@article {pmid40542918,
year = {2026},
author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y},
title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.},
journal = {Science China. Life sciences},
volume = {69},
number = {6},
pages = {1896-1909},
pmid = {40542918},
issn = {1869-1889},
mesh = {*Gene Expression Profiling/methods ; *Transcriptome/genetics ; Fungi/genetics/classification ; *Metagenomics/methods ; Cluster Analysis ; *Eukaryota/genetics ; Clustering Algorithms ; *Software ; High-Throughput Nucleotide Sequencing ; Soil Microbiology ; },
abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.},
}

*Gene Expression Profiling/methods
*Transcriptome/genetics
Fungi/genetics/classification
*Metagenomics/methods
Cluster Analysis
*Eukaryota/genetics
Clustering Algorithms
*Software
High-Throughput Nucleotide Sequencing
Soil Microbiology

@article {pmid41680419,
year = {2026},
author = {Pedrazzini, C and Funari, R and Cucini, C and Nardi, F and Grabenweger, G and Widmer, F and Enkerli, J},
title = {Population genomics identifies Italian and North American origins of Popillia japonica in Switzerland.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41680419},
issn = {2045-2322},
support = {No. 861852//European Union's Horizon 2020/ ; },
mesh = {Animals ; Switzerland ; *Coleoptera/genetics/classification ; Phylogeny ; North America ; Introduced Species ; Italy ; Genetics, Population ; *Metagenomics/methods ; Genomics ; },
abstract = {The Japanese beetle (Popillia japonica), native to Japan, is a major invasive species in North America and Europe. Its colonization of Europe began on the Azores (1970s), followed by Italy (2014) and southern Switzerland (2017). In 2023, the presence of the pest was reported in three areas of Switzerland: Kloten (Canton of Zürich, north-eastern Switzerland), Basel (Canton of Basel-Landschaft, northern Switzerland), and in eastern Canton of Valais (South Switzerland) near the Italian border. In 2024, P. japonica individuals were discovered in several other Swiss Cantons. To trace P. japonica spread and origins in Switzerland, we investigated 42 individuals from infested areas, comprising scattered findings across Switzerland. Phylogenetic and population structure analyses using whole-genome resequencing, including data of previously sequenced samples from Japan, North America, the Azores, Italy, and Southern Switzerland, revealed distinct P. japonica migration patterns. Populations in Basel, Valais, and central Switzerland likely originated from Ticino/Northern Italy via road or rail transport. Conversely, the population near Zürich Airport was identified as an independent introduction from North America, likely through unintentional air transport. These findings offer insights into P. japonica spread across Switzerland, highlighting the need for enhanced monitoring and identification of invasion pathways.},
}

Animals
Switzerland
*Coleoptera/genetics/classification
Phylogeny
North America
Introduced Species
Italy
Genetics, Population
*Metagenomics/methods
Genomics

@article {pmid42045813,
year = {2026},
author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , },
title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42045813},
issn = {1471-2180},
abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome.

METHODS: Fecal samples from 16 Crohn’s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy.

RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the “pyrazinamide resistant rpsA” gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan).

CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05101-9.},
}

@article {pmid42266956,
year = {2026},
author = {Lu, J and Zhong, J and Qiu, W and Zhang, Q},
title = {Intrathecal combined with intravenous eravacycline for the treatment of multisite carbapenem-resistant Acinetobacter baumannii infections (intracranial, pulmonary, and bloodstream) in a post-trauma adolescent female: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1829527},
pmid = {42266956},
issn = {2296-858X},
abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a leading cause of hospital-acquired infection among critically ill patients, with extremely limited therapeutic options, particularly for central nervous system (CNS) infections. Eravacyline, a novel fully synthetic fluorocycline, demonstrates potent in vitro activity against CRAB but exhibits poor penetration across the blood-brain barrier (BBB).

CASE PRESENTATION: A 17-years-old female with severe traumatic brain injury developed concurrent intracranial, pulmonary, and bloodstream CRAB infections. Initial systemic antimicrobial therapy, including intravenous colistin and eravacycline, failed to control the intracranial infection. After switching to a regimen incorporating intrathecal eravacycline (initial dose 2 mg, followed by 5 mg daily) combined with high-dose intravenous cefoperazone-sulbactam and nebulized colistin, the patient showed rapid clinical and microbiological improvement. Serial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) revealed a dramatic reduction in pathogen load, with eventual eradication of CRAB.

CONCLUSION: This case highlights the potential role of intrathecal eravacycline as a salvage therapy for CRAB meningitis, particularly in cases of multifocal, extensively drug-resistant infection. Further pharmacokinetic and safety studies are warranted to optimize its use in CNS infections.},
}

@article {pmid42267106,
year = {2026},
author = {Wu, Y and Gao, Q and Yang, H and Wang, Y and Lang, L and Liu, B and Jiang, X and Li, D and Wang, X and Xun, J and Zhang, Q},
title = {Multi-omics analysis identifies gut microbiota-glutamine axis contributing to the pathogenesis of reflux esophagitis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805181},
pmid = {42267106},
issn = {1664-302X},
abstract = {BACKGROUND: Reflux esophagitis (RE), a common gastroesophageal reflux disease characterized by esophageal mucosal inflammation, is closely associated with gut microbiota dysbiosis and metabolic abnormalities. The glutamine-glutamate metabolic pathway regulates inflammation and mucosal barrier function, but its role in RE and association with gut microbiota remain unclear. This study aimed to characterize gut microbiota and serum metabolites in RE patients via integrated multi-omics (focusing on the gut microbiota-glutamine axis), and verify the activation status of this pathway in RE inflammatory models and the anti-inflammatory effect of its targeted inhibition.

METHODS: RE patients and healthy controls (HCs) were enrolled. Fecal metagenomic sequencing and serum untargeted metabolomics (LC-MS/MS) were performed to identify differential gut microbiota and serum metabolites between the two groups, followed by Pearson correlation analysis to explore their associations. In vitro experiments were conducted on human esophageal epithelial cells (HEECs) divided into four groups: normal, inflammatory, glutamine-supplemented, and inflammatory + glutamine + glutaminase inhibitor (BPTES) groups. qPCR was used to detect the mRNA expression of glutamine-glutamate pathway molecules (GLS, c-Myc, SLC1A5), mucosal barrier markers (ZO-1, Occludin), and pro-inflammatory cytokines (IL-8, IL-6, IL-1β, TNF-α). Intracellular concentrations of glutamine, glutamate, and α-ketoglutarate were measured, and the anti-inflammatory effect of BPTES was verified.

RESULTS: RE patients showed significant differences in gut microbiota diversity and composition compared with HCs, with Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae as dominant taxa. Serum metabolomics revealed elevated glutamine and glutamate in RE patients, which were identified as key differential metabolites related to RE pathogenesis. Pearson analysis revealed that alterations in serum metabolite profiles of RE patients were significantly correlated with changes in gut bacterial abundance. Notably, glutamate-glutamate (Glu-Glu) metabolism exhibited negative correlations with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). In vitro, inflammatory HEECs exhibited increased intracellular glutamine, glutamate, and α-ketoglutarate, upregulated glutamine-glutamate pathway molecules and pro-inflammatory cytokines, and downregulated mucosal barrier markers. Exogenous glutamine alone failed to alleviate inflammation, while combined with BPTES significantly reversed pathway activation and mitigated inflammation in inflammatory HEECs.

CONCLUSION: RE patients exhibit significant gut microbiota dysbiosis (dominated by Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae) and abnormal glutamine metabolism (elevated serum glutamine and glutamate). Pearson analysis reveals that the glutamine-glutamate pathway correlates negatively with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). The glutamine-glutamate pathway is activated in inflammatory esophageal epithelial cells, and targeted GLS inhibition by BPTES reverses pathway activation and mitigates inflammation. These findings highlight the gut microbiota-glutamine axis as potential diagnostic biomarkers and therapeutic targets for RE, providing new insights into pathogenesis and a basis for novel clinical interventions.},
}

@article {pmid42267107,
year = {2026},
author = {Mathyk, BA and Shukla, R and Kumar, V and Mishra, SP and Pandya, S and Patten, N and Gerardi, K and Beatty, HW and Persad, AH and Imudia, AN and Yadav, H and Jain, S},
title = {Parabolic flight induces site specific microbiome changes in women.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1817099},
pmid = {42267107},
issn = {1664-302X},
abstract = {INTRODUCTION: The vaginal microbiome plays a central role in women's health by supporting immune function, maintaining mucosal homeostasis, and preventing infections. Spaceflight and its analogs can induce acute physiological stress, which can alter host microbiome interactions. While other studies have analyzed the microbiome changes at certain body sites, the female-specific microbiome changes have not been explored in depth in space medicine research.

METHODS: Pre- and post-parabolic flight vaginal and oral microbiome were analyzed via metagenomic shotgun sequencing to assess taxonomic composition and metabolic pathways. Host DNA and bad quality sequences were removed using the KneadData tool. Taxonomic and functional profiles were analyzed with MetaPhlAn and HUMAnN. Microbiome data were integrated with stress response parameters including cortisol, proinflammatory cytokines, and urinary short-chain fatty acids.

RESULTS: Both alpha- and beta diversity analysis showed minimal impact of parabolic flight on oral microbiome while vaginal microbiome showed significant differences. Taxonomic profiling showed marked restructuring of the vaginal microbiome, characterized by increased Firmicutes dominance and enrichment of Lactobacillus species, particularly Lactobacillus crispatus and Lactobacillus jensenii, whereas oral microbiome stayed relatively stable. Overall, only 2.54% of oral species showed significant postflight changes compared to 57.9% of vaginal species (p < 0.0001). Random Forest model identified L. crispatus as a key discriminator of postflight vaginal microbiome composition. Metabolic pathway analysis revealed minimal postflight pathway redistribution in saliva samples but greater number of changes in the vaginal microbiome, with significant postflight enrichment of fatty acid biosynthesis and nucleotide metabolism. Vaginal samples demonstrated a threefold greater proportion of altered metabolic pathways compared to oral samples. In addition, urinary acetate, butyrate, and valeric acid levels were significantly reduced postflight. Salivary cortisol increased postflight and positively correlated with L. jensenii.

CONCLUSION: Parabolic flight induces body site-specific microbiome changes in reproductive age women, with greater taxonomic and functional metabolic remodeling in the vaginal microbiome than in the oral microbiome. These findings highlight the sensitivity of the vaginal microbial ecosystem to spaceflight stressors and underscore the need for longitudinal and mechanistic studies to determine the persistence, clinical significance, and potential health implications of these changes during longer duration space missions.},
}

@article {pmid42267128,
year = {2026},
author = {Daurova, A and Daurov, D and Sapakhova, Z and Kanat, R and Abilda, Z and Toishimanov, M and Isgandarov, I and Mukhametov, A and Volkov, D and Shamekova, M and Zhambakin, K},
title = {Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1832403},
pmid = {42267128},
issn = {1664-462X},
abstract = {Abiotic stresses, such as drought, salinity, extreme temperatures, nutrient deficiencies, and heavy metal contamination, severely limit oilseed crop productivity under accelerating climate change. This review synthesizes recent advances in understanding the critical role of soil and plant-associated microbiomes in conferring stress tolerance to major oilseed species, including rapeseed (Brassica napus), sunflower (Helianthus annuus), soybean (Glycine max), and sesame (Sesamum indicum). Beneficial microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and endophytes, enhance plant tolerance through an integrated network of biochemical, physiological, and molecular mechanisms. Biochemically, they modulate phytohormone levels (e.g., IAA and ABA), produce osmoprotectants, and regulate antioxidant systems (e.g., SOD, CAT, POD) to mitigate oxidative damage. Physiologically, these processes contribute to improved root architecture, water-use efficiency, nutrient acquisition, and ion homeostasis under stress conditions. At the molecular level, microorganisms influence gene expression and signaling pathways associated with stress responses, including activation of stress-responsive genes and metabolic adjustments. These interconnected mechanisms collectively strengthen plant resilience by coordinating metabolic regulation, cellular protection, and adaptive responses within the plant-microbiome system. Agroecological practices (soil type, crop rotation, tillage, fertilization) strongly shape microbial community assembly and functional potential, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) reveal stress-driven restructuring and adaptive metabolic shifts in the rhizosphere. Emerging tools such as synthetic microbial consortia (SynComs) and targeted microbiome engineering offer promising, sustainable alternatives to conventional breeding and chemical interventions, enhancing soil health, nutrient cycling, and agroecosystem resilience with reduced environmental footprint. This review presents a comprehensive synthesis with a specific focus on oilseed crops, integrating current knowledge on microbiome dynamics under multiple abiotic stress conditions-an area that remains comparatively underrepresented in the literature. It examines key microbial groups driving adaptation, evaluates omics-based insights into plant-microbiome interactions, identifies critical research gaps, and outlines future directions for microbial inoculants and climate-resilient oilseed production systems.},
}

@article {pmid42267141,
year = {2026},
author = {Hardies, SC and Park, J and Cho, BC and Hwang, CY},
title = {Alishewanella Phage LSH1 from the Sea Surface Microlayer Provides a Novel Minimalistic View of the Siphoviral Hub Structure.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0131},
pmid = {42267141},
issn = {2001-0370},
abstract = {LSH1 is a novel lytic siphovirus isolated, together with its host in the genus Alishewanella, from the surface microlayer of a brackish tidal reservoir in South Korea and characterized with respect to growth properties, genome sequence, gene annotation, mass spectrometry, and electron microscopy. Sequence analysis shows that LSH1 shares only distant similarity to other cultured phages, although a closer metagenomic neighborhood can be defined. LSH1 represents the first isolate from a large, previously unsampled family-level sector of the viral tree. Transmission electron microscopy revealed a tail end distinct from the best structurally characterized siphoviral prototypes and similar in appearance to Salmonella phage Jersey, the prototype of a large structurally uncharacterized group named Guernseyvirinae. Therefore, Jersey was included in the comparative analysis with LSH1. A combination of hidden Markov model comparisons and AlphaFold reconstruction was used to clarify the structural relationships of these phages. Both have structural homologs of portions of the canonical bacteriophage lambda tail hub but lack the lambda components associated with receptor recognition linked to ejection triggering in that system. The LSH1 and Jersey tail hubs are of different sequence lineages, but each represents a relatively minimalistic version of the siphoviral tail hub, with distinct candidates for the structural location of their antireceptors. This study explores the capability of AlphaFold to rapidly augment the relatively few structurally characterized phages with models for diverse variants, fleshing out how much variation there is and perhaps leading to a better treatment of how this variation is evolving.},
}

@article {pmid42267567,
year = {2026},
author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL},
title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.},
journal = {Zoological research},
volume = {47},
number = {3},
pages = {827-842},
doi = {10.24272/j.issn.2095-8137.2025.141},
pmid = {42267567},
issn = {2095-8137},
abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.},
}

@article {pmid42267811,
year = {2026},
author = {Gołębiowska, J and Woodhouse, JN and Tobias-Hünefeldt, SP and Grossart, H-P},
title = {Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0080726},
doi = {10.1128/aem.00807-26},
pmid = {42267811},
issn = {1098-5336},
abstract = {UNLABELLED: Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web.

IMPORTANCE: Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.},
}

@article {pmid42267859,
year = {2026},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70307},
pmid = {42267859},
issn = {2045-8827},
support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; },
abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.},
}

@article {pmid42268526,
year = {2026},
author = {Mohit, and Verma, S and Yadav, A and Venkatesh, V},
title = {Multi-omics insights into immunometabolic dysregulation in neonatal sepsis for precision medicine.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42268526},
issn = {1573-4978},
abstract = {Neonatal sepsis remains a major global health challenge, contributing substantially to morbidity and mortality despite many advances. Conventional diagnostics often fail to capture the disease complexity and immune dysregulation, leading to delayed diagnosis and sub-optimal treatment. Recent advances in multiomics, including genomics, transcriptomics, proteomics, metabolomics and metagenomics are transforming molecular understanding by enabling a precise view of host-pathogen interactions. These approaches also provide critical insights into metainflammation, a state of chronic, low-grade immune and metabolic dysregulation, playing a pivotal role in neonatal immune vulnerability. Integrating multi-omics with meta-inflammatory profiling may support future risk stratification, biomarker discovery, and precision-oriented neonatal sepsis care. However, clinical translation requires further validation, platform standardization, and feasibility assessment in NICU settings. Such insights may establish the foundation of P4 medicine by emphasizing prediction, prevention, personalisation, and participation in neonatal care. Multi-omics integration may support endotype identification, and data-driven clinical communication after adequate validation. Overall, this review highlights how multiomics and metainflammation driven frameworks may improve mechanistic understanding of neonatal sepsis and guide future development of clinically feasible precision-medicine approaches.},
}

@article {pmid42268876,
year = {2026},
author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR},
title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351562},
doi = {10.1371/journal.pone.0351562},
pmid = {42268876},
issn = {1932-6203},
abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.

METHODS: BAL specimens from healthy control volunteers (n = 20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n = 52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).

RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p < 0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p = 0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q < 0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.

CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.},
}

@article {pmid42269300,
year = {2026},
author = {Lo, HY and Hsiao, YT and Wu, YJ and Whang, LM and Chen, WH and Tung, HH},
title = {Persistence and dynamics of antibiotic resistome in a drinking water supply system with booster chlorination.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142622},
doi = {10.1016/j.jhazmat.2026.142622},
pmid = {42269300},
issn = {1873-3336},
abstract = {Due to the extensive use of antibiotics worldwide, the prevalence of antibiotic resistance genes (ARGs) in aquatic environments has become a major public health concern. This study investigated the ARGs in a drinking water supply system, with particular emphasis on booster chlorination in the distribution network. To elucidate the dynamics of the antibiotic resistome, environmental DNA was extracted from water collected from five different sections, and the resistome profiles were subsequently reconstructed with metagenome assembly. Our findings revealed that 35 core ARGs persisted but decreased in concentration during water treatment and early distribution, with genes resistant to bacitracin, multidrug, and rifamycin being the most prominent. However, a notable surge of ARGs was observed at the terminal distribution segment. This increase was linked to changes in the resistome structure, which were primarily associated with shifts in the microbial community and, within the DWDS specifically, also linked to horizontal transfer mediated by mobile genetic elements (MGEs) under chlorine stress from booster chlorination. Microbial communities within the drinking water distribution system (DWDS) shifted distinctly from those in the water treatment plant. Under re-chlorination pressure, the chlorine-tolerant Mycobacteriales and the biofilm-forming Hyphomicrobiales and Rhodobacterales became the predominant taxa. Additionally, metagenome-assembled genomes (MAGs) reconstruction further identified that Hyphomicrobium and Mycobacterium were the main ARG carriers in the DWDS, with the latter as the main putative host for the core ARGs. Overall, this study demonstrated that booster chlorination in the water distribution system while controlling microbial regrowth, may simultaneously facilitate ARG dissemination. These findings highlight the need to optimise re-chlorination practices to balance microbial growth control while minimising ARG proliferation in DWDS.},
}

@article {pmid42269354,
year = {2026},
author = {Petersen, J and Ringel, V and Päuker, O and Frühling, A and Rohde, M and Jarek, M and Spröer, C and Bunk, B and Huber-Fischer, K and Pradella, S and Freese, HM and Koblitz, J and Neumann-Schaal, M and Brinkmann, H},
title = {Think pink 2.0 - Description of Roseobacter cerffii sp. nov., isolated from the chromerid alga Vitrella brassicaformis, and reclassification of Sulfitobacter sabulilitoris as Billmartinia sabulilitoris, gen. nov., comb. nov.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126731},
doi = {10.1016/j.syapm.2026.126731},
pmid = {42269354},
issn = {1618-0984},
abstract = {A Gram-stain-negative, aerobic, pink-pigmented bacterial strain A03A-229[T] was isolated from a non-axenic culture of the chromerid alga Vitrella brassicaformis CCMP3155, which originates from the Great Barrier Reef in Australia. Complete genome sequencing revealed the presence of seven circular replicons, representing one chromosome, two chromids and four plasmids. The 142-kb DnaA-like I chromid, which contains the photosynthesis gene cluster (PGC), traces of ubiquinone-11 and the ability to reduce nitrate are diagnostic for A03A-229[T]. Genomic, physiological, and chemotaxonomic data provided clear evidence that strain A03A-229[T] (= DSM 112523[T] = CECT 31310[T]) represents a new species of the genus Roseobacter, for which the name Roseobacter cerffii sp. nov. is proposed. R. cerffii A03A-229[T] represents the tenth described species of the genus Roseobacter, but phylogenetic (meta-)genome analyses indicated the presence of at least 27 different species. Reconstruction of the metabolic pathways of the genus Roseobacter revealed a highly conserved metabolism with lineage specific adaptations for the formation of compatible solutes and a surprising abundance of four GAPDH genes. The ability to perform aerobic anoxygenic photosynthesis, which is mediated by the PGC, is responsible for the eponymous pink color of this genus, while it only occurs scattered in the sister genus Sulfitobacter. Our phylogenomic analyses provided clear evidence for a distinct taxonomic status of strain Sulfitobacter sabulilitoris HSMS-29[T] (= KACC 19870[T] = NBRC 113549[T]). Based on its phylogenetic position, low average amino-acid identities (AAI) and a PufC-type PGC, we propose the reclassification of this strain as Billmartinia sabulilitoris gen. nov., comb. nov.},
}

@article {pmid42269462,
year = {2026},
author = {Riveros, A and Kwon, H and Impellitteri, CA and Jiang, D},
title = {Nitrate reshapes electron partitioning and Se[0] formation during continuous electro-microbial treatment of mixed selenium oxyanions.},
journal = {Water research},
volume = {303},
number = {},
pages = {126244},
doi = {10.1016/j.watres.2026.126244},
pmid = {42269462},
issn = {1879-2448},
abstract = {Selenium in flue-gas-desulfurization (FGD) wastewater occurs as mixed selenate and selenite oxyanions, and requires both aqueous removal and reduction to elemental selenium to prevent secondary waste generation. Here, we introduce a continuous-flow electro-microbial platform that couples flow-electrode capacitive deionization (FCDI) with bio-electrochemical systems (BES) to achieve voltage-driven removal and bio-mediated reduction within a compact reactor configuration. During 41 days of operation treating mixed selenium oxyanions (10 mg Se L[-1] each) in fortified water samples with FGD-relevant nitrate concentrations (20 mg L[-1]), the system achieved removal efficiencies of 84-95% for selenite and 54-78% for selenate. Nitrate unexpectedly enhanced apparent elemental selenium yield from 70% to 99% under 2 V, but decreased selenium-specific Faradaic efficiency from 20% to 8%, likely due to a combination of electron flux diversion and co-respiration between nitrogen and selenium oxyanions. Metagenomics suggested that genes associated with indirect selenium transformation (cysIJ, trxA/B, gshA/B, and ybbN) were 45-115x more abundant than genes encoding dedicated selenate reductases. Together, these results demonstrate FCDI-BES as a promising platform for treating selenium and potentially other redox-active oxyanions and highlight the importance of studying electron-acceptor competition in similar systems.},
}

@article {pmid42269501,
year = {2026},
author = {Ghose, M and Parab, AS and Manohar, CS},
title = {Metagenome-based analysis of xenobiotic degradation potential in urban mangrove sediments under chronic anthropogenic impact.},
journal = {Marine pollution bulletin},
volume = {231},
number = {},
pages = {119970},
doi = {10.1016/j.marpolbul.2026.119970},
pmid = {42269501},
issn = {1879-3363},
abstract = {Urban mangrove sediments receive continuous inputs of industrial and domestic pollutants, yet the microbial basis of pollutant transformation in these chronically impacted systems remains insufficiently resolved. This study investigated xenobiotic degradation potential in sediments from two urban mangrove locations along the Mandovi estuary, Goa, India, through reanalysis of previously generated shotgun metagenomic data. The assembled metagenomes showed enrichment of degradation pathways associated with aromatic and aliphatic pollutants commonly linked to urban contamination. A high representation of oxidoreductases and related aromatic transformation functions indicated that xenobiotic processing is closely linked to redox regulation and central carbon metabolism. Pathway completeness did not consistently correspond with relative abundance, suggesting that lower-abundance pathways may still retain structurally coherent degradation capacity. Hydrocarbon-specific annotation revealed the coexistence of aerobic and anaerobic activation strategies, consistent with adaptation to the redox heterogeneity of mangrove sediments. Xenobiotic- and hydrocarbon-associated functions were linked mainly to Pseudomonadota, Actinomycetota, Shewanella, and a substantial fraction of unresolved bacterial lineages, indicating that undercharacterized taxa may contribute importantly to pollutant-processing potential. Supportive metagenome-assembled genome analysis showed that recovered genomes encoded complementary subsets of degradation functions, although these genomes should be treated as illustrative examples rather than representatives of the whole community. Comparison between locations revealed similar core degradation functions but variation in secondary pathways, likely reflecting differences in local pollutant inputs and sediment conditions. These results show that urban mangrove microbiomes retain a functionally structured and redox-adapted metagenomic repertoire for xenobiotic and hydrocarbon degradation, highlighting their relevance to pollutant transformation, environmental monitoring, and native community-based bioremediation.},
}

@article {pmid42269618,
year = {2026},
author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M},
title = {Variations in the latitudinal diversity gradients of the ocean microbiome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.016},
pmid = {42269618},
issn = {1934-6069},
abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.},
}

@article {pmid42269619,
year = {2026},
author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y},
title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.009},
pmid = {42269619},
issn = {1934-6069},
abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.},
}

@article {pmid42269751,
year = {2026},
author = {Sun, X and Li, S and Liang, J and Wang, C and Bai, Y and Mao, J and Qu, J},
title = {From Correlation to Causality: Identifying Potential Environmental Drivers of Pathogenic Antibiotic-Resistant Bacteria in River Water Using Causal Machine Learning.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128570},
doi = {10.1016/j.envpol.2026.128570},
pmid = {42269751},
issn = {1873-6424},
abstract = {Pathogenic antibiotic-resistant bacteria (PARB) pose a serious public health threat within the One Health framework, yet identifying their potential environmental drivers in complex aquatic systems remains a challenge. This study systematically compared correlation analysis, explainable machine learning, and causal machine learning within a unified framework. Both Spearman correlation and explainable machine learning identified numerous potentially important factors, notably non-antibiotic pharmaceuticals such as carbamazepine and bezafibrate. However, causal inference via double machine learning, which controls for confounders and interaction effects, revealed a distinctly different driver profile. Under predefined assumptions, this approach estimated potential causal effects for dissolved oxygen, the nitrate-to-ammonium ratio, specific antibiotics (roxithromycin, azithromycin), and non-antibiotic compounds (acenaphthene, 2-chloroanthracene). Taxon-specific analysis further showed that Aeromonas aligned closely with the overall PARB causal profile, whereas Pseudomonas responded primarily to oxidation-reduction potential. Functional profiles suggested potential stress-adaptation mechanisms related to signal transduction and metabolic regulation pathways. By shifting from associative prediction to causal inference, this causal machine learning-guided framework provides a robust analytical basis for identifying environmental drivers and informing targeted management of PARB risks in aquatic ecosystems.},
}

@article {pmid42270066,
year = {2026},
author = {Shi, H and Wang, L and Wu, Y and Cai, B},
title = {Synergistic mechanisms by which arbuscular mycorrhizal fungi regulate hyphosphere bacterial communities and functional genes to suppress potential N2O production under tetracycline stress.},
journal = {Environmental research},
volume = {305},
number = {Pt 2},
pages = {125020},
doi = {10.1016/j.envres.2026.125020},
pmid = {42270066},
issn = {1096-0953},
abstract = {Tetracycline (TC), a widely used veterinary antibiotic, frequently accumulates in agricultural soils and disrupts nitrogen (N) cycling, thereby enhancing nitrous oxide (N2O) emissions. However, biologically based mitigation strategies and their underlying mechanisms remain poorly understood. In this study, a soybean pot experiment was conducted with four treatments: control, arbuscular mycorrhizal fungi (AMF) inoculation, TC addition, and AMF combined with TC. By integrating hyphosphere-specific sampling, potential N2O production rate measurements, 16S rRNA gene sequencing, quantitative PCR, metagenomics, and partial least squares path modeling, we systematically elucidated AMF-mediated regulation of N2O production under TC stress. TC significantly increased potential N2O production rate (+21.2%), primarily by selectively suppressing the terminal denitrification step, as evidenced by reduced nitrous oxide reductase (NOS) activity and decreased abundance of the nosZ gene, resulting in denitrification pathway disruption and N2O accumulation. In contrast, AMF inoculation under TC stress reduced potential N2O production rate by 29.5%, restoring it to control levels. Mechanistically, AMF improved hyphosphere soil properties (e.g., increased SOC and TN and enhanced TC dissipation) and selectively enriched functionally competent and TC-tolerant denitrifiers, particularly nosZ-harboring taxa such as Streptomyces, thereby repairing denitrification pathway completeness. Path modeling further demonstrated that AMF mitigated N2O production both directly by enhancing N-cycling microbial functional capacity and indirectly by optimizing soil physicochemical conditions. Our findings reveal the microbial and molecular mechanisms underlying antibiotic-enhanced N2O emissions and highlight AMF as a low-input, nature-based environmental biotechnology strategy to simultaneously remediate antibiotic-contaminated soils and mitigate agricultural greenhouse gas emissions.},
}

@article {pmid42270094,
year = {2026},
author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B},
title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261460118},
doi = {10.1177/10732748261460118},
pmid = {42270094},
issn = {1526-2359},
abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.},
}

@article {pmid42270219,
year = {2026},
author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y},
title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119489},
doi = {10.1016/j.foodres.2026.119489},
pmid = {42270219},
issn = {1873-7145},
abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.},
}

@article {pmid42270261,
year = {2026},
author = {Vandana, and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP},
title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119548},
doi = {10.1016/j.foodres.2026.119548},
pmid = {42270261},
issn = {1873-7145},
abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.},
}

@article {pmid42270391,
year = {2026},
author = {Nakaya, Y and Hashimoto, K and Fukushima, K and Fatimah, M and Matsumoto, Y and Funauchi, A and Tsukaguchi, A and Yamauchi, K and Miyazaki, A and Iwahashi, Y and Tone, M and Naito, M and Shiroyama, T and Hirata, H and Takeda, Y and Nakamura, S and Kumanogoh, A},
title = {Mycobacterium brisbanense Pulmonary Disease Treated with a Macrolide-Based Multidrug Regimen: A Case Report.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
doi = {10.2169/internalmedicine.7351-26},
pmid = {42270391},
issn = {1349-7235},
abstract = {A 73-year-old woman with a history of tracheostomy for tracheomalacia and bronchiectasis developed a worsening productive cough with progressive nodular/bronchocentric opacities on computed tomography. She was diagnosed with Mycobacterium brisbanense pulmonary disease based on repeated sputum culture results. Antimicrobial susceptibility testing revealed a low minimum inhibitory concentration for clarithromycin, and whole-genome sequencing confirmed the absence of the erm gene. Owing to repeated smear positivity and clinical progression, macrolide-based multidrug therapy was initiated, resulting in both clinical and radiographic improvements. To our knowledge, this is the first reported case of M. brisbanense pulmonary disease in Japan, thus highlighting its potential pathogenicity.},
}

@article {pmid42270613,
year = {2026},
author = {Deng, C and Cai, H and Luo, K and Liu, S and Chen, Q and Sun, W and Ni, J},
title = {Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74161-2},
pmid = {42270613},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.},
}

@article {pmid42270686,
year = {2026},
author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ},
title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53382-x},
pmid = {42270686},
issn = {2045-2322},
abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.},
}

@article {pmid42271018,
year = {2026},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10447-x},
pmid = {42271018},
issn = {2399-3642},
support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; },
abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.},
}

@article {pmid42271211,
year = {2026},
author = {Ying, K and Song, X and Chen, J and Wang, Y and Wu, H and Zhang, Q and Yang, X and Peng, W and Wu, H and Zhang, W and Zhang, Q},
title = {Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05231-0},
pmid = {42271211},
issn = {1471-2180},
support = {2024-SF-124//the Key research and development and transformation plan of Qinghai Province/ ; 2023YFD1801300//the National Key Research and Development Program of China/ ; },
abstract = {The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.},
}

@article {pmid42271238,
year = {2026},
author = {Bi, JG and Wang, YH and Li, PK and Liu, Q and Zheng, X},
title = {Metagenomic insights into regional gut microbiota variation of invasive Spodoptera frugiperda across the Gaoligong Mountains.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05259-2},
pmid = {42271238},
issn = {1471-2180},
support = {202102AA310055//the Supported by the Major Science and Technique Programs of Yunnan Province/ ; YNWRQNBJ2020101//the Young Top Talents of the High-level Talents Training Support Program in Yunnan Province/ ; 202305AM340031//the Lower Nu River, Mountain Agroecosystem, Observation and Research Station of Yunnan Province/ ; 2026J1054//the Yunnan Provincial Department of Education Science Research Fund Project/ ; },
abstract = {BACKGROUND: The invasive pest Spodoptera frugiperda poses a potential threat to the ecological security of western Yunnan, using the Gaoligong Mountains as an important cross-border corridor and overwintering site. However, the potential role of gut microbiota in the local adaptation of S. frugiperda during its invasion remains poorly understood.

METHODS: Adult populations were monitored using sex pheromone traps, and metagenomic sequencing was performed on larval gut microbiota from different regions of the Gaoligong Mountains. The gut microbial composition and functional potential were analyzed, with specific focus on the microbial traits potentially associated with host adaptation and invasion.

RESULTS: S. frugiperda populations persisted year-round in the Gaoligong Mountains, with adult activity peaking from January to May. Microbial diversity was highest in southern samples. Enterococcus, typically dominant in S. frugiperda, displayed low abundance in the central and northern regions. In contrast, Providencia emerged as the dominant genus specifically at the Pianma site (PM, along the China-Myanmar border), where the gut microbiota exhibited higher abundance of site-specific functional genes compared to other regions. These genes encoded proteins including type 1 subunit membrane proteins and outer membrane-targeting proteins. Additionally, the PM samples showed a higher relative abundance of genes K07345, K07347, and K15125. Functional annotation highlighted a strong potential for vancomycin degradation and an enrichment of diverse antimicrobial resistance-associated genes, with adeL being the most abundant.

CONCLUSIONS: These findings suggest that the PM area may represent an important gateway or a priority monitoring site for the transboundary invasion of S. frugiperda, underscoring the urgency of strengthening local management of invasive pests.},
}

@article {pmid42271362,
year = {2026},
author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D},
title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08403-8},
pmid = {42271362},
issn = {1479-5876},
support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.

METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.

RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.

CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.},
}

@article {pmid42271421,
year = {2026},
author = {Stanford, J and Supple, H and Collins, CE and Clarke, ED},
title = {Associations between diet, metabolome, gut microbiota and blood pressure in Australian adults.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01336-4},
pmid = {42271421},
issn = {1475-2891},
abstract = {PURPOSE: Early metabolomic and microbial markers of blood pressure (BP) dysregulation may be detectable before clinical hypertension develops. This exploratory study aimed to examine associations among dietary intake, BP, metabolomic profiles (plasma and urine), and gut microbiota composition. A secondary aim was to assess whether circulating metabolites mediate relationships between significant dietary factors and BP.

METHOD: This was a cross-sectional analysis of baseline data from a randomised cross-over trial. Usual dietary intake was assessed using the Australian Eating Survey (AES)[®] - Heart version Food Frequency Questionnaire. In-clinic BP measurements were measured and participants provided plasma, urine, and stool samples. Plasma and urine were analysed via untargeted metabolomics. Stool samples were collected for shotgun metagenomic sequencing, though metagenomic data was not included in this analysis. Associations between BP, individual metabolites, microbial taxa, and alpha diversity were assessed using linear regression with false discovery rate (FDR) correction. Causal mediation analysis was performed using nonparametric bootstrapping.

RESULT: Thirty-four Australian adults (mean age: 38.4 ± 18.1 years; 52.9% female) had complete data at baseline. Nut intake (servings/day and % energy) was the only dietary factor significantly associated with systolic BP (SBP), with higher intake linked to a 1.13 mmHg reduction. Twenty-nine plasma lipid metabolites were significantly associated with SBP after FDR correction. Of these, nine lipid-related metabolites, particularly 1,2-dilinoleoyl-GPC (18:2/18:2) and 1-linoleoyl-GPC (18:2), were observed to partially mediate the nut-SBP relationship. No urinary metabolites or microbial taxa were significantly associated with BP.

CONCLUSIONS: In this exploratory cross-sectional study, specific lipid metabolites were associated with SBP and partly accounted for the nut-SBP association. These hypothesis-generating findings suggest potential biomarkers of nut intake and BP regulation, warranting confirmation in larger longitudinal, interventional, and mechanistic studies.

TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (Registration number ACTRN12622001321730, Registration date 12/10/2022).},
}

@article {pmid42271469,
year = {2026},
author = {Xing, J and Jiang, Z and Jing, X and Li, Y and Guo, F and Liu, P and Liu, Z and Sun, N},
title = {Analysis of gut microbiota and intestinal mucosal neurotransmitter changes and their correlation in adolescent depression mice.},
journal = {Annals of general psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12991-026-00686-x},
pmid = {42271469},
issn = {1744-859X},
abstract = {BACKGROUND: Adolescent depression is a major mental health disorder with increasing prevalence and substantial long-term consequences. Although growing evidence suggests that the gut-brain axis is involved in depression, the relationships among gut microbiota, intestinal mucosal neurotransmitters, and adolescent depression remain insufficiently understood. This knowledge gap limits a better understanding of the pathophysiological mechanisms underlying adolescent depression and the identification of potential microbiota-related targets. Therefore, this study aimed to investigate alterations in gut microbiota and intestinal mucosal neurotransmitters, as well as their correlations, in an adolescent mouse model of depression.

METHODS: We established an adolescent depression mouse model using chronic unpredictable mild stress (CUMS), and collected data with the Smart video tracking system. We collected intestinal contents and mucosal tissues from mice. We analyzed gut microbial composition using metagenomic sequencing and quantified mucosal neurotransmitters with liquid chromatography-tandem mass spectrometry (LC-MS/MS). We analyzed correlations among gut microbiota, intestinal mucosal neurotransmitters, and behavioral indicators.

RESULTS: Mice in the CUMS group exhibited a significantly reduced sucrose preference rate in the sucrose preference test (P < 0.001); a significantly prolonged immobility time in the forced swim test (P < 0.01); and a significantly decreased total movement distance in the open field test (P < 0.01). No significant intergroup difference was observed in the tail suspension test. Regarding the gut microbiome, the CUMS group showed significantly lower Simpson index (P = 0.018) and Pielou's evenness index (P = 0.022). Beta diversity analysis indicated a statistically significant but modest between-group difference in community structure (ANOSIM R = 0.145, P = 0.03); this finding was supported by PERMANOVA (Bray-Curtis; pseudo-F = 1.675, R² = 0.0897, P = 0.033). LEfSe (Linear discriminant analysis Effect Size) analysis suggested 27 candidate taxa with discriminatory signals between groups (nominal P < 0.05; exploratory). Neurotransmitter analysis demonstrated that levels of 5-HIAA (5-hydroxyindoleacetic acid), 5-HT (serotonin), 5-HTP (5-hydroxytryptophan), and Kyn (kynurenine) in the colon were significantly decreased in the CUMS group, whereas levels of PA (phenylethylamine) and NE (norepinephrine) were significantly elevated (P < 0.05). Spearman correlation analysis found that Lactobacillus and Lactobacillus acidophilus correlated positively with sucrose preference and negatively with immobility in the forced swim test. Lactobacillus acidophilus also showed a positive correlation with 5-HT pathway metabolites: 5-HIAA, 5-HT, 5-HTP, and Kyn.

CONCLUSION: Adolescent mice exposed to CUMS showed depression-relevant behavioral alterations, shifts in gut microbiota composition, and changes in 5-HT pathway metabolites. Gut microbiota dysbiosis was significantly associated with alterations in 5-HT pathway metabolites. Because this study is correlational, causal relationships require validation in future interventional studies.},
}

@article {pmid42271556,
year = {2026},
author = {Kaushik, S and Borck, J and Flatow, E and Frishman, WH and Aronow, WS},
title = {Blood Culture-Negative Infective Endocarditis: A Review.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
pmid = {42271556},
issn = {1538-4683},
abstract = {Blood culture-negative infective endocarditis (BCNIE) represents a diagnostically challenging subset of infective endocarditis in which routine blood cultures remain negative despite fulfillment of Duke-ISCVID diagnostic criteria. BCNIE arises primarily from prior antibiotic exposure, infection with fastidious or nonculturable organisms, or noninfectious conditions that mimic endocarditis. Common fastidious pathogens include Coxiella burnetii, Bartonella species, Brucella species, Tropheryma whipplei, fungi, and nutritionally variant streptococci. Because delayed pathogen identification may postpone targeted therapy, BCNIE is associated with increased diagnostic complexity and substantial morbidity and mortality. Modern evaluation relies on a multimodal strategy integrating serologic testing, prolonged culture incubation, histopathology, advanced molecular diagnostics, and multimodality imaging. Emerging molecular techniques, including 16S/18S polymerase chain reaction and metagenomic next-generation sequencing, have significantly improved microbiologic yield, particularly from excised valve tissue, and are now incorporated into updated Duke-ISCVID criteria. Echocardiography remains central to diagnosis, while cardiac computer tomography and 18 fluoro-2-deoxy-D-glucose positron emission tomography/computer tomography provide complementary value in prosthetic valve disease and detection of periannular complications. Management requires empiric antimicrobial therapy followed by organism-directed treatment once a pathogen is identified, with surgery frequently necessary for heart failure, uncontrolled infection, fungal disease, or structural complications. Multidisciplinary endocarditis teams are increasingly recognized as essential to optimizing outcomes in this complex disease process.},
}

@article {pmid42271557,
year = {2026},
author = {Wassel, MA and Makabe-Kobayashi, Y and Iqbal, MM and Huang, C and Amano, M and Shimizu, A and Mandario, MAE and Takatani, T and Sakakura, Y and Hamasaki, K},
title = {Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42271557},
issn = {2524-4671},
support = {22K05822 and 25K09271//JSPS KAKENHI/ ; No. JURCAOSIRG23-08//Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute, The University of Tokyo/ ; },
abstract = {BACKGROUND: The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.

RESULTS: Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.

CONCLUSIONS: Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.},
}

@article {pmid42271572,
year = {2026},
author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E},
title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag047},
pmid = {42271572},
issn = {1574-6941},
abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.},
}

@article {pmid42272236,
year = {2026},
author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Klarenbeek, N and de Kam, ML and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and de Jong, V and Freyee, B and van Doorn, MBA and Rissmann, R and Niemeyer-van der Kolk, T},
title = {S. aureus colonization and clinical symptoms remain stable upon topical XZ.700 treatment: Results of a double-blind randomized clinical trial in patients with mild to moderate atopic dermatitis.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70630},
pmid = {42272236},
issn = {1365-2125},
support = {//Micreos Human Health B.V./ ; },
abstract = {AIM: Recovering dysbiosis may improve atopic dermatitis (AD) symptoms. XZ.700 is a recombinant chimeric endolysin that specifically targets Staphylococcus aureus and could be a new treatment option for patients with AD. The aim of this first-in-human study was to evaluate the safety, tolerability and efficacy of topical XZ.700 and explore the pharmacodynamic effects in patients with mild to moderate AD.

METHOD AND MATERIALS: This study consisted of Part A and Part B. In Part A, subjects were randomized and received XZ.700 10 μg/g, XZ.700 30 μg/g, XZ.700 100 μg/g or vehicle twice daily for 7 days on nonlesional skin and on all lesions (1% ≤ BSA ≤ 10%). In Part B, subjects received XZ.700 100 μg/g or vehicle on all lesions twice daily for 14 days (1% ≤ BSA ≤ 15%). Clinical scores and patient-reported outcomes were recorded. Pharmacodynamic measurements were taken.

RESULTS: In total, 35 patients completed the study. Tolerability of XZ.700 was acceptable. XZ.700 100 μg/g showed no evidence of effect on cultured S. aureus (estimated difference -52.9% CFU/mL; 95% CI -88.4% to 90.8%), oSCORAD (1.03; 95% CI -5.20 to 7.26) or EASI (-0.534; 95% CI -2.48 to 1.41). Furthermore, XZ.700 treatment did not result in a significant reduction in the relative abundance of S. aureus via metagenomics or other pharmacodynamic outcomes.

CONCLUSION: Tolerability and safety of short-term topical administration of XZ.700 100 μg/g for 14 days were acceptable in most participants; however, some local application-site events occurred, and one hypersensitivity reaction led to discontinuation. XZ.700 did not demonstrate target engagement or clinical benefit vs. vehicle under the tested conditions.},
}

@article {pmid42272618,
year = {2026},
author = {Top, FK and Boussiengui, LG and Sall, NC and Faye, M},
title = {First identification of Molluscum contagiosum poxvirus from human in Senegal.},
journal = {Journal of public health in Africa},
volume = {17},
number = {1},
pages = {1586},
pmid = {42272618},
issn = {2038-9922},
abstract = {Herein, we report on the first identification of a human case of Molluscum contagiosum virus (MOCV) in Senegal. In 2024, a male child living in Diamniadio, Dakar region, with no history of travel, tested positive for MOCV. The aetiology was identified using metagenomic sequencing in the framework of the ongoing preparedness activities for the 2024 mpox public health emergency of international concern (PHEIC). Given the overlapping clinical features of MOCV infection and mpox, further research on MOCV is warranted in the West African region, particularly in the current context of high mpox circulation.},
}

@article {pmid42272701,
year = {2026},
author = {Luo, L and Guo, Z and Chen, W and Zheng, Y and Chen, C and Li, Q and Wang, N and Ji, Y and Hua, J},
title = {Mycobacterium abscessus infection in a young man with cystic fibrosis: a case report and literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1737211},
pmid = {42272701},
issn = {2296-2360},
abstract = {BACKGROUND: Cystic fibrosis (CF) is a rare autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although relatively common in Caucasian populations, CF is rare in China, where it frequently presents with non-specific respiratory symptoms, leading to delayed diagnosis and frequent coinfections with multidrug-resistant pathogens.

CASE REPORT: A 21-year-old man presented with a 6-year history of recurrent productive cough and intermittent fever over the past 6 months. Imaging revealed bronchiectasis with evidence of infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Staphylococcus aureus and Mycobacterium abscessus. Further investigations revealed pancreatic lipomatosis, congenital absence of seminal vesicles, and fat-soluble vitamin deficiencies. CF diagnosis was confirmed by elevated sweat chloride concentration (88 mmol/L) and biallelic CFTR mutations. Clinical stability was achieved through a quadruple antimycobacterial regimen (linezolid, moxifloxacin, azithromycin, and minocycline) combined with systemic supportive care. CFTR modulator therapy was deferred due to limited access and financial constraints.

CONCLUSION: We report a case of CF in a Chinese patient presenting with nontuberculous mycobacterial infection, a condition rarely documented in East Asian populations. We provide a review of the relevant literature, aiming to emphasize the importance of early recognition of CF, personalized antimicrobial strategies, and improved access to essential medications.},
}

@article {pmid42272754,
year = {2026},
author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C},
title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779298},
pmid = {42272754},
issn = {2235-2988},
abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.

METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.

RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P = 0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and γ-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC = 0.946).

CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.},
}

@article {pmid42272841,
year = {2026},
author = {Qiu, X and Qiang, L and Wang, Y and Li, B and Lei, Z and Wang, J},
title = {Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1834558},
pmid = {42272841},
issn = {1663-9812},
abstract = {BACKGROUND: Staphylococcus aureus (SA) remains a global health threat due to its increasing drug resistance and intracellular persistence, which compromise the conventional antibiotic efficacy. Host-directed therapy (HDT) has emerged as a promising alternative by modulating host immunity. With multi-targeting and immunomodulatory properties, traditional Chinese medicine (TCM) monomers represent ideal candidates for HDT. However, their ability to promote host immunity-mediated SA clearance remains largely unexplored.

METHODS: Forty-one TCM monomers potentially regulating host apoptosis, a core mechanism of the host innate immune defense against intracellular pathogens, were screened to identify a compound that promotes the clearance of intracellular SA and methicillin-resistant SA (MRSA). The mechanism was investigated in infected macrophages using transcriptomics, proteomics, molecular dynamics simulations, and biochemical assays. The physiological function of the TCM monomer was examined in infected mice through lung pathology and multi-omics analysis, including transcriptomics, proteomics, metagenomics, and metabolomics.

RESULTS: Triptolide was identified as a potent facilitator of host immunity-mediated intracellular clearance of SA and MRSA, without exerting direct bactericidal effects. Mechanistically, triptolide directly binds to the X-linked inhibitor of apoptosis protein (XIAP), disrupting its interaction with caspases to relieve their inhibition and thereby induce apoptosis. Furthermore, in murine infection models, triptolide treatment reduced bacterial loads, alleviated inflammation, and induced macrophage apoptosis in lungs, concurrently maintaining microbiota homeostasis and improving metabolic function.

CONCLUSION: This study establishes a proof of concept for triptolide as a HDT candidate against SA and MRSA infections, which not only enhances host apoptosis-mediated pathogen clearance but also maintains host microbiota and metabolic homeostasis.},
}

@article {pmid42272967,
year = {2026},
author = {Frisch, S and Aliyazdi, S and Rehner, J and Schmartz, G and Gevaerd, C and Latta, L and Veldung, B and Becker, SL and Keller, A and Schaefer, UF and Loretz, B and Vogt, T and Lehr, CM},
title = {Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.},
journal = {Bioengineering & translational medicine},
volume = {11},
number = {3},
pages = {e70124},
pmid = {42272967},
issn = {2380-6761},
abstract = {Inflammatory skin conditions like Acne inversa are characterized by dysbiosis, an imbalance of commensal and pathogenic bacteria, posing challenges for specific treatments. Consequently, we investigated how biofilm formation, low-nutrition skin environments, and air interfaces influence susceptibility to anti-infective treatments in mixed bacterial cultures. To achieve this in a cost-effective and reproducible manner, we developed a simplified substrate made of gelatin, hyaluronic acid, chondroitin sulphate, and alginate (=Gel-Alg). This in vitro model simulates biofilm cultivation on skin surfaces for aerobic bacteria. We selected Staphylococcus aureus and Staphylococcus epidermidis as two clinically relevant strains, which are also abundant in Acne inversa. We tested single and mixed cultures under different conditions: (i) nutrient broth, (ii) Gel-Alg substrate, (iii) EpiDerm™ commercial skin model, and (iv) ex vivo human skin. Proliferation, measured by colony-forming units, was comparable across most conditions, except for human skin. Metabolic activity, assessed via Presto Blue staining, revealed significant differences. Dual-species cultivation and quantification by viability PMA qPCR indicated dominance of S. epidermidis over S. aureus in skin-like environments. Treatments with biofilm-dissolving rhamnolipids, the antibiotic vancomycin, and combinations thereof demonstrated varying efficacy in single and mixed cultures. While the drug combination could almost completely eradicate staphylococcal biofilms in broth, susceptibility varied in skin-like models and moreover strongly depended on temperature (37°C vs. 32°C). In conclusion, this study suggests that reductionistic models, while mimicking key features, could be valuable for early selective antimicrobial drug development for specific applications like Acne inversa therapy.},
}

@article {pmid42273068,
year = {2026},
author = {Moradi, Z and Alinizi, HR and Mehrvar, M},
title = {Genomic characterization of broad bean wilt virus 1 (Fabavirus alphaviciae) from Iran including phylogenetic relationships.},
journal = {3 Biotech},
volume = {16},
number = {7},
pages = {256},
pmid = {42273068},
issn = {2190-572X},
abstract = {UNLABELLED: The complete genome of a broad bean wilt virus 1 (BBWV1; Fabavirus alphaviciae) isolate (BBWV1-IR) was recovered from an uncultivated Plantago lanceolata plant in Iran by viral metagenomics and validated by RT-PCR. RNA1 (5,779 nucleotides) contains a single ORF encoding replication-associated proteins (Pro-Co, HEL, VPg, Pro, RdRp), while RNA2 (3,414 nucleotides) harbors two overlapping ORFs encoding the large and small coat proteins (LCP and SCP) and two additional proteins (VP47 and VP37). Comparative analyses revealed that BBWV1-IR shared 81-92% and 79.5-83% nucleotide identity in RNA1 and RNA2, respectively, with global isolates. No intragenic recombination was detected; however, reassortment analysis identified three distinct events, including one involving BBWV1-IR, whose RNA1 segment likely originated from Austrian (major) and UK (minor) parental lineages. ORF1 and ORF2a showed substantial variability and high haplotype diversity, with VP37 displaying the greatest nucleotide diversity. Evolutionary analyses indicated that BBWV1 genes were predominantly shaped by negative selection, with essential replication proteins (HEL and Pro) under strong purifying pressure, while VP47 and VP37 experienced more relaxed constraints. A few codons in ORF1 and ORF2a were under episodic positive selection. Phylogenetic analysis clustered 19 non-recombinant isolates into two major clades (A and B), with BBWV1-IR positioned in subclade I of clade A alongside geographically distant isolates, reflecting human-mediated long-distance dispersal. Incongruent clustering of ORF1 and ORF2a in several isolates supports RNA segment reassortment as a key driver of novel variant emergence. Collectively, these findings highlight the roles of mutation, selection, reassortment, and gene flow in shaping BBWV1 evolution, exemplified by the Iranian isolate.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04905-w.},
}

@article {pmid42273206,
year = {2026},
author = {Montgomery, A and Nupp, S and Gray, CR and Jay, ZJ and Edgcomb, V and Hatzenpichler, R},
title = {Tracking active heterotrophic microbial communities in the Guaymas Basin deep biosphere with BONCAT-FACS.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag111},
pmid = {42273206},
issn = {2730-6151},
abstract = {The marine deep biosphere harbors microbial communities that drive organic matter transformations and biogeochemical cycles. Previous work on these communities has focused either on genomic characterization or metabolic activity measurements. However, to understand microbial ecophysiology in the deep biosphere, taxonomic identity and metabolic function must be connected on both single-cell and ecosystem scales. In this work, we optimized a bioorthogonal noncanonical amino acid tagging fluorescence-activated cell sorting (BONCAT-FACS) workflow for low-biomass deep-biosphere sediments obtained during International Ocean Discovery Program Expedition 385 (IODP 385). BONCAT-FACS with 16S rRNA gene amplicon sequencing as well as metagenomics of sediment communities was applied to characterize translationally active communities in hydrothermally altered subsurface sediments of the Guaymas Basin. Our results revealed a heterotrophic microbial population throughout all sediments examined, with taxa translationally active down to our deepest sampling point, 154 m below the seafloor. Based on 16S rRNA gene identities, the translationally active microbial community was dominated by heterotrophic members of the Gammaproteobacteria, Bacilli, Deinococci, and Alphaproteobacteria. These taxa are likely key contributors to cycling the large quantities of hydrothermally altered organic matter in Guaymas Basin sediments. To further elucidate the metabolic capacity of active taxa, we mapped 16S rRNA gene amplicons to metagenome assembled genomes (MAGs) previously obtained from IODP 385. These MAGs contained genes associated with C1 metabolism, carbohydrate degradation, and fermentation, indicating that active taxa leverage these metabolisms for energy conservation. Our results demonstrate that BONCAT-FACS provides high-throughput and single-cell insights into the metabolic activity of microbes in the low-biomass marine subsurface.},
}

@article {pmid42274245,
year = {2026},
author = {Christian, WC and Jay, ZJ and Tolic, N and Nicora, CD and Livingstone, R and Trimmer, S and McDermott, TR and Hatzenpichler, R},
title = {Proteomic stress response by a novel methanogen enriched from the Great Salt Lake.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0041226},
doi = {10.1128/spectrum.00412-26},
pmid = {42274245},
issn = {2165-0497},
abstract = {Methanogenic archaea affect the climate through their production of the greenhouse gas, methane. However, it is unclear how a changing climate and other anthropogenic influences impact methanogen physiology and consequent methane flux. The Great Salt Lake (GSL) is an environment that has been heavily impacted by human activity, more than doubling its salt concentration since the last methanogen was cultured from it in 1985. In this study, we enriched a novel methanogen, for which we propose the name Candidatus Methanohalophilus hillemani, from the GSL at a time when its salinity reached a historical high. Interestingly, Ca. M. hillemani does not increase the expression of energy-conservation or osmotolerance proteins when challenged with salinity or oxygen. In contrast, Ca. M. hillemani prioritizes trace metal uptake and immune functions in response to the presence of the sulfate-reducing bacterium Desulfovermiculus. 16S rRNA gene amplicon data from GSL shore soils with extremely high and variable methane flux indicated the presence of Ca. M. hillemani. Our results show that Ca. M. hillemani is active when challenged with environmental stressors and contributes to the methane flux emanating from the GSL.IMPORTANCEMethanogens are microbes that affect the climate through their production of the greenhouse gas, methane. Changes in climate and land-use patterns are drying up saline lakes, damaging their unique economic and ecological value. As lake levels across the globe fall, it is unclear how methanogens and the amount of methane they produce will concurrently shift. In this study, we measured high methane output from the Great Salt Lake (GSL) across seasons and identified a novel methanogen as part of a larger methanogenic community that is responsible for these emissions. We cultured this novel methanogen from GSL sediments and determined that its methane production was largely unaffected by stress conditions. Our findings indicate that methanogens in saline environments, including a novel cultivated species, may be important and continued sources of methane as salinity increases.},
}

@article {pmid42274374,
year = {2026},
author = {Madi, N and Sayeed, A and Cato, ET and Creasy-Marrazzo, A and Islam, K and Khabir, IU and Islam, T and Khan, ZH and Bhuiyan, TR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ},
title = {Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag286},
pmid = {42274374},
issn = {1537-6613},
abstract = {Virulent bacteriophages (phages) can kill bacterial prey, potentially reducing burden of infection. In cholera, a high phage to Vibrio cholerae ratio is associated with mild dehydration, yet the relative importance of this ratio in disease severity remains unclear. We used machine learning to rank select host, microbial, and environmental factors as determinants of dehydration severity in over 600 cholera patients from across Bangladesh. We found the phage:pathogen ratio ranked among the top classifiers for mild dehydration, behind age and location. We advocate that phage predation be included as a key factor in cholera characterization for scientific, clinical and epidemiological applications.},
}

@article {pmid42275101,
year = {2026},
author = {Zhu, XY and Hopkins, FE and Airs, R and Widdicombe, CE and Wilkinson, B and Tarran, GA and Woodward, EMS and Carrión, O and Curson, ARJ and Ma, Q and Hanwell, L and Yang, GP and Christie-Oleza, JA and Lea-Smith, DJ and Zhang, XH and Todd, JD},
title = {Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag141},
pmid = {42275101},
issn = {1751-7370},
abstract = {Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolise it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.},
}

@article {pmid42275884,
year = {2026},
author = {Zhao, J and Zuo, M and Cao, L and Li, Q and Zhang, R and Wu, H and Yuan, J and Lv, C and Yu, Y and Lu, J},
title = {The neutral and acidic polysaccharides from Ginseng are metabolized by specific gut microbial taxa and confer immunomodulatory effects.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {158},
number = {},
pages = {158400},
doi = {10.1016/j.phymed.2026.158400},
pmid = {42275884},
issn = {1618-095X},
abstract = {BACKGROUND: Ginseng (Panax ginseng C. A. Mey.) exerts immunomodulatory effects partly mediated by its polysaccharides and interactions with gut microbiota. However, due to the structural complexity of ginseng polysaccharides, knowledge of their oral fate and direct microbiota interactions remains limited.

PURPOSE: This study aims to elucidate the oral fate of neutral and acidic polysaccharides in ginseng, analyze core gut microbiota genera and their immunomodulatory effects mechanisms.

METHODS: Structural analysis was conducted on neutral and acidic polysaccharides from ginseng. Thereafter, in vitro digestion and fermentation were performed, with metagenomic and metatranscriptomic profiling. The results were validated in conventional and pseudo‑germ-free immunosuppressed mouse models, and the immunomodulatory mechanisms of the core gut microbiota were investigated.

RESULTS: The in vivo and in vitro findings indicated that neutral and acidic polysaccharides exhibit different digestive properties and gut microbiota degradation patterns, differ in short-chain fatty acid production tendencies, bind to GPR-41/43 receptors, upregulate MAPK-p38 phosphorylation, and promote proliferation of intestinal immune cells.

CONCLUSION: This work systematically elucidated the digestive characteristics of ginseng polysaccharides and laid the groundwork for future studies on the specificity and structure-function relationships of plant-derived polysaccharides.},
}

@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.},
}