@article {pmid42828930,
year = {2026},
author = {Yang, M and Pan, C and Kang, D and Li, J and Ge, Z and Zhang, L and Peng, Y},
title = {Nitrogen starvation coupled with extended anoxic time induces rapid growth of ammonia oxidizers and enrichment of anammox bacteria in low-ammonium wastewater.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127038},
doi = {10.1016/j.watres.2026.127038},
pmid = {42828930},
issn = {1879-2448},
abstract = {Partial nitrification-anammox (PNA) is an energy-efficient autotrophic nitrogen removal process, yet its application to low-ammonium wastewater remains challenging due to the difficulty in selectively suppressing nitrite-oxidizing bacteria (NOB) while maintaining ammonia-oxidizing bacteria (AOB) and anaerobic ammonium oxidation (anammox) bacteria. Here, we developed a chemical-free strategy based on sequential nitrogen starvation and extended anoxic operation to successfully establish one-stage PNA. Long-term reactor operation and cyclic nitrogen conversion performance demonstrated that repeated nitrogen starvation shifted the system from complete nitrification toward partial nitrification, while subsequent extension of the anoxic period promoted anammox activity and finally reached PNA performance. Batch activity tests revealed differential kinetic responses between nitrifiers, with faster AOB activity recovery rates, whereas repeated nitrogen starvation caused greater activity declines in NOB. Community-level microbial composition and functional gene analyses revealed a clear transition from a Nitrospira-dominated community toward an Nitrosomonas-Candidatus Brocadia consortium, accompanied by rapid increase of amoA gene abundance following starvation and enrichment of anammox populations. Genome-resolved metagenomics further revealed distinct succession trajectories among nitrifier populations, with some Nitrospira lineages persisting throughout the operation. Comparative genomic analyses incorporating global wastewater-treatment-plant metagenomes demonstrated that Nitrosomonas possessed greater genomic potential for reactive oxygen species (ROS) defense and redox maintenance than Nitrospira, suggesting a potential mechanism underlying their differential resilience to metabolic stress induced by the imbalance between nitrogen availability and oxygen supply. Nitrogen starvation also selectively reduced non-denitrifying heterotrophic organisms and enhanced the genomic potential for denitrification. Overall, this study demonstrates that a combined nitrogen starvation and oxygen availability strategy can effectively drive PNA establishment in low-strength ammonium wastewater, and provides new insights into stress-induced recovery and ecological selection of nitrifying communities.},
}

@article {pmid42829110,
year = {2026},
author = {Badr, T and Hatem, K},
title = {The regulatory landscape for clinical metagenomics-based diagnostics in Europe: a critical review.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107738},
doi = {10.1016/j.mimet.2026.107738},
pmid = {42829110},
issn = {1872-8359},
abstract = {Metagenomic next-generation sequencing (mNGS) enables broad, untargeted pathogen detection and is increasingly used in the diagnosis of central nervous system infections, infections in immunocompromised or post-transplant patients, ICU patients, and sepsis. This growing clinical role makes the regulatory landscape surrounding mNGS an urgent subject for evaluation, particularly given the phased implementation of the European In Vitro Diagnostic Regulation (IVDR). The transition from the In Vitro Diagnostic Directive (IVDD) to the IVDR marks a shift toward a harmonized, risk-based framework for in vitro diagnostics in the European Economic Area (EEA), but several aspects remain unclear for complex laboratory-developed tests (LDTs) such as clinical mNGS - including the practical implementation of the health institution exemption under Article 5(5), the classification of broad mNGS assays within the current risk tiers, and the scope of required analytical and clinical validation. Notably, validation strategies for mNGS may need to focus on the overall analytical method and intended use rather than on individual target pathogens. Further priorities include harmonized quality requirements, broader availability of external quality assessment (EQA), and clearer frameworks for transferring validated protocols between institutions. This review critically evaluates the current European regulatory framework for clinical mNGS-based LDTs and identifies areas requiring further clarification. Continued collaboration between healthcare institutions, regulators, scientific societies, and industry will be essential to keep requirements proportionate while supporting safe, reliable, and clinically useful implementation of mNGS in routine diagnostics.},
}

@article {pmid42829135,
year = {2026},
author = {Zhan, Y and Li, P and Chen, N and Hu, W and Feng, C},
title = {Enhanced Fe[0]-based autotrophic Cr(VI) biorduction with eggshell as an alternative inorganic carbon source: bioavailability mechanisms and microbial response.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125848},
doi = {10.1016/j.envres.2026.125848},
pmid = {42829135},
issn = {1096-0953},
abstract = {Zerovalent iron-based autotrophic bioreduction of Cr(VI) [FAR-Cr(VI)] is a promising remediation strategy for Cr(VI) contamination in groundwater, but its performance depends on inorganic carbon (IC) delivery and microbial colonization. This study investigated waste derived eggshell as a multifunctional IC source and biostimulatory substrate for enhancing FAR-Cr(VI). Bioreactors were operated with NaHCO3 (LC), CaCO3 (SC), and eggshell (ES) as IC supplements during three consecutive 48 h cycles. The ES biosystem achieved complete Cr(VI) removal (100%) in all cycles, whereas the LC and SC biosystems reached final removal efficiencies of 88.9 ± 0.9% and 93.7 ± 0.6%, respectively. The pseudo-first-order rate constant in the ES biosystem (0.147 h[-1]) was 3.3- and 2.6-fold higher than those in the LC (0.045 h[-1]) and SC (0.057 h[-1]) biosystems. ES promoted denser biofilm formation and significantly increased electron transfer system activity, cell viability and counts. XPS analysis showed higher relative Fe(III) and Cr(III) signals in ES precipitates, indicating more efficient Fe[0] oxidation and Cr(VI) reduction. Metagenomic analysis revealed higher abundances of Fe oxidation genes (feoA and fetA) and Wood-Ljungdahl pathway genes in the ES biosystem, suggesting an ATP-efficient carbon fixation strategy. Component-based experiments showed that calcined eggshell still improved the rate constant by 28.3% over SC, demembraned eggshell by 46.3-78.3%, and the inner membrane provided an additional 39.9-70.5% enhancement beyond demembraned eggshell. These findings indicate that eggshell enhances FAR-Cr(VI) through coupled carrier effects, and native organic, and trace element biostimulation, supporting a "waste-treating-waste" strategy for Cr(VI) contaminated groundwater remediation.},
}

@article {pmid42829285,
year = {2026},
author = {Liu, Y and Liu, Y and Dai, C and Gu, M and Luo, J and Cao, H},
title = {A Kidney Transplant Patient Suffering From Multiple Colonic Ulcers and Hepatic Abscess: A Case Report and Literature Review.},
journal = {Transplantation proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.transproceed.2026.08.003},
pmid = {42829285},
issn = {1873-2623},
abstract = {We present a rare case of colonic mucormycosis with hepatic dissemination after kidney transplantation. Early diagnosis was achieved through rapid metagenomic next-generation sequencing (mNGS) of blood and liver abscess samples, enabling timely intervention. The patient achieved complete clinical recovery with preserved allograft function. Gastrointestinal mucormycosis is extremely rare, reported cases frequently require colectomy (83.3%) and carry a mortality rate approaching 50%. This case highlights key management principles for intestinal mucormycosis in transplant recipients: rapid pathogen identification via mNGS, prompt initiation of dual antifungal therapy against Mucorales, and urgent surgical debridement of necrotic tissue.},
}

@article {pmid42829421,
year = {2026},
author = {Murugan, SB and Thomas, AA and Kene, RD and Rajan, A and Kelgaonkar, A and Rajesh, V and Somanath, A and Mahendradas, P and Deivasenathipathi, G and Majumder, PD},
title = {Current landscape of drug induced retinal vasculitis.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {16},
number = {1},
pages = {},
pmid = {42829421},
issn = {1869-5760},
abstract = {Drug-induced retinal vasculitis (DIRV), a complex diagnostic entity, masquerades as infectious or primary autoimmune diseases. Delineating them is a daunting task. This update aims to consolidate clinical evidence focussing on characteristic "vascular signatures" using advanced multimodal imaging tools. Type III (immune complex-mediated) and Type IV (T-cell-mediated) hypersensitivity pathways were involved in diverse range of drugs causing DRIV. The critical therapeutic strategies are highlighted to prevent permanent ischemic damage. Advances in the recent metagenomic markers are added to aid the clinician from a practical standpoint to aid in preventive and personalised ophthalmic care.},
}

@article {pmid42830273,
year = {2026},
author = {Wang, R and Yang, R and Hu, D and Xin, T and Yang, Z and Guan, Y and Niu, Y},
title = {A 5:2 Intermittent Fasting Regimen Ameliorates High-Fat Diet-Induced MASLD-Associated Skeletal Muscle Impairment in Mice.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {5},
pages = {e70398},
doi = {10.1002/jcsm.70398},
pmid = {42830273},
issn = {2190-6009},
support = {2024ZD0531800//Non-communicable Chronic Diseases National Science and Technology Major Project/ ; 82473614//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; Intermittent Fasting ; *Muscle, Skeletal/pathology/metabolism/physiopathology ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Liver/pathology/metabolism ; *Fasting ; *Non-alcoholic Fatty Liver Disease/etiology ; *Fatty Liver/etiology ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent chronic liver disorder worldwide. Its pathogenesis is closely linked to high-fat diets (HFDs) and is frequently accompanied by decreased skeletal muscle quality. Although intermittent fasting (IF) has been shown to effectively alleviate hepatic steatosis and inflammation, its impact on skeletal muscle quality remains unclear.

METHODS: Eight-week-old male C57BL/6J mice were randomly divided into two groups and fed a normal chow (NC) or 45% HFD for 14 weeks to induce MASLD. Subsequently, the MASLD model mice were subjected to a 5:2 intermittent fasting (IF5:2) regimen for 12 cycles (2 days of fasting per week, with ad libitum HFD feeding on the remaining 5 days). Grip strength, liver weight and quadriceps muscle mass were measured at sacrifice. Serum samples were collected for biochemical analysis and lipopolysaccharide (LPS) measurement. Liver, skeletal muscle and intestinal tissues were harvested for histopathological examination. Faecal samples were analysed by metagenomic sequencing. The mRNA expression of bile acid receptors and inflammatory genes was detected by qRT-PCR. Targeted free fatty acid profiling was performed in liver and skeletal muscle tissues.

RESULTS: Compared with the continuous HFD group, the IF5:2 group showed no significant difference in cumulative energy intake but exhibited significantly reduced body weight, as well as alleviated hepatic steatosis and inflammation. IF5:2 significantly increased grip strength and skeletal muscle cross-sectional area and markedly downregulated mRNA expression of inflammation-related genes in muscle tissue. Regarding intestinal barrier function, the IF5:2 group displayed significantly higher mRNA expression of intestinal tight junction-related genes, a thicker colonic wall and lower serum LPS levels compared with the HFD group. Metagenomic analysis suggested that IF5:2 effectively remodelled HFD-induced gut microbiota dysbiosis and significantly enriched beneficial bacteria including Limosilactobacillus reuteri and Faecalibaculum rodentium, accompanied by significant upregulation of microbial secondary bile acid biosynthesis pathways. mRNA expression levels of bile acid receptors and their downstream regulatory genes in the intestine, liver and skeletal muscle were significantly elevated in the IF5:2 group. IF5:2 treatment significantly reduced free fatty acid levels in the liver and skeletal muscle, which were negatively correlated with the gene expression of bile acid-related receptors in these two tissues.

CONCLUSIONS: Cyclic IF5:2 effectively ameliorates HFD-induced MASLD and protects against skeletal muscle impairment. It represents a promising dietary intervention with dual beneficial effects on alleviating hepatic steatosis and maintaining skeletal muscle quality.},
}

Animals
Mice
Intermittent Fasting
*Muscle, Skeletal/pathology/metabolism/physiopathology
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
Disease Models, Animal
Liver/pathology/metabolism
*Fasting
*Non-alcoholic Fatty Liver Disease/etiology
*Fatty Liver/etiology

@article {pmid42830277,
year = {2026},
author = {Feng, T and Shang, J and Ma, Y and Li, J and Qin, Y and Zhang, J and Cheng, S and Zhang, G and Xie, H},
title = {Metagenomic analysis of rhizosphere soil microbiota in wild and cultivated Notopterygium incisum, an umbelliferae medicinal herb.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42830277},
issn = {1471-2180},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics/methods ; *Apiaceae/microbiology/growth & development ; *Plants, Medicinal/microbiology/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.},
}

*Rhizosphere
*Soil Microbiology
*Metagenomics/methods
*Apiaceae/microbiology/growth & development
*Plants, Medicinal/microbiology/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification

@article {pmid42830300,
year = {2026},
author = {Nguyen, TT and Steen, IH and Stokke, R},
title = {Diverse biosynthetic pathways in Arctic hydrothermal biofilms.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42830300},
issn = {2041-1723},
support = {315427//Norges Forskningsråd (Research Council of Norway)/ ; },
mesh = {*Biofilms ; *Biosynthetic Pathways/genetics ; Arctic Regions ; *Archaea/genetics/metabolism ; *Hydrothermal Vents/microbiology ; *Bacteria/genetics/metabolism ; Metagenome ; Multigene Family ; Metagenomics ; Microbiota/genetics ; Peptide Synthases/genetics/metabolism ; Protein Processing, Post-Translational ; },
abstract = {Biosynthetic gene clusters (BGCs) which encode diverse secondary metabolites are ubiquitous across microbiomes and support critical ecological functions. They also serve as attractive targets for new drug discovery. Here we combined genome-resolved metagenomics with long-read Nanopore RNA sequencing, yielding 1016 bacterial and 124 archaeal medium-to-high quality MAGs from previously unchartered microbial communities in Arctic hydrothermal vent biofilms. We identified 2965 BGCs from 870 metagenome-assembled genomes (MAGs) comprising a distinctive and rich diversity of BGCs, with ribosomally synthesized and post-translationally modified peptides (RiPPs) predominating across all samples. RiPPs and non-ribosomal peptide synthetases (NRPs), also known to encode metabolites with antimicrobial potential, are represented among the most expressed transcripts. Terpenes, though less expressed, contribute to microbial signaling and defense. Notably, we identify hydrogen cyanide (HCN) synthesis pathways in archaeal genomes, challenging the view that cyanogenesis is restricted to bacteria and eukaryotes. Our findings demonstrate that microbial adaptation to extreme environments favors RiPP-based biosynthesis and that HCN may play a role in archaeal ecological interactions. Moreover, microbial communities in Arctic hydrothermal vent biofilms provide a rich reservoir of unique bioactive compounds, with implications for drug discovery.},
}

*Biofilms
*Biosynthetic Pathways/genetics
Arctic Regions
*Archaea/genetics/metabolism
*Hydrothermal Vents/microbiology
*Bacteria/genetics/metabolism
Metagenome
Multigene Family
Metagenomics
Microbiota/genetics
Peptide Synthases/genetics/metabolism
Protein Processing, Post-Translational

@article {pmid42830672,
year = {2026},
author = {Carew, M and Chung, J and Hehir, G and Hoffmann, A and Coleman, R},
title = {Simplifying Macroinvertebrate Biodiversity Assessment: A Standardised Metabarcoding Method for Invertebrate Samples With High Volumes of Debris.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70213},
doi = {10.1111/1755-0998.70213},
pmid = {42830672},
issn = {1755-0998},
support = {LP200100381//Australian Research Council/ ; },
mesh = {Animals ; *Invertebrates/classification/genetics ; *DNA Barcoding, Taxonomic/methods/standards ; *Biodiversity ; Australia ; Fresh Water ; *Metagenomics/methods/standards ; },
abstract = {DNA metabarcoding of freshwater macroinvertebrate samples can provide rapid and accurate identification of species diversity. Processing samples where macroinvertebrates are not separated from net contents can substantially reduce time and cost. We devised and tested a standardised method for processing combined kick/sweep samples using DNA metabarcoding to provide accurate estimates of macroinvertebrate species diversity. Kick and sweep samples were collected from 10 sites across Greater Melbourne known to vary in catchment land use, macroinvertebrate abundance and diversity as well as the type and volume of sampling debris. A sieving, blending and DNA extraction protocol was developed to reduce large debris, rocks and sand in samples, and to concentrate macroinvertebrates for metabarcoding. Variable percentages of the dry weight of samples from each site were used as a source of DNA for metabarcoding. We found that the macroinvertebrate species diversity recovered was mostly consistent when processing different percentages (20%-40%) of dry weight, but a minimum dry weight would be recommended for samples with low total dry weight. We present a method with a laboratory and bioinformatic workflow that enables the cost-effective and reliable processing of large volume samples, like those encountered in freshwater bioassessment. This metabarcoding approach has potential to be applied to any invertebrate biodiversity analysis where invertebrates are not separated from sampling debris, regardless of volume and composition, and used on samples varying in species abundance, diversity and density.},
}

Animals
*Invertebrates/classification/genetics
*DNA Barcoding, Taxonomic/methods/standards
*Biodiversity
Australia
Fresh Water
*Metagenomics/methods/standards

@article {pmid42831335,
year = {2026},
author = {Atayan, AA and Belov, YV and Kuznetsov, MR and Sinyavin, GV and Chernookov, AI and Belykh, EN and Yumasheva, VA and Parfenov, IM},
title = {[Current knowledge of pathophysiology of ischemia-induced intestinal wall damage: comprehensive analysis of pathogenesis and perspectives].},
journal = {Khirurgiia},
volume = {},
number = {10},
pages = {71-79},
doi = {10.17116/hirurgia202610171},
pmid = {42831335},
issn = {0023-1207},
mesh = {Humans ; *Reperfusion Injury/physiopathology/etiology/metabolism/diagnosis ; Intestinal Barrier Function ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation/methods ; *Intestines/blood supply/physiopathology ; *Intestinal Mucosa/metabolism/physiopathology/pathology ; *Ischemia/physiopathology ; Oxidative Stress ; },
abstract = {Intestinal ischemia is still one of the most complex pathological processes and characterized by high mortality and difficulties in early diagnosis. The article presents modern data on pathophysiological mechanisms of ischemia-induced intestinal wall damage. Etiological factors, molecular basis of ischemia-reperfusion injury, role of intestinal microbiota and innovative approaches to diagnosis and therapy are considered. Particular attention is paid to the paradoxical role of reperfusion. Indeed, the last one causes almost 70% of structural damages through activation of NADPH oxidase (NOX-4) and mitochondrial dysfunction. Metagenomic studies revealed a critical decrease in microbiota diversity (Shannon index 1.5-2.0) and butyrate deficiency. This directly correlates with violation of intestinal barrier function. In addition, the authors discuss clinical implications of new data, including probiotics and fecal microbiota transplantation. The article highlights the need for interdisciplinary approach involving microbiologists, clinicians and bioinformaticians to develop personalized strategies to reduce mortality and improve treatment outcomes.},
}

Humans
*Reperfusion Injury/physiopathology/etiology/metabolism/diagnosis
Intestinal Barrier Function
*Gastrointestinal Microbiome/physiology
Fecal Microbiota Transplantation/methods
*Intestines/blood supply/physiopathology
*Intestinal Mucosa/metabolism/physiopathology/pathology
*Ischemia/physiopathology
Oxidative Stress

@article {pmid42831354,
year = {2026},
author = {Mainguy, J and Lemane, T and Bazin, A and Arnoux, J and Gautreau, G and Médigue, C and Calteau, A and Vallenet, D},
title = {PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag948},
pmid = {42831354},
issn = {1362-4962},
support = {//French Alternative Energies and Atomic Energy Commission/ ; 101082304//Horizon Europe Program/ ; //Priority Antibiotic Resistance Research Program (PPR Antibiotic Resistance)/ ; //General Secretariat for Investment (SGPI)/ ; ANR-25-CE45-7210//Agence Nationale pour la Recherche/ ; ANR-21-ESRE-0048//Agence Nationale pour la Recherche under France 2030/ ; //ABRomics/ ; },
abstract = {PanGBank (https://pangbank.genoscope.cns.fr) is a comprehensive open-access database providing precomputed prokaryotic pangenomes at a broad taxonomic scale. Built upon PPanGGOLiN partitioned pangenome graphs, PanGBank addresses the growing need for large-scale comparative genomics through a standardized, regularly updated, and fully accessible resource. The initial release comprises two complementary collections covering >4600 prokaryotic species from the Genome Taxonomy Database (GTDB), encompassing over 393 000 genomes: GTDB_all, maximizing taxonomic and environmental diversity through the inclusion of metagenome-assembled genomes and single-cell amplified genomes, and GTDB_refseq, focusing on high-quality, annotation-rich genomes. Each species-level pangenome integrates graph-based statistical partitions into persistent, shell, and cloud gene families, together with regions of genomic plasticity (panRGP) and co-localized functional modules (panModule). PanGBank offers multiple access modes, including a REST API, a command-line interface, and an interactive web interface. By combining large-scale pangenome resources with advanced graph-based analyses, PanGBank provides a scalable framework for exploring microbial diversity, genome evolution, functional variation, and the dissemination of adaptive traits across prokaryotic populations, as illustrated by a use case on Acinetobacter baumannii pangenome investigating the distribution and evolution of antimicrobial resistance determinants.},
}

@article {pmid42831379,
year = {2026},
author = {Huang, S and Tang, Y and Wang, Z and Li, D},
title = {Biofilm-associated microbial risks in a mega water diversion project: distribution of putative pathogen-associated taxa and concrete biocorrosion potential in the Middle Route canal of the South-to-North water diversion project.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2026.2742367},
pmid = {42831379},
issn = {1029-2454},
abstract = {The ecological assembly of putative pathogen-associated taxa and the biogeochemical potential related to concrete biocorrosion have rarely been examined within an integrated framework in large freshwater diversion systems. We conducted quarterly biofilm sampling at eight stations along the Middle Route canal of the South-to-North Water Diversion Project, and combined 16S rRNA gene amplicon sequencing with shotgun metagenomics to characterize longitudinal and seasonal microbial patterns. Taxonomy-based screening identified 279 putative pathogen-associated ASVs with a mean relative abundance of 3.40%, primarily affiliated with Bacillus and Brevundimonas. Their relative abundance was lowest in the middle reaches, where higher flow velocity and dissolved oxygen may reduce biofilm-associated retention. Total nitrogen accounted for the largest individual contribution among the measured environmental variables (6.13%), whereas normalized stochasticity ratios indicated that stochastic processes predominated in overall community assembly. Metagenomic analysis further revealed spatially structured nitrogen- and sulfur-cycling potential, including biocorrosion-associated taxa such as Thiobacillus and Desulfovibrio, with several related functional pathways showing comparatively higher abundances in upstream biofilms. These findings establish an integrated ecological framework in which stochastic assembly, nutrient-associated selection, and hydrodynamic modulation jointly shape biofilm-associated microbial risks. The study provides critical insights for safeguarding both water-quality monitoring and century-scale infrastructure performance in mega water diversion systems.},
}

@article {pmid42831621,
year = {2026},
author = {Espinoza, JL and Phillips, AJ and Dupont, CL},
title = {Leviathan: fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0097026},
doi = {10.1128/msystems.00970-26},
pmid = {42831621},
issn = {2379-5077},
abstract = {Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing resource requirements, while translated searches in protein space lose classification resolution from ambiguous mapping events. Leviathan's utility is demonstrated through two case studies: a marine plastisphere metagenomics data set analyzing metabolic shifts between early and mature biofilm communities, and a dental caries metatranscriptomics data set where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.IMPORTANCEUnderstanding what microbes can do, not just which ones are present, is central to translating microbiome research into actionable insight. Existing functional profiling tools either rely on fixed reference databases or require complex multi-step pipelines when applied to custom genome collections, and none natively compute per-(pan)genome pathway abundance and graph-based pathway completeness in a single workflow. This limits the ability for researchers to directly compare functional profiles to tangential analyses on their specific genome catalogs. Leviathan addresses this gap with integrated taxonomic and functional profiling against user-defined (pan)genome-resolved references using pseudo-alignment, achieving competitive classification accuracy, with lower resource requirements compared to current methods. Native pangenome support enables routine quantification of metabolic potential and transcriptional activity at both genome and pangenome resolution, revealing functional variation across related strains that single-genome or community-level analyses obscure.},
}

@article {pmid42831635,
year = {2026},
author = {Pfaff, F and Meier, D and Seeholzer, A and Wunderlich, A and Einsiedl, F and Lueders, T},
title = {Impacts of temperature on hydrogenotrophic denitrifying aquifer microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0120626},
doi = {10.1128/aem.01206-26},
pmid = {42831635},
issn = {1098-5336},
abstract = {Groundwater is a globally relevant drinking water resource, yet nitrate pollution from agriculture increasingly threatens its quality, especially in shallow, oxygen-rich aquifers where natural attenuation is limited. This study examined whether gaseous hydrogen can stimulate autochthonous chemolithoautotrophic denitrification in nitrate-polluted, gravel aquifer sediments, and whether this process remains effective across temperatures relevant for laboratory and field conditions. We hypothesized that both microbial community composition and the kinetics of nitrate reduction will change under distinct temperature regimes. Microcosm incubations of sediments from a nitrate-polluted aquifer successfully enriched native hydrogenotrophic denitrifiers. Denitrification activity was quantified at 12°C, 15°C, 20°C, and 25°C, with maximum rates ranging from ~1 to ~1.8 µmol g[-1] sediment day[-1], and average rates generally following the expected kinetic temperature responses. Higher temperatures supported greater microbial biomass and community diversity, including a broader range of denitrifiers. Nevertheless, a single population, a novel strain of Acidovorax defluvii, dominated the community across all temperatures. Unlike the heterotrophic type strain, it possessed a conserved, likely transferable gene cluster for hydrogen oxidation, hydrogen sensing, and CO2 fixation, as revealed by metagenomics. Although complete denitrifiers with hydrogen-oxidation capacity dominated at all temperatures, nitrite accumulated transiently below 15°C. The presence of aerobic respiration genes in all enriched denitrifiers indicates their ability to switch to oxygen as an electron acceptor if available. Our study demonstrates a notable presence of an autochthonous hydrogenotrophic denitrification potential in the studied aquifer and its effective stimulation by hydrogen injection alone. Furthermore, it identifies mass transfer constraints and redox control as targets for future process optimization.IMPORTANCENitrate contamination of groundwater remains a widespread challenge in agricultural regions, and effective in situ remediation strategies are urgently needed. Hydrogen-stimulated chemolithoautotrophic denitrification represents a promising, low-carbon approach, yet its robustness under environmentally relevant temperature conditions has remained unclear. Our findings show that indigenous aquifer microorganisms can rapidly and consistently perform hydrogenotrophic denitrification across a broad temperature range (12-25°C), driven by a dominant Acidovorax species with a specialized hydrogen-oxidizing gene cluster. Identification of a conserved, potentially transferable gene cluster conferring chemolithoautotrophic lifestyle is not only biotechnologically interesting but also contributes to debate about genomic and ecological definitions of microbial species. This demonstrates that hydrogen injection can reliably activate existing microbial potential without requiring bioaugmentation and that temperature-driven shifts in community composition do not compromise nitrate removal. These insights advance the development of hydrogen-based bioremediation strategies for nitrate-impacted aquifers.},
}

@article {pmid42832260,
year = {2026},
author = {Song, X and Jia, S and Chen, L and Cao, C and Chen, Z and Hang, L and Jiang, H and Chen, Z},
title = {Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001847},
pmid = {42832260},
issn = {2057-5858},
mesh = {Antarctic Regions ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; Phylogeny ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Oceans and Seas ; Metagenomics ; Biodiversity ; },
abstract = {Antarctic deep-sea ecosystems harboured unique and metabolically versatile micro-organisms that sustained key biogeochemical processes under extreme polar conditions. However, the genomic diversity and ecological functions of these sedimentary or deep-sea microbial communities remained largely unexplored. Here, we constructed a comprehensive deep-sea microbial dataset of the Antarctic Ocean (dsMDAO) by integrating three newly sequenced Prydz Bay sediment metagenomes with 22 publicly available datasets (9 seawater and 13 sediment samples), spanning water depths of ~300-3500 m. Genome binning yielded 186 metagenome-assembled genomes spanning 19 phyla, including 175 bacteria and 11 archaea, a substantial proportion of which represent previously uncharacterized species. Meanwhile, reads mapping with the available standard Kraken2 database (k2_standard) enabled the expansion of species richness of the dsMDAO database. Furthermore, functional annotation revealed diverse metabolic and ecological potentials, including carbon, nitrogen and sulphur cycling, as well as secondary metabolite biosynthesis, virulence-associated defence and cold-adaptation mechanisms. Sediment microbiomes exhibited higher phylogenetic and functional diversity, enriched in Thaumarchaeota and Chloroflexi, whereas seawater communities were dominated by Proteobacteria with more competitive biosynthetic and interaction potentials. Co-occurrence analyses further indicated complex and competitive networks in seawater versus modular and cooperative assemblages in sediments, reflecting distinct ecological strategies. Collectively, dsMDAO provides the first genome-resolved dataset of Antarctic deep-sea microbiota, revealing the hidden taxonomic and functional diversity that underpins ecosystem resilience in polar oceans. This resource lays a foundation for future ecological, evolutionary and biotechnological exploration of Antarctic microbial dark matter.},
}

Antarctic Regions
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Archaea/genetics/classification/isolation & purification
Metagenome
Phylogeny
*Microbiota/genetics
Geologic Sediments/microbiology
Oceans and Seas
Metagenomics
Biodiversity

@article {pmid42832270,
year = {2026},
author = {Almatrafi, R and Alqurainy, N and Hakami, M and Ajina, R and Alrabiah, S and Arafah, AM and Alotibi, RS and Aldriwesh, MG},
title = {Gut microbiome and healthy ageing: a systematic review of literature.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {10},
pages = {},
doi = {10.1099/mic.0.001779},
pmid = {42832270},
issn = {1465-2080},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Healthy Aging/physiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Aged ; Aging ; Centenarians ; Aged, 80 and over ; Longevity ; },
abstract = {The gut microbiome undergoes compositional and functional changes with ageing. However, microbial signatures specifically associated with healthy ageing, independent of age-related diseases, remain poorly defined. This systematic review aimed to identify compositional and functional features of the gut microbiome associated with healthy ageing. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic search was conducted using PubMed, Web of Science and ScienceDirect for studies published up to January 2026. The search strategy focused on gut microbiome, ageing and healthy terms. Risk of bias was assessed using the Newcastle-Ottawa Scale. Gut microbiome composition was reviewed across five predefined age groups, while the functional pathways were reviewed for older adults and centenarians. The included studies represented several regions, including recognized longevity hotspots, although geographic representation remained limited. Most studies used 16S rRNA gene sequencing (n=24; 58.5%), followed by shotgun metagenomics (n=13; 31.7%), both (n=3; 7.4%) or metaproteomics (n=1; 2.4%). Enrichment of specific taxa such as Akkermansia, Alistipes and Parabacteroides was consistently reported in centenarians, alongside distinct patterns in older adults and long-lived individuals. Functional profiling suggested differences in pathways related to amino acid catabolism, vitamin biosynthesis and pathways potentially linked to immune modulation, inflammatory processes and gut barrier support. This review provides the first structured synthesis of gut microbiome signatures associated with healthy ageing across the lifespan, highlighting consistent functional traits and the need for a wider geographic representation in future research. It supports standardized, multi-omics framework to identify robust biomarkers and potential microbiome-based interventions for promoting healthy ageing.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Healthy Aging/physiology
*Bacteria/classification/genetics/isolation & purification
Metagenomics
RNA, Ribosomal, 16S/genetics
Aged
Aging
Centenarians
Aged, 80 and over
Longevity

@article {pmid42832495,
year = {2026},
author = {Qian, Y and Song, Q and Xie, X and Deng, L},
title = {Codon-aware multi-scale feature fusion for metagenomic sequence classification.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359090},
doi = {10.1371/journal.pone.0359090},
pmid = {42832495},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Codon/genetics ; Algorithms ; Plasmids/genetics/classification ; Humans ; Chromosomes/genetics ; *Metagenome ; },
abstract = {Microorganisms exert profound influences on both natural ecosystems and human society. As the cornerstone of microbial research, metagenomics relies on the precise analysis of large-scale, multi-source genomic data. However, discriminating among diverse sequence types remains a formidable challenge. To address this, we present CamFi (Codon-aware Multi-scale Feature Fusion), a unified framework integrating overlapping nucleotide-triplet representations with multi-scale dilated convolutions for classifying prokaryotic chromosomes, eukaryotic chromosomes, plasmids, and viruses. Benchmark evaluations demonstrate strong mean F1 scores of 97.70% for eukaryotic chromosomes and 94.13% for plasmids. On the CAMI II marine dataset, CamFi achieved a weighted F1 of 82.65%, ranking second among six methods based on reported aggregate metrics. In a balanced four-class benchmark, CamFi attained a macro-F1 of 93.77%, compared with DeepMicroClass (90.03%) and the XGBoost stage of 4CAC (64.66%). These results establish CamFi as a competitive approach for unified metagenomic contig classification under the evaluated conditions.},
}

*Metagenomics/methods
*Codon/genetics
Algorithms
Plasmids/genetics/classification
Humans
Chromosomes/genetics
*Metagenome

@article {pmid42832513,
year = {2026},
author = {Yuan, X and Arany, Á and Formanek, A and Moreau, Y and Lähdesmäki, H and Vatanen, T},
title = {LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2741488},
doi = {10.1080/19490976.2026.2741488},
pmid = {42832513},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Models, Statistical ; Metagenome ; Normal Distribution ; },
abstract = {Longitudinal microbiome data are key to understanding the dynamics of microbial communities and their relationships with the host and environment. However, analysis of such data is challenging due to high dimensionality, compositionality, irregular sampling and temporal dependencies on external covariates. Existing analytical approaches typically address only subsets of these challenges, limiting their ability to yield biologically interpretable insights. We introduce LGTM, a probabilistic modeling framework that combines flexible non-linear longitudinal modeling with interpretable topic-based representations of the microbiome. LGTM simultaneously identifies microbial co-abundance patterns ("topics") and models how their proportions change over time and in relation to host and environmental covariates. Using multiple longitudinal human gut microbiome datasets, we demonstrate that LGTM identifies diverse microbial topics whose major patterns are reproducible across runs, while achieving competitive performance in imputation and forecasting tasks. A key strength of the framework is its interpretability: LGTM yields microbial topics with biologically interpretable taxonomic compositions and directly quantifies associations between covariates and microbial dynamics. LGTM is available at https://github.com/yuanx749/lgtm.},
}

Humans
*Gastrointestinal Microbiome
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Models, Statistical
Metagenome
Normal Distribution

@article {pmid42832582,
year = {2026},
author = {Garamszegi, LZ and Nagy, G and Klein, Á and Szentiványi, T and Vásárhelyi, Z and Markó, G and Zsebők, S and Soltész, Z},
title = {The effect of ULV-based mosquito control on target and non-target organisms in Hungary: An experimental field study.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {10},
pages = {e0014140},
doi = {10.1371/journal.pntd.0014140},
pmid = {42832582},
issn = {1935-2735},
abstract = {Ultra-low volume (ULV) insecticide spraying with deltamethrin as the active ingredient is widely used in mosquito control programs, yet its effectiveness against target mosquitoes and its ecological side effects remain poorly quantified under field conditions in Central Europe. Here, we experimentally evaluated the short-term impact of ground ULV spraying (using deltamethrin + Chrysanthemum cinerariaefolium extract) on both mosquito populations and non-target flying insects in Hungary using a paired before-after-control-impact (BACI) design. Mosquitoes were sampled with BG Sentinel traps, while non-target insects were collected using malaise traps. ULV treatment resulted in a significant reduction in mosquito abundance at treated sites, with an average decline of approximately 47%. Native and invasive mosquito species, including Aedes albopictus and Aedes koreicus, showed similar proportional decreases. However, treatment effectiveness varied substantially among sites and was influenced by initial mosquito abundance and wind conditions. In parallel, malaise trap samples revealed a marked decline in non-target flying insects, with reductions exceeding 40% across multiple taxonomic groups, particularly among small and medium-sized insects, and also when considering pollinator taxa together. Our results indicate that while ULV spraying can temporarily reduce mosquito abundance, it also imposes considerable short-term impacts on non-target insect communities, highlighting trade-offs between vector control and insect conservation within mosquito management programs.},
}

@article {pmid42832605,
year = {2026},
author = {Dong, H and Yang, A and Shan, W and Zhao, C and Li, X and Rui, B and Zhao, J and Wumaier, M and Peng, H and Ma, Y},
title = {First record of Phlebotomus sergenti (Diptera: Psychodidae) in China and its potential epidemiological implications.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {10},
pages = {e0014726},
doi = {10.1371/journal.pntd.0014726},
pmid = {42832605},
issn = {1935-2735},
abstract = {BACKGROUND: Leishmaniasis is a severe parasitic disease transmitted by sand fly bites. Phlebotomus sergenti is a principal vector of Leishmania tropica, causing anthroponotic cutaneous leishmaniasis (ACL) across the Mediterranean, North Africa, South Asia, and West Asia. The Xinjiang Uygur Autonomous Region, located in northwestern China, is a well-recognized endemic focus of visceral leishmaniasis (VL), with sporadic cutaneous leishmaniasis cases also documented in the region. Nevertheless, Ph. sergenti has never been reported in China prior to this study.

Field investigations were carried out in Artux City (July 2023) and Akto County (August-September 2024), Kizilsu Kirghiz Autonomous Prefecture, Xinjiang Uygur Autonomous Region. Sand flies were collected using light traps in livestock pens and residential areas. A total of 2,013 sand fly specimens were collected and 319 of them were identified through morphological examination of the pharynx, spermathecae, and genitalia, combined with molecular analysis of mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cyt b) genes. Among the identified specimens, 145 specimens were identified as Ph. sergenti (36 from Artux City, 109 from Akto County), representing the first record of this species in China. Phylogenetic analysis based on COI and Cyt b sequences showed that Chinese Ph. sergenti populations clustered with those from neighboring countries (e.g., Afghanistan), with no significant genetic differentiation between the two sampling localities. Metagenomic screening of pooled samples revealed the presence of Wolbachia endosymbionts but no detection of Leishmania spp., Trypanosoma spp. or Bartonella spp. in the collected Ph. sergenti specimens.

CONCLUSIONS/SIGNIFICANCE: This study represents the first confirmed record of Ph. sergenti in China, filling a critical gap in the distribution map of this medically important sand fly species. The occurrence of Ph. sergenti at the China-Kyrgyzstan border region suggests potential transboundary dispersal of this vector and underscores the need for enhanced surveillance and cross-border collaborative efforts to monitor the spread of leishmaniasis and other vector-borne diseases in Central Asia.},
}

@article {pmid42832823,
year = {2026},
author = {Saito, H and Makino, R and Yonezawa, H and Fujio, S and Higa, N and Yamahata, H and Adachi, T and Yoshimura, A and Sakiyama, Y and Takashima, H and Hanaya, R},
title = {Intraventricular black fungal hyphal masses caused by Cladophialophora bantiana: illustrative case.},
journal = {Journal of neurosurgery. Case lessons},
volume = {12},
number = {14},
pages = {},
doi = {10.3171/CASE26730},
pmid = {42832823},
issn = {2694-1902},
abstract = {BACKGROUND: CNS fungal infections are rare, life-threatening conditions primarily affecting immunocompromised hosts. While they typically present as brain abscesses, intraventricular proliferation of fungal hyphae is exceedingly rare, and its neuroendoscopic findings have seldom been reported.

OBSERVATIONS: A man in his 80s with a history of malignancies presented with a 1-month history of headache. Brain MRI showed contrast-enhancing lesions along the genu of corpus callosum and lateral ventricles, as well as a nonenhancing lesion protruding into the ventricles. Although these findings were atypical, an endoscopic biopsy was performed because the lesions showed a tendency to enlarge, raising suspicion of a malignant tumor. Neuroendoscopic examination revealed a black-pigmented intraventricular fungal mass, which was partially resected. Shotgun metagenomic analysis identified the pathogen as Cladophialophora bantiana.

LESSONS: C. bantiana exhibits marked neurotropism and is known to cause CNS fungal infections even in immunocompetent individuals. Although intraventricular extension of phaeohyphomycosis is extremely rare and preoperative differential diagnosis remains challenging, a nonenhancing lesion protruding into the ventricles was considered to reflect the presence of fungal hyphae in this case. https://thejns.org/doi/10.3171/CASE26730.},
}

@article {pmid42832944,
year = {2026},
author = {Li, X and Zhang, Z and He, M and Jin, Y and Li, D and Chen, B and Chen, X and Yang, H and Ni, Y and Lu, T and Qian, H},
title = {Risk assessment of antibiotic-resistant bacteria in global lakes and their hotspots.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143801},
doi = {10.1016/j.jhazmat.2026.143801},
pmid = {42832944},
issn = {1873-3336},
abstract = {Freshwater lakes are crucial hotspots that have fueled the global antimicrobial resistance crisis. However, the distribution patterns and health risks of antibiotic-resistant bacteria (ARB) in lakes remain largely unexplored at the global scale. In this study, we comprehensively examined 1268 metagenomic samples from lakes globally and identified 12,866 ARBs spanning 28 phyla. Furthermore, based on the co-carriage of resistance genes, mobile genetic elements, and virulence factors, we developed a three-tiered risk framework. This framework distinguishes a critical-risk group comprising six species (belonging to Enterobacteriaceae, Aeromonadaceae, and Pseudomonadaceae) that are phylogenetically closely related to known pathogens, exhibiting the highest resistance, mobility, and pathogenic potential. Geographically, these critical-risk ARBs are primarily concentrated in low-latitude lakes (Amazon Basin, Central Africa, South/Southeast Asia, and Central America). Using machine learning, we identified temperature and wind speed as the primary driving factors. From a One Health perspective, our results inform a clear action plan and pinpoint low-latitude lakes as the priority targets for surveillance. This highlights the urgent need to include ARB risk stratification in security frameworks for global aquatic ecology.},
}

@article {pmid42833075,
year = {2026},
author = {Wang, X and Wang, J and Rehman, A and Ming, H},
title = {Response mechanisms of marine microbial communities during sulfamethoxazole co-metabolic degradation.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108421},
doi = {10.1016/j.marenvres.2026.108421},
pmid = {42833075},
issn = {1879-0291},
abstract = {Antibiotics, as typical emerging contaminants posing significant ecological risks, are frequently detected in global coastal environments. Their biotransformation in marine environments depends on the stress responses of functional microbial communities, while the underlying response mechanisms remain unclear. Through integrated metagenomic and metabolomic approaches, this study systematically investigated the structural and functional responses of marine microbial communities during the co-metabolic degradation of sulfamethoxazole (SMX), a representative antibiotic. A marine microbial consortium was employed for SMX co-metabolism with alginate, prototypical marine natural organic matter, as the co-substrate. Results revealed that under SMX stress, the microbial community underwent a marked shift in OTU composition, alongside significant increases in richness and diversity. The dominant functional taxon Vibrionaceae exhibited a significant decrease in relative abundance from 97.0% to 82.7%, while Paracoccaceae with SMX degradation potential and other low-abundance (<0.01%) functional taxa were significantly enriched, collectively sustaining stable alginate metabolism and facilitating SMX co-metabolism. Co-occurrence network analysis revealed enhanced interspecies associations. Moreover, the functional profile of the microbial community was profoundly reshaped. Specifically, the microbial community activated adaptive responses, enhancing TCS activation, EPS and endospore production, flagellar motility and chemotaxis, antioxidant capacity and DNA repair, and antibiotic resistance, to mitigate the toxicity of SMX and its intermediates. Concurrently, metabolic strategies were altered via regulation of key pathways (e.g., carbohydrate metabolism and amino acid metabolism), which increased by 7.8% and 17.5% in relative abundance compared to the control, boosting energy supply and SMX-degrading enzyme synthesis to enable SMX co-metabolism. This study provides new insights into the response mechanisms of marine microbial communities to SMX stress and the ecological risk assessment of antibiotics in coastal waters.},
}

@article {pmid42833218,
year = {2026},
author = {Bushnell, B and Schulz, F and Villada, JC},
title = {RandomReadsMG: Rapid, realistic metagenome simulation at terabase scale for benchmarking and experimental design.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101384},
doi = {10.1016/j.xgen.2026.101384},
pmid = {42833218},
issn = {2666-979X},
abstract = {Realistic synthetic metagenomes are essential for benchmarking bioinformatics tools, guiding experimental design, and generating labeled data for artificial intelligence and machine learning. We present RandomReadsMG, an open-source metagenomic read simulator distributed with BBTools. It generates communities containing hundreds to 50,000 genomes in a single command and supports user-defined abundance profiles, configurable within-genome coverage variation, retained read provenance, sequencing errors, and library artifacts. Presets are provided for Illumina, Oxford Nanopore Technologies (ONT), and PacBio sequencing. In benchmarks, RandomReadsMG produced terabase-scale datasets in under 6 h while maintaining bounded memory use. Simulations based on empirical drinking water profiles preserved genome-level depth after remapping. Controlled pathogen spike-ins further showed how simulation can estimate thresholds for read detection and metagenome-assembled genome (MAG) recovery. RandomReadsMG provides a fast, reproducible framework for metagenomics benchmarking, biosurveillance study design, and large-scale synthetic data generation.},
}

@article {pmid42833252,
year = {2026},
author = {van Vorstenbosch, R and Esenkova, EE and Jonkers, DMAE and Elizalde Vilalta, M and de Graaf, MCG and Keszthelyi, D and Pachen, D and van Schooten, FJJ and Mujagic, Z and Smolinska, A},
title = {Investigating the presence of microbiota-based phenotypes in Irritable Bowel Syndrome.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/aeb043},
pmid = {42833252},
issn = {1752-7163},
abstract = {Irritable Bowel Syndrome (IBS) is heterogenous disorder of gut-brain interaction, with a key role for the dysregulated host-gut microbiota interplay. IBS subtyping is based only on symptoms of bowel habits, reflecting limited insight into underlying biological mechanisms. Aims: This study aimed to define microbiota-based IBS phenotypes and to compare these to traditional stool-based subtyping. Methods: The study utilised data from the Maastricht IBS cohort. Gut microbiota composition was analysed using shotgun metagenomic sequencing. Faecal volatile organic compounds (VOCs) were measured by gas chromatography mass spectrometry. Dietary intake and gastrointestinal and mental health symptoms were assessed using a food frequency questionnaire, the Dutch Healthy Diet-15 index, the Gastrointestinal Symptom Rating Scale, and Hospital Anxiety and Depression scores, respectively. Machine-learning approaches were applied to identify microbiota-based phenotypical clusters, which were compared with established Rome III subtypes, and associated with faecal VOCs, gastrointestinal symptom severity, diet and mental health. Results: 178 IBS patients and 134 healthy controls were included. Gut microbiota composition distinguished IBS patients from healthy controls with an AUCROC 0·8. This discriminatory profile was not associated with Rome III subtypes, while statistically significant associations were found with faecal VOCs profiles (i.e. R=0·67, p=4·46e-4) and symptom severity scores of abdominal pain (p=0·05), reflux (p=0·03), and diarrhoea (p=0·01) and depression (p<0·001). Dietary associations varied across clusters. Conclusion: These results suggest that gut microbiota profiling might provide a basis to define relevant IBS endotypes. Further exploration and validation efforts into this direction are needed using longitudinal studies to refine IBS patient stratification ultimately. .},
}

@article {pmid42828686,
year = {2026},
author = {Kazarina, A and Vaškevica, A and Senkāne, DE and Zayakin, P and Hušča, S and Vīksne, K and Pirsko, V and Sokolovska, L and Sergejeva, N and Nakurte, I and Pastare, L and Ruhl, S},
title = {Salivary microbiome responses to chlorhexidine and Coriandrum sativum essential oil mouthwashes in patients with periodontitis in a randomized 2-week clinical trial.},
journal = {Clinical oral investigations},
volume = {30},
number = {10},
pages = {},
pmid = {42828686},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology ; *Saliva/microbiology ; *Chlorhexidine/pharmacology ; *Microbiota/drug effects ; *Oils, Volatile/pharmacology ; Female ; Male ; *Periodontitis/drug therapy/microbiology ; *Coriandrum/chemistry ; Adult ; Middle Aged ; Porphyromonas gingivalis/drug effects ; },
abstract = {OBJECTIVES: To compare the short-term salivary microbiome effects of a Coriandrum sativum essential oil (CSEO) mouthwash, chlorhexidine (CHX) as a benchmark comparator, and water in patients with periodontitis.

MATERIALS AND METHODS: In this randomized three-arm trial, participants with periodontitis rinsed twice daily for 14 days with water, CSEO, or 0.12% CHX. Preclinical anti-Porphyromonas gingivalis and fibroblast cytotoxicity assays informed CSEO concentration selection. Shotgun metagenomic sequencing was performed on 54 saliva libraries, two per participant, from 27 participants sampled at baseline and week 2 (H2O n = 9, CSEO n = 8, CHX n = 10). Alpha diversity, within-subject Bray-Curtis change, and differential abundance were analysed longitudinally.

RESULTS: Both active agents inhibited P. gingivalis in vitro, with CHX showing greater potency. In the clinical trial, no statistically detectable difference between CSEO and water was observed for the primary species-level Bray-Curtis outcome (q = 0.413), alpha diversity (all q ≥ 0.259), or differential abundance. CHX showed greater species-level Bray-Curtis change than water (q = 0.020), lower species-level Simpson diversity (q = 0.014), and broad taxonomic restructuring.

CONCLUSIONS: Under the tested formulation and exposure conditions, CSEO did not produce a statistically detectable group-level salivary microbiome shift relative to water. CHX provided a benchmark for broad ecological perturbation. The CSEO null finding does not exclude modest or heterogeneous effects in a larger cohort.

CLINICAL RELEVANCE: No clinical benefit can be inferred from the absence of a detectable CSEO-associated microbiome shift. Larger studies integrating clinical, inflammatory, and direct functional outcomes are needed.

TRIAL REGISTRATION: ISRCTN79156900, retrospectively registered on 11 May 2026.},
}

Humans
*Mouthwashes/pharmacology
*Saliva/microbiology
*Chlorhexidine/pharmacology
*Microbiota/drug effects
*Oils, Volatile/pharmacology
Female
Male
*Periodontitis/drug therapy/microbiology
*Coriandrum/chemistry
Adult
Middle Aged
Porphyromonas gingivalis/drug effects

@article {pmid42828800,
year = {2026},
author = {Zhao, Z and Zhang, X and Shen, T},
title = {From relative dominance to overproliferation: clarifying microbial and sensory inference in mechanized Hongqu fermentation.},
journal = {International journal of food microbiology},
volume = {463},
number = {},
pages = {112091},
doi = {10.1016/j.ijfoodmicro.2026.112091},
pmid = {42828800},
issn = {1879-3460},
}

@article {pmid42826539,
year = {2026},
author = {Pu, S and Ye, Q and Gao, Z and Zhang, Y and Zhang, S and Zhang, J and Wu, Y},
title = {Williamsia profundi sp. nov., a novel deep-sea Actinomycetota isolate with versatile metabolic potential and specialized ecological adaptability.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126775},
doi = {10.1016/j.syapm.2026.126775},
pmid = {42826539},
issn = {1618-0984},
abstract = {The deep-sea biosphere hosts distinctive microbial communities with specialized adaptive traits, yet the mechanisms underpinning their physiological survival remain largely obscure. In this study a novel Gram-stain-positive, aerobic bacterium, designated strain SKLECPSW1[T], was isolated from the Eastern Indian Ocean at a depth of 5318 m. The strain grows optimally at 32 °C and has a DNA G + C content of 70.0 mol%. Its major fatty acids are C16:0, C18:1 ω9c, and 10-methyl-C18:0. Genome analysis revealed a versatile metabolic repertoire, including complete central carbon metabolic pathways, dissimilatory nitrate reduction to ammonium (DNRA), anaplerotic CO2 fixation, and multiple genes associated with environmental stress responses. Furthermore, CAZyme profiling and 12 putative biosynthetic regions suggested potential for complex carbohydrate processing and secondary-metabolite biosynthesis. Comparative 16S rRNA gene sequence analysis showed that strain SKLECPSW1[T] shared the highest sequence similarity with Williamsia aurantiaca B375[T] (98.3%). Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values with related Williamsia species ranged from 71.15% to 83.35% and 18.8% to 26.6%, respectively, supporting its novel status. Metagenomic analysis of 25 deep-ocean datasets showed broad high-identity genome-wide recruitment in 2 samples, with breadths of 45.60% and 34.64% at ≥95% nucleotide identity, remaining 42.76% and 34.09% at ≥97.5%. Complementary marker-gene analyses further supported the occurrence of low-abundance environmental populations related to W. profundi in these two samples. Collectively, strain SKLECPSW1[T] represents a novel species, for which the name Williamsia profundi sp. nov. is proposed. The type strain is SKLECPSW1[T] (= MCCC 1K09832[T] = JCM 37991[T]).},
}

@article {pmid42826548,
year = {2026},
author = {Huang, P and Zhang, M and Li, Q and Xu, H and Shou, H},
title = {Altered gut microbiota composition and function potential in polycystic ovary syndrome: a multicohort metagenome-assembled genomes study.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {327},
number = {},
pages = {115453},
doi = {10.1016/j.ejogrb.2026.115453},
pmid = {42826548},
issn = {1872-7654},
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) has been associated with gut microbial dysbiosis, but cross-cohort reproducibility and genome-resolved alterations remain insufficiently characterized.

METHODS: We integrated fecal shotgun metagenomic data from three independent PCOS cohorts comprising 169 participants. Taxonomic and functional profiles were generated using MetaPhlAn4 and HUMAnN, while de novo assembly and binning were used to reconstruct species-level genome bins (SGBs). Linear mixed models accounted for cohort heterogeneity. Phylogenetic, co-occurrence network, KEGG-based functional, and prevalence-bias analyses were performed. PCOS classification was evaluated across genus, species, and SGB layers using leakage-safe nested cross-validation and leave-one-cohort-out testing.

RESULTS: PCOS was associated with reduced species richness, contraction of the core microbiota, altered community structure, and lower microbial network connectivity in the two larger cohorts. Eleven species showed differential abundance, including enrichment of Phocaeicola vulgatus and Bacteroides uniformis in PCOS. Genome-resolved analysis recovered 540 dereplicated SGBs, including 32 putative novel species. SGB prevalence bias was phylogenetically structured and remained associated with distinct KEGG Orthology profiles after adjustment for genome length and completeness. PCOS-biased SGBs were enriched in phosphotransferase-system and carbohydrate-utilization functions, whereas Healthy-biased SGBs were enriched in carbon and amino-acid metabolic pathways. Species-level XGBoost achieved the highest internal discrimination (AUC 0.757), but leave-one-cohort-out performance declined substantially, indicating limited cross-cohort generalizability.

CONCLUSIONS: PCOS is associated with multi-resolution gut microbiome alterations, with several community-level features showing cross-cohort reproducibility. These findings extend from community structure to genome-resolved functional programs, refine candidate microbial biomarkers, and highlight the need for external validation before clinical translation.},
}

@article {pmid42826561,
year = {2026},
author = {Zhang, Y and Wu, H and Zhang, X and Wu, Y and Hysen, L and Liu, Y and Zhang, H and Yang, J and Fu, L and Xiao, M and Lu, L and Zhang, Z and Zhang, J and Zhu, D},
title = {Protected area management contexts are associated with variation in Tibetan macaque gut microbiota and antibiotic resistomes.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120878},
doi = {10.1016/j.ecoenv.2026.120878},
pmid = {42826561},
issn = {1090-2414},
abstract = {Protected areas (PAs) are central to global biodiversity conservation and differ in their management contexts and associated patterns of human activity, yet differences in wildlife gut microbiota and antibiotic resistomes across PAs remain poorly understood. This study employed metagenomic analyses to compare the gut microbiota and resistomes of Tibetan macaques (Macaca thibetana) across three PAs in China with differing management contexts: Emeishan Scenic Area (EMS), where ecotourism is prominent; the Tangjiahe sector of Giant Panda National Park (TJH), where ecotourism is permitted but regulated; and Mabian Dafengding National Nature Reserve (MB), where tourist access is prohibited but livelihood-related resource use persists. Results showed that the MB population was characterized by higher gut microbial diversity and antibiotic resistance gene (ARG) abundance, with broader repertoires of potential pathogen taxa and high-risk ARGs. In contrast, potential pathogen signals in EMS and TJH were dominated by a single taxon, while EMS also showed a high-abundance signal of high-risk ARGs dominated by erm(B). Study area, gut microbiota and mobile genetic element (MGE) profiles were independently associated with gut ARG composition. This study provides a new perspective for global wildlife conservation and supports incorporating microbiota and resistome surveillance into protected-area management.},
}

@article {pmid42826574,
year = {2026},
author = {Wu, C and Zhang, H and Chen, L},
title = {Evaluation of protein sequence retrieval via protein language model embeddings and FAISS.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 1},
pages = {109411},
doi = {10.1016/j.compbiolchem.2026.109411},
pmid = {42826574},
issn = {1476-928X},
abstract = {Protein sequence similarity search underpins function annotation, evolutionary analysis, and metagenomic mining, yet conventional alignment-based methods face two persistent difficulties. First, their computational cost grows linearly with database size, making them impractical for billion-scale repositories. Second, their sensitivity declines below 30% sequence identity (the "twilight zone"), limiting remote homolog detection. Protein language models (PLMs) produce evolutionarily informative embeddings through self-supervised learning; however, the systematic integration of PLM embeddings with vector search into online retrieval services, together with experimental characterisation across model variants and index types, has received limited attention. We present ProtFaiss, combining ESM2 embeddings with FAISS approximate nearest neighbour search. On SCOPe40, we evaluate classification accuracy, ranking quality, remote homology sensitivity, retrieval speed, and storage footprint. Ablations spanning index type, model capacity, database scale, pooling strategy, and layer selection characterise the design space. ProtFaiss vector search completes in ∼0.02ms per query - roughly 3×10[5]-fold faster than a BLASTp database scan - and, including ESM2 encoding, the end-to-end latency is ∼30ms, approximately 200-fold faster than BLASTp. ProtFaiss achieves remote homology sensitivity of 7.7% (BLASTp: 6.7%), concentrated in the 15%-25% identity range. A notable finding is that intermediate Transformer layers substantially outperform the final layer: ESM2-650M layer 22 achieves Recall@10 of 0.780, compared with 0.431 for the final layer, suggesting later layers trade global semantic signal for local structural detail. A learned attention-pooling analysis and a preliminary Flat-index evaluation on multi-domain Swiss-Prot proteins further qualify this interpretation: learned pooling partially recovers final-layer performance, whereas intermediate layers remain advantageous in both evaluations. These results support the feasibility of PLM-based retrieval for large-scale protein search; however, generalisability is constrained by the single-domain benchmark.},
}

@article {pmid42826797,
year = {2026},
author = {Cao, B and Yi, Y and Xie, B and Liu, H},
title = {High-sensitivity heavy metal toxicity detection by Acinetobacter baylyi C8: Association with EPS protein deficiency.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135994},
doi = {10.1016/j.biortech.2026.135994},
pmid = {42826797},
issn = {1873-2976},
abstract = {Heavy metal contamination remains a persistent threat to water quality and ecological safety. Although electroactive microorganism (EAM)-based sensing technologies have shown promise for toxicity monitoring, their practical application is constrained by limited sensitivity. Here, we developed a strategy to improve monitoring performance by identifying and exploiting heavy metal-sensitive EAMs from mixed microbial communities. We successfully identified and isolated Acinetobacter baylyi C8 as a highly sensitive strain by integrating metagenomic analysis of mixed EAM communities under metal stress with electrochemical plate-based isolation. In bioelectrochemical sensing systems, C8 showed current-inhibition responses to eight representative heavy metals that were approximately one order of magnitude higher than those of mixed EAMs. For Cd[2+] and Pb[2+], good linear responses were obtained, with detection limits of 0.0157 and 0.0205 mg/L, respectively. C8 also responded consistently to binary and ternary heavy metal mixtures, while common coexisting ions caused little interference with Cd[2+] and Pb[2+] responses. Stable performance was maintained in drinking water, river water, and lake water, with deviations below 5 %. Further analyses showed that the high sensitivity of C8 was associated with low protein content in extracellular polymeric substances (EPS), greater intracellular metal accumulation, and stronger oxidative, metabolic, and electron-transfer disturbances. Overall, this study provides a practical route for identifying heavy metal-sensitive EAMs from mixed communities and highlights their potential for improving bioelectrochemical monitoring of heavy metal toxicity in water environments.},
}

@article {pmid42827076,
year = {2026},
author = {Stensvold, CR},
title = {From patients to populations: biological interpretation in molecular parasitology.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.09.010},
pmid = {42827076},
issn = {1471-5007},
abstract = {Molecular diagnostics have transformed clinical parasitology and molecular epidemiology. As analytical detection continues to improve, biological interpretation must develop alongside it. I would propose integrating complementary evidence and using clinically characterized reference datasets to calibrate biological inference from high-throughput molecular studies, providing a shared interpretative framework from patients to populations.},
}

@article {pmid42827198,
year = {2026},
author = {Tawk, C and El Mouali, Y and Huang, KD and Valkiers, S and Heidrich, V and Gronow, A and Osbelt, L and Rapp, J and Link, H and Segata, N and Typas, A and Strowig, T},
title = {Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42827198},
issn = {2058-5276},
support = {390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1343/15-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1343/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Healthy human gut microbiota is dominated by Bacteroidaceae in industrialized populations and by Prevotellaceae in those with traditional lifestyles, but diet alone is insufficient to explain this dominance of different Bacteroidota. Here we screened 94 dietary components in synthetic gut communities and find that these two bacterial families compete for overlapping nutritional niches. Segatella copri, a key member of Prevotellaceae-rich communities, outcompeted Bacteroidaceae when preferred polysaccharides such as arabinan were available, but this advantage depended on community composition, particularly the presence of Enterobacteriaceae. Metatranscriptomics and targeted metabolomics further revealed that Enterobacteriaceae synergized with dietary components to promote Segatella dominance in human and mouse gut communities. These interactions were validated by using multiple E. coli and Segatella isolates. Analyses of global metagenomes also showed a positive correlation between Segatella-rich non-industrialized microbiomes and Enterobacteriaceae abundance. Our results establish an ecosystem-level dynamic interplay between dietary components and key gut commensals that favour the dominance of Prevotellaceae.},
}

@article {pmid42827448,
year = {2026},
author = {Imokhai, PO and Metellus, R and Karsten, M and Alhoda, M and Gandhi, S and Ogbuefi, C and Carranza, S and Zhang, J and Lee, D and Brooks, A},
title = {An interdisciplinary scoping review of the emerging impact of periocular skincare products on the ocular surface microbiome and tear film stability.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1898798},
pmid = {42827448},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/drug effects ; *Tears/drug effects/chemistry ; *Cosmetics/adverse effects ; *Eye/microbiology/drug effects ; Personal Care Products ; Bacteria/classification/drug effects ; Meibomian Gland Dysfunction ; Meibomian Glands/drug effects ; },
abstract = {BACKGROUND: The healthy ocular surface microbiome consists of Actinobacteria, Proteobacteria, and Firmicutes phyla, with Corynebacterium, Propionibacterium, and Staphylococcus as dominant genera. This microbial environment is essential for maintaining immune homeostasis and barrier integrity.

OBJECTIVE: To synthesize existing evidence on how periocular skincare and cosmetic products affect the ocular surface microbiome, tear film stability, and downstream ocular surface disease.

METHODS: A systematic literature search was conducted across PubMed, Cochrane Library, Embase, Web of Science, and Scopus using Boolean MeSH term strategies. Studies from 2010 to present evaluating microbial composition of the ocular surface and the effects of exogenous exposures (cosmetics, contact lenses, medications) were included.

RESULTS: Preservatives (benzalkonium chloride, parabens), surfactants, retinoids, and essential oils (tea tree oil/terpinene-4-ol) disrupt the ocular surface through non-selective microbial depletion, epithelial cytotoxicity, and lipid emulsification. These mechanisms contribute to meibomian gland dysfunction (MGD), blepharitis, and evaporative dry eye - all associated with characteristic dysbiotic microbiome shifts. Advanced sequencing technologies, including 16S rRNA gene sequencing and shotgun metagenomics, reveal taxon-level changes and functional alterations linked to inflammation and tear film instability.

CONCLUSIONS: Periocular product ingredients represent an underappreciated source of ocular surface dysbiosis. Regulatory gaps under current FDA and MoCRA frameworks limit ingredient-level safety evaluation. Future longitudinal studies using functional metagenomics, metabolomics, and standardized microbiome-specific testing pipelines are urgently needed.},
}

Humans
*Microbiota/drug effects
*Tears/drug effects/chemistry
*Cosmetics/adverse effects
*Eye/microbiology/drug effects
Personal Care Products
Bacteria/classification/drug effects
Meibomian Gland Dysfunction
Meibomian Glands/drug effects

@article {pmid42827647,
year = {2026},
author = {Huang, Z and Liang, J and Pan, Y and Lao, J},
title = {Cryptococcosis in a seemingly immunocompetent patient presenting with knee and lower limb soft tissue infection complicated by meningitis: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1847042},
doi = {10.3389/fmed.2026.1847042},
pmid = {42827647},
issn = {2296-858X},
abstract = {Cryptococcus neoformans typically causes pulmonary or central nervous system (CNS) infections. However, osteoarticular manifestations, particularly as the initial presentation, are rare, especially in immunocompetent hosts. We report the case of a 65-year-old apparently immunocompetent woman admitted for generalized pain following a fall. Ten days post-admission, she developed fever and rapidly progressing soft tissue swelling in the right lower limb and knee. Despite the absence of overt immunodeficiency, the infection disseminated, leading to meningitis. Diagnosis was confirmed via fungal culture of lower limb secretions and metagenomic next-generation sequencing (mNGS) of knee joint tissue. Despite aggressive antifungal therapy, the patient's condition deteriorated, resulting in a fatal outcome. This case underscores the diagnostic challenge of cryptococcal osteoarticular infections in immunocompetent individuals. It highlights the utility of mNGS in diagnosing culture-negative infections and serves as a reminder that cryptococcosis should be considered in the differential diagnosis of fever of unknown origin with musculoskeletal involvement, even in the absence of traditional risk factors.},
}

@article {pmid42827663,
year = {2026},
author = {Li, P and Yang, X and Chen, Y and Wang, L and Cui, Q and Wu, Z and Cao, F},
title = {When metagenomic next-generation sequencing detects Nocardia: from clinical interpretation to immune-based clinical management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1911562},
doi = {10.3389/fcimb.2026.1911562},
pmid = {42827663},
issn = {2235-2988},
mesh = {Humans ; *Nocardia Infections/diagnosis/microbiology/immunology/drug therapy ; *Nocardia/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Female ; Male ; Middle Aged ; Aged ; Immunocompromised Host ; Risk Factors ; Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) increasingly detects Nocardia, but interpreting positive results remains challenging. We aimed to identify host factors and read thresholds that distinguish nocardiosis (ND) from colonization/contamination, and to characterize clinical features linked to immune status.

METHODS: A retrospective analysis from 74 patients at Qilu Hospital of Shandong University from April 2022 to October 2025 was conducted. We assessed mNGS for distinguishing Nocardia infection from colonization or contamination, identified risk factors for nocardiosis, and compared patients' clinical features, imaging findings, and antimicrobial adjustments.

RESULTS: A total of 56 patients with ND and 18 non-ND patients were included. Multivariate logistic regression identified farming exposure, bronchiectasis, and immunocompromised status were significantly associated with ND. An estimated read per million (RPM) thresholds of 56 could distinguish Nocardia infection from colonization/contamination (AUC 0.774; 95% CI, 0.654 - 0.895), with a higher sensitivity than traditional tests (P < 0.001). In ND group, immunosuppressed patients (ISPs) (42.9%) had more pulmonary interstitial fibrosis (29.17% vs. 6.25%, P = 0.03), lymphadenopathy (62.50% vs. 40.63%, P = 0.046) and fungal co-infections (54.17% vs. 18.75%, P = 0.006), while bronchial wall thickening was more common in immunocompetent patients (ICPs) (31.25% vs. 4.17%, P = 0.019). Nocardia was the sole pathogen in 42.9% of true infection cases, and mNGS led to a change in anti-Nocardia management in 87.5% of patients.

CONCLUSION: Our study indicated mNGS is a useful tool for distinguishing Nocardia infection from colonization/contamination, and immune-based phenotyping may guide individualized management strategies for patients with nocardiosis.},
}

Humans
*Nocardia Infections/diagnosis/microbiology/immunology/drug therapy
*Nocardia/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Female
Male
Middle Aged
Aged
Immunocompromised Host
Risk Factors
Adult

@article {pmid42827939,
year = {2026},
author = {Yang, H and Lei, X},
title = {Diagnostic Challenges in mNGS for Pulmonary Mucormycosis Presenting with Imaging Features Resembling Those of Lung Cancer.},
journal = {International medical case reports journal},
volume = {19},
number = {},
pages = {616885},
doi = {10.2147/IMCRJ.S616885},
pmid = {42827939},
issn = {1179-142X},
mesh = {Humans ; *Mucormycosis/drug therapy/diagnosis/diagnostic imaging ; Female ; Antifungal Agents/therapeutic use ; Aged ; *Lung Diseases, Fungal/drug therapy/diagnosis/diagnostic imaging/microbiology ; *Lung Neoplasms/diagnosis/diagnostic imaging ; Amphotericin B/therapeutic use ; Diagnosis, Differential ; *Bronchoalveolar Lavage Fluid/microbiology ; *Rhizopus oryzae/isolation & purification/genetics ; Triazoles/therapeutic use ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Pulmonary mucormycosis is a rare fungal infection with an increasing incidence in clinical reports. Its non-specific presentation often mimics lung cancer, posing significant diagnostic challenges. This report aims to improve clinician recognition of this condition.

CASE PRESENTATION: A 67-year-old woman with diabetes presented with cough and sputum production. Imaging revealed a right hilar mass with bronchial obstruction, mediastinal lymphadenopathy, and cystic cavities (Figure 1A). While initial suspicion favored lung cancer, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) detected Rhizopus oryzae (26,879 sequences), prompting revision of the diagnosis. Antifungal therapy with amphotericin B and posaconazole resulted in clinical improvement. Follow-up imaging at 67 days showed resolution of mucormycosis (Figure 1B).

CONCLUSION: This case highlights the diagnostic challenge of pulmonary mucormycosis masquerading as malignancy. mNGS serves as a valuable tool for early pathogen identification, though its role in therapeutic monitoring requires further investigation.},
}

Humans
*Mucormycosis/drug therapy/diagnosis/diagnostic imaging
Female
Antifungal Agents/therapeutic use
Aged
*Lung Diseases, Fungal/drug therapy/diagnosis/diagnostic imaging/microbiology
*Lung Neoplasms/diagnosis/diagnostic imaging
Amphotericin B/therapeutic use
Diagnosis, Differential
*Bronchoalveolar Lavage Fluid/microbiology
*Rhizopus oryzae/isolation & purification/genetics
Triazoles/therapeutic use
High-Throughput Nucleotide Sequencing
Tomography, X-Ray Computed

@article {pmid42827961,
year = {2026},
author = {Hughes, AE and Castillo-Sevilla, AM and Berlemont, R},
title = {Phylogeny constrains and environment modulates glycoside hydrolase architecture.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100658},
doi = {10.1016/j.crmicr.2026.100658},
pmid = {42827961},
issn = {2666-5174},
abstract = {Glycoside hydrolases (GHs) are central to microbial carbohydrate degradation and frequently occur as multidomain proteins containing accessory domains involved in substrate binding, localization, and retention. However, the extent to which GH multidomain architectures are shaped by phylogeny versus environmental adaptation remains poorly understood. Here, we analyzed 158,829 GH-containing proteins from 17,108 high-quality metagenome-assembled genomes (MAGs) in the GEM catalog, focusing on major GH families involved in polysaccharide and oligosaccharide degradation. We developed domain-domain adjacency networks (DANs) to quantify multidomain organization and compared network weighted architectural similarity across bacterial genera and environments. GH architectures were highly conserved within genera, with bootstrapped DANs displaying stable network properties and distinct lineage-specific architectural similarities, indicating strong phylogenetic constraints on domain organization. Accessory domains associated with substrate targeting and enzyme retention represented approximately 61% of non-catalytic partner domains, highlighting their importance in GH evolution. Although phylogeny was the dominant determinant of multidomain architecture, environmental effects were detected in cosmopolitan genera. Environmental variation had a limited and lineage-dependent influence on GH abundance but more consistently affected the prevalence of multidomain GHs, particularly within GH3, GH13, and GH18 families. These results support a hierarchical model in which phylogeny establishes a conserved framework of GH organization, while environmental pressures fine-tune multidomain architectures. Our study demonstrates that protein domain architecture represents an important and previously underappreciated dimension of microbial functional adaptation and provides a scalable network-based framework for linking enzyme organization to ecological function.},
}

@article {pmid42828099,
year = {2026},
author = {De Smedt, M and Cuypers, WL and Hudda, NU and Delputte, P},
title = {Sequencing the wastewater virome: Current strategies and bioinformatic pitfalls.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117596},
doi = {10.1016/j.isci.2026.117596},
pmid = {42828099},
issn = {2589-0042},
abstract = {Wastewater-based surveillance (WBS) is a powerful tool for monitoring viral pathogens at the population level, complementing clinical surveillance through anonymous and unbiased insights into viral circulation. Wastewater sequencing allows to move beyond detection toward detailed characterization of circulating pathogens. This review outlines the two main sequencing strategies used in WBS: targeted and untargeted approaches. Targeted methods, including amplicon- and probe-based sequencing, provide sensitive detection and recovery of known viruses but are limited in identifying novel pathogens. Untargeted shotgun metagenomic sequencing offers a broader, unbiased view of the wastewater virome, although its performance is challenged by low human viral abundance, complex background signals, and genome assembly challenges. We also discuss key challenges complicating bioinformatic analysis, including limited human viral sequences, co-circulating viral lineages, viral dark matter, reference database limitations, large data volumes, and methodological biases, as well as emerging computational approaches aimed at improving wastewater sequencing analysis and interpretation.},
}

@article {pmid42828306,
year = {2026},
author = {Wayah, SB and Arakawa, K and Philip, K},
title = {From predicted bacteriocins to ecological function.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100662},
doi = {10.1016/j.crmicr.2026.100662},
pmid = {42828306},
issn = {2666-5174},
abstract = {Genome and metagenome mining have uncovered large repertoires of predicted bacteriocin loci, but ecological interpretation has lagged behind discovery. This review uses bacteriocins as a focused model for a broader problem in antimicrobial gene prediction: sequence identifies encoded potential, but it does not establish expression, product deployment, target engagement, or community-level consequence. We distinguish four forms of bacteriocin "silence": transcriptional silence, where loci are not detectably expressed under tested conditions; conditional silence, where expression or activity emerges only under specific environmental or social cues; phenotypic silence, where expression or product formation does not yield detectable activity in routine assays; and ecological silence, where activity is observed but its consequences for coexistence, exclusion, colonization, or community assembly remain unresolved. We also clarify how this framework extends previous reviews of bacteriocin diversity and microbiome-shaping roles by providing an inference-centered taxonomy that separates encoded potential from demonstrated ecological function. Finally, we propose a function-first roadmap for bacteriocin research, including condition-resolved transcriptomics and proteomics, promoter and cue-dissection experiments, expanded target panels, spatially structured assays, defined consortia and microcosms, producer/non-producer comparisons, and explicit tests of resistance, immunity, and fitness consequences. Treating predicted bacteriocin loci as hypotheses rather than conclusions will improve how the field moves from gene catalogs to causal ecological understanding.},
}

@article {pmid42828409,
year = {2026},
author = {Song, Y and Xing, Y and Liu, Y and Zhang, X},
title = {Forensic applications of the skin microbiome: a structured narrative review of donor association, contact inference, and crime-scene reconstruction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1947173},
doi = {10.3389/fmicb.2026.1947173},
pmid = {42828409},
issn = {1664-302X},
abstract = {BACKGROUND: Skin-associated microbial communities are individualized, anatomically structured, temporally dynamic, and readily transferred to contacted surfaces. These properties have generated interest in the skin microbiome as complementary forensic evidence when conventional human DNA or fingerprint evidence is limited.

METHODS: We conducted a structured narrative review guided by the Scale for the Assessment of Narrative Review Articles (SANRA). PubMed/MEDLINE was searched from database inception through 2 August 2026, and reference lists of eligible studies and recent reviews were examined. Peer-reviewed studies were evaluated for relevance to skin microbial individuality, temporal stability, touch transfer, donor or source inference, postmortem interval estimation, analytical standardization, and legal or ethical interpretation. Evidence was synthesized according to study realism, analytical resolution, validation design, and proximity to forensic casework.

RESULTS: The biological basis for forensic use is supported by reproducible inter-individual and body-site variation, including persistent strain- and gene-level features. Controlled studies show that skin-associated communities can be recovered from touched objects and clothing and can support donor differentiation, particularly when targeted markers, microbial single-nucleotide polymorphisms, or metagenomic features are used. Nevertheless, performance estimates are strongly affected by cohort size, body site, substrate, time since deposition, environmental background, contamination, and machine-learning design. Evidence for body-site and biological-trace source inference is promising, whereas postmortem interval estimation, chronological contact reconstruction, and spatial trajectory inference remain exploratory.

CONCLUSION: Skin microbiome profiling should currently be regarded as a source of investigative intelligence and potentially complementary evidence rather than a replacement for human DNA profiling. Translation into practice requires harmonized protocols, realistic multicenter validation, open and representative reference datasets, explicit error-rate reporting, likelihood-based interpretation, and proportionate ethical and legal safeguards.},
}

@article {pmid42322606,
year = {2026},
author = {Sinha, A and Qian, A and Boutin, T and Maurice, CF},
title = {Prophage induction contributes to alterations in the gut phageome during intestinal inflammation.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {117491},
doi = {10.1016/j.celrep.2026.117491},
pmid = {42322606},
issn = {2211-1247},
mesh = {*Prophages/classification/metabolism ; *Gastrointestinal Microbiome ; Virome ; Dextran Sulfate ; Animals ; Mice ; Colitis/chemically induced/immunology/microbiology/virology ; T-Lymphocytes ; Mice, Inbred C57BL ; Datasets as Topic ; Metagenome ; Biodiversity ; *Inflammatory Bowel Diseases/metabolism/microbiology/pathology/virology ; Germ-Free Life ; *Bacteria/growth & development/metabolism/virology ; },
abstract = {Bacteriophages (phages) are abundant members of the gut microbiota and regulators of bacterial communities. During homeostasis, gut phage communities are longitudinally stable and lysogenic replication is dominant. In chronic gut inflammatory disorders, such as inflammatory bowel diseases (IBDs), there are alterations in phage diversity, which may result from changes in phage replication cycles. Here, we use a combination of in vitro, simplified community, and whole-community bioinformatics approaches to investigate whether prophage induction contributes to these alterations. We identify several compounds associated with gut inflammation that induce prophages from commensal gut bacterial isolates. Analyzing data from two mouse models of colitis, we observe that shifts in the composition of temperate phages occur over the course of inflammation, supporting a switch from lysogenic to lytic replication. Collectively, our observations support the idea that prophage induction contributes to alterations in the phageome associated with intestinal inflammation.},
}

*Prophages/classification/metabolism
*Gastrointestinal Microbiome
Virome
Dextran Sulfate
Animals
Mice
Colitis/chemically induced/immunology/microbiology/virology
T-Lymphocytes
Mice, Inbred C57BL
Datasets as Topic
Metagenome
Biodiversity
*Inflammatory Bowel Diseases/metabolism/microbiology/pathology/virology
Germ-Free Life
*Bacteria/growth & development/metabolism/virology

@article {pmid42822631,
year = {2026},
author = {Fu, Q and Ma, X and Sun, B and Liu, X and Wang, D},
title = {Dimethyl Phthalate Disrupts Sulfur Cycling and Triggers Toxic H2S Pollution in Sludge Anaerobic System.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125821},
doi = {10.1016/j.envres.2026.125821},
pmid = {42822631},
issn = {1096-0953},
abstract = {Dimethyl phthalate (DMP), a crucial plastic additive widely employed, has been detected in sewers, sediments, and sewage sludge at elevated levels, particularly in regions where active sulfur cycling occurs. However, the effect of DMP on anaerobic sulfur conversion, especially toxic H2S production, has not been documented. This study aimed to explore the fate of DMP in anaerobic system and its influence on sulfur conversion through both batch and long-term tests using sludge as substrate. Experimental results showed that sludge can effectively adsorb DMP, which conformed to the Freundlich model and pseudo-second-order adsorption kinetic model, with the equilibrium adsorption capacity of DMP in sludge system being 1.024 mg/g. ∼ 85% of DMP was biodegraded in anaerobic system, with monomethyl phthalate (MMP) and phthalic acid (PAA) as its main degradations. Additionaly, DMP presence at 20-200 mg/kg TSS significantly increased H2S gas production by 35.1%-71.7%. Although PAA and MMP can slightly promote H2S production, DMP was the main contributor. Multidimensional analyses showed that DMP spontaneously binds to the EPS of sludge and increases the secretion of EPS, as well as altering its physical and chemical properties (i.e., increasing its direct electron transfer capacity), thereby promoting the bioprocesses of organic sulfur hydrolysis and sulfur containing amino acids degradation. Metagenomic profiling confirmed this metabolic shift, showing an increase in the abundance of hydrolytic bacteria such as Ferruginibacter, as well as an increase in the abundance of organic sulfur metabolic genes such as pepD and aspB, which accelerated sulfide production from organic sulfur hydrolysis. These findings uncover a novel toxicity mechanism where DMP actively trigger hazardous gas emissions, highlighting unrecognized ecological risks in sulfur rich environmental compartments.},
}

@article {pmid42822808,
year = {2026},
author = {Burgess, AL and Bacela-Spychalska, K and Grabner, D and Lipinskaya, T and Johns, T and Bateman, KS and Ross, SH and Stentiford, GD and Bojko, J},
title = {Origins of the Nimaviridae: an ancient virus from the hepatopancreas of an invasive crustacean.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108756},
doi = {10.1016/j.jip.2026.108756},
pmid = {42822808},
issn = {1096-0805},
abstract = {The only recognised member of the Nimaviridae is white spot syndrome virus (WSSV), which causes billions in annual losses in the shrimp industry; this virus belongs to the Whispovirus genus. Many manuscripts are published each year that highlight the importance of understanding and controlling this virus, as well as attempting to figure out its origin. The evolutionary history of this economically important pathogen has been particularly difficult to unravel. Recently, several endogenous and exogenous nimaviruses have been discovered from decapod crustaceans, allowing insight into their genetic diversity, evolution, and virulence. We characterise an exogenous nimavirus infecting the hepatopancreas of the invasive amphipod, Dikerogammarus haemobaphes, putatively named 'Dikerogammarus haemobaphes amphinimavirus' (DhAV). Histopathology and fluorescence in situ hybridisation (FISH) are used to demonstrate that the virus primarily infects the nuclei of hepatopancreatic epithelia, similarly to their viral relatives, nudiviruses. Metagenomic tools were used to complete the circular 231,466 bp viral genome, which encodes a predicted 103 ORFs. Phylogenetic analysis suggests that this virus is an early diverging member of the Nimaviridae. The characterisation of DhAV opens doors to further evolutionary study, offering the potential to explore the genomic events that precede the emergence of one of aquacultures most deadly pathogens.},
}

@article {pmid42822929,
year = {2026},
author = {Nayak, SK and Bhattacharyya, P and Pradhan, C and Padhy, SR and Parida, SP and Das, A and Moharana, A and Rath, M and Nayak, A},
title = {Soil functional microbial pathways related to GHGs emissions of coastal degraded mangroves-rice ecologies in Sundarban, India: A soil metagenomic approach.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {344-357},
doi = {10.1016/j.jes.2025.12.050},
pmid = {42822929},
issn = {1001-0742},
mesh = {India ; *Wetlands ; *Soil Microbiology ; *Greenhouse Gases/analysis ; Oryza ; Methane/analysis ; Metagenomics ; *Environmental Monitoring ; Soil/chemistry ; },
abstract = {Mangroves and their adjacent rice ecologies play a critical role in regulating greenhouse gas (GHGs) emissions, particularly in tropical coastal wetlands. This study assessed the impact of mangrove degradation on methane (CH4) and nitrous oxide (N2O) emissions by comparing two distinct ecosystems; degraded mangroves, and adjacent rice system in the Sundarban, India. Annual CH4 and N2O emissions were quantified and linked to soil microbial energy metabolism pathways; methanogenesis, methanotrophy, sulphur (S), and nitrogen (N) metabolism by using whole-genome metagenomic analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs was used for functional microbial pathway analysis. Acetoclastic pathway was found to be the dominant CH4 production pathway in rice, where relatively low soil salinity favored CO2 to CH4 conversion. Methane oxidation was higher in degraded mangroves, driven by the serine and xylulose monophosphate pathways, reflecting microbial adaptation to saline and alkaline conditions. The assimilatory pathway (AMP) dominated S metabolism, with adenosine phosphosulfate kinase more abundant in degraded mangroves and adenosine triphosphate sulfurylase in rice ecology. Denitrification was the primary N pathway in degraded mangroves and adjacent rice systems, while dissimilatory nitrate reduction to ammonium (DNRA) prevailed in rice. A higher abundance of enzymes involved in acetate to methane production pathway was observed in rice systems, indicating greater CH4 production potential, whereas a higher abundance of phosphoserine aminotransferase in serine pathways in degraded mangroves suggested relatively higher potential for CH4 oxidation. These results demonstrate that targeted microbial management in mangrove-rice ecologies could serve as a promising strategy for climate change mitigation in coastal ecology.},
}

India
*Wetlands
*Soil Microbiology
*Greenhouse Gases/analysis
Oryza
Methane/analysis
Metagenomics
*Environmental Monitoring
Soil/chemistry

@article {pmid42822935,
year = {2026},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Feng, B and Zhang, B and Zhang, S and Fu, J},
title = {Sulfate addition enhanced antibiotic resistance in lake sediments by enriching resistant bacteria and promoting the potential of horizontal gene transfer.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {405-416},
doi = {10.1016/j.jes.2026.04.061},
pmid = {42822935},
issn = {1001-0742},
mesh = {*Lakes/microbiology/chemistry ; *Sulfates/analysis ; *Geologic Sediments/microbiology/chemistry ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Lake sediments represent a typical reservoir of antibiotic resistance genes (ARGs), an emerging contaminant. As a key nutrient for sediment microorganisms, elevated sulfate levels can profoundly influence sulfur cycling and related microbial processes. However, the impact of sulfate loads on the profiles of ARGs in lake sediments remains poorly understood. This study utilized a microcosm experiment to examine how sulfate addition at various concentrations (200, 400, and 600 mg/kg dry weight) affects the sediment resistome, via metagenomic analysis. Sulfate addition significantly increased sediment sulfides and the relative abundance of sulfate-reducing genes (SRGs). Notably, the high sulfate treatment (600 mg/kg) resulted in a significant rise in the relative abundance of ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), indicating an increased potential for resistance dissemination under high sulfate loading. The relative abundance of horizontal transfer related genes, including those mediating cell membrane permeability and type IV secretion system, was enhanced by sulfate addition, potentially promoting ARG dissemination. Linear regression identified strong positive relationships between the abundance of ARGs and abundances of both MGEs and VFGs. Sulfate addition enriched specific antibiotic-resistant bacteria (ARBs) carrying SRGs that were identified via network analysis. The genera Burkholderia, JACDDX01, and Hylemonella showed marked enrichment, with increases of 16.7 %, 13.2 %, and 94.6 %, respectively. Overall, the rise in ARG abundance under sulfate addition shows close links to specific ARBs and enhanced horizontal transfer. These findings have implications for understanding sulfate-driven changes in sediment resistome and assessing environmental risk in sulfate-enriched lake ecosystems.},
}

*Lakes/microbiology/chemistry
*Sulfates/analysis
*Geologic Sediments/microbiology/chemistry
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid42822967,
year = {2026},
author = {Xu, H and Hei, S and Yang, G and Fu, W and Zhang, X and Liang, P and Pan, B and Huang, X},
title = {Sustained anaerobic valorization of refractory wastewater into bioenergy via abiotic-biotic hybrid systems: Unraveling synergistic hydrolysis and optimized interspecies electron transfer.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {762-775},
doi = {10.1016/j.jes.2026.02.030},
pmid = {42822967},
issn = {1001-0742},
mesh = {*Waste Disposal, Fluid/methods ; *Wastewater/chemistry ; Anaerobiosis ; Bioreactors ; Hydrolysis ; Electron Transport ; },
abstract = {Anaerobic digestion (AD) of refractory industrial wastewater remains challenging due to structural recalcitrance and thermodynamic limitations. While abiotic-biotic hybrid systems incorporating electroactive materials (EMs) offer promise, their long-term efficacy and mechanisms at a system level, particularly with real industrial waste streams, are underexplored. This study demonstrates the sustained, system-level enhancement of anaerobic valorization using magnetite (Mag)- or pyrogenic carbon (PC)-amended reactors during 140-day continuous operation treating real membrane-making wastewater laden with N,N-dimethylformamide (DMF). EMs-augmented systems achieved superior COD removal of 75.5 % or 67.0 % and methane production of 255 or 228 mL/(g VSS·day), respectively, at an organic loading rate of 10.0 g COD/(L·day), representing an 88.5 % or 68.6 % increase in methanogenesis over the control. The enhancement stemmed from EMs synergistically boosting enzymatic hydrolysis to deconstruct refractory amide bonds and conjugated structures, and redirecting interspecies electron transfer (IET) pathways with greater efficiency and conductivity. Mag excelled under shock loads due to conductive Fe(III/II) lattice, whereas PC performed better under moderate loads leveraging pseudocapacitive functionalities. Microbial evolution revealed EM-specific colonization of hydrolytic/acidogenic consortia and IET-active methanogens. Metagenomic reconstruction indicated EMs enhanced cleavage of recalcitrant bonds, redirected DMF biodegradation toward (di)methylamine dehydrogenases-catalyzed hydrolysis pathway, and stimulated CO2-reducing/acetoclastic methanogenesis. Furthermore, EMs appeared to reconstruct intra-extracellular IET channels via membrane-spanning redox-active complexes, reinforcing energy conservation and stress resilience while channeling electrons from fermentation to methanogenesis. These findings establish a sustainable strategy for valorizing recalcitrant wastewater into bioenergy, offering insights into microbial electron flux redirection in abiotic-biotic systems.},
}

*Waste Disposal, Fluid/methods
*Wastewater/chemistry
Anaerobiosis
Bioreactors
Hydrolysis
Electron Transport

@article {pmid42822992,
year = {2026},
author = {Wickström, R and Sheikh, ZB and Hirsch, LJ},
title = {Recognizing NORSE and FIRES - clinical course, diagnosis and evaluation.},
journal = {Seminars in pediatric neurology},
volume = {59},
number = {},
pages = {101294},
doi = {10.1016/j.spen.2026.101294},
pmid = {42822992},
issn = {1558-0776},
mesh = {Humans ; *Status Epilepticus/diagnosis/etiology/physiopathology ; },
abstract = {New-onset refractory status epilepticus (NORSE) is a rare but severe neurological condition affecting both children and adults without prior epilepsy and without an identifiable acute cause at presentation. A substantial proportion of patients progress to super-refractory status epilepticus, which is associated with high morbidity and mortality. Despite its clinical severity, diagnostic strategies remain heterogeneous and are largely based on expert consensus due to limited high-quality evidence. This article summarizes current concepts in the definition, clinical recognition, and diagnostic evaluation of NORSE and its subtype febrile infection-related epilepsy syndrome (FIRES). Early identification is critical, as the clinical course, often characterized by a prodromal phase followed by rapidly escalating, treatment-refractory seizures, may provide important diagnostic clues. A structured diagnostic approach is essential and should include early, broad investigation for infectious, autoimmune, paraneoplastic, metabolic, and genetic etiologies, combined with continuous reassessment as new clinical information emerges. Key diagnostic tools include comprehensive blood and cerebrospinal fluid analyses, continuous EEG monitoring, and early neuroimaging, supplemented by advanced techniques such as cytokine panels, metagenomic sequencing and genetic testing when indicated. However, in more than half of cases, no etiology is identified, and patients are classified as having cryptogenic NORSE. Given the potential for treatable causes and the impact of early targeted therapy, timely and systematic evaluation is essential. We here provide an overview of current diagnostic strategies and propose a practical framework to support clinicians managing this complex condition.},
}

Humans
*Status Epilepticus/diagnosis/etiology/physiopathology

@article {pmid42823503,
year = {2026},
author = {Bayer, T and Meinert, H and Wei, R and Bornscheuer, UT},
title = {Advances in amidases and urethanases as depolymerization biocatalysts.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {42823503},
issn = {1552-4469},
support = {953214//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Stable chemical bonds as well as noncovalent interactions define the properties of industrial chemicals and materials, including polyesters such as polyethylene terephthalate (PET), polyamides (nylons) and polyurethanes. The resistance of plastics to hydrolysis contributes to the global issues of waste accumulation and environmental pollution. Recently identified metagenomic enzymes act on highly stable ester, amide and carbamate bonds in small molecules as well as pretreated polymeric materials. However, depolymerization activities, particularly for nylons and polyurethanes, remain too low to facilitate the efficient treatment of plastic waste. This Perspective highlights the natural diversity of different hydrolase superfamilies suitable for deconstructing synthetic polymers and examines their catalytic features. We also discuss strategies for discovering biocatalysts and tailoring their properties by protein engineering-both assisted by bioinformatics and (ultra)high-throughput screening tools. The combination of these approaches and thorough process analyses will be required to advance hydrolase-based depolymerization of plastics beyond the current recycling schemes for PET.},
}

@article {pmid42824003,
year = {2026},
author = {Qi, G and Wu, Z and Chen, J and Zhang, D and Wang, Q},
title = {Gut microbiota characteristics of gastric cancer patients across distinct pathological stages and their associations with tumor and paratumor mucosal microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1897107},
pmid = {42824003},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; China ; Aged ; Feces/microbiology ; Metagenomics ; Neoplasm Staging ; Dysbiosis ; },
abstract = {Gastric cancer (GC) is closely associated with microbial dysbiosis; however, the spatial-temporal characteristics of the gut, paracancerous, and intratumoral microbiomes, as well as their interrelationships during tumor progression, remain insufficiently defined. This study aimed to characterize these microbiomes in 85 GC patients from Northwest China using shotgun metagenomic sequencing and functional annotation. Clinical samples included feces, tumor tissues, and paratumor mucosal tissues (≥5 cm from the tumor margin), enabling comprehensive profiling of microbial composition at the phylum, genus, and species levels, as well as functional pathway analysis. The results showed that the microbial community was dominated by Firmicutes and Bacteroidetes (combined relative abundance >75%), maintaining structural stability across tumor stages II-IV (Stage I n=2 is only descriptively reported and excluded from formal statistical testing), thereby supporting the "core microbiota resilience" hypothesis. PERMANOVA revealed that tumor stage had a statistically significant yet modest effect on community structure (R[2] = 0.039, P = 0.032). MaAsLin2 identified stage-associated differential genera: Roseburia and Megamonas decreased with advancing stage, whereas Lactobacillus and Enterobacter were enriched in advanced stages (III/IV). Functional pathway analysis revealed stage-specific metabolic remodeling: Stage II was enriched in DNA repair, glycolysis, aromatic amino acid, and nucleotide biosynthesis pathways; Stage IV showed enrichment in protein deamination/demethylation, pyruvate fermentation, and coenzyme metabolism pathways. Correlation analysis further revealed a characteristic pattern of "pathogen enrichment and beneficial bacteria depletion." Fusobacterium nucleatum and Helicobacter pylori exhibited strong positive correlations with GC, whereas short-chain fatty acid-producing bacteria such as Roseburia and Faecalibacterium prausnitzii showed significant negative correlations, particularly in paracancerous tissues. We established multi-layered taxonomic correlation profiles based on intra-cohort microbial shifts, in which Bacteroides stercoris and Bifidobacterium pseudocatenulatum exhibited the most pronounced stage-related abundance changes in the fecal microbiota across tumor stages. Overall, this study systematically delineates the structural stability, stage-specific functional remodeling, and interrelated dynamics of gut, paracancerous, and intratumoral microbiomes in gastric cancer. These findings provide descriptive baseline data of cross-compartment microbiome variation within gastric cancer patients across tumor stages, which only deliver preliminary correlative clues of GC-related microbial shifts and require further multi-cohort verification with non-cancer control populations.},
}

Humans
*Stomach Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome
Female
Male
*Bacteria/classification/genetics/isolation & purification
Middle Aged
China
Aged
Feces/microbiology
Metagenomics
Neoplasm Staging
Dysbiosis

@article {pmid42824150,
year = {2026},
author = {Rabbani, SA and El-Tanani, M and Matalka, II and Sharma, S and Saini, M and Kumar, R},
title = {From surveillance to intelligence: a scoping review of machine learning for antimicrobial resistance surveillance intelligence across One Health.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1922265},
pmid = {42824150},
issn = {2296-2565},
mesh = {*Machine Learning ; Humans ; *One Health ; *Drug Resistance, Bacterial ; *Population Surveillance/methods ; Predictive Learning Models ; Animals ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a leading global health threat requiring coordinated surveillance across human, animal, environmental, and genomic systems. Machine learning is increasingly applied to AMR data, yet its contribution to actionable surveillance intelligence, rather than prediction alone, remains poorly defined.

OBJECTIVE: To map how machine-learning approaches generate AMR surveillance intelligence, to characterise their validation and implementation maturity, and to propose a framework distinguishing technical prediction from actionable surveillance intelligence.

METHODS: We conducted a scoping review following JBI methodology and PRISMA-ScR reporting. PubMed/MEDLINE, Scopus, and Web of Science were searched from January 2015 to May 2026 for studies applying machine learning or related methods to AMR surveillance intelligence. Two reviewers independently screened and charted records. Of 1,985 records, 66 met eligibility and formed the working evidence base; 41 studies (40 core empirical and one supporting preprint) were appraised against TRIPOD+AI- and PROBAST-aligned reporting, validation, and implementation-readiness domains.

RESULTS: Machine learning was applied across five clusters: clinical and electronic-health-record risk prediction and decision support; genomic and whole-genome-sequencing prediction; MALDI-TOF-based rapid resistance prediction; wastewater and metagenomic surveillance; and environmental, animal, food-chain, and One Health early warning. Prediction and risk stratification predominated, but validation maturity was limited: most studies were retrospective or internally validated, with few using external, cross-country, temporal, prospective, or drift-focused evaluation. On appraisal, discrimination was reported in 31 of 41 studies (76%) and explainability in 26 (63%); by contrast, external or temporal validation was present in only 15 (37%), calibration in 5 (12%), prospective evaluation in 1 (2%), and operational deployment with measured clinical or public-health impact in a single study (2%).

CONCLUSION: Machine learning can support AMR surveillance intelligence across clinical, genomic, diagnostic, environmental, and One Health settings, but the evidence demonstrates technical feasibility far more convincingly than operational readiness. Realising this transition will require external and prospective validation, calibration and drift monitoring, transparent and equitable reporting, workflow integration, and explicit linkage of model outputs to clinical and public-health action. We propose a One Health AMR Surveillance Intelligence Framework to organise this shift from data generation toward actionable, adaptive surveillance intelligence.},
}

*Machine Learning
Humans
*One Health
*Drug Resistance, Bacterial
*Population Surveillance/methods
Predictive Learning Models
Animals

@article {pmid42824179,
year = {2026},
author = {Manoharan, RK and Han, KI and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and Chaudhary, J and Shin, HD},
title = {Gut health and microbiome modulation by the heat-killed postbiotic beLP1[®] in adults with excess weight: a randomized, placebo-controlled trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1919277},
pmid = {42824179},
issn = {2296-861X},
abstract = {BACKGROUND: Overweight is linked to gut microbiota dysbiosis and gastrointestinal (GI) symptoms that impair quality of life.

METHODS: This 84-day randomized, double-blind, placebo-controlled study evaluated the gut-health effects of heat-killed Lactiplantibacillus plantarum (beLP1[®]) in otherwise healthy adults (aged 18-45 years) within the BMI range of 25-35 kg/m[2] and a ≥3-month history of mild-to-moderate GI discomfort, confirmed by Gastrointestinal Symptom Rating Scale (GSRS). In this trail 140 adults were allocated in a 1:1 ratio to receive either daily beLP1[®] (>30 billion cells) (n = 70) or placebo (n = 70). A total of 103 participants completed the study without protocol deviations and were included in the primary per-protocol (PP) analysis (beLP1[®]: n = 49; Placebo: n = 54). This predefined analysis directly compares the beLP1[®] and placebo arms using analysis of covariance (ANCOVA), supplemented by two independent-sample Student's t-tests. The primary endpoint was change in gastrointestinal symptoms via the GSRS, secondary endpoints included the Perceived Stress Scale (PSS), the Digestion-associated Quality of Life Questionnaire (DQLQ), Tumor Necrosis Factor-alpha (TNF-α), lipid parameters, Dual-Energy X-ray Absorptiometry (DEXA), and gut microbiome diversity by metagenomic Next-Generation Sequencing (NGS).

RESULTS: Compared to placebo, beLP1[®] significantly reduced total Gastrointestinal Symptom Rating Scale (GSRS) scores at Day 42 (p = 0.0215) and Day 84 (p = 0.0394), with prominent improvements in abdominal pain (p = 0.0205) and dyspeptic syndrome (p = 0.0303) domains. Significant reductions in perceived stress (p = 0.0004) and improvements in digestion-associated quality of life (p = 0.0008) were concurrently achieved. Metagenomic analysis revealed a favorable modulation of the gut microbiota, characterized by an enrichment of several short-chain fatty acid-producing bacteria and a significant reduction in multiple opportunistic pathogens. No significant changes occurred in serum TNF-α, lipid profiles, or DEXA body composition metrics.

CONCLUSION: Overall, beLP1[®] safely and progressively alleviates GI symptoms, reduces stress, and optimizes microbiome composition in adults with excess weight. ClinicalTrials.gov: NCT05820737.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT05820737?cond=NCT05820, identifier NCT05820737.},
}

@article {pmid42824567,
year = {2026},
author = {Wu, B and Wei, W and Zhang, K and Zhang, S},
title = {Pancreatic microbiota composition and diversity in pancreatitis-associated infection: a systematic review with focus on infected pancreatic necrosis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1916175},
pmid = {42824567},
issn = {1664-302X},
abstract = {UNLABELLED: Pancreatitis-associated intra-abdominal infection (PA-IAI), particularly infected pancreatic necrosis (IPN), is a serious complication of severe acute pancreatitis and contributes substantially to late morbidity and mortality. Sequencing-based technologies have expanded the detection of microorganisms in pancreatic infection; however, the characteristics of pancreatic microbiota and their clinical relevance have not been systematically summarized. A systematic literature search was conducted in seven electronic databases to identify studies evaluating pancreatic microbiota in patients with pancreatitis-associated infection. Studies reporting microbial composition or diversity using sequencing-based approaches were included. Study characteristics, microbial findings, diversity patterns, clinical outcomes, and methodological details were systematically extracted and synthesized. Six studies involving 235 participants were included; 188 participants contributed pancreatic or peripancreatic microbiota data. Most available evidence was derived from patients with IPN. Sequencing-based approaches generally detected a broader range of microbial taxa than conventional culture, with enteric-associated microorganisms frequently detected, while phylum-level dominance varied among studies. Reported diversity patterns varied between studies and could not be directly compared because of methodological heterogeneity. Although IPN was associated with worse clinical outcomes, current evidence did not demonstrate that specific microbial taxa or microbiota characteristics independently predicted mortality, organ failure, or treatment response. Current evidence indicates that pancreatic microbiota in pancreatitis-associated infection, particularly IPN, are characterized by frequent detection of enteric-associated microorganisms and substantial methodological heterogeneity. Sequencing-based approaches may provide additional microbiological information beyond conventional culture and may influence clinical management; however, whether sequencing-guided management changes improve antimicrobial stewardship or patient-centered outcomes remains uncertain. Future prospective studies using standardized microbiome workflows are required to determine the clinical significance of pancreatic microbial characteristics.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295285, identifier: CRD420261295285.},
}

@article {pmid42824881,
year = {2026},
author = {Esberg, A and Jönsson, D and Persson, P and Eriksson, L and Haworth, S and Johansson, I},
title = {Cross-platform, multi-cohort identification of a caries microbial signature.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2737699},
pmid = {42824881},
issn = {2000-2297},
abstract = {OBJECTIVE: To identify a robust salivary microbial signature associated with caries using a cross-platform, multi-cohort design.

DESIGN: Full-length 16S rRNA gene sequencing (ONT) and shotgun metagenomics (MET) were performed in a derivation cohort with matched data (n = 463). Associations between the oral microbiome and caries were evaluated using confounder-adjusted linear models with nested cross-validation. Identified species were incorporated into microbial risk scores and tested in two independent ONT-based cohorts (n = 3,457 and n = 215).

RESULTS: ONT and MET shared community structure despite differences in sequencing depth and detection sensitivity. Inter-individual ecological distances were moderately correlated (Spearman ρ = 0.48), with significant Procrustes alignment (r = 0.60), and mean relative abundances of shared species were strongly correlated (ρ = 0.75), but agreement at the individual species level was more variable. Ten species were consistently associated with caries across platforms and analytical approaches. Risk scores based on these species were strongly associated with caries burden in the derivation cohort (R[2] = 0.46 for MET; R[2] = 0.42 for ONT) and replicated in independent cohorts (mean R[2] = 0.27 and 0.10). Detection- and abundance-based scores performed similarly and combining them provided minimal additional predictive value. Detection-based scores showed a slightly greater incremental contribution to model fit. Leave-one-out analyses confirmed that associations were not strongly driven by individual species.

CONCLUSIONS: Key ecological features of the oral microbiome are reproducible across sequencing platforms. The microbial signature of caries can be summarised using a detection-based risk score which may have potential uses in caries risk assessment.},
}

@article {pmid42825217,
year = {2026},
author = {Zhu, Y and Zhang, J and Wei, Y and Zhou, S and Qin, X},
title = {Biochar application alters soil properties and microbial gene profiles in a continuous cassava cropping system.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21731},
pmid = {42825217},
issn = {2167-8359},
mesh = {*Manihot/growth & development ; *Soil Microbiology ; Rhizosphere ; *Charcoal/pharmacology ; *Soil/chemistry ; Nitrogen/metabolism ; Metagenome ; *Microbiota/genetics ; Nitrogen Cycle ; },
abstract = {Continuous cassava cropping can lead to soil degradation and disturbances in soil microbial functions, threatening the sustainability of cassava production systems. To address these challenges, this study examined the effects of biochar on soil physicochemical properties and microbial functional profiles in a continuous cassava cropping system. Two biochar application rates (0 and 3 Mg ha[-1]) were applied, and metagenomic sequencing was conducted to evaluate microbial community composition and functional genes related to carbon and nitrogen cycling in rhizosphere and bulk soils. The results demonstrated that biochar was associated with higher soil pH, soil organic matter, and available nutrient content, with a stronger effect in rhizosphere soil. Biochar application altered the genetic potential of microbial communities, particularly in the rhizosphere soil. In terms of functional categories, biochar was related to higher gene abundances in "homologous recombination" and "DNA replication" categories (Kyoto Encyclopedia of Genes and Genomes (KEGG) database), as well as the "replication, recombination, and repair" category (evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database) in rhizosphere soil. Biochar also affected the abundance of carbon cycling genes, particularly in the rhizosphere. The abundance of the aerobic respiration-related gene coxA was increased, while the abundance of the anaerobic fermentation gene L-lactate dehydrogenase (LDH) was decreased. Additionally, in rhizosphere soil, biochar significantly increased the abundance of norB (denitrification), GDH2 (nitrogen mineralization), and nifD (nitrogen fixation), while decreasing the abundance of genes involved in nitrogen assimilation (gltB), assimilatory nitrate reduction (nirA), nitrogen mineralization (cynS), and nitrogen uptake (nrtA, nasF, cynA, nrtC, and nasD). Together, these results suggest that biochar application may enhance nutrient availability and reshape microbial functional potential primarily in the cassava rhizosphere, providing field evidence for biochar use in continuous cassava cropping.},
}

*Manihot/growth & development
*Soil Microbiology
Rhizosphere
*Charcoal/pharmacology
*Soil/chemistry
Nitrogen/metabolism
Metagenome
*Microbiota/genetics
Nitrogen Cycle

@article {pmid42825336,
year = {2026},
author = {Wernike, K and Pfaff, F and Zeiske, S and Höper, D and Beer, M},
title = {Two incursions, two viruses: emergence of a second novel Shamonda virus clade, Germany, 2026.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {31},
number = {39},
pages = {},
doi = {10.2807/1560-7917.ES.2026.31.39.2600756},
pmid = {42825336},
issn = {1560-7917},
mesh = {Animals ; Germany/epidemiology ; Cattle ; Phylogeny ; *Orthobunyavirus/genetics/isolation & purification/classification ; Genome, Viral ; *Cattle Diseases/virology/epidemiology ; },
abstract = {Following the emergence of Shamonda virus (SHAV) in Europe in 2026, we identified a second, genetically distinct SHAV clade in cattle in Germany. Consistent differences across all three genome segments together with divergent regional distribution patterns indicate independent introductions. We have designated the two clades as SHAV Europe 1 (SHAV-EU1) and SHAV Europe 2 (SHAV-EU2). The unexpected co-circulation of these two clades has important implications for diagnostics, surveillance, host range assessment, risk evaluation and control measures.},
}

Animals
Germany/epidemiology
Cattle
Phylogeny
*Orthobunyavirus/genetics/isolation & purification/classification
Genome, Viral
*Cattle Diseases/virology/epidemiology

@article {pmid42825496,
year = {2026},
author = {Lin, Y and Chen, Y and Gao, A and Pan, A and Wang, W and Du, C and Liu, B and Wang, H},
title = {A Posterior-Only Revision Surgery Protocol with Selective Cement Preservation for Post-Vertebral Augmentation Infection.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/72994},
pmid = {42825496},
issn = {1940-087X},
mesh = {Humans ; *Reoperation/methods ; *Bone Cements ; Female ; Retrospective Studies ; Aged ; Male ; Spinal Fusion/methods ; Polymethyl Methacrylate/chemistry ; Middle Aged ; },
abstract = {Post-vertebral augmentation infection is uncommon but clinically serious, especially in older patients with multiple comorbidities and fragile spinal bone stock. Revision surgery is challenging because surgeons must eradicate infection, decompress neural structures when needed, restore stability, and decide whether polymethylmethacrylate cement can be safely preserved. This article describes a posterior-only protocol for diagnosing and treating post-vertebral augmentation infection and illustrates the workflow with a retrospective representative cohort treated between January 2015 and December 2024. Among 48 surgically treated patients, 12 underwent cement removal, and 36 underwent selective cement preservation when all predefined preservation conditions were satisfied, and no mandatory removal or intraoperative conversion criterion was present. The protocol emphasizes diagnosis confirmation, compartment-focused debridement, staged cement-decision logic, microbiological sampling including metagenomic next-generation sequencing, posterior stabilization, and postoperative reassessment. The median follow-up duration in the representative cohort was 14.0 months (interquartile range, 12.0-28.5 months). In selected patients, the cement-preservation pathway was associated with lower unadjusted operative burden, whereas final infection control, computed tomography-confirmed fusion, pain improvement, and complication rates were descriptively similar between groups. This protocol is intended for spine surgeons managing post-PVA infection when a posterior-only corridor can address the active infected compartment and provide stable reconstruction.},
}

Humans
*Reoperation/methods
*Bone Cements
Female
Retrospective Studies
Aged
Male
Spinal Fusion/methods
Polymethyl Methacrylate/chemistry
Middle Aged

@article {pmid42826078,
year = {2026},
author = {Abubakar, TM and Mohd Zain, NA},
title = {Wastewater surveillance of tetracycline resistance genes: a global bibliometric and trend analysis.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/10934529.2026.2740561},
pmid = {42826078},
issn = {1532-4117},
abstract = {Tetracycline resistance genes (TRGs) in wastewater pose environmental and public health risks through antimicrobial resistance dissemination. However, the global development of wastewater surveillance for TRG monitoring remains insufficiently characterized. Scopus-indexed TRG wastewater surveillance research (2001-2025) was analyzed using bibliometric methods, yielding 700 articles after screening. Data were cleaned using biblioMagika[®] and OpenRefine, with VOSviewer used for keyword co-occurrence analysis. Temporal trends were assessed using the Mann-Kendall test, Sen's slope estimator, and Hamed-Rao correction for serial autocorrelation. Publication output increased significantly (τ = 0.891, P = 1.15 × 10[-9]; Sen's slope ≈ 3.84 publications/year) and remained significant after autocorrelation correction (N/N* ≈ 3.16, P = 6.16 × 10[-4]). China and the United States led publication output (370 and 99 publications, respectively), while publication volume was not significantly associated with normalized citation impact (r = 0.163, P = 0.436). Environmental science and microbiology dominated. Six thematic clusters centered on antibiotic resistance genes, horizontal gene transfer, metagenomics, and wastewater treatment. TRG wastewater surveillance research is expanding rapidly, highlighting the need for international collaboration, methodological standardization, and capacity building within a One Health framework.},
}

@article {pmid42826257,
year = {2026},
author = {Wu, X and Zang, T and Liu, Y and Xu, B},
title = {Suspected allergic bronchopulmonary candidiasis in a patient with concurrent multidrug-resistant bacterial pneumonia: A case report.},
journal = {Medicine},
volume = {105},
number = {40},
pages = {e50977},
doi = {10.1097/MD.0000000000050977},
pmid = {42826257},
issn = {1536-5964},
mesh = {Humans ; Male ; Aged ; *Pneumonia, Bacterial/drug therapy/complications ; Drug Resistance, Multiple, Bacterial ; Anti-Bacterial Agents/therapeutic use ; Candida albicans/isolation & purification ; Immunoglobulin E/blood ; *Candidiasis/diagnosis ; },
abstract = {RATIONALE: Allergic bronchopulmonary candidiasis (ABPC) is a rare pulmonary hypersensitivity disorder; diagnosis is difficult because Candida albicans is usually a respiratory commensal.

PATIENT CONCERNS: A 70-year-old man with hypertension and prior cerebral infarction was admitted for sudden right limb weakness (6.5 hours) and diagnosed with hemorrhagic cerebral infarction in the intensive care unit.

DIAGNOSES: Persistent fever and pulmonary infiltrates developed despite broad-spectrum antibiotics. Total immunoglobulin E (IgE) was 2181 IU/mL; sputum grew C albicans + carbapenem-resistant Pseudomonas aeruginosa; bronchoalveolar lavage fluid metagenomic next-generation sequencing detected C albicans, P aeruginosa, Klebsiella pneumoniae, EBV, and HSV-1. ABPC was suspected alongside multidrug-resistant bacterial pneumonia.

INTERVENTIONS: Ceftazidime-avibactam (2.5 g q8h) + nebulized polymyxin B (0.5 M IU q12h); oral voriconazole (400 mg q12h loading, then 200 mg q12h); IV methylprednisolone 40 mg/d.

OUTCOMES: Clinical improvement on combined therapy; respiratory stabilization within 2 weeks; intensive care unit transfer out. Follow-up chest computed tomography showed resolution of infiltrates; total IgE fell from 2181 to 995 IU/mL (-54%). Discharged with hemorrhagic cerebral infarction, hypertension, carbapenem-resistant Pseudomonas pneumonia, K pneumoniae co-infection, and ABPM.

LESSONS: Persistent infiltrates with high IgE and Candida isolation should suggest ABPM, not intensified antibiotics. ABPC can occur in older patients without asthma. Early corticosteroids plus antifungals yield rapid improvement. Metagenomic next-generation sequencing complements conventional testing but cannot confirm ABPC alone.},
}

Humans
Male
Aged
*Pneumonia, Bacterial/drug therapy/complications
Drug Resistance, Multiple, Bacterial
Anti-Bacterial Agents/therapeutic use
Candida albicans/isolation & purification
Immunoglobulin E/blood
*Candidiasis/diagnosis

@article {pmid42815260,
year = {2026},
author = {Zhao, Y and Zhao, X and Lian, J and Wang, S and Ning, Q and Xu, Q and Zhang, Z and Zong, J and Wang, S},
title = {Microbiome-guided prioritization of Corynebacterium striatum in diabetic foot ulcers and preclinical evaluation of tanshinone IIA.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158803},
doi = {10.1016/j.phymed.2026.158803},
pmid = {42815260},
issn = {1618-095X},
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by impaired healing and infection, but microbial signatures linked to glycemic status and their therapeutic relevance remain unclear.

PURPOSE: To identify DFU taxa associated with glycemic status and test whether microbiome-guided prioritization can inform evaluation of Tanshinone IIA (Tan IIA).

STUDY DESIGN: Clinical metagenomic discovery followed by in vitro functional and multi-omics analyses, biophysical studies, and in vivo evaluation.

METHODS: Wound samples from 54 DFU patients underwent HbA1c-stratified shotgun metagenomics. A prioritized patient-derived Corynebacterium striatum isolate was assessed for Tan IIA antibacterial and antibiofilm activity, multi-omics responses, and candidate-protein binding. Topical Tan IIA was tested in non-inoculated and C. striatum-inoculated diabetic wounds.

RESULTS: C. striatum was enriched in higher-HbA1c wounds and positively associated with continuous HbA1c (β = 0.422, 95% CI 0.095-0.748; P = 0.011; q = 0.064). Tan IIA inhibited the isolate (MIC = 64 μ g/ml), reduced biofilm biomass, and induced stress, redox, cell-envelope, and metabolic responses. SPR supported binding to MurD and TrxB. On day 14, wound closure was significantly greater in inoculated wounds (93.40% vs. 78.80%; adjusted P = 0.0187). In inoculated wounds, Tan IIA reduced EUB338-positive bacterial signal and viable counts versus vehicle (8.587 vs. 8.847 log10 CFU/g; adjusted P =  0.0480).

CONCLUSION: HbA1c-stratified metagenomics prioritized C. striatum as a glycemic-status-associated candidate. These findings support microbiome-guided preclinical evaluation of plant-derived Tan IIA as a topical candidate for infected DFUs.},
}

@article {pmid42815267,
year = {2026},
author = {Liu, L and Li, Y and Pan, X and Zhang, K and Yang, F and Liu, D and Sun, W and Li, P and Du, B},
title = {Fermented Polygonatum kingianum polysaccharide exerts enhanced anti-obesity effects by modulating the gut microbiota-GDCA-TGR5 axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158824},
doi = {10.1016/j.phymed.2026.158824},
pmid = {42815267},
issn = {1618-095X},
abstract = {Probiotic-fermented Polygonatum kingianum polysaccharide (FPKP0) was previously confirmed to exhibit enhanced anti-adipogenic activity in 3T3-L1 cells in vitro owing to altered structural, prompting an examination of whether this modified FPKP0 exerts superior anti-obesity effects in vivo via related mechanism in high-fat diet-fed mice. Physiological results showed that FPKP0 outperformed unfermented PKP0 accounting for reducing body weight, improving blood lipids, alongside alleviating hepatic steatosis and colonic damage. Correspondingly, FPKP0 reshaped the gut microbiota by boosting beneficial genera (especially Akkermansia muciniphila) and suppressing harmful bacteria (e.g., Dubosiella, Helicobacter). Integrated metagenomic and metabolomic analyses identified A. muciniphila and Glycodeoxycholic acid (GDCA) as the key microbial and metabolic factors with the in vivo effects of FPKP0. A strong positive correlation (ρ = 0.83) between A. muciniphila abundance and GDCA levels suggests a potential relationship between microbial remodeling and bile acid metabolism following FPKP0 intervention. Further mechanistic exploration suggested that TGR5 may serve as a downstream receptor associated with FPKP0-related changes in GDCA. Molecular docking and immunoblotting indicated a GDCA-TGR5 interaction and activation of the Gsα-PKA-CREB-UCP1 cascade to stimulate energy expenditure. This enhanced in vivo anti-obesity effect of FPKP0 may involve modulation of the gut microbiota (AKK)-bile acid (GDCA)-TGR5 axis, supporting the potential of FPKP0 as a functional food additive to combat obesity and related disorders.},
}

@article {pmid42815303,
year = {2026},
author = {Qiu, J and Yan, J and Cao, L and Xu, Y and Zhang, X and Zhai, Y and Bai, J},
title = {Temporal shifts in the dominance of tolerant taxa reshape microbial functional potentials from substrate utilization to stress resistance in sediments contaminated with sulfonated methyl phenolic resin.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {126985},
doi = {10.1016/j.watres.2026.126985},
pmid = {42815303},
issn = {1879-2448},
abstract = {Sulfonated methyl phenolic resin (SMP), a widely used additive in water-based drilling fluids, accumulates in sediments due to its low degradability. Bioremediation is a promising strategy for SMP removal, but the microbial responses to SMP remain unclear. Here, we conducted microcosm experiments to compare microbial composition and functional potentials between early and late exposure stages across a SMP concentration gradient. The results showed that SMP exposure reduced microbial diversity and increased the relative dominance of putatively tolerant taxa. Microbial response asynchrony increased and was positively correlated with resistance potential. Life-history proxies indicated contrasting patterns between exposure stages, with lower 16S rRNA gene copy number and longer predicted minimum doubling time at the early stage and the opposite pattern at the late stage. Additionally, degradation- and resistance-related functional genes were enriched at the early and late stages, respectively. At the metagenome-assembled genome (MAG) level, abundant MAGs at the late exposure stage exhibited high resistance potential. Overall, our results showed that SMP could exert a double-edged sword effect on microorganisms, acting as both a stressor and a carbon source, thereby inducing stage-specific microbial functional transitions.},
}

@article {pmid42815610,
year = {2026},
author = {Dong, H and Li, Y and Aziz, P and Song, M and Yan, L and Chen, Z and Fohrer, N and Messyasz, B and Li, Y},
title = {Physicochemical and microbial regulators of contrasting diffusive greenhouse gas fluxes in Danjiangkou Reservoir.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125819},
doi = {10.1016/j.envres.2026.125819},
pmid = {42815610},
issn = {1096-0953},
abstract = {Reservoirs play a key role in the global greenhouse gas (GHG) balance through carbon and nitrogen cycling, yet the spatiotemporal variation in GHG fluxes from large drinking-water reservoirs and the underlying regulatory mechanisms remain unclear. This study investigated the seasonal dynamics of CO2, CH4, and N2O diffusive fluxes in Danjiangkou Reservoir and examined their physicochemical and microbial associations. In August, when water levels were low and water temperatures were high, the mean CO2 flux was close to zero (5.59 ± 10.74 mg·m[-2]·h[-1]), with both source and sink fluxes observed among sites; the reservoir showed net CO2 emission during the other sampling periods (40.89 ± 8.88 mg·m[-2]·h[-1]). CH4 and N2O exhibited both source and sink fluxes without consistent seasonal patterns. Mixed-effects models and random-forest analyses consistently identified total dissolved solids (TDS) as a major predictor of all three GHG fluxes, whereas pH, dissolved oxygen, and inorganic nitrogen showed gas-specific associations. Metagenomic analyses indicated a reorganization of microbial functional potential with changing water levels: under high-water conditions, the relative contributions of nitrogen-transformation markers, including nitrate reduction, NO-to-N2O conversion, and dissimilatory nitrate reduction to ammonium, were higher; under low-water conditions, carbon-fixation markers, including those associated with the Calvin cycle and the 3-hydroxypropionate cycle, accounted for larger proportions of the target functional profile. Genus-level annotations identified Polynucleobacter as a prominent CO2-associated taxon, Methylibium and Methylocystis as prominent CH4-associated taxa, and Nitrospira and Haliscomenobacter as candidate N2O-associated taxa. Together, these findings describe spatiotemporal GHG flux patterns and their physicochemical and microbial associations, providing a basis for further investigation of reservoir GHG budgets and potential mitigation strategies.},
}

@article {pmid42815804,
year = {2026},
author = {Chang, K and Xie, H and Wang, Y and Na, W and Liu, C and Liu, Y},
title = {Ozone disinfection effectively reduces pathogenic microbial nucleic acid background in mNGS laboratories.},
journal = {Journal of microbiological methods},
volume = {250},
number = {},
pages = {107728},
doi = {10.1016/j.mimet.2026.107728},
pmid = {42815804},
issn = {1872-8359},
abstract = {For the first time, this report confirmed under real-laboratory-contamination scenarios that ozone disinfection effectively reduces microbial nucleic acid background in mNGS laboratories, with consistent and efficient disinfection performance. With the global advancement of standardized clinical application of mNGS technology, the results provide a practical strategy to control laboratory contamination, reduce false-positive risks, and maintain a low nucleic acid baseline. This method addresses the difficulty of eliminating persistent contamination in mNGS laboratories and offers a direct reference for environmental decontamination of metagenomic sequencing laboratories worldwide.},
}

@article {pmid42816384,
year = {2026},
author = {Kondo, S and Kumar, N and Hamahata, N},
title = {Aseptic Meningitis Unmasking Coccidioidomycosis of the Central Nervous System Outside an Endemic Region.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
doi = {10.2169/internalmedicine.7538-26},
pmid = {42816384},
issn = {1349-7235},
abstract = {A 20-year-old male presented with persistent aseptic meningitis. Cerebrospinal fluid (CSF) showed neutrophil-dominant pleocytosis, high protein, low glucose, and an opening pressure >55 cmH2O. Fluid metagenomic next-generation sequencing detected Coccidioides immitis/posadasii and subsequent culture confirmed the diagnosis. The retrospective history revealed residence in Arizona approximately six months prior to hospitalization. Antifungal therapy was escalated, and the patient was transferred to a tertiary neurocritical care center for advanced neurocritical care. This case demonstrates that geographic bias can delay the recognition of coccidioidal meningitis outside endemic regions. Clinicians should therefore obtain a patient's travel history even if the patients have only a remote travel history.},
}

@article {pmid42816497,
year = {2026},
author = {Zhou, F and Pan, S and Ma, C and Sun, W and Ye, Y and Zhu, DZ and Xiong, J and Li, C and Zhang, J and Gan, J and Sun, X and Lu, D and Gan, H},
title = {Humic acid's sheltering effect paradoxically promotes antibiotic resistance gene dissemination during peroxymonosulfate water treatment.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42816497},
issn = {2041-1723},
support = {52070103//National Natural Science Foundation of China (National Science Foundation of China)/ ; LMS26E090008//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; },
mesh = {*Peroxides/pharmacology/chemistry ; Animals ; *Humic Substances/analysis ; *Water Purification/methods ; Caenorhabditis elegans/microbiology ; Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Microbial/genetics ; Oxidative Stress/drug effects ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Advanced oxidation processes (AOPs) utilizing peroxymonosulfate (PMS) are increasingly deployed for water disinfection, yet their impact on the dissemination of antibiotic resistance genes (ARGs) remains poorly understood. Here, we conducted field surveys in three aquaculture ponds in eastern China and employed a Transwell-based horizontal gene transfer (HRT) sorting assay, metagenomics, and transcriptomics to investigate the underlying mechanisms. We found that PMS-treated waters harbored significantly higher intracellular ARG burdens compared to untreated or chlorinated systems. Mechanistically, the ubiquitous humic acid (HA) acts as a selective radical scavenger, protecting bacteria from lethal oxidative damage while stimulating type IV pilus-mediated uptake of extracellular ARGs. This interaction redirects HGT from conjugation toward natural transformation. Crucially, this protective effect is oxidant-specific: HA effectively quenches PMS-derived radicals but provides no defense against direct electrophilic attack by chlorine. Furthermore, predation experiments using Caenorhabditis elegans demonstrate that this "sheltering effect" facilitates the accumulation of ARGs in nematodes, decoupling resistance acquisition from oxidative stress intensity. These findings highlight a critical risk pathway in which some water treatment chemicals can promote the spread of resistance, necessitating a reassessment of oxidant selection based on their specific chemical mechanisms.},
}

*Peroxides/pharmacology/chemistry
Animals
*Humic Substances/analysis
*Water Purification/methods
Caenorhabditis elegans/microbiology
Gene Transfer, Horizontal/drug effects
*Drug Resistance, Microbial/genetics
Oxidative Stress/drug effects
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid42817081,
year = {2026},
author = {Pushp, and Paliwal, A},
title = {Fungal Keratitis: A Narrative Review with a Focus on Antifungal Resistance and Emerging Therapies.},
journal = {Infectious disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715265490828260921074616},
pmid = {42817081},
issn = {2212-3989},
abstract = {Corneal infection that can cause blindness, fungal keratitis has shown an increasing prevalence worldwide, especially in tropical and subtropical areas, where it significantly increases the risk of unilateral corneal blindness. The epidemiology, molecular etiology, diagnosis, antifungal resistance, and changing treatment of fungal keratitis are all reviewed in this article. Geographic diversity is evident in epidemiological patterns, with filamentous fungi such as Aspergillus and Fusarium predominating in warm climes, and an increasing number of reports of Candida species in temperate and healthcare-associated settings. Disease incidence and outcomes have been further affected by post-COVID-19 changes in ophthalmic treatment, extensive corticosteroid exposure, delayed presentations, and environmental factors, including climate fluctuations and increased airborne spore loads. Rapid stromal invasion, enzyme-mediated tissue damage, biofilm development, and host immune dysregulation are key factors determining severity, according to molecular findings. For improved detection, including in culture-negative and polymicrobial cases, diagnostic advancements focus on combining traditional microscopy and culture with in vivo confocal microscopy, MALDI-TOF MS, targeted PCR, and metagenomic next-generation sequencing. Time to treatment is being reduced by rapid point-of-care techniques like tear β-D-glucan tests, LAMP, CRISPR/Cas platforms, and AI-based image analysis. The necessity for systematic susceptibility testing and antifungal management is supported by rising antifungal resistance, particularly rising MIC trends in Fusarium and Aspergillus species, which exhibit variable susceptibility to azoles and amphotericin B, highlighting the need for species-specific antifungal susceptibility testing. The evolving epidemiology, molecular etiology, and new developments in fungal keratitis diagnosis are covered in this article. Additionally, it emphasizes new therapeutic approaches, including advanced drug delivery systems, advances in antifungal resistance management, and potential avenues for improved management. The article presents a narrative review focusing on recent developments in the epidemiology, molecular mechanisms, diagnosis, antifungal resistance, and treatment options for fungal keratitis.},
}

@article {pmid42817572,
year = {2026},
author = {Kundral, S and Giang, PD and Kirk, AM and Buczynski, JB and Arachchige, KSA and Khare, SK and Bernhardt, PV and Evans, PN and Guddat, LW and Bell, SG and De Voss, JJ},
title = {Structural and Functional Characterisation of a Metagenome-Derived CYP108D18 Reveals an Unusual Dioxygen-Bound State and Selective Hydrocarbon Hydroxylation.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70451},
pmid = {42817572},
issn = {1751-7915},
support = {DP210103970//Australian Research Council/ ; },
mesh = {*Cytochrome P-450 Enzyme System/metabolism/chemistry/genetics/isolation & purification ; Hydroxylation ; *Metagenome ; *Oxygen/metabolism ; *Sphingomonadaceae/enzymology/genetics ; Escherichia coli/genetics/metabolism ; Enzyme Stability ; Hot Springs/microbiology ; Protein Binding ; Monoterpenes/metabolism ; Australia ; Gene Expression ; Molecular Docking Simulation ; Cloning, Molecular ; Substrate Specificity ; Recombinant Proteins/genetics/metabolism/isolation & purification/chemistry ; Temperature ; },
abstract = {Cytochrome P450 enzymes form a large superfamily of monooxygenases capable of oxidising diverse substrates. Among them, members of the CYP108 family are recognised for their role in monoterpenoid oxidation. In this study, we report the identification and characterisation of a new CYP108 family member, CYP108D18, from a metagenome-assembled genome derived from microbial communities in a geothermal hot spring located in northern Queensland, Australia. Taxonomic binning associated CYP108D18 with a Novosphingobium species, a genus well-known for its bioremediation potential. CYP108D18 was heterologously expressed in Escherichia coli, yielding 640 nmol L[-1] of culture, and purified to homogeneity. The enzyme exhibited moderate thermostability, with a [15]T50 value of 47°C ± 1°C. Spectroscopic substrate binding assays revealed that while CYP108D18 bound monoterpenoids similarly to other CYP108 enzymes, it showed higher affinity and pronounced larger heme spin-state shifts with aromatic hydrocarbons such as phenylcyclohexane and phenanthrene. Subsequent in silico docking and spectral-binding studies also suggested that CYP108D18 may accommodate larger plant-derived sesquiterpenes, indicating a potential role in their metabolism. Reconstitution of CYP108D18 with spinach ferredoxin and ferredoxin reductase resulted in the oxidation of phenylcyclohexane to trans-4-phenylcyclohexanol. Molecular dynamics simulations and ONIOM (QM/MM) calculations supported selective hydrogen abstraction at the cyclohexane C4 position, rationalising trans-4-phenylcyclohexanol as the predominant product. The high-resolution crystal structure of substrate-free CYP108D18 revealed a bound dioxygen ligand positioned above the heme iron, an unusual feature among P450 structures. Both substrate-free and phenylcyclohexane-bound structures revealed a persistent open conformation, suggesting the absence of a canonical open-to-closed transition upon ligand binding. Spectroelectrochemical analysis showed a heme redox potential of -451 mV versus NHE for the substrate-free CYP108D18, shifting subtly to -409 mV upon phenylcyclohexane binding, which contributes to reduced activity with non-native [2Fe-2S] ferredoxins.},
}

*Cytochrome P-450 Enzyme System/metabolism/chemistry/genetics/isolation & purification
Hydroxylation
*Metagenome
*Oxygen/metabolism
*Sphingomonadaceae/enzymology/genetics
Escherichia coli/genetics/metabolism
Enzyme Stability
Hot Springs/microbiology
Protein Binding
Monoterpenes/metabolism
Australia
Gene Expression
Molecular Docking Simulation
Cloning, Molecular
Substrate Specificity
Recombinant Proteins/genetics/metabolism/isolation & purification/chemistry
Temperature

@article {pmid42817813,
year = {2026},
author = {Wang, L and Yu, S and Huang, J and Meng, Y and Zhao, C and Gan, Y and Hu, W and Yang, Y},
title = {Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70579},
doi = {10.1111/mec.70579},
pmid = {42817813},
issn = {1365-294X},
support = {2023YFD1801900//National Key Research and Development Program of China/ ; 2025KYPT0066//National Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock/ ; 32460897//National Natural Science Foundation of China/ ; Q2022002//'Grassland Talents' Youth Innovation and Entrepreneurship Talent Project of Inner Mongolia Autonomous Region/ ; 2025-Gui-Yan-1-36//Hohhot R&D Investment Incentive Program/ ; },
mesh = {Animals ; *Microbiota/genetics ; Birds/microbiology/virology ; *Ecosystem ; Bacteria/genetics/classification ; *Biodiversity ; Arthropod Vectors/microbiology/virology ; Fungi/genetics/classification ; Phylogeny ; Grassland ; Sequence Analysis, DNA ; Virome ; Viruses/classification/genetics ; },
abstract = {Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito- and bird-associated communities. Ecological network analyses revealed substantial cross-host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system-wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host-associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.},
}

Animals
*Microbiota/genetics
Birds/microbiology/virology
*Ecosystem
Bacteria/genetics/classification
*Biodiversity
Arthropod Vectors/microbiology/virology
Fungi/genetics/classification
Phylogeny
Grassland
Sequence Analysis, DNA
Virome
Viruses/classification/genetics

@article {pmid42817903,
year = {2026},
author = {Olasupo, OA and Olaniyan, OP and Akinde, SB and Adesoye, AA and Ajadi, FA and Obire, O and Oladipo, EK and Sule, WF and Oyinloye, OE and Salami, AA and Fajoyegbe, ES and Ajani, AJ and Ojo, O},
title = {Metagenomic Characterisation of Antibiotic Resistance in Anaerobic Digesters and Their Implications for Environmental Health.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70400},
pmid = {42817903},
issn = {1758-2229},
mesh = {*Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Metagenome ; },
abstract = {Antimicrobial resistance (AMR) in environmental systems represents an emerging One Health challenge, with anaerobic digesters potentially serving as reservoirs of resistance-associated genetic features. This study analysed four publicly available anaerobic digester shotgun metagenomic datasets (M2, M3, M12 and M17) retrieved from the NCBI Sequence Read Archive to characterise microbial functions, resistance-associated annotations and antibiotic target loci. The datasets were generated using Illumina HiSeq 2000 sequencing and analysed through quality assessment, assembly, functional annotation and resistome profiling. A total of 1082 resistance-associated annotations were identified, with the highest abundance detected in M2 (348), followed by M12 (276), M17 (259) and M3 (205). Detected annotations were associated with diverse antimicrobial categories, including aminoglycosides, quinolones, beta-lactams, tetracyclines, glycopeptides, macrolides and sulfonamides. Several frequently detected loci, including rpoB, rpoC, gyrA, gyrB, EF-Tu, EF-G, Ddl and KasA, were interpreted as antibiotic target or housekeeping loci rather than confirmed acquired resistance genes. Exploratory co-abundance analysis identified strong associations among functionally linked loci, including rpoB-rpoC and gyrA-gyrB, likely reflecting shared genomic occurrence or functional relationships. These findings highlight the resistome potential of anaerobic digesters while emphasising the need for host-resolved metagenomics, mobile genetic element analysis and mutation-level characterisation to clarify environmental AMR risks.},
}

*Metagenomics
*Anti-Bacterial Agents/pharmacology
Anaerobiosis
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects/isolation & purification/classification
*Metagenome

@article {pmid42818131,
year = {2026},
author = {Parker, E and Oladipo, F and Levy, JI and Ope-Ewe, OO and Soumare, H and Andersen, K and Happi, AN and Happi, CT},
title = {Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.22.26363641},
pmid = {42818131},
abstract = {Population-scale pathogen surveillance is limited worldwide, particularly in resource-constrained settings, where clinical systems only monitor select priority pathogens and reach only those who can access healthcare. Wastewater-based epidemiology addresses many of these gaps, offering cost-effective surveillance that is adaptable across diverse implementation contexts. In Lagos, Nigeria, a high enteric pathogen burden coincides with a complex sanitation landscape. However, circulating pathogen diversity in Lagos is largely uncharacterised outside of outbreak contexts. Here we characterize human-associated pathogen diversity in Lagos with virus-enriched metagenomic and metatranscriptomic sequencing of untreated wastewater sampled from open drainage canals from July-August 2024. We detected a diverse human-associated virome dominated by enteric adenoviruses, astroviruses and caliciviruses. We recovered numerous partial and near-complete genomes from pathogens of public health concern, including noroviruses, enteroviruses and sapoviruses. Although our enrichment targeted viruses, we detected diverse bacterial pathogens, including recurrent detection of Vibrio cholerae , other enteric bacteria, and zoonotic pathogens such as Streptococcus suis. We also detected antimicrobial resistance genes, including aminoglycoside, beta-lactam and fluoroquinolone resistance and clinically important genes such as mcr . Together, these results establish a regional baseline of pathogen diversity and demonstrate the utility of virus-enriched sequencing for integrated wastewater surveillance.},
}

@article {pmid42818146,
year = {2026},
author = {Song, L},
title = {Lossless compression of protein databases for efficient and accurate metagenomic sequence classification with Centrifuger.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752512},
pmid = {42818146},
issn = {2692-8205},
abstract = {We present a lossless compression algorithm for indexing a protein database while supporting fast taxonomic classification in the method Centrifuger. The algorithm is a new scheme of the previously proposed run-block compression algorithm to reduce the size of the Ferragina-Manzini (FM) index, and it scales better with alphabet size than the original. On the RefSeq prokaryotic and viral protein sequences, Centrifuger reduces the memory footprint by over a third compared to the method Kaiju that builds on a plain FM-index, while having comparable running time. Furthermore, the compressed FM-index is lossless and can locate matches of arbitrary length, which helps Centrifuger achieve greater accuracy than Kraken2, a k-mer-based taxonomic classification method. We leverage the computational efficiency of Centrifuger to create an index of size 182 GB for classifying the reads against the full nr database that contains about 250 billion amino acid characters. Using this index, Centrifuger reveals different SARS-CoV-2 infection states and viral transcriptome profiles across human cell types from single-cell RNA-seq data.},
}

@article {pmid42818234,
year = {2026},
author = {Oliver, A and Podell, S and Allen, EE},
title = {Diverse genome organization strategies for polysaccharide utilization in the oceans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.21.753266},
pmid = {42818234},
issn = {2692-8205},
abstract = {Carbohydrate-active enzymes (CAZymes) drive the turnover of polysaccharides in the oceans. However, the scale of diversity in polysaccharide utilization and genome organization strategies has yet to be characterized, particularly in marine ecosystems. In this paper, we introduce mpcgcdb.com as an interactive web catalog for marine CAZyme gene clusters, their associated metagenome-assembled genomes, and relevant enzyme families found in marine metagenomic samples. This database contains nearly 290,000 marine CAZyme gene clusters from more than 22,000 genomes, enabling user-initiated exploratory visualizations for genome organization networks and enzyme phylogeny. This tool will assist researchers in developing hypotheses about gene function, connecting species to metabolic niches, and identifying gaps where future work is needed to understand different pathways in marine glycan cycling.},
}

@article {pmid42818264,
year = {2026},
author = {Ge, Y and Li, E and Mustafa, H and Varabyou, A and Salzberg, SL},
title = {Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.22.753623},
pmid = {42818264},
issn = {2692-8205},
abstract = {Accurate taxonomic classification in metagenomics is often compromised by low-complexity sequences, which lead to chance matches that in turn cause sequences to be misclassified. Here we present Kmask, an entropy-based masking tool implemented for use either standalone or as part of Kraken [1,2] database construction, which replaces low-entropy regions with Ns. Using a sliding window size aligned with Kraken's default k-mer length and parameters optimized across 12 control bacterial genomes spanning a broad range of GC content, Kmask efficiently removes low-complexity sequences while retaining high-complexity regions. To benchmark performance, we applied Kmask to a newly constructed database, Microbial2025, that contains over 71,000 bacterial, archaeal, viral, and fungal genomes, and we then classified human reads against both masked and unmasked versions of the database using KrakenUniq [2]. We found that Kmask substantially reduced misclassifications, driving down the false positive rate to 5.78% from 7.52%. Notably, Kmask performed comparably to an SDUST-masked [3] database, achieving a similar false positive rate (5.78% vs. 5.17%) while masking out fewer bases (1.33% vs. 1.85%). We also tested Kmask on a database of human cancer sequences, where we found that it eliminated many false positives caused by low-complexity matches between bacterial genomes and human DNA. These results demonstrate that Kmask is an effective method for masking low-complexity sequences in large microbial databases, thus improving the accuracy of metagenomic classification.},
}

@article {pmid42818341,
year = {2026},
author = {Li, T and Yang, Y and Cho, SH and Howell, BR and Wu, Z and Yin, W and Elison, JT and Huynh, KM and Ahmad, S and Yap, PT and Li, G and Wang, L and Zhu, H and Lin, W and , },
title = {Microbes on the Mind: Multi-modal Neuroimaging Reveals Gut-Brain Axes in Infants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.23.753825},
pmid = {42818341},
issn = {2692-8205},
abstract = {The gut microbiome undergoes rapid maturation after birth and has been associated with cognition and mental health, yet its relation to early brain development remains poorly defined. We analyzed 223 typically developing children aged 0-3 years with multimodal MRI and paired fecal shotgun metagenomics. Microbiome-wide association analyses identified associations with cortical morphology, white-matter microstructure, and functional connectivity. Ridge-regularized canonical correlation analysis identified two principal covariance patterns: a structural-metabolic mode and a functional-taxonomic mode. Sparse canonical partial least squares recovered the principal CCA score and phenotype patterns within the same sample. Longitudinal canonical-score slopes were not significantly correlated; in autoregressive cross-lag models, however, neuroimaging CCA1 scores predicted microbiome CCA1 scores 1-6 months later. These results indicate cross-domain covariance and temporal ordering within the measured windows but do not establish causality.},
}

@article {pmid42818393,
year = {2026},
author = {Falahati Khanaman, S and Shrestha Gurung, BD and Aryal, S and Geza Nisrania, M and Gadhamshetty, V and Gnimpieba, E},
title = {Predictors Recover Most of the Metagenomic Signal for Antibiotic Resistance Gene Occurrence: A Cross-City Test of Geographic Transferability in Urban Wastewater.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.24.753270},
pmid = {42818393},
issn = {2692-8205},
abstract = {Antibiotic resistance genes (ARGs) travel from cities into rivers and coastal waters through wastewater treatment plants. Monitoring them normally requires metagenomic sequencing, which is sufficiently costly that most utilities can sample only occasionally. Weather and location data are freely available on a daily basis for virtually any location worldwide, making them attractive predictors for identifying where limited sequencing resources should be prioritized. However, whether such models generalize to previously unseen cities remains largely untested, as most published studies train and evaluate models within the same catchments, thereby assessing interpolation rather than geographic transferability. To address this gap, we paired 235 wastewater metagenomes collected from five European cities with 23 abiotic predictors spanning geospatial, meteorological, hydrological, radiative, and temporal domains. Model performance was evaluated using leave-one-group-out (LOGO) cross-validation, in which all samples from one city were withheld for testing while the remaining cities were used for training. CatBoost achieved a median LOGO ROC-AUC of 0.929 and a median F1-score of 0.750. Using freely available environmental reanalysis predictors (meteorological, hydrological, radiative, geospatial, and temporal) - without any metagenomic sequencing - CatBoost achieved a mean ROC-AUC of 0.722, recovering 78% of the predictive performance of the full omics-integrated model. Removing latitude and longitude reduced ROC-AUC by only 0.003, whereas replacing random cross-validation with city-wise validation reduced ROC-AUC by 0.052. Predictive performance varied across ARG classes, ranging from a ROC-AUC of 0.981 for β-lactam resistance genes to 0.762 for glycopeptide resistance genes. These findings demonstrate that freely available environmental reanalysis predictors - spanning meteorological, hydrological, radiative, geospatial, and temporal domains - recover 78% of the predictive signal for antibiotic resistance gene occurrence in urban wastewater, allowing scarce sequencing capacity to be directed to the catchments where it changes a decision.},
}

@article {pmid42818437,
year = {2026},
author = {Wang, L and Zhang, Y and Nguyen, SM and Peters, BA and Qi, Q and Burk, RD and Kaplan, R and Thyagarajan, B and Daviglus, M and Shu, XO and Ma, S and Dai, Q and Shrubsole, MJ and Zheng, W and Yu, D},
title = {Discovery and Validation of Gut Microbiome Features Associated with Dietary Patterns in U.S. Black/African and Hispanic/Latino Populations.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.04.26362286},
pmid = {42818437},
abstract = {BACKGROUND: Large-scale studies examining dietary patterns and gut microbiome have focused predominantly on European ancestry populations; evidence from other ancestry groups remains limited.

OBJECTIVES: We conducted a two-stage study to evaluate associations of multiple dietary patterns with gut microbiome diversity and composition among Black/African American adults and validate significant findings in a Hispanic/Latino population in the US.

METHODS: Included were 514 Black participants from the Southern Community Cohort Study (SCCS) and 2,133 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Diet was collected by food frequency questionnaires or 24-h dietary recalls at cohort enrollment. Gut microbiome profiling was performed by shotgun metagenomic sequencing of stool samples collected during cohort follow-up. Five dietary patterns - Healthy Eating Index (HEI), Dietary Approaches to Stop Hypertension (DASH), Empirical Dietary Inflammatory Potential (EDIP), Empirical Dietary Index for Hyperinsulinemia (EDIH), and Ultra-Processed Foods (UPF) - were examined for associations with microbiome diversity and composition by linear regression after data transformation and confounders adjustment. Microbial taxa with FDR<0.1 and their constituent lower-level features identified in SCCS were targeted for validation in HCHS/SOL.

RESULTS: In SCCS, HEI, DASH, EDIP, or EDIH were associated with the relative abundances of 14 microbial taxa, primarily members of families Coriobacteriaceae and unclassified Firmicutes, as well as species Lactococcus lactis and Clostridium sp. AF20-17LB . Among these, the inverse associations of genus Collinsella and its species C. aerofaciens with HEI or DASH were validated in HCHS/SOL (all P <0.05). Additionally, Collinsella and C. aerofaciens were associated with higher odds of obesity in SCCS (BMI≥ 30 kg/m2; OR [95%CI]:1.24 [1.01, 1.53] and 1.32 [1.07, 1.63], respectively).

CONCLUSIONS: Healthier dietary patterns were consistently associated with lower abundances of Collinsella and C. aerofaciens in Black/African and Hispanic/Latino Americans. Further research should clarify causal pathway linking diet, gut microbiome, and health outcomes across diverse populations.},
}

@article {pmid42818523,
year = {2026},
author = {Chen, D and Wang, Y and Portik, DM and Nearing, J and Nickols, WA and Wilkinson, JE and Christiani, DC and Nguyen, LH and Franzosa, EA and Spengler, JD and Huttenhower, C and Thompson, KN},
title = {Microbial transmission and ecology of human and environmental microbial communities in childcare centers.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10207669/v1},
pmid = {42818523},
issn = {2693-5015},
abstract = {Background Early-life microbial exposures profoundly impact lifelong health trajectories by shaping immune maturation and modulating disease risk, e.g. as described by the "hygiene hypothesis." Childcare facilities represent a critical yet understudied source of microbial exposures where preschool-aged children spend 7-10 hours daily during key developmental periods. This study presents the first multi-omic and multi-kingdom investigation of microbial transmission and community ecology across childcare environments, integrating microbiome samples from both high-touch and low-touch surfaces with children's nasal and oral microbiomes, using full-length 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing paired with short-read (SR) and long-read (LR) metagenomic sequencing. This combination provides enhanced species-level taxonomic resolution and improved recovery of genomes and genomic elements compared to conventional short-read approaches. Results Our findings revealed distinct microbial signatures across environments, with human-associated microorganisms predominating in high-touch areas, while greater taxonomic diversity characterizes low-touch areas. Specifically, on high-touch surfaces, several bacterial and fungal species were shared between host and environmental communities, such as food-associated Lactococcus lactis and Streptococcus thermophilus , suggesting defined transmission routes via host shedding, environmental exposures, and food consumption. With improved genomic resolution and reconstruction from paired SR and LR metagenomics, we identified novel lateral gene transfer (LGT) events enriched for mobile elements, DNA-interacting domains, and adaptive elements such as antibiotic resistance and virulence factors. These methods also shed light on viral ecology, such as Caudoviricetes bacteriophages ubiquitous across host and environmental communities with phylogenetically-differentiated niche- and bacterial host-specific lineages. The positive relationship between the host prediction frequency and its community relative abundance suggested host abundance (availability)-driven phage-bacteria population dynamics. Conclusions This work highlights previously understudied components of early-life microbial exposures in childcare environments with enhanced resolution and provides methods for identifying potential pathogen reservoirs, tracking transmission routes, and developing targeted interventions.},
}

@article {pmid42818648,
year = {2026},
author = {Xia, H and Wen, Y and Li, X and Hu, L and Yuan, Y and Tian, J and Li, S and Zhan, Y and Dang, X and Lin, Y and Li, L and Chen, Y and Zhang, Y and Guan, Y and Wang, J},
title = {A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1938149},
pmid = {42818648},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; *Databases, Genetic ; *Bacteria/genetics/classification/isolation & purification ; *Genome, Microbial ; Computational Biology/methods ; Cohort Studies ; Biocuration ; },
abstract = {INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) enables broad, untargeted pathogen detection, but its analytical performance depends on host depletion strategy, reference database composition, and alignment methodology. We developed the Clinical Microbial Genomic Database (CMGD), a clinically focused reference resource prioritizing medically relevant taxa.

METHODS: CMGD was manually curated, clinically stratified, and included more than 18,000 microbial species. We evaluated host-depletion references, alignment and classification strategies, six published clinical cohorts, and 30 retrospective mNGS-positive clinical samples.

RESULTS: The combined GRCh38-T2T reference achieved the highest human-read depletion rate while minimizing microbial-read loss. CMGD provided broader target-species coverage than the standard Kraken2 database, and BWA-CMGD showed lower erroneous assignment rates overall, although Kraken2 yielded higher unique species-level assignment rates for many shared taxa. Across six published clinical cohorts, CMGD achieved 91.0% detection concordance with BLAST-NT and a strong read-count correlation (R[2] = 0.97). In 30 retrospective samples, CMGD and NT showed strong correlations for total mapped reads (R[2] = 0.99) and uniquely mapped reads (R[2] = 0.89), with concordance correlation coefficients of 0.99 and 0.92, respectively. High sequence-mapping accuracy did not ensure reliable species-level discrimination for highly homologous taxa such as Escherichia coli and Shigella flexneri.

DISCUSSION: Clinically stratified database curation improves the analytical performance, computational efficiency, and interpretability of mNGS-based pathogen detection. Species-complex-level reporting may be more appropriate when species-level discriminatory evidence is insufficient. Prospective multicenter validation is required to establish clinical diagnostic utility.},
}

Humans
*Metagenomics/methods
High-Throughput Nucleotide Sequencing
*Databases, Genetic
*Bacteria/genetics/classification/isolation & purification
*Genome, Microbial
Computational Biology/methods
Cohort Studies
Biocuration

@article {pmid42818693,
year = {2026},
author = {Landsittel, JA and Howe, A and Kuehn, S and Lee, KK and Mani, M},
title = {The ecological context of enzymatic variation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.09.750510},
pmid = {42818693},
issn = {2692-8205},
abstract = {Among the challenges in understanding microbial ecosystems is the presence of physics at vastly different scales. Reactions, catalyzed by enzymes but regulated at the level of the cell, propel the flux of carbon and nitrogen through our atmosphere. Compounding this is the presence of pervasive enzyme sequence variation; this variation has been shown to contain coevolving modes of amino acids which encode the enzyme's evolutionary history. In this work, we take steps towards bridging the gap between the enzymatic variation present in an ecosystem and its subsequent activity. We employ the reduction of nitrate by NarG as a model system, which acts as an essential step in the nitrogen cycle by mediating both the return of di-nitrogen to the atmosphere and the assimilation of nitrate into biomass. Considering both metagenomic reconstructions as well as functional data from soil nitrate reducers, we find that sequence variants of enzymes obey predictable responses to environmental fluctuations. That is, while prior community-level metagenomic studies have characterized the response of bacterial strains to the environment, our study provides an enzyme variant level sequence-to-response map. Further, we demonstrate that a simple statistical model can predict the organismal phenotype from variant sequence; in soil samples not originally seen by that model, the prediction of a variant's reduction rate correlates with how much cells with that variant grow in abundance.},
}

@article {pmid42818746,
year = {2026},
author = {Qihong, L and Juan, W and Xue, T and Zhiheng, D and Dongyan, C and Lili, Y and Feiqiu, W and Sixi, L and Shilin, L},
title = {Scrub typhus triggers hemophagocytic lymphohistiocytosis in children: metagenomic next-generation sequencing enables rapid diagnosis.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1888645},
pmid = {42818746},
issn = {2296-2565},
mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology ; Male ; *Scrub Typhus/complications/diagnosis ; Female ; Child, Preschool ; Child ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; Adolescent ; Metagenomics ; },
abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome. Rapid identification of the underlying trigger is critical for effective clinical management. This study describes the clinical features and diagnostic approach for scrub typhus-associated HLH in children, emphasizing the role of metagenomic next-generation sequencing (mNGS).

METHODS: We retrospectively analyzed 12 pediatric patients diagnosed with scrub typhus-associated HLH at Shenzhen Children's Hospital between July 2023 and July 2025. Demographic, clinical, laboratory, and treatment data were analyzed. The diagnostic timeline was systematically evaluated, including patient's delay, doctor's delay, and mNGS turnaround time.

RESULTS: The median age was 7.5 years (range: 3-13.7), with a male-to-female ratio of 1:2. All patients presented with prolonged fever (median duration: 9 days). Common clinical findings included eschar (66.7%), lymphadenopathy (100%), hepatomegaly (58.3%), and splenomegaly (66.7%). Notably, four patients (33.3%) were initially misdiagnosed as having Kawasaki disease. All patients met the HLH-2004 criteria, with prominent hyperferritinemia (median: 5,355 ng/mL) and elevated sCD25 (median: 5,065 U/mL). Peripheral blood mNGS confirmed the diagnosis of scrub typhus in all patients (median sequence reads: 333). Cerebrospinal fluid (CSF) mNGS was positive for Orientia tsutsugamushi in four out of five patients tested, and cytokine profiling revealed elevated levels of IL-6, IL-10, and IFN-γ. Basic CSF parameters, including white blood cell count, protein, and glucose, are reported for all patients who underwent lumbar puncture. Severe complications included pulmonary hemorrhage (n = 3) and shock (n = 3). All patients survived following targeted antibiotic and immunomodulatory therapy.

CONCLUSION: Scrub typhus is a significant trigger for secondary HLH in children from endemic areas. mNGS may facilitate rapid etiological diagnosis and timely targeted therapy. CSF mNGS and cytokine analysis may be considered in severe cases, though further validation is warranted. We also acknowledge that our study demonstrates feasibility rather than superiority of mNGS over conventional diagnostic methods.},
}

Humans
*Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology
Male
*Scrub Typhus/complications/diagnosis
Female
Child, Preschool
Child
Retrospective Studies
High-Throughput Nucleotide Sequencing
Adolescent
Metagenomics

@article {pmid42818833,
year = {2026},
author = {Perez, RK and Prakash, H and Jaynes, D and Huang, P and Deegan, J and Hopkins, L and Ross, M and Minor, M and Payne, K and Ayvaz, T and Clark, JR and Boerwinkle, E and Tisza, MJ and Maresso, AW},
title = {Wastewater Metagenomic Virome Analysis of the 2026 World Cup in Texas.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.04.26362178},
pmid = {42818833},
abstract = {Mass gatherings are thought to create conditions for pathogen introduction and spread, yet whether such events measurably alter the viral community of a city has rarely been tested against an extensive historical baseline. We analyzed 5,137 hybrid-capture metagenomic wastewater samples collected from 55 sites across 17 Texas cities between June 2022 and July 2026, spanning the 2026 FIFA World Cup. We asked (1) whether host-city viral community composition during the tournament departed from its established summer-to-summer range, (2) whether targeted respiratory viruses rose above their characteristic summer trend, and (3) whether the load of rare and novel taxa was elevated in host cities relative to non-host cities. Despite the plausibility of these hypotheses, we detected no tournament-associated perturbations. Although based on a single event, these findings favor continuous wastewater surveillance over event-triggered deployment, both for detecting introductions that arrive unpredictably and for supplying the baseline against which any event should be judged.},
}

@article {pmid42818860,
year = {2026},
author = {Zhang, R and Chen, Y and Hou, D},
title = {Functional organization outweighs spatial separation in structuring microbial communities across a petroleum-hydrocarbon groundwater plume.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938677},
pmid = {42818860},
issn = {1664-302X},
abstract = {OBJECTIVE: Petroleum-hydrocarbon plumes in groundwater are shaped by hydrological transport, redox conditions, and indigenous microbial activity. However, it remains unclear whether spatial differences among groundwater microbiomes primarily reflect physical separation among wells or ecological reorganization associated with distinct attenuation states within a plume.

METHODS: We integrated hydrogeological context, petroleum-hydrocarbon concentrations, hydrochemical variables, and shotgun-metagenomic profiles from 15 groundwater monitoring wells at a petroleum-hydrocarbon-impacted site. Community beta diversity, spatial and functional distance relationships, permutation-based group tests, and exploratory composite indices of natural attenuation potential and taxonomic-functional diversity were evaluated.

RESULTS: Genus-level community dissimilarity increased with estimated spatial distance (Mantel r = 0.240, p = 0.034), but was more strongly associated with functional-module dissimilarity (r = 0.670, p = 0.001). Biodegradation potential remained associated with community dissimilarity after controlling for spatial distance (partial Mantel r = 0.428, p = 0.001). Operational attenuation states explained 35.4% of genus-level compositional variation (PERMANOVA p = 0.008). High natural attenuation potential and high taxonomic-functional diversity occurred in partly distinct wells.

CONCLUSION: The results indicate that groundwater microbiome turnover within the plume is spatially structured but is more closely coupled to functional reorganization than to distance alone. Joint consideration of hydrological setting, microbial degradation potential, and functional diversity may improve groundwater natural-attenuation assessment.},
}

@article {pmid42819055,
year = {2026},
author = {Jingjing, T and Nannan, Y and Jingjie, Z and Ping, C and Yankun, Z},
title = {Presumed Candida tropicalis endogenous endophthalmitis with multifocal systemic Candida albicans abscesses: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1951092},
pmid = {42819055},
issn = {2296-858X},
abstract = {BACKGROUND: Endophthalmitis is a kind of infectious diseases that seriously threatens vision; Endogenous fungal endophthalmitis (EFE) accounts for 2% to 8% of all endophthalmitis, and is rare and often misdiagnosed in clinical practice. Different strains of Candida may have organ orientation differences, and mixed infections have also been reported in literature.

CASE REPORT: A 72 year old male patient was admitted to the hospital due to fever for 5 months and decreased vision in both eyes. The patient's left vitreous fluid underwent metagenomic next-generation sequencing (mNGS), which revealed the presence of Candida tropicalis (1 sequence detected); The fungal culture of vitreous humor and the blood culture sent for testing at the same time was negative. Candida albicans was detected in the culture of surgical specimens for renal and lumbar lesions. The core clinical feature of this case is the inconsistency of pathogen detection between the whole body and the eyes. Due to mNGS only detected one Candida tropicalis sequence and the vitreous fungal culture was negative, this case should be considered as a suspected Candida tropicalis endophthalmitis clinically diagnosed. It may be a mixed invasive infection of Candida albicans and Candida tropicalis, and there may be differences in organ orientation between the two strains (Candida albicans prefers kidney and bone tissues, while Candida tropicalis is invasive to intraocular tissues), forming a zoning colonization pattern. However, this explanation still lacks conclusive microbiological evidence. The patient received local and systemic antifungal treatment in both eyes, and underwent bilateral vitrectomy. The systemic infection was controlled, and the left eye vision improved from near blindness to 0.25 (8 months) with some recovery in visual function.

CONCLUSION: EFE is prone to misdiagnosis, and high-risk individuals should undergo pathogen testing as soon as possible. mNGS is a rapid identification tool, but caution should be exercised when single sequence detection and negative culture occur. When the pathogens are inconsistent, alternative explanations such as contamination and sequential infection should be excluded. The combination of comprehensive antifungal therapy and surgical treatment is effective,Clinical physicians need to establish a global mindset and pay attention to the intrinsic relationship between systemic lesions and eye damage.},
}

@article {pmid42819200,
year = {2026},
author = {Wu, L and Bao, Y and Pu, J and Zhang, L and Huang, J and Xi, X and Luo, L},
title = {Post-vertebroplasty lumbar spondylodiscitis due to Cutibacterium modestum.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1905143},
pmid = {42819200},
issn = {2296-858X},
abstract = {Percutaneous vertebroplasty-associated spinal infection is uncommon but may cause progressive vertebral destruction and can mimic tuberculous spondylitis on imaging. The detection of low-virulence skin commensals such as Cutibacterium species in deep specimens also creates a diagnostic challenge because contamination and true infection must be distinguished. We report a 78-year-old man who developed recurrent progressive low back pain shortly after percutaneous vertebroplasty for an L2 compression fracture. Baseline computed tomography (CT) and contrast-enhanced magnetic resonance imaging (MRI) showed destructive spondylodiscitis centered at L2/3, with adjacent vertebral body and disc-space involvement, paravertebral inflammatory extension, and bilateral psoas abscess-like collections, initially suggesting tuberculous spondylitis. However, molecular testing for the Mycobacterium tuberculosis complex and targeted sequencing for mycobacterial drug-resistance genes were negative, and histopathology demonstrated acute and chronic inflammatory necrotic changes without typical tuberculous granulomas. Metagenomic next-generation sequencing of aspirated fluid identified a high abundance of Cutibacterium modestum, which was subsequently detected again in lesion tissue and peripheral blood by targeted high-throughput sequencing. Given the repeated detection in deep-site specimens, exclusion of tuberculosis and other competing diagnoses, compatible clinical and imaging findings, and improvement after targeted antimicrobial therapy and percutaneous stabilization, C. modestum was considered the most probable causative pathogen. These findings suggest that pathogen attribution in post-vertebroplasty spinal infection should rely on integrated clinical, microbiological, pathological, and therapeutic evidence rather than on imaging findings alone. Integrated clinico-microbiological assessment may improve pathogen attribution for rare low-virulence organisms in postoperative spinal infection.},
}

@article {pmid42819311,
year = {2026},
author = {Shen, R and Liu, S and Yu, P and Xie, S and Xie, Q and Wang, Q and Pan, Y and Zhang, Z and Wang, Z and Zhao, W},
title = {Integrative hologenomic analysis reveals apolipoprotein D-associated host-microbe metabolic crosstalk linked to fat deposition in Jinhua pigs.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1915318},
pmid = {42819311},
issn = {1664-302X},
abstract = {BACKGROUND: Adipose deposition is a complex trait shaped by both host genetics and environmental factors, including the gut microbiota. While quantitative trait loci (QTLs) and candidate genes underlying fat accumulation have been extensively identified in diverse pig breeds, the hologenomic regulatory networks integrating host genetic variation and microbial signals remain to be fully deciphered.

METHODS: In this study, we utilized a strictly controlled dietary cross-fostering model involving Jinhua and Landrace×Yorkshire pigs across developmental stages (day60, day90 and day180). We integrated population genetics, eQTL analysis, transcriptomics, metagenomics and metabolomics to elucidate the host-metabolite-microbe axis.

RESULTS: Phenotypic analysis revealed a robust genetic trait for high backfat thickness in Jinhua pigs, independent of dietary intervention. Through F ST analysis and eQTL mapping, we pinpointed a strongly differentiated locus (13_133481393_A_G) that was nearly fixed in JH pigs (allele frequency 0.95) and was associated with upregulation of APOD. In our multi-omics dataset, this locus was linked to shifts in cecal gene expression that were consistent with a pro-adipogenic program, which coincided with an intestinal metabolic profile marked by elevated oleic acid and reduced oleoylethanolamide. This metabolic niche, in turn, directionally recruited synergistic microbes, specifically Eubacterium sp. AM28-29 and Blautia, which functioned as biochemical amplifiers to further accelerate lipid accumulation.

CONCLUSION: Our study establishes a hologenomic framework demonstrating how foundational genetic selection (APOD) shapes the host-microbe metabolic interplay to drive complex production traits. This study offers novel molecular targets and a theoretical framework for precision breeding and nutritional modulation of meat quality in livestock.},
}

@article {pmid42819442,
year = {2026},
author = {Li, Y and Yu, Z and Shen, M and Cui, S and Yang, X},
title = {Adult Epstein-Barr virus encephalitis: a retrospective case report series with metagenomic next-generation sequencing-based diagnosis.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1861146},
pmid = {42819442},
issn = {1664-2295},
mesh = {Humans ; Female ; *Encephalitis, Viral/diagnosis/cerebrospinal fluid/drug therapy ; Middle Aged ; Retrospective Studies ; Male ; High-Throughput Nucleotide Sequencing ; *Epstein-Barr Virus Infections/diagnosis/cerebrospinal fluid/drug therapy/complications ; Aged ; Metagenomics ; Adult ; Magnetic Resonance Imaging ; Herpesvirus 4, Human/genetics ; Antiviral Agents/therapeutic use ; },
abstract = {BACKGROUND: EBV encephalitis is uncommon in adults, and its diagnosis and management remain challenging, particularly in patients with underlying medical conditions.

METHODS: We retrospectively analyzed seven adult patients with EBV encephalitis confirmed through cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) between December 2021 and January 2024.

RESULTS: Six patients (86%) were female, with a median age of 59 years. Five patients had significant underlying conditions, including malignancies (n = 2), systemic lupus erythematosus (n = 1), and EBV-associated hemophagocytic lymphohistiocytosis (HLH, n = 2). Common clinical presentations included fever (86%), impaired consciousness (86%), neck stiffness (57%), headache (43%), and decreased muscle strength (43%). CSF analysis revealed elevated protein levels (57%) and leukocytosis (71%). Magnetic resonance imaging (MRI) identified encephalitis-associated lesions in three of six patients (50%), whereas computed tomography (CT) was largely unremarkable. All patients received antiviral therapy, and five additionally received corticosteroids. Three patients recovered, whereas four died, with all deaths occurring in patients with concurrent malignancies or HLH.

CONCLUSION: MRI is the preferred imaging modality for suspected encephalitis, and CSF-mNGS is an essential pathogen detection assay. Underlying conditions such as malignancies and HLH are associated with poor clinical outcomes.},
}

Humans
Female
*Encephalitis, Viral/diagnosis/cerebrospinal fluid/drug therapy
Middle Aged
Retrospective Studies
Male
High-Throughput Nucleotide Sequencing
*Epstein-Barr Virus Infections/diagnosis/cerebrospinal fluid/drug therapy/complications
Aged
Metagenomics
Adult
Magnetic Resonance Imaging
Herpesvirus 4, Human/genetics
Antiviral Agents/therapeutic use

@article {pmid42819443,
year = {2026},
author = {Lutsiv, T and Thompson, HJ and Fiehn, O and Gareau, MG and Borowsky, AD and Chen, BH and Hussan, H},
title = {A Distinct Host-Microbiome Signature Underlies the Accelerated Malignant Potential of Colorectal Laterally Spreading Tumors.},
journal = {Gastro hep advances},
volume = {5},
number = {12},
pages = {101102},
pmid = {42819443},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Laterally spreading tumors (LST) are flat colorectal neoplasms with an accelerated risk of malignant transformation and interval colorectal cancer. Despite their clinical importance, the molecular and microbial mechanisms underlying LST's aggressive biology remain poorly understood. Thus, we aimed to characterize the transcriptomic and microbial landscape of LST in comparison with paired protruding lesions and the adjacent normal colonic tissue.

METHODS: Formalin-fixed, paraffin-embedded tissues from 36 samples were obtained from 15 adults and analyzed using RNA sequencing and 16S rRNA gene amplicon sequencing. Patterns of the differential gene expression were assessed using Gene Set Enrichment Analysis and Ingenuity Pathway Analysis. Microbial community composition and its predicted functional capacity were evaluated with analysis of compositions of microbiomes with bias correction in QIIME 2 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, respectively.

RESULTS: Compared with paired protruding lesions and normal tissue, LST exhibited a distinct protumorigenic transcriptomic profile marked by the activation of MYC, E2F, mTOR, DNA damage, and senescence-associated secretory phenotype pathways, as well as robust proinflammatory signaling driven by TNF, NF-κB, IL-1, and IL-17. LST tissue also demonstrated a permissive environment for genomic instability. Microbiome analysis revealed enrichment of Fusobacterium and depletion of beneficial taxa, including Lactococcus, accompanied by predicted suppression of carbohydrate fermentation and short-chain fatty acid production, as well as altered sulfur metabolism. Fusobacterium abundance correlated with increased TNF expression, supporting a microbiota-driven inflammatory niche in LST.

CONCLUSION: LST are characterized by a unique inflammatory/metabolic/senescence axis that distinguishes them from other paired colorectal tissue samples. This procarcinogenic signature is driven by a Fusobacterium-enriched and carbohydrate-fermentation-depleted microbial ecosystem. These findings highlight the gut microbial ecosystem as a critical cofactor in LST pathogenesis and further support that combined host/microbiota-targeted strategies may improve colorectal cancer prevention in this population. Given the exploratory nature and limited cohort size, these findings require validation in larger prospective cohorts with metagenomic and metabolomic integration.},
}

@article {pmid42819542,
year = {2026},
author = {Feng, B and Chen, Y and Chen, Y and Feng, J and Yu, Z and Guo, F and Ruan, J},
title = {Case Report: Coinfection of influenza A and Chlamydia psittaci pneumonia.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1895006},
pmid = {42819542},
issn = {2296-858X},
abstract = {The coinfection of influenza A and Chlamydia psittaci pneumoniae is rarely described in China. However, the clinical features of these diseases pose a significant diagnostic challenge. Therefore, it is necessary to report and review such a potentially fatal case. We report an 89-year-old male patient requiring admission to the intensive care unit with acute hypoxemic respiratory failure, shock and MODS. He presented with fever, fatigue, anorexia and dyspnea. The patient exhibited severe hypoxemia, shock, hepatic dysfunction (elevated liver enzymes and serum bilirubin), acute kidney injury and a SOFA score of 17. Mechanical ventilation (MV) and venous-venous extracorporeal membrane oxygenation (VV-ECMO) were established for respiratory support. The initial diagnosis focused on influenza A for his positive influenza A nucleic acid. However, the patient's imaging presentation was not coupled with viral pneumonia, which raised suspicion for other pathogens. Metagenomic next-generation sequencing (mNGS) detected coinfection of C psittaci, influenza A H3N2 virus, and Klebsiella pneumoniae in bronchoalveolar lavage fluid. Concurrent targeted NGS (tNGS) detected C. psittaci in blood. Omadacycline and baloxavir marboxil were prescribed. The patient's condition improved, and he was successfully weaned from VV-ECMO and MV. He was discharged and recovered on day 60 of the follow-up. This case underscores the diagnostic complexity of coinfection and the use of NGS testing in this severe condition and the role of omadacycline in psittacosis.},
}

@article {pmid42819899,
year = {2026},
author = {, },
title = {Correction: Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1981765},
doi = {10.3389/fmicb.2026.1981765},
pmid = {42819899},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1924993.].},
}

@article {pmid42820078,
year = {2026},
author = {Cao, Z and Luo, J and Zhuang, H and Li, X and Ban, Y and Ouyang, Y and Hu, J and You, P and Liu, X and Liang, Q and Zhang, Z},
title = {Severe Vibrio vulnificus Sepsis without Typical Wound Exposure in a Patient with Chronic Liver Disease and Diabetes: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {644649},
pmid = {42820078},
issn = {1178-6973},
abstract = {BACKGROUND: Vibrio vulnificus, a Gram-negative bacillus, is frequently present in warm estuarine and coastal waters and is a notable pathogen responsible for seafood-related fatalities globally. Infection typically arises from ingesting contaminated seafood or exposure of skin wounds to tainted seawater, resulting in primary or secondary sepsis, as well as severe skin and soft tissue infections.

CASE PRESENTATION: Upon hospital admission, a 51-year-old man with chronic gastritis, long-term alcohol use, type 2 diabetes, thrombocytopenia, and active hepatitis B and C presented with acute right upper quadrant abdominal pain, high fever, and a history of consuming raw fish (sashimi) before symptom onset, suggesting a foodborne infection. Despite denial of recent seawater exposure or seafood handling, his condition rapidly deteriorated, resulting in septic shock, moderate acute respiratory distress syndrome, and necrotizing fasciitis of the left lower extremity within 72 hours. Laboratory findings revealed severe thrombocytopenia, hyperlactatemia, multiple organ dysfunction, and metabolic acidosis. Vibrio vulnificus was identified via peripheral blood metagenomic next-generation sequencing. Whole-exome sequencing incidentally detected a heterozygous missense variant in the DOCK2 gene (c.4511C>T, p. Thr1504Met), classified as a variant of uncertain significance. In silico analyses suggested a benign effect, leaving any potential link to disease severity undetermined without functional confirmation.

CONCLUSION: Severe V. vulnificus sepsis may develop through foodborne transmission, even in the absence of typical exposure to seawater or seafood handling. Disease severity in this patient was primarily influenced by chronic liver disease, alcohol abuse, and diabetes. Clinicians should watch for V. vulnificus infection in patients with these risk factors who present with septic shock or rapidly progressive soft tissue infections, regardless of exposure history.},
}

@article {pmid42820214,
year = {2026},
author = {Sola, M and Paravel, A and Auger, S and Chatel, JM and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Veiga, P and Frioux, C and Mariadassou, M and Berland, M},
title = {NeighborFinder: an R package inferring local microbial network around a species of interest.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag201},
pmid = {42820214},
issn = {2635-0041},
abstract = {MOTIVATION: Understanding interactions from microbiome data is a central aspect in microbial ecology, as it provides insights into ecosystem stability, disease mechanisms, and can be used to design synthetic communities. Current network inference tools reconstruct global networks from co-abundance data, which means they capture the overall correlation structure for the entire set of taxa considered. These approaches are computationally intensive and suboptimal when the focus is on the local neighborhood of one or a few taxa of interest.

RESULTS: We introduce NeighborFinder, a local network inference method that enables the targeted discovery of direct neighbors around a species of interest. Using cross-validated multiple linear regression with ℓ 1 penalty and microbiome-specific filters, our approach infers interpretable species-centered interactions, with F1 score ≥ 0.95 on simulated cohorts ranging from 250 to 1000 samples. This method is well-suited for large metagenomic datasets and is particularly valuable for exploratory studies where the targeted hypotheses outweigh the need for global community structure. The approach complements existing methods by being biologically intuitive and computationally efficient.

The R package is available on CRAN https://CRAN.R-project.org/package=NeighborFinder. The data and source code used to calculate performances and produce the use case example can be found respectively at: https://doi.org/10.57745/UPITJ0 and https://doi.org/10.57745/HJLWW4.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}

@article {pmid42820688,
year = {2026},
author = {Yang, X and Wu, J and Wang, T and Li, Z and Xi, Y and Zhao, L and Luo, M and Xie, X and Zhao, G and Zhou, H and Zhang, L},
title = {GCF-anchored and target-oriented mining of metagenomic BGC space for bioactive product discovery.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0109826},
doi = {10.1128/spectrum.01098-26},
pmid = {42820688},
issn = {2165-0497},
abstract = {Microbial natural products are vital for drug discovery, yet pervasive genomic fragmentation and data volume hinder the translation of metagenomic biosynthetic gene clusters (BGCs) into therapeutic leads. We present metasynBGC, a target-oriented framework that employs a "function-first" logic using experimentally validated gene cluster families (GCFs) as evolutionary templates and functional beacons. This dual-path strategy enables (i) template-guided reconstruction of fragmented BGCs via conserved biosynthetic synteny, and (ii) high-resolution prioritization of complete BGCs based on therapeutic potential. Applying metasynBGC to large-scale public metagenome-assembled genome (MAG) data sets, we uncovered hidden biosynthetic potential, including BGC0001089_plus, a novel bacillaene-like variant containing an additional functional pksF gene. Simultaneously, bioactivity-prioritized mining of nonribosomal peptide synthetase (NRPS) BGCs, coupled with deep learning and chemical synthesis, yielded six novel compounds. These molecules exhibited diverse in vitro cytotoxic profiles across seven cancer cell lines, with [Formula: see text] values as low as 38.04 µM. Compounds D and E showed potent activity and pronounced cell-line selectivity. By transforming microbial "dark matter" into an actionable reservoir of therapeutic leads, metasynBGC provides a practical target-oriented strategy for linking metagenomic BGC mining with downstream experimental validation. The scripts used in this study are publicly available at https://github.com/Shirly-Yang/metasynBGC.IMPORTANCEThe vast chemical diversity hidden within metagenomic data remains largely inaccessible because biosynthetic gene clusters (BGCs) are often highly fragmented. Our study introduces metasynBGC, a target-oriented framework designed to bridge these gaps by using well-characterized BGCs within gene cluster families (GCFs) as templates to reconstruct incomplete biosynthetic pathways. Unlike traditional methods, metasynBGC integrates a dual-path discovery engine: it performs priority-driven mining to precisely locate naturally intact clusters while reconstructing fragmented ones using representative BGC members as guides. We demonstrate its efficacy by identifying and synthesizing novel compounds with notable cytotoxic activity, providing a validated "sequence-to-molecule" pipeline. This work offers a scalable framework for the systematic discovery of therapeutic candidates from uncultivated microbes and expands our capacity to interpret genomic "dark matter." By enabling the functional validation of complex molecules from fragmented data, metasynBGC facilitates the translation of metagenomic data sets into promising leads for therapeutic development.},
}

@article {pmid42820708,
year = {2026},
author = {Islam, MR and Sarkar, R and Dey, SS and Ahmed, I and Patwary, MRH and Hasan, Z and Mishu, MA and Ahmed, MM and Chowdhury, A},
title = {Metagenomic profiling and temporal dynamics of antimicrobial resistance genes across hospital wastewaters in Dhaka, Bangladesh.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0075526},
doi = {10.1128/spectrum.00755-26},
pmid = {42820708},
issn = {2165-0497},
abstract = {UNLABELLED: Hospital wastewater (HWW) in Bangladesh is often discharged into municipal sewage and water bodies without adequate treatment. It raises concern that hospitals may act as reservoirs and amplification points for clinically important antimicrobial resistance genes (ARGs). However, culture-independent data on the composition, mobility, and seasonal behavior of these genes in Bangladeshi hospital wastewater remain limited. Here, we combined single monsoon time-point baseline shotgun metagenomic sequencing with longitudinal qPCR to characterize wastewater from three tertiary hospitals in Dhaka and a nearby community wastewater line across three seasonal sampling points. Across sites based on baseline metagenomic profiling, the putative resistome was dominated by aminoglycoside, sulfonamide, macrolide-lincosamide-streptogramin (MLS), tetracycline, and β-lactam resistance, primarily associated with Actinomycetota and Pseudomonadota. Hospital effluents contain putative clinically important genes, including the vanA cluster, blaVIM, blaOXA-232, blaIMP, and blaKPC. Metagenomic analysis linked many putative ARGs to plasmid-predicted contigs, transposition, or integration modules, while virulence profiling showed enrichment of putative genes related to adhesion, motility, iron acquisition, and secretion, particularly in MHWW-2. Exploratory network co-occurrence from baseline metagenomics primarily suggested fecal-derived gut commensals, alongside pathogens, as reservoirs and putative vectors for ARG input into the wastewater system. Longitudinal qPCR showed higher absolute loads of selected ARGs at the pre-winter sampling point, and the class 1 integron gene (intI1LC) tracked total ARG burden across seasonal transitions. These findings identify hospital wastewater in Dhaka primarily as a dynamic reservoir of clinically important and potentially mobile resistance determinants, and support its use as a target for wastewater-based AMR surveillance.

IMPORTANCE: Wastewater surveillance can provide early warning of AMR, but in Bangladesh, it is rarely applied beyond culture or single-gene PCR, limiting detection of emerging, mobile, and facility-specific threats. This study integrates metagenomics with longitudinal qPCR to connect which resistance genes are present with who carries them and how they change seasonally across multiple hospitals. We show that hospital effluents contain a shared background resistome yet disproportionately concentrate last-line resistance in taxa that include clinically important lineages, with signals rising toward pre-winter. By placing high-risk putative ARGs in putative plasmid, integron, and transposase contexts and alongside virulence repertoires from baseline metagenomic profiling, our results identify plausible genomic mechanisms that may contribute to spread beyond hospitals. These findings position hospital effluents in Dhaka preliminarily as dynamic reservoirs of clinically important, mobile AMR and support wastewater-based epidemiology for sustained surveillance and risk mitigation.},
}

@article {pmid42820737,
year = {2026},
author = {Liu, T and Smeds, J and Nilsson, M and Öquist, M and Bertilsson, S},
title = {Depth-stratified boreal peatland microbiomes reveal recurring community organization and methane-cycling potential.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag111},
pmid = {42820737},
issn = {1574-6941},
abstract = {Microbial communities in peatlands vary with depth, but most studies have been limited in spatial extent or replication, constraining assessment of general community patterns. We characterized microbial community structure and metabolic potential across replicated depth profiles in seven boreal peatlands in Sweden. Combining 16S rRNA gene sequencing and shotgun metagenomics, we identified recurring vertical stratification across sites. Microbial richness declined with depth, and core taxa including Rice Cluster II, Terriglobales, Subgroup 2, Roseiarcus, Methylocystis, and Candidatus Solibacter were shared across locations. Functional gene profiles revealed depth-related reorganization of carbon-cycling potential, with hydrolytic and fermentative functions relatively more abundant near the surface and acetogenic and methanogenic pathways more prominent in deeper anoxic horizons. Gene-centric analyses indicated an important contribution of Rice Cluster II-related methanogens to hydrogenotrophic methanogenesis, while co-occurrence networks identified a depth-conserved syntrophic module centered on this lineage. Environmental variables showed depth-specific associations with microbial communities. Despite geographic separation and site-specific variation among peatlands, recurring depth-resolved microbial assemblages and functional profiles were observed, suggesting that common environmental constraints associated with peat development contribute to broad patterns of microbial community organization and carbon-cycling potential.},
}

@article {pmid42820741,
year = {2026},
author = {Napier, BA and Merrill, BD and Krieger, M and Gevers, D and Reid, G},
title = {Formulations containing co-biotic compounds mediate microbiome function and composition without increased gas production in an ex vivo gastrointestinal model.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131126},
doi = {10.1128/aem.01311-26},
pmid = {42820741},
issn = {1098-5336},
abstract = {UNLABELLED: Dietary supplement formulations that contain co-biotics or compounds that modulate biological processes in both the host and microbiome to confer a health benefit are an emerging strategy to fine-tune both host physiology and gut microbiome function. Here, we evaluated three novel formulations containing co-biotic compounds (DM-02, a multivitamin; AM-02, formulated for energy and focus; and PM-02, formulated to promote sleep) for their effects on human gut microbiome composition and function. The three formulations and untreated control (Unt-Ctrl) were subjected to upper gastrointestinal digestion, after which the digesta were exposed to 24-h simulated colonic fermentation in the validated ex vivo systemic intestinal fermentation research (SIFR) technology (n = 6 healthy adults). Outcomes included pH, short-chain fatty acid (SCFA) and gas production, ultra-deep metagenomic profiling, and untargeted metabolomics of post-colonic supernatants, each compared to Unt-Ctrl. All three formulations significantly reduced pH (3%-4%) and increased total SCFAs (9%-11%) and acetate (9%-12%), with AM-02 and PM-02 also increasing butyrate by 20% and propionate by 7%-8%, without increasing gas production. Each formulation significantly enriched specific SCFA- and B-vitamin-producing taxa. AM-02 significantly increased the abundance of two pyruvate fermentation to acetate/lactate pathways. PM-02 significantly increased the abundance of two tryptophan biosynthesis pathways, accompanied by an increase in available tryptophan and the abundance of tryptophan-producing microbes. All three formulations increased the availability of microbiome-derived metabolites, indicating microbiome functional modulation by the treatments. These findings support clinical evaluation of these novel formulations as a strategy to enhance microbiome composition and function.

IMPORTANCE: The gut microbiome produces metabolites, including short-chain fatty acids, B vitamins, and tryptophan derivatives, that are critical regulators of host physiology, from energy metabolism and gut barrier integrity to sleep and immune function. While probiotics introduce live microorganisms, and prebiotics selectively feed existing microbes, co-biotics represent a distinct category of compounds that simultaneously modulate host cell biology and microbiome activity. Despite growing interest in co-biotic supplementation, the impact of complete co-biotic-containing formulations on gut microbiome composition and functional output has not been evaluated. Using a validated ex vivo gastrointestinal model inoculated with fecal microbiota from six healthy adults, we demonstrate that three supplement formulations containing co-biotic compounds consistently increased production of health-associated metabolites, selectively enriched beneficial microbial taxa, and modulated functional metabolic pathways, all without increasing gas production. These findings establish a mechanistic foundation for the clinical investigation of co-biotic formulations as targeted, tolerable interventions for optimizing gut microbiome function across diverse human populations.},
}

@article {pmid42820871,
year = {2026},
author = {Zhang, J and Liang, C and Jiang, F and Zhao, X and Zhang, T},
title = {Seasonal and Regional Dietary Heterogeneity Is Associated With Gut Microbiota Differentiation in Przewalski's Gazelle (Procapra przewalskii).},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70215},
pmid = {42820871},
issn = {1749-4877},
support = {2025-ZJ-J09//Innovation Platform Construction Project of Qinghai Province/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University/ ; },
abstract = {Wild ungulates on the Qinghai-Tibet Plateau experience seasonal shifts in food resources, yet integrated evidence linking diets with gut microbiota and metabolic profiles remains limited. We combined fecal DNA metabarcoding, 16S rRNA sequencing, metagenomics, and untargeted metabolomics to analyze diet, gut microbiota composition, functional pathways, and fecal metabolic profiles in 82 fecal samples of Przewalski's gazelle (Procapra przewalskii) from three regions. Seasonal comparisons were conducted within each region and regional comparisons within each season. Winter diets showed regional specificity, with Poaceae and Cyperaceae enriched in the N region, Poaceae and Fabaceae in the S region, and Iridaceae in the W region, whereas summer diets shifted toward forb families including Asteraceae, Apiaceae, Brassicaceae, and Polygonaceae. Gut microbiota composition and KEGG Level 3 functions differed between seasons. Representative taxa enriched in winter included UCG-007 within Oscillospiraceae, Akkermansia, Mailhella, and Papillibacter, whereas taxa enriched in summer included Candidatus Saccharimonas, [Eubacterium]_brachy_group, and Colidextribacter. Representative pathways included Biosynthesis of cofactors, Biosynthesis of nucleotide sugars, Biosynthesis of various nucleotide sugars, and Glyoxylate and dicarboxylate metabolism in winter, whereas representative pathways in summer included the Phosphotransferase system (PTS), Ribosome, Aminoacyl-tRNA biosynthesis, and Peptidoglycan biosynthesis. Fecal metabolomic profiles differed among regions within both seasons, and dietary dissimilarity was significantly correlated with metabolomic, genus-level microbial, and KEGG Level 3 functional dissimilarities. Correlation analyses linked LEfSe-identified plant families to dominant genus-level taxa and KEGG Level 3 pathways. Together, these results support a close link between dietary variation and changes in gut microbiota composition, functional potential, and fecal metabolic profiles.},
}

@article {pmid42822169,
year = {2026},
author = {Zhou, Y and Zhang, M and Zhai, Y and Zhang, Y and Zhang, A and Wang, B and Song, J and Wang, M and Zheng, Y},
title = {Microbial functional differentiation and flavor formation across layer exchange in cereal vinegar fermentation: Multi-omics insights and targeted bioaugmentation.},
journal = {International journal of food microbiology},
volume = {463},
number = {},
pages = {112088},
doi = {10.1016/j.ijfoodmicro.2026.112088},
pmid = {42822169},
issn = {1879-3460},
abstract = {Spatial heterogeneity is common in cereal vinegar fermentation, but microbial and metabolic changes across the layer-exchange process remain unclear. We combined metagenomics and metatranscriptomics with physicochemical, organic-acid, and volatile profiling to investigate layer-associated changes during Tianjin Duliu mature vinegar (TDMV) fermentation and guide bioaugmentation. Before exchange, the frequently turned upper layer consumed ethanol at 1.14 times the lower-layer rate, rapidly accumulated acetic acid, and was enriched in Acetobacter and Komagataeibacter. The lower layer retained more ethanol and lactic acid, was enriched in lactic acid bacteria and yeasts, and contained more ethyl esters. After upward transfer, the original lower-layer Cupei rapidly accumulated acetic acid as several ethyl esters decreased; after downward transfer, the original upper-layer Cupei acidified more slowly while phenethyl alcohol, phenethyl acetate, ethyl lactate, and 2,3-butanediol increased. Genus-level transcript profiles showed that Acetobacter-affiliated transcripts related to acetaldehyde oxidation and the acetolactate/acetoin branch were more pronounced in upper-positioned Cupei, whereas LAB-affiliated lactate-forming transcripts were prominent in the lower layer. At the 100-kg scale, a targeted two-strain treatment using Lactobacillus helveticus and Acetobacter pasteurianus increased substrate conversion efficiency from 47.35 ± 1.36% to 51.19 ± 0.32% and final total acid by approximately 9.7% in both portions. In a → A, day-17 acetic acid was 43.8% higher than in the control, but the difference was not significant at the endpoint. The bioaugmentation samples showed changes in aroma-related volatile composition. These findings support complementary microbial functional differentiation across Cupei positions and inform position-targeted regulation of TDMV fermentation.},
}

@article {pmid42822223,
year = {2026},
author = {Liao, M and Qiu, Y and Wu, Z and Zhao, S and Ji, Y and Lin, N and Ma, J and Abraham, EN and Liu, G and Feng, Y},
title = {Nature-based solution-inspired electroactive ecological floating bed: a technology for carbon-nitrogen removal and ecological performance assessment in aquaculture Tailwater.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127010},
doi = {10.1016/j.watres.2026.127010},
pmid = {42822223},
issn = {1879-2448},
abstract = {The remediation of polluted aquaculture water and sediment, which severely threatens aquatic ecosystems, is of paramount importance. In this study, a Nature-based Solution (NbS) of electroactive ecological floating bed coupled with an oxygen-producing submerged plants system (EEFB-PS) was designed, where a conductive floating-bed matrix functioned as an integrated biocathode embedded within the rhizosphere and was coupled to the anode in the sediment. Under a 12 h light/dark condition, submerged plants induced diel DO oscillations that enabled nitrification in the daytime and electroautotrophic denitrification at night, as supported by distinct nitrate-reduction signals in cyclic voltammetry (CV) and differential cyclic voltammetry (DCV). Compared with the control system, EEFB-PS achieved a low effluent concentration of COD (7.2 mg/L), TN (1.3 mg/L), NH4[+]-N (0.1 mg/L), and NO3[-]-N (1.1 mg/L), and enhanced nitrogen removal dominated by microbially mediated pathways. 16S rRNA and metagenomics revealed enrichment of electroactive and nitrogen-cycling bacteria (e.g., Geobacter and Nitrospira) and functional shifts toward intensified denitrification/DNRA. Notably, the abundance of nosZ gene, which encodes nitrous oxide reductase, was significantly up-regulated (by 13.8-fold), demonstrating the system's high potential to mitigate N2O emissions. Meanwhile, EEFB-PS significantly mitigated the Global Warming Potential (GWP) to 4.6 mg CO2-eq m[-2]h[-1] by suppressing methanogenesis and promoting methane oxidation modules. Moreover, EEFB-PS rebalanced the aquatic food web by shifting phytoplankton dominance from Chlorophyta to Bacillariophyta, reducing phytoplankton density while increasing zooplankton abundance, thereby mitigating eutrophication risk. In summary, EEFB-PS demonstrates a rhizosphere-integrated, low carbon emission ecotechnology that couples with electron supply, plant-driven process, and microbial functional succession for aquaculture tailwater treatment and ecological restoration.},
}