@article {pmid42258415,
year = {2026},
author = {Pan, S and Chen, H and Sun, J and Xu, X and Gao, C},
title = {Species Identification And Antibiotic Susceptibility Testing Of The Nocardia Genus: Advances And Clinical Challenges.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {231},
pages = {},
doi = {10.3791/69977},
pmid = {42258415},
issn = {1940-087X},
mesh = {*Nocardia/drug effects/classification/genetics/isolation & purification ; Humans ; *Anti-Bacterial Agents/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Microbial Sensitivity Tests/methods ; Nocardia Infections/microbiology/drug therapy/diagnosis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The genus Nocardia comprises bacteria widely distributed in nature that can cause infections in both humans and animals. Due to their diverse clinical manifestations and prolonged culture time, infections are frequently misdiagnosed or overlooked. In recent years, advances in biological techniques have markedly improved molecular diagnostic methods, enabling more precise species identification. However, the increasing issue of antimicrobial resistance poses significant challenges for clinical management, particularly among immunocompromised patients, for whom treatment is more complex. Although multiple therapeutic agents are currently available, rising resistance rates highlight the critical importance of antibiotic susceptibility testing. This review discusses molecular identification methods for Nocardia species, including recent advances in 16S rRNA gene sequencing, multilocus sequence analysis (MLSA), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), and metagenomic next-generation sequencing (mNGS). The advantages and limitations of each technique are explored, with particular emphasis on their applications in detecting antibiotic resistance. The review also examines the clinical implementation of these molecular technologies, highlighting their contributions to rapid Nocardia identification, improved diagnostic accuracy, and reduced misdiagnosis. Finally, current limitations and future research directions are discussed, with particular attention to challenges related to cost, sensitivity, and standardization.},
}

*Nocardia/drug effects/classification/genetics/isolation & purification
Humans
*Anti-Bacterial Agents/pharmacology
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Microbial Sensitivity Tests/methods
Nocardia Infections/microbiology/drug therapy/diagnosis
RNA, Ribosomal, 16S/genetics

@article {pmid42258525,
year = {2026},
author = {Siegers, JY and Auerswald, H and Maquart, PO and Szentiványi, T and Guillebaud, J and Hoem, T and Li, X and Suor, K and Pum, L and Khun, L and Nuon, S and Chea, K and Heang, V and Bienes, KM and Su, YCF and Duong, V and Nouhin, J and Boyer, S and Karlsson, EA},
title = {Discovery of a novel coltivirus in a newly identified Bat Bug Species (Heteroptera: Cimicidae) in Cambodia.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {6},
pages = {e0014372},
doi = {10.1371/journal.pntd.0014372},
pmid = {42258525},
issn = {1935-2735},
abstract = {Bats and their ectoparasites are significant reservoirs and potential vectors of emerging zoonotic pathogens, yet the viral diversity within bat-associated arthropods remains poorly characterized. This study reports the identification of a novel coltivirus (order Reovirales), provisionally designated Stricticimex coltivirus (SCCV), in a newly described bat bug species, Stricticimex phnomsampovensis, collected from cave-dwelling wrinkle-lipped free-tailed bats (Mops plicatus) in Cambodia. Metagenomic sequencing and phylogenetic analysis revealed that SCCV clusters within the Coltivirus genus, showing closest similarity to Tai Forest Reovirus (TFRV) previously isolated from African bats. SCCV was detected in 18.4% of examined bat bugs and successfully isolated in VeroE6 cells, with replication confirmed in multiple mammalian cell lines. The discovery of SCCV extends the known diversity and geographic range of coltiviruses and highlights bat ectoparasites as overlooked hosts of potentially zoonotic viruses. These findings underscore the importance of integrated One Health surveillance targeting both bats and their ectoparasites to better assess the risk of pathogen spillover in biodiverse regions with high human-animal contact.},
}

@article {pmid42258549,
year = {2026},
author = {Vanhnollat, C and Chonephetsarath, S and Somlor, S and Vungkyly, V and Soulaphy, T and Vongsanga, S and Etobayeva, IV and Bigot, T and Wong, G and Letizia, AG and Brey, PT and Buchy, P and Vongphayloth, K},
title = {Detection and genetic characterization of Tembusu virus and other flaviviruses from mosquitoes in Lao PDR.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351023},
doi = {10.1371/journal.pone.0351023},
pmid = {42258549},
issn = {1932-6203},
mesh = {Animals ; *Flavivirus/genetics/isolation & purification/classification ; Laos ; Phylogeny ; Female ; *Culicidae/virology ; Genome, Viral ; *Mosquito Vectors/virology ; Flavivirus Infections/virology ; Humans ; Mosquito-Borne Diseases ; },
abstract = {BACKGROUND: Lao People's Democratic Republic (Lao PDR), located in Southeast Asia and known for its rich biodiversity, is part of a region recognized as a hotspot for emerging and re-emerging infectious diseases. Among flaviviruses, dengue virus (DENV) and Japanese encephalitis virus (JEV) are recognized public health threats. However, other reemerging mosquito-borne flaviviruses may also infect humans and cause diseases. Despite that, their distribution and public health impact in Lao PDR are not well understood due to limited past surveillance.

METHODOLOGY: Mosquitoes were collected using CDC light traps from 2021 to 2024, as part of vector and pathogen surveillance studies conducted across six provinces. A total of 2,548 female mosquitoes, representing 100 species from 11 genera, were collected and morphologically identified. Of these, 1,622 mosquitoes were pooled into 1,008 "mini pools" according to species and collection site. The pools were screened for flaviviruses by nested RT-PCR. Positive samples were further analysed by metagenomic sequencing, and coding-complete genomes were recovered and subjected to phylogenetic analysis.

PRIMARY RESULTS: We recovered thirteen coding-complete genomes through metagenomic sequencing, which included one Tembusu virus (TMUV) strain (TMUV/Mos_L010) from Culex vishnui mosquitoes and 12 other insect-specific flaviviruses (ISFVs). Phylogenetic analysis placed TMUV/Mos_L010 in cluster 3, closely related to a TMUV strain known to be pathogenic to dolphins in Thailand, with more than >99% bootstrap support for amino acid homogeneity. The detected ISFVs were part of the classical insect-specific flavivirus (cISFV) lineage and were further classified into five subgroups according to their associated mosquito genera: Aedes (1), Anopheles (1), Culex (2), and Uranotaenia (1).

CONCLUSIONS: This study documents the first detection of TMUV in Laotian mosquitoes and extends the known distribution of cluster 3 TMUV strains. The discovery of diverse ISFVs shows the rich and underexplored virome among Laotian mosquito populations. These findings highlight the need for enhanced arbovirus surveillance and ecological research to assess zoonotic risks of spillover infections in Southeast Asia.},
}

Animals
*Flavivirus/genetics/isolation & purification/classification
Laos
Phylogeny
Female
*Culicidae/virology
Genome, Viral
*Mosquito Vectors/virology
Flavivirus Infections/virology
Humans
Mosquito-Borne Diseases

@article {pmid42258623,
year = {2026},
author = {Mosquera, RA and Magana-Ceballos, IG and De Jesus Rojas, W and Huang, X and Koochak, H and Tellez, ME and Castillo-Moguel, JA and Bishehsari, F and Mahdavinia, M and Ramos-Benitez, MJ and Harris, T and Yadav, A and Owens, K and Lemus-Rangel, R and Romero, M and Zuleta, S and Luz, A and Baltazar-Fernandez, A and McBeth, KE and Hashmi, S and Rosario Ortiz, G and Santoyo-Rios, J and Loyo-Rodriguez, JF and Colasurdo, GN},
title = {Multi-Omics Analysis Defines Endotypes and Systemic Inflammation in Primary Ciliary Dyskinesia: A Comparison with Healthy Controls.},
journal = {Annals of the American Thoracic Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/annalsats/aaoag152},
pmid = {42258623},
issn = {2325-6621},
abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic airway inflammation and progressive lung injury. The inflammatory profile and systemic involvement remain poorly defined. We applied integrated multi omics (transcriptomics, proteomics, and metagenomics) to characterize inflammatory signatures and explore saliva as a noninvasive marker of systemic inflammation. These findings may support improved disease characterization and inform therapy and monitoring.

METHODS: This cross sectional, multicenter study included participants with PCD and healthy controls from Houston, Texas; Puerto Rico; and Mexico. Demographic and clinical data were collected in the absence of acute infection. Oral swabs underwent a bulk inflammatory transcriptomic profiling of 590-genes using NanoString nCounter® and microbiome evaluation via metagenomic sequencing. High sensitivity NULISA™ proteomic profiling of 250-proteins was performed on both saliva and plasma, with results correlated across omic layers. Pathway and gene set analyses were conducted using nSolver Advanced Analysis.

RESULTS: Seventy-six participants were enrolled: 51 with PCD and 25 healthy controls. PCD patients, especially those older than 10 years and those with microtubular defects, showed markedly elevated inflammatory gene and protein expression in saliva and plasma. Five inflammatory endotypes were identified: Neutrophilic protease dominant, Dipeptidyl Peptidase 1(DPP‑1) profile (78%); neutrophilic recruiting, high‑Th17 (71%); eosinophilic dominant, high‑Th2 (51%); Th2/Th17‑high (47%), and Th2/Th17‑low (25%). PCD demonstrated increased neutrophil, and CD45‑related gene expression and activation of ten inflammatory pathways, including NF‑κB, oxidative stress, T‑cell-receptor, TREG, Th17, TNF, Th1, Th2, TGF-B signaling, and TLR (P < .01). Saliva and plasma showed strong molecular concordance. Microbiome analysis revealed significant shifts in diversity and abundance linked to inflammatory pathways.

DISCUSSION: These findings show that PCD is characterized by baseline inflammatory activity with marked endotypic heterogeneity, most frequently involving neutrophilic-immune pathways driven by DPP1-associated protease activity and Th17-mediated neutrophil recruitment, while a distinct subset of patients demonstrates a Th2-predominant inflammatory endotype. Salivary inflammatory profiling, which closely mirrors plasma, may offer a practical, non-invasive approach to capturing this patient-level heterogeneity and monitoring systemic immune activity and treatment response, especially with the new anti-inflammatory medications for bronchiectasis.},
}

@article {pmid42259326,
year = {2026},
author = {Martins, MF and Govindan, R and Almaghlouth, NK and Kirby, JE and Kentoffio, KJ and Farmakiotis, D and Le-Mahajan, A},
title = {A fatal case of Legionella micdadei prosthetic valve endocarditis diagnosed by plasma microbial cell-free DNA metagenomic sequencing.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(26)00223-9},
pmid = {42259326},
issn = {1474-4457},
abstract = {We report a fatal case of Legionella micdadei prosthetic valve endocarditis in a patient who was immunocompromised, characterised by an indolent outpatient course followed by rapid clinical deterioration into mixed shock secondary to valve dehiscence and sepsis. The diagnosis was made by plasma microbial cell-free DNA metagenomic next-generation sequencing (mcfDNA-mNGS) and confirmed by buffered charcoal yeast extract culture of valve tissue. This case underscores the diagnostic limitations of conventional methods in culture-negative endocarditis, the evolving role of mcfDNA-mNGS in culture-negative endocarditis, and the absence of current culture-negative endocarditis guidelines addressing timely diagnosis for patients who are at risk of rapid deterioration. In this Grand Round, we briefly review the state of diagnostics for culture-negative endocarditis and the particularities of Legionella endocarditis. We also propose a framework for deciding when to consider early metagenomic testing, balancing the potential strengths of this technology with its limitations and cost.},
}

@article {pmid42259450,
year = {2026},
author = {Yang, W and Wang, X and Li, H and Liu, W and Chen, Z and Ren, B and Guo, T and Guo, J},
title = {Enhanced co-removal of nitrate and tetracycline from wastewater by iron-nitrogen-doped carbon: synergistic role of pyridinic nitrogen and iron.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135105},
doi = {10.1016/j.biortech.2026.135105},
pmid = {42259450},
issn = {1873-2976},
abstract = {Co-pollution of nitrate and tetracycline (TC) poses a critical barrier to efficient biological treatment due to impaired electron transfer, diminished microbial metabolic activity, and disrupted community structure. To address this challenge, this study synthesized an iron-nitrogen-doped carbon material (Fe-NC) featuring electron-withdrawing pyridinic nitrogen and Fe active sites. Under co-contaminated conditions, the nitrate and TC removal efficiencies of the TC/Fe-NC200 system were 100 % and 96 %, which were 21.27 and 2.18 times higher than those of the TC system. Material characterization indicated that Fe-NC might act as an electron transfer station, promoting the removal of nitrate and TC through Fe[3+]/Fe[2+] cycling. Electrochemical analyses showed that Fe-NC promotes the secretion of cytochrome c and flavin mononucleotide, accelerating extracellular electron transfer. Enzyme activity assays indicated that Fe-NC enhances intracellular electron transfer by activating key redox enzymes and upregulating associated gene expressions. Electron transfer system activity and metagenomic analysis further demonstrated that Fe-NC improves microbial respiration and increases the abundance of dominant taxa such as Bacteroidota (11.96 %) and Chryseobacterium (12.00 %), which support both TC degradation and microbial stress tolerance. These mechanistic insights establish a novel, bio-electroactive function for Fe-NC, in which the synergistic effects of Fe redox cycling and pyridinic nitrogen coordination led to improved electron flow, microbial function, and pollutant breakdown. This work not only reveals a previously unexplored pathway for biological co-removal of nitrate and antibiotics but also provides a scalable strategy for enhancing bioremediation efficiency in complex wastewater systems.},
}

@article {pmid42259455,
year = {2026},
author = {Wang, Y and Huang, Y and Yin, D and Gong, B and Fan, G},
title = {A segmented electron donor dosing strategy for enhancing thiosulfate-driven partial denitrifying efficiency: Insights into sulfur oxidation pathway, electron transfer and metagenomic microbial ecology.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135106},
doi = {10.1016/j.biortech.2026.135106},
pmid = {42259455},
issn = {1873-2976},
abstract = {Thiosulfate-driven partial denitrification (TPD) is a highly efficient denitrification process that exhibits good stability when coupled with Anammox. This study aimed to enhance the performance of the TPD system by employing different electron donor dosing strategies. The data show that the NO3[-]-N removal efficiency (NRE) and NO2[-]-N accumulation efficiency (NAE) in the segmented dosing group reached 98 % and 90 %, respectively. The study indicates that segmented electron donor dosing significantly enhances the activity of the electron transport chain. Specifically, Complex I and Complex III are associated with electron utilization by nitrate reductase (Nar) and nitrite reductase (Nir). The increased activity of Complex I and the inhibited activity of Complex III in the segmented dosing group contribute to improved NRE and NAE. Metagenomic analysis revealed that Thiobacillus predominated and served as the key functional species for Nar, Nir, and sulfur oxidation. Combined with qPCR analysis, segmented dosing significantly increased the expression levels of functional genes and elevated the NarG/(NirK + NirS) ratio, which further facilitated the accumulation of NO2[-]-N. Furthermore, the segmented dosing group possessed a complete sulfur oxidation pathway capable of fully oxidizing S2O3[2-] to SO4[2-], suggesting a reduced metabolic potential for S[0] production within the system. Overall, this study offers a potential strategy for ensuring a stable supply of nitrite in future anaerobic ammonium oxidation processes.},
}

@article {pmid42259841,
year = {2026},
author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y},
title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01038-z},
pmid = {42259841},
issn = {2055-5008},
abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.},
}

@article {pmid42260308,
year = {2026},
author = {Li, L and DU, L},
title = {[Clinical value of cerebrospinal fluid metagenomic next genera-tion sequencing in diagnosing neonatal intracranial infections].},
journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences},
volume = {},
number = {},
pages = {1-10},
doi = {10.3724/zdxbyxb-2025-0965},
pmid = {42260308},
issn = {1008-9292},
abstract = {OBJECTIVES: To evaluate the diagnostic performance of cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) for neonatal intracranial infections and its impact on clinical decision making.

METHODS: A retrospective observational study was conducted. Neonates admitted to the Children's Hospital, Zhejiang University School of Medicine from 2020 to 2025 with suspected intracranial infection who underwent CSF mNGS were enrolled. The sensitivity of mNGS and its concordance with CSF culture and PCR were calculated. Clinical impact was assessed using predefined criteria, and samples were categorized into positive impact and no impact groups to identify independent factors influencing the clinical utility of mNGS.

RESULTS: Among 61 neonates with suspected intracranial infection, 48 were confirmed. Pathogens were identified in 18 cases, of which 9 were detected exclusively by mNGS, accounting for 50% of etiological diagnoses. The sensitivity of mNGS was 31.3% (95% CI: 18.7%-46.3%), higher than that of culture PCR (18.8%, 95% CI: 8.9%-32.6%), but the difference was not statistically significant (P=0.15). The positive and negative concordance rates between mNGS and culture PCR were 66.7% (95% CI: 29.9%-92.5%) and 76.9% (95% CI: 60.7%-88.9%), respectively. mNGS positively influenced clinical decisions in 37.7% (23/61) of patients: 12 cases with positive results guided etiological diagnosis and treatment adjustment, and 11 cases with negative results led to antibiotic de escalation or discontinuation. Multivariate analysis identified a positive mNGS result as an independent factor associated with positive clinical impact (OR = 22.127, P<0.01).

CONCLUSIONS: CSF mNGS provides valuable support in etiological diagnosis and clinical decision making for neonatal intracranial infections.},
}

@article {pmid42251735,
year = {2026},
author = {Dennu, L and Devic, M and Rigonato, J and Falciatore, A and Lozano, JC and Vergé, V and Mariac, C and Joli, N and Jaillon, O and Sabot, F and Bouget, FY},
title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: insights into genetic diversity and function of outlier chromosomes.},
journal = {The Plant journal : for cell and molecular biology},
volume = {126},
number = {5},
pages = {e70982},
doi = {10.1111/tpj.70982},
pmid = {42251735},
issn = {1365-313X},
support = {ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; },
abstract = {Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes (MAGs). Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40° to 78° N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: While MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the big outlier chromosome, a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome, associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish B. prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets.},
}

@article {pmid42251775,
year = {2026},
author = {Sahnan, S and Morandini, V and Ferrer, M and Onrubia, A and Torralvo, C and Kaján, GL and Harrach, B and Varsani, A and Kraberger, S},
title = {Four lineages of adenoviruses identified in raptors sampled in Spain.},
journal = {Virology},
volume = {623},
number = {},
pages = {110990},
doi = {10.1016/j.virol.2026.110990},
pmid = {42251775},
issn = {1096-0341},
abstract = {Adenoviruses infect a wide range of vertebrate species from fish to humans, including an especially large number of avian species. This study utilized viral metagenomic workflow coupled with targeted PCR to identify and characterize adenoviruses from cloacal swabs collected from 50 black kites (Milvus migrans), 11 ospreys (Pandion haliaetus), and 35 common kestrels (Falco tinnunculus) sampled in Spain. A total of eleven adenoviral genomes were determined from black kites (n = 8) and common kestrels (n = 3). Amino acid pairwise comparison of the DNA polymerase protein coupled with phylogenetic analysis shows that these viruses fall into four adenovirus lineages: two in the genus Aviadenovirus (raptor adenovirus 2 and 3) and two in the genus Siadenovirus (raptor adenovirus 1 and 4). The genomes of raptor adenovirus 1 and raptor adenovirus 2 belong to the classified species Siadenovirus raptoris and Aviadenovirus falconis, respectively, whereas raptor adenovirus 3 and 4 represent putative new species. This study expands the known host range of raptor-infecting viruses in the species Siadenovirus raptoris and Aviadenovirus falconis to include black kites and common kestrels, respectively. We also expand on the diversity knowledge of adenoviruses in black kites.},
}

@article {pmid42251975,
year = {2026},
author = {Chen, C and Wang, M and Sun, L and Cheng, X and Deng, H and Li, RH},
title = {Phosphorus metabolism regulates the trade-off between phosphorus removal and sludge reduction.},
journal = {Bioresource technology},
volume = {458},
number = {},
pages = {135096},
doi = {10.1016/j.biortech.2026.135096},
pmid = {42251975},
issn = {1873-2976},
abstract = {Sludge reduction decreases the phosphorus export flux through waste sludge discharge, thereby increasing the risk of effluent phosphorus instability. However, the regulatory role of phosphorus in sludge reduction remains unclear. Here, side-stream phosphorus recovery was introduced into an anaerobic side-stream reactor (ASSR) based sludge reduction system to redirect phosphorus export from sludge discharge to physicochemical recovery, enabling investigation of how phosphorus flux redistribution regulates sludge reduction. Two parallel systems, a conventional ASSR system (SBR-ASSR) and an ASSR system coupled with phosphorus recovery (SBR-ASSR-PR), were comparatively evaluated using phosphorus mass balance, endogenous respiration analysis, cryptic growth modeling, and metagenomic profiling. Phosphorus recovery increased total phosphorus removal from 77.8% to 97.3% and total nitrogen removal from 72.5% to 82.1%, while reducing the observed sludge yield by 28%. Phosphorus mass balance showed that 34.7% of influent phosphorus was rerouted through the recovery pathway, reducing phosphorus discharge via waste sludge from 74.9% to 57.5%. The resulting lower system phosphorus levels restructured microbial metabolic allocation, suppressing biosynthesis while enhancing decay and substrate reutilization, with the cryptic growth contribution increasing from 35.9% to 46.9%. Metagenomic profiling corroborated this metabolic shift, revealing significant changes in key genes and pathways related to phosphorus cycling, energy maintenance, and denitrification. These findings show that phosphorus metabolism can regulate microbial growth-decay allocation, and that side-stream phosphorus recovery can coordinate nutrient removal, phosphorus recovery, and sludge minimization by restructuring internal phosphorus fluxes and microbial metabolic allocation.},
}

@article {pmid42252081,
year = {2026},
author = {Wang, F and Xie, J and Fu, T and Pu, K and Wu, Q and Li, Q},
title = {Negative CSF mNGS Results and Early Shunt Placement in Post-Infectious Hydrocephalus: A Retrospective Cohort Study.},
journal = {World neurosurgery},
volume = {},
number = {},
pages = {125104},
doi = {10.1016/j.wneu.2026.125104},
pmid = {42252081},
issn = {1878-8769},
abstract = {OBJECTIVE: To evaluate the impact of pre-shunt cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) guidance on the timing of ventriculoperitoneal (VP) shunt surgery and clinical outcomes in patients with post-infectious hydrocephalus (PIH), and to explore the value of mNGS in different clinical scenarios.

METHODS: In this retrospective cohort study, we included 42 patients with PIH who underwent VP shunt surgery at our institution between January 2019 and December 2025. Patients were divided into two groups according to whether pre-shunt CSF mNGS was performed: the mNGS group (n = 19) and the non-mNGS group (n = 23). Primary outcomes included recovery to shunt time (RTS), first negative to shunt time (NTS), decisional shunt to actual shunt time (DTS), and postoperative antibiotic time (PAT). Secondary outcomes included postoperative hospital stay (POHS), functional outcomes (mRS and GCS), POD 90 mortality, infection recurrence, and reoperation.

RESULTS: Compared with the non-mNGS group, the mNGS group demonstrated significantly shorter NTS (3 [IQR 1-4] days vs. 9 [IQR 4.5-17] days, P = 0.002), DTS (2 [IQR 1-3.5] days vs. 8 [IQR 6-18] days, P < 0.001), and PAT (0 [IQR 0-2] days vs. 4 [IQR 0-10] days, P = 0.010). No significant differences were observed between the two groups in RTS (P = 0.135), functional outcomes, mortality, infection recurrence, or reoperation.

CONCLUSIONS: Pre-shunt CSF mNGS testing significantly shortens NTS, DTS, and PAT in patients with PIH without compromising clinical outcomes. The mNGS-guided shunt strategy is safe and feasible, supporting its potential clinical application.},
}

@article {pmid42252233,
year = {2026},
author = {Dou, ZX and Liu, C and Zhang, Y and Wang, ZQ and Zhao, L},
title = {[A case of microsporidial keratoconjunctivitis].},
journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology},
volume = {62},
number = {6},
pages = {468-472},
doi = {10.3760/cma.j.cn112142-20251002-00402},
pmid = {42252233},
issn = {0412-4081},
abstract = {A 15-year-old male patient presented with recurrent photophobia, lacrimation, and blurred vision in both eyes for 3 years. He had been repeatedly diagnosed with "bilateral keratitis (unknown etiology)"at other hospitals and failed to respond to multiple topical medications. Initially diagnosed as bilateral Thygeson superficial punctate keratitis, he was treated with 0.5% loteprednol etabonate suspension eye drops and other medications. However, his symptoms worsened after 3 weeks of treatment. Subsequently, corneal epithelial tissue metagenomic testing and scrape cytological examination were performed, confirming the diagnosis of bilateral microsporidial keratoconjunctivitis. The treatment regimen was adjusted to topical application of 1% voriconazole eye drops, 0.3% gatifloxacin ophthalmic gel, and 0.1% tacrolimus eye drops. After 3 weeks of treatment, the patient's visual acuity in both eyes recovered to 1.0, conjunctival hyperemia was alleviated, and corneal epithelial punctate infiltration and fluorescein staining improved. One month after treatment, his symptoms were basically relieved, with the corneal infiltration and palpebral conjunctival papillae resolved. No recurrence was observed during the one-year follow-up.},
}

@article {pmid42252320,
year = {2026},
author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W},
title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55351-w},
pmid = {42252320},
issn = {2045-2322},
support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; },
abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.},
}

@article {pmid42252423,
year = {2026},
author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ},
title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05199-x},
pmid = {42252423},
issn = {1471-2180},
support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Química Valaner-MGI Mexico/ ; },
abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.},
}

@article {pmid42252476,
year = {2026},
author = {Wei, C and Wang, Y and Chen, Z},
title = {Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02445-2},
pmid = {42252476},
issn = {2049-2618},
abstract = {BACKGROUND: The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood.

RESULTS: Here, we present the Archaeal Viral Genome Database (AVGD), a comprehensive survey of archaeal viruses across eight distinct habitat types, including 3708 archaeal viral genomes, with genome sizes ranging from 3 to 188 kb, identified from 64,521,709 putative viral genomes using 40 public metagenomic datasets, an integrated public viral genome database (IGN), and pig gut viral databases. Our analysis revealed that the majority (92.93%) of archaeal viruses in the AVGD belong to the class Caudoviricetes. Phylogenetic analysis showed that many archaeal viruses diverged with their respective habitats. Using CRISPR spacer matching, we characterized the host composition of these archaeal viruses and uncovered competitive interaction networks between archaeal viruses and other archaeal viruses targeting the same host or different hosts. Furthermore, we identified 129,067 coding genes from 3708 archaeal viral genomes, most of which were associated with essential archaeal viral cellular functions, including replication, assembly, and packaging. Archaeal viruses also encoded a variety of auxiliary metabolic genes, anti-CRISPR (Acr) proteins for evading host immunity, and DNA methyltransferases for escaping host restriction-modification systems.

CONCLUSIONS: Together, this study provides a valuable resource and offers new insights into the ecological roles and host interactions of archaeal viruses across diverse environments. Video Abstract.},
}

@article {pmid42252506,
year = {2026},
author = {Galtier, A and Warinner, C and Velsko, IM},
title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag136},
pmid = {42252506},
issn = {1759-6653},
abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.},
}

@article {pmid42252693,
year = {2026},
author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W},
title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag145},
pmid = {42252693},
issn = {1751-7370},
abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.},
}

@article {pmid42252802,
year = {2026},
author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M},
title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {3},
pages = {e70324},
doi = {10.1002/jcsm.70324},
pmid = {42252802},
issn = {2190-6009},
support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; },
abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.

METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67 ± 8 years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.

RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4 kg/m2), WL (mean -6.5 vs. -0.2 kg), survival (median 5 vs. 13 months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p < 0.001) but not for other clinical covariables (e.g., cancer type) (all p > 0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p < 0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p > 0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial β-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p < 0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p < 0.05; 2025: Myoviridae, Siphoridae, p < 0.05) but also single-stranded (2022: Inoviridae, Microviridae, p < 0.05; 2025: Inoviridae; p < 0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).

CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.

TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).},
}

@article {pmid42253890,
year = {2026},
author = {Liu, Y and Xie, H and Song, Z and Huang, M and Li, M},
title = {Massive ascites and adnexal masses mimicking malignancy: A case report of Chlamydia trachomatis infection diagnosed by metagenomic next-generation sequencing.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02616},
pmid = {42253890},
issn = {2214-2509},
abstract = {OBJECTIVE: Chlamydia trachomatis (C. trachomatis) is the most commonly reported bacterial sexually transmitted infection among sexually active women. Although often asymptomatic or associated with non-specific clinical manifestations, it can cause inflammatory exudates and encapsulated fluid collections that are similar to adnexal masses on imaging. In rare cases, it may also present with massive ascites, a constellation of findings that may mimic ovarian malignancy.

CASE: We report the case of a 32-year-old female with a nearly 3-month history of abdominal pain, adnexal masses and massive ascites. The initial workup did not reveal obvious evidence of infection and cytological examination showed no malignant cells. However, advanced gynecological originated cancer could not be fully excluded. Metagenomic next-generation sequencing (mNGS), which detected C. trachomatis in ascitic fluid, facilitated the diagnosis. The patient showed satisfactory clinical improvement following doxycycline treatment.

CONCLUSION: For young, sexually active women presenting with unexplained ascites and adnexal masses, after excluding malignancy and common infectious diseases such as tuberculosis, C. trachomatis infection should be considered. Modern etiological detection methods, such as mNGS, can be employed to facilitate the diagnosis.},
}

@article {pmid42254105,
year = {2026},
author = {Habib, E and Urooj, I and Barry, HD and Awais, M and Kumari, M and Hajj, F},
title = {AI-programmable therapeutics via metagenomic foundation models for rare phage-mediated autoimmune modulations: early translational risks and benefits.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3905-3906},
pmid = {42254105},
issn = {2049-0801},
}

@article {pmid42254157,
year = {2026},
author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A},
title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3348-3359},
pmid = {42254157},
issn = {2049-0801},
abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.},
}

@article {pmid42254407,
year = {2026},
author = {Liang, Y and Hu, J and Wang, Z},
title = {A case of severe psittacosis in a hemodialysis patient-the critical role of detailed medical history and next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1825118},
pmid = {42254407},
issn = {2296-858X},
abstract = {An 80-year-old male patient on maintenance hemodialysis was admitted with "high fever and cough." Pulmonary imaging suggested pneumonia, but his condition deteriorated rapidly despite empirical broad-spectrum antimicrobial therapy (covering bacteria, atypical pathogens, and fungi), progressing to respiratory failure and delirium. He was transferred to the intensive care unit for continuous renal replacement therapy. Routine microbiological tests (blood culture, sputum culture, respiratory pathogen PCR) were all negative. Detailed history revealed that the patient had kept a parrot for over a month prior to illness onset. Metagenomic next-generation sequencing of blood and sputum specimens detected abundant Chlamydia psittaci sequences. Following confirmation, treatment was adjusted to oral minocycline combined with intravenous azithromycin. The patient's temperature gradually normalized, neuropsychiatric symptoms resolved, and pulmonary imaging showed marked improvement, ultimately leading to successful discharge. This case highlights the importance of considering zoonotic pathogens in immunocompromised patients with refractory pneumonia. Detailed history-taking and metagenomic next-generation sequencing (mNGS) technology are crucial for early diagnosis. Early use of mNGS should be strongly considered in immunocompromised patients with severe pneumonia unresponsive to empiric therapy and negative routine workup, particularly when epidemiological clues such as bird exposure are present.},
}

@article {pmid42254409,
year = {2026},
author = {Kong, H and Pan, J and Liu, J and Liang, M and Liu, L and Niu, H and Li, Y},
title = {Successful management of severe Pneumocystis jirovecii pneumonia with inhaled nitric oxide and individualized ventilatory strategies in an immunosuppressed patient: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1808578},
pmid = {42254409},
issn = {2296-858X},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have improved survival in extensive-stage small-cell lung cancer (SCLC) but may cause checkpoint inhibitor pneumonitis (CIP). Management of CIP often requires prolonged high-dose corticosteroids, leading to profound immunosuppression and increased risk of opportunistic infections. Among these, Pneumocystis jirovecii pneumonia (PJP) is a life-threatening complication in non-HIV patients and carries higher mortality than HIV-associated PJP. Early etiological diagnosis is therefore essential. We report a case of severe PJP diagnosed by metagenomic next-generation sequencing (mNGS) and successfully managed with comprehensive respiratory support.

CASE PRESENTATION: A 69-year-old HIV-negative man with extensive-stage SCLC received four cycles of etoposide-platinum chemotherapy plus adebrelimab. Subsequently, CIP developed and required prolonged high-dose methylprednisolone therapy. He was transferred to our hospital for progressive dyspnea. Evaluation showed severe hypoxemia (PaO₂/FiO₂ 185 mmHg) and markedly elevated serum 1,3-β-D-glucan (3327.99 pg./mL). Bronchoalveolar lavage fluid mNGS identified P. jirovecii as the predominant pathogen, with Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans indicating mixed pulmonary infection. The patient received trimethoprim-sulfamethoxazole, cefoperazone-sulbactam, and caspofungin. Worsening respiratory failure required endotracheal intubation and mechanical ventilation. Lung recruitment maneuvers, individualized positive end-expiratory pressure titration, and adjunctive inhaled nitric oxide progressively improved oxygenation, allowing successful extubation and eventual discharge.

CONCLUSION: Severe PJP should be considered in non-HIV patients receiving corticosteroids for CIP. mNGS enabled rapid pathogen identification and targeted therapy. Comprehensive respiratory support, including optimized mechanical ventilation and inhaled nitric oxide, may be valuable in managing life-threatening opportunistic infections in immunosuppressed patients.},
}

@article {pmid42254474,
year = {2026},
author = {Sparaciari, FE and Saylors, K and Chan, M and Perez, S and Firth, C and Horwood, PF and Karlsson, EA},
title = {Operationalizing metagenomic data from environmental surveillance for one health decision-making in live animal markets: Findings from a multisectoral workshop in Cambodia.},
journal = {Dialogues in health},
volume = {8},
number = {},
pages = {100312},
pmid = {42254474},
issn = {2772-6533},
abstract = {BACKGROUND: Live animal markets (LAMs) are recognized as hotspots for zoonotic disease emergence. Environmental surveillance (ES), particularly when paired with metagenomic sequencing, offers an advanced and actionable approach to pathogen detection in high-risk settings. However, the complexity of metagenomic data and the lack of user-friendly communication tools hinder its integration into routine public health decision-making.

METHODS: We conducted an exploratory qualitative participatory workshop study with descriptive analysis. A three-day multisectoral workshop was held in Phnom Penh, Cambodia, in May 2024, bringing together stakeholders from health, agriculture, and environment sectors to explore how metagenomic ES data can be visualized, understood, and applied. Through simulation exercises, surveys, and interviews, the workshop evaluated user preferences for data formats, thresholds for action, and decision-making strategies.

FINDINGS: In total, 52 participants attended the workshop and ten completed semi-structured interviews. Participants discussed their preferred familiar visualizations (bar, pie, and line charts) and intuitive color-coded thresholds (e.g., traffic-light schemes). While digital dashboards were welcomed, analog, printer-friendly formats remained essential due to infrastructure constraints. Key barriers to ES integration included limited bioinformatics capacity, lack of inter-ministerial coordination, and minimal ES prioritization at the provincial level.

INTERPRETATION: Metagenomic ES data can inform public health actions when visualization tools are tailored to end-user needs and embedded in multisectoral governance. This exploratory participatory workshop generated preliminary stakeholder-informed insights and an initial draft roadmap for future implementation planning in Cambodia. Further expert-led and funded work is needed to validate visualization tools, pathogen-specific thresholds, escalation pathways, and operational use under real-world surveillance conditions.},
}

@article {pmid42254492,
year = {2026},
author = {Chang, Z and Wang, X and Zhao, M and Zhang, X and Li, S and Liu, Y and Zhang, S and Wang, J and Wang, X},
title = {MARM: a framework for malignancy risk prediction from host-derived CNV in bronchoalveolar lavage fluid mNGS data with microbial admixture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1846545},
pmid = {42254492},
issn = {1664-302X},
abstract = {Early identification and risk assessment of malignancy are essential for improving clinical decision-making and patient outcomes. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) data contain both microbial and host-derived signals, and a key challenge in extending such data to tumor-associated applications is the robust extraction of host features with discriminative value for malignancy from this complex, admixed background. To address this problem, we developed MARM, a malignancy risk prediction method centered on host-derived copy number variation (CNV). Using host-derived reads from BALF mNGS data, MARM performs genome-wide window-based coverage quantification, normalization and bias correction, reference baseline construction, and principal component-based denoising to derive window-level CNV features for malignancy risk modeling. In addition, a pseudo-label-based extension strategy was introduced to incorporate weakly labeled samples through high-confidence screening, and the performance of XGBoost, Random Forest, and generalized linear models (GLM) was systematically evaluated using CNV features, microbial features, and combined features. Models built on host-derived CNV features consistently outperformed those based on microbial features and achieved performance comparable to combined-feature models, while joint modeling did not provide a stable additional benefit. These findings indicate that, under the current data setting and feature construction strategy, CNV represents a more stable and informative discriminative signal than microbial features. Among the evaluated classifiers, XGBoost showed the best compatibility with window-level CNV features and outperformed Random Forest and GLM overall. On the independent validation set, the pseudo-label-enhanced MARM achieved the best overall performance, with a sensitivity of 0.686, specificity of 0.975, accuracy of 0.847, and Youden index of 0.671. By contrast, microbial features did not show stable independent discriminative ability, and combined modeling did not yield clear or sustained performance gains. Together, these results indicate that, in microbially admixed BALF mNGS data, host-derived CNV is more suitable than the evaluated microbial features as the core modeling signal for malignancy risk prediction. MARM provides a new methodological framework for malignancy prediction in complex clinical samples and offers a reference for deeper exploitation of host-derived signals in mNGS data and related auxiliary diagnostic applications.},
}

@article {pmid42254517,
year = {2026},
author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P},
title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801806},
pmid = {42254517},
issn = {1664-302X},
abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.

METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.

RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC = 0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7α,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.

CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.},
}

@article {pmid42254837,
year = {2026},
author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM},
title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag082},
pmid = {42254837},
issn = {2730-6151},
abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.},
}

@article {pmid42255303,
year = {2026},
author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W},
title = {Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1726191},
pmid = {42255303},
issn = {1664-462X},
abstract = {Biochar, a soil amendment with diverse regulatory functions, has been widely applied to enhance soil conditions. However, its underlying mechanism for alleviating continuous cropping obstacles, from the perspective of rhizosphere microbe-metabolite-plant coupling, remains to be further elucidated. Using cucumber (Cucumis sativus L.) as the model crop, this study explored the rhizosphere-mediated effects of biochar application under continuous cropping conditions via the analytical methods of metagenomics and metabolomics. Six biochar application rates (0, 5, 10, 20, 30, and 40 t ha[-][1]) were tested. All biochar treatments significantly improved cucumber yield by 20%-50%, with the C30 and C40 treatments producing the most pronounced yield enhancement. C10, C20, C30 and C40 treatments had a positive effect on cucumber quality, soil physicochemical properties and enzymatic activities. Vitamin C and soluble protein peaked in C20, whereas some sugar indicators decreased across all biochar treatments. Urease activity was significantly elevated under C20, C30, and C40 treatments. Notably, the C40 treatment led to marked increases in total nitrogen, available phosphorus, and sucrase activity. Biochar amendments also enriched key bacterial phyla involved in carbon and nitrogen cycling, including Actinobacteria, Bacteroidetes, Chloroflexi, and Bacillota. Medium to high application rates (C20, C30, C40) upregulated various secondary metabolic pathways associated with biotic stress resistance, including the biosynthesis pathways of phenylpropanoids, various alkaloids, and the metabolic pathway of phenylalanine. High biochar application rate (C40) characterized lipid metabolism as the core responsive pathway and significantly downregulated galactose metabolism. This study reveals that biochar application represents a promising strategy to mitigate continuous cropping obstacles of cucumber by enhancing nutrient cycling, enzyme activities, soil metabolite composition, and the rhizosphere microbial community in facility systems of the cold and arid northern regions of China.},
}

@article {pmid42255362,
year = {2026},
author = {Sun, Y and Kei, K and Qiu, JW and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the feather duster worm, Sabellastarte sp. h YS-2021 (Sabellida: Sabellidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {274},
pmid = {42255362},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Sabellastarte sp. h YS-2021 (feather duster worm; Annelida; Polychaeta; Sabellida; Sabellidae). The genome sequence has a total length of 1 786.39 megabases. Most of the assembly (97.94%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.35 kilobases. From the metagenome data, we recovered 5 bins, of which one was a high-quality MAG.},
}

@article {pmid42255501,
year = {2026},
author = {Huo, S and Liu, W and Lv, C and Liu, B and Xue, J and Hong, Y and Hao, Y and Chen, M and Xu, A and Tan, X and Feng, X and Li, S},
title = {The re-emergence of psittacosis in China: a scoping review of epidemiology, diagnostics, and One Health priorities.},
journal = {Science in One Health},
volume = {5},
number = {},
pages = {100158},
pmid = {42255501},
issn = {2949-7043},
abstract = {Psittacosis caused by Chlamydia psittaci has re-emerged in China as sporadic cases and localized outbreaks. However, current knowledge remains fragmented across the clinical, veterinary, epidemiological, and public health fields. This scoping review mapped studies on psittacosis in China, identified major knowledge gaps, and defined priorities for research, clinical management, and prevention and control. Following the Arksey and O'Malley framework and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR), China National Knowledge Infrastructure (CNKI), Wanfang, PubMed, Web of Science, and Embase were searched for studies published between 1 January 1985 and 31 December 2025 and synthesized eligible studies with descriptive statistics and thematic analysis. A total of 424 studies were included. Research interest showed recent sharp increases and was concentrated in Eastern and Central China. Case reports and series dominated the literature, whereas analytic epidemiology, standardized surveillance, and high-resolution molecular studies remained limited. Reported cases were most often documented in middle-aged and older adults with avian exposure, including pet birds and poultry, and the reported occurrence showed a winter-spring pattern. Pneumonia was the predominant clinical presentation, and severe cases could progress to acute respiratory distress syndrome and multi-organ dysfunction. Metagenomic next-generation sequencing (mNGS) was the most frequently reported diagnostic method in recent studies, while PCR and serology remained important complementary tools. Overall, the literature is growing rapidly, but remains uneven in geographic coverage, study design, and integration across human, animal, and environmental sectors. These findings support broader One Health surveillance, stronger analytic and molecular epidemiology, and more standardized approaches to diagnosis, source investigation, and prevention in China.},
}

@article {pmid42256215,
year = {2026},
author = {Li, C and Ye, X and Chen, Y and Shen, M and Zhou, Z and Jiang, H and Hu, L and Pan, H and Shen, D and Lin, Y and Wang, L},
title = {Pathogen spectrum of pulmonary infections in kidney transplant recipients and the diagnostic value of mNGS: a sputum and BALF study based on clinical decision-making.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1742153},
pmid = {42256215},
issn = {2235-2988},
abstract = {BACKGROUND: Pulmonary infection is a common and severe post-transplant complication in kidney transplant recipients (KTRs). Their long-term immunosuppression results in an extremely complex pathogen spectrum. Compared with conventional etiological detection methods, metagenomic next-generation sequencing (mNGS) enables rapid and broad-spectrum pathogen identification. However, compared with bronchoalveolar lavage fluid (BALF), research on the diagnostic value of sputum - used as a non-invasive sample - for pulmonary infections in KTRs remains limited.

METHODS: A retrospective study included 77 kidney transplant recipients (KTRs) with pulmonary infections admitted from July 2021 to January 2025. BALF (n=37) or sputum (n=40) was collected for mNGS. Ninety-two non-immunosuppressed patients with pulmonary infections, treated during the same period and with BALF for mNGS, were also included. We compared pathogen profiles between the two groups and evaluated the diagnostic performance for KTRs pulmonary infections between BALF and sputum.

RESULTS: The pathogen spectrum in KTRs was dominated by viruses (43.0%) and opportunistic fungi (20.0%), whereas bacteria (67.97%) predominated in the non-immunosuppressed group. The co-infection rate was significantly higher in KTRs than in the non-immunosuppressed group (67.57% vs. 35.87%, P<0.001). In the KTRs cohort, the sputum group had a much higher prevalence of heart disease than the BALF group (52.5% vs. 2.7%, P<0.001). The positive detection rates of sputum and BALF mNGS showed no statistical difference (97.5% vs. 91.89%, P = 0.268), but sputum mNGShad a higher concordance rate with the clinical composite diagnosis (95.0%) compared to BALF mNGS (81.08%). In both specimen types, mNGS achieved a significantly higher pathogen detection rate than conventional tests (P<0.001 for both), with poor agreement between the two approaches (Kappa < 0.2).

CONCLUSION: The pathogen spectrum of pulmonary infections in KTRs differs significantly from that in non-immunosuppressed patients. It is characterized by a predominance of viruses and opportunistic fungi. mNGS is superior to conventional methods for making an etiological diagnosis. Non-invasive sputum mNGS is a valuable diagnostic alternative in KTRs, particularly for patients unable or unwilling to undergo invasive procedures.},
}

@article {pmid42256221,
year = {2026},
author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V},
title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826972},
pmid = {42256221},
issn = {2235-2988},
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.},
}

@article {pmid42256253,
year = {2026},
author = {Huang, W and Wang, S and Zhang, Y and Gao, M and Zhong, N and Hao, C and Janak, LP and Wang, L and Meng, S and Zhao, W and Zeng, S},
title = {Streptococcus mutans exacerbates gut microbiota dysbiosis in SHANK3 [-/-] autism model mice via the oral-gut axis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2681259},
pmid = {42256253},
issn = {2000-2297},
abstract = {BACKGROUND AND OBJECTIVE: Autism spectrum disorder (ASD) is associated with gut microbiota dysbiosis, yet the impact of oral pathobiont translocation via the oral-gut axis remains unclear. This study investigated how Streptococcus mutans (S. mutans), a primary cariogenic pathogen, influences gut microbial structure and function in an ASD mouse model.

METHODS: SHANK3 knockout (SHANK3[-/-]) and wild-type (WT) mice were divided into four groups: WT control, WT S. mutans-gavaged (WT-S.m), SHANK3[-/-] control, and SHANK3[-/-] S. mutans-gavaged (SHANK3-S.m). Mice were gavaged with S. mutans UA159 twice weekly for five weeks, followed by fecal metagenomic sequencing (n = 6 per group).

RESULTS: S. mutans translocated to the gut in both gavaged groups but did not achieve enhanced colonization in SHANK3[-/-] mice. S. mutans gavage significantly altered the gut microbiota structure in both WT and SHANK3[-/-] mice. In the ASD model, S. mutans gavage led to a significant enrichment of potential pathobionts (e.g. Duncaniella dubosii, Muribaculum gordoncarteri) and a decrease in beneficial bacteria (e.g. Bacteroides caecimuris, Bacteroides faecium). LEfSe analysis identified Parascardovia denticolens and Bacteroides heparinolyticus as specific biomarkers for the SHANK3-S.m group. Microbial networks showed reduced stability in SHANK3-S.m mice, with Enterocloster bolteae as a key node. Functional analysis revealed suppressed butanoate metabolism and enhanced neuroinflammation-related pathways.

CONCLUSION: Although S. mutans colonized only transiently, it provoked exacerbated ecological instability and pro-inflammatory metabolic alterations in ASD model mice, underscoring the role of the oral-gut-brain axis in ASD.},
}

@article {pmid42256259,
year = {2026},
author = {Dewan, A and Mascellino, MT},
title = {Computational and multi-omics systems biology for precision microbiome therapeutics.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1842701},
pmid = {42256259},
issn = {2813-4338},
abstract = {The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka-Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications-including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling-illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML-GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches - metabolic compatibility modeling and data-driven responder stratification - suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges-such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models-are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.},
}

@article {pmid42256958,
year = {2026},
author = {Elendu, C and Debua, AT and Okolo, EH and Sadiq, HO},
title = {Immune Checkpoint Inhibitor Pneumonitis Complicated by Invasive Pulmonary Aspergillosis in COPD: Diagnostic and Therapeutic Challenges.},
journal = {Clinical case reports},
volume = {14},
number = {6},
pages = {e72755},
pmid = {42256958},
issn = {2050-0904},
abstract = {Checkpoint inhibitor-associated pneumonitis complicated by invasive pulmonary aspergillosis represents a diagnostic challenge in ICI-treated patients, particularly those with COPD receiving corticosteroid therapy. Persistent or worsening respiratory abnormalities despite immunosuppressive treatment should prompt reassessment for superimposed fungal infection, including bronchoscopy, BALF analysis, and microbiologic testing to facilitate diagnosis and targeted therapy.},
}

@article {pmid42257244,
year = {2026},
author = {Moulignier, A and Heran, F and Lallemand, F and Bourdillon, P},
title = {Human Pegivirus Encephalitis With Brain Detection and Response to Sofosbuvir Ledipasvir.},
journal = {Annals of clinical and translational neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/acn3.70450},
pmid = {42257244},
issn = {2328-9503},
abstract = {Human pegivirus (HPgV-1) has been associated with severe encephalomyelitis in immunocompromised patients. Its neurological spectrum remains poorly defined. We report a slowly progressive encephalitis in a person living with well-controlled HIV, characterized by white matter abnormalities and inflammatory cerebrospinal fluid (CSF). HPgV RNA was detected in CSF and brain tissue by metagenomic sequencing, with no alternative pathogen identified. Following off-label treatment with sofosbuvir/ledipasvir, the patient showed sustained clinical improvement, normalization of CSF findings, and disappearance of detectable HPgV RNA. This observation expands the clinical context of HPgV-1 detection and supports further investigation of its role in central nervous system disease.},
}

@article {pmid42257696,
year = {2026},
author = {Nebauer, DJ and Nelson, T and Romanis, C and Neilan, BA and Timms, VJ},
title = {Taxonomy bias in metagenome-assembled genome recovery.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001736},
pmid = {42257696},
issn = {2057-5858},
abstract = {The recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing is rapidly expanding the availability of representative genomes. However, this practice may skew the representation of specific taxa in real-world datasets. This bias is attributed primarily to the known inefficiencies of sequence-by-synthesis platforms in amplifying GC-rich and AT-rich sequence fragments. Here, we recover 216 medium- and high-quality MAGs from an Australian wetland site. Notably, no MAGs were recovered for some dominant cyanobacterial and proteobacterial species known to be present. A new protocol involving read-based classification and alignment to the MAG dataset demonstrated the highly efficient recovery of low-GC organisms in the Actinobacteria and Bacteroidota phyla. Additionally, the recovery of lost taxonomic information was demonstrated through unmatched sample mapping. The findings suggest a bias towards the recovery of smaller, low-GC organisms in MAG recovery, potentially skewing the global representation of microbial diversity. Our pipeline is made publicly available as a tool to help researchers estimate taxonomic losses following MAG recovery efforts.},
}

@article {pmid41654194,
year = {2026},
author = {Wei, P and Zhang, L and Hu, Q and Zhu, A and Zhuang, Z and Zhang, Z and Zhang, S and Chen, J and Xiong, X and Qu, B and Zhang, Y and Chen, L and Xu, Z and Chen, Z and Zhong, Q and Xing, X and Li, X and Gao, J and He, Y and Xie, G and Shang, J and Guo, X and Jiang, J and Shi, Y and Zhao, J and Wang, Y and Zhao, J and Jin, Y},
title = {Integrated multiplex PCR and metatranscriptomics reveal upper-lower airway microbial landscapes in pediatric respiratory infections.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {58-69},
pmid = {41654194},
issn = {1995-820X},
mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; *Multiplex Polymerase Chain Reaction/methods ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Male ; Child, Preschool ; Infant ; *Microbiota/genetics ; Child ; *Bacteria/genetics/classification/isolation & purification ; Nasopharynx/microbiology/virology ; Gene Expression Profiling ; Viruses/genetics/isolation & purification/classification ; Metagenomics ; },
abstract = {Despite widespread use of multiple PCR, a substantial proportion of pediatric acute respiratory tract infections (ARTIs) lack identifiable pathogens and are classified as unknown etiology. The microbial characteristics and clinical relevance of these cases remain unclear. In this study, we compared the airway microbiomes of PCR-positive and PCR-negative ARTIs and examined their relationships with sampling site and disease severity. A total of 514 hospitalized children with ARTIs were enrolled. Nasopharyngeal swabs (NS) and bronchoalveolar lavage fluid (BALF) samples were tested using a 22-target multiplex PCR panel and subsequently stratified by pathogen status for pooled metatranscriptomic sequencing to profile active microbial communities, viral genotypes, and antibiotic resistance genes. PCR identified common respiratory pathogens in 77.0% of NS and 54.1% of BALF samples. Metatranscriptomic analysis showed that PCR-negative pools displayed markedly lower viral activity and comparatively higher bacterial transcript abundance, with notable enrichment of Pseudomonas. Microbial signatures differed between upper and lower airway samples and across clinical severity, with severe cases demonstrating increased bacterial burden and Pseudomonas enrichment, whereas mild infections exhibited relatively stronger viral signals. Under current thresholds, antibiotic resistance genes were detected in patient pools but not in healthy controls. Overall, PCR-negative pediatric ARTIs exhibited distinct, bacteria-enriched microbial profiles. Integrating metatranscriptomics with PCR enhances pathogen characterization and reveals site- and severity-related microbial patterns that may support diagnostic evaluation and clinical management.},
}

Humans
*Respiratory Tract Infections/microbiology/virology
*Multiplex Polymerase Chain Reaction/methods
Bronchoalveolar Lavage Fluid/microbiology/virology
Female
Male
Child, Preschool
Infant
*Microbiota/genetics
Child
*Bacteria/genetics/classification/isolation & purification
Nasopharynx/microbiology/virology
Gene Expression Profiling
Viruses/genetics/isolation & purification/classification
Metagenomics

@article {pmid42250135,
year = {2026},
author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M},
title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42250135},
issn = {1573-0972},
abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.},
}

@article {pmid42250463,
year = {2026},
author = {Xia, L and Lu, L and Liu, M and Jiao, J and Liu, L and Meng, L and Liu, Y and Li, W and Lu, C and Ma, B},
title = {Proposal of Edaphobacterium genomatis gen. nov., sp. nov. within the family Casimicrobiaceae from metagenome-assembled genomes in accordance with the SeqCode.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126735},
doi = {10.1016/j.syapm.2026.126735},
pmid = {42250463},
issn = {1618-0984},
abstract = {Casimicrobiaceae strains inhabit various environments, but their ecological roles in natural soils remain mostly unclear. By actively targeting specific high-altitude datasets during our Global Mollisols Genomic Atlas (GMGA) mining efforts, we discovered a previously unknown lineage within this family. This novel group is represented by five metagenome-assembled genomes (MAGs) recovered from oligotrophic soils in the Southern Brazilian Highland Grasslands, a unique environment within the broad Pampas black soil region. Phylogenetic and comparative genomic analyses showed these five MAGs form a distinct monophyletic clade within Casimicrobiaceae. Their novel taxonomic status is supported by Average Nucleotide Identity (ANI) thresholds, showing clear divergence from all known reference genomes. Functional annotations suggest a chemoorganotrophic lifestyle with microaerobic respiration capacity, while trace-gas scavenging genes indicate potential lithoheterotrophy for maintenance energy under nutrient limitation. Additionally, an autonomous ACC deaminase system and specialized nutrient scavenging pathways (organophosphonate and taurine utilization) highlight its adaptive capacity for rhizosphere interactions and survival in oligotrophic environments. Screening 22,976 public metagenomes demonstrated a widespread global distribution, primarily inhabiting diverse soil (86.4%) and plant-associated (7.0%) environments. Based on these analyses, we propose the name Edaphobacterium genomatis gen. nov., sp. nov. for this novel taxon following the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data) rules. Our results uncover hidden species diversity and highlight the specific functional roles of uncultured microbes in nutrient-limited highland niches within fertile black soil regions.},
}

@article {pmid42250813,
year = {2026},
author = {Kadam, R and Jo, S and Panwar, NL and Kim, T and Park, J},
title = {Metagenomic insights into metabolic limitations and biosafety implications of rendered pig carcass anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135081},
doi = {10.1016/j.biortech.2026.135081},
pmid = {42250813},
issn = {1873-2976},
abstract = {Global livestock production has intensified, increasing the biosecurity and environmental risks associated with animal mortality management. This study evaluated the feasibility of anaerobic digestion (AD) as a sustainable valorization route for rendered pig carcasses using long-term performance monitoring and whole-metagenome shotgun sequencing. During operation at an organic loading rate (OLR) of 1.0-2.0 kg-VS/m[3]/d, the reactor achieved peak methane (CH4) yields of 400-430 mL-CH4/g-VS and an organic matter removal efficiency > 70%. The buffering capacity generated through carcass proteolysis contributed to maintaining reactor performance under increasing loading conditions. However, increasing the OLR to 3.0 kg-VS/m[3]/d triggered process instability, decreasing the CH4 yield and increasing the total volatile fatty acids (TVFAs) to > 6,000 mg/L, specifically dominated by propionic and butyric acids. Metagenomic analysis identified a specialized consortium dominated by the syntrophic acetogen Cloacamonas and acetoclastic methanogen Methanosaeta during reactor operation at moderate OLRs. Functional profiling revealed that although the community possessed efficient hydrolytic and syntrophic acetate oxidation pathways, propionic acid accumulation and lower completeness of propionate oxidation pathways suggested potential limitations in syntrophic propionate oxidation at elevated OLRs. Furthermore, biosafety-related assessments suggested that AD may offer potential biocontainment advantages over traditional carcass disposal methods based on reduced prevalence of antimicrobial resistance genes and virulence-associated factors. These findings provide a metabolic framework for optimizing carcass-based AD as a viable substrate for renewable energy recovery.},
}

@article {pmid42250815,
year = {2026},
author = {Xie, C and Li, D and Li, J and Li, J and Yin, M and Wu, Y and Zhang, C and Luo, R and Zhu, Y and Zhang, Z and Zheng, Z and Peng, Y},
title = {Molecular mechanism of anammox granular sludge disintegration caused by polyethylene terephthalate micro/nanoplastics: a new perspective based on quorum sensing.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135060},
doi = {10.1016/j.biortech.2026.135060},
pmid = {42250815},
issn = {1873-2976},
abstract = {Quorum sensing (QS) regulates the synthesis and secretion of extracellular polymeric substances (EPS), which are essential for maintaining the structural stability of anaerobic ammonium oxidation (Anammox) granular sludge. However, the molecular mechanism linking polyethylene terephthalate micro/nanoplastics (PET-MNPs)-induced QS disruption to EPS inhibition remains unclear. This study investigated the effects of two PET-MNP sizes (80 μm and 300 nm) on Anammox granular sludge under different exposure concentrations. PET-MNPs significantly reduced nitrogen removal performance and caused surface cracking, structural loosening, and granule disintegration. EPS analysis showed that PET-MNPs decreased EPS content, altered protein secondary structure, and increased hydrophilic functional groups, thereby weakening sludge bioadhesion. Metagenomic and metatranscriptomic analyses indicated that PET-MNPs inhibited the abundance and expression of genes involved in the Anammox process, tricarboxylic acid cycle, glycolysis/gluconeogenesis, and Wood-Ljungdahl pathway, resulting in insufficient ATP, NADH, and metabolic precursors required for EPS synthesis. Meanwhile, methionine and fatty acid metabolism were suppressed, limiting precursor supply for acyl-homoserine lactone (AHL) synthesis. Molecular docking showed that PET oligomers could stably bind to LuxR and potentially hinder AHL-LuxR complex formation. Exogenous AHL supplementation promoted EPS re-secretion, confirming the important role of QS imbalance in PET-MNPs-induced EPS reduction. Overall, PET-MNPs destabilized Anammox granular sludge through the combined effects of particle-induced physical damage and oligomer-mediated molecular interference. This study elucidates the molecular mechanism of MNP-induced Anammox granule disintegration and provides a theoretical basis for assessing the ecological risks of emerging pollutants in biological wastewater treatment.},
}

@article {pmid42250818,
year = {2026},
author = {Liu, Y and Qian, Z and Peng, Y and Zhang, T and Li, Z and Shi, S and Gu, H},
title = {Enhancing ethanol-driven chain elongation via iron speciation: impacts on metabolic flux and dual FAB/RBO pathway activation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135088},
doi = {10.1016/j.biortech.2026.135088},
pmid = {42250818},
issn = {1873-2976},
abstract = {Anaerobic chain elongation (CE) has emerged as a promising technology for upgrading low-value organic substrates into high-value medium-chain fatty acids (MCFAs); however, achieving targeted metabolic flux and efficient electron transfer remains challenging. To address this, this study explores the role of iron speciation in enhancing chain elongation (CE) driven by ethanol. Two iron-modified activated carbons, Fe3O4@AC and ZVI@AC, were evaluated to assess their impact on microbial metabolic networks. Results revealed that Fe3O4@AC significantly enhanced caproate production (4600.0 mg/L) and electron transfer efficiency (87.0 %), while ZVI@AC triggered a diversion towards alcohol production (940.61 mg/L n-butanol). The superior performance of Fe3O4@AC was attributed to its semiconductive properties, which facilitated interspecies electron transfer (potentially via DIET-like mechanisms) and balanced electron flow, promoting the activation of both fatty acid biosynthesis (FAB) and reverse β-oxidation (RBO) pathways. Metagenomic analysis revealed a shift in microbial community composition, with Massilibacterium enrichment under Fe3O4@AC, highlighting the importance of tailored material design for targeted MCFA production. These findings provide insights into optimizing microbial metabolism for enhanced CE efficiency.},
}

@article {pmid42250890,
year = {2026},
author = {Ticho, AL and McRae, AN and Cifuentes, L and Fredrick, T and Anazco, D and Espinosa, MA and Garcia Cordova, JM and Romanos, M and Villamarin, J and Johnson, S and Lennon, R and Hurtado Andrade, MD and Chen, J and Camilleri, M and Acosta, AJ},
title = {A subphenotype of obesity with reduced enteroendocrine GLP-1 synthesis and enhanced tirzepatide response.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.05.019},
pmid = {42250890},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Obesity is a heterogeneous disease characterized by different pathophysiological and behavioral traits that influence response to GLP-1-based therapies. We previously identified an obesity phenotype characterized by fast gastric emptying and increased postprandial hunger. We aimed to elucidate pathophysiologic mechanisms in this phenotype by evaluating plasma enteroendocrine hormones and mucosal gene expression, and to evaluate treatment response to tirzepatide across subphenotypes.

METHODS: 483 adults with obesity underwent solid meal gastric emptying (SGE) by scintigraphy, postprandial appetite assessment using visual analog scale (VAS), and plasma enteroendocrine hormone profiling. Gaussian mixed modeling identified phenotypic clusters. Associations with plasma short-chain fatty acids (SCFAs) and fecal metagenomics were explored. A separate cohort (n=31) underwent colonic mucosal biopsies with quantification of GCG (GLP-1) and PYY mRNA. Retrospective evaluation of weight loss in participants treated with tirzepatide among each cluster was performed (n=61).

RESULTS: Three clusters were identified based on SGE and GLP-1. One cluster demonstrated fast SGE, increased postprandial hunger, and discordantly low postprandial GLP-1 (termed dc-GE/GLP-1; n=130, 26.9%), as well as lower plasma PYY and CCK. dc-GE/GLP-1 showed higher plasma SCFA levels, without significant differences in fecal microbial composition. Compared with concordant clusters (c-GE/GLP-1; n=353, 73.1%), dc-GE/GLP-1 had decreased mucosal mRNA expression of GCG (GLP-1) and PYY. At 6-months of tirzepatide, dc-GE/GLP-1 was associated with greater weight loss compared with c-GE/GLP-1 (21.5% vs 11.7%).

CONCLUSIONS: We identified a subphenotype of obesity with fast gastric emptying and discordantly low GLP-1 plasma levels, reduced mucosal hormone synthesis, and enhanced weight loss to tirzepatide. Further studies are needed to identify mechanisms contributing to GLP-1 deficiency in this subphenotype of obesity.},
}

@article {pmid42251226,
year = {2026},
author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR},
title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.},
journal = {Journal of natural medicines},
volume = {},
number = {},
pages = {},
pmid = {42251226},
issn = {1861-0293},
support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; },
abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.},
}

@article {pmid42251252,
year = {2026},
author = {Lockwood, S and Ranaivoson, HC and Randriambolamanantsoa, TH and Razanajatovo, N and Raharinosy, V and Ahyong, V and Héraud, JM and Dussart, P and Lacoste, V and Brook, CE},
title = {Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13715-7},
pmid = {42251252},
issn = {1471-2334},
support = {P200A210054//U.S. Department of Education/ ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; },
abstract = {BACKGROUND: Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed.

METHODS: We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis.

RESULTS: We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n = 24; n = 8 previously diagnosed) and rhinovirus (n = 18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus.

CONCLUSION: mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.},
}

@article {pmid42251689,
year = {2026},
author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X},
title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag090},
pmid = {42251689},
issn = {1536-4844},
support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; },
abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.

METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.

RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P = .040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P < .05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.

CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.},
}

@article {pmid42251704,
year = {2026},
author = {Farace, PD and Marrero Diaz de Villegas, R and Mon, ML and Soria, MA and Talia, PM},
title = {Structural insights into predicted thermophilic GH5 cellulases for industrial lignocellulose bioconversion.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/07391102.2026.2683872},
pmid = {42251704},
issn = {1538-0254},
abstract = {Lignocellulosic biomass can be converted into biofuels and other valuable bioproducts, but it must first undergo physicochemical and enzymatic degradation. Among the various enzymes involved in lignocellulose degradation, thermophilic glycoside hydrolase family 5 (GH5) cellulases have gained significant attention given their ability to sustain enzymatic activity at temperatures exceeding 60 °C. These high temperatures not only accelerate enzymatic reactions, improving reaction rates and process efficiency, but also enhance substrate solubility and reduce the risk of microbial contamination, making them highly valuable for the paper, food, feed, pharmaceutical, and biofuel industries. In this work, we identified five GH5 cellulases with predicted thermophilic properties from termite gut metagenomes and evaluated their structural features using machine-learning classification, comparative structural modeling, interatomic contact analysis, and temperature-dependent flexibility simulations. The candidates, spanning GH5 subfamilies 2, 25, 37, 39, and 40, displayed high structural confidence (pLDDT > 90) and aliphatic indices comparable to those of thermophilic references. Analysis of amino acid composition analysis revealed enrichment in aromatic and charged residues. Hydrophobic contact densities were consistently higher than in mesophilic controls and aligned with thermophilic benchmarks. Temperature-dependent flexibility simulations showed restrained RMSF profiles, more closely resembling the thermophilic reference enzyme than to the mesophilic control. These findings are consistent with a thermophilic profile, pending experimental confirmation, and provide useful insights for the selection and engineering of GH5 cellulases for high-temperature biotechnological applications.},
}

@article {pmid42248407,
year = {2026},
author = {Tan, Y and Sun, J and Chen, X and Wang, Y and Zhang, C and Gong, L and Cui, X},
title = {Chronic Papillary Conjunctivitis as a Novel Ocular Manifestation of Rickettsia felis Infection: A Case Report.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108861},
doi = {10.1016/j.ijid.2026.108861},
pmid = {42248407},
issn = {1878-3511},
abstract = {PURPOSE: To report the first case of chronic papillary conjunctivitis caused by Rickettsia felis infection.

CASE: A 27-year-old man presented with a four-year history of unilateral papillary conjunctivitis refractory to multiple antibiotic courses. Examination revealed tarsal conjunctival injection, papillary hypertrophy, mucopurulent discharge, and eyelid laxity with entropion. The patient had a history of cat ownership for 5-6 years, suggesting possible exposure to the cat flea, and remained systemically asymptomatic without fever, rash, or lymphadenopathy. Metagenomic next-generation sequencing (mNGS), serology, and histopathology confirmed Rickettsia felis infection. Given the chronic intracellular nature of the infection, the patient received an extended 2-month course of oral doxycycline (100 mg twice daily) combined with topical therapy, with marked improvement observed by week 8 and subsequent entropion repair surgery.

CONCLUSION: This represents the first reported case of chronic, isolated rickettsial conjunctivitis without systemic involvement or Parinaud's oculoglandular syndrome features. This case highlights the importance of considering rickettsial infection in chronic, treatment-refractory conjunctivitis and demonstrates the value of metagenomic sequencing for diagnosis.},
}

@article {pmid42248728,
year = {2026},
author = {van Dorst, J and Taylor, N and Pushpakumara, BLDU and Tan, ZT and Buchanan, DD and Haber, PS and Nash, E and Visser, S and Volovets, A and Sivam, S and Ooi, CY},
title = {Genotoxic pks + E. coli is strongly associated with ileocolonic neoplasia in adults with Cystic Fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.05.016},
pmid = {42248728},
issn = {1873-5010},
abstract = {BACKGROUND: Polyketide synthase island-positive (pks+) Escherichia coli is a genotoxic gut bacterium linked to colorectal cancer (CRC) tumorigenesis via the genotoxin colibactin. In adults with Cystic Fibrosis (CF), there is an increased incidence and earlier development of CRC but the biological mechanisms underlying this increased risk remain incompletely understood. We aimed to determine the prevalence of pks+ E. coli in adults with CF.

METHODS: Stool samples and DNA were analyzed from the SCREENCF study cohort. Metagenomic libraries were sequenced on the NovaSeq X Plus platform, using Illumina protocols. Detection of the pks island was assessed with polymerase chain reaction (PCR) targeting the clbB gene.

RESULTS: Of the 49 CF participants; pks+ E. coli was detected in 1/35 (3%) of the no pathology (NORMAL) group, 5/12 (42%) in the adenomatous polyps (AP) group, and 2/2 (100%) in the ileocolonic cancer (ICC) group. Individuals with any ileocolonic neoplasia were 34 times more likely to harbor pks+ E. coli than those with NORMAL colonoscopy findings (OR = 34.0, 95% CI 5.00-691, p = 0.002). The presence of pks+ E. coli correlated with higher overall E. coli burden (p = 0.0009), but not with fecal inflammation, other genotoxic bacterial species or overall bacterial composition.

CONCLUSION: pks+ E. coli is infrequently detected among adults with CF, but its presence is associated with ileocolonic neoplasia, indicating a potential role in pathogenesis. If validated in larger cohorts, pks+ E. coli could provide a clinically meaningful biomarker for early detection, risk stratification and a potential target for precision intervention.},
}

@article {pmid42248819,
year = {2026},
author = {Peng, D and Zhou, J and Xiong, M and Chen, Y and Zhang, Y and Hu, Y and Yang, Y and Xu, J and Zheng, Y and Xu, D},
title = {Gut Microbiota Dysbiosis Drives Lethal Bacterial Enteritis in Sturgeons: Insights From Ex Vivo Cultivation and Metagenomic Investigations.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70218},
doi = {10.1111/jfd.70218},
pmid = {42248819},
issn = {1365-2761},
support = {D-8006-25-0392//Shanghai Aquatic Wildlife Conservation and Research Center/ ; K2025-02-08-00-12-F00043//Shanghai Municipal Commission of Agriculture and Rural Affairs/ ; },
abstract = {The Chinese sturgeon (Acipenser sinensis) and Yangtze sturgeon (A. dabryanus) are critically endangered flagship species. To investigate the intestinal microbial changes associated with bacterial enteritis in captive populations, we integrated bacterial isolation with metagenomic sequencing to characterize both healthy and maladjusted gut microbiomes. Healthy sturgeons exhibited a stable microbiota dominated by the beneficial Cetobacterium. In contrast, enteritis was consistently associated with severe dysbiosis, characterized by the depletion of these commensals and the massive expansion of opportunistic pathogens, notably Aeromonas and Citrobacter. Culture-based analyses identified A. veronii, C. freundii and Plesiomonas shigelloides as the dominant cultivable bacteria from diseased individuals; these isolates harboured diverse virulence traits and were multidrug-resistant. Crucially, both sturgeon species showed highly similar microbial responses and pathogenic profiles during enteritis. These findings indicate that sturgeon enteritis is closely correlated with a dysbiosis-driven syndrome. Establishing the healthy baseline provides a critical theoretical foundation for screening autochthonous probiotics and developing targeted pathogen control strategies. Furthermore, the striking cross-species commonality validates the Yangtze sturgeon as a viable surrogate model for advancing disease management and conservation in the difficult-to-breed Chinese sturgeon.},
}

@article {pmid42248870,
year = {2026},
author = {Vasquez, YM and Romero, MF and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F},
title = {Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73437-x},
pmid = {42248870},
issn = {2041-1723},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; },
abstract = {Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.},
}

@article {pmid42249277,
year = {2026},
author = {Guanglin, W and Xiuwen, K and Rong, H},
title = {Awake VV-ECMO for severe pneumonia caused by Elizabethkingia anophelis: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13735-3},
pmid = {42249277},
issn = {1471-2334},
abstract = {BACKGROUND: Elizabethkingia anophelis is phenotypically similar to E. meningoseptica and is often misidentified by conventional methods, delaying appropriate therapy. Awake venovenous extracorporeal membrane oxygenation (VV-ECMO) avoids complications of deep sedation and mechanical ventilation, but its role in severe pulmonary infection with rare pathogens remains underexplored.

CASE PRESENTATION: We report a 62-year-old male with chronic hepatitis B who developed type I respiratory failure and septic shock unresponsive to conventional support. VV-ECMO was initiated on January 23, and awake ECMO management was implemented to preserve spontaneous breathing and cough reflex. Serial metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid revealed influenza A H1N1, Aspergillus fumigatus, and multidrug-resistant bacteria (Detailed mNGS results are provided in Supplementary Table 2). On day 32, sputum culture suggested E. meningoseptica, but subsequent mNGS identified E. anophelis (322,376 reads). The anti-infective regimen was adjusted to minocycline-based combination therapy. Under awake ECMO support, the patient's infection markers gradually improved, and he was successfully weaned from ECMO on day 38 and from mechanical ventilation thereafter. He was discharged after recovery.

CONCLUSION: This case demonstrates that awake ECMO can serve as an effective respiratory support platform in complex severe pneumonia. When conventional testing reports E. meningoseptica, clinicians should suspect possible E. anophelis infection, and timely mNGS is recommended for accurate species identification. Minocycline-based combination therapy appears promising for E. anophelis infections.

CLINICAL TRIAL: Not applicable.

CLINICAL PEARL: In critically ill patients with suspected Elizabethkingia infection, do not rely solely on phenotypic identification; use mNGS to distinguish Elizabethkingia anophelis from Elizabethkingia meningoseptica, and consider early minocycline-based therapy.},
}

@article {pmid42249286,
year = {2026},
author = {Qiu, X and Li, W and Zhang, M and Lei, S and Chen, H and Wang, X and Miao, Y and Yu, Z and Wu, Y and Hou, Z},
title = {The impact of hydrogen sulfide on gut microbiota of diabetic mice with lower limb arterial ischemia.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05167-5},
pmid = {42249286},
issn = {1471-2180},
support = {H2020206490//Natural Science Foundation of Hebei Province/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; H2024206134//Key Project of Natural Science Foundation of Hebei Province (Class A)/ ; },
abstract = {BACKGROUND: The prevalence of hindlimb ischemia (HLI) associated with diabetes mellitus (DM) is high. However, its prevention and treatment face significant challenges. This study explored the effects of hydrogen sulfide (H2S) intervention in mice with DM and HLI, while concurrently investigating its regulatory effects on gut microbial homeostasis.

METHODS: The diabetic model in C57BL/6J mice was established through intraperitoneal injection of streptozotocin. The HLI model was created by ligating and severing the femoral artery, with subsequent initiation of a 21-day exogenous H2S intervention. Fecal samples from the mice were collected at four time points: before model establishment, 3 days after successful induction of the diabetes model, 3 days after establishment of the HLI model, and after 21 days of H2S intervention for metagenomic analysis. Body weight, blood glucose levels, and hindlimb blood flow in the mice were monitored. Additionally, functional assessment and histopathological examination of the ischemic skeletal muscle were performed to evaluate contractile and morphological properties.

RESULTS: H2S administration significantly enhanced hindlimb blood perfusion and restored plasma H2S concentrations in diabetic mice with HLI, concurrently improving both function and morphological integrity of the ischemic skeletal muscle. Bacterial abundance at the phylum level showed changes over the course of the experiment, particularly in Bacteroidetes and Firmicutes. In the DM + HLI group, the Firmicutes-to-Bacteroidetes ratio was significantly elevated; however, H2S treatment downregulated this alteration. H2S intervention modulated the abundance of various bacterial species, increasing Lactobacillus murinus and Faecalibacterium prausnitzii, while simultaneously downregulating inflammation-related bacteria such as Ruminococcus sp. JE7A12. Microbial network analysis revealed that the DM + HLI and H2S groups had lower network complexity than the control group. Furthermore, functional metagenomic profiling identified 28 differentially expressed genes, which were annotated to 8 primary and 30 secondary KEGG pathways, with 6 genes specifically enriched in carbohydrate metabolism pathways.

CONCLUSION: Exogenous H2S administration improved hindlimb blood perfusion, restored contractile function, and preserved morphological integrity of ischemic skeletal muscle in diabetic mice with HLI. Concurrently, H2S treatment altered the abundance of gut microbiota, improving microbial balance. Targeting the gut microbiota via H₂S suggests a potential translational avenue that warrants causal investigation for the treatment of diabetic limb ischemia. Further studies are warranted to establish causal relationships and elucidate the underlying mechanisms linking H2S, gut microbiota, and vascular recovery.},
}

@article {pmid42249504,
year = {2026},
author = {Liu, Y and Xie, Y and Yang, J and Deng, Y and Liu, D and Chang, J and Tang, J and Zhao, H and Chen, X and Tian, G and Liu, G and Cai, J and Jia, G},
title = {Integrated gut metagenomic and muscle proteomic analysis reveals the role of dietary fermented extruded brewers' spent grain in enhancing pork quality through the gut-muscle axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42249504},
issn = {1674-9782},
support = {No. 2021ZDZX0009//Sichuan Science and Technology Program/ ; },
abstract = {BACKGROUND: The fact that feeding pigs with probiotic-fermented agricultural by-products improves pork quality has been repeatedly demonstrated and widely applied, but the underlying mechanisms remain unclear. This study explored the effects of fermented extruded brewers' spent grain (FEBSG) on meat quality in growing-finishing pigs, as well as its regulatory mechanisms.

METHODS: Sixty Duroc × Landrace × Yorkshire pigs (52.25 ± 2.10 kg) were randomly assigned to five dietary treatments, in which FEBSG replaced 0, 5%, 10%, 15%, and 20% of soybean meal (SBM). The experiment spanned 10 weeks.

RESULTS: Compared with the control, 20% FEBSG significantly increased final body weight, average daily feed intake, and average daily gain, while decreasing feed to gain ratio (P < 0.05). Both 15% and 20% FEBSG improved carcass characteristics and meat quality, including higher carcass weight, loin eye area, and intramuscular fat content, along with lower drip loss and shear force (P < 0.05). These treatments also enhanced flavor-related amino acids and unsaturated fatty acids (P < 0.05), and improved umami and sweet taste profiles. Moreover, 20% FEBSG increased muscle fiber density and reduced fiber diameter, upregulated MyHC I, MyHC IIa, PGC-1α, AMPKα1, TFAM, and SDH activity, and downregulated MyHC IIb and LDH activity (P < 0.05). Proteomic analysis identified 69 differentially expressed proteins, with enrichment in AMPK and PPAR signaling pathways. Metagenomic analysis revealed increased abundance of short-chain fatty acid-producing bacteria, including Clostridium, Lactobacillus, Prevotella, and Bartonella. Correlation analysis demonstrated associations between gut microbiota diversity and meat quality traits, as well as between dominant microbial genera and differentially expressed proteins, volatile fatty acids, muscle fiber characteristics, and the AMPK/PGC-1α/TFAM signaling pathway.

CONCLUSIONS: Partial replacement of SBM with FEBSG positively influenced growth performance and pork quality in pigs, with the underlying mechanisms may involve the activation of the AMPK/PGC-1α/TFAM signaling pathway via the gut-muscle axis, thereby enhancing mitochondrial biogenesis, muscle development, and metabolism.},
}

@article {pmid42249511,
year = {2026},
author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H},
title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42249511},
issn = {2049-2618},
support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.

RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced naïve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of naïve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.

CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.},
}

@article {pmid42249581,
year = {2026},
author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W},
title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.},
journal = {Microbial biotechnology},
volume = {19},
number = {6},
pages = {e70397},
doi = {10.1111/1751-7915.70397},
pmid = {42249581},
issn = {1751-7915},
support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; },
abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.},
}

@article {pmid42249721,
year = {2026},
author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W},
title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {11},
pages = {e70422},
doi = {10.1111/mec.70422},
pmid = {42249721},
issn = {1365-294X},
support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; },
abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.},
}

@article {pmid42250066,
year = {2026},
author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W},
title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42250066},
issn = {1559-0291},
support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; },
abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.},
}

@article {pmid42250131,
year = {2026},
author = {Gao, X and Qin, R and Li, S and Yang, Y and He, J},
title = {Congenital tuberculosis transmitted via the placenta: identification by metagenomic next-generation sequencing.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42250131},
issn = {1435-4373},
support = {grant number: kryc-yq-2127//Kuanren Talents Program of the second affiliated hospital of Chongqing Medical University/ ; },
abstract = {BACKGROUND: Congenital tuberculosis (CTB) is a rare disease with high mortality in neonates. Early diagnosis is crucial but often delayed due to atypical clinical and imaging manifestations.

CASE PRESENTATION: We report a 36-day-old female infant presenting with recurrent fever. Laboratory data showed leukocytosis and neutrophilia with mildly elevated C-reactive protein. Chest computed tomography revealed extensive ground-glass opacities, multiple subpleural nodules, and necrotic hilar and mediastinal lymphadenopathy. The asymptomatic mother was subsequently found to have diffuse miliary nodules on chest CT. Conventional tuberculosis tests (acid-fast smear, culture, GeneXpert, T-SPOT.TB) were negative in both the infant and mother. Metagenomic next-generation sequencing (mNGS) of the placental tissue detected 10 specific Mycobacterium tuberculosis sequences, and Ziehl-Neelsen staining confirmed acid-fast bacilli. Both mother and infant responded well to anti-tuberculosis therapy.

CONCLUSIONS: CTB should be considered in neonates with persistent pulmonary infection unresponsive to broad-spectrum antibiotics. Examination of placental tissue using mNGS is a valuable diagnostic tool for confirming transplacental tuberculosis transmission.},
}

@article {pmid42242079,
year = {2026},
author = {Yang, F and Zhang, M and Tan, Y and Yuan, Z and Liu, W and Wu, Y and Li, F},
title = {Alkaline woody peat shifts CO2 emissions to CH4 by modulating microbial cross-feeding in Cd-contaminated paddy soil.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142498},
doi = {10.1016/j.jhazmat.2026.142498},
pmid = {42242079},
issn = {1873-3336},
abstract = {Alkaline organic amendments are widely used to remediate cadmium (Cd)-contaminated paddy soils by alleviating acidification and reducing Cd bioavailability, yet their impacts on greenhouse gas emissions remain unclear. Here, we examined how alkaline woody peat (WP) regulates carbon fluxes and microbial interactions in Cd-contaminated paddy soil. Anaerobic incubation and greenhouse pot experiments, together with in situ methane monitoring and metagenomic analyses, were used to compare alkaline-modified WP with acidic WP, CaO alone, and unamended controls. Alkaline WP (AWP-2) increased soil pH from 5.5 to 7.35 and decreased exchangeable Cd from 32% to 13%, confirming its remediation effectiveness. However, this was accompanied by marked changes in greenhouse gas emissions: methane production increased by up to 3.9-fold, while carbon dioxide emissions declined. Metagenomic analyses showed that alkaline WP strongly enriched methanogenic archaea, particularly Methanosarcina, whose relative abundance reached 26.6% compared with 4.2% in the control, while suppressing microbial populations associated with CO2-generating pathways. Functional gene profiles revealed increased abundance of mcrA and reduced representation of genes involved in complete acetate oxidation (maeA, pdc, sucA, porA, aceE, and icd). Genome-resolved analysis further showed that some microbes positively associated with methanogens lacked key genes involved in acetate oxidation to CO2 (e.g., aceE), suggesting a reduced capacity for CO2 generation from acetate and a greater tendency to retain carbon as acetate, thereby potentially favoring acetoclastic methanogenesis. Overall, these results highlighting a potential trade-off between Cd remediation and greenhouse gas mitigation and the need to incorporate microbially driven carbon fluxes into environmental risk assessments of alkaline amendments in contaminated paddy soils.},
}

@article {pmid42242448,
year = {2026},
author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F},
title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.06.001},
pmid = {42242448},
issn = {1995-820X},
abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.},
}

@article {pmid42242497,
year = {2026},
author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and , and Segre, JA and Sereti, I and Kong, HH},
title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.05.019},
pmid = {42242497},
issn = {1523-1747},
abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia (ICL), a rare clinical syndrome with obscure cause, and people living with HIV (PLWH) are two etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to characterize the multi-kingdom taxonomic diversity of skin microbiomes in patients with ICL and PLWH who were followed longitudinally before and after antiretroviral therapy (ART) initiation. Compared with healthy individuals, the skin microbiomes of patients with ICL and ART-naïve PLWH showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses (HPVs) and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy individuals. In PLWH, high-oncogenic-risk HPV types persisted after 2 months of ART but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.},
}

@article {pmid42243106,
year = {2026},
author = {Lee, M and Kim, D and Song, JH and Park, SJ and Chang, JY},
title = {Efficacy of Lactococcus lactis WiKim0124 in Fat-, Sucrose-, and Fat/Sucrose-Induced Obesity Models.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00915-3},
pmid = {42243106},
issn = {2396-8370},
support = {KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; },
abstract = {Lactococcus lactis WiKim0124 (WiKim0124), a probiotic strain isolated from kimchi, has previously shown anti-obesity effects in high-fat diet (HFD) models. This study investigated whether WiKim0124 and its formulated version, SW01, exert consistent anti-obesity efficacy across distinct diet-induced obesity models through modulation of host lipid metabolism and gut microbial function. In 3T3-L1 adipocytes and FFA-treated HepG2 cells, both treatments inhibited lipid accumulation and modulated lipid metabolism-related markers, indicating enhanced fatty acid oxidation and reduced lipogenesis. In C57BL/6 J mice fed HFD, high-sucrose (HSuc), or HFD + HSuc diets, daily oral administration of WiKim0124 or SW01 significantly reduced body weight gain, adipose tissue mass, and hepatic lipid accumulation. WiKim0124 and SW01 significantly enhanced fatty acid oxidation pathways, as evidenced by increased expression of the markers PPARα, CPT-1α, and UCP2. Gut microbiota analysis showed increased Bacteroidetes and enrichment of Akkermansia muciniphila in treated groups. Shotgun metagenomic functional profiling revealed enhanced short-chain fatty acid-related pathways and enzymes, with distinct patterns depending on treatment and dietary stressors. Microbial functional responses were most pronounced in the HFD + HSuc model, supporting a diet-dependent mode of probiotic action. Together, these findings demonstrate consistent anti-obesity efficacy of WiKim0124 and support the translational potential of its formulated application through integrated modulation of host metabolism and gut microbial function.},
}

@article {pmid42243452,
year = {2026},
author = {Das, R and Medhi, MC and Tamang, B},
title = {Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02062-0},
pmid = {42243452},
issn = {2191-0855},
abstract = {Traditional fermented rice beverages are produced through complex microbial fermentation processes that influence their physicochemical characteristics and metabolite composition. In this study, metagenomic sequencing and GC-MS/MS-based metabolomics were integrated to characterize four indigenous rice beverages: Black Rohi Modh (BR), Rohi Modh (RH), Jou Bidwi (JOU), and Sai Mod (SM). All beverages were mildly acidic, with pH values ranging from 4.1 to 4.5 and titratable acidity between 0.58 and 0.72% lactic acid. Ethanol content varied among samples, with BR showing the highest concentration (8.13% v/v), followed by JOU and RH (approximately 5.5% v/v), while SM exhibited the lowest level (4.28% v/v). Antioxidant activity differed across beverages, with RH and BR demonstrating higher DPPH radical scavenging activity and SM showing the highest ferric reducing antioxidant power (96.93 µmol/mL). Metagenomic analysis generated 57.69 Mb of assembled sequences, identifying 48 microbial phyla and 1,785 species, with Eukarya accounting for 66.12% of the total community. Ascomycota predominated in BR and JOU, whereas Bacillota was more abundant in RH. The genus Saccharomyces was consistently dominant across samples. Functional annotation indicated enrichment in metabolic pathways related to carbohydrate and amino acid metabolism, as well as genes associated with ethanol biosynthesis and retinol metabolism pathways, reflecting microbial metabolic potential rather than direct vitamin production. Metabolomic profiling identified 113-167 metabolites per beverage, with 93 compounds shared among all samples. Correlation analysis revealed significant associations between Saccharomyces cerevisiae and short-chain fatty acids (ρ = 0.62-0.71, FDR < 0.05), indicating a strong positive relationship between microbial abundance and metabolite production.},
}

@article {pmid42243513,
year = {2026},
author = {Yi, J and Zhao, Y and Li, Z and Chen, A and Tang, Z and Zheng, L and Ge, H and Yu, Q and Liu, W and Xiang, J and Tang, J},
title = {M.globosa promotes lung cancer progression and M2 macrophage polarization through oxidative phosphorylation.},
journal = {NPJ precision oncology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41698-026-01528-5},
pmid = {42243513},
issn = {2397-768X},
support = {2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2403084//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; },
abstract = {The lungs are colonized by a variety of microbes which play a significant role in lung cancer progression. In this study, we conducted an in-depth analysis of metagenomic sequencing data obtained from alveolar lavage fluid (ALF) samples of patients with non-small-cell lung cancer (NSCLC) at different clinical stages. The nested qPCR was used to validate the abundance of key fungi and establish a correlation between fungi abundance and patient prognosis. We found that elevated levels of M.globosa correlated with patients at stage1B-3 and worse prognosis. M.globosa enhanced the proliferation of lung cancer cells and promoted tumor growth in vivo by promoting M2-like macrophage polarization, which was primarily driven by oxidative phosphorylation (OXPHOS) activation. The inhibition of OXPHOS in tumor-bearing mice using metformin significantly retarded the tumor growth induced by M. globosa. Together, our clinical observations and experimental findings suggest that intracellular M. globosa infection may contribute to lung cancer progression through immunometabolic remodeling of macrophages.},
}

@article {pmid42243631,
year = {2026},
author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW},
title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {},
number = {},
pages = {},
doi = {10.1093/jamia/ocag088},
pmid = {42243631},
issn = {1527-974X},
support = {//S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; //UTHealth Houston Seed/ ; //Baylor College of Medicine/ ; //Alkek Foundation Seed/ ; },
abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.

MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.

RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.

DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.

CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.},
}

@article {pmid42243719,
year = {2026},
author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS},
title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09123-3},
pmid = {42243719},
issn = {1471-2229},
support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; },
abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.

RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.

CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).},
}

@article {pmid42243998,
year = {2026},
author = {Li, S and Sun, Y and Tong, X and Zhang, Z and Ma, X and Li, D and Min, L},
title = {Near-complete inhibition of rumen methanogenesis via microbial and enzymatic modulation using a low dose of Asparagopsis taxiformis combined with 3-nitrooxypropanol.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42243998},
issn = {1674-9782},
support = {SKXRC2025487//Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 2024CXTD13//Guangdong Modern Agro-industry Technology Research System/ ; 202408440440//China Scholarship Council/ ; NYQS202613//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; 2026A1515010802//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) from ruminants represents a major contributor to agricultural greenhouse gas emissions. The red seaweed Asparagopsis taxiformis (A. taxiformis) is a highly effective CH4 emission inhibitor, but its large-scale application is restricted by limited biomass availability. This study evaluated whether reducing the inclusion level of A. taxiformis (0.32% dry matter, DM) combined with 3-nitrooxypropanol (3-NOP; 0.05% DM) could maintain a high inhibitory efficacy, and elucidated the underlying microbial mechanisms through in vitro fermentation and metagenomics analysis.

RESULTS: The combined treatment decreased CH4 production by 98.21% (P < 0.01) without impairing DM degradation, and markedly shifted rumen fermentation towards propionate, lowering the acetate-to-propionate ratio (1.59 vs. 2.65; P < 0.01). Metagenomic profiling revealed substantial reductions in the abundance of Methanobrevibacter and Ruminococcus, along with increased levels of propionate-associated bacteria such as Prevotella, Treponema, Eubacterium, and Selenomonas (P < 0.01). Functionally, the combined treatment downregulated key enzymes in hydrogenotrophic and methylotrophic methanogenesis, including methyl-coenzyme M reductase (EC:2.8.4.1) and tetrahydromethanopterin S-methyltransferase (EC:2.1.1.86), thereby blocking terminal methanogenic steps.

CONCLUSIONS: Collectively, these results demonstrate that co-supplementation with A. taxiformis and 3-NOP achieves near-complete methanogenesis inhibition at drastically reduced seaweed dosage through coordinated changes in fermentation patterns, microbial community structure, and methanogenic enzymatic pathways. This approach provides a practical strategy to overcome biomass limitations of A. taxiformis and warrants validation in long-term in vivo trials.},
}

@article {pmid42244002,
year = {2026},
author = {Ansari, MH and Staubach, F and Alacatli, N and Obbard, DJ},
title = {A diverse gut virome in natural populations of Drosophila melanogaster.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00585-2},
pmid = {42244002},
issn = {2524-4671},
abstract = {BACKGROUND: Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.

RESULTS: Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.

CONCLUSIONS: Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.},
}

@article {pmid42244030,
year = {2026},
author = {Wang, Y and Zhang, Y and Feng, L and Han, Q and Yu, Q and Li, H},
title = {Host Ecology Shapes Gut Pathogen Evolution: An Eco-Evolutionary Trade-Off in Plateau Wildlife.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70344},
doi = {10.1111/1462-2920.70344},
pmid = {42244030},
issn = {1462-2920},
support = {32471575//National Natural Science Foundation of China/ ; },
abstract = {The intestinal tracts of plateau wildlife function as crucial reservoirs for diverse pathogens. However, the mechanisms through which host ecology influences pathogen community assembly and their interactions remain unclear. By comparing the subterranean-living plateau zokor (Eospalax baileyi) with the aboveground plateau pika (Ochotona curzoniae) across a two-and-a-half-year study, this work provides evidence that the distribution and transmission dynamics of pathogens, virulence factor genes (VFGs), and pathogen-host interaction (PHI) genes are determined by animals' distinct niches. The results demonstrate a clear eco-evolutionary trade-off: the plateau zokor, inhabiting stable yet pathogen-enriched burrow systems, exhibited higher abundances of pathogens, VFGs, and PHI genes in its gut, and formed complex co-occurrence networks. In contrast, the plateau pika, under diverse environmental exposure, possessed higher pathogen and gene diversity but lower overall abundance, alongside simpler interaction networks indicative of opportunistic colonization. Metagenomic binning indicated a close association among VFGs, PHI genes, and mobile genetic elements (MGEs), pointing to their possible joint transfer. Additionally, animal weight and precipitation were identified as key drivers of pathogen dynamics. These findings indicate that the gut sits at the crossroads of animal and environmental health, highlighting how host-mediated pathogen evolution across distinct niches shapes the broader One Health dynamics of the plateau ecosystem.},
}

@article {pmid42244179,
year = {2026},
author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H},
title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71330},
pmid = {42244179},
issn = {1469-8137},
support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; },
abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.},
}

@article {pmid42244577,
year = {2026},
author = {Ettinger, CL and Eisen, JA},
title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.28.596327},
pmid = {42244577},
issn = {2692-8205},
abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.},
}

@article {pmid42244712,
year = {2026},
author = {Iranzo, J and Wolf, YI and Koonin, EV},
title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.25.727639},
pmid = {42244712},
issn = {2692-8205},
abstract = {BACKGROUND: Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome?

RESULTS: We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors.

CONCLUSIONS: Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.},
}

@article {pmid42244725,
year = {2026},
author = {Steinberger, AJ and Nickodem, CA and Leite de Campos, J and Kates, AE and Goldberg, TL and Safdar, N and Sethi, AK and Shutske, JM and Ruegg, PL and Suen, G and Hite, JL},
title = {Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.22.726633},
pmid = {42244725},
issn = {2692-8205},
abstract = {Antimicrobial use (AMU) in agricultural systems is frequently linked to antimicrobial resistance (AMR). Yet, the scale at which AMU reshapes host-associated resistomes remains unclear. This gap arises, in part, from the scarcity of farm-level AMU data from commercial production systems. Here, we combine detailed AMU records from commercial dairy farms with metagenomic analyses of bovine fecal resistomes from calves, lactating cows, sick cows, and cull cows. At a broad level, resistome profiles were similar regardless of farm AMU. Resistance associated with historically common antibiotics, such as tetracyclines, was frequent on low- and high-AMU farms, indicating that some resistance classes are ubiquitous in dairy systems regardless of current AMU. In contrast, resistance to other drug classes varied systematically with AMU. Higher AMU was associated with increased resistance to aminoglycosides, β-lactams, and macrolides, drug classes that are critical for treating mastitis and bovine respiratory disease. Resistance gene richness and diversity were highest in calves, underscoring the importance of accounting for host traits alongside AMU when evaluating resistance patterns. Together, these findings underscore the need for detailed, farm-level AMU data to understand how management practices shape AMR and to inform strategies for sustaining the effectiveness of existing antimicrobials in agricultural and public-health contexts.},
}

@article {pmid42244773,
year = {2026},
author = {Espinoza, JL and Dupont, CL and Phillips, A},
title = {Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.14.664802},
pmid = {42244773},
issn = {2692-8205},
abstract = {Functional profiling of metagenomes and metatranscriptomes is essential for understanding microbial community capabilities, yet current methods require computationally expensive translated-search alignments that scale poorly to the large genome-resolved reference databases now common in the field. We introduce Leviathan, an open-source software package for integrated taxonomic and functional profiling that operates at both genome and pangenome resolution. Leviathan combines Sylph for ultra fast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against genome-resolved gene catalogs, bypassing the translated-search step that dominates runtime in existing approaches. For each (pan)genome, Leviathan functional profiling produces dual metrics: pathway abundance from aggregated gene-level quantification and pathway coverage from graph-based assessment of enzymatic step completeness. On CAMI-I and CAMI-II datasets, Leviathan achieved up to 74-fold faster runtimes and 14-fold lower memory usage compared to HUMAnN, while improving genome-level assignment accuracy by up to 12% and pangenome-level accuracy by up to 5%. We demonstrate Leviathan's applicability through two case studies: a marine plastisphere metagenomics dataset where differential coverage analysis revealed metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where pangenome-resolved co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.},
}

@article {pmid42245494,
year = {2026},
author = {Hu, Z and Chen, C},
title = {Revealing gut microbiota profiles and their influencing factors in commercial boars of three breeds by a large-scale metagenome study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1825304},
pmid = {42245494},
issn = {1664-302X},
abstract = {Boars play a critical role in pig production. Numerous studies have reported important effects of the gut microbiota on pig production traits. However, whether the gut microbiota is associated with reproduction traits in boars remains largely unknown. Understanding the gut microbial composition and its influencing factors in large-scale boar populations is an essential first step to investigate this association. In this study, shotgun metagenomic sequencing was performed on fecal samples of 1,651 commercial boars from three breeds raised in three pig farms to uncover their gut microbial structures. We observed significant differences in boar gut microbial compositions across three breeds, even when raised in the same farm. Permutational multivariate analysis of variance (PERMANOVA) within-farm breeds and with-age stages found that the effect size of each factor on boar gut microbial composition varied across farms and age stages. Breeds accounted for 2% ~ 9% of the variance of boar gut microbial compositions in different farms. We then identified gut microbial taxa enriched in each boar breed using MaAsLin2. Lactic acid and butyrate-producing taxa, such as Lactobacillus amylovorus and Faecalibacterium prausnitzii, were enriched in Duroc boars; Akkermansia muciniphila and Lactobacillus reuteri showed the enrichment in Landrace boars, accompanied by increased relative abundance of Enterobacteriaceae members. Meanwhile, the species from Bacteroides, Prevotella, and Treponema had higher abundances in the gut of Large White pigs than in the other two pig breeds. We also identified bacterial species enriched in each of the three age stages. These breed and age-associated microbial enrichment patterns might reflect the combined effects of long-term genetic selection of pig breeds, age, and differences in feeding diets. The results of this study provide important insights for further investigating the effects of gut microbiota on boar reproductive traits and for developing strategies to modulate the gut microbiota to improve boar health and production performance.},
}

@article {pmid42245495,
year = {2026},
author = {Kuźniar, A and Das, AP and Goraj, W},
title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820854},
doi = {10.3389/fmicb.2026.1820854},
pmid = {42245495},
issn = {1664-302X},
}

@article {pmid42245502,
year = {2026},
author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M},
title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1825173},
pmid = {42245502},
issn = {1664-302X},
abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.},
}

@article {pmid42245511,
year = {2026},
author = {Otto, SJG and McLeod, L and McCarthy, EL and Funk, T and Lacoste, SR and Chai, Z and Links, MG and Barlow, LD and Gow, SP and Ramsay, D and Zaheer, R and McAllister, TA and Stothard, P and Hill, JE and Waldner, CL},
title = {Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1806062},
pmid = {42245511},
issn = {1664-302X},
abstract = {INTRODUCTION: The risk to humans and animals from antimicrobial resistance (AMR) has increased the emphasis on antimicrobial stewardship in food animal agriculture. Current stewardship recommendations include increasing diagnostic laboratory testing to inform antimicrobial use for bovine respiratory disease (BRD) management in beef feedlot production, yet the performance of newer molecular and sequencing-based diagnostic tests in commercial settings remains poorly characterized.

METHODS: Using nasopharyngeal swabs collected from commercial feedlot calves as part of Canadian surveillance, this study evaluated diagnostic laboratory testing approaches for detecting key bacterial BRD pathogens (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasmopsis bovis) and associated AMR genes. Bayesian latent class models (BLCMs) were applied to compare traditional culture and antimicrobial susceptibility testing (AST) or qPCR with long-read metagenomic sequencing and recombinase polymerase amplification (RPA). Differences in detection of target bacteria and phenotypic or genotypic AMR were assessed across the early feeding period and between age cohorts.

RESULTS: This represents the first large-scale field evaluation of a recently developed, long-read metagenomic sequencing protocol implemented by a commercial laboratory for detecting BRD bacteria and AMR in respiratory samples (n = 760) collected by private veterinarians from western Canadian beef feedlots. Detection patterns for BRD bacteria and AMR using culture/AST and metagenomics were often similar between fall-placed calves and yearlings, but with differences from RPA. Detection of BRD bacteria had low sensitivity (< 65% for most organisms/tests), but higher specificity (>90% for all organisms/tests). Detection of macrolide and tetracycline resistance had low but variable sensitivity, with higher estimates for AST compared to metagenomics and RPA, and higher but variable specificity (>90% for most resistance outcomes/tests). Despite not using any targeted enrichment, metagenomic sequencing detected M. bovis although with a sensitivity lower than qPCR or RPA. Estimates of predictive value were most informative across the largest range of prevalence for AST, followed by metagenomics and then RPA.

DISCUSSION: This work demonstrates the potential for large scale implementation of long-read metagenomic sequencing to support antimicrobial stewardship and AMR surveillance for feedlot cattle. The estimates of clinical diagnostic performance and predictive values provide evidence-based guidance for three different laboratory tests for BRD management.},
}

@article {pmid42245748,
year = {2026},
author = {Li, JZ and Guan, SY and Zhang, JF and Zheng, JN},
title = {Acute Q Fever in an Elderly Traveler with Multiple Comorbidities Diagnosed by Blood mNGS and Resolved with Omadacycline.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {610202},
pmid = {42245748},
issn = {1178-6973},
abstract = {This article reports a case of acute Q fever in a 61-year-old man. The patient mainly presented with high fever and cough. Extensive multi-system investigations failed to identify an etiology. On the fourth day of admission, the diagnosis of acute Q fever was confirmed by rapid detection of Coxiella burnetii nucleic acid sequence by blood metagenomic Next-Generation Sequencing (mNGS). With the treatment of intravenous omadacycline, the fever was controlled within 24 hours and the clinical symptoms significantly improved. Subsequent sequential therapy with oral doxycycline was administered, and the patient was discharged successfully. This case highlights the value of mNGS in the rapid diagnosis of rare or zoonotic pathogens in patients with fever of unknown origin, especially in patients with potential exposure to endemic areas. Furthermore, the novel tetracycline antibiotic omadacycline, demonstrating favorable efficacy and safety despite the patient's liver dysfunction, offers a valuable treatment option for rapid control of acute Q fever symptoms, especially in severe cases or those intolerant to doxycycline.},
}

@article {pmid42245929,
year = {2026},
author = {Yan, W and Wang, X and Shi, K and Wang, L},
title = {Atypical Legionella pneumophila encephalopathy lacking respiratory symptoms and radiographic lesions: A Case Report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1828042},
pmid = {42245929},
issn = {2296-858X},
abstract = {This report details an unusual case of Legionella pneumophila encephalopathy in a 29-year-old male who presented with acute altered consciousness and extreme agitation, notably lacking any respiratory symptoms or typical meningeal signs. Extensive imaging, including chest CT and cranial MRI, revealed no pulmonary infiltrates or structural brain lesions. Cerebrospinal fluid (CSF) analysis demonstrated an aseptic profile with elevated protein, and CSF metagenomic sequencing returned negative. The diagnostic dilemma was ultimately resolved using whole-blood targeted next-generation sequencing (tNGS), which detected Legionella sequences. The patient achieved a rapid and complete neurological recovery following a combined regimen of levofloxacin and high-dose glucocorticoids. This case underscores that Legionella infection can manifest as an isolated, toxin- and immune-mediated encephalopathy without preceding clinical pneumonia. It highlights the critical rescue value of early molecular screening (such as tNGS) in unexplained encephalopathy and supports the judicious use of early steroid intervention to halt the aseptic neurotoxic cascade.},
}

@article {pmid42246002,
year = {2026},
author = {Ren, JM and Zhang, XY and Liu, XP and Pei, LH and Jiang, WP and Zhang, XM and Ding, H and Huang, JS},
title = {Specimen-specific differences in clinical metagenomic sequencing reporting patterns in hospitalized patients: a single-center retrospective observational study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1823283},
pmid = {42246002},
issn = {2235-2988},
abstract = {Clinical metagenomic next-generation sequencing (mNGS) is increasingly used in hospitalized patients, but finalized reporting patterns vary across specimen types in routine practice. We conducted a single-center retrospective observational study using routine clinical mNGS data from January 1, 2024, to December 31, 2025. A specimen-specific first-order design retained only the first eligible mNGS order per patient within each specimen category during the study window. Orders were grouped as bronchoalveolar lavage fluid (BALF), blood, cerebrospinal fluid (CSF), and tissue for primary comparisons; heterogeneous "Other" specimens were described separately. The primary endpoint was report-interpreted any-positive at the order level. We summarized specimen-specific report-interpreted positivity, pathogen-group detection, the most frequently reported organisms ranked by order-level report presence, and mixed detections among positive orders. ICU-associated analyses were included as contextual descriptive stratification only. The cohort included DNA-only orders and a subset of PMseq-RNA-tested orders; RNA virus analyses were restricted to PMseq-RNA-tested orders, and DNA-only orders were treated as not tested for RNA virus fields. Among 1, 981 included specimen-specific first orders, BALF accounted for 973, blood 473, CSF 240, and tissue 122. Report-interpreted any-positive differed by specimen type, with BALF highest (876/973, 90.0%; 95% CI, 88.0-91.8%), followed by tissue (95/122, 77.9%; 95% CI, 69.7-84.3%), blood (343/473, 72.5%; 95% CI, 68.3-76.3%), and CSF (63/240, 26.2%; 95% CI, 21.1-32.2%). Among positive orders, at least 2 distinct standardized pathogens were reported in 672/876 BALF orders (76.7%), 182/343 blood orders (53.1%), 39/95 tissue orders (41.1%), and 8/63 CSF orders (12.7%). Across the four primary specimen groups, the most frequently reported organisms included Epstein-Barr virus (n = 485), Candida albicans (n = 285), and cytomegalovirus (n = 262), together with Klebsiella pneumoniae and Acinetobacter baumannii; these rankings reflect report-level frequency rather than adjudicated pathogenic roles, particularly for latency- or reactivation-prone viruses. Of included orders, 277 (14.0%) underwent PMseq-RNA testing. These findings characterize specimen-specific differences in clinical mNGS reporting patterns and provide a specimen-context-aware reference for interpreting routine inpatient reports.},
}

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

@article {pmid42247317,
year = {2026},
author = {Zeng, Y and Wang, S and Zhang, Q and Miao, H and Xu, J and Li, W},
title = {Successful management of Legionella pneumonia in an immunocompromised infant presenting with generalized pustular rash: A case report.},
journal = {Science progress},
volume = {109},
number = {2},
pages = {368504261458101},
doi = {10.1177/00368504261458101},
pmid = {42247317},
issn = {2047-7163},
abstract = {Legionella infection is rare in children, and extrapulmonary manifestations are even less commonly reported. Cutaneous involvement, particularly in the form of generalized pustular eruptions, may present significant diagnostic and therapeutic challenges, especially in immunocompromised patients. We report a male infant under 6 months with X-linked severe combined immunodeficiency (XL-SCID) who presented with a disseminated pustular rash as the predominant clinical feature. Initial blood and pus cultures were negative, and empirical antimicrobial therapy showed limited clinical response. Metagenomic next-generation sequencing (mNGS) was subsequently performed and identified Legionella as the causative pathogen. Based on this finding, the antimicrobial regimen was adjusted to include a macrolide antibiotic combined with trimethoprim-sulfamethoxazole (TMP-SMX), resulting in significant clinical improvement and eventual recovery. This case highlights the atypical presentation of Legionella infection with predominant cutaneous manifestations in children, particularly in the context of primary immunodeficiency, and underscores the diagnostic value of mNGS in cases with inconclusive conventional testing. Early application of advanced molecular diagnostics and timely optimization of targeted antimicrobial therapy are crucial for improving outcomes in rare and complex pediatric infections.},
}

@article {pmid42247440,
year = {2026},
author = {Levade, I and Delisle, B and Fournier, É and Therrien, C},
title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350663},
doi = {10.1371/journal.pone.0350663},
pmid = {42247440},
issn = {1932-6203},
abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.},
}

@article {pmid42247515,
year = {2026},
author = {Piñero, M and Librado, P},
title = {Genomic evidence for limited entomophagy in ancient Europeans.},
journal = {Science advances},
volume = {12},
number = {23},
pages = {eaec6939},
doi = {10.1126/sciadv.aec6939},
pmid = {42247515},
issn = {2375-2548},
abstract = {To meet the rising food demands of our growing population, the Food and Agriculture Organization proposed edible insects as sustainable sources of animal protein. Although hundreds of million people already consume insects around the tropics, western societies remain averse to entomophagy. To trace whether ancient Europeans consumed insects, we here apply two complementary genomic approaches. Metagenomic screening on 745 ancient anatomically modern human dental calculus returned limited insect DNA traces, with read abundances well below those observed in Neanderthals, western chimpanzees, and gorillas. In addition, genes encoding stomach-expressed chitinases show two of the most significant signatures of latitudinal differentiation genome-wide. Clines are consistent with evolutionary benefits of entomophagy in tropical regions and with expression quantitative trait locus data supporting low chitin digestibility in present-day Europeans. Ancient genomes confirm that both clines already existed at the onset of agriculture and persisted despite massive migrations. Together, our findings support occasional and possibly incidental insect consumption in Europe over the past ~9000 years.},
}

@article {pmid42247592,
year = {2026},
author = {Boulay, A and Németh, V and Criel, B and Stock, M and De Baets, B and Galiez, C and Rousseau, E and Briers, Y and Vázquez, R},
title = {PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
doi = {10.1093/database/baag033},
pmid = {42247592},
issn = {1758-0463},
support = {#325947//FRQNT/ ; //NSERC/ ; 1S91526N//FWO/ ; 1S38519N//FWO/ ; #307935//FRQS/ ; 01P10022//BOF/ ; },
abstract = {As biology becomes increasingly data-driven, so does the field of phage lysins, enzymes that degrade bacterial cell walls and offer promising alternatives to traditional antibiotics. Five years ago, we introduced PhaLP, a centralized resource for Phage Lytic Protein sequences and associated metadata to support global research efforts. Here, we present PhaLP 2.0, an enhanced database designed to address key challenges in computational lysin research by integrating newly identified lysins from thousands of metagenomes. To expand the known diversity of lysins beyond that of cultured phages, we developed SUBLYME, a protein-embedding-based machine-learning Software designed to Uncover and classify Bacteriophage Lysins from Metagenomic datasets. Using embeddings derived from the well-curated sequences of the original PhaLP database, we trained support vector machines to distinguish lysins from non-lysins in viromes and classify them as endolysins or virion-associated lysins. The models achieved an average F1 score of 98% on held-out clusters. SUBLYME enabled the discovery of 743 000 new lysin sequences from EnVhogDB, a virome-derived protein database, increasing the number of known lysin clusters 40-fold, from 1000 to 40 000. SUBLYME and PhaLP 2.0 are accessible online at https://github.com/Rousseau-Team/sublyme and https://phalp.ugent.be, respectively. Together, these advances establish PhaLP 2.0 as a comprehensive and scalable portal for lysin discovery, classification, and sequence analysis, paving the way for future antibacterial applications and evolutionary insights.},
}

@article {pmid42247807,
year = {2026},
author = {Sadia, H and Amin, A and Khalid, N and Ahmed, I},
title = {Antimicrobial resistance and virulence in polymicrobial chronic wound infections: A metagenomic perspective.},
journal = {Journal of infection and public health},
volume = {19},
number = {8},
pages = {103280},
doi = {10.1016/j.jiph.2026.103280},
pmid = {42247807},
issn = {1876-035X},
abstract = {BACKGROUND: Chronic wound infections represent a significant clinical and public health challenge due to their polymicrobial nature and the increasing burden of antimicrobial resistance (AMR). Conventional culture-based diagnostics often fail to capture the full microbial diversity and resistance potential associated with these infections.

METHODS: Chronic wound samples persisting for more than 15 days were collected from patients at a tertiary-care hospital in Pakistan. Samples are categorized into five groups: lower leg (ll-H1), upper leg (ul-H2), foot (ft-H3), chest (ct-H4) and catheter (ca-H5). Shotgun metagenomic sequencing was employed alongside routine culture-based methods to characterize microbial communities, antimicrobial resistance genes, and virulence determinants. Taxonomic and functional profiling were performed to assess microbial diversity and resistance patterns across wound subgroups.

RESULTS: Metagenomic analysis revealed a predominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Clinically relevant pathogens, including Achromobacter xylosoxidans, Staphylococcus aureus, and Pseudomonas aeruginosa, were frequently detected, along with less commonly reported taxa such as Achromobacter insolitus and Stenotrophomonas maltophilia. Multiple antimicrobial resistance gene clusters and biofilm-associated virulence factors were identified, indicating substantial multidrug resistance potential. Site-specific analysis showed that Pseudomonas aeruginosa dominated ul-H2 (∼32%), while Enterobacter hormaechei was most abundant in ft-H3 (∼40%). Culture-based methods primarily recovered common aerobic pathogens, whereas metagenomics detected additional opportunistic and unculturable taxa, highlighting the limitations of routine diagnostics. Resistome analysis identified ARGs conferring resistance to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and macrolides.

CONCLUSIONS: Chronic wound infections in Pakistan harbor diverse polymicrobial communities with substantial antimicrobial resistance and virulence potential. Shotgun metagenomics provides a more comprehensive characterization than culture-based methods by detecting additional pathogens and resistance determinants across wound sites. These findings support the integration of metagenomic diagnostics to improve clinical decision-making, strengthen antimicrobial stewardship, and guide infection control strategies in resource-limited healthcare settings.},
}

@article {pmid42248018,
year = {2026},
author = {Park, S and Shin, JH and Lee, HH and Lee, JG},
title = {Cover crop incorporation maintains the methane oxidation potential and lowers methane emissions in plastic-film-mulched upland arable soils.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130115},
doi = {10.1016/j.jenvman.2026.130115},
pmid = {42248018},
issn = {1095-8630},
abstract = {Plastic film mulching can transform upland arable soils from sinks for methane (CH4) into sources by limiting gaseous exchange and creating hypoxic microsites. We explored whether incorporating cover crops can help reduce CH4 emissions by maintaining methanotroph functional potential in the presence of mulching. We conducted a field experiment in an upland maize field to compare NPK fertilization and cover crop incorporation, both with and without mulching. We combined CH4 flux measurements with methane oxidation potential (MOP) assays and shotgun metagenomics to analyze CH4-cycling communities and functional gene profiles. Cover crop incorporation under mulching (M-CC) reduced cumulative CH4 emissions by 55% compared with NPK fertilization under mulching (M-NPK) and maintained 17% higher MOP. By contrast, particulate methane monooxygenase (pMMO) genes did not show a uniform enrichment under M-CC. However, M-CC demonstrated higher abundances of genes associated with hydrogenase activity, single-carbon (C1) metabolism, electron transport, and antioxidant biosynthesis. Specifically, there was a 21% to 67% increase in hydrogenase genes, a 14% to 55% rise in C1 metabolism genes, a 28% to 54% increase in electron transport genes, and a remarkable 280% elevation in the antioxidant biosynthesis gene egtD. Using plastic film mulching with incorporated cover crops maintained MOP and promoted greater microbial biomass and metabolic flexibility. These effects were linked to lower CH4 emissions and reduced yield-scale CH4 emissions, all without compromising maize yield.},
}

@article {pmid42248101,
year = {2026},
author = {Xu, Z and Zhang, L and Zhu, D and Zhi, S and Ashbolt, NJ and Li, G and Luo, W and Nghiem, LD},
title = {Optimising composting to reduce plasmid and integrative conjugative element conjugation to minimise antibiotic resistomes in livestock manure for safe organic fertilisation.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142573},
doi = {10.1016/j.jhazmat.2026.142573},
pmid = {42248101},
issn = {1873-3336},
abstract = {Antimicrobial resistance is a critical threat to organic fertilizer production from livestock manure by composting. This study provides new insights to the dynamics of antimicrobial resistance genes (ARGs) during composting to propose strategies for their elimination. Results from genome-resolved metagenomics, meta-analysis, and quantitative assessment showed temperature and moisture content as key factors governing ARG dynamics during composting. Although integrative conjugative elements (ICE) could be transferable by some thermophilic bacteria, composting temperature to above 60 °C reduces mobile ARGs driven by plasmid conjugation for elimination. Further controlling moisture content to low than 60% inhibits the secretion of extracellular polymeric substances to restrain ARG rebound by ICE conjugation, particularly at the maturation stage of composting. These results are significantly useful for China, where swine manure accounted for most of livestock manure-derived ARGs (91.5%). Applying findings from this study to optimise the composting of livestock manure could reduce ARG proliferation by up to 59.3% in China.},
}

@article {pmid42248258,
year = {2026},
author = {Guo, Y and Jia, X and Chen, Y and Xu, S and Ming, T and Kong, F and Xu, J},
title = {Inhibiting methanogenesis with medium-chain fatty acids: strategy for rapid start-up and stable operation of food waste chain elongation systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135078},
doi = {10.1016/j.biortech.2026.135078},
pmid = {42248258},
issn = {1873-2976},
abstract = {Converting food waste (FW) into medium-chain fatty acids (MCFAs) via chain elongation (CE) is an economical and eco-friendly approach, but methanogenic competition remains a key challenge limiting CE efficiency. Traditional inhibition methods (e.g., pH regulation, hydraulic/solids retention time control, chemical additives) require strict operation or external inputs, causing non-specific microbial inhibition, high costs and environmental risks. Innovatively, MCFAs can inherently suppress methanogens with obvious advantages. However, their inhibition mechanisms and dependence on concentration and carbon chain length remain unclear. This study investigated the effects of butyric acid (C4), caproic acid (C6), and caprylic acid (C8) at different concentrations on methane production, medium- and short-chain fatty acids accumulation, and microbial dynamics in FW anaerobic fermentation. The results indicated that the inhibitory effect was primarily driven by undissociated fatty acids, with the potency increasing with longer carbon chain lengths. Notably, C8 at a low undissociated concentration (0.05 mM) completely inhibited methanogenesis. Higher concentrations of C4, C6, and C8 effectively sustained hydrolysis and acidogenesis while promoting CE and leading to the accumulation of caproic acid and caprylic acid. Metagenomic analysis showed that a decline in methanogenesis-related functional genes was accompanied by an increase in reverse β-oxidation related functional genes. These findings provide a feasible strategy for rapid start-up and stable operation of FW-based CE systems, and present a sustainable route for FW valorization toward high-value biochemicals.},
}

@article {pmid42248259,
year = {2026},
author = {Gai, T and Zhang, J and Zhang, S and Zhang, L and Li, X and Wu, Y and Yang, Y and Liu, X and Shi, G and Yang, M},
title = {Performance and mechanisms of a biochar-enhanced partial nitritation/anammox process for the treatment of silane tower wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135083},
doi = {10.1016/j.biortech.2026.135083},
pmid = {42248259},
issn = {1873-2976},
abstract = {The increasing discharge of silane tower wastewater, characterized by high ammonia (NH4[+]-N) and the presence of silane derivatives, poses significant challenges to biological nitrogen removal processes. In this study, a partial nitritation/anammox (PN/A) sludge system was enhanced through the addition of sludge-derived biochar (SBC). The results demonstrated that SBC effectively improved the nitrogen removal performance of PN/A sludge during the treatment of silane tower wastewater. Under low-proportion silane tower wastewater conditions, SBC rapidly promoted R2 sludge granulation within 19 d during phase I. During phase IV, when 100% silane tower wastewater was used as the influent, the NH4[+]-N and total nitrogen removal efficiencies of R2 were stably maintained at 80%-83%. These improvements were mainly attributed to the ability of SBC to promote sludge granulation, enrich functional microorganisms, and enhance extracellular electron transfer (EET) performance. SBC addition enabled the sludge to maintain higher levels of tightly bound extracellular polymeric substances rich in hydrophobic amino acids (HAAs). This study found that SBC-promoted EET was more strongly associated with anammox bacteria than with ammonia-oxidizing bacteria, resulting in a more pronounced enhancement of specific anammox activity than specific ammonia oxidation rate. Metagenomic and metatranscriptomic analyses further revealed that SBC enhanced the biosynthetic pathways and transcriptional expression of genes associated with HAA synthesis in PN/A sludge. Overall, this study provides a novel enhancement strategy for the application of PN/A processes in the treatment of complex industrial wastewater with high NH4[+]-N concentrations.},
}

@article {pmid42248305,
year = {2026},
author = {Janes, VA and Stalenhoef, JE and Van der Putten, B and Koster, L and Jakobs, ME and Van Dissel, JT and De Jong, MD and Schultsz, C and Mende, DR},
title = {Metagenomic sequencing as a diagnostic tool for urine culture negative febrile urinary tract infection.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106783},
doi = {10.1016/j.jinf.2026.106783},
pmid = {42248305},
issn = {1532-2742},
abstract = {OBJECTIVES: The diagnosis of febrile urinary tract infection (fUTI) by urine culture is hampered by antibiotic pre-treatment. We investigated urine metagenomics to diagnose fUTI in patients with positive blood but negative urine cultures.

METHODS: We performed shotgun metagenomic sequencing on 41 culture-positive and 19 culture-negative urine samples from fUTI patients, comparing urine metagenomics to blood and urine culture including antimicrobial susceptibility testing (AST). mOTUs3.1 performed metagenomic pathogen detection and ResFinder2.0 antimicrobial drug resistance (AMR) gene detection (standard settings). Whole genome sequencing (WGS) was performed on blood culture isolates from culture-negative urine samples. BWA-MEM and sylph aligned metagenomic pathogen reads to their respective WGS assemblies.

RESULTS: Metagenomics detected the blood culture isolate in 39/41 culture-positive and 17/19 culture-negative urine samples. 11/19 urine culture-negative patients were pre-treated with antibiotics, versus 8/41 urine culture-positives. The blood culture isolate was the most abundant pathogen in 33/41 culture-positive and 15/19 culture-negative urine samples. A median of 93.2% of pathogen-specific metagenomic reads mapped to their WGS assemblies with a median ANI of 98.7% (n=11). Genotypic AMR detection and phenotypic AST matched in 38-96% of cases.

CONCLUSIONS: Urine metagenomics successfully detected the causative pathogen in urine culture-negative fUTI patients. Genotypic AMR prediction requires further investigation.},
}

@article {pmid41551460,
year = {2026},
author = {Cornman, RS and Hepner, MJ and Otto, CRV},
title = {The Appalbees menu: a multiyear, multilocus metagenetic assessment of pollen foraging by Appalachian Bombus affinis workers.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20284},
pmid = {41551460},
issn = {2167-8359},
mesh = {Animals ; Bees/physiology ; *Pollen/genetics/classification ; Virginia ; West Virginia ; DNA Barcoding, Taxonomic ; Appalachian Region ; *Feeding Behavior ; Metagenomics ; Pollination ; },
abstract = {BACKGROUND: Detailed studies of foraging behavior are needed for scientific management of the endangered rusty-patched bumblebee (Bombus affinis) in the disjunct and ecologically differentiated habitats it presently occupies. Current knowledge gaps hinder recovery planning but are challenging to redress through direct observation of rare interactions in the field.

METHODS: We used genetic metabarcoding to characterize the taxonomic composition of pollen collected by B. affinis workers in the Appalachian mountains of Virginia and West Virginia from 2021-2023. We developed a custom sequence database of the regional flora and compared results for two independent genetic loci, internal transcribed spacer 1 and internal transcribed spacer 2 (ITS1 and ITS2).

RESULTS: While ITS2 consistently detected more plant diversity, results from the two loci were broadly concordant with a few notable exceptions. The plant genera Hydrangea, Actaea, Rhododendron, Tilia, and (unexpectedly) Laportea were prominent in midsummer samples, with Rubus a consistent contributor in late spring and early summer. Pea flowers (family Fabaceae) were relatively infrequent but the genera Securigera and Trifolium were detected before the Hydrangea bloom and again in late summer afterwards. The diversity of forage plants was highest in late summer, driven primarily by various genera of Asteraceae. Comparing the current data with previous work indicates regional differentiation in forage plants between Appalachia and the upper Midwest, but also allows 'consensus' forage sources that are supported by multiple lines of evidence and shared between regions to be tabulated. These results should help managers focus survey efforts for this endangered species and plan habitat enhancements.},
}

Animals
Bees/physiology
*Pollen/genetics/classification
Virginia
West Virginia
DNA Barcoding, Taxonomic
Appalachian Region
*Feeding Behavior
Metagenomics
Pollination

@article {pmid42012700,
year = {2026},
author = {Chen, J and Xi, M and Hu, W and He, R and Zhang, W and Zhang, Y and Chen, X and Chen, J},
title = {Adult Onset of MSMD Caused by IL-12Rβ1 Variants: Report of a Young Woman with NTM Infection Lacking Bacille Calmette-Guérin (BCG)-induced Diseases.},
journal = {Journal of clinical immunology},
volume = {46},
number = {1},
pages = {},
pmid = {42012700},
issn = {1573-2592},
support = {23141901900//the Shanghai Science and Technology Innovation Action Plan，experimental animal research project/ ; 23PJD073//the Shanghai Pujiang Program/ ; ynms202306//Basic Research Project of the Sixth People's Hospital of Shanghai/ ; },
abstract = {UNLABELLED: Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by increased susceptibility to infections caused by weakly virulent mycobacteria (such as nontuberculous mycobacteria (NTM) or the Bacillus Calmette–Guérin (BCG) vaccine) in otherwise healthy individuals. In this study, we described a 29-year-old patient with MSMD due to NTM infection identified using metagenomic next-generation sequencing (mNGS) testing. The patient showed a poor response to standard antimycobacterial treatment. Therefore, we performed whole-exome sequencing (WES) and identified three heterozygous variants in IL-12Rβ1 (Ala131Thr, Arg323* and Arg561*). The two deleterious IL-12RB1 variants, Arg323* and Arg561*,were shown to be in trans (paternal and maternal, respectively). Further investigation revealed that two of these variants (Arg323* and Arg561*) could affect the binding between IL-12Rβ1 and IL-12Rβ2, leading to a weakened response of CD4[+] T cells to stimulation with IL-12 plus tuberculosis antigen (TbAg), with reduced expression levels of IFN-γ and its downstream target p-STAT4. However, these variants did not affect the CD4[+] T-cell response to glucan stimulation, as the three heterozygous variant loci do not interfere with the aggregation of IL-12Rβ1 and IL-23R. This autosomal recessive, partial IL-12Rβ1 deficiency ultimately resulted in the patient developing disseminated NTM infection. In clinical treatment, we combined IFN-γ with standard antimycobacterial therapy. The patient showed only a partial response to therapy. Therefore, as detection techniques continue to advance, it is important for clinicians to increase their understanding of MSMD to enable faster and more accurate diagnosis and treatment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10875-026-02009-x.},
}

@article {pmid42235671,
year = {2026},
author = {Peng, D and Liu, X and Wang, L and Pan, Y and Kang, B and Liu, X and Xu, R and Cheng, Y},
title = {A multi-omics signature of microplastic exposure and its clinical, metabolic, and microbial correlates in colorectal cancer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128426},
doi = {10.1016/j.envpol.2026.128426},
pmid = {42235671},
issn = {1873-6424},
abstract = {Microplastics (MPs) are emerging environmental contaminants with potential human health implications, yet their distribution and biological effects in colorectal cancer (CRC) remain unclear. Here, we investigate the presence of MPs in blood, tumor, and peri-tumor tissues from CRC patients using a multi-omics approach. We find that MPs, particularly polyvinyl chloride (PVC) and polyethylene (PE), are more abundant in tumor and peri-tumor tissues than in blood. Tissue-specific MPs were associated with clinical traits, serum metabolites, and gut microbes. Functional analysis suggested MP-related alterations in microbial pathways involving carbohydrate metabolism, fatty acid degradation, and bile acid biosynthesis. Our findings provide the first integrative evidence suggesting potential links between MPs exposure to metabolic and microbial dysregulation in CRC patients.},
}

@article {pmid42235696,
year = {2026},
author = {Tang, P and Shuai, H and Yang, Z and Cen, Q and Mao, Y and Wang, J and Zhou, Y},
title = {Contributions and mechanisms of bioclogging-induced oxygen-limited microsites to nitrogen removal in porous media.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135059},
doi = {10.1016/j.biortech.2026.135059},
pmid = {42235696},
issn = {1873-2976},
abstract = {Nitrate (NO3[-]-N) in wastewater treatment plant (WWTP) effluents has become a contributing factor to the increasing eutrophication risk in receiving waters, whereas the relatively high dissolved oxygen (DO, approximately 7-8 mg L[-1]) in effluents constrains NO3[-]-N removal. Constructed wetland systems based on porous media are major technologies for advanced treatment of WWTP effluents. Although bioclogging in such systems is usually regarded as a negative phenomenon, it may create favorable anoxic microenvironments for denitrification through transport confinement. In this study, vertical saturated flow-through porous-media columns were established to systematically elucidate how bioclogging reshapes oxygen transport and drives microbial functional reorganization under bulk-oxic conditions. The results showed that hydraulic conductivity (k) decreased from 27.5 and 18.1 cm s[-1] in Groups A and B, respectively, to < 0.03 cm s[-1], while NO3[-]-N removal increased from 61 to 64% during start-up to 88-91% at day 24. The two-dimensional plate experiment directly captured the full evolution of pore-scale oxygen-limited microenvironments from discrete patches to connected structures. DO heatmaps further showed that bioclogging-induced transport confinement generated nested confined oxygen-limited microsites within an otherwise bulk-oxic flow field. Denitrification-related genes were enriched in the clogging-affected upper and intermediate layers, indicating that efficient denitrification was more likely associated with bioclogging-induced confined oxygen-limited microsites than simply with medium depth. Metagenomic analysis further revealed a metabolic division of labor within the microbial community, with Ectobacillus mainly associated with upstream nitrate reduction, Nitrospira and Chitinophagaceae playing complementary roles in downstream steps, and Ignavibacterium exhibiting genomic signatures consistent with enhanced organic-carbon metabolism and potential reducing-equivalent generation. Overall, bioclogging coupled bulk-oxic and locally oxygen-limited functions through transport confinement and community-level metabolic partitioning, providing new mechanistic insights into stable nitrogen removal under high-DO effluent conditions.},
}