@article {pmid41759875,
year = {2026},
author = {Nuranindita, R and Natanegara, S and Wusono, AD and Amirudin, FA and Hitipeuw, D and Rahayu, AA and Daud, MM and Yuwanita, MR and Qanita, NG and Saputra, EY and Jun, H and Jeon, BY and Lee, MR and Ju, JW and Malik, MDA and Garjito, TA and Han, JH and Muh, F},
title = {Metatranscriptomic analysis of Anopheles species from Menoreh Hills endemic area in Central Java, Indonesia.},
journal = {Acta tropica},
volume = {277},
number = {},
pages = {108033},
doi = {10.1016/j.actatropica.2026.108033},
pmid = {41759875},
issn = {1873-6254},
mesh = {Animals ; *Anopheles/microbiology/virology/genetics/classification ; Indonesia ; *Microbiota ; *Mosquito Vectors/virology/microbiology ; Bacteria/classification/genetics/isolation & purification ; Gene Expression Profiling ; Transcriptome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The mosquito microbiome plays a crucial role in vector competence and disease transmission dynamics, yet comprehensive metatranscriptomic analyses of Anopheles species microbiomes remain limited, particularly in malaria-endemic regions like the Menoreh Hills of Central Java, Indonesia. This study aimed to characterize the microbial and viral community compositions of five Anopheles species and their potential implications for vectorial capacity.

METHODS: Metatranscriptomic analysis was performed on five Anopheles species (An. barbirostris, An. flavirostris, An. kochi, An. maculatus, and An. vagus) collected from the Menoreh Hills endemic area using RNA sequencing, taxonomic classification, and functional annotation approaches.

RESULTS: Proteobacteria emerged as the dominant bacterial phylum across all species, with variations in relative abundance of other taxa. Baculoviridae emerged as the overwhelmingly dominant viral family across all species, with other families including Bunyavirales, Herpesvirales, and Nucleocytoviricota present at much lower abundances. Diversity indices revealed An. vagus with the highest microbial diversity and An. barbirostris with the lowest. Adherence-related virulence factors were predominant, particularly in An. maculatus and An. vagus, while carbohydrate-active enzymes AA1 and GT35 were abundant across all species.

CONCLUSIONS: This study examines microbiome and virome across five Anopheles species from Menoreh Hills. Betabaculovirus dominated virome, while bacterial and fungal communities showed species-specific patterns. Analyses revealed virulence differences. Study limitations include pooled samples. The results provide data for malaria research.},
}

Animals
*Anopheles/microbiology/virology/genetics/classification
Indonesia
*Microbiota
*Mosquito Vectors/virology/microbiology
Bacteria/classification/genetics/isolation & purification
Gene Expression Profiling
Transcriptome
Metagenomics
*Viruses/classification/genetics/isolation & purification

@article {pmid42260359,
year = {2026},
author = {Lu, F and Li, Y and Chen, X and Chen, Y and Li, C and Nong, G and Liu, J and Wei, Q},
title = {Community-acquired pseudomonas aeruginosa pneumonia in immunocompetent children: a study of 7 cases.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13768-8},
pmid = {42260359},
issn = {1471-2334},
support = {AD22035219//Guangxi Clinical Research Center for Pediatric disease/ ; 2025GXNSFAA069702//The National Natural Science Foundation of Guangxi/ ; },
abstract = {BACKGROUND: To characterize the clinical features and outcomes of community-acquired Pseudomonas aeruginosa (PA) pneumonia in immunocompetent children.

METHODS: A retrospective analysis was conducted on seven immunocompetent children with community-acquired PA pneumonia hospitalized between January 2015 and June 2025. Pneumonia was defined by acute respiratory symptoms with new radiographic infiltrates. PA infection was confirmed by culture from sterile sites/lower respiratory tract or metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid.

RESULTS: All patients were male (n = 7). Age distribution was as follows: 1-12 months (n = 3), 13-36 months (n = 1), 37-60 months (n = 1), and ≥ 61 months (n = 2). Median age at onset was 18.0 months (IQR: 8.0-123.0). All patients presented acutely with fever and cough; two developed respiratory failure within 72 h. Additional clinical features included dyspnea (n = 4), lung rales (n = 4), hemoptysis (n = 3), chest pain (n = 2), and wheezing (n = 1). Chest imaging showed lobar consolidation (n = 5) or mass-like consolidation (n = 2). A total of seven cases were identified, with PA confirmed by culture in four patients and by mNGS of bronchoalveolar lavage fluid in three patients. All isolates were susceptible to anti-pseudomonal β-lactam antibiotics except aztreonam. Complications included definite or suspected empyema (n = 5), pyopneumothorax (n = 3), and bacteremia (n = 2). Three patients required pediatric intensive care, two received invasive mechanical ventilation, two underwent closed thoracic drainage, and one required decortication. There were no deaths, but 4 patients sustained significant residual lung injury secondary to necrotizing pneumonia.

CONCLUSION: Although rare, community-acquired PA pneumonia in immunocompetent children is associated with severe disease and pulmonary complications. Initial therapy with anti-pseudomonal β-lactam antibiotics appears effective in improving outcomes. Repeated cultures are recommended in the cases who remain symptomatic.},
}

@article {pmid42260652,
year = {2026},
author = {Le Moigne, A and Andrei, AŞ and Pernthaler, J},
title = {Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02442-5},
pmid = {42260652},
issn = {2049-2618},
abstract = {BACKGROUND: Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-"functional dispersal limitation"-explained variation in cellobiose use.

RESULTS: Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of "functional dispersal limitation." We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.

CONCLUSIONS: Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.},
}

@article {pmid42260783,
year = {2026},
author = {Hao, M and Sha, Y and Gao, J and Niu, J and Xu, Y},
title = {Concurrent Spinal Dural Arteriovenous Fistula and Varicella-Zoster Virus Meningoencephalitis Unmasked by Corticosteroid-Associated Deterioration: A Case Report on the Diagnostic Value of Serial mNGS.},
journal = {Current medical imaging},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115734056496224260602072444},
pmid = {42260783},
issn = {1573-4056},
abstract = {BACKGROUND: Concurrent spinal dural arteriovenous fistula (SDAVF) and varicella-zoster virus (VZV) meningoencephalitis are exceptionally rare, and overlapping features can delay diagnosis. This case adds to the literature by illustrating how corticosteroid exposure before exclusion of vascular and infectious mimics may be followed by neurological deterioration, and by emphasizing the diagnostic value of serial metagenomic next-generation sequencing (mNGS).

CASE PRESENTATION: A 48-year-old man developed insidious bilateral lower-limb weakness that progressed to numbness, sphincter dysfunction, and near-paralysis. Initial spinal magnetic resonance imaging showed diffuse thoracolumbar cord lesions; cerebrospinal fluid studies were mildly inflammatory, and myelitis was suspected. He received methylprednisolone pulse therapy followed by oral corticosteroids without improvement. One month later, he presented with fever, severe headache, vomiting, worsening paralysis, and altered mental status. Cerebrospinal fluid demonstrated marked pleocytosis, hypoglycorrhachia, and elevated protein, and mNGS detected abundant VZV sequences. Brain imaging showed hydrocephalus, meningeal enhancement, multifocal ischemic lesions, and intracranial arterial stenoses, consistent with VZV meningoencephalitis and vasculopathy. After external ventricular drainage, intravenous acyclovir, dexamethasone for cerebral edema, and empirical anti-tuberculosis therapy, serial mNGS showed a reduced VZV burden. Repeat spinal imaging revealed tortuous perimedullary vessels and hemosiderin deposition, and angiography confirmed SDAVF from the left T10 intercostal artery. The fistula was coagulated. At 12-month follow-up, he regained slight right-leg movement and partial sensory recovery above L1.

CONCLUSION: Progressive myelopathy with atypical inflammatory features should prompt vascular evaluation and pathogen testing. Serial mNGS can identify coexisting infection, guide therapy, and help avoid hazardous empirical corticosteroid use when the diagnosis remains uncertain.},
}

@article {pmid42261054,
year = {2026},
author = {Foster, NR and Holman, LE and Armbrecht, L and Courtin, J and Jensen, T and Pedersen, MW and Schreiber, L and Schroeder, H and Seersholm, FV and Zampirolo, G and Bohmann, K and Zimmermann, HH},
title = {A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70152},
doi = {10.1111/1755-0998.70152},
pmid = {42261054},
issn = {1755-0998},
support = {101105307//European Union's Horizon Europe Marie Sklodowska-Curie Actions/ ; 856488//European Union's Horizon 2020 Research and Innovation Program/ ; //Independent Research Fund Denmark/ ; DP250100886//Australian Research Council (ARC)/ ; DP250103420//Australian Research Council (ARC)/ ; },
abstract = {Recovering ancient DNA from environmental samples is transforming the way we understand historical ecosystems. While high-throughput sequencing of the total DNA in environmental samples (shotgun metagenomic sequencing) reveals the taxonomic contents of these samples, the genetic signals of some taxa (e.g., eukaryotes) can be weak compared to the background levels of DNA from organisms such as bacteria, requiring deep sequencing approaches that are costly. Thus, to increase cost-effectiveness, pre-sequencing enrichment of target DNA can be advantageous. One technique to enrich this target DNA is hybridisation capture, where short RNA or DNA baits are designed to match, bind and isolate specific stretches of DNA. Hybridisation capture has previously been applied to recover DNA from ancient skeletal remains, but it is only beginning to emerge as an approach to characterise organisms from ancient environmental samples. Thus, there is limited information on establishing hybridisation capture workflows for ancient environmental DNA applications, including the limitations and advantages. This mini review focuses on establishing a roadmap for the applications of hybridisation capture to ancient environmental DNA samples.},
}

@article {pmid42262077,
year = {2026},
author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y},
title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113225},
doi = {10.1128/spectrum.01132-25},
pmid = {42262077},
issn = {2165-0497},
abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.

IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.},
}

@article {pmid42262118,
year = {2026},
author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P},
title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050126},
doi = {10.1128/msystems.00501-26},
pmid = {42262118},
issn = {2379-5077},
abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.},
}

@article {pmid42262136,
year = {2026},
author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G},
title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028426},
doi = {10.1128/msystems.00284-26},
pmid = {42262136},
issn = {2379-5077},
abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.

IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.},
}

@article {pmid42262316,
year = {2026},
author = {Gao, B and Chen, L and Xu, W and Liu, G and Wei, M and Shen, W and Tu, P and Shan, J},
title = {Uncovering the Hidden Risks: How PLA and PLGA Microplastics Disrupt Gut Microbiota and Metabolic Health.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.5c00556},
pmid = {42262316},
issn = {1520-5010},
abstract = {Biodegradable plastics are often promoted as an eco-sustainable alternative to conventional polymers. However, their potential to degrade into microplastics still poses significant health risks. Commonly used materials such as polylactic acid (PLA) and poly(lactic-co-glycolic acid) (PLGA) have been widely adopted across various industries. While the toxicity of PLA microplastics has been studied extensively, the biological effects of PLGA microplastics remain largely unknown. Through metagenomic sequencing and untargeted metabolomic profiling, we evaluated the impacts of both PLA and PLGA microplastics on gut bacteria, fungi, virulence factors, microbial metabolic pathways, and metabolites in feces, serum, and liver tissue in this study. Our results demonstrate that both types of biodegradable microplastics disrupt gut microbiota and host metabolic homeostasis. PLA exposure provoked more pronounced changes in gut bacteria, fungi, virulence factors, and fecal and hepatic metabolites. In contrast, microbial metabolic pathways and serum metabolites were more strongly affected by PLGA. Several altered features were common to both microplastics, including enrichment of hepatic metabolic pathways related to valine, leucine, and isoleucine biosynthesis; one-carbon pool by folate; glycine, serine, and threonine metabolism; pantothenate and CoA biosynthesis; taurine and hypotaurine metabolism; and cysteine and methionine metabolism. Other disturbances were material-specific, such as UMP biosynthesis pathways, which were altered exclusively by PLA, while palmitate biosynthesis and unsaturated fatty acid biosynthesis were affected only by PLGA. These findings advance our understanding of the distinct and shared health risks posed by different biodegradable microplastics, providing a clearer basis for assessing their long-term safety.},
}

@article {pmid42262390,
year = {2026},
author = {Weissman, JL and Walling, A and Ducklow, H and Zakem, EJ},
title = {Genomic Traits Associated with Copiotrophy Decouple from Maximum Growth Rate Predictions Along Temperature Gradients.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag147},
pmid = {42262390},
issn = {1751-7370},
abstract = {Maximum growth rate is often used as a primary axis of functional variation in studies of microorganisms, in part because emerging tools make it straightforward to estimate from genomic and metagenomic data. However, temperature, via its influence on reaction kinetics, may act as a confounder in studies that measure genomic signatures of growth optimization across environments. Observations suggest that growth optimization need not always indicate rapid growth. For example, strong temperature gradients are the norm across much of the world's oceans, where deep-ocean microbes show elevated signals of genomic growth optimization relative to the faster-growing communities at the surface. Looking across environments, we find a negative relationship between genomic growth optimization and optimal growth temperature, leading to the potential decoupling of genomic traits associated with copiotrophy from maximum growth rate, particularly when measured along a temperature gradient. Our results suggest that, as a result of temperature's confounding effects, genomic signatures of growth optimization often better predict the ecological roles and functional genomic content of microorganisms than do growth rates themselves. Finally, we suggest reframing copiotrophy as growth beyond a thermodynamic baseline maximum growth rate, rather than in relation to a static rate cutoff.},
}

@article {pmid42263510,
year = {2026},
author = {Ergunay, K and Bourke, BP and Kamau, M and Fustec, B and Osborne, CJ and Mutura, J and Lebunge, R and Ochieng, G and Onyango, T and Cruz, A and Campos, M and Pott, MC and Romero, U and Deakins, AG and Paoli, J and Liao, HM and von Fricken, ME and McDermott, EG and Jiang, L and Grieco, JP and Achee, NL and Linton, YM},
title = {Unbiased long read metagenomic screening reveals diverse jingmen tick virus genomes across continents.},
journal = {Virology},
volume = {623},
number = {},
pages = {110999},
doi = {10.1016/j.virol.2026.110999},
pmid = {42263510},
issn = {1096-0341},
abstract = {Jingmen tick virus (JMTV) is an emerging tick-associated virus related to flaviviruses. Substantial information gaps remain on the epidemiology and public health impact of JMTV, despite evidence for symptomatic human infections, detection in potential zoonotic reservoirs and widespread global circulation. Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) of various life stages from locations of spillover risk across continents, from Eastern Africa (Kenya), Central America (Belize), and North America (Arkansas, United States). Signals of virus detection were observed in 32.9% of the pooled samples comprising adult, nymph and larvae stages. JMTV genome segments were assembled in 16.7% of the pools with initial virus detection. Adult ticks comprising Amblyomma gemma, Hyalomma rufipes, Rhipicephalus. evertsi and Rhipicephalus pulchellus from Kenya yielded complete JMTV genome assemblies. Evidence for tick-associated arbo-jingmenviruses was described for the first time in Belize, identified as complete genome segments encoding for non-structural virus proteins in pooled larvae. Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades and genomic underrepresentation in many regions with documented virus activity. Further investigations and expanded screening are needed to elucidate JMTV and arbo-jingmenvirus global epidemiology.},
}

@article {pmid42263617,
year = {2026},
author = {Chen, C and Li, J and Wang, F and Cheng, M and Sheng, T and Ahmed, Z and Hu, J and Zhou, Y},
title = {Auxiliary fermentation with Pediococcus acidilactici C1 reshapes flavor formation in sufu: An integrated metagenomic, flavoromic and non-targeted metabolomic deciphering.},
journal = {Food chemistry},
volume = {521},
number = {},
pages = {149979},
doi = {10.1016/j.foodchem.2026.149979},
pmid = {42263617},
issn = {1873-7072},
abstract = {Sufu, a traditional Chinese fermented soybean product, relies on spontaneous microbial succession for flavor, leading to high variability. Starter-assisted fermentation improves flavor; this study explores sufu flavor differences and mechanisms between spontaneous and Pediococcus acidilactici C1-inoculated processes. The findings demonstrated that inoculation with P. acidilactici C1 markedly enhanced the diversity and concentration of flavor compounds in sufu. Notably, 12 key taste-active free amino acids were detected, with glutamate up by 14% and aspartic acid showing an approximate 20-fold increase. A total of 15 key volatile flavor compounds were characterized, among which 8 were newly uncovered, namely ethyl 2-methylbutanoate, ethyl acetate, ethyl butyrate, ethyl caprylate, ethyl 2-ethylhexanoate, ethyl propionate, isoamyl acetate and 3-octanol. Metagenomics revealed enrichment of genes related to carbohydrate transport, amino acid/lipid metabolism, while non-targeted metabolomics confirmed metabolic remodeling. Multi-omics analyses showed P. acidilactici C1 reprogrammed carbon flux and boosted amino acid/lipid-derived volatile biosynthesis, enabling flavor-enhancing starter development.},
}

@article {pmid42263645,
year = {2026},
author = {Xing, Y and Huang, X and Luo, J and Wei, D and Chen, H and Sun, X},
title = {Active carbon-fixing microbes and their role in carbon fixation in mangrove sediments.},
journal = {Marine pollution bulletin},
volume = {231},
number = {},
pages = {119962},
doi = {10.1016/j.marpolbul.2026.119962},
pmid = {42263645},
issn = {1879-3363},
abstract = {Mangroves are vital blue carbon ecosystems, yet the microbial drivers of carbon fixation in their soils remain poorly understood. Here, this study investigated the patterns of drivers carbon-fixing microbes and their functional genes across three representative mangrove bays in the Beibu Gulf of the South China Sea (Lianzhou Bay, Maowei Sea and Zhenzhu Bay) using an integrated geochemical and metagenomic approach. The findings showed that: (1) the distribution of total organic carbon (TOC) in mangrove soils was significantly influenced by tidal zonation and mangrove plants, with TOC content in the mid-tidal zone consistently exceeding that in adjacent mudflats by 1.5- to 2.3-fold (p < 0.01); (2) potential dominant carbon fixation pathways inferred from soil microbial communities may vary significantly across different areas, including chemolithoautotrophic taxa (e.g., Nitrospira, Thiobacillus), phototrophic cyanobacteria (e.g., Synechococcus, Cyanobium), and mixotrophic assemblages. Correspondingly, the relative abundances of key functional genes (e.g., narH, narG, fabB, oadB) exhibited significant differences among these bays; (3) environmental factors including salinity, nutrients, and heavy metals jointly influenced the accumulation of carbon fixation genes and their microbial hosts, collectively explaining 63.9% of community variation at the species level. This study provides a mechanistic understanding of microbial functional diversity that underpins carbon cycling in mangrove soils, offering quantitative insights for the conservation and management of blue carbon ecosystems under anthropogenic pressures.},
}

@article {pmid42263665,
year = {2026},
author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, AM and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, D and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, J and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA},
title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2026020270},
pmid = {42263665},
issn = {2473-9537},
abstract = {Plant-based whole foods may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing auto-HCT for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary endpoints were feasibility and tolerability, defined by successful enrollment, and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24‑hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial is registered at ClinicalTrials.gov (NCT06559709).},
}

@article {pmid42263908,
year = {2026},
author = {Figueroa-Ortiz, C and Schoninger, S and Chan, JL and Bermudez, TA and Li, Y and Cander, S and Mcgonagle, B and Bacon, CW and Kalchiem-Dekel, O and Chawla, M and Lin, R and Tamari, R and Shaffer, BC and Perales, MA and Redelman-Sidi, G and Shahid, Z and Loganathan, R and Kamboj, M and Papanicolaou, G and Lee, YJ},
title = {Tuberculosis After Allogeneic Hematopoietic Cell Transplant: A 15-Year Case Series Highlighting Diagnostic Challenges.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.06.007},
pmid = {42263908},
issn = {2666-6367},
abstract = {BACKGROUND: Tuberculosis (TB) is an uncommon but potentially fatal complication after allogeneic hematopoietic cell transplant (HCT). Diagnosis is often delayed due to nonspecific clinical presentations, limited sensitivity of screening tests for latent TB infection, and slow turnaround of conventional TB diagnostic methods.

OBJECTIVE: The study aim is to describe the clinical and diagnostic characteristics of allogeneic HCT recipients with TB in the era of molecular and sequence based diagnostic methods.

STUDY DESIGN: We conducted a retrospective review of microbiologically confirmed TB cases among HCT recipients at a tertiary cancer center from 2010 to 2025. We detail clinical, demographic, and diagnostic characteristics including metagenomic next-generation sequencing (mNGS) testing of bronchoalveolar lavage (BAL) and blood (Eurofins Viracor, Lenexa, KS) for two individuals.

RESULTS: Ten patients were diagnosed with active TB at a median of 122 days post-HCT (range: 36-2,557). The median age was 53 years, and 6 were males. Except for one patient, all patients were foreign-born. Pre-HCT TB screening was performed in 7 patients; however, only 3 had positive (tuberculin skin test, n=1; interferon-gamma release assay [IGRA], n=2), and 1 had indeterminate IGRA results. All patients had abnormal CT chest findings compatible with latent TB. Nine of 10 patients presented with either fever or cough, while one patient was asymptomatic with incidental radiographic abnormalities. TB was diagnosed by MTB PCR in 8 cases, 4 patients had disseminated TB, and 3 died. mNGS results were available in two patients. In both cases MTB was detected in BAL, and in one, MTB was detected in the blood. Among 9 patients with available susceptibility testing data, moxifloxacin resistance was identified in one case.

CONCLUSIONS: In our cohort, post-HCT TB occurred mainly in foreign-born patients. Infection was diagnosed early after transplant and was frequently disseminated, with high mortality. These results underscore the limitations of current screening methods, and the diagnostic challenges of post-HCT TB.},
}

@article {pmid42263990,
year = {2026},
author = {Meng, Q and Zeng, W and Zhang, J and Liu, H and Li, S and Peng, Y},
title = {Efficient nutrient removal from low C/N municipal wastewater using a phototrophic biofilm system integrating simultaneous nitrification-denitrification and phosphorus removal (SND).},
journal = {Environmental research},
volume = {},
number = {},
pages = {124859},
doi = {10.1016/j.envres.2026.124859},
pmid = {42263990},
issn = {1096-0953},
abstract = {Microalgae-bacteria systems based on phosphorus-accumulating organisms (PAOs) offer low-energy and low-carbon-emission solutions for wastewater treatment, but their performance declines with low carbon-to-nitrogen (C/N) ratios municipal wastewater. In this study, a phototrophic biofilm system capable of coupling simultaneous nitrification-denitrification with phosphorus removal (P-SNDPRB) was developed to enhance low C/N ratios (3.32-4.11) municipal wastewater treatment. Before biofilm integration, total nitrogen (TN) removal was below 75%. After integration, TN removal increased to over 82%, while organic matter and phosphorus removal efficiencies remained at 85% and 90% in the P-SNDPRB system, respectively. Microalgae photosynthesis supplied oxygen to the biofilm, enabling denitrification. Chemometric and metagenomic analyses revealed denitrification and phosphorus accumulating metabolism (PAM) as key pathways for nitrogen and phosphorus removal. Flow cytometry sorting showed that biofilm spatial distribution promoted synergistic interactions among Accumulibacter, Competibacter, Nitrosomonas, Chlorella, and Cyanobacteria, further enhancing nitrogen and phosphorus removal. This study provides a low-energy and sustainable approach for the treatment of municipal wastewater with a low C/N ratio.},
}

@article {pmid42264042,
year = {2026},
author = {Zheng, Y and Li, X and Jia, Z and Qi, Y and Yin, H},
title = {Microbial-mediated attenuation of carbonaceous organics within urban sewers: Insights from in-pipe sediments microbial communities and metagenomic analyses.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135134},
doi = {10.1016/j.biortech.2026.135134},
pmid = {42264042},
issn = {1873-2976},
abstract = {Sewer sediments consist of diverse microbial communities that actively engage in the degradation of carbonaceous organics, adversely impacting influent quality of wastewater treatment plants. Yet, the underlying biological mechanisms within actual sewers remains underexplored. This study elucidated the microbial-mediated attenuation mechanisms in actual gravity sewers, with integrated approaches including sediments scanning electron microscopy, flow cytometry, extracellular polymeric substances (EPS) characterization, and metagenomic sequencing. Along the 3.56 km trunk sewer, chemical oxygen demand and five-day biological oxygen demand decreased by 55.1 % and 53.9 %, respectively. A spatial shift from anoxic to anaerobic conditions was observed along the sewer, accompanied by increased sediment microbial cell density (2.17 × 10[6]-2.57 × 10[7] cells/g SS) and EPS accumulation (2.22-17.69 mg/g VSS). The downstream enrichment of tryptophan- and tyrosine-like EPS components was consistent with the formation of larger and denser sediment aggregates (21.45-51.55 μm). Metagenomic analysis revealed a spatial shift in carbonaceous organics transformation potential, with upstream sediments enriched in fermentation-related microbial communities and genes associated with simple organic hydrolysis, while downstream reaches showed higher relative abundances of genera and genes associated with complex fatty acid and amino acid transformation through Embden-Meyerhof-Parnas pathway and tricarboxylic acid cycle. Downstream enrichment of pentose phosphate pathway-related genes further supported increased microbial resilience and biosynthetic potential under low-oxygen conditions. These findings underscore the sewer's role as pre-bioreactors, and strengthening sewer maintenance to minimize sediments accumulation is crucial for preventing excessive in-sewer organic matter loss.},
}

@article {pmid42264047,
year = {2026},
author = {Xu, YY and Tan, X and Dang, CC and Zhao, ZC and Fang, R and Fan, L and Ren, NQ and Xie, GJ and Wu, YN},
title = {Metagenomic insights into Thermus-mediated sulfur oxidation, nitrogen cycling, and thermoadaptation in thermophilic autotrophic denitrification bioreactors.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135137},
doi = {10.1016/j.biortech.2026.135137},
pmid = {42264047},
issn = {1873-2976},
abstract = {Thermus species are widely recognized as a key group of heterotrophic denitrifiers mediating carbon, nitrogen, and sulfur cycling in geothermal habitats, and have attracted extensive research attention for their thermostable enzyme resources. However, their autotrophic denitrification potential remains poorly characterized, and the systems-level mechanisms underlying their thermal adaptation remain incompletely understood. This study presents three high-quality metagenome-assembled genomes (MAGs) of Thermus from autotrophic sulfur-based denitrification bioreactors. These MAGs encode the complete genetic potential for the Calvin-Benson-Bassham cycle, reductive tricarboxylic acid cycle, and 3-hydroxypropionate bicycle for inorganic carbon fixation. Thermus strains employ a distinct sulfide oxidation route: HS[-] is first oxidized to polysulfides or glutathione persulfide by fccAB, then condensed with sulfite to form thiosulfate via rhodanese, and finally completely oxidized to sulfate by complete sox cluster. T. scotoductus (MAG1) carries genes for nitrate reduction (narGHI) and dissimilatory nitrate reduction to ammonium (nrfA and nrfH). As conspecific strains, MAG2 and MAG3 harbor abundant denitrification genes (nar, nirK, norBC), indicating strong substrate-driven metabolic plasticity. A protein-protein interaction network further elucidated the systems-level thermoadaptive survival mechanisms of T. scotoductus, identifying chaperone-mediated protein homeostasis and DNA repair-dependent genomic stability as core adaptive strategies, alongside orphan nodes (e.g., aceE, lpd, nuoC) with potential independent functions. Collectively, these findings advance our understanding of Thermus' metabolic plasticity, offer valuable thermostable resources for high-temperature wastewater treatment and industrial applications, and bridge critical knowledge gaps in the autotrophic metabolism and thermoadaptive regulation of thermophilic bacteria-laying a robust genomic foundation for the development and optimization of high-temperature biotechnological processes.},
}

@article {pmid42264152,
year = {2026},
author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TTB},
title = {Enteral Iron Dose Effect on Iron Storage, Intestinal Barrier, and Gut Microbiome in Preterm Infants: A Randomized Clinical Trial.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101389},
doi = {10.1016/j.ajcnut.2026.101389},
pmid = {42264152},
issn = {1938-3207},
abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.

OBJECTIVE: To compare the effects of two enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.

METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/day, or a higher dose of 6 mg/kg/day of total enteral iron. The primary outcome was the fecal microbiome after 2 weeks on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 weeks postmenstrual age were also evaluated.

RESULTS: Among 151 randomized infants who received study iron (77 low-dose; 74 high-dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/day had higher post-treatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/day. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.

CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/day was associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/day dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants.

TRIAL REGISTRATION: Clinicaltrials.gov NCT04497012.},
}

@article {pmid42264207,
year = {2026},
author = {Laovechprasit, W and Avila-Reyes, VA and Stacy, BA and Young, KT and Harris, HS and Tuttle, AD and Sirpenski, G and Kennedy, AE and Innis, CJ and Norton, TM and Zirkelbach, B and Stanton, JB},
title = {Surveillance of gastrointestinal viruses of free-ranging and rehabilitated Sea turtles in the United States.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105966},
doi = {10.1016/j.meegid.2026.105966},
pmid = {42264207},
issn = {1567-7257},
abstract = {Sea turtle populations are imperiled globally, primarily due to anthropogenic threats. However, non-anthropogenic factors, such as infectious diseases, can affect their population stability. Viruses are common causes of gastrointestinal disease in many species, and gastrointestinal signs are regularly observed among sea turtles, but little is known about enteric viruses in sea turtles. Establishing basic knowledge of viral diversity and evolutionary relationships is a necessary step towards understanding potential health impacts. This study investigated the viral genome contents of seventy-seven gastrointestinal specimens from six species of sea turtles with varying health conditions from the Atlantic and Pacific coasts of the United States. Forty-eight, non-plant and non-bacteria infecting viruses were detected (≥5 viral-like reads per sample) through random RNA sequencing. Detected viral sequences were then confirmed and characterized by semi-targeted, strand-switching sequencing, which provided deeper sequencing metrics allowing for phylogenetic characterization (>10× depth) for nineteen viruses across eight viral families, including seven putative novel viral species, one putative novel genus, and eleven likely novel viral sequences from taxa that lack established species demarcation criteria. Sixteen RNA viruses were characterized: four double-stranded RNA viruses (Partitiviridae, Totiviridae, and Picobirnaviridae), eleven positive-sense single-stranded RNA viruses (Caliciviridae, Dicistroviridae, unclassified Hepelivirales, and unclassified Picornavirales), and one negative-sense bisegmented RNA virus (Chuviridae). Three DNA viruses were also identified (Parvoviridae, Circoviridae, and unclassified Cressdnaviricota). Viruses identified in this study were often genetically related to viruses previously known to infect aquatic invertebrates and fish. This study provides baseline knowledge of viral communities in sea turtles and will serve as a foundation for future hypothesis-driven research to understand their relevance to sea turtle health.},
}

@article {pmid42264211,
year = {2026},
author = {Bhadelia, N and Gikandi, I and Lassmann, B},
title = {Regional Signals Preceding the 2026 Bundibugyo Virus Disease Outbreak.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108862},
doi = {10.1016/j.ijid.2026.108862},
pmid = {42264211},
issn = {1878-3511},
abstract = {BACKGROUND: The May 2026 Bundibugyo virus disease (BVD) outbreak in the Democratic Republic of the Congo was declared a Public Health Emergency of International Concern after substantial undetected community transmission. We describe regional surveillance signals detected by the Biothreats Emergence, Analysis, and Communications Network (BEACON), our open access event based surveillance program, in the weeks preceding outbreak declaration.

METHODS: We reviewed BEACON reports of VHF-compatible illness clusters detected in the transboundary DRC-Uganda-Burundi-South Sudan region during March-April 2026, prior to the May 15 laboratory confirmation of BDBV.

RESULTS: BEACON detected four temporally proximal VHF-compatible illness signals: (1) March 9, North Kivu Province-suspected Ebola case under investigation with unresolved laboratory results; (2) March 10, Kasaï Province-fatal hemorrhagic illness with secondary cases and negative Ebola PCR; (3) March 30, Burundi-35-case undiagnosed cluster near the DRC border with 5 deaths, negative testing for major filoviruses and >200 pathogens, pending metagenomic sequencing; (4) April 22, South Sudan-three suspected VHF cases with negative initial testing. All four signals shared a similar diagnostic phenotype: VHF-compatible presentation, mobilization of investigation teams, negative initial testing, and no publicly reported confirmed etiology. None were formally reported to have been resolved.

CONCLUSIONS: Our detection of four unresolved VHF signals preceding the confirmed BDBV outbreak highlights gaps in formal follow-up mechanisms for negative cases and fragmented regional diagnostic coordination. In light of confirmed BDBV circulation and Africa CDC's identification of 10 countries at high risk for spread, these preceding signals warrant urgent retrospective investigation and laboratory.},
}

@article {pmid42264215,
year = {2026},
author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and , and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH},
title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.05.024},
pmid = {42264215},
issn = {1523-1747},
abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare inborn error of immunity (IEI) caused by hyperfunctional pathogenic variants in CXC chemokine receptor 4 (CXCR4), predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and potential reduction in bacterial infection frequency. Here, we investigated skin microbiomes of 11 patients with WHIM syndrome using shotgun metagenomics, compared to healthy controls. WHIM skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in WHIM syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.},
}

@article {pmid42264245,
year = {2026},
author = {Zhao, Y and Zhang, Y and Tang, S and Peng, T and Bagadi, AH and Jia, X and Wei, Z and Han, J and Li, L and Liu, X and Kong, W and Song, S and Wei, C and Wang, J},
title = {Structural elucidation and gut barrier-protective effects of a glucomannan polysaccharide fraction from Lanzhou lily bulbs.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152899},
doi = {10.1016/j.ijbiomac.2026.152899},
pmid = {42264245},
issn = {1879-0003},
abstract = {Food-derived dietary polysaccharides have attracted increasing attention as functional ingredients for ulcerative colitis (UC) management. In this study, a homogeneous polysaccharide, designated LDP, was isolated from the bulbs of Lilium davidii var. willmottiae (Lanzhou lily). Structural analyses showed that LDP had a weight-average molecular weight (MW) of 5.082 × 10[3] g/mol and was mainly composed of alternating →4)-α-D-Manp-(1 → and →4)-β-D-Glcp-(1 → residues with minor branching. Conformational analysis and molecular dynamics (MD) simulations indicated that LDP adopted an extended semi-flexible coil conformation in aqueous solution. In dextran sulfate sodium (DSS)-induced colitis mice, LDP markedly alleviated disease symptoms, as evidenced by improved survival, reduced body weight loss, a lower disease activity index and attenuated histopathological injury. Mechanistically, LDP enhanced intestinal barrier integrity, significantly increased acetic acid levels and partially restored short-chain fatty acid (SCFA)-associated beneficial taxa, including Lactobacillaceae, Bifidobacterium, Allobaculum and members of Erysipelotrichaceae/Erysipelotrichia. Integrated metagenomic, proteomic, Western blot and immunological analyses further indicated that LDP attenuated intestinal inflammation by suppressing the TAB1/MAP2K4-centered MAPK signaling pathway, as evidenced by reduced TAB1 and MAP2K4 expression and decreased p38 phosphorylation, and by restoring the Th17/Treg balance in mesenteric lymph nodes (MLNs). These findings suggested that LDP alleviated DSS-induced colitis through coordinated regulation of gut microbiota, microbial metabolism, MAPK inflammatory signaling and mucosal immunity.},
}

@article {pmid42264341,
year = {2026},
author = {Zhu, K and Sun, W and Wang, Z and Zha, Y and Qu, X and Wang, B and Zhang, H},
title = {Environmental ubiquity but limited host taxonomic distribution of co-occurring metal(loid)-resistance genes and persistent organic pollutant-transformation genes in global inland waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128552},
doi = {10.1016/j.envpol.2026.128552},
pmid = {42264341},
issn = {1873-6424},
abstract = {Human activities have transformed inland waters into reservoirs of co-contamination by heavy metals and persistent organic pollutants, driving microbial adaptation through metal-resistance genes (MRGs) and POP-transformation genes (POPTGs). However, the global biogeography and ecological drivers of these co-occurring functional genes and their hosts remain unresolved. Here, leveraging 1,593 metagenomes, we investigate the global distribution, microbial hosts, co-occurrence patterns, and drivers of MRGs and POPTGs in inland waters. Key MRG subtypes (e.g., ruvB, pstB, arsB) and POPTGs (e.g., hdt, linJ, bphA) co-occurred in phylogenetically constrained hosts-predominantly Proteobacteria (e.g., Pseudomonas, Acidovorax)-exhibiting dual resistance to Cr/Cu and transformation of aromatic/chlorinated POPs. The positive correlations linked MRG-POPTG to mobile genetic elements, suggesting horizontal gene transfer accelerates multi-pollutant resistance. Our findings highlight known POPTGs and MRGs occur together, which is ubiquitous in the environment but restricted to a limited number of taxa (approximately 3.8% ratio of the total 4129 non-redundant MAGs). Finally, a global map of MRG-POPTG-carrying MAGs (MPCMs) abundance is generated, where climatic and anthropogenic factors explained MPCMs hot spots in South Asia, Southeast Asia, South America.},
}

@article {pmid42264402,
year = {2026},
author = {Li, C and Tan, Y and Ma, S and Wang, J and Bai, W and Li, Z and Gao, S and Zhao, Q and Qin, J and Ye, Z},
title = {Concentration-dependent roles of hydrazine in immobilized denitrifying biofilm for industrial wastewater treatment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135122},
doi = {10.1016/j.biortech.2026.135122},
pmid = {42264402},
issn = {1873-2976},
abstract = {Hydrazine-bearing industrial wastewater is challenging to treat biologically because hydrazine can simultaneously act as a reducing substrate and a microbial inhibitor. In this study, an immobilized denitrifying biofilm system was used to evaluate the concentration-dependent effects of hydrazine on denitrification performance, electron contribution, and microbial response under anoxic conditions. Under sufficient co-substrate conditions, 5-10 mg/L hydrazine was effectively removed, with a maximum removal efficiency of approximately 94%, while stable denitrification was maintained. Nitrogen-15 isotope tracing showed that approximately 31% of the electrons released from hydrazine oxidation were transferred to denitrification-coupled nitrate reduction, indicating that hydrazine can partially contribute reducing equivalents in the denitrifying biofilm. However, elevated hydrazine concentrations impaired hydrazine oxidation and denitrification, induced nitrite and ammonium accumulation, and reduced carbon utilization. Mechanistic analyses showed that this deterioration was associated with oxidative stress, membrane damage, and inhibition of key enzymes, particularly nitrite reductase and hydroxylamine oxidoreductase. Metagenomic analysis further revealed a stress-induced shift in the microbial community from central carbon metabolism toward compensatory pathways. Overall, this study provides mechanistic and process-level insights into the feasibility and operational limitations of using immobilized denitrifying biofilms for treating hydrazine-bearing industrial wastewater.},
}

@article {pmid42264404,
year = {2026},
author = {Li, Z and Wang, L and Wang, B and Wang, S and Liu, T and Peng, Y},
title = {Controlled transition from anammox to partial denitrification-anammox system enhanced nitrogen removal: Microbial community succession and organic matter management.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135121},
doi = {10.1016/j.biortech.2026.135121},
pmid = {42264404},
issn = {1873-2976},
abstract = {Integrated partial denitrification-anammox (PDA) offers a sustainable strategy for mainstream wastewater treatment. However, the dynamic transitions and microbial mechanisms during the shift from anammox to coupled PDA remain inadequately characterized. In this study, a PDA system was systematically established by the gradual replacement of nitrite with nitrate and controlled increases in acetate concentrations. Subsequently, acetate was replaced with sludge fermentation liquor (SFL) as the organic carbon source. The process achieved progressive enhancement in nitrogen removal, which stabilized at 93.9%-96.1%. The contribution of anammox in nitrogen removal accounted for > 74% of influent total nitrogen. Concurrently, the mean particle size increased from 85.6 μm to 387.5 μm, and this granulation process significantly improved the stability of the PDA system. 16S rRNA sequencing revealed a marked enrichment of Candidatus Brocadia (0.3% to 4.6%) and Thauera (5.8% to 17.3%). Furthermore, metagenomic analysis confirmed the high abundance of anammox-related genes (hdh, hzs) and higher abundance of the genes encoding nitrate reductase (narG/H/I, napA/B) compared to nitrite reductase genes (nirS/K). This metabolic bias reinforced the PD ecological niche, ensuring stable PDA functionality when SFL was used as the carbon source. Notably, enhanced activity of polysaccharide and protein hydrolase highlighted the critical roles of hydrolysis and acidogenesis in sustaining non-competitive PD performance, particularly under SFL conditions. This study provides a potentially reproducible strategy for the cultivation of PDA communities from anammox inoculum, elucidating microbial dynamics and functional stability during process transitions. These findings provide valuable insights for efficient wastewater treatment by replacing external chemical carbon sources to improve the recovery and utilization of sludge resources.},
}

@article {pmid42264456,
year = {2026},
author = {Wildbur, C and Dawson, RA and Roy, S and Ah-Peng, C and Espenberg, M and Hernández, M},
title = {Carbon monoxide oxidizers in soils of different ages from Piton de la Fournaise volcano.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag062},
pmid = {42264456},
issn = {1574-6941},
abstract = {Volcanic soils provide a unique environment for studying microbial colonization and succession due to their extreme conditions and distinct geochemical profiles. This study focused on carbon monoxide (CO)-oxidizing microbial communities in volcanic soils at Piton De La Fournaise, Réunion island. Soil samples from three sites (corresponding to eruptions in 1401, 1559, and 2007) were analyzed to assess microbial community structure using 16S rRNA gene sequencing and metagenomic analysis to identify functional genes involved in CO oxidation. Phylum-level analysis showed higher relative abundance of Acidobacteriota and Chloroflexota, lower abundances of Actinomycetota and Bacteroidota, and relatively stable levels of Pseudomonadota, while class-level patterns included rising Alphaproteobacteria and Acidobacteriia, with Ktenobacteria emerging in the 1401 site. CO dehydrogenase-related genes were found in 17 metagenome-assembled genomes across all sites. The CO consumption rate by microbes in soils was measured. CO-oxidizing microbes were present across soil ages, with detectable activity in the 2007 site and greatest activity in the 1401 site, suggesting that these microbes actively use CO as an energy source even in soils with primary vegetation, contrary to general understanding. The findings suggest intricate dynamics of microbial succession in volcanic soils and may challenge conventional expectations about community complexity over time.},
}

@article {pmid42265111,
year = {2026},
author = {Campese, L and Longo, A and Pelletier, E and Delmont, TO and Ambrosino, L and Miralto, M and Mele, BH and Alberti, A and Labadie, K and Oliveira, PH and Perdereau, A and Wincker, P and , and Iudicone, D},
title = {Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07571-y},
pmid = {42265111},
issn = {2052-4463},
support = {101082021//MARCO-BOLO/ ; ID: 862923//AtlantECO/ ; 101081642//OBAMA-NEXT/ ; },
abstract = {Marine ecosystems are hotspots of biodiversity and biogeochemical activity, yet much of their complexity remains largely inaccessible without genome-resolved data. Here we present a curated dataset of 52 eukaryotic metagenome-assembled genomes (MAGs) reconstructed from samples collected between April 2019 and January 2020 at three NEREA (Naples Ecological REsearch for Augmented observatories) sites in the Gulf of Naples. NEREA is a coastal observatory integrating physical, chemical and biological measurements with state-of-the-art metagenomics. The eukaryotic MAGs have an average completeness of ~55% and genome size of ~20 Mb. Predicted proteins were functionally annotated against UniProtKB, InterPro, and eggNOG databases, and each MAG was taxonomically classified using a curated RNA polymerase A reference dataset. The recovered MAGs encompass diverse eukaryotic lineages, primarily Ochrophyta, Chlorophyta and Haptophyta. Building on the Tara Oceans eukaryotic MAG legacy, this release represents the first reconstruction of eukaryotic MAGs from a coastal time series, enabling temporal and functional analyses of eukaryotic plankton.},
}

@article {pmid42265123,
year = {2026},
author = {Murchie, TJ and Cocker, SL and Baleka, S and Vogel, NA and Natola, L and Karpinski, E and Tirlea, D and Barrera, MA and Grant, DM and Morien, E and Long, GS and Rutledge, LY and Zazula, GD and Jensen, BJ and Froese, DG and Poinar, HN},
title = {Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42265123},
issn = {2041-1723},
abstract = {Permafrost-preserved ground squirrel (Urocitellus) burrows in Yukon, Canada contain coprolites (palaeofaeces) that span from the Holocene to at least the Middle Pleistocene (~700 kya). Using shotgun metagenomics and targeted enrichment, we recover a rich, multi-taxon spectrum of ancient environmental DNA from these pellets, including: plants, insects, microbes, and megafauna consistent with eastern Beringian ecosystems. These coprolites consistently preserve an abundance of eukaryotic DNA, enabling the assembly of >18 mitochondrial genomes (ground squirrel, snowshoe hare, steppe bison, horse, and mammoth), and revealing previously unrecognized diversity within Arctic Urocitellus, including a ~700 kya lineage that predates divergence among several extant clades. Characteristic damage patterns, positive/negative controls, and in silico taxon validations strongly support aDNA authenticity, and comparisons with regional permafrost datasets indicate minimal post-depositional leaching. These results show that permafrost coprolites can yield high-resolution records of Quaternary ecosystems and multi-organism population histories, providing a powerful complement to sedimentary and skeletal ancient DNA.},
}

@article {pmid42265319,
year = {2026},
author = {Gionchetta, G and Lee, J and Hansen, O and Beck, K and Bürgmann, H},
title = {Invasion dynamics of antimicrobial-resistant E. coli in river biofilms: impacts on the resistome, microbiomes, and horizontal gene transfer.},
journal = {npj antimicrobials and resistance},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44259-026-00232-5},
pmid = {42265319},
issn = {2731-8745},
support = {ID 100010434//La Caixa Foundation/ ; 186531/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {River biofilms are frequently exposed to invasion by antibiotic-resistant bacteria (ARB) due to episodic or chronic wastewater inputs, yet the ecological processes governing the fate of invaders and their resistance plasmids remain poorly understood. We experimentally exposed river-grown biofilms from sites differing in microbial diversity and wastewater impact to a genetically tagged ARB Escherichia coli carrying a transferable IncPα plasmid with the nptII resistance gene. Over two weeks, we tracked invader and plasmid dynamics using qPCR and plasmid-to-genome ratios as a proxy for horizontal gene transfer (HGT), complemented by 16S rRNA gene sequencing and metagenomics. Both quantification approaches yielded consistent results: the invader transiently established in all biofilms, peaking within 48 h and declining to near-background levels after 14 days. Decreasing plasmid-to-genome ratios indicated limited HGT and progressive plasmid loss. Biofilms impacted by wastewater showed slower declines, suggesting greater plasmid persistence in disturbed environments and increased abundance of specific indigenous antimicrobial resistance genes of public health concern. While the overall resistome exhibited short-lived shifts, and indigenous resistomes remained largely stable. These findings demonstrate that invader-biofilm interactions are dynamic and shaped by community context, supporting the One Health framework and highlighting how environmental conditions modulate antimicrobial resistance risks in freshwater ecosystems.},
}

@article {pmid42265550,
year = {2026},
author = {Lu, R and Dumonceaux, T and Anzar, M and Zovoilis, A and Antonation, K and Barker, D and Corbett, C and Nadon, C and Robertson, J and Eagle, SHC and Lung, O and Rudar, J and Surujballi, O and Wajnberg, G and Laing, C},
title = {MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06497-x},
pmid = {42265550},
issn = {1471-2105},
support = {CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; },
abstract = {BACKGROUND: Plasmids and viruses are two types of mobile genetic elements (ME), that rely on host cells to reproduce and propagate themselves. Recently, metagenomics has greatly facilitated the discovery and characterization of new plasmids and viruses, which relies on accurate identification of these reads in metagenomes. Some state-of-the-art tools can identify plasmid or viral reads, while others are able to identify the probable host or source species of these reads. Since the Minimizer-based Naïve Bayes Classifier (MNBC) tool accurately classifies chromosomal and viral reads to the species level, we extended it to develop the MNBC-ME tool that can also identify plasmid reads and their putative host species.

RESULTS: A standard reference- and test-sequence framework using simulated variable-length reads was used to benchmark MNBC-ME with eleven other state-of-the-art tools for ME identification: DeepMicroClass, geNomad, PPR-Meta, viralVerify, Plasmer, PlasClass, PlasX, VIBRANT, DeepVirFinder, HOTSPOT, and MOSTPLAS. MNBC-ME was the most consistent tool at classifying chromosomal, viral and plasmid reads of variable lengths, in contrast to the other tools whose precision or recall dropped below 50% in some circumstances. MNBC-ME also exceeded 65% and 70% performance in predicting host genus and family of plasmid reads, respectively.

CONCLUSIONS: MNBC-ME is tool for identification of both short and long viral- and plasmid-originated reads across a wide variety of read types. It also identifies potential low-level host taxa for plasmid reads, and source taxa for chromosomal and viral reads. It is freely available at https://github.com/ComputationalPathogens/MNBC-ME and can be found as the 'mnbc-me' package in bioconda.},
}

@article {pmid42265587,
year = {2026},
author = {Liang, X and Li, J and Liu, P and Lai, Z and Huang, S and Xie, F and Jin, W and Mao, S},
title = {Rumen ecological distribution of Pichia yeasts and their effects on rumen fermentation and microbial community.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05281-4},
pmid = {42265587},
issn = {1471-2180},
support = {32272896//The National Natural Science Foundation of China/ ; 32361143788//The National Natural Science Foundation of China/ ; QTPY2026017//The Fundamental Research Funds for the Central Universities/ ; },
abstract = {Yeast supplementation has been widely studied to enhance rumen fermentation and feed efficiency, yet developing efficient yeasts adapted to the rumen environment remains a challenge. In this study, two rumen-derived Pichia strains (Pichia membranifaciens M12 and Pichia kudriavzevii Y4) were evaluated using in vitro rumen fermentation experiments, including a control and three supplementation groups (2 × 10[5], 2 × 10[6], and 2 × 10[7] CFU/mL) for each strain. Results indicated that the two strains did not affect pH but significantly reduced concentrations of ammonium nitrogen (NH3-N) and microbial crude protein (MCP). At 24 h, NH3-N decreased by up to 13.3% and MCP by 18.5%, while at 48 h, NH3-N showed a reduction of up to 22.0% and MCP decreased by up to 5.7%. P. membranifaciens significantly increased the concentration of total volatile fatty acids by 15.4% and elevated the proportions of acetate and propionate at 48 h. Microbial community analysis revealed that these shifts in fermentation parameters were associated with an altered bacterial community structure. Specifically, P. membranifaciens enriched cellulolytic bacteria (Ruminococcus), while reducing amylolytic and proteolytic taxa (Prevotella), and promoted the propionate‑producer (Succiniclasticum). These findings suggested that P. membranifaciens has the potential to influence rumen microbiota. Further examination of the in vivo prevalence of Pichia yeasts species via ITS (n = 72; average parity 2.8 ± 1.1) revealed a lower prevalence and relative abundance for P. membranifaciens compared to P. kudriavzevii. Metagenomic analysis (n = 8; average parity 2.7 ± 0.9) detected both species at low abundances. Overall, this study indicated that rumen-derived Pichia yeasts have the capacity to modulate rumen fermentation, with P. membranifaciens warranting further in vivo evaluation.},
}

@article {pmid42265917,
year = {2026},
author = {Nakamura, K and Okazaki, A and Motooka, D and Matsumoto, N and Hasegawa, Y and Fukuda, S and Yabe, M and Sugiura, A and Yatsuka, Y and Fushimi, T and Onuki, T and Aida, Y and Ohtake, A and Murayama, K and Okazaki, Y},
title = {Nanopore-based haplotype-resolved X-chromosome inactivation analysis for clinical severity assessment in X-linked disorders: an AIFM1 family study with proof-of-concept application to a mosaic PDHA1 carrier.},
journal = {HGG advances},
volume = {},
number = {},
pages = {100632},
doi = {10.1016/j.xhgg.2026.100632},
pmid = {42265917},
issn = {2666-2477},
abstract = {X-chromosome inactivation (XCI) modifies disease severity in females with X-linked variants, but clinically applicable high-resolution assessment remains limited. We report a family with an AIFM1 variant showing marked intrafamilial phenotypic variability and evaluated whether haplotype-resolved nanopore sequencing can inform clinical interpretation. Targeted long-read sequencing was performed in a severely affected hemizygous male, his asymptomatic heterozygous mother, and a severely affected heterozygous sibling. In the hemizygous male, the sample served as a technical control, with all reads mapping to a single haplotype, consistent with a hemizygous X chromosome. Among heterozygous carriers with the identical variant (c.506C>T; p.Pro169Leu), XCI correlated with severity: the affected sibling showed 84% skew favoring activation of the pathogenic allele, whereas the mother showed preferential inactivation (20%). This family-based study shows that using nanopore sequencing for haplotype-resolved X-inactivation (XCI) analysis may provide a practical framework for selected X-linked disorders with variable expressivity.},
}

@article {pmid42266244,
year = {2026},
author = {Lin, X and Du, Y and Mai, H and Zhang, X},
title = {Voriconazole-Induced Agranulocytosis in a Cirrhotic Patient with Influenza-Associated Pulmonary Aspergillosis: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {607868},
pmid = {42266244},
issn = {1178-6973},
abstract = {The diagnosis and treatment of influenza-associated pulmonary aspergillosis (IAPA) present significant challenges, and voriconazole, as the first-line treatment for IAPA, rarely causes the serious adverse event of agranulocytosis. We first report a case of voriconazole-associated agranulocytosis in a patient with IAPA complicated by cirrhosis and systematically describe the complete process of diagnosis, treatment, and adverse event management. A 68-year-old male with a history of liver cirrhosis presented with cough, dyspnea, and fever. Testing confirmed influenza A, and chest computed tomography (CT) showed diffuse bilateral pulmonary inflammation. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and culture detected Aspergillus fumigatus, confirming the diagnosis of IAPA. The patient received voriconazole. On Day 20 of hospitalization, agranulocytosis developed and resolved after voriconazole discontinuation and granulocyte colony-stimulating factor (G-CSF) administration, consistent with voriconazole-associated agranulocytosis. After neutrophil recovery, voriconazole was resumed with leukocyte support and close monitoring of complete blood counts (CBC) and drug levels. At one-month follow-up, no recurrence of infection or agranulocytosis was observed. This case emphasizes the value of mNGS in timely diagnosis of IAPA, underscores the importance of closely monitoring CBC in such patients during triazole antifungal therapy, and proves the feasibility of resuming antifungal treatment-including the cautious re-administration of the initially sensitizing agent under strict monitoring-after the correction of agranulocytosis. These findings contribute to a better understanding of the disease and may help to optimize its clinical management.},
}

@article {pmid42266457,
year = {2026},
author = {Stach, TL and Deep, A and Madge Pimentel, I and Buchner, D and Borton, MA and Soares, AR and Starke, J and Bornemann, TLV and Rehsen, PM and Dreger, KL and Boenigk, J and Vos, M and Leese, F and Beisser, D and Probst, AJ},
title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf079},
pmid = {42266457},
issn = {2730-6151},
abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g. upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.},
}

@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.},
}