene integration in mammalian systems. These platforms establish R2 as a viable all-RNA programmable system for targeted genomic integration. Future directions include reprogramming the DNA-binding specificity of R2 through protein engineering to target loci, optimizing integration fidelity and efficiency, and mining diverse R2-like elements from metagenomic data. With continued optimization and rigorous safety validation, R2-derived platforms could supplant current nuclease-dependent editors in applications requiring high-fidelity, large-cargo integration.},
}

@article {pmid42761643,
year = {2026},
author = {Wang, X and Hu, WP and Wu, YX and Hua, JL and Cheng, ZX and Wang, X and Liu, L and Zhang, J},
title = {Blood mNGS-Detected Epstein-Barr Virus in ICU Patients with Pneumonia: Associations with Disease Severity Markers and Inflammatory Burden.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {596241},
doi = {10.2147/IDR.S596241},
pmid = {42761643},
issn = {1178-6973},
abstract = {BACKGROUND: Epstein-Barr virus (EBV) is frequently detected in critically ill patients, but the clinical meaning of EBV reported by blood metagenomic next-generation sequencing (mNGS) in ICU patients with pneumonia remains unclear.

METHODS: This retrospective secondary analysis used data from a prospective multicenter cohort of patients with suspected sepsis. Data included demographics, clinical variables, radiological findings, blood culture and mNGS results, cytokine levels, and 30-day mortality.

RESULTS: A total of 184 ICU patients with pneumonia were included and classified as EBV-positive (n=34) or EBV-negative (n=150) according to blood mNGS. EBV-positive patients had lower serum albumin and systolic blood pressure, higher qSOFA score distribution, more frequent sepsis at enrollment, higher C-reactive protein and procalcitonin levels, higher PaCO2, and lower serum calcium. Pneumocystis jirovecii was numerically more frequent in EBV-positive patients but was not independently associated with EBV positivity after adjustment. In exploratory cytokine analysis, EBV-positive patients showed higher TRAIL levels and more frequent IL-17 detection. In an exploratory multivariable model, lower serum albumin and sepsis at enrollment remained associated with EBV positivity. 30-day mortality did not differ significantly between groups.

CONCLUSION: In ICU patients with pneumonia, blood mNGS-detected EBV was associated with markers of disease severity and inflammatory burden. However, these associations do not establish clinically significant EBV reactivation, and no statistically significant difference in 30-day mortality was observed between groups.},
}

@article {pmid42761748,
year = {2026},
author = {Ubani, O and Ngole-Jeme, VM},
title = {Dataset characterising dominant bacterial phylotypes across animal manure-enriched composting microcosms for crude oil waste sludge bioremediation.},
journal = {Data in brief},
volume = {69},
number = {},
pages = {113198},
doi = {10.1016/j.dib.2026.113198},
pmid = {42761748},
issn = {2352-3409},
abstract = {The dataset provides a complete record of microbial, functional, physicochemical, and contaminant dynamics from controlled co-composting microcosms designed to remediate petroleum refinery sludge using targeted animal manure amendments. Five treatments-cow, pig, horse, and poultry manures, as well as an unamended control-were monitored over 300 days. The study incorporated amplicon-based 16S rRNA gene sequencing, functional gene inference, culture-based validation, bulk chemistry, and chromatographic analyses. Illumina MiSeq profiling of the V1-V3 regions identified 359 bacterial genera (raw OTU-level assignments prior to quality and abundance filtering) across 17 phyla, with taxonomic inventories structured from phylum to genus. Alpha and beta diversity measures demonstrated treatment-dependent community assembly, with the highest richness and diversity observed in cow-manure microcosms-pig and poultry amendments selectively enriched hydrocarbon-degrading taxa, including Pseudomonas. Functional predictions generated using PICRUSt2 (NSTI = 0.02-0.16) indicated enrichment of pathways involved in xenobiotic degradation, aromatic compound metabolism, and benzoate catabolism. These predictions were supported by culture-based evidence, including redox indicator screening and detection of the cbzE gene, which encodes catechol 2,3-dioxygenase, a key enzyme in chlorobenzoate/chlorocatechol degradation pathways and functionally analogous to the widely recognised xylE gene in aromatic hydrocarbon-degrading microorganisms. Collectively, these determinations provide complementary genomic and phenotypic evidence for the biodegradation potential of the microbial community and its capacity to transform aromatic and other environmentally relevant xenobiotic compounds. Additional datasets document total organic carbon, nitrogen, and phosphorus profiles of feedstocks and sludge. At the same time, Soxhlet extraction GC-MS measurements quantify polycyclic aromatic hydrocarbon (PAH) attenuation, with up to 99.9% removal achieved for multiple compounds in pig, horse, and poultry-amended systems. Through the combination of taxonomic profiling, PICRUSt2-based functional inference, chemical transformation analyses, and degradation kinetic measurements, this dataset affords a comprehensive characterisation of microbial community structure, predicted metabolic potential, and biodegradation performance associated with crude oil sludge co-composting at the sampled time point.},
}

@article {pmid42762131,
year = {2026},
author = {Xiang, Q and Li, Y and Yang, J},
title = {Translational efficiency guides microbial community remodeling.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2736907},
doi = {10.1080/19490976.2026.2736907},
pmid = {42762131},
issn = {1949-0984},
mesh = {*Microbiota ; Metagenomics ; *Microbial Interactions ; *Bacteria/genetics/metabolism ; *Protein Biosynthesis ; },
abstract = {While metagenomics provides compositional insights, its correlative nature limits causal community remodeling. Overcoming this, in a recent Cell study, Moyne et al. introduced the Microbial Interaction and Niche Determination (MIND) framework. By leveraging translational efficiency to map resource competition and niche partitioning, MIND establishes a mechanistic blueprint for rational engineering.},
}

*Microbiota
Metagenomics
*Microbial Interactions
*Bacteria/genetics/metabolism
*Protein Biosynthesis

@article {pmid42762368,
year = {2026},
author = {Cirak, S and Grieshaber, V and Müller, P and Chao, CM},
title = {The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.},
journal = {Molecular and cellular pediatrics},
volume = {13},
number = {1},
pages = {},
pmid = {42762368},
issn = {2194-7791},
abstract = {In severe childhood-onset neuromuscular disease (NMD), ventilatory muscle weakness and ineffective airway clearance drive recurrent infections and chronic colonization that is often culture-negative, polymicrobial, or both. The lung microbiome framework offers a unifying model: altered microbial immigration, elimination, and growth can produce dysbiosis with pathobiont expansion and antimicrobial resistance (AMR). We propose that pediatric NMD may follow a distinct developmental trajectory in which early-life secretion stasis, viral insults, and frequent antibiotics perturb immune-microbiome crosstalk during lung growth, potentially "imprinting" long-term community structure. However, NMD-specific airway microbiome data remain sparse because most studies rely on culture or upper-airway sampling. Oxford Nanopore Technologies (ONT) long-read sequencing enables real-time metagenomics with AMR gene detection and can deliver same-day profiles (as short as ~ 6 h from sample to result in optimized workflows), but requires robust low-biomass controls and, in some settings, polishing or hybrid strategies to mitigate higher per-read error. A major limitation of metagenomic sequencing of respiratory samples is the high proportion of host DNA, bacterial reads may account for only about 1-5% of the total sequencing reads. We review microbiome principles relevant to pediatric NMD, summarize current evidence, and outline ONT-enabled study designs and translational priorities.},
}

@article {pmid42753439,
year = {2026},
author = {Wang, B and Zhu, K and Wang, Z and Sun, W and Zha, Y and Wang, H and Zhang, Y and Zhang, Y and Song, Y and Zhang, H},
title = {Biogeographical pattern of persistent organic pollutant-transformation genes and their hosts across global inland waters.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143613},
doi = {10.1016/j.jhazmat.2026.143613},
pmid = {42753439},
issn = {1873-3336},
abstract = {Persistent organic pollutants (POPs) remain widespread in inland waters despite decades of regulation, yet the global distribution and ecological controls of microbial POP transformation potential remain largely unresolved. Here, we analyzed 1593 metagenomic samples from inland waters across six continents to investigate the biogeography, microbial hosts, and environmental drivers of POP transformation genes (POPTGs). We identified four major POP categories, with polychlorinated POP transformation genes dominating both water and sediment habitats. Sediments harbored significantly higher POPTG richness and abundance than water columns, highlighting their role as global reservoirs of POP transformation capacity. Unexpectedly, POPTG diversity displayed hump-shaped latitudinal pattern. Proteobacteria were the dominant POPTG carriers, and widespread host taxa generally possessed broader transformation repertoires. Nearly half of POPTG-carrying species were shared between habitats, while frequent associations with mobile genetic elements suggested potential horizontal dissemination of transformation traits. Structural equation modeling revealed that host diversity, anthropogenic pressure, and mean annual temperature collectively explained 38% of POPTG abundance variation, with host diversity exerting the strongest effect. Our findings establish a global framework linking microbial ecology with POP transformation potential and provide insights into predicting natural attenuation and remediation capacity of inland waters under environmental change.},
}

@article {pmid42753600,
year = {2026},
author = {Huang, Q and Zhang, Y and Bais, C and Liu, Y},
title = {Metagenome-resolved evidence that soluble factors in granular activated carbon-amended reactor effluent reprogram propionate metabolism and methanogenic pathways.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130925},
doi = {10.1016/j.jenvman.2026.130925},
pmid = {42753600},
issn = {1095-8630},
abstract = {Granular activated carbon (GAC) enhances anaerobic digestion performance, yet the mechanisms underlying reactor-scale improvements remain incompletely understood, particularly how GAC affects biomass not attached to its surface. Here, sludge from a non-GAC up-flow anaerobic sludge blanket reactor was incubated with 0.45-μm-filtered effluents from non-GAC and GAC-amended reactors under repeated propionate loading, followed by genome-resolved metagenomics. GAC-reactor effluent increased methane yield from 64 ± 3% to 76 ± 3% (p < 0.01) in the absence of GAC particles. A non-redundant catalog of 170 quality-filtered metagenome-assembled genomes (MAGs) was recovered, enabling pathway- and gene-set quantification. Genomic potential for both major propionate-oxidation routes increased in the GAC-effluent group relative to the non-GAC group, with a larger increase for the methylmalonyl-CoA (MMC) route than for the dismutation route (1.289- versus 1.221-fold). Accordingly, the MMC-to-dismutation preference ratio was 5.60% higher in the GAC-effluent group, alongside a broader carrier base. Cobamide potential shifted toward remodeling and cobamide-dependent use rather than increased de novo corrin-ring synthesis. Candidate electron-transfer architectures were also rebalanced: PilA-associated carriers became less prominent, whereas maturation-supported multiheme cytochrome carriers increased from 22.96% to 34.90% of community abundance, although H2/formate-module carriers remained prevalent. Quorum-sensing systems underwent pathway- and carrier-specific redistribution, while all eight curated extracellular-polysaccharide modules showed higher mean gene abundance in the GAC-effluent composite. These findings show that a filter-passing effluent fraction can extend GAC-associated effects beyond direct particle contact and link enhanced methanogenesis to a broader, redistributed network of metabolic, redox, and coordination capacities. This expands the mechanistic framework of conductive-material-assisted anaerobic digestion and provides a basis for harnessing GAC-derived functions throughout the reactor.},
}

@article {pmid42753610,
year = {2026},
author = {Feng, Y and Xu, G and Wu, D and Sun, D and Shao, Q and Xu, H},
title = {Community-level eDNA decay patterns in marine zooplankton: Implications for optimizing eDNA-based marine environmental monitoring.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120341},
doi = {10.1016/j.marpolbul.2026.120341},
pmid = {42753610},
issn = {1879-3363},
abstract = {Environmental DNA (eDNA) has the potential to greatly transform marine ecological monitoring, yet its capacity for accurate biodiversity estimates is constrained by its decay process. Previous research has largely focused on laboratory-cultured single species, and thus the dynamics of mixed-species eDNA from natural communities remain poorly understood. Here, we conducted a 10-day time-series experiment to track the community-level eDNA decay process following the complete removal of zooplankton, employing an integrated approach of morphological analysis, quantitative PCR (qPCR), metabarcoding, and metagenomics. Our results reveal that the decay of marine zooplankton eDNA is a complex, heterogeneous process. Total community eDNA declined rapidly during the first two days (0-2 d), followed by a slower decline (4-10 d), as quantified by qPCR. Crucially, the taxonomic composition of the detectable eDNA pool changed substantially over time: the relative read abundance of copepods declined sharply after only two days, whereas that of medusae persisted high throughout the experiment. Furthermore, methodological comparison revealed significant discrepancies in temporal trajectories between metabarcoding and metagenomics regarding the detected community composition. To optimize eDNA-based marine environmental monitoring, we propose matching target taxa and molecular methods to the temporal scale of interest. Short-lived signals of copepods might support timely, near-snapshot assessments of recent environmental change by eDNA metabarcoding, whereas long-lived medusa eDNA appears to integrate occurrence over time. Taxon-specific signal persistence and method-dependent detectability should therefore be considered when interpreting eDNA monitoring data. This framework can strengthen the reliability of eDNA-based biodiversity assessments and support more effective marine ecosystem monitoring.},
}

@article {pmid42753987,
year = {2026},
author = {Benech, N and Guarino-Vignon, P and McLellan, P and Campidelli, C and Sergeant, M and Joubert, F and Truong, S and Barbier, P and Sandoz, E and Ruffié, P and Sedda, D and Delmeule, A and Pradat, P and Landman, C and Bourrier, A and Marchand, L and Alric, L and Scanzi, J and Cassir, N and Dureault, A and Piet, E and Gallet, S and Botelho-Nevers, E and Roussel-Gaillard, T and Cuerq, C and Ader, F and Guillet, M and Rolhion, N and Grill, JP and Lamaziere, A and Chatel, JM and Pechine, S and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 Strain for the prevention of multiple-recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.09.002},
pmid = {42753987},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Recurrent Clostridioides difficile infection (rCDI) results from persistent microbiome dysfunction and impaired colonization resistance. Although fecal microbiota transplantation (FMT) is effective, defined and scalable alternatives are needed. We evaluated whether a single commensal strain could restore key microbiome functions and prevent recurrence.

METHODS: We assessed Faecalibacterium prausnitzii EXL01 in a murine CDI model and a multicenter, open-label single-arm phase I trial including adults with ≥3 CDI episodes. Following vancomycin preconditioning, patients received oral EXL01 for 8 weeks with 8-week follow-up. Primary endpoint was safety. Secondary endpoints included recurrence at week 8. Longitudinal stool samples underwent shotgun metagenomics and metabolomics. Outcomes were benchmarked against matched FMT cohorts. Additional in vitro and murine studies of EXL01 were performed.

RESULTS: In mice, EXL01 reduced C. difficile burden and intestinal inflammation in an antibiotic-disrupted murine model. Six patients were treated; no treatment-related serious adverse events occurred. Five of six patients (83.3%) remained recurrence-free at week 8, comparable to matched FMT cohorts. EXL01 was detectable in stool up to 8 weeks post-treatment. Multi-omics analyses showed that EXL01 engraftment was correlated with restoration of bile acid metabolism, including reduced primary bile acids and increased secondary bile acids, and increased short-chain fatty acid production, particularly butyrate, despite limited taxonomic recovery. EXL01 selectively deconjugated bile acids in vitro.

CONCLUSIONS: A single, well-characterized bacterial strain was associated with restoration of key microbiome functions and low recurrence rates in high-risk rCDI. These findings support precision microbiome therapeutics targeting ecosystem function rather than taxonomic complexity. Controlled trials are ongoing. (clinicaltrials.gov; NCT06306014).},
}

@article {pmid42754030,
year = {2026},
author = {Yang, M and Luo, Y and Wu, S and Jia, W and Chen, H and He, F and Cheng, R},
title = {Oral supplementation of 6'-sialyllactose in early-life enhances cognitive function in mice via modulating gut microbiota and promoting brain myelination.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-29049},
pmid = {42754030},
issn = {1525-3198},
abstract = {This study aimed to investigate the effects of early-life oral supplementation with 6'-sialyllactose (6'-SL) on neurobehavioral development in mice and the potential mechanisms involving the microbiota-gut-brain (MGB) axis. Neonatal mice received daily oral gavage of saline or 6'-SL from birth to postnatal day (PND) 21. Behavioral tests (Y-maze, open field, light-dark box, forced swim test) were conducted from PND 37-41. Fecal metagenomics and short-chain fatty acid (SCFA) levels were assessed, and brain gene expression was analyzed by RNA sequencing and reverse transcription quantitative real-time PCR (RT-qPCR) at PND 21 and PND 42. Our findings revealed that 6'-SL supplementation enhanced cognitive function in growing mice, as evidenced by improved performance in the Y-maze test. Early-life 6'-SL supplementation exerts profound and sustained regulatory effects on the gut microbiota and SCFA. At PND 21, 6'-SL enriched Akkermansia muciniphila and elevated acetate, isobutyrate, and isovalerate, while suppressing Enterococcus. At PND 42, Akkermansia muciniphila and Escherichia were further enriched, while Alistipes and Duncaniella were inhibited. Meanwhile, acetate, isobutyrate and propionate levels remained elevated. Notably, these changes were observed not only at the end of the intervention but also persisted at PND 42, indicating a sustained long-term effect of 6'-SL supplementation. In contrast, most myelin genes were altered only to a small extent at PND 21, compared with their marked upregulation in the PFC at PND 42 (Mbp, Mog, Olig1, Sox10, Egr2, Vegfa). Correlation analysis revealed that the abundance of Akkermansia muciniphila was positively correlated with isobutyrate levels, Escherichia showed a positive correlation with propionate levels, while Enterococcus was negatively correlated with acetic acid. These SCFA were positively associated with myelin gene expression. Further, these genes were positively associated with cognitive performance, suggesting their potential involvement in cognitive function. Thus, 6'-SL enhances spatial cognition in early-life mice through a mechanism involving gut microbiota and SCFA modulation, subsequent upregulation the transcription of prefrontal myelination-related gene. This study provides novel insights into the mechanisms by which 6'-SL regulates early brain development via the MGB axis and offers critical theoretical support for nutritional supplementation strategies in infancy.},
}

@article {pmid42754171,
year = {2026},
author = {Palanga, E and Pinel-Galzi, A and Filloux, D and Pinault, A and Kpemoua, KE and Ali, E and Julian, C and Richard, D and Poulicard, N and Roumagnac, P and Hébrard, E},
title = {New insights into phylogenetic diversity of maize yellow mosaic virus revealed by viral sequences from Togo.},
journal = {Virus research},
volume = {},
number = {},
pages = {199804},
doi = {10.1016/j.virusres.2026.199804},
pmid = {42754171},
issn = {1872-7492},
abstract = {Maize yellow mosaic virus (MaYMV) (Polerovirus MAYMV, Solemoviridae) is an emerging virus with a global distribution in maize and other cereals. Transmitted by aphids in a circulative, non-propagative manner, MaYMV forms icosahedral particles and possesses a positive-sense, single-stranded RNA genome. Three distinct phylogenetic groups of MaYMV have been described in Asia, East Africa and Latin America. In this study, 19 genomes from Togo and Burkina Faso were sequenced using Virion-Associated Nucleic Acid-Based Metagenomics (VANA) combined with classical RT-PCR to constitute the first dataset of West African MaYMV genomic sequences. Phylogenetic analyses of global dataset of 92 genomic sequences revealed two sub-lineages within the African strain. We also identified 15 recombinant MaYMV genomes involving intra- and inter-continental exchanges. A comparative analysis of non-recombinant sequences was conducted and identified 19 molecular signatures in proteins P0, P1, P4 and P5. Notably, residue K/R 253 in P5 was lineage-specific and is located near conserved polero- and luteovirus residues known to be involved in aphid interactions, suggesting a potential role in viral transmission.},
}

@article {pmid42754770,
year = {2026},
author = {Petri, RM and Ricci, S and Jelinski, M and Hund, A},
title = {Observational study of the microbiome of perforated abomasal ulcers in unweaned beef calves in Canada.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42754770},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Abomasum/microbiology/pathology ; *Cattle Diseases/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Stomach Ulcer/veterinary/microbiology ; Canada ; Bacteria/classification/genetics/isolation & purification ; Male ; *Microbiota ; },
abstract = {In western Canada, perforating abomasal ulcers (AU) are generally diagnosed postmortem in beef calves up to 2 months of age. Certain microbes have been associated with AU, but the evidence is circumstantial. Thus, analyzing the abomasal microbiome in calves with and without AU may provide insight into the etiology of the disease. Using 16S rRNA gene sequencing, abomasal tissues from Western Canadian beef calves, with (n = 27) and without AU (n = 17), were analyzed for microbial diversity. No significant differences were seen between microbiomes of AU and CON calves despite numerical differences in abundance. Therefore, a subsample of 18 tissues (12 AU, 6 CON) were analyzed using untargeted metagenomic sequencing for determination of phylogeny, and the presence of antimicrobial resistance genes (ARGs). Staphylococcaceae (1.5%), Campylobacteraceae (1.4%) and Enterobacteriaceae (1.4%) were seen across all samples. Differential abundance analysis revealed Streptomyces spp. REN17 to be less abundant in AU calves, suggesting a potential association between Streptomyces spp. and calf gut health. An ARG associated with polymyxin resistance was found to be differentially abundant in calves with a history of antimicrobial therapy. Although differences were observed in the predicted metabolic functions among groups, none reached statistical significance. In our study, no consistent microbial signature associated with AU was identified, despite the differential abundance of individual taxon, nor did prior antimicrobial therapy associate to the growth of specific microbiota. To better understand the potential role of the abomasal microbiota in AU etiology and the impact of early life interventions in beef calves, a larger sample size is needed.},
}

Animals
Cattle
*Abomasum/microbiology/pathology
*Cattle Diseases/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Stomach Ulcer/veterinary/microbiology
Canada
Bacteria/classification/genetics/isolation & purification
Male
*Microbiota

@article {pmid42754901,
year = {2026},
author = {Zhou, C and Fu, B and Hou, X and Wu, WM and Khan, A and Li, C and Han, H and Li, X},
title = {Untapped enzymatic potential: dehalogenase- and peroxidase-driven PVC degradation by gene carriers in Tibetan plateau pikas.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42754901},
issn = {2049-2618},
mesh = {Animals ; *Lagomorpha/microbiology/metabolism ; Biodegradation, Environmental ; *Polyvinyl Chloride/metabolism ; *Hydrolases/metabolism/genetics ; Tibet ; Rhodococcus/enzymology/genetics/metabolism ; *Microplastics/metabolism ; *Peroxidase/metabolism/genetics ; *Bacteria/classification/genetics/enzymology/isolation & purification ; },
abstract = {BACKGROUND: Wide distribution of polyvinyl chloride microplastics (PVC-MPs) has been documented in remote regions such as the Qinghai-Tibet Plateau (QTP). Microbial degradation of plastics is frequently coupled with lignocellulose-degrading enzymatic machinery. As a ubiquitous biological sampler on the QTP, the herbivore plateau pika (Ochotona curzoniae), which harbors diverse lignocellulose-degrading enzymes, represents a promising reservoir for novel PVC-degrading enzymes.

RESULTS: In this study, a PVC-MPs feeding trial of plateau pikas revealed gut microbiota recruitment of plastic degraders. Subsequent enrichment experiment yielded a PVC-degrading consortium that depolymerized PVC into long-chain alkanes, with Rhodococcus and Leifsonia identified as PVC-response specialist and generalist, respectively. Multi-omics analysis supported a putative degradation pathway initiated by haloalkane dehalogenase (HLD) and involving oxidases. Furthermore, novel RhHLD (from Rhodococcus MAG) released 11.5 mg L[-1] chloride ions from PVC films, whereas dye-decolorizing peroxidase LeDyP from Leifsonia MAG generated PVC-degrading intermediates. Analysis of 39 metagenomic datasets further confirmed that haloalkane dehalogenase and dye-decolorizing peroxidase are prevalent in the gut of wild pikas.

CONCLUSIONS: This study elucidates the PVC-degrading potential of herbivore gut microbiota and expands the catalytic toolkit for plastic bioremediation, underscoring the bioprospecting potential in extreme ecosystems Video Abstract.},
}

Animals
*Lagomorpha/microbiology/metabolism
Biodegradation, Environmental
*Polyvinyl Chloride/metabolism
*Hydrolases/metabolism/genetics
Tibet
Rhodococcus/enzymology/genetics/metabolism
*Microplastics/metabolism
*Peroxidase/metabolism/genetics
*Bacteria/classification/genetics/enzymology/isolation & purification

@article {pmid42755253,
year = {2026},
author = {Gupta, KH and Israni, AK and Onyeaghala, G},
title = {Gut microbial metabolism of immunosuppressive drugs: from metagenomic associations to functional enzyme biomarkers.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001314},
pmid = {42755253},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: Inter-individual variability in immunosuppressant exposure remains a major challenge in transplantation. Pharmacogenomics and host-related factors contribute to this variability, with increasing evidence suggesting that the gut microbiome is also an important determinant of drug metabolism. This review summarizes recent advances in microbiome-mediated metabolism of immunosuppressive drugs like tacrolimus and mycophenolate and highlights emerging functional approaches to identify clinically relevant microbial enzymes.

RECENT FINDINGS: Microbial β-glucuronidases contribute to the enterohepatic recirculation of mycophenolic acid by deconjugating mycophenolic acid glucuronide, influencing systemic exposure and gastrointestinal toxicity. In parallel, gut bacteria such as Faecalibacterium prausnitzii can directly metabolize tacrolimus into less active metabolites, potentially contributing to variability in drug exposure and dose requirements. Recent studies further demonstrate that metaproteomic and enzyme activity-based approaches provide greater functional resolution than metagenomics alone for identifying microbiome-associated drug metabolism pathways.

SUMMARY: Current evidence supports a significant role for the gut microbiome in immunosuppressant pharmacokinetics and functional microbial enzymes represent promising biomarkers of immunosuppressant disposition. Moving beyond gene-level associations toward the functional characterization of microbial enzymes through the integration of metaproteomics, metabolomics, and enzyme activity assays with pharmacokinetic modeling may facilitate development of microbiome-based biomarkers and microbiome-guided precision dosing strategies in transplantation. Future integration of microbiome-derived functional data into therapeutic drug monitoring and pharmacokinetic models may improve individualized immunosuppressive therapy and transplant outcomes.},
}

@article {pmid42755618,
year = {2026},
author = {Li, L and Luo, Y and Liu, S and Liang, C and Ruan, H and Peng, P and Huang, Z},
title = {Genome-resolved gut metagenomics identifies an Escherichia coli-Collinsella signature associated with Wagner 4 gangrenous diabetic foot ulcers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1893357},
pmid = {42755618},
issn = {1664-3224},
mesh = {Humans ; *Escherichia coli/genetics ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Gastrointestinal Microbiome/genetics ; *Actinobacteria/genetics ; Metagenome ; Male ; Female ; Feces/microbiology ; },
abstract = {Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1-3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1-3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. To prioritize robust candidates, we combined two complementary approaches: random forest (RF) stability selection, which identified 24 MAGs with reproducibly high classification importance across resampled folds, and covariate-adjusted MaAsLin2 differential-abundance testing. Intersecting the results of both approaches prioritized three MAGs supported by each method: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG signature (out-of-bag AUC = 0.703) retained much of the discriminatory information captured by the broader 24-MAG RF classifier, with concordant, opposing abundance directions across classifier interpretation, differential-abundance testing, and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli-Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response, or recovery.},
}

Humans
*Escherichia coli/genetics
*Diabetic Foot/microbiology
*Metagenomics/methods
*Diabetes Mellitus, Type 2/complications/microbiology
*Gastrointestinal Microbiome/genetics
*Actinobacteria/genetics
Metagenome
Male
Female
Feces/microbiology

@article {pmid42755623,
year = {2026},
author = {Xu, Z and Wang, Y and Zhang, X and Guo, F and Chen, J and Geng, H and Li, Y and Gao, Y},
title = {Application of metagenomic next-generation sequencing in gastrointestinal infections in children after allogeneic hematopoietic stem cell transplantation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1868295},
pmid = {42755623},
issn = {2235-2988},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Child, Preschool ; Male ; Child ; Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Viruses/classification/isolation & purification/genetics ; Transplantation, Homologous/adverse effects ; *Gastrointestinal Diseases/microbiology/diagnosis/etiology/virology ; Diarrhea/microbiology ; Adolescent ; Bacterial Infections/microbiology/diagnosis ; },
abstract = {BACKGROUND: Gastrointestinal infections are the leading cause of death for pediatric patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT). Conventional microbiological testing (CMT) often fails to identify the pathogens, resulting in delayed diagnosis and poor treatment outcomes. Metagenomic next-generation sequencing (mNGS) offers a promising method that does not require cultivation, but its application in this specific situation has not been fully studied.

METHODS: 185 fecal samples were collected from 96 children who underwent HSCT and suffered from diarrhea. All samples were simultaneously subjected to mNGS and CMT testing. The diagnostic performance, pathogen spectrum and prevalence of gastrointestinal infection pathogens were systematically analyzed and compared.

RESULTS: Compared with CMT, mNGS detected significantly more bacteria, viruses and atypical pathogens. Among the pathogens detected by mNGS in the 185 fecal samples, the predominant bacteria were Pseudomonas spp. (28 cases), Clostridioides spp. (28 cases), Campylobacter spp. (25 cases), Acinetobacter spp. (16 cases), and Staphylococcus aureus (13 cases). Clostridioides spp. exhibited a significantly higher detection rate in fecal samples from patients receiving CsA-based combination therapy (p=0.01099) and those with bone marrow from unrelated donors (p=0.03188). Pseudomonas aeruginosa (p = 0.03038) and Campylobacter spp.(p = 0.00549) were detected significantly more frequently in patients within the early phase (1-30 days). The detection rate of Adenovirus was markedly decreased during the intermediate phase (31-100 days) (p = 0.01458). Furthermore, Polyomavirus showed a significantly increased detection rate in patients with short-term diarrhea (1-3 days) (p=0.03451).

CONCLUSION: Our findings highlight the substantial superiority of mNGS over CMT in pathogen detection, with a broader coverage encompassing bacteria, viruses, and atypical organisms. It uncovers complex polymicrobial and viral-bacterial co-infections, delineates infection dynamics linked to immune reconstitution. Integrating mNGS into the diagnostic workflow holds great potential for enabling precision antimicrobial therapy and improving outcomes in this high-risk population.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Child, Preschool
Male
Child
Feces/microbiology/virology
Infant
Bacteria/classification/isolation & purification/genetics
Viruses/classification/isolation & purification/genetics
Transplantation, Homologous/adverse effects
*Gastrointestinal Diseases/microbiology/diagnosis/etiology/virology
Diarrhea/microbiology
Adolescent
Bacterial Infections/microbiology/diagnosis

@article {pmid42755660,
year = {2026},
author = {Wei, W and Yan, P and Wang, F and Wang, Q and Li, C and Bai, X and Zhang, Y and Bao, Y and Li, J and Yu, K},
title = {Sarcopenia in patients with active ulcerative colitis: associations with serum metabolites and gut microbiota.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1942104},
pmid = {42755660},
issn = {2296-861X},
abstract = {BACKGROUND: Sarcopenia has garnered increasing attention in ulcerative colitis (UC) owing to its association with adverse clinical outcomes; however, its pathogenesis in the context of UC remains insufficiently characterized.

METHODS: Hospitalized patients aged 18-70 years with active UC were consecutively enrolled at the Department of Gastroenterology, Peking Union Medical College Hospital, and age-matched healthy controls (HCs) were recruited. Body composition was assessed by bioelectrical impedance analysis (BIA), and muscle strength was evaluated by handgrip strength. Sarcopenia was diagnosed in accordance with the Asian Working Group for Sarcopenia (AWGS) 2025 consensus. Serum high-sensitivity C-reactive protein (hsCRP) of patients was recorded at admission. Intestinal barrier function was evaluated by serum diamine oxidase (DAO). Serum metabolites were profiled by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Gut microbiota composition and functional pathways were analyzed using metagenomic sequencing.

RESULTS: Fifty-seven patients with active UC and 35 HCs were enrolled. The prevalence of sarcopenia, myopenia, and low muscle strength in the UC cohort was 40.4, 50.9, and 64.9%, respectively. Serum hsCRP was significantly higher in UC patients with sarcopenia (p = 0.011), whereas serum DAO showed no significant difference between UC patients with and without sarcopenia. Primary bile acids (BAs), conjugated BAs, and conjugated primary BAs were significantly increased, while hippuric acid, valerylcarnitine, and 2-methylbutyrylcarnitine were significantly decreased, in sarcopenic relative to non-sarcopenic UC patients (all p < 0.05). However, the association between serum hippuric acid and sarcopenia was not significant after adjusting for disease activity and hsCRP. At the genus level, Bacteroides and Streptococcus were the most prominently decreased and increased taxa in sarcopenic UC patients, respectively. Metagenomic functional analysis revealed that the relative abundance of the protein digestion and absorption pathway was significantly lower in sarcopenic UC patients (p = 0.030).

CONCLUSION: UC-related sarcopenia exhibits notable associations with systemic inflammation, gut dysbiosis, and perturbations in circulating metabolites, including BAs and acylcarnitines.},
}

@article {pmid42755900,
year = {2026},
author = {Wu, T and Wang, G and Xu, N and Xu, K and Chen, G},
title = {Case Report: A cluster of cases with rash associated with Chlamydia pneumoniae infection.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1922611},
pmid = {42755900},
issn = {2296-858X},
abstract = {We report a case of clustered rashes among teenagers associated by Chlamydia pneumoniae (CP) infection. Most patients only presented with rashes without significant fever or other respiratory tract symptoms. Metagenomic next-generation sequencing (mNGS) of blood samples identified the culprit - the nucleic acid sequence of CP was detected in the peripheral blood of the index case. The results of targeted next-generation sequencing (t-NGS) of throat swabs further supported the presence of CP. After antibiotic treatment, the patients' conditions improved. In this case, we should have a systematic understanding of rashes and mucositis caused by respiratory tract infections to facilitate further diagnosis and treatment.},
}

@article {pmid42755932,
year = {2026},
author = {Pascual, J and Martínez-Blanch, JF and Amaro, C and Roig, FJ},
title = {Editorial: Advances in immunity and microbiome: exploring key interactions and innovations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1933468},
doi = {10.3389/fimmu.2026.1933468},
pmid = {42755932},
issn = {1664-3224},
}

@article {pmid42756064,
year = {2026},
author = {Zhang, G and Huang, Y and Gong, Z and Xu, C and Ding, X and Cai, W and Wu, J},
title = {Multi-omics analyses unveil gut microbiota and metabolites signatures in deoxycholic acid-associated intestinal inflammation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917982},
pmid = {42756064},
issn = {1664-302X},
abstract = {OBJECTIVE: High-fat diet (HFD) is closely related to the increased incidence of inflammatory bowel disease (IBD), and excessive fecal deoxycholic acid (DCA) induced by HFD makes significant contribution to the colonic inflammation. However, the precise mechanisms remain unclear. This study aims to explore the association between DCA-induced alteration of gut microbiota as well as related metabolites and intestinal inflammation.

METHODS: Wild-type C57BL/6 J mice were orally administrated with or without 0.2% DCA for 12 weeks, then the alteration of gut microbiota signature and fecal metabolites were analyzed by metagenomic sequencing and widely-targeted metabolomics, respectively. The colonic tissue injury was confirmed by histopathological analysis and pro-inflammatory cytokines production was determined by qPCR and ELISA.

RESULTS: DCA administration induced gut microbiota dysbiosis and fecal metabolomic profile disturbance, accompanied with significantly increased expression of pro-inflammatory cytokines in intestine, including TNF-α, IL-6 and IL-1β, and obvious tissue damage. Specifically, α-diversity of gut microbiota was greatly reduced by excessive DCA, and abundance analysis together with linear discriminant analysis of effect size (LEfSe) identified Bacteroides and Desulfovibrio as potential biomarkers of DCA exposure. Excessive DCA significantly decreased the abundance of Eubacterium plexicaudatum, bacterium 1xD42-87 and Ruminococcus flavefaciens, which were positively correlated with the downregulation of multiple metabolites reported to possess anti-inflammatory activities, especially indoles, vitamin D3 and alpha-CEHC. Meanwhile, DCA administration dramatically increased the abundance of Parabacteroides distasonis and Bacteroide acidifacien, which were positively correlated with the upregulation of metabolites reported to have pro-inflammatory properties, including multiple bile acid metabolites such as chenodeoxycholic acid, glycochenodeoxycholic acid and lithocholic acid. Spearman correlation analysis emphasized the important effects of aforementioned microbiota and metabolites in the association between DCA and intestinal inflammation.

CONCLUSION: Our study revealed that excessive DCA led to concurrent alterations of gut microbiota and metabolites, which exhibited significant correlations with intestinal inflammation, suggesting a potential indirect regulatory pathway that may involve gut microbiota. Targeting DCA-related gut microbiota or metabolites might represent a promising intervention for HFD-associated colonic inflammation.},
}

@article {pmid42756159,
year = {2026},
author = {Jiang, P and Zhou, M and Liao, Y and Du, W and Liu, M},
title = {Associations of the gut mycobiome and its cross-kingdom interactions with estrus return in post-weaning sows revealed by metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1892244},
pmid = {42756159},
issn = {1664-302X},
abstract = {Post-weaning estrus return is a critical determinant of reproductive efficiency in the swine industry. While the gut microbiome, particularly bacteria, has been significantly associated with estrus return in sows, the role of the gut mycobiome and its cross-kingdom interactions with bacteria in this context remains largely unexplored. Here, we employed fecal metagenomics to characterize the gut mycobiome in 85 sows and investigated its association with post-weaning estrus return. A total of 22 fungal species were significantly associated with estrus return. Normal-return sows were characterized by increased abundance of Arxiozyma slooffiae (formerly Kazachstania slooffiae) and decreased abundances of Malassezia pachydermatis and Alternaria rosae. Moreover, we uncovered cross-kingdom interactions between fungi and bacteria associated with estrus return, where Arxiozyma slooffiae showed a positive correlation with Prevotella spp. enriched in normal-return sows. These interactions were predicted to involve the exchange of metabolites, including Fe[2+], thiamine, and nicotinate. Fungal biomarkers demonstrated good discriminatory power for distinguishing normal-return and non-return sows (AUC = 0.906), and the combination with bacterial biomarkers further enhanced the performance (AUC = 0.947). Integrated multi-omics analysis revealed extensive associations between gut fungi and hormones and hormone-related compounds, as well as microbial functional pathways. Notably, Arxiozyma slooffiae was positively correlated with phytoestrogens (including daidzein and genistein) and the steroid hormone biosynthesis pathway but negatively correlated with testosterone. Collectively, these findings provide comprehensive insights into the role of the gut mycobiome and its cross-kingdom interactions in sow reproductive performance.},
}

@article {pmid42756787,
year = {2026},
author = {Fang, Q and Gong, X and Mao, S and Ren, D and Chen, H and Pan, M and Huang, X and Chen, J and Chen, X and Wu, H and Zheng, Y},
title = {Pilot Surveillance Program on Pneumonia with Public Health Risk - Shanghai Municipality, China, 2024-2025.},
journal = {China CDC weekly},
volume = {8},
number = {35},
pages = {1096-1103},
pmid = {42756787},
issn = {2096-7071},
abstract = {China's surveillance for pneumonia of unknown etiology, established in 2004, is vital for identifying novel pathogens early. However, limited cases have been reported, indicating potential challenges regarding sensitivity and operational efficiency.

WHAT IS ADDED BY THIS REPORT?: A pilot surveillance program to detect pneumonia with public health risk was implemented in Shanghai between October 2024 and July 2025. The system was established using an optimized workflow involving refined case definitions, tiered laboratory testing network, and joint expert risk assessment process. Forty-six cases were identified in medical institutions at different levels, demonstrating the system's operational feasibility.

The pilot provides a framework for a proactive paradigm for monitoring emerging respiratory threats. Future surveillance should prioritize identifying case clusters and specific epidemiological links (e.g., suspicious animal contact and travel history). Applying advanced diagnostics, including metagenomic sequencing, and integrating multi-source data with information technology are crucial next steps for building a more responsive surveillance system.},
}

@article {pmid42756829,
year = {2026},
author = {Elmaghrabi, MM and Alghofaili, SA and Mahmoud, MM and ElKharashy, AK and Kulsum, SN},
title = {Metagenomic-driven predictive biosafety and contamination traceability in stem cell manufacturing: Translating outbreak genomics into regenerative medicine.},
journal = {Regenerative therapy},
volume = {33},
number = {},
pages = {101170},
pmid = {42756829},
issn = {2352-3204},
abstract = {Stem cell manufacturing and regenerative medicine laboratories are highly vulnerable to microbial contamination due to complex processing workflows, extensive manipulation, prolonged culture conditions, and continuous environmental exposure. Conventional microbiological methods remain fundamental for laboratory quality control; however, they may underestimate concealed resistance determinants, microbial diversity, contamination pathways, and transmission dynamics. Recent advances in metagenomic sequencing have transformed outbreak investigation, resistome characterization, and genomic surveillance, providing unprecedented opportunities for contamination monitoring and biosafety management. This review proposes a translational biosafety framework that integrates metagenomic surveillance with contamination traceability systems in stem cell manufacturing and regenerative medicine laboratory environments. The review discusses contamination challenges, limitations of conventional microbiological diagnostics, metagenomic surveillance approaches, predictive biosafety concepts, genomic traceability systems, corrective and preventive action (CAPA) integration, and future artificial intelligence (AI)-assisted monitoring strategies. Lessons from sequencing-based outbreak investigations involving multidrug-resistant microorganisms highlight the potential utility of metagenomic surveillance for early detection of contamination, microbial source attribution, resistome characterization, environmental monitoring, and contamination traceability. Integrating sequencing-guided diagnostics with laboratory traceability systems and CAPA-based quality management may shift biosafety practices from reactive contamination control toward proactive predictive biosurveillance. The proposed framework may strengthen contamination prevention, improve manufacturing reproducibility, support regulatory compliance, and enhance the reliability of stem cell processing and regenerative medicine applications. Future studies are needed to standardize sequencing-guided biosafety workflows and evaluate their implementation in academic, research, and clinical-grade stem cell manufacturing laboratories.},
}

@article {pmid42756860,
year = {2026},
author = {Yao, C and Lei, L and Wang, W and Jiang, L and Yang, W and Sheng, Y and Liu, Z and Qian, X},
title = {Global intI1 abundance quantifies livestock antimicrobial-resistance risk.},
journal = {Environmental science and ecotechnology},
volume = {33},
number = {},
pages = {100759},
pmid = {42756860},
issn = {2666-4984},
abstract = {Livestock farming environments are major reservoirs of antimicrobial resistance (AMR), yet scalable genetic indicators that quantitatively capture AMR risk remain limited. The class 1 integrase gene intl1 is a hallmark of class 1 integrons (CL1s), which couple gene capture with horizontal transfer capacity and have emerged as leading candidates. However, their suitability as a direct proxy for livestock-associated AMR risk has not been rigorously tested at scale. Here we show that the abundance of intI1 functions as a robust quantitative indicator of livestock-associated AMR risk. Using a custom Class 1 Integrase Database expanded by 63.5% and integrating 4017 livestock metagenomes, 9625 livestock-derived isolate genomes, and approximately 1.2 million human clinical isolate genomes, we demonstrate that intI1 abundance tracks host- and geography-dependent risk patterns, that livestock CL1s carry compact, conserved resistance-cassette arrays matching clinical spectra, and that nearly all are plasmid-borne, with their efficient dissemination facilitated by Tn402, ISCR, and IS110 family elements. A random-forest model trained on these data predicts global intI1 abundance and associated risk with high accuracy (R [2] = 0.93), revealing persistent hotspots across Asia, sub-Saharan Africa, and South America over two decades. These findings establish intI1 as a practical, single-platform proxy that can be incorporated into One Health surveillance and early-warning systems.},
}

@article {pmid42758039,
year = {2026},
author = {Agudelo, C and Nsereko, M and Ainebyona, A and Andama, A and Castro, R and Leung, SRM and Nakafeero, J and Nannyonga, G and Nolan, K and Teran, L and Wambi, P and Young, MG and Kato-Maeda, M and Cattamanchi, A and Jaganath, D and Wobudeya, E and Wolf, AR},
title = {Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciag573},
pmid = {42758039},
issn = {1537-6591},
abstract = {BACKGROUND: Stool-based molecular tests provide noninvasive options for pediatric tuberculosis (TB) diagnosis, but have lower sensitivity compared to sputum-based tests. Untargeted metagenomic sequencing (mNGS) on stool could improve sensitivity and identify new gene targets for molecular testing.

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

RESULTS: We analyzed 176 stool samples of children with a median age of 3.6 years (IQR, 1-6 years). Against the MRS, the sensitivities of mNGS with positive TB defined as ≥ 1, 2, or 5 sequence fragments were 35.5% (95% CI 19%-55%), 25.7% (12%-45%), and 19.4% (13%-25%) respectively, and specificities 92.64% (87%-96%), 97% (93%-99%), and 99.3% (96%-100%). Stool Xpert Ultra had similar sensitivity (22.6%) to stool mNGS considering all samples tested. In a head-to-head comparison, stool mNGS had lower sensitivity than stool Xpert Ultra (38.5% vs. 53.8%, difference -15.3%, 95% CI 14-68 to 25-81). mNGS utilized rRNA, virulence proteins and membrane proteins not targeted in current PCR-based platforms.

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

@article {pmid42758297,
year = {2026},
author = {Xu, H and Zhong, T and Li, J},
title = {The link of oral microbiome diversity to stroke risk: Evidence from the National Cohort Study in the United States.},
journal = {The International journal of neuroscience},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/00207454.2026.2736054},
pmid = {42758297},
issn = {1563-5279},
abstract = {OBJECTIVE: To assess whether oral microbiome diversity and periodontal health are independently associated with stroke prevalence in a U.S. adult cohort, with implications for risk stratification in physical medicine and rehabilitation.

METHODS: We analyzed cross-sectional data from 4,438 adults in the National Health and Nutrition Examination Survey (NHANES) 2009-2012, using survey-weighted logistic regression to evaluate associations between stroke and oral microbiome β-diversity (unweighted UniFrac), α-diversity (Shannon, Simpson), and clinical periodontal measures (probing depth, clinical attachment loss, and tooth count), adjusting for age, sex, race/ethnicity, education, income, smoking, alcohol consumption, body mass index, and diabetes.

RESULTS: In crude models, each 1-mm increase in mean probing depth was associated with higher stroke odds (odds ratio [OR] = 1.89, 95% confidence interval [CI] = 1.39-2.56), as was each 1-mm increase in clinical attachment loss (OR = 1.50, 95% CI = 1.32-1.71); each additional tooth was associated with lower odds (OR = 0.91, 95% CI = 0.88-0.94). After stepwise adjustment, attachment loss (OR = 1.23, 95% CI = 1.04-1.46; P = 0.017) and tooth count (OR = 0.96, 95% CI = 0.92-0.99; P = 0.024) remained significant, whereas probing depth did not (OR = 1.30, 95% CI = 0.90-1.88; P = 0.156). A threshold effect was observed at approximately 1.46 mm for probing depth. β-Diversity clusters did not differ in stroke prevalence after adjustment (global P = 0.61), and neither α-diversity index was significant in the stepwise- or fully-adjusted models (Shannon fully-adjusted OR = 1.29, 95% CI = 0.97-1.72; P = 0.081). Periodontal associations were consistent across sex and age strata; the non-significant findings in younger participants were attributable to limited statistical power.

CONCLUSION: Clinical periodontal measures, particularly attachment loss and tooth count, were associated with stroke prevalence independently of traditional cardiovascular risk factors, whereas oral microbiome diversity indices were not. These measures may serve as readily accessible markers for refining stroke risk assessment. The cross-sectional design precludes causal inference, and findings require validation in prospective cohorts with adjudicated stroke outcomes and metagenomic profiling before clinical translation. Nevertheless, these results support integrating oral health assessment into routine stroke risk evaluation and highlight periodontal inflammation as a potentially modifiable contributor to cerebrovascular disease.},
}

@article {pmid42758523,
year = {2026},
author = {Lan, G and Li, X and Lu, Z and Zhang, Y and Feng, F and Liu, J and Wu, W and Liu, J and Zhou, Y and Gu, J and Ma, R and Qi, D},
title = {Gut Microbiome Functional Reprogramming Reflects Divergent Social Strategies in a Wild Primate.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70185},
pmid = {42758523},
issn = {1749-4877},
support = {2025JZG01//Foundation for Non-Invasive Research on Golden Snub-Nosed Monkeys in Baihe Nature Reserve/ ; CAZG2025C13//Chengdu Research Base of Giant Panda Breeding/ ; 32570615//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a critical interface between host physiology and environmental challenges, yet its role in mediating behavioral strategies in socially complex mammals remains unclear. Using metagenomic sequencing of wild golden snub-nosed monkeys (Rhinopithecus roxellana), we investigated how social status (one-male unit [OMU] leaders vs. all-male unit [AMU] individuals) and seasonal variation (winter-spring [WS] and summer-autumn [SA]) shape gut microbial structure and function. We found that seasonal shifts drive primary microbial restructuring, but social status exerts a strong influence, particularly during the SA mating season. OMU leaders maintained stable microbial communities enriched in energy conservation and cellular maintenance pathways including methane metabolism and peptidoglycan biosynthesis. In contrast, AMU individuals exhibited highly plastic microbiomes potentially suited for competition, with enhanced functions in environmental sensing (e.g., flagellar assembly and two-component systems) and nitrogen metabolism. AMU gut microbiomes also showed reduced diversity in SA, indicating specialization for competitive readiness. These results demonstrate that the gut microbiome is functionally compartmentalized by social status, providing distinct metabolic toolkits that align with divergent behavioral strategies-investment in unit fitness for OMU leaders versus risk-taking for AMU individuals. Our study reveals the gut microbiome is closely associated with social adaptation in primate societies, serving as a dynamic indicator of divergent behavioral strategies.},
}

@article {pmid42758594,
year = {2026},
author = {Khoo, BY and Sadasiv, MS},
title = {A clinician's guide to infectious diseases diagnostics: principles, pitfalls, and stewardship.},
journal = {Postgraduate medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/postmj/qgag134},
pmid = {42758594},
issn = {1469-0756},
abstract = {Accurate interpretation of infectious diseases diagnostic tests requires a comprehensive understanding of test principles, performance characteristics, and the cognitive discipline of diagnostic stewardship. While contemporary modalities range from traditional culture to high-throughput metagenomics, postgraduate trainees may struggle to reconcile complex laboratory data with the clinical context. This educational primer aims to bridge the gap between laboratory science and bedside decision-making. We first distinguish between analytical (limit of detection) and clinical sensitivity, emphasizing how disease prevalence dictates predictive values. We then move beyond theoretical limitations to identify clinician-modifiable pre-analytical variables, such as specimen collection techniques, that directly affect diagnostic test performance. A core framework for Diagnostic Stewardship is introduced, focusing on the test-treatment threshold and the critical distinction between organism detection and active infection. Through illustrative case studies, we apply clinical reasoning strategies to resolve common pitfalls, including serological cross-reactivity, polymerase chain reaction inhibition in critical samples, and prozone phenomena. Enhanced diagnostic competence requires more than memorizing test characteristics; it demands the integration of stewardship principles, awareness of cognitive biases, and active collaboration with other healthcare professionals. This review provides a structured approach for trainees to navigate the complexities of modern infectious disease diagnostics. Key messages Infectious disease tests should be interpreted in light of the syndrome, pre-test probability and the timing, and type of specimen tested. NAAT positivity detects nucleic acid, not necessarily viable organisms or active disease. Most avoidable microbiological diagnostic errors begin before the sample reaches the laboratory. Discordant test results should trigger a deliberate diagnostic pause and, when needed, discussion with the laboratory.},
}

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42759123,
year = {2026},
author = {Guo, X and He, Z and Wang, X and Ren, H and Ren, B and Zhang, J and Liu, P and Song, Z and Zhao, B},
title = {Sustained nitrogen release and nitrogen-cycling functional genes jointly shape NH3-N2O loss trade-offs under long-term controlled-release fertilization.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130951},
doi = {10.1016/j.jenvman.2026.130951},
pmid = {42759123},
issn = {1095-8630},
abstract = {Simultaneously mitigating ammonia (NH3) volatilization and nitrous oxide (N2O) emissions without compromising crop productivity remains a critical challenge in sustainable nitrogen management. Drawing on a long-term field experiment established in 2013, this study integrated multi-year gaseous nitrogen loss measurements with metagenomic sequencing to assess the performance of polymer-coated fertilizer (PCF) and sulfur-coated fertilizer (SCF) relative to conventional urea (CU) in intensive maize production. Both coated urea treatments substantially suppressed NH3 losses relative to CU, with PCF achieving consistent reductions of 72.3%-92.8% and SCF showing more variable reductions of 28.8%-89.7%. However, sustained nitrogen release from coated urea concurrently stimulated N2O production, with increases of 8.3%-114.3% under PCF and 15.5%-88.9% under SCF. Critically, NH3 mitigation substantially outweighed the N2O penalty, enabling PCF to reduce the combined NH3 and N2O losses by 39.8%-69.5% and yield-scaled losses by 45.9%-70.9%, respectively, while enhancing crop yield by 4.7%-11.2%. Soil enzyme assays and metagenomic analyses suggested that NH3 suppression was associated with reduced urease activity and enrichment of archaeal ammonia oxidation and downstream nitrification genes under PCF, whereas elevated N2O emissions were correlated with sustained soil inorganic nitrogen replenishment that appeared to override concurrent declines in denitrification genes. These findings suggest that PCF reduces the combined NH3 and N2O losses while sustaining crop productivity, although the N2O penalty outweighed the climate benefit of NH3 mitigation in three of four years. The net environmental performance of controlled-release fertilizers therefore depends on the indicators evaluated and was associated with nitrogen release dynamics and the corresponding functional gene networks.},
}

@article {pmid42759371,
year = {2026},
author = {Ge, L and Yang, S and Zeng, X and Huang, Y and Lai, H and Wang, Y and Mei, Y and Zhao, N},
title = {Unlocking the metabolomics and metagenomics code of phenyl moiety chromophore profiles underlying naturally occurring yellow color of dry-salted radish.},
journal = {Food chemistry},
volume = {529},
number = {},
pages = {151190},
doi = {10.1016/j.foodchem.2026.151190},
pmid = {42759371},
issn = {1873-7072},
abstract = {The aim of this study was to investigate the molecular basis and the role of biotic and abiotic factors in the development of naturally occurring yellow color of dry-salted radish by analyzing color, physicochemical properties, amino acid profile, glucosinolates and myrosinase activity, metabolomics and metagenomics. Results showed that metabolites of phenyl-containing amino acids (Trp, Phe, Try, carboline, indole, pyrrolidone), curcuminoids (curcumin, gingerol), polyphenols and flavonoids were the major chromophores for color of dry-salted radish. Additionally, chromophore formation involved assistance with pyrrole-containing compounds, glucosinolates and isothiocyanates. Low Aw (<0.7) was the key abiotic factor to facilitate the chromophore formation by enriching the genera of Lactiplantibacillus, Lacticaseibacillus, Pediococcus, Levilactobacillus and Halomonas, and promoted gene functions linked to metabolism of Trp, Phe, Try, curcuminoids, polyphenol, flavonoid, phenyl, pyrrolidone, transport of amino acid and ions, hyperosmotically responsive system. Capitalizing on this finding would empower the development of dry-salted vegetables with appealing and stable color.},
}

@article {pmid42748823,
year = {2026},
author = {Yang, R and Liu, C and Liu, J and Liu, Y and Wang, C and Guo, D and Zhou, J and Tai, X and Zhang, G and Zhang, B},
title = {Antibiotic resistome patterns across wheat soil microdomains under cadmium exposure and their associations with rhizosphere metabolite profiles.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143642},
doi = {10.1016/j.jhazmat.2026.143642},
pmid = {42748823},
issn = {1873-3336},
abstract = {The co-contamination of heavy metals and antibiotic resistance genes (ARGs) poses an increasing challenge to agroecosystems, yet its relationships with rhizosphere metabolism and microbial communities remain poorly understood. We integrated metagenomic sequencing, untargeted metabolomics, and absolute qPCR in a wheat pot experiment to characterize resistome patterns across unplanted bulk soil (O), root-zone soil (PS), and rhizosphere soil (PR) under three Cd treatments. At the booting stage, observed ARG subtype richness and total TPM-normalized ARG abundance were higher in root-associated compartments, whereas responses to cadmium within PR were heterogeneous and non-monotonic. Absolute qPCR broadly supported enrichment of selected resistance genes in root-associated soils. Community analyses identified Pseudomonadota and Actinomycetota as potential ARG-associated taxa. Metabolomic differentiation between PR and O was substantially greater than the differences among Cd treatments within PR, while metabolite-ARG associations partly reflected compartment-level covariation. ARG and metal resistance gene abundances showed strong covariation relationship, and contig-level analysis identified genetic contexts consistent with potential linkage among resistance determinants across both control and Cd-amended treatments. Overall, spatial differentiation among soil microdomains was more consistent than treatment-associated Cd patterns. These findings identify the wheat rhizosphere as an important zone of ARG enrichment under Cd exposure while highlighting the need for host-resolved and functional validation.},
}

@article {pmid42749142,
year = {2026},
author = {Zhang, Y and Wang, H and Ling, Y and Wang, H and Wang, S and Wang, X and Liu, F},
title = {Carbon-sulfur regulation for deep nitrogen removal in Arundo donax straw/elemental sulfur-amended surface flow constructed wetlands: Metagenomic and metabolomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135874},
doi = {10.1016/j.biortech.2026.135874},
pmid = {42749142},
issn = {1873-2976},
abstract = {Plant-derived carbon can sustain heterotrophic denitrification in low carbon-to-nitrogen (C/N) constructed wetlands, but how the relative loading of elemental sulfur (S[0]) and solid carbon regulates mixotrophic nitrogen removal remains unclear. In this study, six surface flow constructed wetlands (SFCWs) amended with different Arundo donax straw/S[0] ratios were operated for 96 days to treat simulated secondary effluent. Under the tested conditions, the 1:1 ratio (450 g/450 g) showed the best performance, with a stable-period total inorganic nitrogen (TIN) removal efficiency of 77.6 ± 5.7 % and a relatively low net SO2-4 accumulation per unit TIN removed (1.47 mg SO2-4/mg N). Insufficient S[0] weakened late-stage NO-3-N removal; the excess S[0] configuration showed HS[-]/S[2-] accumulation and was associated with a higher risk of dissimilatory nitrate reduction to ammonium without improving nitrogen removal; and carbon-limited configurations showed insufficient electron donor availability. Vertical profiles showed that carbon release and NO-3-N reduction were concentrated in the lower layers. Metagenomic analysis showed that the 1:1 configuration enriched representative functional taxa, including hydrolytic/fermentative bacteria (Clostridium), sulfur-transforming bacteria (Sulfuritalea, Thiobacillus), and nitrogen reduction-related taxa (Azonexus). Functional gene abundances suggested greater potential for anaerobic carbon oxidation and sulfur transformation in the 1:1 configuration. Metabolomic analysis indicated substrate-associated changes in sulfur-related metabolites and in pathways related to nicotinamide adenine dinucleotide and coenzyme A. Network analysis further showed that carbon metabolism and sulfur transformation were closely associated with nitrogen removal performance. These results provide new insights into substrate regulation of mixotrophic denitrification in SFCWs treating low C/N wastewater.},
}

@article {pmid42749360,
year = {2026},
author = {Zhang, K and Gorelik, MG and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G},
title = {Divergent microbial preludes to necrotising enterocolitis defined by gut phages and bacterial resistomes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338976},
pmid = {42749360},
issn = {1468-3288},
abstract = {BACKGROUND: Translating microbiome correlations into robust predictive features for complex gut disorders remains elusive, partly due to oversimplified models of pathogenesis and neglect of the virome, a key player in microbial ecosystems. Necrotising enterocolitis (NEC), a devastating disease of preterm infants with no reliable clinical predictors, exemplifies this challenge.

OBJECTIVE: To determine the predictive potential of the gut prophageome and polymicrobial aetiologies for NEC.

DESIGN: We applied integrated metagenomic and metatranscriptomic analyses and machine learning to 1825 longitudinal stool samples from 43 preterm infants who later developed NEC and 86 gestational age-matched and birthweight-matched controls across three US hospitals. We characterised gut prophageome acquisitions and their association with clinical exposures, including antibiotics, diet and pharmacotherapies. To predict NEC risk, we integrated pre-onset prophageome, antibacterial resistome and bacteriome profiles with neonatal pathology, stratifying the cohort by disease onset timing (early: ≤40 days; late: >40 days) for separate analysis.

RESULTS: NEC cases exhibited distinct viral diversity trajectories before disease onset. Early-onset NEC was best predicted by phage-bacterial interaction signatures (75% accuracy, 81% sensitivity). Metatranscriptomics revealed increased phage DNA abundance with low gene expression, suggesting a lysogenic lifestyle that may stabilise pathobionts. These phages encode metabolic genes potentially enhancing pathobiont resilience. Late-onset NEC was best predicted by antibacterial resistome profiles (83% accuracy).

CONCLUSION: The gut prophageome serves as both a source of pre-symptomatic predictive signals and an active modulator of NEC pathogenesis, with distinct microbial mechanisms driving early-onset and late-onset disease. These polymicrobial etiologies inform strategies for early detection, risk stratification and the development of microbiome-targeted preventive and therapeutic interventions.},
}

@article {pmid42749361,
year = {2026},
author = {Qian, Z and Han, J and Lyu, B and Ainiwaer, A and Zhao, Q and Wang, S and Cheng, J and Li, Y and Sun, Y and Zhang, X and Lu, Y},
title = {Longitudinal gut microbiome dynamics during immunotherapy identify microbial features of clinical benefit in advanced primary liver cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339115},
pmid = {42749361},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiome has been linked to immune checkpoint inhibitor (ICI) outcomes, but the temporal dynamics of microbial communities during treatment remain poorly characterised.

OBJECTIVE: To characterise gut microbiome trajectories during ICI therapy and evaluate whether on-treatment microbial states improve the identification and generalisability of pretreatment biomarker signatures.

DESIGN: We performed a large prospective longitudinal shotgun metagenomic study of 315 patients with advanced primary liver cancer receiving ICI-based therapy, profiling 777 serial stool metagenomes collected at baseline and at approximately 3-month intervals on treatment. Responders (durable clinical benefit ≥6 months) contributed extended follow-up beyond 18 months. On-treatment windows were used for feature discovery; baseline-trained models were evaluated across all nine public ICI cohorts (n=1204).

RESULTS: Responders showed higher baseline alpha diversity and distinct community structure. Longitudinal profiling revealed marked ecological remodelling during therapy in both response groups, characterised by reduced network connectivity, increased modularity and strong time point specificity of discriminatory species. Using the on-treatment contrast at ~6 months (T2) as a discovery window, we identified a 16-species panel. A baseline model built from this panel outperformed models based on baseline-only feature discovery and generalised across nine public ICI studies. The resulting gut microbiome-derived immunotherapy outcome score stratified overall and progression-free survival in the discovery cohort (HRs 0.49 and 0.44) and across multiple external datasets, including stable-disease subsets.

CONCLUSION: The gut microbiome undergoes structured ecological remodelling during ICI therapy; on-treatment longitudinal windows improve pretreatment signature portability and support microbiome-guided stratification in immuno-oncology.},
}

@article {pmid42749373,
year = {2026},
author = {Gao, H and Shen, J and Chen, D and Mol, BW and Hu, W and Liang, Z and Bai, X and Han, X and Zhu, J and Wang, H and Liu, X and Su, C and Chen, Y and Weng, R and Liu, Y and Li, W and Zhang, D},
title = {Labour induction in low-risk women at 39 weeks of gestation: a randomised trial in China (LIRIC) - protocol of an open label, randomised controlled trial.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e123251},
pmid = {42749373},
issn = {2044-6055},
mesh = {Humans ; Female ; Pregnancy ; China ; *Labor, Induced/methods ; *Cesarean Section/statistics & numerical data ; Randomized Controlled Trials as Topic ; Infant, Newborn ; Gestational Age ; Adult ; Infant ; Pregnancy Trimester, Third ; Perinatal Mortality ; },
abstract = {INTRODUCTION: The A Randomized Trial of Induction Versus Expectant Management (ARRIVE) first demonstrated that elective induction of labour (IOL) at 39 weeks in low-risk pregnancies reduced the likelihood of caesarean section (CS) without compromising perinatal safety; however, the generalisability of these findings remains debated, leading to uncertainty in clinical practice. The Labour Induction in Low-risk Women at 39 Weeks of Gestation: a Randomised Trial in China (LIRIC) aims to evaluate whether 39-week elective IOL reduces CS rates compared with expectant management while exploring its impact on infant neurodevelopment and multiomics profiles.

METHODS AND ANALYSIS: This is a single-centre, open-label, randomised controlled trial in China. A total of 1074 low-risk pregnant women (nulliparous or multiparous) will be randomly assigned (1:1 ratio) to either 39-week IOL or expectant management. The primary outcome is the CS rate. Secondary outcomes include a composite of severe neonatal morbidity and perinatal mortality and infant neurodevelopmental scores (Bayley Scales of Infant Development; Bayley-4 and Ages and Stages Questionnaires; ASQ-3), among others. Data analysis will follow the intention-to-treat principle. Biospecimen will be collected for metagenomic and metabolomic analyses, with results to be reported separately.

ETHICS AND DISSEMINATION: The protocol has been approved by the Ethics Committee of Women's Hospital, School of Medicine, Zhejiang University. Informed consent will be obtained from all participants. Results will be disseminated via peer-reviewed journals, and standardised infant developmental reports will be provided to participants to enhance study benefit.

TRIAL REGISTRATION NUMBER: NCT07082530.},
}

Humans
Female
Pregnancy
China
*Labor, Induced/methods
*Cesarean Section/statistics & numerical data
Randomized Controlled Trials as Topic
Infant, Newborn
Gestational Age
Adult
Infant
Pregnancy Trimester, Third
Perinatal Mortality

@article {pmid42749445,
year = {2026},
author = {Agusetyaningsih, I and Lestari, DA and Pandupuspitasari, NS and Setiaji, A and Philco, SV and Sugiharto, S},
title = {Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {3},
pages = {100775},
doi = {10.1016/j.jgeb.2026.100775},
pmid = {42749445},
issn = {2090-5920},
abstract = {Antibiotic resistance is a growing global health concern, with poultry systems acting as important reservoirs of antibiotic resistance genes (ARGs). However, resistome and functional profiles of indigenous chickens raised under traditional systems remain underexplored. This study aimed to characterize the antibiotic resistome, virulence factor genes, and metabolic potential of gut microbiota in Indonesian Kedu chickens using a shotgun metagenomic approach. Digesta samples from five gastrointestinal segments of 21 healthy adult chickens were analyzed through high-throughput sequencing. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Antibiotic Resistance Genes Databases (ARDB), while virulence factors and functional genes were annotated using Virulence Factor Database (VFDB), Clusters of Orthologous Groups (COG), and Carbohydrate-Active EnZymes (CAZy) databases. Results revealed a diverse resistome dominated by multidrug resistance and efflux pump mechanisms, with prominent genes associated with fluoroquinolone, tetracycline, β-lactam, and glycopeptide resistance. The detection of clinically relevant ARGs suggests that genetic determinants associated with antimicrobial resistance are present in the gut microbiota of traditionally raised Kedu chickens, although metagenomic data alone cannot determine whether these genes are actively expressed or confer phenotypic resistance. Virulence factor analysis showed functions related to adherence, immune evasion, iron acquisition, quorum sensing, and efflux activity, reflecting strong microbial adaptability. Functional profiling demonstrated enrichment in translation, carbohydrate and amino acid metabolism, genome maintenance, and cell envelope biogenesis. Additionally, CAZyme analysis indicated a high capacity for complex polysaccharide degradation, supporting efficient utilization of fiber-rich traditional diets. In conclusion, this study provides a comprehensive metagenomic overview of antibiotic resistance and functional potential in Kedu chicken gut microbiota, emphasizing the importance of incorporating indigenous poultry into antimicrobial resistance surveillance within a One Health framework.},
}

@article {pmid42750334,
year = {2026},
author = {Zhang, S and Xiao, L and Mo, G},
title = {[Progress in the application of bronchoalveolar lavage fluid in the diagnosis of infectious lung diseases].},
journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology},
volume = {42},
number = {9},
pages = {844-850},
pmid = {42750334},
issn = {1007-8738},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/cytology/immunology ; *Lung Diseases/diagnosis/microbiology/immunology ; },
abstract = {Bronchoalveolar lavage fluid (BALF) contains diverse cellular components and pathogens, directly reflecting the local immune status at sites of pulmonary infection. By detecting pathogens such as bacteria, fungi, and viruses within these samples and analyzing changes in the immune cell composition and cytokine levels, it will help to assess the immune microenvironment of infected lung regions and to predict disease prognosis. In recent years, the application of artificial intelligence in BALF analysis has significantly enhanced the efficiency of cell classification and counting. Combined with molecular diagnostic methods such as metagenomic next-generation sequencing, this approach deeply explores the diagnostic value of immune cells, pathogens, and their molecular characteristics in BALF for infectious lung diseases. It will provide more precise support for early disease identification, personalized treatment, and clinical decision-making.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology/cytology/immunology
*Lung Diseases/diagnosis/microbiology/immunology

@article {pmid42750336,
year = {2026},
author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YPR},
title = {Alamandine/MrgD pathway modulates gut-bone marrow axis in ageing.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70656},
pmid = {42750336},
issn = {1476-5381},
support = {AG056881/NH/NIH HHS/United States ; P20GM103442/NH/NIH HHS/United States ; U42 OD010918/NH/NIH HHS/United States ; },
abstract = {BACKGROUND AND PURPOSE: Ageing is associated with colon epithelial barrier disruption and up-regulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in ageing via modulating gut-BM axis.

EXPERIMENTAL APPROACH: Mice, 2-3 (Young) or 22-24 months (Old), were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Faecal microbiome was analysed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Caecal or serum bacterial metabolites were analysed and the caecal supernatants (CS) were tested for myelopoietic potential.

KEY RESULTS: MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in ageing was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels and this was antagonized by NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the microbiota with decreased Bacillota/Bacteroidota in ageing. Ala decreased the CD80[+] and increased CX3CR[+] macrophages in the Old colons. Old-CS induced myelopoiesis in BM cells with higher number of pro-inflammatory macrophages, which was prevented by Ala treatment.

CONCLUSIONS AND IMPLICATIONS: Targeting Ala/MrgD pathway is a promising approach for ameliorating the inflammatory stress in ageing by restoring homeostasis in the gut-BM inter-organ communication.},
}

@article {pmid42750565,
year = {2026},
author = {Pothikamjorn, TL and Gonzales, JA},
title = {Molecular biomarker profiling in noninfectious uveitis: a chronological review of discovery.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
pmid = {42750565},
issn = {1531-7021},
abstract = {PURPOSE OR REVIEW: Noninfectious uveitis (NIU) encompasses a heterogeneous group of immune-mediated intraocular inflammatory diseases whose complexity has driven systematic molecular biomarker discovery. This review presents NIU molecular biomarkers organized by biological category; autoantigens, human leukocyte antigens (HLA) and genetic markers, cellular immune subsets, cytokines, chemokines, and multiomics platforms including proteomics, microbiome metagenomics, metabolomics, and single-cell transcriptomics with each category presented in strict chronological order of landmark discovery.

RECENT FINDINGS: We present a review organized along two nested timelines. Categories are presented in the order they historically emerged in the field, and within each category, landmark discoveries appear in chronological sequence. This allows the reader to trace how each biomarker category evolved: from foundational autoantigen identification in experimental uveitis models, through the genomic revolution of HLA association studies, into cellular immunophenotyping, cytokine profiling of aqueous humor, chemokine mapping of intraocular trafficking, and finally the emerging omics platforms that may potentially anchor precision medicine in NIU. Each biomarker is paired in line with its linked targeted therapeutic.

SUMMARY: Biomarker research has transformed the understanding of NIU from a clinically defined syndrome into a group of molecularly distinct immune disorders. Advances spanning autoantigens, genetics, immune-cell profiling, cytokines, chemokines, and multiomics have revealed novel pathogenic mechanisms and therapeutic targets. Integration of these biomarkers with targeted therapies may accelerate the transition toward precision medicine in uveitis care.},
}

@article {pmid42750609,
year = {2026},
author = {Ma, X and Zhong, L and Wang, T and Zhang, Y and Liu, X and Ma, S and Dang, D},
title = {Clinical and etiological characteristics of severe community-acquired pneumonia: A two-center retrospective analysis from Xi'an and Jiaxing in China.},
journal = {The Journal of international medical research},
volume = {54},
number = {9},
pages = {3000605261489324},
doi = {10.1177/03000605261489324},
pmid = {42750609},
issn = {1473-2300},
mesh = {Humans ; *Community-Acquired Pneumonia/microbiology/epidemiology ; Male ; Female ; Retrospective Studies ; China/epidemiology ; Aged ; Severity of Illness Index ; Anti-Bacterial Agents/therapeutic use ; Sputum/microbiology ; *Community-Acquired Infections/microbiology ; },
abstract = {ObjectiveThis study was conducted to evaluate the baseline clinical profile, causative pathogens, and treatment patterns of severe community-acquired pneumonia across two medical centers (Xi'an and Jiaxing) from January 2023 to August 2025.MethodsWe extracted data regarding medical profile, demographic characteristics, comorbidities, laboratory parameters, treatments during hospitalization, and outcomes for these patients from electronic records. Pathogens were detected using a combination of sputum culture/throat-swab polymerase chain reaction with metagenomic next-generation sequencing or targeted next-generation sequencing.ResultsAmong the 204 severe community-acquired pneumonia patients, majority were men (72.55%, 95% confidence interval: 66.05%-78.21%); the age range of the population was 65-79 years (41.18%, 95% confidence interval: 34.65%-48.03%), and chronic obstructive pulmonary disease was the predominant chronic pulmonary condition, present in 28.92% of the study participants. Laboratory evaluations revealed high illness severity scores (Acute Physiology and Chronic Health Evaluation II score: 19.00 (14.00, 24.00) and Sequential Organ Failure Assessment score: 7.00 (6.00, 10.00)). Pathogens were identified using metagenomic next-generation sequencing or targeted next-generation sequencing of blood/sputum/bronchoalveolar lavage fluid and polymerase chain reaction of sputum culture/throat-swab in 117 and 85 cases, respectively. Klebsiella pneumoniae was the most common pathogen, present in 20.10% of the participants (95% confidence interval: 15.18%-26.13%), followed by coronavirus 2019 (16.18%, 95% confidence interval: 11.76%-21.85%), and influenza A virus (12.75%, 95% confidence interval: 8.85%-18.02%). Most frequently administered medicines were β-lactam/β-lactamase-inhibitor combinations (89.22%) and carbapenems (60.78%). All patients received respiratory support, with 15.69% undergoing continuous renal-replacement therapy and 5.39% receiving extracorporeal membrane oxygenation. The in-hospital mortality rate was 38.73% (79/204, 95% confidence interval: 32.31%-45.56%).ConclusionSevere community-acquired pneumonia, which is most often caused by K. pneumoniae in our region, regularly complicates chronic obstructive pulmonary disease and other chronic pulmonary diseases, requires broad-spectrum antibiotics and life-support, and is associated with a relatively high mortality rate.},
}

Humans
*Community-Acquired Pneumonia/microbiology/epidemiology
Male
Female
Retrospective Studies
China/epidemiology
Aged
Severity of Illness Index
Anti-Bacterial Agents/therapeutic use
Sputum/microbiology
*Community-Acquired Infections/microbiology

@article {pmid42750770,
year = {2026},
author = {Saha, S and Dutta, M and Bosu, A},
title = {Reframing Technology and Ethics in Corneal Xenotransplantation: A Scoping Review of Standards and Safety in Ophthalmology.},
journal = {Health care science},
volume = {},
number = {},
pages = {},
pmid = {42750770},
issn = {2771-1757},
abstract = {Xenotransplantation offers a potential solution to the critical global organ shortage by allowing the transplantation of organs from non-primate animals to humans. To address the critical barriers of biological safety, zoonotic infections, and immunological rejection, this review evaluates current innovations in genetically engineered donor species strategies and assesses existing ophthalmological standards, employing specific expression of human regulatory proteins (hCD46/hCD55) and genetically modified triple knockout (GGTA1/B4GalNT2/CMAH), biophysical thresholds, porcine cytomegalovirus screening, bacterial/mycotic cultures, and DNA sequencing for unidentified organisms. Employing a snowball strategy across PubMed Central, ResearchGate, and Wiley Online Library, 47 articles were selected and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews. The feasibility of xenotransplantation relies heavily on advancements in donor technology and genotype transparency, animal husbandry and biosafety, infectious testing and surveillance, recipient monitoring and lifetime surveillance, biosafety incident and response plan, data governance, sharing and oversight, and animal welfare and social license, necessitating pathogen observation, biosecure storage, bioexclusion monitoring, and good manufacturing practice-style manual, quantitative polymerase chain reaction for porcine cytomegalovirus, porcine reproductive and respiratory syndrome virus, hepatitis E virus, alongside porcine endogenous retrovirus-A/B/C; metagenomic sequencing initially, followed by 1, 3, 6, and 12 months, and subsequently once every year, systematic and preliminary persistent sampling evaluations, independent data safety monitoring board, collaborative guidelines, encrypted databases, and data retention. The integration of endothelium-protective human genes, including hA20 or hHO-1, into genetically altered donor corneas in non-human primate xenografts, is expected to minimize initial post-transplant endothelial cell density loss by ≥ 20% compared to existing models. While clustered regularly interspaced short palindromic repeats-based modifications offer transformative potential for xenotransplantation, their reliability currently depends on establishing stringent biosafety standards.},
}

@article {pmid42750901,
year = {2026},
author = {Musleh, L and Montilli, M and Ammendolia, MG and Sciarra, A and Riccioli, A and Maurizi, L and Longhi, C},
title = {More than an infection: the ecological puzzle of recurrent urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1927507},
pmid = {42750901},
issn = {2235-2988},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology ; Recurrence ; Microbiota ; Reinfection/microbiology ; Host Microbial Interactions ; Dysbiosis ; Urinary Tract/microbiology ; },
abstract = {Recurrent urinary tract infections (rUTIs) represent one of the most common infectious conditions worldwide, yet their pathophysiology extends far beyond repeated episodes of acute bacterial cystitis. Increasing evidence indicates that recurrence may arise through overlapping mechanisms including reinfection from intestinal or periurethral reservoirs, intracellular bacterial persistence, microbial dysbiosis, impaired mucosal immunity and chronic inflammatory remodelling of the bladder microenvironment. Current diagnostic frameworks remain largely based on symptom-based definitions and standard urine culture, approaches that incompletely capture the biological complexity of recurrent disease. This limitation is evident even at the definitional level, where clinically pragmatic categories often fail to reflect the heterogeneous mechanisms underlying recurrence. Advances in expanded urine culture techniques, metagenomics and metabolomics have reshaped the understanding of the urinary tract as a dynamic ecological system interconnected with vaginal, intestinal and prostatic microbial compartments. These approaches have identified diverse microbial communities, virulence-associated functional profiles and host-microbe interactions linked to recurrence-prone phenotypes. Significant challenges continue to persist in elucidating the biological mechanisms driving recurrence. Addressing these gaps is essential to improve disease characterization and support the development of more effective diagnostic and therapeutic approaches.},
}

Humans
*Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology
Recurrence
Microbiota
Reinfection/microbiology
Host Microbial Interactions
Dysbiosis
Urinary Tract/microbiology

@article {pmid42751327,
year = {2026},
author = {De La Hoz, A and Kovac, V and Woolley, AE and Issa, NC and Letourneau, A and Baden, LR and Hammond, SP and Little, JS},
title = {Plasma Microbial Cell-Free DNA Sequencing for the Diagnosis of Chronic Disseminated Candidiasis in Patients with Hematologic Malignancies.},
journal = {Open forum infectious diseases},
volume = {13},
number = {9},
pages = {ofag543},
pmid = {42751327},
issn = {2328-8957},
abstract = {Diagnosis of chronic disseminated candidiasis (CDC) is frequently delayed because clinical manifestations are nonspecific and conventional diagnostic tests have limited sensitivity. We describe a series of 19 CDC cases in which plasma microbial cell-free DNA sequencing was performed due to diagnostic uncertainty. Results influenced antifungal management in most cases.},
}

@article {pmid42751339,
year = {2026},
author = {Segura, MG and Schwem, B and Sakamuri, RM and Grimes, CZ and Horne, M and Wanger, A and Truong, TT and Lieberman, JA and Litvinseva, AP and Ostrosky-Zeichner, L and Smith, DJ},
title = {Molecular Evidence of Autochthonous Environmental Acquisition of Fonsecaea Pediatric Infection in the United States.},
journal = {Open forum infectious diseases},
volume = {13},
number = {9},
pages = {ofag529},
pmid = {42751339},
issn = {2328-8957},
abstract = {Fonsecaea species cause chromoblastomycosis and phaeohyphomycosis, but links between environmental exposure and infection are poorly defined. We describe a 4-year-old boy with finger swelling after oak tree laceration in Houston, Texas. Broad-range polymerase chain reaction identified F. pedrosoi or F. monophora, and metagenomic sequencing of tree bark and soil detected Fonsecaea DNA.},
}

@article {pmid42751541,
year = {2026},
author = {Victor, MP and Al Shehri, N and Grevskott, DH and Alarif, WM and Ali, AM and Marathe, NP},
title = {High-throughput sequencing dataset of raw and treated wastewater from Jeddah, Saudi Arabia.},
journal = {Data in brief},
volume = {68},
number = {},
pages = {113174},
pmid = {42751541},
issn = {2352-3409},
abstract = {Wastewater is a major point source of pollution and antimicrobial resistance (AMR) in the environment. The aim of this study was to determine the microbiota and antimicrobial resistance genes present in both the influent and effluent from a biological wastewater treatment plant situated in Jeddah Second Industrial City, Saudi Arabia, using metagenomics. Water samples were collected, and the DNA extracted from these samples was subjected to metagenomic sequencing (one influent and one effluent) using Illumina NovaSeq. Our analysis yielded ∼88 Gigabases. The predominant bacterial genera identified were Actinomycetota, Psuedomonadota, and Bacillota, and β-lactamases emerged as the most common class of resistance genes. Eventhough these are unreplicated single observations they are expected to be a valuable resource for researchers focusing on wastewater studies, especially in the middle East, offering insights into bacterial diversity and the spectrum of resistomes associated with these microbial communities.},
}

@article {pmid42751774,
year = {2026},
author = {Shao, J and Hung, W and Yin, P and Huang, P and Zhao, W and Yu, L and Tian, F and Chen, W and Xu, J and Zhai, Q and Li, J and Zhao, J},
title = {Efficacy of Bifidobacterium animalis subsp. lactate BL-99 in relieving functional constipation: a randomized placebo-controlled clinical trial.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03175c},
pmid = {42751774},
issn = {2042-650X},
abstract = {Current therapies for functional constipation (FC) often exhibit limited long-term efficacy. Probiotics, particularly Bifidobacterium animalis subsp. lactis BL-99 (BL-99), may offer a novel approach to alleviate FC symptoms. This randomized, double-blind, placebo-controlled trial (No. WXSY-YXLL-AF/SC-11/01.0) enrolled 41 FC patients who completed the full 6-week study. Participants were randomly assigned to receive either BL-99 (1 × 10[11] colony-forming units per day) or placebo for 4 weeks in this population trial. After completing the 4-week intervention period, administration was discontinued and participants entered a 2-week observation following-up period for continued monitoring. Primary endpoint data collected after trial completion were the changes in the Patient Assessment of Constipation Symptoms (PAC-SYM, 12-item scale) score, evaluated on the first day (0 day), the 28th day (week 4), and the 42th day (week 6). Secondary outcomes included fecal metagenomic profiling to evaluate gut microbiota alterations. After 4 weeks of intervention, the BL-99 group demonstrated significant reductions in PAC-SYM scores compared to the placebo, particularly in domains of "abdominal discomfort" (Δ = 1.8 vs. 0.9, p = 0.007) and "pain during defecation" (Δ = 2.1 vs. 1.0, p = 0.003). These improvements persisted at the 2-week post-treatment follow-up (p < 0.05). Metagenomic analysis revealed that BL-99 enriched Bifidobacterium and Faecalibacterium while suppressing Clostridium species, shifting gut microbiota composition closer to that of the healthy controls. Functional annotation highlighted significant downregulation of infection-related pathways (e.g., bacterial invasion and LPS biosynthesis) and metabolic disease-associated pathways (e.g., insulin resistance) in the BL-99 group (q < 0.05). This trial suggests that 4-week BL-99 supplementation effectively alleviates FC symptoms, partially through microbiota modulation and metabolic pathway regulation. The sustained post-treatment effects warrant further investigation into its long-term benefits.},
}

@article {pmid42752346,
year = {2026},
author = {Pothikamjorn, TL and Doan, TA and Hinterwirth, A and Stewart, JM and Gonzales, JA},
title = {Metagenomic Deep Sequencing Identifies Gene Mutations Associated with Chemotherapeutic Resistance in Vitreoretinal Lymphoma.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/09273948.2026.2677102},
pmid = {42752346},
issn = {1744-5078},
abstract = {PURPOSE: To identify gene mutations associated with chemotherapeutic resistance in patients with vitreoretinal lymphoma (VRL) using metagenomic deep sequencing (MDS) of intraocular specimens.

METHODS: Patients with VRL confirmed by cytopathology and immunohistochemistry, flow cytometry, and/or polymerase chain reaction for MYD88, were included. Intraocular specimens underwent MDS of the host genome. Gene mutations were identified and cross-referenced with the Catalogue of Somatic Mutations in Cancer database to determine associations with chemotherapeutic resistance.

RESULTS: Forty-nine patients with VRL underwent MDS, with six specimens from four patients revealing eight gene mutations associated with chemotherapeutic resistance. Four specimens from three patients harbored mutations associated with methotrexate resistance, the mainstay of VRL treatment. In one patient, serial sampling from the initial vitrectomy and two subsequent recurrences revealed distinct resistance-associated mutations at each time point. Despite multi-agent therapy including rituximab, consolidation regimens, and lenalidomide, this patient ultimately succumbed to the disease, whereas the other three patients remained in long-term remission.

CONCLUSIONS: Our findings demonstrated that specific gene mutations associated with chemotherapeutic resistance may be harbored by VRL. The detection of different resistance mutations at sequential time points in one patient may reflect clonal selection, treatment pressure, or variable detection sensitivity. The ability to easily sample ocular fluid and detect different mutations associated with tumor recurrence or persistence may provide insights into tumor pathogenesis and could inform prognosis and influence treatment decisions. These findings establish a foundation for developing targeted PCR assays for identified resistance genes, which could transform clinical practice in VRL.},
}

@article {pmid42752928,
year = {2026},
author = {Maurya, S and Sharma, P and Yadav, BNS and Gupta, GP and Tiwari, N and Yadav, RK},
title = {Fungi to the rescue: recent advances, mechanistic insights and omics-based perspectives in heavy metal mycoremediation.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42752928},
issn = {1432-072X},
mesh = {Biodegradation, Environmental ; *Metals, Heavy/metabolism ; *Fungi/metabolism/genetics ; Multiomics ; Proteomics ; *Environmental Pollutants/metabolism ; },
abstract = {Heavy metal (HM) contamination arising from rapid industrialization poses critical threats to global ecosystem integrity and public health. Conventional physicochemical approaches are limited by high costs, incomplete removal, and toxic waste generation, necessitating sustainable alternatives. Mycoremediation, which harnesses the remarkable, diverse capacities of fungi to tolerate and mitigate HM stress through sophisticated biological mechanisms, has emerged as a promising and sustainable approach to address HM pollution. This review examines the sources and ecotoxicological impacts of HM pollution, alongside the intracellular and extracellular mechanisms underlying fungal tolerance and removal, including biosorption, precipitation, membrane transport, antioxidant defense, chelation, bioaccumulation, and biotransformation. It further synthesizes fungal-based bioremediation strategies, while examining how metagenomic, metatranscriptomic, transcriptomic, proteomic, and metabolomic approaches are advancing understanding of fungal community structure and active detoxification pathways. This work uniquely integrates community- and isolate-level multi-omics data, explicitly bridges mechanistic understanding with omics-driven insights, and extends this into translational roadmap for applied bioremediation.},
}

Biodegradation, Environmental
*Metals, Heavy/metabolism
*Fungi/metabolism/genetics
Multiomics
Proteomics
*Environmental Pollutants/metabolism

@article {pmid42753294,
year = {2026},
author = {Saleh, ZH and El Enbaawy, MI and Kamal, MA and Mahmoud, H and Hassan, M},
title = {Heat stress, respiratory dysbiosis, and poultry pathobiome: A comprehensive review of chronic respiratory disease in chickens.},
journal = {Veterinary microbiology},
volume = {322},
number = {},
pages = {111225},
doi = {10.1016/j.vetmic.2026.111225},
pmid = {42753294},
issn = {1873-2542},
abstract = {The poultry respiratory microbiome is increasingly recognized as a critical determinant of poultry health, mucosal immunity, and host resistance to opportunistic pathogens. Chronic Respiratory Disease (CRD) exerts a severe economic toll on the global broiler industry. While conventionally attributed to specific etiological agents such as Mycoplasma gallisepticum, disease progression is fundamentally tied to broad ecological dysbiosis within the respiratory tract. This comprehensive review synthesizes current knowledge on the functional roles and compositional dynamics of the poultry respiratory microbiome in both healthy and diseased states. Notably, we acknowledge the emerging threat of climate change, elucidating how heat stress physically and immunologically disrupts the respiratory mucosal microenvironment, acting as a primary catalyst for microbiome destabilization and CRD susceptibility. By shifting the paradigm from a single-pathogen model to a comprehensive pathobiome perspective, we detail the microbial shifts that characterize CRD. Furthermore, because investigating this low-biomass environment presents unique analytical challenges, we critically evaluate current technical methodologies. We address critical bottlenecks in sample collection, DNA extraction biases, and the comparative efficacy of 16S rRNA amplicon versus shotgun metagenomic sequencing. Ultimately, this synthesis provides a foundational framework for optimizing diagnostic methodologies and developing microbiome-targeted interventions -such as next-generation probiotics- to mitigate CRD in an era of escalating environmental stressors.},
}

@article {pmid42753435,
year = {2026},
author = {Xue, P and Huang, B and Wang, Y and Zhao, L and Mao, L},
title = {Environmental fate and risk of diverse oxygenated isomeric prothioconazole biotransformation products in soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143509},
doi = {10.1016/j.jhazmat.2026.143509},
pmid = {42753435},
issn = {1873-3336},
abstract = {Isomeric biotransformation products (TPs) of organic pesticides substantially expand structural diversity and may exhibit distinct environmental behaviors compared with their parent compounds. However, the formation mechanisms and ecological risks of such isomers (regioisomers) in soil remain poorly understood. In this study, the triazole fungicide prothioconazole (PTC) was incubated in agricultural soil, and 21 isomeric TPs were identified and classified into six structural groups using high-resolution mass spectrometry (HR-MS) based on diagnostic fragmentation patterns. These secondary oxygenated isomeric TPs were derived from three primary intermediates (PTC-desthio, PTC-dehydrated, and PTC-S-methyl) via site-selective oxygenation. Toxicity predictions indicated substantial variability among isomers, with certain hydroxylated derivatives exhibiting higher predicted ecotoxicity than others, challenging the assumption that biotransformation necessarily leads to detoxification. Metagenomic analysis showed that PTC exposure significantly altered the soil microbial community, enriching genes associated with xenobiotic degradation and central carbon metabolism. Notably, functional microbial shifts, particularly involving the genus Acinetobacter, were strongly associated with specific isomer profiles. These results suggest a potential link between microbial metabolic responses and the formation of structurally diverse isomeric TPs. The widespread occurrence of such isomers highlights that assessments based solely on parent compounds may underestimate the environmental fate and risks of PTC in agroecosystems.},
}

@article {pmid42709897,
year = {2026},
author = {Guss, HD and Francioli, YZ and Grover, EN and Hill, A and Zou, W and Wade, KJ and Pike, H and Gopalan, SS and Yang, L and Bo, Z and Pollock, DD and Carlton, EJ and Castoe, TA},
title = {Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014202},
doi = {10.1371/journal.pntd.0014202},
pmid = {42709897},
issn = {1935-2735},
mesh = {Animals ; Humans ; *Schistosoma japonicum/genetics/isolation & purification/classification ; China/epidemiology ; Genetic Variation ; *Schistosomiasis japonica/epidemiology/parasitology/transmission/prevention & control ; Genome, Helminth ; Snails/parasitology ; Metagenomics ; Disease Eradication ; },
abstract = {In China, sustained snail control, environmental management, and mass drug administration with praziquantel reduced schistosomiasis to near-elimination levels, yet re-emergence in Sichuan Province during the early 2000s exposed vulnerabilities in elimination efforts. We used population genomics to investigate the multi-scale population processes underlying Schistosoma japonicum re-emergence in Sichuan. We sequenced whole genomes from 270 miracidia collected from 53 human hosts across 17 villages in 2007, one year after re-emergence was documented. Population genomic analyses identified a broadly cohesive regional schistosome population with weak geographic structuring. Genome-wide diversity remained substantial, and demographic reconstructions revealed no recent decline in effective population size, suggesting that parasite populations had not undergone regional demographic collapse prior to re-emergence and were likely maintained in non-human reservoir hosts. At finer spatial scales, several villages exhibited reduced genomic diversity and elevated inbreeding, consistent with localized transmission maintained by relatively small founding populations. Estimates of pairwise genetic relatedness revealed dense within-village sibling clusters alongside second- and third-degree relationships spanning villages, and rare first- and second-degree cross-village links, supporting predominantly local transmission embedded within a connected regional transmission network. Genomic inference of minimum reproducing worm pairs identified substantial heterogeneity in host-level worm burden, ranging from one to eleven adult worm pairs, although uneven sampling limited absolute estimates. Together, these findings indicate that parasite persistence in this near-elimination setting was sustained by interacting processes operating across multiple biological scales, including diverse regional parasite populations, localized transmission networks connecting villages, and marked heterogeneity in host-level worm burden. More broadly, this work demonstrates how population genomics can reconstruct otherwise hidden patterns of parasite persistence and transmission, providing a valuable complement to conventional epidemiological surveillance in complex, multi-host parasite systems.},
}

Animals
Humans
*Schistosoma japonicum/genetics/isolation & purification/classification
China/epidemiology
Genetic Variation
*Schistosomiasis japonica/epidemiology/parasitology/transmission/prevention & control
Genome, Helminth
Snails/parasitology
Metagenomics
Disease Eradication

@article {pmid42743804,
year = {2026},
author = {Chen, ZY and Gao, FZ and Li, P and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Multi-omics evidence reveals robust airborne-human resistome connectivity driven by high-risk ARGs and mediated by Staphylococcus.},
journal = {Environment international},
volume = {216},
number = {},
pages = {110525},
doi = {10.1016/j.envint.2026.110525},
pmid = {42743804},
issn = {1873-6750},
abstract = {Airborne microbiomes are considered an important source of human antimicrobial resistance (AMR) exposure, yet multi-omics evidence linking airborne and human nasal resistomes remains limited. Here, we integrated metagenomic sequencing and whole-genome sequencing of antibiotic-resistant Staphylococcus isolates to investigate the connectivity between air and human nasal resistomes in dairy farm environments. Metagenomic taxonomic profiling showed that Staphylococcus was prominent in total suspended particles (TSP) and consistently detected across all samples. Among environmental reservoirs, TSP resistomes exhibited the strongest similarity to human nasal resistomes. This connectivity was supported by multiple lines of evidence, including highly similar resistome profiles, extensive homologous antibiotic resistance gene (ARG) pairs, strain-level similarity of resistant Staphylococcus isolates, and conserved mobile ARG genetic contexts. Notably, this connectivity was primarily driven by high-risk ARGs, while Staphylococcus was frequently associated with mobile ARGs and represented the only shared pathogenic genomes carrying both ARGs and virulence factor genes between airborne and nasal samples. Although lower ARG diversity, nasal resistomes exhibited higher ARG burden, risk scores, antibiotic-resistant bacterial genome abundance, and prevalence of resistant Staphylococcus. Occupational exposure further increased total and high-risk ARG burdens among farm workers. Together, these findings indicate that TSP can serve as an important route of occupational AMR exposure, with high-risk ARGs and Staphylococcus contributing to connectivity between airborne and nasal resistomes. Incorporating the host microbiome may therefore provide a more complete assessment of human-associated AMR exposure within a One Health framework.},
}

@article {pmid42743807,
year = {2026},
author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C},
title = {Involvement of cross-genus phages in bacterial resistance to chlorine disinfection.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126886},
doi = {10.1016/j.watres.2026.126886},
pmid = {42743807},
issn = {1879-2448},
abstract = {Chlorine disinfection resistance in pathogenic microorganisms poses severe environmental concerns and public health risks. While phages play critical roles in host adaptation to environmental stress, how poly-host phages contribute to bacterial resistance to chlorine disinfectants remains poorly understood. Here, we investigated shifts in the population dynamics, transcriptional profiles, and function potentials of cross-genus phage-bacterial communities under exposure to chlorine disinfectants in a continuously operated anaerobic-anoxic-oxic system over a 92-day period, using integrated metagenomic and metatranscriptomic approaches. In the presence and absence of chlorine disinfectants, the genomic abundance and diversity of phage and bacterial communities showed similar variation trends, and the community structures of both exhibited clear differences. A strong significant positive correlation was observed between phage and bacterial diversity under chlorine exposure (R = 0.975, p = 0.00,057), whereas no significant correlation was detected in the absence of chlorine disinfection (R = -0.314, p = 0.613), suggesting that chlorine disinfectants may enhance phage-bacteria interactions. Host-associated phages exhibited high consistency with their corresponding putative hosts in terms of genomic abundance (M[2] = 0.0945, p = 0.001) and transcript abundance (M[2] = 0.3668, p = 0.001), and they were also significantly correlated with cross-genus phages in both genomic abundance (R = 0.97, p < 2.2e-16) and transcript abundance (R = 0.83, p < 2.2e-16), which collectively suggests the critical role of cross-genus phages in the resistance of microbial communities to chlorine disinfectants. Bipartite association network analysis shows that cross-genus phages carry highly homologous genes to their putative hosts and may be involved in the horizontal transfer of these genes among bacteria. These homologous genes are involved in DNA repair, redox balance regulation, environmental stress adaptation and efflux pump functions, suggesting a synergistic role between cross-genus phages and their putative hosts in chlorine resistance. Our findings reveal that cross-genus phages can contribute to the resistance of bacterial communities to chlorine disinfectants, providing the theoretical foundation for evaluating the role of poly-host phages in microbial communities.},
}