@article {pmid42754330,
year = {2026},
author = {Na, SI and Kim, J and Kim, SY and Park, J and Cho, YJ},
title = {SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {9},
pages = {e2606011},
doi = {10.71150/jm.2606011},
pmid = {42754330},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; RS-2023-00301850//Ministry of Education/ ; RS-2026-25491179//Ministry of Science and ICT/ ; 2024ER210600//Korea National Institute of Health research project/ ; },
mesh = {*Microbiota ; Internet ; *Software ; Bacteria/classification/genetics ; *Computational Biology/methods ; Workflow ; Metagenomics/methods ; },
abstract = {Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.},
}

*Microbiota
Internet
*Software
Bacteria/classification/genetics
*Computational Biology/methods
Workflow
Metagenomics/methods

@article {pmid42767308,
year = {2026},
author = {Zhao, Y and Zheng, M and An, J and Xiu, W and Yao, J and Qi, Z and Wu, H and Lv, Y and Liu, X},
title = {Characterization and soil remediation performance of a natural polycyclic aromatic hydrocarbon-degrading bacterial consortium (PD1).},
journal = {Environmental research},
volume = {308},
number = {Pt 2},
pages = {125717},
doi = {10.1016/j.envres.2026.125717},
pmid = {42767308},
issn = {1096-0953},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent and toxic soil contaminants that pose significant risks to environmental and human health. In this study, a natural PAHs-degrading microbial consortium (PD1) was enriched from coal gangue backfill soil using phenanthrene as the sole carbon source. PD1 features Acidovorax and Pigmentiphaga as the dominant functional genera. The consortium achieved 70% phenanthrene removal within 3 days in liquid culture and demonstrated robust soil remediation performance, with 74.7% and 89.5% removal within 3 and 9 days, respectively, significantly outperforming native conditions. PD1 also degraded fluoranthene, pyrene, and benzo[a]anthracene, and exhibited strong tolerance to As(III) at concentrations up to 50 mg/L, while maintaining stable activity during long-term storage at 4°C. Metagenomic and metatranscriptomic analyses, together with the tentative annotation of two early-stage intermediates, supported a proposed major route for PHE degradation in PD1. The cooperative interactions among various functional microorganisms within the consortium drive the efficient degradation of PHE. These results establish PD1 as a robust, synergistic consortium with strong potential for the bioremediation of PAHs-contaminated soils.},
}

@article {pmid42767310,
year = {2026},
author = {Guo, Y and Song, Z and Xie, H and Kong, Q and Bai, L and Zhang, J},
title = {Coupled Salinity-Redox Gradients Shape Dissolved Organic Matter characteristics and Its Linkages with microbial Functional Potential in Intertidal Sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125713},
doi = {10.1016/j.envres.2026.125713},
pmid = {42767310},
issn = {1096-0953},
abstract = {Estuarine intertidal sediments occur in freshwater-seawater mixing zones where hydrological processes simultaneously alter salinity and redox conditions, potentially regulating dissolved organic matter (DOM) transformation and microbial processes. However, how DOM and its interactions with microbial communities respond to salinity and redox gradients in natural intertidal environments remains poorly understood. Here, surface sediments and porewater from the Yellow River Estuary were analyzed by integrating constructed composite salinity and redox indicators, spectroscopy-based two-dimensional correlation analysis, metagenomics, and multivariate statistics. Results showed that overall DOM variation was significantly associated with both gradients, with redox showing stronger links to chromophoric and protein-like components, molecular-weight properties, and redox-sensitive aromatic, phenolic, oxygen-containing structures. In contrast, neither gradient was significantly associated with whole-community taxonomic composition or functional potential, whereas carbon- and nitrogen-related taxa and functions showed environmental associations. Multiple analyses consistently indicated that DOM covaried with selected functional modules, with more reducing conditions linked to DOM accumulation and fermentation-related functions, and higher salinity linked to microbially derived DOM and substrate-utilization functions. Variation partitioning attributed 20.7% of DOM variation and 39.6% of the main joint DOM-microbe pattern to the shared salinity-redox fraction, while redox retained a significant unique association with DOM (20.3%). Exploratory path models further suggested that DOM characteristics may link salinity-redox gradients to selective rather than community-wide microbial functional variation. Together, these findings support considering salinity and redox as a coupled environmental background and highlight DOM chemistry as a potential interface between their variation and selective microbial functional responses in intertidal sediments.},
}

@article {pmid42767353,
year = {2026},
author = {Cao, Y and Peng, K and Zhou, Z and Shang, J and Liu, Z and Gao, Y and Wang, Z and Zhang, D and Li, R},
title = {Alterations in the gut resistomes of endangered wild equids associated with anthropogenic activities: Insights for One Health surveillance.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129195},
doi = {10.1016/j.envpol.2026.129195},
pmid = {42767353},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) are emerging environmental contaminants, but how human-associated management practices are associated with mobile resistomes in endangered wildlife remains poorly resolved. Here, we used fecal metagenomics to compare Przewalski's horses, Mongolian khulans, and domestic horses from Xinjiang, China, including Przewalski's horses from a protected area and a captive-breeding setting under human management. Across 47 fecal metagenomes, we identified 380 ARG subtypes, 23 metal resistance gene (MRG) types, and 26 mobile genetic element (MGE) subtypes. Przewalski's horses and domestic horses carried higher ARG burdens than Mongolian khulans, whereas Mongolian khulans showed a higher MRG burden. Within Przewalski's horses, captive individuals had higher ARG and MGE loads than protected-area individuals, with enrichment of tet(W), lnu(C), vanYG1, transposase genes, and IS91. Co-occurrence networks and structural equation modeling indicated that the captive management setting was positively associated with IS91, which in turn was linked to ARG enrichment and ARG-MRG co-occurrence. Genome-resolved analysis recovered 590 medium- to high-quality metagenome-assembled genomes (MAGs) and revealed that MAGs co-carrying ARGs, MRGs, and MGEs were predominantly assigned to anaerobic gut genera, including Prevotella, Alloprevotella, Cryptobacteroides, and Limivicinus. These findings suggest that human-associated wildlife habitats are associated with increased mobility potential of gut resistomes through the enrichment of MGEs and resistance carrying host bacteria. Endangered equids may therefore act as sentinels for AMR reservoirs at wildlife-human-environment interfaces, supporting ARG and MGE monitoring in protected-area and captive management programs.},
}

@article {pmid42767827,
year = {2026},
author = {Nikitina, D and Suk, KT and Torre, A and Idilman, R and Alvares-da-Silva, MR and Lauridsen, MM and Fagan, AC and Kreivenaite, E and Sharma, SP and Nielsen, EJ and Turan, D and Jahagirdar, V and Michalczuk, MT and Khoruts, A and Bojja, SH and Lee, HW and Skieceviciene, J and Sikaroodi, M and Kupcinkas, J and Gillevet, PM and Bajaj, JS},
title = {Hospitalisation in cirrhosis is linked to distinct gut microbiome structural and functional profiles: a multinational metagenomic study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339378},
pmid = {42767827},
issn = {1468-3288},
abstract = {BACKGROUND: Hospitalisations represent major clinical events in cirrhosis, yet prediction based on clinical variables alone remains limited.

OBJECTIVE: Given the role of the gut microbiome in disease progression, we evaluated whether gut metagenomic profiles are associated with 90-day hospitalisation and provide additional prognostic information beyond clinical features in a multinational outpatient cirrhosis cohort.

DESIGN: We enrolled 679 outpatients with cirrhosis from seven countries and performed stool metagenomic profiling, including taxonomic, functional pathway and antibiotic resistance gene (ARG) analyses, with 90-day follow-up. Machine learning models were developed using clinical and microbiome features for predicting non-elective hospitalisations.

RESULTS: 25% of patients required hospitalisation within 90 days. Hospitalised patients had more advanced cirrhosis, lower microbial diversity which was consistent across countries despite marked variation in microbial composition. Diet had a modest influence on microbiome structure. After adjustment for country, disease severity, cirrhosis aetiology and treatment, 19 bacterial species remained independently associated with hospitalisation, including enrichment of Enterococcus faecium and Veillonella rogosae and depletion of multiple commensal taxa. Functional profiling demonstrated coordinated taxonomic-functional alterations focusing on complex carbohydrate degradation pathways, glycan biosynthesis, lipid and nucleotide salvage pathways and association with antimicrobial resistance mechanisms. The combined clinical-microbiome model significantly outperformed both the clinical-only (area under the curve (AUC) 0.79) and microbiome-only (AUC 0.74) models, achieving an AUC of 0.84.

CONCLUSION: Gut microbiome composition and function are associated with short-term hospitalisation risk and provide additional prognostic information beyond clinical variables in a multicountry cohort. Hospitalisation, regardless of country, is characterised by loss of short-chain fatty acid-producing taxa, functional shifts, ARG and pathway changes.},
}

@article {pmid42767973,
year = {2026},
author = {Han, KH and Yang, J},
title = {Beyond conventional immunosuppression: tailoring perioperative management protocols for clinical xenotransplantation.},
journal = {Clinical transplantation and research},
volume = {},
number = {},
pages = {},
doi = {10.4285/ctr.26.0054},
pmid = {42767973},
issn = {3022-7712},
abstract = {Clinical xenotransplantation offers a conceptually unlimited supply of donor organs, owing to transformative advances in gene-editing technologies. However, the pharmacological and physiological distinctions between allo- and xenotransplantation pose a major challenge. Unlike allografts, xenografts simultaneously trigger complement-amplified humoral rejection, thromboregulatory incompatibility driven by porcine-human molecular mismatch, and species-specific innate inflammatory cascades. However, conventional calcineurin-based immunosuppression provides no meaningful coverage for these pathways. We analyzed these differences to provide the mechanistic foundation for a dedicated perioperative framework. The proposed framework encompasses immunologic assessment; porcine cytomegalovirus (PCMV)/roseolovirus-free donor certification; intensified induction; third-generation anti-CD154 monoclonal antibodies with pharmacokinetically verified trough targets; normothermic machine perfusion with anti-inflammatory perfusate supplementation; and thromboregulatory rescue protocols incorporating tranexamic acid, heparin, and antiplatelet agents. Furthermore, we aimed to address consumptive coagulopathy; targeted suppression of macrophage- and neutrophil-driven innate inflammatory cascades, alongside activation of xenoreactive natural killer cells; and multimodal surveillance integrating flow cytometry, donor-derived cell-free DNA, and metagenomic sequencing for porcine endogenous retrovirus and PCMV monitoring. By combining compassionate-use failure analysis with prospective trial design aligned with the 2026 International Society for Heart and Lung Transplantation consensus statement, this review proposes a standardized perioperative management protocol that is applicable to clinical xenotransplantation.},
}

@article {pmid42767975,
year = {2026},
author = {Burge, K and Velsko, IM and Salazar-García, DC and Uriarte, MH and Lomba Maurandi, J and Warinner, C},
title = {Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70201},
pmid = {42767975},
issn = {1755-0998},
support = {//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; //National Science Foundation/ ; },
mesh = {Animals ; *Microbiota ; *Mouth/microbiology ; *Gene Library ; Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; DNA, Single-Stranded/genetics ; Neanderthals ; *Metagenomics/methods ; },
abstract = {DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (< 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.},
}

Animals
*Microbiota
*Mouth/microbiology
*Gene Library
Humans
*DNA, Ancient
Sequence Analysis, DNA
DNA, Single-Stranded/genetics
Neanderthals
*Metagenomics/methods

@article {pmid42768024,
year = {2026},
author = {Kong, C and Jin, Y and Liu, G and Guo, Y and Guo, F and Ma, Y},
title = {Eggerthella lenta disrupts the gut vascular barrier to drive colorectal cancer liver metastasis.},
journal = {Cell discovery},
volume = {12},
number = {1},
pages = {},
pmid = {42768024},
issn = {2056-5968},
abstract = {Distant metastasis is the leading cause of death in colorectal cancer (CRC), and the gut vascular barrier (GVB) is the first obstacle to hematogenous spread. To investigate whether GVB function is directly influenced by metastasis-associated bacteria, we analyzed two cohorts comprising 20 healthy controls, 82 non-metastatic CRC patients, and 65 patients with liver or lung metastases. Multi-omics approaches (metagenomic sequencing and single-cell RNA sequencing) and gnotobiotic mouse models were employed to examine gut microbes that are linked to GVB disruption and metastasis. Patients with CRC liver metastasis exhibited impaired GVB and bacterial colonization at metastatic sites. Eggerthella lenta was enriched in patients with elevated expression of plasmalemmal vesicle-associated protein-1 (PV-1), a GVB injury marker, and its abundance was correlated with metastasis and recurrence. In vitro and in vivo, E. lenta compromised endothelial tight junction and GVB integrity, enhancing CRC cell migration and liver metastasis. Mechanistically, E. lenta adhered to endothelial cells and activated endoplasmic reticulum (ER) stress via a TLR4-dependent pathway, promoting autophagy and apoptosis. The knockdown of PERK attenuated ER stress, prevented autophagy and apoptosis, and downregulated the expression of ZO-1 and Claudin-5 induced by E. lenta. These findings highlight the clinical potential of microbiota-targeted strategies and PERK inhibition in the treatment of E. lenta-associated CRC metastasis.},
}

@article {pmid42768105,
year = {2026},
author = {Dong, D and Walsh, AM and Vatanen, T and Weingart, G and Khdhiri, M and Stampfer, MJ and Vehik, K and Franzosa, EA and Huttenhower, C and Wang, DD and , },
title = {Gut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42768105},
issn = {2522-5812},
abstract = {Prospective evidence linking early-life microbiome development and host genetics with type 1 diabetes (T1D) risk is limited. Here, we describe how gut microbiome maturation and host genetics influence T1D risk in the TEDDY study. We analysed 12,151 longitudinal metagenomes and host genetic data from 887 children at high genetic risk for T1D followed for up to 6 years. We identify three microbiome maturational patterns: Early Matured, Late Matured and Early Plateaued, driven primarily by non-linear changes in species from the Bifidobacterium and Ruminococcus genera. The Early Matured pattern is enriched in galactose metabolism and exhibits higher production of aromatic amino acids and B-group vitamins at early follow-ups, whereas the Early Plateaued pattern has increased microbial production of branched-chain amino acids. Notably, the Early Plateaued pattern is associated with a threefold elevated risk of T1D, whereas other patterns are not associated with T1D risk. Furthermore, we find that host genetic variants related to antimicrobial and antiviral immune responses modify the association between the Late Matured pattern and T1D risk. These findings highlight the role of early microbial exposures and host genetics in T1D susceptibility.},
}

@article {pmid42768289,
year = {2026},
author = {DeVito, A and Kimm-Drapeau, AL and Higgins, WJ and Montecillo, M and Bernstein, MN and Wright, S and Li, C and Bal, I and Dadhania, DM and Selbach, F and Lee, JR},
title = {Serial Blood Microbiome Profiles in Kidney Transplant Recipients Reveal Evidence of Circulating Gut and Non-Gut Derived Microbial DNA.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70323},
doi = {10.1111/tid.70323},
pmid = {42768289},
issn = {1399-3062},
support = {R21 AI 173849/NH/NIH HHS/United States ; R01DK139249/NH/NIH HHS/United States ; R01AI184528/NH/NIH HHS/United States ; UL1TR002384//National Center for Advancing Translational Sciences of the National Institutes of Health/ ; 539291308//German Research Foundation/ ; },
abstract = {BACKGROUND: In this study, we sought to investigate the utility of 16S rRNA gene sequencing of whole blood in kidney transplant recipients and to assess a link between the gut microbiota and the blood microbiota.

METHODS: We recruited 63 kidney transplant recipients who provided 163 whole blood specimens over the first 140 days after transplantation. We profiled the blood microbiome using 16S rRNA gene sequencing of the V4-V5 hypervariable region. We additionally evaluated the gut microbiota via metagenomic sequencing in a subset of kidney transplant recipients who had matched blood specimens.

RESULTS: We generated a median of 19 959 sequences per blood specimen. We discovered that most whole blood microbiome profiles consisted of mitochondrial DNA (mean relative blood abundance greater than 99%) with minimal microbial DNA detected. Out of the 163 blood specimens, 83 (51%) had detectable microbial 16S rRNA sequences and there were 92 distinct taxa detected at the genus level. Among the 51 kidney transplant recipients, blood microbial 16S sequences were persistently detected in 10 kidney transplant recipients over time, intermittently detected in 29 kidney transplant recipients over time, and not detected in 12 kidney transplant recipients over time. Among 76 matched blood-fecal specimens, 9 blood specimens had detectable gut microbial 16S sequences, which were also detected in 3 of the 9 fecal specimens.

CONCLUSION: Our study finds minimal detection of bacterial DNA in the blood microbiome in kidney transplant recipients and evidence of gut bacterial DNA in the bloodstream of kidney transplant recipients.},
}

@article {pmid42768305,
year = {2026},
author = {Avershina, E and Birkeland, EE and Bucher-Johannessen, C and Rounge, TB},
title = {CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734649},
pmid = {42768305},
issn = {1949-0984},
mesh = {Humans ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/classification/immunology/isolation & purification/virology ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems ; Plasmids/genetics ; Feces/microbiology ; Middle Aged ; Metagenome ; Norway ; Female ; Diet ; Bacteriophages/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.},
}

Humans
*Interspersed Repetitive Sequences
*Bacteria/genetics/classification/immunology/isolation & purification/virology
*Gastrointestinal Microbiome/genetics
*CRISPR-Cas Systems
Plasmids/genetics
Feces/microbiology
Middle Aged
Metagenome
Norway
Female
Diet
Bacteriophages/genetics
Gastrointestinal Tract/microbiology

@article {pmid42768386,
year = {2026},
author = {Pateriya, D and Tanwar, A and Sharma, VK},
title = {Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {42768386},
issn = {1757-4749},
support = {INSACOG//Biotechnology Industry Research Assistance Council/ ; BT/PR50613/MED/32/981/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {The human microbiome serves as a reservoir of antibiotic resistance genes (ARGs), collectively known as the resistome, which has crucial implications for human health. However, the distribution of ARGs across diverse bacterial taxa and their variation across populations, disease states, and body sites remain less well understood. Here, we comprehensively profiled the human resistome using genomic and metagenomic data. Our analysis included 4,744 species-representative gut bacterial genomes and 452 oral bacterial genomes, along with gut metagenomic data from 10,230 individuals across 58 studies encompassing 5,388 healthy and 4,842 disease-associated samples, including underexplored non-Western cohorts. Our analysis revealed variation in the gut resistome across population groups and countries. The oral microbiome exhibited a distinct resistome profile with lower ARG prevalence compared to the gut. Across multiple datasets, ARG abundance was generally higher in inflammatory bowel disease samples compared to healthy samples. Pathogenic taxa such as Enterobacter, Citrobacter, Escherichia, and Klebsiella carried the highest number of ARGs, including clinically relevant ARGs, whereas abundant commensals like Bacteroides and Prevotella contributed to the baseline resistome. Notably, population-level differences in ARG composition appeared to be linked to microbial community structure. Shared ARGs between commensal and pathogenic bacteria provided clues to horizontal gene transfer. These findings provide crucial insights into the ecological and population-level factors shaping the gut resistome, highlighting the roles of both pathogens and commensals in the maintenance and dissemination of antimicrobial resistance.},
}

@article {pmid42768390,
year = {2026},
author = {Macey, MC and Ilieva, V and Stephens, BP and Tatton, B and Balcha, E and Schwenzer, SP and McGenity, TJ and Miruts, H and Gomez, F and Cavalazzi, B and Olsson-Francis, K},
title = {Metagenomic insights into the taxonomic and metabolic diversity of the microbiome of Lake Karum in the Danakil Depression, Ethiopia.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42768390},
issn = {2524-6372},
support = {Grant agreement No 871149//Europlanet 2024 RI project - Expert Exchange/ ; Grant Agreement No 654208//Europlanet 2020 RI project - Transnational Access/ ; Expanding Excellence in England, grant number 124.18//Research England/ ; },
abstract = {BACKGROUND: Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes.

RESULTS: The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including Candidatus Bipolaricaulota and Candidatus Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the Candidatus Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage.

CONCLUSION: This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.},
}

@article {pmid42768760,
year = {2026},
author = {Sidorov, R and Li, L and Dadvar, A and Ahmad, I and Spring, S and Overmann, J and Römling, U},
title = {Archaeal Genes Code for GGDEF Domain Proteins With Diguanylate Cyclase Activity.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.70117},
pmid = {42768760},
issn = {1365-2958},
support = {2022-04865//Swedish Research Council for Natural and Engineering Sciences/ ; //Karolinska Institutet KI Funds 2023/ ; },
abstract = {Cyclic di-GMP is ubiquitous in Bacteria, including members of the deepest branching phyla, but has not yet been detected in Archaea. Thus, whether cyclic di-GMP was present as a signaling nucleotide in the last universal common ancestor (LUCA) of Bacteria and Archaea remains unknown. In this work, bioinformatic analyses and structural modelling identified GGDEF domain proteins in archaeal isolates and encoded by metagenomes of confirmed archaeal origin. In particular, in bacterial model organisms, phenotypic and in vivo assays, in combination with catalytic mutants, suggest that selected archaeal GGDEF domain proteins possess diguanylate cyclase activity. These include the complex RECS-PAS/PAC-PocR-GGDEF-HD-GYP domain protein of Methanocella arvoryzae MRE50, a member of the Stenosarchaea order Methanocellales. While cyclic di-GMP signaling proteins are ubiquitous in Bacteria, their presence seems to be more sporadic in Archaea. It is currently unclear whether cyclic di-GMP signaling proteins have been lost in some lineages, secondarily introduced by horizontal gene transfer into others, or whether both scenarios have occurred.},
}

@article {pmid42769519,
year = {2026},
author = {Rudi, K and Majaneva, S and Ray, JL and Sundt, M and Martin, J and Angell, IL and Nylund, S and Refseth, GH and Keeley, N and Snipen, LG},
title = {Contrasting associations between microbiota respiratory strategies and seafloor macrofauna.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag230},
pmid = {42769519},
issn = {2730-6151},
abstract = {Microbe-macrofauna associations are central to coastal benthic ecosystems, yet the microbial functions that underpin these remain poorly understood. To address functional microbe-macrofauna associations, we analyzed 245 seafloor samples from Norwegian and Icelandic coastal zones, encompassing 1204 macrofaunal taxa, 121 543 zero-radius operational taxonomic units, and 302 high-quality metagenome-assembled genomes (MAGs). We first analyzed potential confounding factors and found that macrofauna showed the strongest association with a north-south geographic gradient, while overall there was a concordance for metadata associations. We found that macrofaunal assemblages were positively correlated with either a Bacteroidota-enriched cluster of MAGs ("BA"; n = 178 MAGs) or a cluster enriched in Actinomycetota and Pseudomonadota ("AP"; n = 124 MAGs). Functionally, the AP cluster was enriched in oxidases, cytochrome c-based respiratory processes, and fatty-acid β-oxidation. In contrast, the BA cluster showed enrichment in hydrolases, polysaccharide-degradation functions, and microaerobic/anaerobic respiration via cytochrome bd. Macrofaunal taxa associated with BA tended to have higher tolerance values for anthropogenic disturbance than those associated with AP, although this association was weak. Taken together, these results identify contrasting microbial respiratory strategies that co-vary with macrofaunal assemblages, while further experimental work is required to establish directionality and mechanism.},
}

@article {pmid42769662,
year = {2026},
author = {Goodall, T and Jones, B and Thorpe, AC and Griffiths, RI and Gweon, HS and Read, DS and Pywell, R and Busi, SB},
title = {Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag250},
pmid = {42769662},
issn = {2730-6151},
abstract = {Restoring agriculturally degraded habitats to species-rich grasslands is a vital conservation objective. During restoration, how the soil resistome matures alongside microbial community composition and function remains unclear. Here, we tested two competing hypotheses: whether the soil resistome co-occurs through a microbial structural maturation, in which soil restoration is associated with higher-order biotic interactions, or whether antimicrobial resistance (AMR) is instead associated with the competitive pressures and high bacterial taxonomic richness found in disturbed, eutrophic arable land. Using a unique land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly following the cessation of agricultural activity. Our results demonstrate that AMR abundance increases significantly with restoration age, reaching a maximum in >143-year-old soils. The strongest predictor of this rise in AMR abundance was an increasing microbial eukaryotic signature rather than increasing microbial density, suggesting that resistome expansion is not associated with generalized spatial competition, but rather, co-occurs with structural maturation of the microbiome. We observed an order of magnitude increase in antibiotic biosynthetic potential, dominated by the emergence of streptomycin clusters. Microbial reorientation during soil maturation mirrors the expansion of a core resistome comprised of ancient, intrinsic mechanisms, such as Major Facilitator Superfamily (MFS) efflux pumps and RNA Polymerase-Binding Protein A (RbpA) target protection, in older soils. We demonstrate that endogenous AMR is a hallmark of healthy, restored soil ecosystems rather than a marker of anthropogenic soil degradation.},
}

@article {pmid42769680,
year = {2026},
author = {Zelca, E and Gudra, D and Karklina, D and Ustinova, M and Lunge, M and Fridmanis, D and Rumba-Rozenfelde, I and Daugule, I},
title = {New Insights into the Composition of the Early-Life Gut Microbiome: A Metagenomic Analysis of Fecal Samples in Children Up to 18 Months of Age.},
journal = {Pediatric gastroenterology, hepatology & nutrition},
volume = {29},
number = {5},
pages = {359-373},
pmid = {42769680},
issn = {2234-8646},
abstract = {PURPOSE: To determine the gut microbiome composition and associated factors in infants.

METHODS: Cross-sectional study was conducted in primary healthcare centers including healthy children up to 18 months of age. Parents of children answered a questionnaire and bring a fecal sample of their child. Fecal samples were analyzed using shotgun sequencing. The relative abundances of taxonomic profile were detected and compared with associated factors.

RESULTS: In the study were included 91 children. The most abundant taxonomic units belonged to phyla: Bacillota, Bacteroidota, Actinobacteria. In contrast, the most abundant species were Bifidobacterium longum and Bifidobacterium breve, demonstrating an age-appropriate microbial composition. The viral fraction mainly consisted of bacteriophages, with the most abundant viral family being Tospoviridae. Nevertheless, more than 50 rather new taxonomic entities were observed to cause shifts in the taxonomic units of the infant gut microbiome in association with perinatal antibacterial therapy, type of delivery, feeding type in the first 6 months of life. Higher relative abundance of Kitasatospora spp. MMS16 BH015 was associated with C-section and antibacterial treatment during delivery. A total of 302 antimicrobial resistance genes were identified, the most frequently encountered genes were associated with glycopeptide antibiotic resistance: vanG, vanT, vanW, vanY and adeF. The distribution of ARGs did not differ among different age groups.

CONCLUSION: Metagenomic sequencing provides broader insights into the composition of the gut microbiome, emphasizing the presence of unusual species associated with environmental and perinatal factors. Perinatal antibacterial treatment may have a greater impact on the infant microbiome than was previously estimated.},
}

@article {pmid42769757,
year = {2026},
author = {Hu, B and Gao, Q and Hui, J and Wang, M and Gao, H and Li, K and Zheng, J and Dai, Z and Liu, S and Liu, H},
title = {Gut Enterococcus faecium derived leucic acid mediates the antiobesity effect of dietary fiber.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70173},
pmid = {42769757},
issn = {2770-596X},
abstract = {Obesity is a globally prevalent metabolic disorder closely associated with gut microbiota dysbiosis. However, the precise roles of gut microbiota and microbial metabolism in this disease remain unclear. Through fecal metagenomic data mining and clinical cohort validation, we identified a gut bacterial strain with anti-obesity potential, Enterococcus faecium (E. faecium). It inhibited adipocyte enlargement, dyslipidemia, and hepatic steatosis in obese mice by metabolizing leucine to produce leucic acid (LEA). Colonization with E. faecium or exogenous LEA supplementation improved obesity-associated metabolic phenotypes. Mechanistically, E. faecium metabolized leucine into LEA via putative branched-chain amino acids metabolic enzymes. The bacterium-derived LEA regulated mitochondrial oxidative phosphorylation and thus alleviated obesity. Furthermore, using a high-content screening system and an in vitro fermentation model, we found that the dietary fiber glucomannan exerted anti-obesity effects by promoting the growth of E. faecium. This study reveals the critical role of microbial metabolism and LEA production in ameliorating the onset and progression of obesity, providing a theoretical basis for dietary fiber intervention strategies targeting the gut microbiota.},
}

@article {pmid42769923,
year = {2026},
author = {Ren, M and Wang, J},
title = {Genome reduction in marine ammonia-oxidizing archaea driven by elevated temperature.},
journal = {mLife},
volume = {},
number = {},
pages = {},
pmid = {42769923},
issn = {2770-100X},
abstract = {Marine ammonia-oxidizing archaea (AOA) have evolved into diverse lineages and ecological niches. However, less is known about the impact of environmental factors on their genomic evolution. By integrating 281 AOA metagenome-assembled genomes (MAGs) around global oceans, we revealed that AOA genome size decreased with elevated temperature across the two predominant genera Nitrosopumilus and Nitrosopelagicus. This was supported by their contrasting temperature preferences, with the large-genome Nitrosopumilus commonly occupying cold waters and the genome-reduced Nitrosopelagicus preferring warm waters. We further found a warm-like subclade diverging from the cold-adapted Nitrosopumilus and a cold-like subclade from the warm-adapted Nitrosopelagicus. These divergences were accompanied by the enrichment of functional genes associated with adaptation to temperature fluctuation. Our results highlight the role of temperature in shaping genomic reduction and phylogenetic divergence in marine AOA, with implications for nitrogen cycling under ocean warming.},
}

@article {pmid42770038,
year = {2026},
author = {Saktaganov, N and Ongarbayeva, N and Klivleyeva, N and Glebova, T and Baimukhametova, A and Kalkozhayeva, M and Aliyev, A and Komissarov, A and Yolshin, N and Fadeev, A and Danilenko, D and Ibragimov, P and Karamendin, K},
title = {Metagenomic characterization of the porcine respiratory virome on farms in northern Kazakhstan.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1926297},
pmid = {42770038},
issn = {2297-1769},
abstract = {Studies of the porcine respiratory virome are essential for understanding the complex viral communities in the porcine respiratory tract and their roles in health and disease. Characterizing the respiratory virome provides insights into the diversity, prevalence, and dynamics of pathogenic and commensal viruses, thereby facilitating the identification of emerging and previously unrecognized respiratory pathogens. Metagenomic next-generation sequencing (mNGS) is a method for analyzing viral communities, enabling comprehensive monitoring of circulating and co-detected pathogens in animals. In this study, mNGS on the Illumina platform was used to characterize the porcine respiratory virome in Kazakhstan. The study included 150 nasopharyngeal swabs collected from commercial pig farms in northern Kazakhstan. Viral sequences were assigned to the families Parvoviridae, Herpesviridae, Picornaviridae, Astroviridae, and Anelloviridae. High coverage was achieved for Porcine cytomegalovirus, Porcine parvovirus 5, and Porcine parvovirus 7, including reconstruction of a nearly complete PPV7 genome. Significant variability in mapped read counts and sequencing depth was observed across samples, reflecting heterogeneity in the detection of viral nucleic acids within the sampled population. Phylogenetic analysis showed that all identified viruses belong to globally circulating evolutionary lineages and do not form new divergent clusters. Moreover, respiratory and gastrointestinal virus sequences were often detected simultaneously in nasopharyngeal samples, indicating a complex composition of viral nucleic acids in the upper respiratory tract of pigs. Pigs are important reservoirs and intermediate hosts for zoonotic viruses. Metagenomic studies contribute not only to animal health and disease control but also to One Health initiatives by strengthening early warning systems for pathogens with epidemic or pandemic potential. The results demonstrate the high viral diversity in domestic pigs in Kazakhstan and confirm the effectiveness of mNGS as a tool for epizootiological surveillance and molecular monitoring of viral infections in livestock.},
}

@article {pmid42770043,
year = {2026},
author = {Wuopio, J and Graells, T and Lin, YT and Schillemans, T and Moll, JM and Eklund, AC and Nielsen, HB and Larsson, A and Engström, G and Orho-Melander, M and Johnson, LS and Ärnlöv, J},
title = {Associations between sodium intake and gut microbiota composition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1889723},
pmid = {42770043},
issn = {2296-861X},
abstract = {INTRODUCTION: High salt intake is associated with adverse health outcomes. Emerging evidence highlights the importance of the gut microbiome in human health, but large-scale human data on salt intake and the microbiome are limited. We examined the cross-sectional association between estimated 24-h sodium excretion (est24hNa) and the gut microbiome in a population-based cohort.

METHODS: We included 9,220 participants from the Swedish SCAPIS cohort with available shotgun metagenomic sequencing of fecal samples and urine analyses. We estimated the 24-h sodium excretion using the Kawasaki formula. Alpha diversity was assessed using the Shannon and inverse Simpson indices, and beta diversity using Bray-Curtis dissimilarity. Functional potential was evaluated using Gut Microbial Modules. Associations were analyzed using mixed linear regression models.

RESULTS: Alpha diversity was inversely associated with est24hNa, but associations were attenuated after adjustment for BMI and were not significant in fully adjusted models. Beta diversity was associated with est24hNa, although the explained variance was small (R2 < 0.001). Higher est24hNa was associated with 75 microbial species, including lower abundance of 27 species and higher abundance of oral-associated taxa such as Streptococcus spp. and Veillonella. It was also associated with increased abundance of pathways involved in microbial energy metabolism and carbohydrate fermentation.

CONCLUSION: Higher est24hNa was associated with selected gut microbiome features, including a higher abundance of several oral-associated taxa and differences in inferred functional capacity for energy metabolism and carbohydrate fermentation. These findings identify microbial patterns associated with sodium exposure that may be relevant to cardiometabolic health.},
}

@article {pmid42770203,
year = {2026},
author = {Pramanik, S and Banerjee, S and Mondal, A and Kundu, A and Biswas, R and Dam, B and Mandal, S and Rath, J},
title = {Metagenomic insights into microbial biodeterioration of terracotta in the 18th-century-old temple Jor Mandir.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2026.2734111},
pmid = {42770203},
issn = {1029-2454},
abstract = {Microbial colonisation represents a significant yet underexplored factor contributing to the biodeterioration of terracotta heritage structures in tropical environments. Here, we present a comprehensive multi-analytical investigation of the Jor Mandir complex, an eighteenth-century terracotta monument in eastern India. Culture-based analysis revealed morphologically distinct cyanobacteria that were not detected by metagenomics, underscoring the complementarity of the two approaches. Amplicon sequencing of a composite biofilm sample revealed a microbial community dominated by Cyanobacteria (44.18%), followed by Actinobacteriota (18.61%), Proteobacteria (14.30%), Chloroflexi (10.16%), Acidobacteriota (7.38%), and other minor phyla. Stress-tolerant coccoid taxa such as Chroococcidiopsis and Aphanocapsa, along with filamentous genera including Leptolyngbya, Lyngbya, Oscillatoria, and Phormidium, and heterocystous nitrogen-fixing genera such as Scytonema, Nostoc, and Calothrix, were identified. These organisms exhibited biochemical adaptations, including the production of scytonemin and carotenoids, which contributed to photoprotection and substrate weathering. Elemental profiling indicated associations between the aluminosilicate terracotta matrix and surface-associated biofilm material. GC-MS analysis revealed a range of organic compounds, including fatty acid methyl esters, hydrocarbons, phenolic compounds, and phthalate derivatives, reflecting the chemically complex nature of the biofilm matrix. PICRUSt2-based functional reconstruction further indicated a biofilm community with predicted pathways related to biosynthetic processes, biodegradation pathways, and energy metabolism. Together, these descriptive observations provide a site-specific baseline profile of microbial colonisation and biofilm-associated characteristics on the terracotta surfaces of the Jor Mandir complex and highlight the value of integrating microbiological and physicochemical approaches in future monument monitoring and conservation studies.},
}

@article {pmid42771225,
year = {2026},
author = {Castells, M and Benítez-Galeano, MJ and Maya, L and Casaux, ML and Slimovich, L and Saravia, A and Lizasoain, A and Fraga, M and Giannitti, F and Rodríguez-Osorio, N and Colina, R},
title = {Shotgun metagenomic sequencing and genetic characterization of four enteric viruses in a dairy farm suffering a diarrhea outbreak of undetermined cause in adult cattle.},
journal = {Archives of virology},
volume = {171},
number = {10},
pages = {},
pmid = {42771225},
issn = {1432-8798},
support = {FCE_3_2022_1_172734//Agencia Nacional de Investigación e Innovación/ ; PL_27//Instituto Nacional de Investigación Agropecuaria/ ; },
mesh = {Animals ; Cattle ; *Cattle Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Disease Outbreaks/veterinary ; Phylogeny ; Feces/virology ; Female ; Uruguay/epidemiology ; Genome, Viral ; Shotgun Sequencing ; Dairying ; Metagenomics ; *Enterovirus Infections/veterinary/virology/epidemiology ; Torovirus/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Diarrhea is an acute disease of cattle that has been extensively studied in calves; however, it has been far less investigated in adult cattle, despite its significant impact on milk production and animal health. In this study, we investigated an outbreak in a dairy herd in Uruguay for which initial diagnostic testing for the main known pathogens yielded negative results. Therefore, the outbreak was further investigated in depth using shotgun metagenomic sequencing, molecular virology assays and viral isolation. Of the three fecal samples from affected cows that were submitted for diagnostic testing and were negative for the main enteric pathogens, including BCoV, two were positive for bovine torovirus (BToV) by RT-qPCR. Next-generation sequencing-based virome analysis revealed over 3,300 viral operational taxonomic units (vOTUs), predominantly bacteriophages, but also eukaryotic viruses from 11 families. The complete genome of BToV was obtained and a putative novel protoparvovirus species was characterized. In addition, two distinct enteroviruses belonging to the species Enterovirus fitauri and Enterovirus idromi were identified. Notably, Enterovirus idromi had previously been reported exclusively in dromedaries; its detection in cattle expands the known host range of this species. Furthermore, the Enterovirus idromi strain appears to represent an interspecies recombinant enterovirus. These results highlight the importance of emerging approaches such as next-generation sequencing for identifying novel pathogens in cattle diseases and may serve as a basis for evaluating their potential role in disease pathogenesis, as well as for incorporating them into routine initial diagnostic testing.},
}

Animals
Cattle
*Cattle Diseases/virology/epidemiology
*Diarrhea/veterinary/virology/epidemiology
*Disease Outbreaks/veterinary
Phylogeny
Feces/virology
Female
Uruguay/epidemiology
Genome, Viral
Shotgun Sequencing
Dairying
Metagenomics
*Enterovirus Infections/veterinary/virology/epidemiology
Torovirus/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing

@article {pmid42771532,
year = {2026},
author = {Igwe, AN and Afkhami, ME},
title = {Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001835},
pmid = {42771532},
issn = {2057-5858},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; California ; *Microbiota/genetics ; *Fungi/classification/genetics/isolation & purification ; Metagenomics/methods ; Ecosystem ; Metagenome ; },
abstract = {Environmental filtering and buffering are complementary processes responsible for stabilizing ecosystem services across landscapes. The extent to which either of these processes structures microbial composition and functions in extreme soil systems can be highly context-dependent, requiring site-specific examination to elucidate general principles of community function under stress. Serpentine soils have high amounts of heavy metals and magnesium and low levels of plant nutrients and exist in close proximity to nutrient-rich and plant-productive nonserpentine soils, making them an ideal system for evaluating selection and redundancy under stress. Combining biogeographical field surveys and shotgun metagenomic sequencing of microbiomes from 23 pairs of serpentine and nonserpentine soils across California, we investigated selection and functional redundancy between disparate soil types. We hypothesized that the strong selective pressure present in serpentine soils would result in distinct bacterial and functional profiles. Bacterial and fungal community taxonomic compositions were indeed distinct between serpentine and nonserpentine soils, while archaeal communities were similar between soil types. In contrast, functional repertoires of all microbial community groups were largely similar between soil types, with many of the same taxa carrying out functions across soil types. Still specialized functions in serpentine soils represented adaptations to stress in contrast to the carbon-rich environment of nonserpentine soils. For example, specialized functions - such as siderophore biosynthesis proteins, which are involved in the biosynthesis of iron-chelating compounds - were distinctive features of serpentine soils and specialized functions notably had similar functional redundancy but distinct taxa carrying out the functions across soil types. These results highlight taxa that perform the functions that have been selected for survival in an extreme soil ecosystem and the functions that are most at risk in the face of environmental disturbances.},
}

*Soil Microbiology
*Soil/chemistry
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
California
*Microbiota/genetics
*Fungi/classification/genetics/isolation & purification
Metagenomics/methods
Ecosystem
Metagenome

@article {pmid42772044,
year = {2026},
author = {McLeod, L and Lehmann, M and Otto, SJG and Lacoste, SR and McCarthy, EL and Links, MG and Waldner, CL},
title = {Deep nasopharyngeal swabs are more sensitive than short nasal swabs for identifying antimicrobial resistance genes in bovine respiratory pathogens examined using long-read metagenomic sequencing.},
journal = {Research in veterinary science},
volume = {212},
number = {},
pages = {106414},
doi = {10.1016/j.rvsc.2026.106414},
pmid = {42772044},
issn = {1532-2661},
abstract = {Challenges in sample collection have contributed to the limited use of diagnostic testing in bovine respiratory disease (BRD) management. Short nasal swabs (SNS) offer a practical and cost-effective alternative to deep nasopharyngeal swabs (DNPS) for sampling the upper respiratory tract, but gaps remain in understanding the efficacy of SNS for detecting clinically relevant bacteria and associated antimicrobial resistance genes (ARGs) compared to DNPS. This study compared detection of BRD-associated bacteria and ARGs between SNS and DNPS samples collected from 207 fall-placed calves at a research feedlot, using a recently developed long-read metagenomic sequencing protocol. More total reads and base pairs were identified from DNPS than SNS for Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Bibersteinia trehalosi, while no difference was detected for Mycoplasmopsis bovis. Additional bacteria of potential interest were also identified. Bacterial reads and total base pairs identified as Mesomycoplasma dispar, Moraxella bovoculi, and Mannheimia bovis were higher in DNPS compared to SNS, while reads identified as Moraxella bovis were higher in SNS. The prevalence of samples in which ARGs were detected within reads identified as M. haemolytica, P. multocida, H. somni or B. trehalosi was greater in DNPS samples compared to SNS for tetracyclines (OR = 1.6, P = 0.02), macrolides (OR = 2.3, P < 0.001), sulfonamides (OR = 2.5, P < 0.001), and aminoglycosides (OR = 2.5, P < 0.001). Overall, for the sequencing protocol used in this study, DNPS performed better than SNS for the detection of BRD bacteria and associated ARGs.},
}

@article {pmid42772074,
year = {2026},
author = {Zhang, R and Li, G and Hou, D},
title = {Decoupling petroleum-hydrocarbon burden from metagenomic degradation potentials identifies subsurface layers with constrained intrinsic bioremediation potential.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143676},
doi = {10.1016/j.jhazmat.2026.143676},
pmid = {42772074},
issn = {1873-3336},
abstract = {Petroleum-hydrocarbon concentrations delineate contaminated soil but do not indicate whether contaminant burden is matched by indigenous degradation potential. We integrated total petroleum hydrocarbons (TPH) in the C10-C40 range with four process-specific metagenomic degradation potentials to identify subsurface layers where intrinsic bioremediation may be constrained. We collected 36 depth-resolved soil samples from six boreholes at a former refinery, including 22 with matched metagenomic profiles. CANT-HYD annotation identified 135 nonredundant genes across 15 hidden Markov models, representing aerobic and anaerobic degradation potentials for aromatic hydrocarbons and alkanes. TPH was positively associated with aerobic aromatic potential before adjustment (Spearman's ρ = 0.543, q = 0.0448), but not after accounting for depth and borehole. TPH also showed no significant overall association with the four-dimensional potential profile (partial R[2] = 0.073, p = 0.349). Site-relative screening identified seven nonexclusive high-burden/low-potential flags across five layers that were robust to threshold and borehole-exclusion tests. In adjusted models, the four-potential block was associated with genus-level community composition (marginal R[2] = 0.274, p = 0.0337), whereas TPH showed no independent association. These results indicate that petroleum-hydrocarbon burden did not correspond consistently to the four metagenomic degradation potentials. This framework prioritizes subsurface layers for targeted, process-specific assessment of intrinsic bioremediation.},
}

@article {pmid42772147,
year = {2026},
author = {Li, T and Guo, T and Wang, P and Zhi, Z and Cao, Y and Cui, M and Zhang, J},
title = {Age-dependent dynamics of cecal caproic acid in free-range Lueyang black-boned chickens and its effects on primary myoblasts.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107762},
doi = {10.1016/j.psj.2026.107762},
pmid = {42772147},
issn = {1525-3171},
abstract = {The age-dependent dynamics of cecal caproic acid and its effects on chicken myoblasts remain poorly characterized. A total of 560 female Lueyang black-boned chickens were allocated to cage-reared (CR) or free-range (FR) systems, with seven replicate units per system and 40 birds per unit. Cecal samples were collected at 120, 150, 180, and 360 d of age. Age-dependent microbial and metabolic profiles were characterized within FR chickens using shotgun metagenomics and untargeted metabolomics, whereas caproic acid abundance was compared between CR and FR chickens. Primary chicken myoblasts were used to assess cellular responses to caproic acid. Cecal caproic acid abundance was higher in FR than in CR chickens (P < 0.05). Within FR chickens, its abundance increased at 150 d, declined at 180 d, and increased again at 360 d. These dynamics coincided with age-related differences in microbial community composition and predicted carbohydrate-processing functions. The metabolite cluster containing caproic acid was positively associated with breast muscle yield and negatively associated with lipid-related traits. Caproic acid reduced myoblast viability at 500 μmol/L after 24 and 48 h and at 100-500 μmol/L after 72 h. Treatment with 300 or 400 μmol/L for 48 h reduced EdU incorporation and PCNA and CCND1 mRNA expression and their corresponding protein abundances. It also increased the proportion of cells in G0/G1 and increased apoptosis, without detectable between-group differences in culture-medium pH. The p-AMPK/AMPK and p-p38/p38 ratios increased, whereas the p-ERK/ERK ratio decreased (P < 0.05). MYOD1 mRNA expression also increased following caproic acid treatment (P < 0.05). Together, these findings identify caproic acid as an age-responsive cecal metabolite with direct effects on myoblast proliferation and survival in vitro. They provide evidence for a potential link between cecal metabolic variation and muscle-cell responses in chickens.},
}

@article {pmid42772223,
year = {2026},
author = {Deng, Y and Miao, L and Xu, Y and Huang, C and Liang, S and Ni, T and Chen, Y and Hou, J and You, G},
title = {Low-light and tannin functionalization promote high-density filamentous cyanobacterial biofilms for low-C/N aquaculture tailwater treatment: Stratified structures and metabolic networks.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {126986},
doi = {10.1016/j.watres.2026.126986},
pmid = {42772223},
issn = {1879-2448},
abstract = {Algal-bacterial biofilms show great promise for treating aquaculture tailwater with low carbon-to-nitrogen (C/N), yet their practical application is hindered by limited light penetration, which restricts biomass accumulation and reduces algal-to-bacterial ratios. Here, we developed a tannin-functionalized optical fiber (OTL) system that integrates internal light delivery with a bio-flocculant tannin interface to promote the formation of high-density cyanobacterial biofilms. The OTL system achieved removal efficiencies of 95.73%, 96.93%, 84%, and 89% for NH4[+]-N, NO3[-]-N, COD, and PO4[3][-]-P, respectively, and increased biofilm biomass by 2.37-fold compared with illuminated bare fibers (OL). Multiscale imaging and spectral analyses showed that the middle biofilm layer harbored the highest cyanobacterial-to-bacterial ratio. Filamentous cyanobacteria enriched in this layer secreted abundant exopolysaccharides, forming a robust biological scaffold that recruited coccoid cyanobacteria and heterotrophic bacteria and generated a stratified architecture favorable for mass transfer and algal-bacterial interactions. Metagenomics analysis identified Desertifilum as the dominant filamentous cyanobacterium in OTL. The relative abundances of exopolysaccharide biosynthesis and export genes, including wzx, wzy, and wza, were 1.11- to 1.22-fold higher in OTL, indicating enhanced potential for exopolysaccharide polymerization and export. Metagenome-assembled genomes further revealed that complex exopolysaccharides produced by Desertifilum were degraded by epiphytic bacteria such as Flavobacterium and Sediminibacterium, supplying bioavailable carbon to Thauera and establishing a cooperative metabolic network associated with enhanced nitrogen uptake, nitrate reduction, and coupled GS/GOGAT-mediated nitrogen assimilation. This study demonstrates that optical fiber-guided photochemical regulation can engineer stratified, high-density algal-bacterial biofilms, offering a nature-inspired and low-carbon strategy for aquaculture tailwater treatment and ecological water restoration.},
}

@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.},
}