@article {pmid42283754,
year = {2026},
author = {Chen, X and Fang, Z and Li, S and Wu, Q and Liu, W and Xiang, L and Liu, Q and Tan, L and Weng, Q},
title = {Isolation and genomic analysis of a novel Pseudomonas phage from karst cave in China.},
journal = {Archives of virology},
volume = {171},
number = {7},
pages = {},
pmid = {42283754},
issn = {1432-8798},
abstract = {Bacteriophages (phages) in extreme environments like karst caves remain largely unexplored. Here, we report vB_Psp_JHDO137a, a novel phage isolated from cave sediment infecting Pseudomonas sp. The 41,530-bp dsDNA genome places it within the genus Ghunavirus (family Autographiviridae). Notably, its genome lacks auxiliary metabolic genes (AMGs), in contrast to AMG-rich profiles reported in cave metagenomic surveys and underscoring the necessity of isolation-based approaches to complement environmental sequencing data.},
}

@article {pmid42283827,
year = {2026},
author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K},
title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02807-1},
pmid = {42283827},
issn = {1432-184X},
support = {No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; },
abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.},
}

@article {pmid42284845,
year = {2026},
author = {Wang, W and Sun, X and Hao, R and Li, F},
title = {Algal community composition drives lake greenhouse gas emissions via dissolved organic matter transformation and microbial processing.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130177},
doi = {10.1016/j.jenvman.2026.130177},
pmid = {42284845},
issn = {1095-8630},
abstract = {Lakes are important sources of greenhouse gases, yet bloom-driven emissions are often assessed from total algal biomass, ignoring algal functional composition. This study examined how cyanobacteria (Microcystis aeruginosa), green algae (Chlorella vulgaris), diatoms (Cyclotella meneghiniana), and dominance-based mixtures regulate DOM transformation and CO2/N2O production under eutrophic conditions. It integrated to pure-culture experiments, water-sediment microcosms, sterilization controls, DOM fluorescence spectroscopy, gas monitoring, and metagenomics to resolve an algae-DOM-microbe-gas cascade. Cyanobacteria produced protein-like DOM and stimulated carbon mineralization, with CO2 exceeding 20 mmol L-1 by day 36; cyanobacteria-dominant mixtures followed a similar high-CO2 trajectory. Green algae generated tyrosine-like DOM and caused the strongest NO2[-] accumulation, reaching 5.21 mg L[-1] by day 21, corresponding to the highest N2O production; this pattern also occurred in green-algae-dominant mixtures. Diatom-only and diatom-dominant treatments favored humic-like DOM, organic carbon retention, and the weakest short-term CO2/N2O accumulation. Sterilization reduced inorganic carbon and greenhouse gas production, supporting microbial control. Background summer metagenomics provided functional context, showing algal-DOM turnover potential through carbon metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and the TCA cycle, while nirK and other nitrogen genes indicated capacity for substrate-driven incomplete nitrogen reduction. Functional differentiation among Candidatus_Planktophila, Limnohabitans, Rhodoferax, and Cyanobium linked DOM processing with potential gas-production pathways. These results show algal community composition, rather than biomass alone, regulates greenhouse gas production by shaping DOM quality, nutrient intermediates, and microbial C-N pathways. Incorporating algae composition into greenhouse gas assessment, this novel algae-DOM-microbe-gas framework provides mechanistic support for improving eutrophication management and lake-emission mitigation.},
}

@article {pmid42284910,
year = {2026},
author = {Fu, J and Li, Z and Hu, C and Yao, L and Cao, M and Dong, Y and Wang, P and Liang, Y and Tong, L and Shi, J},
title = {Metagenomic insights into the distribution and potential influencing factors of antibiotic resistance genes in historically polluted lake sediments.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {298},
number = {},
pages = {107898},
doi = {10.1016/j.aquatox.2026.107898},
pmid = {42284910},
issn = {1879-1514},
abstract = {Lake sediments serve as time-integrated archives of the evolution and persistence of environmental antibiotic resistance genes (ARGs), providing insights into how sustained environmental pressures shape resistome structure in human-impacted lake systems. Industrially polluted lakes, as systems subjected to strong anthropogenic disturbance, are characterized by high-intensity contaminant loading in sediments; however, the accumulation patterns and environmental factors associated with ARG persistence in such environments remain poorly understood. This study investigated the horizontal and vertical distributions and potential influencing factors of ARGs along sediment depth gradients (0-40 cm, 40-80 cm, and 80-120 cm) in a lake historically polluted by industrial activities (Ya'er Lake). Results indicated that bacitracin (27.3-43.6%) and multidrug resistance genes (25.4-33.1%) dominated the resistome, with pronounced enrichment in shallow sediments near discharge outlets, reflecting the influence of legacy pollution inputs. ARGs exhibited significant vertical stratification (p < 0.05): highest abundance in shallow layers, peak diversity in middle layers, and shifts with depth of key subtypes. Host-tracking assigned ARGs to 34 major genera across four phyla, with Pseudomonadota, Actinomycetota, Bacillota, and Thermodesulfobacteriota identified as the major ARG hosts. Microbial communities and mobile genetic elements (MGEs) jointly shaped ARG persistence, with shallow sediments showing broader host-MGE coupling and deeper sediments showing stronger signatures of environmental filtering and selective MGE-mediated maintenance. Overall, ARGs shifted from surface enrichment associated with historical wastewater inputs to a more selective persistence pattern with burial depth, indicating contaminated lake sediments as long-term reservoirs and potential dissemination sources of ARGs.},
}

@article {pmid42284942,
year = {2026},
author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.},
journal = {Water research},
volume = {303},
number = {},
pages = {126258},
doi = {10.1016/j.watres.2026.126258},
pmid = {42284942},
issn = {1879-2448},
abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.},
}

@article {pmid41748614,
year = {2026},
author = {Ma, Z and Xu, X and Peng, W and Zhang, T and Chen, Z and Cao, S and Zhang, F and Wang, Y and Xiao, H and Zhang, Y and Liu, Z and Liu, Z and Xue, H and Long, Q and Hou, T and Wang, W and Liu, Y and Jin, Z and Zhang, M and Peng, Y and Wen, J and Gaut, B and Zhou, Y},
title = {Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41748614},
issn = {2041-1723},
support = {32300191//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32372662//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Vitis/genetics/physiology ; Polymorphism, Single Nucleotide ; Genome, Plant/genetics ; *DNA Transposable Elements/genetics ; Climate Change ; *Adaptation, Physiological/genetics ; Genetic Variation ; Genetics, Population ; Genomics ; Metagenomics ; Plant Breeding ; *Acclimatization/genetics ; },
abstract = {Amur grape (Vitis amurensis Rupr.) is widely recognized for its cold tolerance traits and serves as a valuable genetic resource for breeding climate-resilient grape cultivars. Here, we construct a graph pangenome reference (Vampan_V1.0) and generate a variant map comprising 48,308,434 short variants and 127,094 TE-associated structural variants (TEVs) using deep resequencing data from 330 samples across 31 natural populations covering the species' distribution range. We discover a biased accumulation of SNPs around TEVs and identify 823 candidate adaptive genes associated with environmental variables. Using machine learning-based genetic offset models, we further show that putative adaptive TEVs significantly reduce genetic offsets by 7.3% to 8.2% under future climate scenarios. Our study shows the power of a graph-based pangenome to resolve complex variation and highlights the impact of TEVs on genetic diversity, local adaptation, and resilience to future climate change, providing insights into utilizing crop wild relatives in climate-resilient crop breeding.},
}

*Vitis/genetics/physiology
Polymorphism, Single Nucleotide
Genome, Plant/genetics
*DNA Transposable Elements/genetics
Climate Change
*Adaptation, Physiological/genetics
Genetic Variation
Genetics, Population
Genomics
Metagenomics
Plant Breeding
*Acclimatization/genetics

@article {pmid42275949,
year = {2026},
author = {Zheng, Y and Su, F and Li, H and Wu, H and Cui, P and Song, F},
title = {Wetland succession reshapes microbial degradation of plant- and microbial-derived carbon.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130154},
doi = {10.1016/j.jenvman.2026.130154},
pmid = {42275949},
issn = {1095-8630},
abstract = {Plant- and microbial-derived organic carbon require distinct microbial enzymes, but how wetland succession regulates these substrate-specific degradation pathways in estuarine soils remains unclear. We collected 0-10 cm soils from four wetland types in the Liaohe River Estuary, China-tidal flat, restored wetland, Suaeda salsa wetland, and reed wetland-with three independent replicate sites per type. Shotgun metagenomic sequencing, CAZy annotation, taxonomic annotation, co-occurrence networks, and Mantel tests were used to examine CAZyme genes targeting plant-, fungal-, and bacterial-derived carbon. We identified 16,346,752 CAZyme-encoding sequences assigned to 749 families. Carbon-cycling gene composition differed significantly among wetland types (ANOSIM R = 0.37, p = 0.034). Gene diversity was higher in early to mid-successional stages, whereas the abundances of plant-, fungal-, and bacterial-derived carbon degradation genes increased along succession. Lignocellulose-degrading genes were most enriched in reed wetland, including AA3, CBM9, and CE1. Microbial hosts shifted markedly, with Bacteroidota increasing from 8.53% to 38.28% among plant-derived carbon degraders. Plant-derived carbon degrader networks were densest in tidal flat soils, suggesting a transition from stress-associated microbial associations to resource-specialized assemblages. Environmental controls were substrate-specific: plant-derived genes correlated only with nitrate, fungal-derived genes with moisture, nitrogen, salinity, and electrical conductivity, and bacterial-derived genes with none of the measured variables. These findings reveal substrate-specific microbial mechanisms linking wetland succession to carbon turnover and identify Bacteroidota, AA3, and nitrate availability as candidate indicators for restoration assessment and carbon-sequestration management.},
}

@article {pmid42276429,
year = {2026},
author = {Kang, X and He, P and Zhang, H and Lü, F},
title = {Multi-omic insights into thermal regulation of the resistome through composting-simulating microcosm system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135119},
doi = {10.1016/j.biortech.2026.135119},
pmid = {42276429},
issn = {1873-2976},
abstract = {Composting is a crucial biosecurity practice that stabilizes organic waste and reduces biological hazards prior to land application, with temperature as a major driver of resistome succession. However, compost temperature is a dependent, composite factor jointly determined by microbial metabolism and management practices. The regulatory pathways of temperature on resistome remain unclear. In this study, temperature gradients from 50°C to 65°C were applied to biowaste in a composting-simulating microcosm system to investigate the genomic and functional regulatory pathways of antimicrobial resistance genes (ARGs) using high-temporal-resolution metagenomic and metatranscriptomic analyses. The succession dynamics of ARGs under temperature-controlled incubation were demonstrated from the ecological niche perspective. Our results revealed that the genomic potential and transcriptional activity of ARGs responded asynchronously to temperatures. ARG sensitivity to temperature was category-specific, with 60°C representing a critical threshold for genomic-level removal of ARGs. The context-anchored members drove the resistome's response trends during temperature-controlled incubation, while abundance-based dynamics did not show significant kinetic shift under elevated temperatures. Temperature shaping the resistome through intra-lineage ARG reduction within context-anchored members rather than community succession. Unassociated fragment members showed transient abundance fluctuations at 55°C. Both context-anchored and unassociated fragment ARG carriers maintained transcriptional homeostasis during temperature-controlled incubation. Viruses had a limited impact on the community resistome. Our study demonstrated temperature-driven regulation of the resistome, providing a basis for optimizing ARG management in composting.},
}

@article {pmid42276430,
year = {2026},
author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Pan, X},
title = {Industrial red mud establishes redox-active interfaces to steer metabolic pathways toward chain elongation in sludge anaerobic fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135151},
doi = {10.1016/j.biortech.2026.135151},
pmid = {42276430},
issn = {1873-2976},
abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) provides a promising route for sludge valorization, but is often limited by inefficient hydrolysis and restricted interspecies electron transfer. This study evaluated industrial red mud (RM) as a conductive and alkaline regulator to enhance anaerobic chain elongation (CE). With 5 g/L RM addition, MCFAs yield reached 12.6 g COD/L, representing a 164% increase over the control. Spectroscopic analysis showed that the strong alkalinity of RM altered protein secondary structures, facilitating substrate hydrolysis while maintaining stable pH favorable for CE. Increased release of humic-like substances was observed, and electrochemical evidence suggested that the adsorption of these redox mediators onto the RM surface potentially facilitated the formation of redox-active interfaces, which contributed to the enhanced electron transfer capacity. Microbial network analysis demonstrated that RM acted as a topological hub, restructuring the community into a synchronized syntrophic consortium (hydrolysis-acidogenesis-CE) and highly enriching key CE bacteria. Metagenomic analysis revealed an increase in the abundance of genes encoding conductive membrane proteins (cytochromes and Mtr-associated), suggesting a potential enhancement in direct interspecies electron transfer. Meanwhile, RM increased the gene abundance of the CE key pathway (reverse β-oxidation pathway), thereby favoring the genetic potential for MCFAs accumulation. These findings establish a sustainable 'waste-treating-waste' framework, utilizing RM-driven electron reservoirs to facilitate the high-value conversion of WAS in anaerobic systems.},
}

@article {pmid42276515,
year = {2026},
author = {Hassanien, A and Saadaoui, I and Sayadi, S},
title = {Archaea as a Resource for Sustainable Biotechnology: From Extremophiles to Valuable Products.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2026.06.006},
pmid = {42276515},
issn = {1638-6183},
abstract = {Archaea, a remarkable domain of microorganisms, possess extraordinary survival capabilities that enable them to thrive in the most extreme environments on Earth, including high temperatures, extreme pH, oxygen-deprived habitats, and high salinity. Modern ecological studies have revealed their broad distribution and ecological roles, but traditional culture techniques do not accurately capture the structure of archaeal communities in such settings. This review provides an integrated and up-to-date synthesis of tools used to assess archaeal biodiversity, with particular emphasis on high-throughput culture-independent strategies, including metagenomics, functional metagenomics, and multi-omics. We also provide a quantitative, up-to-date mapping of archaeal biodiversity and bioproduct research (2010-2024), highlighting methodological trends and underexplored niches that are not emphasized in previous reviews. These advancements in archaeal studies have allowed scientists to investigate numerous archaeal strains for potential biotechnological applications and products, and to explore novel genes that lead to the discovery of new metabolites and bioactive molecules. Building on this framework, we critically analyze the current and emerging biotechnological applications of archaea. focusing on metabolites, enzymes, biopolymers, and biofuels, as well as identifying the major scientific and technical bottlenecks that hinder their translation into industrial scale. Finally, we outline key research priorities for utilizing archaeal resources in development of more sustainable and environmentally friendly biotechnologies.},
}

@article {pmid42276765,
year = {2026},
author = {Diao, Y and Li, J and Wang, L and Zhang, Q and Xu, C and Peng, A and Lu, C and Lai, B and Chen, R and Chen, J and Pei, X},
title = {Microbiological characteristics of granulomatous lobular mastitis revealed by metagenomic sequencing.},
journal = {Journal of clinical pathology},
volume = {},
number = {},
pages = {},
doi = {10.1136/jcp-2026-210744},
pmid = {42276765},
issn = {1472-4146},
abstract = {AIMS: Granulomatous lobular mastitis (GLM) is a rare, chronic, benign inflammatory disease of the breast with an unclear aetiology. This study aimed to characterise the microbial features of GLM using metagenomic next-generation sequencing (mNGS) and to provide potentially relevant microbial clues for clinical evaluation.

METHODS: Twenty fresh lesion tissue samples were collected from 15 female patients with GLM, including one representative sample per patient and five additional deep tissue samples. Clinical data collection, mNGS, bioinformatics analysis and data interpretation were performed to characterise the microbial profiles of GLM lesions.

RESULTS: In this study, all patients presented with palpable breast masses, breast pain and abscess formation. More than half showed increased white blood cell counts, neutrophil percentages, C reactive protein levels and erythrocyte sedimentation rates together with decreased lymphocyte percentages. Based on genus-level filtering, mNGS identified 16 bacterial genera, 14 fungal genera and 3 viral genera, revealing a complex but bacteria-dominated microbial profile. The most frequently detected bacterial genera were Corynebacterium, Cutibacterium, Acinetobacter, Staphylococcus and Hathewaya, with marked interpatient variation in relative abundance, while fungal profiles were relatively more concentrated. In five patients with both superficial and deep tissue samples, microbial profiles differed across sampling depths, particularly for bacterial composition.

CONCLUSIONS: mNGS revealed a complex, bacteria-dominated microbial profile in GLM lesions and indicated that sampling depth may influence the detected microbial profiles. These findings may provide useful clues for clinical evaluation, but the pathogenic significance of these micro-organisms remains to be elucidated.},
}

@article {pmid42277004,
year = {2026},
author = {Clark, JR and Chirman, D and Prakash, H and Terwilliger, A and McNeese, M and Ross, M and Tisza, M and Javornik Cregeen, SJ and Hopkins, L and Deegan, J and Troisi, CL and Boerwinkle, E and Mena, K and Wu, F and Kimata, JT and Johnson, M and Gregory, D and Fletcher, FE and Giordano, TP and Maresso, AW},
title = {Statewide multi-year wastewater sequencing reveals dual origins of HIV-1 signal.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74140-7},
pmid = {42277004},
issn = {2041-1723},
support = {U19AI14429//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30AI161943//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01DA059394//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; },
abstract = {Human immunodeficiency virus 1 (HIV-1) is a retrovirus which has infected 90 million people and resulted in over 40 million deaths. Despite advances in diagnostics, treatment, and prophylaxis, HIV-1 continues to spread due to undiagnosed and untreated infections. Traditional monitoring methods are ineffective when access to testing is limited or people do not seek care, particularly given the long period between infection and symptom onset, allowing undetected transmission to continue. Here, we use a hybrid-capture sequencing approach to track HIV-1 signal in municipal wastewater in 15 different cities over nearly 3 years. We obtain near-complete genomic coverage of HIV-1, enabling detailed genomic analysis. Surprisingly, there are a substantial number of research-associated retroviral vector sequences recovered. Using computational competitive mapping, we identify specific genomic regions that differentiate authentic HIV-1 from vector-derived inputs. In an exploratory analysis of sites with available clinical data, wastewater-derived circulating HIV-1 reads show a positive correlation with community-level HIV diagnosed prevalence that was robust to exclusion of individual high-prevalence sites. This study identifies lentiviral vector contamination as a confounding factor in wastewater HIV-1 detection, recovers authentic circulating HIV-1 signal through an original classification framework, and provides initial evidence that the resulting signal tracks community HIV burden.},
}

@article {pmid42277027,
year = {2026},
author = {Wacker, EM and Rühlemann, MC and Franke, A and Ellinghaus, D},
title = {TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42277027},
issn = {2041-1723},
support = {EL 831/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Metagenomic shotgun sequencing data from over 600,000 metagenomes are publicly available in repositories such as NCBI's Sequence Read Archive (SRA). Technically advanced and easy-to-use best-practice metagenome software workflows for raw data pre-processing, assembly of metagenome-assembled genomes, and taxonomic and functional annotation of metagenome-assembled genomes are needed for reproducible analysis and harmonization of large-scale metagenomic datasets. We introduce TOFU-MAaPO (Taxonomic Or FUnctional Metagenomic Assembly and PrOfiling), a portable, automated single-command Nextflow pipeline for large-scale analysis of metagenomic short-read sequencing data. It analyzes metagenome files locally or directly from the SRA using accession or study IDs. In a benchmark against three established metagenome software pipelines, the TOFU-MAaPO workflow yielded 12%, 42% to 77% more high-quality metagenome-assembled genomes, likely reflecting the integration of multiple complementary binning tools with a unified refinement strategy. Using its assembly-free taxonomic abundance profiling module, we also automatically downloaded 16,462 uniquely identifiable and accessible human gut metagenome samples from the SRA and taxonomically annotated them against the Genome Taxonomy Database on a high-performance cluster in less than 55 hours, including download time. TOFU-MAaPO makes large metagenome projects more accessible to individual research groups and is freely available at https://github.com/ikmb/TOFU-MAaPO .},
}

@article {pmid42277260,
year = {2026},
author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C},
title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {42277260},
issn = {1546-1718},
abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.},
}

@article {pmid42277454,
year = {2026},
author = {Amoia, SS and Giampetruzzi, A and Antònio, LF and Tomàs Pais da Cunha, A and Minafra, A},
title = {A new putative carlavirus identified by metagenomic analysis in a wild weed in Angola.},
journal = {Archives of virology},
volume = {171},
number = {7},
pages = {},
pmid = {42277454},
issn = {1432-8798},
abstract = {A metagenomic analysis was performed by high-throughput sequencing (HTS) to identify viruses infecting a wild weed collected in Seles (Angola), which exhibited clear yellowing symptoms. The analysis led to the discovery of a putatively novel carlavirus, tentatively named 'Seles weed carlavirus'. The complete genome sequence, consisting of 8,597 nucleotides, poly-A tail excluded, exhibited the typical organization of members of the genus Carlavirus, including the replicase polyprotein (ORF1); the triple gene block (ORFs 2-4); the coat protein (ORF5) and an RNA-binding protein (ORF6). The replicase polyprotein and coat protein gene regions of the newly described virus shared the highest amino acid sequence identity with the corresponding sequences of cowpea mild mottle virus (51.40%) and Hainan betaflexivirus (63.08%), respectively. The infection was further confirmed by RT-PCR with multiple specific targeted primer pairs, whose related amplicons were cloned and sequenced.},
}

@article {pmid42277703,
year = {2026},
author = {Cumley, N and Quick, J and Brier, T and Wilkinson, S and Kent, C and Hassan-Smith, Z and Loman, N and Hassan-Smith, G},
title = {Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13276-9},
pmid = {42277703},
issn = {1471-2334},
abstract = {BACKGROUND: Central nervous system infections (CNSI) contribute significantly to global disability and mortality, but the causative agent is often undetected. Metagenomic sequencing offers the potential to enhance diagnostic sensitivity, particularly in cases of unusual or partially treated infections. However, caution is required in interpretation of metagenomics data due to technical artefacts from contamination or non-specific read mapping which can reveal a broad spectrum of biologically plausible but diagnostically unlikely organisms.

METHODS: This study compares the performance of metagenomic sequencing with standard clinical microbiology methods using cerebrospinal fluid (CSF) from patients with CNSI and non-infected control samples. To evaluate sensitivity of different laboratory approaches, we sequenced DNA and RNA metagenomic libraries extracted from CSF, using both cell-free and cellular fractions. We then devised a set of simple, easily interpreted yet rigorous filters tailored for clinical metagenomics to generate a framework for result interpretation that can be readily applied by clinical scientists.

RESULTS: We demonstrate that composite filtering strategies are essential to reduce misleading signals and support standardised workflows. Additionally, our results suggest that a cell-free sample preparation approach can improve confidence in identifying clinically relevant pathogens, highlighting the impact of sample preparation on results quality.

CONCLUSION: In this study we describe a reproducible method that can be incorporated into a practical framework for clinical application of metagenomic sequencing in CNSI diagnostics.},
}

@article {pmid42277905,
year = {2026},
author = {Serrano-Gómez, G and Zaida, S and Pons-Tarín, M and Mayorga, L and Maria, TC and Natalia, B and Francisco, G and Manichanh, C},
title = {Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis.},
journal = {Biomarker research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40364-026-00950-y},
pmid = {42277905},
issn = {2050-7771},
support = {PI20/00130//Instituto de Salud Carlos III/ ; PID23-147387OB-100//Ministerio de Ciencia, Innovación y Universidades/ ; SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; },
abstract = {BACKGROUND: First-degree relatives of patients with inflammatory bowel disease (IBD) carry elevated disease risk and offer a unique window into preclinical gut microbiome alterations. We investigated whether familial IBD risk is associated with intermediate, disease-specific, or shared gut microbiome configurations in both Crohn's disease (CD) and ulcerative colitis (UC), the two main form of IBD.

METHODS: Using shotgun metagenomics, we analysed fecal samples from CD (n = 68) and UC (n = 77) patients, their healthy first-degree relatives (CD-HFDRs, n = 37; UC-HFDRs, n = 30), and unrelated healthy controls (HCs, n = 497), integrated species-level taxonomy, MetaCyc functional pathways, and virulence factor gene (VFG) profiling, with differential abundance analyses adjusted for relevant covariates.

RESULTS: HFDRs exhibited preserved alpha diversity but intermediate dysbiosis relative to patients and HCs. CD-HFDRs shared CD-associated taxonomic alterations, including depletion of Faecalibacterium prausnitzii, and enrichment of adherence- and invasion-associated VFGs, with 16 of 18 HFDR-enriched VFGs also elevated in CD patients. CD-HFDR functional pathway profiles nonetheless closely resembled those of HCs, revealing a dissociation between taxonomic and functional dysbiosis. Random forest classifiers distinguished HFDRs from HCs with strong performance: species- and VFG-based models achieved an AUCs of 0.966 in CD, and 0.946 in UC. Top predictive features were depletion of F. prausnitzii and enrichment of the E. coli adhesin gene fdeC. UC-HFDRs showed subtler alterations but comparable classifier performance.

CONCLUSIONS: IBD first-degree relatives harbour a transitional gut microbiome between health and disease, more pronounced in CD, with F. prausnitzii depletion and pathobiont virulence genes emerging as robust microbiome-based risk indicators.},
}

@article {pmid42278013,
year = {2026},
author = {Mei, Z and Zhou, H and Du, H and Liu, K and Gao, C and Sheng, Z and Gong, Y},
title = {Heat Stress Induces Metabolic and Physiological Imbalance in Laying Hens, Accompanied by Hepatic Transcriptomic, Cecal Microbial, and Metabolomic Alterations.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/ani16111578},
pmid = {42278013},
issn = {2076-2615},
support = {2023ZD0405203//the Biological Breeding-National Science and Technology Major Project/ ; 2023ZD0407106//the Biological Breeding-National Science and Technology Major Project/ ; HBZY2023B007//the Hubei Fund for Seed Industry High-Quality Development Project/ ; 2025HBSTX4-04//the Earmarked Fund for Hubei Agriculture Research System/ ; 2018YFE128100//the National Key Research and Development Program of China/ ; 2023BBA029//he Major Program of Hubei Province/ ; },
abstract = {Heat stress is a major constraint to productivity and physiological homeostasis in laying hens. This study investigated integrated responses to acute heat stress using a multi-omics approach, including performance traits, serum biochemical parameters, histology, hepatic transcriptomics, cecal metagenomics, and metabolomics. Acute heat stress impaired productive performance, as reflected by changes in egg production and reduced eggshell strength, and induced systemic physiological disturbances, including increased stress- and injury-related blood indicators and disrupted metabolic and electrolyte balance. Histological analysis confirmed liver and intestinal tissue damage. Hepatic transcriptomics revealed inflammatory activation and suppression of metabolic pathways, particularly those involved in lipid metabolism, energy production, and redox homeostasis. Cecal metagenomic and metabolomic analyses showed altered microbial composition and functional potential, along with disruptions in amino acid, lipid, and energy metabolism. Collectively, these findings suggest that acute heat stress is associated with coordinated inflammatory responses and metabolic reprogramming, together with liver and intestinal injury and gut microbiota-metabolite alterations. The study provides a framework for understanding early heat stress responses and highlights potential targets for nutritional and microbiota-based interventions in poultry production. Importantly, serum biochemical indicators such as D-lactic acid and aspartate aminotransferase may serve as potential early biomarkers for monitoring heat-stress-induced physiological disturbances.},
}

@article {pmid42278142,
year = {2026},
author = {Yuan, Z and Xie, F and Ding, Y and Li, X and Ghonaim, AH and Jiang, C and Ren, M and Li, S},
title = {Dietary Fiber Levels Modulate Intestinal Mucosal Architecture and the Microbiome-Metabolome Axis to Support Immune Homeostasis in Brooding Wanxi White Geese.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/ani16111709},
pmid = {42278142},
issn = {2076-2615},
abstract = {Dietary fiber is a critical determinant of intestinal health, yet its optimal inclusion level for WWG during the critical brooding period remains undefined. This study aimed to evaluate the effects of varying dietary CF levels (approximately 3%, 5%, and 9%) on the intestinal morphology, immune function, and microbiome-metabolome axis of brooding WWG. A total of 120 one-day-old goslings were randomly assigned to the three dietary treatments for a 28-day trial. Histological analysis revealed that the 9% CF diet significantly improved gut morphology, yielding superior villus-to-crypt ratios in the jejunum and ileum. Molecular assays indicated that higher fiber levels (5-9%) upregulated the expression of nutrient transporters (SGLT1 and GLUT2). Concurrently, the 9% CF diet effectively suppressed the potent pro-inflammatory cytokine TNF-α in the jejunum while appropriately upregulating IL-6 and NF-κB, indicating enhanced mucosal immune vigilance and structural maturation. Multi-omics integration (shotgun metagenomics and LC-MS metabolomics) demonstrated that specific fiber levels significantly shifted microbial abundances, specifically enriching Bacteroidetes and Actinobacteria. These microbial shifts were strongly correlated with enriched metabolic pathways, notably lysine biosynthesis and purine metabolism, which synergistically support mucosal homeostasis. Collectively, these findings demonstrate that a 9% dietary CF inclusion is an effective nutritional strategy to optimize intestinal architecture and microbial-metabolic profiles in brooding WWG.},
}

@article {pmid42278211,
year = {2026},
author = {Shematorova, EK and Shpakovski, GV},
title = {Molecular Evolution of the Archaeal DNA-Dependent RNA Polymerase: Cooperative Changes in Subunit Composition and Specific Domains of Small Subunits.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114679},
pmid = {42278211},
issn = {1422-0067},
support = {thematic plan 1ф.4.1//National Research Center "Kurchatov Institute"/ ; },
abstract = {The subunit composition and tertiary structure of DNA-dependent RNA polymerases in archaea, bacteria, and eukaryotes are currently well understood. The single RNA polymerase of archaea resembles the nuclear RNA polymerase II of eukaryotes in its composition and consists of 10-12 subunits. Perhaps the only exception that seems to confirm this rule is the Rpo8 subunit (homologue of the eukaryotic Rpb8), which only some classes of archaea have. The development of metagenomic sequencing has led to a significant revision of the classification system of prokaryotes, in particular to the identification of a number of new Archaea evolutionary lineages. This makes it possible to analyze the subunit composition and structure of RNA polymerase of all currently isolated archaeal phyla. Our analysis shows that the Rpo8 subunit is present only in the RNA polymerase of Archaea species from the Thermoproteota of the Thermoproteati superphylum and from the whole superphylum Promethearchaeati, formerly known as the Asgard. After analyzing the changes in the small Rpo6 subunit (homologue of eukaryotic Rpb6), functionally interacting with Rpo8, we noticed that the largest number of changes in the primary and domain structures of this small subunit occurred in archaeal phyla that lack Rpo8. Shortened forms of Rpo6 without N- or C-terminal regions were observed only in representatives of archaea with an RNA polymerase that does not contain the Rpo8 subunit. Our analysis shows that the changes in Rpo6 are an adaptation of a multisubunit transcription complex to the disappearance of Rpo8. Most likely, the Rpo8 subunit was present in the RNA polymerase of the Last Common Ancestor of Archaea (LCAA) and, in the course of evolution, disappeared in the superphyla Euryarchaeota and Nanobdellati and two divisions of the Thermoproteati superphylum: Bathyarchaeota and Thaumarchaeota.},
}

@article {pmid42278252,
year = {2026},
author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B},
title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114714},
pmid = {42278252},
issn = {1422-0067},
support = {101079425//Centre of Biotechnologie of Sfax/ ; },
mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; },
abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.},
}

*Metagenomics/methods
Tunisia
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Archaea/genetics/classification
Shotgun Sequencing
Phylogeny
*Bacteria/genetics/classification
Metagenome

@article {pmid42278256,
year = {2026},
author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M},
title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114723},
pmid = {42278256},
issn = {1422-0067},
support = {RAC# 2240005//King Faisal Specialist Hospital & Research Centre/ ; },
abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.},
}

@article {pmid42278324,
year = {2026},
author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y},
title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114794},
pmid = {42278324},
issn = {1422-0067},
support = {24-14-00059//Russian Science Foundation/ ; },
abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.},
}

@article {pmid42278475,
year = {2026},
author = {Ermakov, VS and Falah, K and Nigam, SK},
title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114942},
pmid = {42278475},
issn = {1422-0067},
support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; },
abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.},
}

Animals
*Organic Anion Transport Protein 1/metabolism/genetics
Signal Transduction
Mice
*Kidney/metabolism/microbiology
*Fatty Acids, Volatile/metabolism
Mice, Knockout
*Gastrointestinal Microbiome
Humans

@article {pmid42278495,
year = {2026},
author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E},
title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114969},
pmid = {42278495},
issn = {1422-0067},
support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; },
mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; },
abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.},
}

Humans
*gamma-Aminobutyric Acid/metabolism/biosynthesis
*Brain/metabolism/physiology
Animals
*Probiotics
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism
*Brain-Gut Axis

@article {pmid42278559,
year = {2026},
author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH},
title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27115036},
pmid = {42278559},
issn = {1422-0067},
support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; },
mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; },
abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.},
}

Animals
*Titanium/toxicity/chemistry
*Zebrafish/microbiology
*Dysbiosis/microbiology/chemically induced
*Gills/microbiology/drug effects
*Bacterial Translocation/drug effects
*Gastrointestinal Microbiome/drug effects
*Nanoparticles/toxicity
RNA, Ribosomal, 16S/genetics
*Metal Nanoparticles/toxicity/chemistry

@article {pmid42278576,
year = {2026},
author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T},
title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27115052},
pmid = {42278576},
issn = {1422-0067},
mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; },
abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.},
}

Humans
Female
*Lactobacillus/genetics/physiology
*Vagina/microbiology/virology
*Candida/genetics/physiology
*Cervix Uteri/microbiology/virology
*Papillomavirus Infections/virology/microbiology
*Mycobiome/genetics
Metagenomics/methods
Adult
Microbiota
Shotgun Sequencing
Middle Aged
*Human Papillomavirus Viruses/genetics

@article {pmid42278616,
year = {2026},
author = {Gajic, I and Jovicevic, M and Kekic, D and Kabic, J and Vicic, I and Lukovic, B and Tomic, A and Sovljanski, O and Skoric, M and Sikanic, I and Jankovic, M and Smitran, A and Bozic, L and Golic, B and Basic, J and Karabasil, N and Opavski, N},
title = {Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27115092},
pmid = {42278616},
issn = {1422-0067},
support = {7042//Scientific Fund of the Republic of Serbia/ ; },
abstract = {Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization.},
}

@article {pmid42279294,
year = {2026},
author = {Newell, LF and Twohey, E and Sweetnam, J and Skendzel, S and Stingle, J and Vartanian, KA and Davis, BA and Layman, CE and Carbone, L and Ray, K and Fei, SS and Karstens, L and He, FC and El Jurdi, N and Blaes, AH and Meyers, G and Cook, RJ and Baraki, A and Dengel, DR and Holtan, SG},
title = {Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.},
journal = {Cancers},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/cancers18111710},
pmid = {42279294},
issn = {2072-6694},
abstract = {Background: Chemotherapy and radiation accelerate aging of multiple systems, including the immune and musculoskeletal systems. Resistance training may mitigate some of the late physiologic effects of cancer therapy. Methods: We developed a community-based pilot study of resistance training for long-term cancer survivors meeting criteria for pre-frailty or frailty (N = 8; 6 allogeneic hematopoietic cell transplant, 1 autologous hematopoietic transplant, 1 breast cancer survivor) and their caregivers (N = 8 healthy controls) consisting of a baseline assessment, 10 weeks of personalized resistance training at least once weekly as a group and as many additional times on an individual basis as their schedule allowed, and an end-of-study assessment to measure change in strength and body composition. Blood samples were collected at the start of the study and after the 10-week training program to assess changes in peripheral blood mononuclear cell DNA methylation patterns, gene expression measured by RNA sequencing, and stool microbiome analysis using metagenomics. The median number of resistance training sessions was 25 sessions. Results: Cancer survivors and controls both more than doubled their squat and press volume after 10 weeks. At baseline, cancer survivors exhibited a pro-inflammatory transcriptomic and epigenetic profile with elevated interferon signaling and reduced naïve T cell signatures compared to healthy controls, consistent with immune senescence. After 10 weeks of resistance training, these differences normalized, suggesting that exercise exerted anti-inflammatory and immune-restorative effects in cancer survivors at both gene expression and methylation levels. Ten fecal microbial pathways that were lower in relative abundance in patients compared with controls at baseline were no longer significantly different post-exercise. Conclusions: Our data suggest that in addition to beneficial changes in body composition, resistance training may exert an immune restorative effect in cancer survivors.},
}

@article {pmid42279452,
year = {2026},
author = {Yang, L and Meng, W and Yang, T and Zhu, Y and Wang, Z},
title = {Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/diagnostics16111582},
pmid = {42279452},
issn = {2075-4418},
abstract = {With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation.},
}

@article {pmid42279756,
year = {2026},
author = {Abaalkhail, MA and Mohamed, SHS and Aljurbua, MS and Alkhuraisi, RA and Aladhadh, M},
title = {Microbial Diversity of Spontaneously Fermented Camel Milk.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/foods15111969},
pmid = {42279756},
issn = {2304-8158},
abstract = {Camel milk is widely consumed in the world's arid and semi-arid regions because of its favorable nutritional profile and associated human health benefits. The indigenous microbiota of raw camel milk is diverse and composed of different bacterial and fungal groups. This community drives spontaneous milk fermentation, resulting in a variety of traditional products, including Gariss, Shubat, Chal, Dhanaan, Lfrik, and Suusac (or Suusa), depending on geographic region and cultural practice. This fermented milk has improved sensory, nutritional, and health profiles, as well as an extended shelf life, compared to raw milk. Fermentation alters the microbial community structure, with lactic acid bacteria (LAB) consistently becoming dominant, while yeasts and molds are also detected in some products. These patterns have been identified using both culture-dependent and culture-independent approaches, including 16S rRNA gene sequencing and whole-genome shotgun metagenomics. However, the milk's microbial composition is highly variable and is influenced by the original composition, geographical location, fermentation and hygiene practices. The detection of opportunistic pathogens such as E. coli, Salmonella and Listeria in some traditional products raises important food safety concerns. This review presents current knowledge on fermented camel milk microbiology using a cross-regional approach, identifying key gaps in microbial safety and process standardization to support wider acceptance and potential commercialization.},
}

@article {pmid42280335,
year = {2026},
author = {Barba-de la Rosa, AP and Treviño, S and Ovando-Vázquez, C and De León-Rodríguez, A and Calva-Cruz, OJ and Barrera-Pacheco, A and Espitia-Rangel, E},
title = {Dietary Supplementation with Amaranth Protein Isolate Modulates the Gut Microbiota in Children with Overweight and Obesity: A Nonrandomized Trial.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/nu18111690},
pmid = {42280335},
issn = {2072-6643},
support = {A3-S-37825//Consejo nacional de ciencia y tecnologia mexico/ ; },
mesh = {Humans ; Child ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Amaranthus/chemistry ; Body Mass Index ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/blood ; *Plant Proteins/administration & dosage/isolation & purification/pharmacology ; *Overweight/microbiology ; Cholesterol/blood ; Insulin/blood ; Triglycerides/blood ; Feces/microbiology ; },
abstract = {BACKGROUND: Overweight and obesity are chronic diseases that result from complex interactions including genetics, environment, eating behaviors, and limited access to a healthy diet. Amaranth protein (AmProt) has several health benefits, but no studies have examined its effects on the modulation of children's gut microbiota. The work aimed to analyze serum levels and changes in gut microbiota in children aged 8-10 years with different body mass index (BMI) values after supplementation with AmProt.

METHODS: Participating children were allocated into three groups according to their BMI: normal weight (NW), overweight (OW), and with obesity (OB). Children received AmProt for 90 days. Levels of fasting blood glucose, cholesterol, triglycerides, and insulin were analyzed before and after diet supplementation. HOMA-IR and adinopectin/leptin ratio were evaluated. Feces were collected and metagenome analysis was carried out.

RESULTS: No changes in glucose levels were observed across groups and treatments; however, cholesterol and triglycerides levels tended to decrease. The HOMA-IR value increased in relation to BMI and no changes were observed after treatment. Firmicutes were highly abundant in all groups. The lower abundance of Ruminococcus was observed in the OW and OB groups. In the OW group, Blautia, Butyricicoccus, and Roseburia were also observed in increased abundance. In all groups, AmProt consumption tended to increase the abundance of Coproccus, Prevotella, and Collinsella. Conclusions: Supplementation of the children's diet with AmProt showed an improvement in serum cholesterol and triglyceride levels, which could be related to changes in the microbiota related to lipid metabolism.},
}

Humans
Child
Male
Female
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
*Amaranthus/chemistry
Body Mass Index
Blood Glucose/metabolism
*Pediatric Obesity/microbiology/blood
*Plant Proteins/administration & dosage/isolation & purification/pharmacology
*Overweight/microbiology
Cholesterol/blood
Insulin/blood
Triglycerides/blood
Feces/microbiology

@article {pmid42280338,
year = {2026},
author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ},
title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/nu18111694},
pmid = {42280338},
issn = {2072-6643},
support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.

METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.

RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.

CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.},
}

Humans
*Synbiotics/administration & dosage
*Metagenomics/methods
Child, Preschool
*Autism Spectrum Disorder/microbiology/therapy
Male
Child
Female
Pilot Projects
Feces/microbiology
*Gastrointestinal Microbiome
Treatment Outcome
*Precision Medicine/methods

@article {pmid42280669,
year = {2026},
author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W},
title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/plants15111632},
pmid = {42280669},
issn = {2223-7747},
support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; },
abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.},
}

@article {pmid42280715,
year = {2026},
author = {Beckett, T and Hesse, U},
title = {Transcriptome Profiling of Leaves and Roots from Rooibos (Aspalathus linearis) Using Oxford Nanopore Sequencing.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/plants15111679},
pmid = {42280715},
issn = {2223-7747},
support = {PMDS22062326365//National Research Foundation/ ; N/A//Rooibos Council of South Africa/ ; },
abstract = {Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low stress tolerance. Transcriptome data can serve to identify molecular markers for improved stress response, which would speed up selection and facilitate the establishment of breeding programmes. Previously, rooibos leaf transcriptomes have been sequenced using Illumina, which yields short reads, hampering correct reassembly of full-length transcripts. Here, we established Oxford Nanopore-based, long-read transcriptome analysis for leaf and root samples from rooibos. We report on potential pitfalls in data pre-processing (PolyA tail trimming and rRNA removal), and compare two assemblers (RATTLE and RNA-Bloom2) and two clustering algorithms (VSEARCH and CD-HIT). The best assembly comprising 169,122 transcripts was generated using RNA-Bloom2 with short-read polishing, followed by CD-HIT clustering. Of the 95,054 predicted proteins, only 67% were also present in the Illumina dataset. The remainder comprised substantially shorter, mostly full-length sequences from a wide range of primary and secondary biosynthesis pathways. Functional annotation indicated that this transcriptome represents a high-quality, comprehensive resource for data mining. In the leaf fraction, comparative transcriptomics identified overexpressed rooibos transcripts potentially involved in photosynthesis, photorespiration and carbon fixation. In the roots, overexpressed transcripts encoded enzymes potentially involved in regulation of root growth and secondary metabolite biosynthesis. These transcripts may represent first targets for molecular marker development.},
}

@article {pmid42281243,
year = {2026},
author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE},
title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2685381},
doi = {10.1080/19490976.2026.2685381},
pmid = {42281243},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; },
abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Feces/microbiology
Biomarkers/urine/blood
Female
Adult
Male
*Diet
Australia
*Bacteria/classification/genetics/isolation & purification/metabolism
Cross-Over Studies
Middle Aged
Metabolome
Metabolomics
Blood Pressure

@article {pmid42281420,
year = {2026},
author = {Góngora, E and Altshuler, I and Ellis, M and Okshevsky, M and Greer, CW and Whyte, LG},
title = {In Situ Mesocosm Experiment Shows the Capability of the Microbial Community of a Canadian High Arctic Shoreline to Degrade the New Generation of Ship Fuels.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10583},
pmid = {42281420},
issn = {1520-5851},
abstract = {The warming effects of climate change are leading to a reduction in sea ice, which could open new shipping routes across the Arctic, leading to the possibility of hydrocarbon spills washing onto a shoreline. The behavior and biodegradability of new low-sulfur fuels (LSFs), currently being used by vessels worldwide, has not been assessed on Arctic beaches. We deployed mesocosm experiments on a remote Canadian high Arctic beach for 33 days using two LSFs (marine diesel and ultra-low-sulfur fuel oil, ULSFO) and Bunker C fuel oil (currently being phased out). Bunker C was mostly removed from beach sediments by natural attenuation (14.6% biodegradation, 62.8% nonbiological removal), while the LSFs were more easily biodegraded (37.6-72.8% biodegradation, 2.9-10.0% nonbiological removal). Native beach sediment microorganisms, including putatively novel taxa, adapted to the presence of fuel by expressing multiple aliphatic hydrocarbon biodegradation genes, but only few aromatic hydrocarbon degradation genes. Our results suggest that, while not as biodegradable as marine diesel, ULSFO appears to be a more environmentally friendly alternative to Bunker C due to its higher biodegradability under in situ Arctic environmental conditions. However, limited aromatic hydrocarbon biodegradation under cold and nutrient-poor environmental conditions could negatively affect the efficacy of natural attenuation.},
}

@article {pmid42282013,
year = {2026},
author = {Dobbler, PT and Ravi, A and Větrovský, T and Pěchoučková, E and Nemec, A and Kyselková, M},
title = {Single-contig bacterial genomes recovered from cattle fecal metagenomes at farms with variable antibiotic use.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9715194/v1},
pmid = {42282013},
issn = {2693-5015},
abstract = {Cattle feces represent a complex microbial reservoir with implications for animal health and the environmental dissemination of microorganisms and antibiotic resistance genes. Metagenomic studies have shown that cattle fecal communities are dominated by Bacillota and Bacteroidota, whereas low-abundance taxa, including potential pathogens, often remain underrepresented due to methodological detection limits. Here, we present 84 single-contig, medium- to high-quality metagenome-assembled genomes (MAGs) recovered from cattle feces after enrichment for bacteria able to grow in acetate-supplemented minimal medium. The MAGs were classified within the phyla Actinomycetota (20 MAGs), Bacillota (5), Bacteroidota (21), Patescibacteriota (5), and Pseudomonadota (33), with 41 MAGs representing putative novel taxa at species to family level. Nineteen MAGs carried antibiotic resistance genes and six MAGs were assigned to opportunistic pathogenic species. This dataset thus provides a genomic resource for studies of bacterial diversity and antimicrobial resistance at the animal-environment interface within a One Health framework.},
}

@article {pmid42282041,
year = {2026},
author = {Schutz, C and Queiroz, A and Mota, T and Ward, A and Barr, D and Janssen, S and Shey, M and Wilkinson, R and Wilkinson, K and Burton, R and Lelouvier, B and Andrade, B and Meintjes, G},
title = {Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9856875/v1},
pmid = {42282041},
issn = {2693-5015},
abstract = {Background: HIV-associated tuberculosis (HIV-TB) results in unacceptably high mortality rates despite appropriate treatment. Patients hospitalized with HIV-TB often have disseminated tuberculosis and sepsis syndrome which may result in gastro-intestinal barrier dysfunction and facilitate microbial product translocation. Microbial product translocation may contribute to HIV-TB deaths by driving systemic inflammation. Objectives: To assess microbial product translocation and gastrointestinal epithelial damage in patients hospitalized with HIV-TB and the association with 12-week mortality and biomarkers of tuberculosis dissemination. To describe the bacterial blood microbiome (abundance and diversity) in patients with HIV-TB, its association with mortality and tuberculosis dissemination and compare to outpatient controls. Methods: Patients hospitalized with a new diagnosis of HIV-TB were enrolled and prospectively followed for 12 weeks. Markers of microbial product translocation and gastrointestinal damage were measured in a subset (n=373) and bacterial 16s rDNA was quantitated and metagenomic sequencing performed in 235 patients. Microbial product translocation and gastrointestinal epithelial damage marker concentrations were compared between hospitalized patients who died and survivors and inpatients compared to HIVpositive outpatient controls. Logistic regression analysis was performed to determine associations with mortality. Bacterial abundance, diversity and immune perturbation was measured and analysed across patient outcome groups and in patients with tuberculosis dissemination. Results: Patients hospitalized with HIV-TB had significantly higher concentrations of bacterial 16s rDNA, soluble CD14 (sCD14), lipopolysaccharide binding protein (LBP), trefoil factor 3 (TFF3) and lower endotoxin core antibody IgM (EndoCAB), compared to outpatient controls. Soluble CD14 and TFF3 were significantly higher and EndoCAB lower in inpatients who died versus survivors. TFF3 was independently associated with mortality. LPS, sCD14, LBP, EndoCAB and TFF3 showed significant trends in patients with positive biomarkers of tuberculosis dissemination. Metagenomic sequencing showed higher diversity in hospitalised HIV-TB patients compared to controls, but diversity was not different between outcome groups. Mycobacterium genus proportions were increased in hospitalised patients who died compared to survivors. Conclusion: We found evidence of increased gastrointestinal epithelial damage and microbial product translocation in patients hospitalized with HIV-TB and in patients with positive biomarkers for tuberculosis dissemination, however, only TTF3 (a marker of gastrointestinal epithelial damage), was independently associated with mortality.},
}

@article {pmid42282268,
year = {2026},
author = {Frame, LA and Warren, A and Al Qalam, A and Corr, PG and Farah, M and Karam, M and Rangoussis, K and Fahim Devin, M and Celikkol, Z and Gordon, L and Villarreal, D and Catto, E and Udam, Y and Thompson, K and Lubinski, O and Samman, A and Badawi, A and Hack, H and Hunter, M and Hines, I and Servetas, S and Jackson, SA and Hasan, NA and Kogan, M},
title = {Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2679810},
pmid = {42282268},
issn = {2993-3935},
abstract = {BACKGROUND: Associations between the gut microbiome and cognitive decline remain inconsistent, reflecting methodological variability, small cohorts, and limited integration of behavioral and lifestyle factors. The microbiota-gut-brain axis may influence cognition through metabolic, immune, and neuroendocrine pathways affecting mood, decision-making, and health behaviors.

METHODS: This prospective, proof-of-concept study integrated multidimensional phenotyping with metagenomic sequencing (shotgun) in adults (50-90 y) around Washington, DC. Participants were classified as healthy controls (HC) or mild cognitive impairment (MCI) by clinical history; early Alzheimer's disease (eAD) participants were unable to complete study requirements. Longitudinal assessment used Boston Cognitive Assessment (BoCA), patient-reported outcomes (PROMIS-29), dietary intake and quality (DietID™), readiness-for-change (adapted URICA), at-home stool sample collection.

RESULTS: Seventeen participants completed sufficient assessments (HC n = 11; MCI n = 6). Substantial overlap in gut microbiome composition was observed between HC and MCI. Poorly characterized or uncommon taxa drove trends; unassigned taxa were common. Assessment revealed high diet quality and variability in dietary patterns and key components (vegetables, whole grains, fat, fish). Participants demonstrated high readiness to engage in nutritional behavior change, with individuals with MCI reporting greater concern about maintaining changes and a stronger desire for external support.

CONCLUSIONS: Integrating multidimensional phenotyping with metagenomics is feasible in cognitive decline. Findings highlight biological and behavioral heterogeneity, limitations of species-level inference, and diet and behavioral readiness as modifiable contextual factors.},
}

@article {pmid42282663,
year = {2026},
author = {Torres-Morales, J and Dewhirst, F and Kauffman, KM and Mark Welch, J and Borisy, G},
title = {Site-specialization of human oral Porphyromonas species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.02.729646},
pmid = {42282663},
issn = {2692-8205},
abstract = {Site-specificity within the human oral cavity reflects adaptation mechanisms such as genome divergence and metabolic specialization. Members of the genus Porphyromonas are distributed across oral sites in health and disease, yet the specific distribution of taxa and the functional basis of their site-specificity remain poorly understood. We analyzed 1,242 metagenomes from nine oral sites in healthy individuals and 24 subgingival plaque samples from individuals with periodontitis. Competitive mapping to a dereplicated genus-level pangenome of 84 reference genomes, combined with phylogenomic, gene-level detection, and functional profiling, revealed distinct site-specific distribution patterns, ecotype differentiation, and metabolic specialization across Porphyromonas taxa. Porphyromonas pasteri was the most abundant and widespread taxon in healthy subjects, comprising two ecotypes--one mucosal, one plaque-associated. Porphyromonas gingivalis was rare in healthy subjects but present in periodontal disease, although detected in only half of periodontitis samples. P. gingivalis exhibited the broadest metabolic repertoire, suggestive of a survival strategy adaptive to disparate conditions. In contrast, Porphyromonas catoniae, restricted to healthy dental plaque, lacked biosynthetic pathways for cobalamin, biotin, and serine, implying nutritional dependency on other taxa or the host. Porphyromonas endodontalis, detected in subgingival plaque across both health and disease, also lacked several metabolic pathways. A 44 kb conjugative element identified in P. gingivalis was detected across healthy and periodontitis subgingival plaque microbiomes independently of the P. gingivalis chromosome, indicating horizontal transfer. These findings reveal genomic divergence and complex metabolic specialization among Porphyromonas taxa, refining our understanding of their role in the ecological structure of the human oral microbiome.},
}

@article {pmid42282812,
year = {2026},
author = {Jiang, AK and Grant, MR and Arp, G and Dufault-Thompson, K and Clarke, AM and Li, Y and Lehman, D and Jarmusch, AK and Hall, B and Jiang, X},
title = {Discovery of BilV reveals a multienzymatic basis for bilirubin reduction across vertebrate gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.01.729425},
pmid = {42282812},
issn = {2692-8205},
abstract = {Gut bacteria reduce bilirubin to urobilinogen, allowing it to be excreted through feces and urine, but studies have long noted a heterogeneous mixture of partially reduced bilirubin-derived intermediates, suggesting that multiple enzymes are involved. Here we identify bilirubin vinyl reductase (BilV), a novel Old Yellow Enzyme family reductase encoded in the genomic neighborhood of the known bilirubin reductase (bilR). Using heterologous expression and LC-MS/MS, we show that BilR acts on the methine bridges in the bilirubin reduction pathway; co-expression with BilV enables vinyl-group reduction and complete conversion to urobilinogen. In bacterial genomes, bilV co-occurs primarily with the bilR -insertion subtype and is largely absent alongside bilR -short. Analysis of 1,197 gut metagenomes across 14 vertebrate species reveals that this differential co-occurrence shapes pathway availability across hosts: carnivores and omnivores carry balanced bilR and bilV , whereas avian microbiomes, dominated by bilR -short, are depleted for bilV . These findings establish that bilirubin reduction to urobilinogen involves two enzymes with complementary regioselectivity, and that their distribution across vertebrate gut microbiomes varies in concert with host bile pigment chemistry.},
}

@article {pmid42283066,
year = {2026},
author = {Zhang, J and Liang, J and Lv, F and Guo, Z},
title = {Maternal vaginal colonization screening for term singleton pregnancy: comparative evaluation of metagenomic next-generation sequencing (mNGS) versus real-time quantitative PCR (qPCR).},
journal = {Practical laboratory medicine},
volume = {50},
number = {},
pages = {e00542},
pmid = {42283066},
issn = {2352-5517},
abstract = {OBJECTIVE: To investigate the distribution characteristics of potential high-risk pathogens for early-onset neonatal infection in maternal vaginal secretions, and to perform a head-to-head comparative evaluation of detection performance for target pathogens between metagenomic next-generation sequencing (mNGS) and real-time quantitative polymerase chain reaction (qPCR), with conventional bacterial culture as the reference standard.

METHODS: A total of 294 valid maternal vaginal secretion samples were prospectively collected and tested in parallel using qPCR, mNGS, and conventional bacterial culture. The Chi-square test was used to compare the differences in pathogen detection rates among the three methods. Receiver operating characteristic (ROC) curve was plotted to calculate the area under the curve (AUC) and 95% confidence interval (CI), to systematically evaluate the detection performance of the two methods for target pathogens.

RESULTS: The spectrum of potential early-onset neonatal pathogens in maternal vaginal secretions, ranked by detection rate, was as follows: Staphylococcus aureus, Streptococcus agalactiae, Ureaplasma urealyticum, Listeria monocytogenes, and Campylobacter fetus. The detection rates of these target pathogens by qPCR, mNGS, and bacterial culture showed high consistency, with no statistically significant difference in detection rates among the three methods (all P > 0.05). ROC curve analysis showed that the AUC values of both qPCR and mNGS for the above major pathogens were all above 0.90, which were significantly different from the null hypothesis of AUC = 0.5 (all P < 0.05), indicating good detection performance; while there was no significant difference in AUC values between qPCR and mNGS (all P > 0.05). In addition, Listeria monocytogenes (3 cases) and Campylobacter fetus (1 case) were only detected by qPCR and mNGS, while not isolated by conventional culture.

CONCLUSION: This head-to-head comparative study confirms that both mNGS and targeted qPCR have high accuracy and consistency for detecting potential early-onset neonatal pathogens in maternal vaginal secretions. We propose a tiered antenatal screening strategy for maternal vaginal pathogenic colonization: qPCR is recommended as the first-line tool for routine antenatal screening due to its high cost-effectiveness and rapid turnaround time, while mNGS is reserved for high-risk pregnant women (e.g., preterm premature rupture of membranes, clinical chorioamnionitis), culture-negative suspected infection cases, or scenarios requiring comprehensive pathogen profiling, to take full advantage of its unbiased, broad-spectrum detection capability. This integrated screening strategy requires further prospective validation with paired neonatal clinical outcome data to confirm its value in the prevention and early intervention of early-onset neonatal infection.},
}

@article {pmid42283067,
year = {2026},
author = {Wei, F and Wang, X and Lv, H and Xia, H and Gan, G and Chen, X and Liu, X and Chen, H and Zhao, L},
title = {Identification of a potential novel Staphylococcus species via genomic sequencing: A neonatal infection case report.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02631},
pmid = {42283067},
issn = {2214-2509},
abstract = {BACKGROUND: Coagulase-negative Staphylococci (CoNS) are common symbiotic Gram-positive bacteria colonizing human skin and mucous membranes with lower virulence than Staphylococcus aureus. As crucial pathogens of neonatal infections, they often harbor multiple drug resistance genes and can induce neonatal pneumonia, sepsis, suppurative meningitis, and other clinical manifestations.

CASE PRESENTATION: A preterm neonate at 29[+1] weeks' gestation complicated by respiratory distress syndrome and pneumonia received empirical ceftazidime and penicillin for 8 days. The condition initially improved but suddenly deteriorated on postnatal day 17 with septic shock, fever, and anemia. Routine tests suggested Staphylococcus capitis infection, and targeted anti-infective and supportive treatments relieved symptoms. Given the inconsistenty between the infection severity and that of typical Staphylococcus infections, metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) were further performed, identifying a potential novel Staphylococcus species closely related to Staphylococcus warneri. Nevertheless, the origin of this potential novel species remains unclear, which needs further verification.

CONCLUSION: For neonates with sudden clinical deterioration, intractable infection or ambiguous conventional microbial results, mNGS and WGS facilitate accurate pathogen identification and treatment adjustment. This potential novel strain discovery highlights the importance of enhanced vigilance against bacterial multidrug resistance and the emergence of potential novel pathogens in neonatal care.},
}

@article {pmid42283460,
year = {2026},
author = {Tothero, GK and Keffer, JL and Emerson, D and Fleming, EJ and Chan, CS},
title = {Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0176825},
doi = {10.1128/msystems.01768-25},
pmid = {42283460},
issn = {2379-5077},
abstract = {The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59-3.04 Mb) than those of Groups 2 (4.55-6.06 Mb) and 3 (3.94-5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.IMPORTANCEResearchers have long noted differences in metal oxidation, morphology, and ecology among Sphaerotilus-Leptothrix, but longstanding confusion over phylogeny and genus boundaries led to inconsistent taxonomic classification between the two genera. This confusion stems from previous work that used isolates that are unavailable or lost distinguishing traits in culture, and from limited genomic data. Furthermore, the Leptothrix type strain L. ochracea has never been isolated. This study provides molecular evidence that substantiates calls to reassign some Leptothrix members to the genus Sphaerotilus but adds to an emerging body of evidence that Group 1 L. ochracea and now L. toolikensis represent a functionally distinct lineage. While genomic similarity metrics left taxonomic divisions unclear, integrating metabolic potential with phylogeny resolved genus boundaries based on clear functional groupings. This polyphasic approach for delineating genera clarifies longstanding taxonomic confusion and refines our understanding of functional diversity both across and within Sphaerotilus-Leptothrix lineages.},
}

@article {pmid42283524,
year = {2026},
author = {Hashimoto, K and Fukushima, K and Nakamura, S and Kida, H},
title = {Reply to Rojas-Ponce, "Operational considerations for implementing culture-free mycobacterial sequencing in routine laboratory settings".},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0056426},
doi = {10.1128/jcm.00564-26},
pmid = {42283524},
issn = {1098-660X},
}

@article {pmid42283633,
year = {2026},
author = {Gomez-Gallego, T and Udaondo, Z and Palacios-Ferrer, R and Díaz-Martínez, L and Ramos, JL},
title = {Development of advanced bioinformatic profiles to improve the detection and functional understanding of fungal acid phosphatases.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0210625},
doi = {10.1128/aem.02106-25},
pmid = {42283633},
issn = {1098-5336},
abstract = {We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.},
}

@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.},
}