@article {pmid42726613,
year = {2026},
author = {Chen, S and Guan, Q and Zhou, D and Duan, L and Hu, J},
title = {SPFuseRanker: A Multi-Importance Score Fusion Framework for Core Microbiome Identification in Metagenomic Data.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3733474},
pmid = {42726613},
issn = {2998-4165},
abstract = {Clinical metagenomic data are typically high-dimensional, sparse, and zero-inflated, and are often characterized by limited sample sizes and measurement noise. In addition, different feature-importance methods may produce inconsistent taxon rankings, which limits the stability of single-method feature selection and complicates the identification of candidate core microbiome members. To address this issue, we propose SPFuseRanker, a score-fusion-based ranking framework for integrating multiple microbial importance measures in metagenomic data. The method constructs a consensus score vector by combining heterogeneous importance signals, including statistical tests, correlation analysis, univariate classification performance, and tree-based feature importance. A top-weighted distance function based on Softmax normalization is introduced to emphasize highly ranked taxa during the fusion process. The optimization of the fused score vector is formulated as a minimum-distance problem and solved using a genetic algorithm (GA). We evaluate the proposed method using both synthetic simulations and a real-world systemic lupus erythematosus (SLE) gut microbiome dataset. Experimental results show that SPFuseRanker achieves more stable ranking performance compared with several representative rank aggregation and score fusion methods, particularly in terms of ranking consistency and robustness under noise. In addition, the selected candidate microbial taxa demonstrate improved predictive performance in disease classification tasks, suggesting their potential relevance to SLE-associated microbial signatures. Overall, SPFuseRanker provides a practical framework for integrating multi-source importance information and may serve as a useful tool for candidate core microbiome identification in metagenomic studies.},
}

@article {pmid42727121,
year = {2026},
author = {Huo, P and Han, T and Hou, J and Zhang, T and Gao, P and Li, J},
title = {Organic matter and greenhouse gas dynamics across contrasting hydrological states in intermittent rivers.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126849},
doi = {10.1016/j.watres.2026.126849},
pmid = {42727121},
issn = {1879-2448},
abstract = {As intermittent rivers expand globally, understanding how contrasting hydrological conditions relate to organic matter (OM) characteristics and greenhouse gas (GHG) dynamics is important. We investigated CO2 and N2O dynamics across contrasting low-flow (LF) and high-flow (HF) campaigns in intermittent rivers. Pore-water GHG concentrations consistently exceeded those in overlying water, suggesting an important internal GHG pool. During the LF campaign, higher chlorophyll-a concentrations coincided with lower overlying-water CO2 concentrations, whereas the HF campaign showed greater soil-OM contribution, higher DOC, a stronger humic-like/aromatic DOM signature, and higher dissolved CO2. Multivariate RDA explained substantial joint CO2-N2O variation (adjusted R[2] = 0.720 in LF and 0.668 in HF); nutrients retained large unique fractions in both campaigns, while the OM-associated fraction was larger in HF. Metagenomic profiles linked pore-water CO2 to multiple carbon-processing and respiratory functions. Pore-water N2O was less clearly associated with broad microbial-community turnover but showed stronger relationships with substrate balance and denitrification-related functional composition. Higher N2O coincided with lower WDOC/NO3[-]-N; CLR-based analyses further showed significant associations between N2O and denitrification-related gene profiles, with the relative representation of nosZ versus nirK/nirS decreasing as N2O increased. These patterns were consistent with greater incomplete-denitrification potential under relatively low carbon availability. Across three thin boundary layer (TBL) model parameterizations, estimated CO2 emissions were consistently higher in the HF campaign, whereas the direction of the N2O flux contrast varied among models. These findings highlight distinct environmental and microbial associations of CO2 and N2O across contrasting hydrological states in intermittent rivers.},
}

@article {pmid42727124,
year = {2026},
author = {Yang, H and Hoque, MM and Zhao, J and Dovom, HA and Hai, FI and Jiang, G},
title = {Wastewater-derived gut microbiome: global patterns and associations with population health.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126898},
doi = {10.1016/j.watres.2026.126898},
pmid = {42727124},
issn = {1879-2448},
abstract = {Urban wastewater systems aggregate gut microbiome signals from large populations, enabling exploration of their associations with population-level health patterns. However, it remains unclear whether wastewater-derived gut microbiome (WGM) simply represents a composite of individual gut microbes or whether it forms structured ecological patterns with potential relevance to population-level health-burden gradients. We analyzed 661 untreated wastewater metagenomes from 220 cities across 97 countries spanning all inhabited continents to characterize the global WGM. WGM exhibited broad phylogenetic diversity, with more than 95% of detected genera occurring in over 80% of samples worldwide. Co-occurrence network analysis revealed distinct, densely connected modules and structurally heterogeneous hub and bridging taxa, indicating organized network architecture that was not explained by abundance alone. Under the iCAMP framework, WGM turnover was predominantly classified as dispersal limitation across climate zones, continents, development levels, and sampling years. We then explored associations between WGM and population-level health indicators using a multi-model machine-learning framework. Across 21 health-burden indicators covering non-communicable diseases, infectious diseases, injuries, and mental health conditions, WGM-based classification of low- versus high-burden countries exceeded shuffled-label expectations for 19 indicators. Recurrently selected WGM taxa were identified across multiple feature-selection strategies. Together, these results show that operationally defined WGM profiles show reproducible structure and broad associations with country-level health-burden indicators.},
}

@article {pmid42727145,
year = {2026},
author = {Li, Z and Luo, S and Yang, X and Liang, Y and Feng, Z and Yang, S and Yuan, K and Yang, Y and Ming, L and Yu, K and Zhang, J and Luan, T and Chen, B},
title = {Concurrence of antibiotic resistance genes in plasmid genomes shape environmental resistomes.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143571},
doi = {10.1016/j.jhazmat.2026.143571},
pmid = {42727145},
issn = {1873-3336},
abstract = {Horizontal transfer of plasmid-associated antibiotic resistance genes (ARGs) plays a pivotal role in environmental antibiotic resistance dissemination. Here, we characterized ARG concurrence patterns in plasmid genomes and examined plasmid-associated ARGs across 106 environmental metagenomes. Approximately half of known ARG subtypes (257) occurred in plasmid genomes, and nearly one-quarter of plasmids carried ARGs, including "super plasmids" harboring over 20 ARG subtypes spanning 10 antibiotic categories. Aminoglycoside resistance genes (AmRGs) exhibited the highest concurrence frequency (CF) with other ARGs in plasmid genomes, followed by beta-lactam and sulfonamide resistance genes. Many high-risk ARGs preferentially coexisted with AmRGs (45.6% of total AmRGs CF). Environmental metagenomes revealed distinct plasmid-associated ARG profiles between polluted and relatively pristine environments, with significantly greater diversity and abundance under anthropogenic pollution. Five widespread ARG subtypes occurred across all environmental media, whereas polluted environments contained more unique ARGs. Co-occurrence networks identified AmRGs as "hubs" linking multiple ARG subtypes in environmental resistomes. Plasmid-ARG interaction networks further showed more complex potential plasmid-mediated concurrent dissemination in polluted environments. Collectively, use of aminoglycosides is more likely to cause co-transmission of multiple plasmid-related ARGs than other antibiotics, and CF of ARGs is proposed as an important supplementary factor for evaluating ARG dissemination under anthropogenic antibiotic stress.},
}

@article {pmid42727147,
year = {2026},
author = {Xu, QJ and Liu, XR and Sima, M and Zheng, YF and Zhao, HP and Alvarez, P},
title = {Hydrogen-supported biodefluorination of unsaturated perfluorinated carboxylic acids.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143544},
doi = {10.1016/j.jhazmat.2026.143544},
pmid = {42727147},
issn = {1873-3336},
abstract = {PFMeUPA (i.e., (E)-perfluoro(4-methylpent-2-enoic acid) is a unsaturated perfluorohexanoic acid wtih emerging concern due to its potential to cause developmental toxicity. Here, we investigate the sustainable biological treatment of PFMeUPA under anoxic conditions by delineating batch degradation potential and continuous-flow reactor dynamics using hydrogen (H2) as the sole electron donor. In batch assays inoculated with anaerobic digestion sludge, an enriched hydrogenotrophic consortium achieved near-complete removal of 50 μM PFMeUPA over 90-days with a stoichiometric release of 125 μM fluoride (F[-]), representing a 26% defluorination extent that corresponds to the cleavage of two C-F bonds per molecule. The continuous-flow H2-based membrane biofilm reactor (MBfR) harboring this enriched anaerobic biofilm was operated for 130 days, achieving 100% removal of 5 μM PFMeUPA and 20% of defluorination at a hydraulic retention time (HRT) = 6 h. Transformation product identification using high-resolution mass spectrometry suggests dominance of reductive defluorination and a shift toward hydrogenated byproducts at later stages. Metagenomic results indicate the enrichment of microbial taxa including Hydrogenophaga (hp_bin.22) and and Azonexus (hp_bin.19) genomes, which carry genes for hydrogen metabolism (hoxH) and fluoride efflux pumps (crcB). This work demonstrates the feasibility of hydrogen-supported biological treatment for unsaturated perfluorinated carboxylic acids from contaminated water. SYNOPSIS: We demonstrate reductive defluorination of branched PFAS by a H2-fed biofilm, with co-occurring hydrogenase and fluoride exporter genes in Hydrogenophaga and Azonexus as potential biodefluorination biomarkers.},
}

@article {pmid42727395,
year = {2026},
author = {Zhao, X and Sun, J and Sun, WL and Sun, X and Zhang, YH and Zhang, PD},
title = {Functional convergence of rTCA-related carbon-fixation potential and biochemical residue accumulation in seagrass sediments.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108398},
doi = {10.1016/j.marenvres.2026.108398},
pmid = {42727395},
issn = {1879-0291},
abstract = {Seagrass meadows are globally significant blue carbon ecosystems, yet the microbial and biochemical mechanisms driving sediment organic carbon (SOC) accumulation remain poorly understood. To address this, we employed an integrated approach combining metagenomic sequencing, biochemical assays, and structural equation modeling to investigate carbon cycling in the seagrass and adjacent unvegetated sediments of Swan Lake, China. A total of 115,179 carbon fixation genes and 119,615 decomposition genes were identified, revealing distinct microbial community structures among the habitats. Seagrass sediments harbored more diverse carbon-fixing (CFMs) and decomposing microorganisms (CDMs), with 83 medium-to high-quality metagenome-assembled genomes (MAGs) recovered. While neutral community model analysis indicated that stochastic processes predominantly governed community assembly, functional analyses highlighted specific drivers of sequestration. The reductive tricarboxylic acid (rTCA) cycle emerged as the dominant carbon fixation pathway, with key genes (e.g., aclA, korA) showing strong positive correlations with SOC. Conversely, decomposition pathways for starch and lignin were negatively associated with SOC. Furthermore, seagrass sediments exhibited elevated concentrations of total amino sugars (TAS) and lignin phenols (TLP), which linked significantly to carbon fixation rather than decomposition. PLS-SEM revealed statistically significant associations among seagrass traits, environmental variables, microbial carbon-fixation potential, biochemical residue pools, and SOC, supporting a mechanistic pathway in which enhanced microbial functional potential drives the accumulation of recalcitrant biochemical residues, thereby facilitating long-term carbon retention in sediments. These findings emphasize the pivotal role of microbial anabolism and the accumulation of biosynthetic residues in sediment carbon storage, suggesting a functional convergence in seagrass-driven carbon sinks.},
}

@article {pmid42727575,
year = {2026},
author = {Deng, ZL and Safaei, N and McHardy, AC},
title = {Metax enables accurate cross-domain taxonomic profiling of metagenomes.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.08.024},
pmid = {42727575},
issn = {1097-4172},
abstract = {Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomic profiler that integrates coverage-based probabilistic modeling with an expectation-maximization framework to distinguish true microbial signals from artifacts. Across >600 samples from host-associated, environmental, wastewater, and low-biomass clinical settings, including benchmarks with limited reference representation, Metax improved profiling accuracy, achieving on average 55% higher F1 scores and 45% lower Bray-Curtis dissimilarity than other methods. Moreover, this broad evaluation demonstrated that Metax resolved bacterial and viral signatures of peri-implantitis in oral microbiomes and revealed signals suggestive of reagent-borne contaminants and reference misassemblies in plasma-cell-free DNA. By leveraging genome-wide coverage evidence, Metax enables robust cross-domain profiling across diverse sample types and sequencing depths, including settings where reference databases are highly incomplete.},
}

@article {pmid42727829,
year = {2026},
author = {Xu, P and Li, L and Wei, Y and Xu, Y and Zhang, Y and Ye, W and Peng, X},
title = {Divergent responses of the rhizosphere microbiome to organic amendments sustain cadmium immobilization and low crop Cd accumulation after remediation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135835},
doi = {10.1016/j.biortech.2026.135835},
pmid = {42727829},
issn = {1873-2976},
abstract = {This study integrated a two-stage immobilization-cultivation experiment to evaluate the effects of three immobilization strategies (inorganic, organic, and organo-mineral amendments) and two fertilization modes (mineral fertilizer alone and partial substitution with organic fertilizer) on soil cadmium (Cd) immobilization and plant Cd accumulation. During the immobilization phase, the organo-mineral strategy achieved the highest Cd immobilization efficiency of 69.5%. In the cultivation phase, the use of mineral fertilizer alone led to Cd remobilization, whereas organic substitution maintained or even enhanced immobilization, reducing shoot Cd accumulation in pak choi by up to 58.3%. Notably, the combined organic immobilization and organic substitution treatment (OP) was particularly effective: despite not having the lowest soil available Cd, it achieved the lowest plant Cd accumulation (2.83 mg·kg[-1]). Genomic analysis indicated that the OP treatment enriched core metagenome-assembled genomes (MAGs), including MAG8/Pelagerythrobacter, MAG13/Sphingomicrobium, and MAG30/VAYN01, which contained the highest abundances of genes related to extracellular polymeric substance (EPS) synthesis, phosphorus mobilization, and complexation-precipitation, suggesting the potential of these microbes to enhance EPS secretion and phosphate precipitation for rhizospheric Cd interception. This functional potential, along with the measured high EPS content (259.88 mg·kg[-1]) and low plant Cd accumulation in the OP group, provides coherent correlative evidence supporting the hypothesis that an "EPS barrier-chemical precipitation" mechanism synergistically reduces Cd migration to root surfaces. Collectively, continuous organic management can maintain soil fertility, enhance Cd immobilization, and promote low-Cd crop production, offering an efficient strategy for the safe utilization of remediated farmland.},
}

@article {pmid42727916,
year = {2026},
author = {Song, D and He, L},
title = {Functional Potential of C-N-S-Fe-As Cycling in Shallow Clay Layers and Its Influence on Arsenic Migration and Transformation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125667},
doi = {10.1016/j.envres.2026.125667},
pmid = {42727916},
issn = {1096-0953},
abstract = {Clay layers are important reservoirs, reaction interfaces, and potential release sources of arsenic (As) in shallow groundwater systems. However, microbial functions within these layers and their regulatory mechanisms for As migration and transformation remain insufficiently understood. Clay sediments from different depths in a shallow borehole of the Jianghan Plain were selected in this study. The functional potential of microbially mediated C-N-S-Fe-As cycling was systematically evaluated. Its potential influence on As migration and transformation in clay layers was also assessed. The results show that vertical variations in mineral composition and grain-size structure provide differentiated microenvironments. These microenvironments may support microbial colonization, organic matter preservation, and redox reactions. The microbial C-N-S-Fe-As metabolic potential in clay layers shows clear vertical differentiation. Nitrification- and oxidation-related genes are relatively enriched in the upper clay layer. This enrichment may form an oxidative barrier favorable for As adsorption and immobilization. Carbon degradation and fermentation can provide electron donors for Fe(III) reduction, nitrate reduction, and sulfate reduction in the middle clay layer. Within the studied profile, the middle interval may represent a key geochemical zone for As activation and mobilization. Microbial Fe(III) reduction is more likely to be the key process driving reductive dissolution of As-bearing iron oxides and As release. Fe/S reduction-related functions are generally weakened in the lower clay layer. Accordingly, the As transformation flux is relatively limited. A site-specific vertical microbial functional zonation pattern is proposed for the studied clay profile. This pattern consists of an upper oxidative immobilization barrier, a middle reductive release core, and a lower low-activity transformation zone. This site-specific study provides insights into the potential microbial geochemical role of clay layers in high-As groundwater formation in the Jianghan Plain.},
}

@article {pmid42728037,
year = {2026},
author = {Gurnani, B and Kaur, K},
title = {Innovations in the diagnosis of Pythium insidiosum keratitis: molecular advances and the path to point-of-care testing.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2026.2733166},
pmid = {42728037},
issn = {1744-8352},
abstract = {INTRODUCTION: Pythium insidiosum keratitis is an aggressive, vision-threatening corneal infection that closely mimics fungal keratitis clinically and on smear microscopy, frequently delaying targeted therapy and appropriate surgical intervention. Rapid and reliable molecular diagnosis is therefore critical, particularly given the small-volume, low-biomass nature of corneal specimens encountered in routine ophthalmic practice worldwide, especially in endemic regions with limited diagnostic infrastructure.

AREAS COVERED: This review summarizes advances in molecular diagnostics for Pythium insidiosum keratitis, including conventional and nested PCR, duplex and multiplex PCR, real-time PCR, high-resolution melt analysis, loop-mediated isothermal amplification (LAMP), colorimetric LAMP, metagenomic sequencing, and CRISPR-based platforms. Key diagnostic targets such as ITS, 18S rRNA, COX2, and PinsEXO1 are evaluated for analytical sensitivity, specificity, turnaround time, contamination control, and applicability in endemic, resource-limited settings and peripheral ophthalmic centers with limited infrastructure and limited availability of trained personnel.

EXPERT OPINION: Future progress will depend on integrating robust molecular targets with closed-tube, contamination-resistant amplification platforms within tiered diagnostic systems. Colorimetric LAMP offers immediate translational potential, while PinsEXO1-based assays enhance specificity. CRISPR-based detection and microfluidic integration remain promising but require rigorous validation in ocular specimens before routine clinical adoption in diverse real-world settings globally, across varied healthcare systems and populations.},
}

@article {pmid42728095,
year = {2026},
author = {Hernandez-Valencia, JC and Ramírez, JD},
title = {Culture-free genomics: a shift toward genome-wide applications in chagas disease and leishmaniasis.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2026.2733187},
pmid = {42728095},
issn = {1744-8352},
abstract = {INTRODUCTION: Chagas disease and leishmaniasis remain major neglected tropical diseases, with diagnosis and surveillance constrained by low parasite burden, multiclonal infections, and complex parasite biology. Traditional culture-dependent and targeted molecular approaches fail to capture the full genomic diversity of Trypanosoma cruzi and Leishmania spp. limiting clinical and epidemiological utility. High-throughput sequencing has enabled a shift toward culture-free genomic approaches, allowing direct parasite DNA analysis from host-derived samples.

AREAS COVERED: We review the evolution from early sequencing to second- and third-generation platforms, highlighting culture-free detection and genomic surveillance. We discuss enrichment strategies (selective whole-genome amplification (SWGA) and capture-enrichment sequencing (CES)) addressing low parasite DNA abundance in complex samples, alongside metagenomics and portable sequencing for field-based surveillance and diagnostics. Biological and technical challenges are examined, including genomic complexity, structural variation, life-cycle-driven plasticity, and fragmented reference genomes across T. cruzi discrete typing units (DTUs) and Leishmania species. We further explore how direct-from-host data can improve diagnostics, enhance transmission surveillance, support treatment monitoring, and guide control strategies.

EXPERT OPINION: Culture-free genomic approaches represent a transformative advance in kinetoplastid research, providing resolution that culture-dependent methods cannot deliver. Their diagnostic contribution is at present largely indirect, operating through the identification of improved molecular and serological targets rather than through sequencing as the assay itself. Persistent barriers of cost, infrastructure, standardization, and bioinformatics capacity, together with the absence of formal clinical validation, currently confine these methods to research and surveillance settings. Successful translation will require methodological innovation, expanded genomic resources, and investment to bridge the gap between research and public health.},
}

@article {pmid42728602,
year = {2026},
author = {Akintunde, DM and Burton, R and Olaleye, M and Akintunde, OO and Idris, SH},
title = {Antimicrobial resistance in Noma control: a costly neglect within existing neglect.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {42728602},
issn = {1348-8945},
abstract = {INTRODUCTION: Noma is a severe gangrenous orofacial disease affecting malnourished children aged 2-6 years in extreme poverty, with 85-90% mortality if untreated. Recently classified as a Neglected Tropical Disease, it is managed mainly with empirical broad-spectrum antibiotics. Antimicrobial resistance (AMR) threatens to undermine treatment, yet AMR remains largely absent from Noma research and policy. This review examines AMR prevalence and drivers in Noma, identifies knowledge and policy gaps, and proposes recommendations.

METHODS: We reviewed literature on Noma microbiology and documented AMR, plus WHO NTD and AMR policy documents. Community and health system factors and surveillance capacity in Noma-endemic regions, primarily Sub-Saharan Africa, were synthesized.

RESULTS: Noma lesions show marked dysbiosis with frequent detection of Fusobacterium necrophorum, Prevotella spp., Staphylococcus aureus, Pseudomonas aeruginosa, and a novel "Treponema sp. A". A 25-year retrospective analysis found that >92% of patients presented late, requiring prolonged antibiotics. Direct AMR data are scarce. Case reports documented MDR-Escherichia coli in Afghanistan (2012), Vancomycin-resistant Enterococci in South Korea (2022), ESBL E. coli in Mali (2021), Serratia marcescens (Ticarcilline, amoxicillin, and sulfamethoxazole-trimethoprim) and Pseudomonas aeruginosa (Rifampicin) in Chad (2014); and Pseudomonas aeruginosa (penicillins, carbapenems, aminoglycosides, sulfamethoxazole-trimethoprim, and nitrofurantoin) in Italy (2015). A recent metagenomic study reported high β-lactam and metronidazole resistance determinants, especially in Prevotella spp. Drivers include empirical broad-spectrum antibiotic use, self-medication, irrational prescribing, and weak diagnostics, with only a small share of laboratories across 14 SSA countries performing routine bacteriology and susceptibility testing. Policy gaps persist: WHO NTD and AMR strategies are siloed, anaerobes are excluded from GLASS surveillance, and Noma guidelines lack AMR triggers.

CONCLUSION: AMR risks reversing gains in Noma control, and treatment centers may become AMR amplification sites without stewardship. Given limited microbiology data, we recommend adding AMR indicators to WHO and national Noma strategies, integrating anaerobic AMR surveillance at sentinel sites, generating Noma-specific antibiograms, and mandating antimicrobial stewardship in Noma programs. Mainstreaming AMR in Noma research and policy is essential to preserve therapeutic options.},
}

@article {pmid42728927,
year = {2026},
author = {Olsson, B and Thorén, MH and Eriksson, O and Johannesson, H},
title = {Spatial structure and growth dynamics of fairy rings formed by Marasmius oreades.},
journal = {Royal Society open science},
volume = {13},
number = {8},
pages = {rsos260575},
doi = {10.1098/rsos.260575},
pmid = {42728927},
issn = {2054-5703},
abstract = {Despite the long-term fascination of fairy ring-forming fungi, many aspects of their biology remain unresolved. It is not known why the mycelium grows as an annular structure, rather than a solid disc, or why it grows radially outwards. Different theories have been suggested, but none have been tested experimentally with molecular resolution. Here, we undertook a metagenomic approach to study the growth dynamics of the fairy ring-forming fungus Marasmius oreades. We confirmed that M. oreades grows as an open ring by detecting its DNA in metagenomes of soil collected along transects from two fairy rings. We showed that the mycelia forming rings are dikaryotic by identifying two mating-type alleles and showing genome-wide heterozygosity. We tested five hypotheses for the mechanism of radial outgrowth using transplantation experiments. The results were most consistent with a transient-escape hypothesis, and suggest that the mycelium avoids inhibitory factors present at the back edge of the mycelial growth front. Our study demonstrates the power of metagenomics for studying fungi, showing that detailed genomic information can be recovered directly from soil. This approach enables the investigation of cryptic aspects of fungal biology, such as the growth of fairy ring-forming fungi, in natural settings that would otherwise remain hidden.},
}

@article {pmid42728975,
year = {2026},
author = {Prada, C and Lopez, JV and Jones, N and Pruzinsky, N and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the spiny sea fan, Muricea muricata (Pallas, 1766) (Malacalcyonacea: Plexauridae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {512},
doi = {10.12688/wellcomeopenres.27232.1},
pmid = {42728975},
issn = {2398-502X},
abstract = {We present a genome assembly from a Muricea muricata specimen (spiny sea fan; Cnidaria; Anthozoa; Malacalcyonacea; Plexauridae). The genome sequence has a total length of 453.40 megabases. Most of the assembly (98.45%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.29 kilobases. Gene annotation of this assembly by Ensembl identified 52 164 protein-coding genes. From the metagenome data, we recovered five bins, of which three were high-quality MAGs.},
}

@article {pmid42729027,
year = {2026},
author = {Avelino, C and Karp, R and Baker, A and Metz, S and Sweet, M and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the lesser starlet coral, Siderastrea radians (Pallas, 1766) (Scleractinia: Rhizangiidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {493},
doi = {10.12688/wellcomeopenres.27286.1},
pmid = {42729027},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Siderastrea radians (lesser starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 807.19 megabases. Most of the assembly (94.17%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.38 kilobases. Gene annotation of this assembly by Ensembl identified 47 051 protein-coding genes. From the metagenome data, we recovered two binned metagenomes assigned to the bacterial phylum Bacteroidota and class Bacteroidia.},
}

@article {pmid42729039,
year = {2026},
author = {Stewart, JM and Medina, M and Bruckner, A and May, L and Moffitt, ZJ and Lopez, JV and Woodley, CM and Metz, S and Sweet, M and Pruzinsky, N and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the maze coral, Meandrina meandrites (Linnaeus, 1758) (Scleractinia: Meandrinidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {469},
doi = {10.12688/wellcomeopenres.27184.1},
pmid = {42729039},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Meandrina meandrites (maze coral; Cnidaria; Anthozoa; Scleractinia; Meandrinidae). The genome sequence has a total length of 551.16 megabases. Most of the assembly (99.25%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.2 kilobases. Gene annotation of this assembly by Ensembl identified 30 464 protein-coding genes. We recovered two bins from the metagenome data.},
}

@article {pmid42729217,
year = {2026},
author = {Zhang, H and Zhou, J and Chen, Y and Wang, X and Luo, X and Yang, G and Gui, Z and Wang, S and Zhang, Y and Chen, J},
title = {Case Report: Reversible neurological involvement associated with Chlamydia psittaci infection: clinical, cerebrospinal fluid and neuroimaging features of three fully documented cases.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1932046},
doi = {10.3389/fmed.2026.1932046},
pmid = {42729217},
issn = {2296-858X},
abstract = {BACKGROUND: Chlamydia psittaci infection presents mainly as severe pneumonia, but a subset of patients develop neurological symptoms. Previous reports are largely single cases and frequently lack cerebrospinal fluid (CSF) data, opening pressure and follow-up imaging, which makes the mechanism of neurological involvement difficult to determine.

METHODS: We retrospectively analysed three patients with C. psittaci infection confirmed by metagenomic next-generation sequencing (mNGS), all of whom developed neurological manifestations and had complete clinical, CSF, neuroimaging and follow-up data. Exposure history, neurological phenotype, laboratory and CSF parameters, opening pressure, treatment and outcome were collected. Potential explanations for neurological involvement were interpreted in the context of the clinical findings and published literature.

RESULTS: All three patients (two men and one woman; aged 50-72 years) reported pigeon or poultry exposure. Two presented with encephalopathy/delirium and one with headache. Opening pressures were 160, 230 and 90 mmH₂O; none exceeded 250 mmH₂O. CSF white-cell counts were 0-2/mm³, with mild protein elevation in one patient, and the CSF pathogen tests performed were negative. This mismatch between neurological manifestations and routine CSF findings met the study's operational description of CSF-clinical dissociation. Two patients had reversible splenial lesions consistent with cytotoxic lesions of the corpus callosum (CLOCCs). Hypoalbuminemia was present in all three patients, whereas hyponatremia and coagulation abnormalities occurred in selected cases. Neurological symptoms resolved within 4-7 days after pathogen-directed therapy, and all patients recovered completely during follow-up.

CONCLUSIONS: In these three fully documented cases, C. psittaci-associated neurological involvement was short-lived and reversible. The clinical-CSF mismatch was consistent with the hypothesis that unmeasured indirect processes may have contributed, but it did not establish a mechanism or exclude low-burden direct CNS infection. Reversible splenial lesions consistent with CLOCCs were a notable imaging finding. Co-detected organisms and systemic complications limited pathogen-specific causal attribution. Clinical improvement was temporally associated with pathogen-directed therapy.},
}

@article {pmid42729221,
year = {2026},
author = {Rout, AK and Tripathy, PS and Dey, S and Kumar, N and Kumar, G and Parida, PK and Singh, A and Dehury, B and Pandey, PK and Behera, BK},
title = {Metagenomic insights into antibiotic resistance genes and virulence factors in sediments of river Yamuna.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938385},
doi = {10.3389/fmicb.2026.1938385},
pmid = {42729221},
issn = {1664-302X},
abstract = {Riverine sediments serve as critical reservoirs of microbial diversity and functional genes, reflecting both natural ecological processes and anthropogenic impacts. In the present study, we employed a shotgun metagenomic approach to investigate microbial community composition, antimicrobial resistance (AMR) genes, and virulence factors in sediments collected from three environmentally distinct locations of the Yamuna River near Agra, India, representing BSA, TGY, and YEA. The sediment DNA was subjected to high-throughput Illumina sequencing, followed by quality control, assembly, and open reading frame prediction. Taxonomic classification and diversity analyses were performed using MEGAN6 and R-based statistical tools, while AMR genes were identified from predicted metagenomic proteins using the Resistance Gene Identifier (RGI) against the CARD database, with high-confidence perfect and strict hits retained; ARGs were interpreted independently of species-level host assignment. Virulence factors were assessed through presence-absence profiling of functionally relevant gene categories. The results revealed pronounced spatial heterogeneity in microbial communities, with increasing taxonomic diversity, functional complexity, and evenness from BSA to TGY and YEA. TGY and YEA composite samples showed greater observed representation of high-confidence AMR gene predictions spanning multiple drug classes and resistance mechanisms, alongside a diverse repertoire of virulence-associated genes linked to motility, adhesion, and secretion systems. In contrast, the BSA site harbored a comparatively simpler resistome and virulome. Overall, this study highlights Yamuna River sediments as important reservoirs of resistance and virulence determinants and underscores the need for long-term genomic surveillance to inform risk assessment, pollution control, and sustainable river management strategies.},
}

@article {pmid42729271,
year = {2026},
author = {Qi, M and Zeng, Y and Ruan, B and Wang, Q},
title = {Streptococcus suis meningitis complicated with communicating hydrocephalus: complete clinical and radiological resolution with non-neurosurgical management-A case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1888345},
doi = {10.3389/fmed.2026.1888345},
pmid = {42729271},
issn = {2296-858X},
abstract = {BACKGROUND: Streptococcus suis (S. suis) meningitis is a severe zoonotic central nervous system infection, with permanent sensorineural hearing loss as its most common long-term sequela. Hydrocephalus is an extremely rare and underrecognized complication of S. suis meningitis, and no case of communicating hydrocephalus secondary to S. suis meningitis managed successfully with non-neurosurgical therapy has been formally documented.

CASE PRESENTATION: A 52-year-old man presented with 8 days of progressive dizziness and gait imbalance. Contrast-enhanced magnetic resonance imaging (MRI) confirmed communicating hydrocephalus with diffuse leptomeningeal enhancement and no ventricular obstruction. Cerebrospinal fluid (CSF) cultures remained persistently negative, while metagenomic next-generation sequencing (mNGS) identified S. suis within 48 h with a relative abundance of 92.60%. Guideline-recommended targeted antimicrobial therapy combined with short-course adjunctive dexamethasone achieved complete clinical and radiological resolution without neurosurgical intervention. The patient remained asymptomatic with intact bilateral hearing at the 10-month follow-up.

CONCLUSION: To our knowledge, this is the first reported case of S. suis meningitis-associated communicating hydrocephalus successfully managed without neurosurgery. Accurate hydrocephalus subtyping via contrast-enhanced MRI and rapid pathogen identification via mNGS may help inform clinical decision-making regarding the potential for non-neurosurgical management in carefully selected patients.},
}

@article {pmid42729285,
year = {2026},
author = {Yang, S and Fan, Z and Wu, R and Duan, L and Sun, J},
title = {The first reported case of Balamuthia amoebic encephalitis initially presenting as anti-NMDAR encephalitis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1929027},
doi = {10.3389/fmed.2026.1929027},
pmid = {42729285},
issn = {2296-858X},
abstract = {Balamuthia mandrillaris (B. mandrillaris) is a highly pathogenic free-living amoeba that can invade the central nervous system and cause Balamuthia amoebic encephalitis (BAE). BAE is associated with an extremely high mortality rate, and no treatment regimen with well-established efficacy is currently available. We report a case of BAE in a 63-year-old man who was initially diagnosed with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis. Because the patient initially exhibited no overt signs of infection and metagenomic next-generation sequencing (mNGS) failed to identify any pathogens in the cerebrospinal fluid (CSF), the presence of frequent seizures and anti-NMDAR antibodies in the CSF initially led the treating clinicians to a diagnosis of anti-NMDAR encephalitis. As the disease progressed, multiple intracranial lesions developed. Repeat mNGS subsequently detected B. mandrillaris in the CSF, thereby establishing the diagnosis of BAE. Despite combination antimicrobial therapy, the patient's condition failed to improve, and he ultimately died. This case underscores the importance of maintaining a high index of suspicion for amoebic infection in patients with encephalitis, as B. mandrillaris infection may elicit autoimmune responses early in the disease course and mimic autoimmune or other noninfectious forms of encephalitis.},
}

@article {pmid42729392,
year = {2026},
author = {Du, Q and Tian, Z and Wang, J and Xu, X},
title = {Severe pulmonary vein stenosis presenting with infection-like pulmonary findings after radiofrequency ablation for atrial fibrillation: A case report.},
journal = {Respiratory medicine case reports},
volume = {63},
number = {},
pages = {102495},
doi = {10.1016/j.rmcr.2026.102495},
pmid = {42729392},
issn = {2213-0071},
abstract = {We report a case of severe pulmonary vein stenosis(PVS) with complete pulmonary vein occlusion(PVO) after radiofrequency ablation for atrial fibrillation(AF). A 51-year-old man presented to the respiratory department with chest tightness, dyspnea, and chest pain. Early chest computed tomography (CT) revealed inflammatory changes in the left lung and bilateral pleural effusions, and the patient responded poorly to antibiotic therapy. He had undergone radiofrequency catheter ablation for AF 5 months prior. On admission, inflammatory markers were not significantly elevated, procalcitonin was negative, and bronchoalveolar lavage fluid (BALF) culture and metagenomic next-generation sequencing (mNGS) revealed no definitive pathogenic infection. Subsequent cardiac CTA showed non-visualization of the left inferior pulmonary vein and stenosis of the left superior pulmonary vein near the left atrium, leading to a diagnosis of post-ablation pulmonary vein occlusion and stenosis. The patient underwent pulmonary vein stenting at another hospital, with follow-up CTA demonstrating restored opacification distal to the stents without intraluminal filling defects. This case highlights the need for prompt evaluation of pulmonary vein patency when focal pulmonary infection-like changes, chest pain, or pleural effusion occur after atrial fibrillation ablation when infection is not confirmed.},
}

@article {pmid42729475,
year = {2026},
author = {Zhang, M and He, L and Xin, H and Huang, T and Wang, F and Wang, L},
title = {Metagenomic profiling of blood-associated microbial DNA signatures in leukemia-associated febrile neutropenia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917043},
doi = {10.3389/fmicb.2026.1917043},
pmid = {42729475},
issn = {1664-302X},
abstract = {Febrile neutropenia (FN) is a life-threatening complication of chemotherapy, but the low microbial biomass of blood makes shotgun metagenomic profiles highly sensitive to technical background. We reanalyzed 47 publicly available patient sequencing runs representing 43 unique patient-timepoint samples from 19 SRA-labeled patients, together with 23 no-template-control (NTC) runs spanning 21 sequencing batches. To distinguish reference-catalogue content from progressively stronger evidence of patient-associated signal, we applied batch-matched NTC correction together with nested abundance thresholds and a feature-specific global NTC envelope. CheckM2 evaluated 1,013 bins; 13 met completeness ≥50% and contamination <10%, and dereplication yielded 11 draft MAG representatives. Ten representatives showed positive patient-to-control abundance excess, but only four showed recurrent support above both threefold matched-control abundance and the global NTC envelope. Functional annotations were therefore interpreted as reference-genome homologs rather than evidence of expression, phenotype, viability or bloodstream origin. Matched-control correction retained 19 read-level ARG types, but only seven subjects contributed complete longitudinal ARG-profile contrasts, limiting reliable temporal inference. The resulting run-resolved, nested evidence framework identified a subset of microbial DNA and ARG signals that remained detectable under increasingly stringent control criteria while distinguishing them from catalogue-level or background-sensitive signals. These findings support cautious reporting of patient-enriched microbial DNA and ARG signals rather than inference of a resident blood microbiome or clinical resistance phenotype.},
}

@article {pmid42729502,
year = {2026},
author = {Tagele, SB and Kassa, AS and Tilahun, S and Zegeye, WA},
title = {Editorial: Harnessing genomics to revolutionize plant disease management and preservation of soil biodiversity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1901274},
doi = {10.3389/fmicb.2026.1901274},
pmid = {42729502},
issn = {1664-302X},
}

@article {pmid42729572,
year = {2026},
author = {Leontyev, DV and Schnittler, M and Shchepin, ON},
title = {Short-read genome skimming enables molecular barcoding of old myxomycete collections.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e201932},
doi = {10.3897/imafungus.17.201932},
pmid = {42729572},
issn = {2210-6340},
abstract = {This study evaluates the effectiveness of Illumina-based genome skimming for barcoding myxomycete herbarium collections ranging from 29 to 91 years in age. We successfully retrieved partial sequences of the standard marker gene (nucSSU) in all cases, as well as additional markers (mtSSU, EF1a, and COI) for certain collections. Altogether, 28 genes were recognized in the studied material. In a 33-year-old specimen of Lindbladia tubulina, the assembly reached an N50 of 4.19 kb, enabling the recovery of extended functional loci. The input genomic DNA quantity emerges as the primary determinant of sequencing success. Samples with high DNA yields provide representative amounts of contigs coming confirmedly (matching sequences in the NCBI nucleotide database) or potentially (no-hit fraction) from myxomycetes, regardless of specimen age. In addition to target DNA, we revealed distinct signals of both anthropogenic contamination (human DNA and skin microflora) and natural substrate inhabitants, including oribatid mites and bacteria from dead wood, soil, and grass litter. Thus, even in old collections, metagenomic data still carry information regarding the substrate upon which the myxomycete developed. The results demonstrate that short-read genome skimming may help to integrate historical type material of myxomycetes into contemporary phylogenetic research. This method overcomes the length-dependent limitations of traditional Sanger sequencing, thus providing a roadmap for the future of museomics in myxomycetology.},
}

@article {pmid42729674,
year = {2026},
author = {Li, Y and Ye, Z and Fei, M},
title = {Case Report: Early bilateral capsular contraction syndrome associated with Epstein-Barr virus-positive uveitis after cataract surgery.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1901790},
doi = {10.3389/fmed.2026.1901790},
pmid = {42729674},
issn = {2296-858X},
abstract = {OBJECTIVE: To report a case of capsular contraction syndrome complicated by viral uveitis during the early postoperative period after bilateral cataract surgery.

METHODS: A retrospective case report was conducted.

RESULTS: A 74-year-old woman with no significant medical history developed bilateral capsular contraction syndrome one month after bilateral cataract surgery. Further ophthalmic evaluation revealed bilateral uveitis. Laboratory testing and metagenomic next-generation sequencing identified Epstein-Barr virus (EBV) in both peripheral blood and aqueous humor samples.

CONCLUSION: EBV-associated uveitis may have contributed to the early development of bilateral capsular contraction syndrome in this patient after cataract surgery. In patients presenting with postoperative uveitis accompanied by capsular contraction, underlying viral infection should be considered as a potential contributing factor.},
}

@article {pmid42729922,
year = {2026},
author = {Cong, J and Xu, W and Zhang, Y and Ding, X and Cui, S and Chi, X and Yang, X},
title = {Gut microbiota dynamics and metabolic pathways associated with bleomycin-induced pulmonary fibrosis progression.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21693},
doi = {10.7717/peerj.21693},
pmid = {42729922},
issn = {2167-8359},
mesh = {Animals ; *Bleomycin ; *Pulmonary Fibrosis/chemically induced/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome ; Mice ; Disease Progression ; *Metabolic Networks and Pathways ; Disease Models, Animal ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Lung/pathology ; },
abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a progressive respiratory disease characterized by epithelial injury, aberrant repair and excessive extracellular matrix deposition. Although the gut-lung axis is increasingly implicated in respiratory disorders, stage-resolved characterization of gut microbiota taxonomic and functional potential during PF development is limited.

METHODS: We established a bleomycin-induced murine PF model and performed cross-sectional shotgun metagenomic sequencing of fecal samples from separate cohorts at three defined stages: baseline (control), day 7 (early fibrosis; M7), and day 14 (established fibrosis; M14). Microbial taxonomy, alpha/beta diversity, and predicted functional capacity were inferred using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZymes (CAZy) annotations; associations were assessed using Procrustes and Spearman correlation analyses.

RESULTS: Histopathology and immunohistochemistry confirmed progressive fibrogenesis with increased TGF-β1 and α-SMA expression. Compared with baseline, bleomycin-treated groups exhibited stage-specific shifts in gut microbial composition, including depletion of mucin-associated taxa (e.g., Prevotella, Akkermansia muciniphila) and expansion of Muribaculaceae- and Clostridiaceae-affiliated taxa. Alpha and beta diversity metrics differed across groups. KEGG/CAZy-based annotations revealed predicted, stage-dependent changes in microbial metabolic potential, including early reductions in pathways related to amino acid and glycan metabolism (M7) and later increases in predicted starch/sucrose catabolism, phosphotransferase system (PTS) representation, and secondary bile acid biosynthesis (M14). Correlation analyses linked compositional shifts to these predicted functional changes.

CONCLUSION: In a stage-resolved, cross-sectional study, bleomycin-associated pulmonary fibrosis was accompanied by compositional and predicted functional alterations in the gut microbiota. These data identify candidate taxa and predicted pathways for follow-up mechanistic testing, but functional (metabolomic) and causality experiments are required to confirm whether and how microbial changes contribute to PF pathogenesis.},
}

Animals
*Bleomycin
*Pulmonary Fibrosis/chemically induced/microbiology/pathology/metabolism
*Gastrointestinal Microbiome
Mice
Disease Progression
*Metabolic Networks and Pathways
Disease Models, Animal
Mice, Inbred C57BL
Feces/microbiology
Male
Lung/pathology

@article {pmid42730546,
year = {2026},
author = {Lipovac, J and Angevin, L and KrižanoviC', K},
title = {Using Mapping-Profiles to Refine Strain-Level Metagenomic Classification.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261485334},
doi = {10.1177/15578666261485334},
pmid = {42730546},
issn = {1557-8666},
abstract = {Metagenomic classification at the strain level remains challenging due to high sequence similarity among closely related genomes, which leads to ambiguous read mappings and frequent false-positive strain detections. Reducing such errors improves the reliability of strain-level analyses, which is critical for applications such as pathogen detection. We introduce StrainRefine, a post-mapping refinement method that analyzes read-reference mapping profiles to resolve ambiguous assignments among highly similar genomes. The method represents candidate reference genomes using binary profiles that capture read-support patterns and measures similarity between references based on profile overlap. The method clusters references based on similar mapping profiles, filters weakly supported genomes, and reassigns reads to representative references, reducing redundant reporting of near-identical strains. StrainRefine substantially reduces false-positive strain detections while preserving recall and improving agreement between predicted and true abundance profiles. On large-scale metagenomic datasets, it achieves a substantially improved precision-recall balance compared with existing mapping-based approaches, with the standalone method obtaining the highest read-level classification accuracy on the most complex evaluated dataset. Unlike many strain-level tools designed for individual species, StrainRefine operates without prior assumptions about sample composition or curated species-specific reference collections, while still achieving comparable performance in single-species settings on species-specific reference databases. These results highlight mapping-profile similarity as an effective signal for improving strain-level metagenomic classification.},
}

@article {pmid42730617,
year = {2026},
author = {Xu, T and Zhu, P and Wang, Y and Jia, C and Hou, X and Zhang, Y and Liu, H and Song, J and He, M and Li, F and Hao, D and Zhao, Y and Zhang, X and Chen, B and Xu, J and Ma, B},
title = {High-Throughput Dual Resonance and Non-Resonance Mode Raman-Activated Cell Sorting With Low-Volume Harvesting.},
journal = {Small methods},
volume = {},
number = {},
pages = {e71037},
doi = {10.1002/smtd.71037},
pmid = {42730617},
issn = {2366-9608},
support = {2022YFF0713104//National Key Research and Development Program of China/ ; PTYQ2026YZ0075//Research Instrument Development Project of Chinese Academy of Sciences/ ; WZ[2024]007//Chishui River Middle Basin, Watershed Ecosystem, Observation and Research Station of Guizhou Province/ ; 2025TSGCCZZB0170//Innovation Capacity Improvement Project for Sci-Tech SMEs of Shandong Province/ ; },
abstract = {Raman-activated cell sorting (RACS) platforms are limited by inflexibility in tackling different Raman signals and inability to export the sorted cells in a sufficiently low volume for downstream processing. Here, we present a generally applicable RACS platform that tackles these challenges. For adaptive dual-mode operation that supports diverse spontaneous Raman signals, microfluidic optical tweezers are designed with switchable capture strategies, with a high-throughput in-stream mode (up to 834 events/min) for resonance Raman signals with short exposures (<0.1 s) for resonance-Raman-based screening, and a high-precision out-stream mode (up to 50 events/min) for non-resonance Raman detection with extended exposures (>0.1 s). Moreover, to achieve low-volume concentrated harvesting, an on-chip storage and centralized harvesting mechanism delivers target cells in uniform 10 µL suspensions with >97% purity. Using the in-stream mode for resonance Raman screening, we isolated a Yarrowia lipolytica mutant with 77% increased β-carotene production in just one sorting round directly from a mutant library. Employing the out-stream mode for non-resonance Raman detection, we enriched phosphate-solubilizing bacteria from wastewater with nearly 100% recovery in concentrated 10 µL volumes, enabling direct function-targeted mini-metagenomics. This high-throughput dual-mode RACS platform with low-volume cell harvesting greatly expands the application of label-free live-cell sorting via metabolic phenome.},
}

@article {pmid42730659,
year = {2026},
author = {Kumar, M and Narayanankutty, A and Nair, G and Kulkarni, R and Shouche, Y},
title = {Standardized Workflow for Human Fecal Sample Collection and Automated Deoxyribonucleic Acid Extraction Using a Magnetic Particle Processor.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {235},
pages = {},
doi = {10.3791/73312},
pmid = {42730659},
issn = {1940-087X},
mesh = {*Feces/microbiology/chemistry ; Humans ; Workflow ; *DNA/isolation & purification ; *DNA, Bacterial/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; Magnetics/methods ; *Specimen Handling/methods/standards ; },
abstract = {Gut microbiome sequencing has become an important approach for investigating microbial community dynamics in healthy and diseased states. Alterations in microbial composition have been associated with several lifestyle- and age-related disorders, including diabetes, leukemia, and neurodegenerative diseases. Because different microorganisms exhibit distinct physiological characteristics and environmental requirements, standardized fecal sample collection, transport, and processing are essential to preserve sample integrity and minimize technical variability. Variations introduced during pre-analytical handling and deoxyribonucleic acid (DNA) extraction can influence downstream microbiome analyses and affect data interpretation. The goal of this protocol is to provide a standardized workflow for human fecal sample collection and automated DNA extraction using the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit (nucleic acid extraction kit) and the KingFisher Flex System (automated magnetic particle processor). The workflow integrates controlled sample handling with automated nucleic acid extraction to reduce manual variability and improve procedural consistency. The protocol includes standardized fecal sample collection, storage, preparation, automated extraction, and nucleic acid recovery from complex fecal matrices. Representative results demonstrate successful recovery of DNA suitable for downstream applications, including 16S ribosomal ribonucleic acid (rRNA) gene sequencing and shotgun metagenomic sequencing. The standardized workflow supports reproducible sample processing, facilitates scalability for microbiome studies, and promotes greater consistency across experiments. The visual demonstration provides practical guidance for implementing standardized fecal sample processing and automated nucleic acid extraction for gut microbiome research.},
}

*Feces/microbiology/chemistry
Humans
Workflow
*DNA/isolation & purification
*DNA, Bacterial/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics
Magnetics/methods
*Specimen Handling/methods/standards

@article {pmid42731191,
year = {2026},
author = {Yang, MT and Bai, T and Zhao, JX and Zhang, M and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Zhu, XQ and Elsheikha, HM and Liu, R and Zhang, XX},
title = {Interkingdom remodeling of the intestinal bacteriome and virome during Toxoplasma gondii infection in rats.},
journal = {Veterinary parasitology},
volume = {348},
number = {},
pages = {110925},
doi = {10.1016/j.vetpar.2026.110925},
pmid = {42731191},
issn = {1873-2550},
abstract = {Toxoplasma gondii infection is associated with intestinal microbiome disruption, but its effects on genome-resolved bacterial populations, the gut virome, and bacteriome-virome relationships remain poorly understood. Using previously generated shotgun metagenomic datasets from 36 intestinal samples collected from 18 Sprague-Dawley rats across control, acute, and chronic infection groups, we reconstructed 294 quality-filtered, non-redundant bacterial metagenome-assembled genomes (MAGs) and identified 899 medium-to-high-quality viral operational taxonomic units (vOTUs) from assembled metagenomic contigs. Infection was associated with reduced bacterial richness in the small intestine during both acute and chronic stages and lower Shannon diversity during chronic infection. In contrast, large-intestinal α-diversity remained stable despite significant compositional reorganization. Taxonomic changes included increased Lactobacillus intestinalis, Limosilactobacillus reuteri, and Prevotella sp900547005, together with decreased Rothia sp002492045 and Akkermansia muciniphila. Functional profiling revealed region- and stage-specific changes in predicted bacterial metabolic potential, including reduced energy-related pathways and carbohydrate-active enzyme abundance. The virome also showed significant compositional changes in both intestinal regions. Quimbyviridae and Podoviridae_crAss-like viruses decreased in the small intestine during chronic infection, while Quimbyviridae, Flandersviridae, and Podoviridae_crAss-like viruses showed stage-specific decreases in the large intestine. Predicted bacterial hosts were assigned to 48.39% of vOTUs, with Lachnospiraceae and Ruminococcaceae being the most frequently linked families. Trans-kingdom networks further revealed region-specific positive and negative abundance correlations between bacterial and viral taxa. These findings extend previous microbiota-metabolome observations by integrating genome-resolved bacteriome analysis with contig-based virome profiling, providing a foundation for future mechanistic studies of toxoplasmosis-associated microbiome remodeling.},
}

@article {pmid42731219,
year = {2026},
author = {Xie, B and Hua, X and Geng, L and Li, K and Liu, G and Fang, Y and Zhao, T and Lu, C and Zhang, C and Han, Z and Yu, B and Li, X},
title = {Cecal microbiota regulates meat quality of Yanshan red jade broilers: insights from metagenomics and targeted metabolomics.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107619},
doi = {10.1016/j.psj.2026.107619},
pmid = {42731219},
issn = {1525-3171},
abstract = {This study aimed to elucidate the molecular mechanism of cecal microbiota regulating muscle flavor in Yanshan red jade broilers with natural body weight variation. Eighteen-week-old hens were selected for this study. Targeted metabolomics was applied to determine the fatty acid and amino acid composition of muscle. Metagenomic sequencing was used to analyze the structure and function of cecal microbial communities. A regulatory network between gut microbiota and meat flavor was constructed via correlation analysis. The results showed that the high-weight female (HF) group had significantly better slaughter performance and leg muscle intramuscular fat (IMF) than the low-weight female (LF) group. Metabolomic analysis identified a total of 38 fatty acids and 25 amino acids. The HF group was enriched in umami amino acids such as arginine and serine, while the LF group had higher content of long-chain polyunsaturated fatty acids (PUFAs) and 1-methyl-l-histidine. Metagenomic analysis showed that Eubacterium and Anaerostipes were the characteristic bacteria in the HF group, while Odoribacter was dominant in the LF group. Functional annotation identified a total of 12 differential metabolic pathways, including core pathways such as lipid metabolism and amino acid synthesis. The association network showed that Eubacterium sp. An11 enhanced growth performance and umami quality by promoting muscle protein deposition, Odoribacter_splanchnicus affected muscle nutritional characteristics by regulating fatty acid metabolism, and Pseudoflavonifractor_capillosus was involved in both growth and flavor regulation. This study provides theoretical support and functional strain targets for flavor improvement of high-quality broilers and precise nutritional regulation of gut microbiota.},
}

@article {pmid42731224,
year = {2026},
author = {Kerek, Á and Hetyésy, M and Tornyos, GÁ and Kaszab, E and Fehér, E and Jerzsele, Á and Tóth, T and Zsédely, E and Fébel, H},
title = {Timing of an antioxidant-acidifier feed additive modulates growth performance and cecal microbiota in broiler chickens during enrofloxacin exposure.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107639},
doi = {10.1016/j.psj.2026.107639},
pmid = {42731224},
issn = {1525-3171},
abstract = {Nutritional interventions targeting oxidative stress and gut ecology may help sustain broiler performance during antimicrobial perturbation. This study evaluated the timing-dependent effects of an antioxidant-acidifier feed additive, alone or combined with enrofloxacin, on growth performance and cecal microbiota in broilers. A total of 1,200 Ross 308 male broilers were assigned to six treatments (4 pens/treatment; 50 birds/pen) and reared to 42 d: control, enrofloxacin (d15-19), additive for 4 weeks (A4; d15-42), A4+enrofloxacin, additive for 6 weeks (A6; d1-42), and A6+enrofloxacin. The additive was included at 4% of the diet, providing fumaric acid, heat-stable vitamin C, and all-rac-α-tocopheryl acetate. Performance traits were recorded by phase and overall. Cecal contents were collected from 2 birds/pen on d14, d20, and d42 and analyzed by shotgun metagenomic sequencing; microbiota analyses were conducted on pen-level aggregated profiles. Growth performance showed modest, timing-dependent numerical differences: A4 had numerically higher finisher and overall average daily gain, whereas A4+enrofloxacin was associated with lower overall gain than enrofloxacin alone. Cecal community structure was driven primarily by sampling time point. No detectable enrofloxacin-associated separation was observed at d20, whereas a trend toward separation was evident at d42. By d42, only limited genus-level differences were detected, with the strongest signal observed for Phocaeicola in the targeted differential abundance analysis. Overall, additive timing influenced growth responses and cecal microbiota trajectories during enrofloxacin exposure, supporting the importance of supplementation timing when nutritional strategies are used to improve robustness under antibiotic perturbation.},
}

@article {pmid42720301,
year = {2026},
author = {Gauthier, NPG and Kapoor, V and Gaston, DC and Prasad, N and Nwaobia, P and Kraft, CS and Mittar, D},
title = {When tests don't fit the rules: regulatory challenges for agnostic metagenomic next-generation sequencing in infectious diseases diagnostics.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0098726},
doi = {10.1128/jcm.00987-26},
pmid = {42720301},
issn = {1098-660X},
abstract = {Metagenomic next-generation sequencing (mNGS) enables agnostic detection of bacteria, viruses, fungi, and parasites from clinical specimens. Patient access is restricted due to their current regulatory classification as Laboratory Developed Tests, which are offered by a limited number of laboratories. While patient access may be expanded through Food and Drug Administration authorization of mNGS-based in vitro diagnostics, some regulatory requirements for achieving this classification can be challenging to apply due to the agnostic nature of mNGS. For example, existing guidelines recommend organism-by-organism performance characterization similar to targeted molecular tests involving fixed analytes with stable detection thresholds. This mini-review synthesizes validation and regulatory challenges unique to mNGS-based diagnostics and describes how laboratories and developers currently navigate available pathways. We focus on core analytical and clinical validation challenges, including discussion on the central role of bioinformatics pipelines and reference databases. We then summarize practical considerations for regulatory engagement, labeling, clinical-facing reporting, and alignment of mNGS assays to existing quality system frameworks. Finally, we outline future oversight considerations, including the need to distinguish mNGS from multiplexed PCR paradigms and the potential value of modular, component-based regulatory approaches that separately evaluate reagents, instruments, software, and databases, enabling system-level oversight rather than organism-by-organism validation. Together, these considerations aim to support risk-appropriate, scalable oversight, and accelerate adoption of mNGS in clinical microbiology.},
}

@article {pmid42720994,
year = {2026},
author = {Halle-Smith, JM and Fung, K and Efstathiou, E and Tovey, N and Stockton, J and Iqbal, TH and Moss, P and Beggs, AD and Roberts, KJ},
title = {The Effect of Pancreatic Exocrine Insufficiency and Pancreatic Enzyme Replacement Therapy on Gut Microbiome Composition in Pancreatic Disease: A Prospective Cohort Study.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002709},
pmid = {42720994},
issn = {1536-4828},
abstract = {OBJECTIVES: Increasing evidence demonstrates that pancreatic exocrine insufficiency (PEI) is associated with harmful changes to the gut microbiome. The mainstay of PEI treatment is with pancreatic enzyme replacement therapy (PERT), which has been shown to lead to significant survival benefit in pancreatic disease. The aim of this study was to determine how treatment of PEI with PERT affects gut microbiome composition.

METHODS: This is a prospective observational cohort study of patients being treated for pancreatic disease at a single centre. PEI status of patients was assessed at the time of recruitment using published diagnostic criteria. Pre-PERT samples were taken before treatment was started and post-PERT samples were taken after at least 4 weeks of treatment. To profile the gut microbiome composition, shotgun metagenomic sequencing was performed with DNA extracted from stool samples.

RESULTS: 25 patients with pancreatic disease were included. The abundance of pathogenic bacteria, such as Viridans group Streptococcus and Campylobacter species, was significantly increased in the gut microbiome of patients with PEI compared to those without PEI. Following PERT treatment, analysis of the gut microbiome of treated patients showed a significant reduction in the abundance of multiple pathogenic species, such as those from Viridans group Streptococci, compared to untreated PEI patients.

CONCLUSIONS: Treatment with PERT leads to significant changes in the gut microbiome composition of patients with pancreatic disease. Changes include a significant reduction in potentially pathogenic bacteria and so may contribute to the survival benefits seen with PERT treatment in pancreatic disease.},
}

@article {pmid42721651,
year = {2026},
author = {Chi, HY and Nakanishi, H and Takada, A and Yoneyama, K and Sakai, K and Saito, K},
title = {Development of a novel universal primer set with high sensitivity and specificity for detection of diatom.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {86},
number = {},
pages = {102991},
doi = {10.1016/j.legalmed.2026.102991},
pmid = {42721651},
issn = {1873-4162},
abstract = {The diatom test has long been used as an ancillary examination in the diagnosis of drowning. The conventional diatom test requires the handling of strong acids and depends on the investigator's skill and expertise. Several issues are also associated with the diatom test, such as sample contamination and diatom loss during testing. We have developed a novel primer set for detecting diatoms using real-time PCR. The primers were designed based on the rbcL gene as a marker, and the amplicon length was 68 bp. A high detection sensitivity (0.1 pg DNA) was achieved for all diatom species tested, and no amplification was observed using DNA from cyanobacteria or humans, demonstrating that the primer set has high specificity. Evaluation of the method's detection limit based on diatom counts using laser capture microdissection showed that the limit varied by species, ranging from 1 to 40 individuals. Diatoms were detected in various environmental water samples, including river and seawater, and in lung tissues from drowning autopsies. Although there are limitations to genus-level identification, this primer set was applicable to metagenomic analysis. Since this primer set is highly sensitive and specific and can detect diatoms even when their DNA is degraded, it has the potential for application in forensic practice. Furthermore, this method may enable validation of the premise underlying the diatom test-namely, that diatoms can disseminate to closed organs via the systemic circulation.},
}

@article {pmid42721830,
year = {2026},
author = {Męcik, M and Stefaniak, K and Harnisz, M and Czatzkowska, M and Felis, E and Bajkacz, S and Sawicki, J and Krawczyk, K and Paukszto, Ł and Korzeniewska, E},
title = {From regionalization to homogenization: Nationwide metagenomic assessment of priority pathogens and the resistome in Polish hospital wastewater.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143526},
doi = {10.1016/j.jhazmat.2026.143526},
pmid = {42721830},
issn = {1873-3336},
abstract = {Hospital wastewater (HWW) is a critical hotspot for the dissemination of antibiotic resistance genes (ARGs) and pathogens. This study provides the first comprehensive metagenomic characterization of HWW across Poland, analyzing 64 medical facilities across two seasons via Nanopore long-read sequencing (total of 128 HWW samples). The HWW microbiome was mostly dominated by Proteobacteria, Bacteroidota, and Firmicutes. Multivariate analysis confirmed a significant seasonal shift in the resistome. Winter samples exhibited geographic regionalization, with localized hotspots of specific ARGs, including vancomycin resistance (operon van) and carbapenemase genes (blaOXA, blaNDM). Conversely, summer samples showed a significant trend toward nationwide homogenization, characterized by a uniform distribution of ESBL genes (blaTEM, blaCTX-M) and multidrug resistance (MDR) determinants, alongside the persistence of localized clinical hotspots. Klebsiella pneumoniae emerged as a central network hub, particularly in summer, showing strong correlations with ESBLs. Quantitative genomic co-occurrence analysis revealed a functional division within dominant taxa: while environmental species like Acinetobacter johnsonii comprised the general background microbiome, clinical pathogens such as Acinetobacter baumannii served as primary vectors, showing frequent associations with high-risk ARGs. Environmental and opportunistic bacteria, such as Aeromonas spp. and Citrobacter spp., were identified as putative 'bridge hosts' associated with mobile resistance determinants and potentially contributing to HGT. The findings indicate that seasonal factors, such as increased temperature and sub-inhibitory antibiotic concentrations, may contribute to the transition from regionalized to homogenized resistance profiles, demonstrating that background resistome convergence can coexist with point-source clinical outbreaks. This seasonal "blurring" of regional boundaries positions HWW as an active vector for large-scale antimicrobial resistance (AMR) dissemination. These results underscore the urgent need for nationwide metagenomic surveillance and advanced wastewater treatment strategies within the "One Health" framework to mitigate the environmental spread of WHO priority pathogens.},
}

@article {pmid42722168,
year = {2026},
author = {Liu, Y and Li, B and Najman, MA and Huang, S and Qi, Y and Kim, DH and Sim, YB and Kim, SH and Ratnaweera, H and Zhang, H and Shi, X},
title = {Steering carbon and nitrogen toward biopolymer recovery in synthetic municipal wastewater using an intertidal wetland sediment-seeded biofilm-based reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135837},
doi = {10.1016/j.biortech.2026.135837},
pmid = {42722168},
issn = {1873-2976},
abstract = {Recovering value-added biopolymers from municipal wastewater offers a promising route to improve the sustainability of wastewater treatment. In this study, two moving bed biofilm reactors (MBBRs) seeded with intertidal wetland sediment (IWS) (Riws) and conventional activated sludge (AS) (Ras) were operated in parallel for synthetic municipal wastewater treatment and biopolymer recovery. A higher total nitrogen (TN) removal efficiency was achieved in the Riws than in the Ras (92.4 ± 0.5% and 80.1 ± 3.8%, respectively). Moreover, Riws achieved a higher alginate-like exopolymers (ALE) yield than Ras, reaching 374.3 ± 10.5 mg/g VSS compared with 242.6 ± 8.4 mg/g VSS. The recovered ALE from Riws also contained more protein (890.0 ± 11.7 mg/g ALE) and showed a higher alginate-equivalent response (598.6 ± 32.5 mg/g ALE). Estimated COD and nitrogen partitioning further showed that ALE-associated COD accounted for 17.5% of influent COD in Riws and 6.9% in Ras, while ALE protein-associated N represented 19.1% and 5.9% of influent TN, respectively. Moreover, metagenomic analysis showed that the mature Riws biofilm had higher abundances of genes associated with nitrogen assimilation and denitrification, together with genes involved in ALE biosynthesis, and extracellular-polymer regulation through quorum sensing and c-di-GMP-related pathways. These functional differences were consistent with the greater retention of wastewater carbon and protein-associated nitrogen in recoverable ALE in Riws. These results demonstrate that inoculum selection can effectively regulate microbial assembly and redirect wastewater carbon and nitrogen toward extracellular biopolymer synthesis and recovery, providing a feasible strategy for wastewater valorization.},
}

@article {pmid42722277,
year = {2026},
author = {Xue, X and Ge, Y and Meng, T and Chen, Y and Zhou, L and Xu, D},
title = {Anthropogenic disturbance enhances bacteria-mediated resistome transmission across the sediment-benthos-demersal fish trophic continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129137},
doi = {10.1016/j.envpol.2026.129137},
pmid = {42722277},
issn = {1873-6424},
abstract = {Aquatic ecosystems are important environmental reservoirs of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), yet how anthropogenic disturbance influences their distribution and cross-niche transmission through benthic food webs remains poorly understood. Here, we systematically characterized resistome and virulome profiles across trophic niches, including sediments, benthic invertebrates and demersal fishes, along a gradient of anthropogenic disturbance in Gehu Lake, China. Metagenomic analysis identified 1,645 ARG and 1,939 VFG subtypes, with both gene pools exhibiting pronounced niche differentiation. Sediments harbored the highest abundance and diversity of both gene pools, whereas animal-associated niches exhibited substantial but host-dependent attenuation. Notably, anthropogenic disturbance significantly altered ARG and VFG profiles across all ecological niches, with stronger effects in sediments and benthic organisms than in fish guts, and was generally associated with higher ARG and VFG abundance and diversity. Integrative source-tracking and bacteria-gene association network analyses further demonstrated that bacterial transmission was the primary vector mediating the cross-trophic dissemination of both gene pools. Anthropogenic disturbance reshaped bacterial community structure across niches and enhanced bacterial migration along the food chain, as reflected by the increased contribution of bacteria derived from upstream trophic compartments. KEGG functional profiling suggested that these transmitted bacterial assemblages processed enhanced metabolic and adaptive capacities functions such as xenobiotic degradation. Among the enriched bacterial lineages, Pseudomonadota, Actinomycetota and Bacillota were dominant and showed a higher propensity to harbor ARGs and VFGs, thereby facilitating their persistence, amplification and trophic transfer. Collectively, our findings reveal a disturbance-driven, microbiome-mediated mechanism underlying the co-dissemination of ARGs and VFGs across aquatic food webs, highlighting the critical role of host-associated microbial selection in amplifying environmental health risk.},
}

@article {pmid42722642,
year = {2026},
author = {Jiang, D and Soo, N and Tan, CY and Dankwa, S and Wang, HY and Theriot, BS and Xue, K and Hill, D and Ardeshir, A and Bain, JR and Heston, SM and Hurst, JH and Siddiqui, NY and Van Rompay, KKA and Cervantes-Barragan, L and Smith, JP and Song, R and Roper, J and Kelly, MS and Hudgens, MG and De Paris, K and Permar, SR and Goswami, R and Surana, NK},
title = {Commensal bacteria inhibit viral infections via a tryptophan metabolite.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42722642},
issn = {2041-1723},
support = {P01 AI117915//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01 AI178377//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30 AI064518//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R03 AI142341//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R56 DK140173//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Tryptophan/metabolism ; Virus Replication ; Cytomegalovirus/physiology ; *Bacteria/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; HIV Infections/microbiology/metabolism/virology ; SARS-CoV-2/physiology ; Transaminases/metabolism/genetics ; Cytomegalovirus Infections/microbiology/metabolism ; Symbiosis ; Feces/microbiology ; *Virus Diseases/microbiology ; },
abstract = {Clinical outcomes following viral exposures exhibit substantial interindividual variability. Although developing evidence suggests commensal bacteria modulate viral infections, the specific bacteria and mechanisms remain underexplored. Here, we define a pathway by which viral infections are inhibited by specific tryptophan-catabolizing bacteria. Using HIV as a model, we bioinformatically associated and experimentally validated several bacterial species that inhibited viral replication. This activity required the aromatic amino acid aminotransferase (ArAT) to metabolize tryptophan into 3-indolelactic acid, which agonizes the aryl hydrocarbon receptor (AhR). Given that AhR regulates multiple viral infections, we found that commensal bacteria also inhibit cytomegalovirus (CMV) in an ArAT-dependent manner. Finally, we used fecal shotgun metagenomic data to confirm that ArAT is associated with improved disease outcomes in three distinct human cohorts at-risk for HIV, CMV, or symptomatic COVID-19. Taken together, our results provide mechanistic insight into how commensal bacteria impact viral infections, thereby adding to an emerging field focused on host-commensal-virus interactions.},
}

Humans
*Tryptophan/metabolism
Virus Replication
Cytomegalovirus/physiology
*Bacteria/metabolism
Receptors, Aryl Hydrocarbon/metabolism
HIV Infections/microbiology/metabolism/virology
SARS-CoV-2/physiology
Transaminases/metabolism/genetics
Cytomegalovirus Infections/microbiology/metabolism
Symbiosis
Feces/microbiology
*Virus Diseases/microbiology

@article {pmid42723024,
year = {2026},
author = {Guo, WM and Zhang, XH and Yang, X and Chen, F and Gao, ZX and Tian, DY and Tian, DL},
title = {Rashless varicella-zoster virus encephalitis diagnosed by metagenomic next-generation sequencing: two case reports.},
journal = {BMC neurology},
volume = {26},
number = {1},
pages = {},
pmid = {42723024},
issn = {1471-2377},
mesh = {Humans ; Male ; Aged ; *Encephalitis, Varicella Zoster/diagnosis/cerebrospinal fluid/drug therapy/complications ; *High-Throughput Nucleotide Sequencing/methods ; *Herpesvirus 3, Human/genetics ; Metagenomics/methods ; Magnetic Resonance Imaging ; Acyclovir/therapeutic use ; },
abstract = {BACKGROUND: Varicella-zoster virus (VZV) can cause a range of central nervous system (CNS) infections, but early diagnosis is difficult when typical skin rash is absent. Rashless VZV encephalitis may present with nonspecific clinical, cerebrospinal fluid (CSF), and neuroimaging findings and can mimic autoimmune encephalitis, primary central nervous system lymphoma, or other disorders. We report two cases of rashless VZV encephalitis diagnosed by CSF metagenomic next-generation sequencing (mNGS), with subsequent neurological complications.

CASE PRESENTATION: Case 1 was a 68-year-old man admitted with fever, seizures, and impaired consciousness. Brain magnetic resonance imaging (MRI) showed multifocal abnormal signals. CSF analysis revealed marked pleocytosis and elevated protein levels, and CSF cytology showed suspected atypical lymphocytes, leading to early consideration of autoimmune encephalitis and primary central nervous system lymphoma. CSF mNGS detected VZV, and rashless VZV encephalitis was diagnosed. The patient improved after intravenous acyclovir combined with a short course of dexamethasone. On day 45 after disease onset, follow-up MRI showed a new acute cerebral infarction adjacent to the posterior horn of the left lateral ventricle. Recurrent CSF pleocytosis and persistent protein elevation suggested possible VZV-associated vasculopathy. After repeated antiviral treatment, he improved again, and no recurrence was observed during more than 3 years of follow-up. Case 2 was a 74-year-old man admitted with fever, low back pain, vomiting, and impaired consciousness. Brain MRI showed multifocal abnormal signals, and CSF analysis revealed marked inflammatory changes. CSF mNGS detected VZV, supporting the etiological diagnosis of rashless VZV encephalitis. The patient improved after intravenous acyclovir combined with a short course of dexamethasone. On day 14 after disease onset, he developed urinary retention, impaired defecation sensation, and bilateral lower-limb weakness, suggesting possible lumbosacral nerve root or cauda equina involvement. Suspected VZV-related Elsberg syndrome was considered. His urinary and bowel dysfunction recovered at 2 months after disease onset.

CONCLUSIONS: Rashless VZV encephalitis may be diagnostically challenging because early clinical, CSF, and neuroimaging findings are nonspecific. CSF mNGS can support etiological diagnosis, and careful follow-up is needed to detect delayed vascular and lumbosacral nerve root complications.},
}

Humans
Male
Aged
*Encephalitis, Varicella Zoster/diagnosis/cerebrospinal fluid/drug therapy/complications
*High-Throughput Nucleotide Sequencing/methods
*Herpesvirus 3, Human/genetics
Metagenomics/methods
Magnetic Resonance Imaging
Acyclovir/therapeutic use

@article {pmid42723054,
year = {2026},
author = {Zhao, J and Chen, X and Wang, X and Cui, Y and Zhuge, J and Zhang, Y and Zhang, L and Yan, Y and Fang, H and Hua, Z and Li, G},
title = {Metagenomic-based quantification of Pseudomonas aeruginosa burden links microbiome collapse to mortality in severe community-acquired pneumonia.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {25},
number = {1},
pages = {},
pmid = {42723054},
issn = {1476-0711},
support = {2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Humans ; *Community-Acquired Pneumonia/mortality/microbiology ; *Pseudomonas aeruginosa/genetics/isolation & purification ; Female ; *Microbiota ; Retrospective Studies ; *Pseudomonas Infections/mortality/microbiology ; Metagenomics ; Male ; Aged ; Middle Aged ; Lung/microbiology ; *Community-Acquired Infections/microbiology/mortality ; ROC Curve ; Metagenome ; High-Throughput Nucleotide Sequencing ; Prognosis ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (sCAP) remains a major cause of mortality in critically ill patients, Pseudomonas aeruginosa (P. aeruginosa) is a frequent pathogen associated with poor prognosis in this population. While metagenomic next-generation sequencing (mNGS) is widely used for pathogen detection, its value in quantifying pathogen abundance and linking it to lung microbiome alterations remains unclear.

OBJECTIVES: This study investigated the association between P. aeruginosa abundance quantified by mNGS and lung microbiome alterations and clinical outcomes in sCAP patients.

METHODS: This multicenter retrospective study included 130 patients with sCAP caused by P. aeruginosa from five hospitals (September 2021-June 2025). Patients were stratified into low, medium, and high abundance groups according to mNGS-derived reads per ten million (RPTM) values of P. aeruginosa. Lung microbiome diversity and community structure were analyzed, and differences between groups were assessed using appropriate statistical methods. The association between P. aeruginosa abundance and clinical outcomes was evaluated using correlation analysis, sankey diagram, receiver operating characteristic curve, grey zone analysis and logistic regression.

RESULTS: A total of 130 patients with sCAP due to P. aeruginosa were stratified into low, medium, and high abundance groups based on mNGS-derived RPTM value. Microbial diversity decreased progressively with increasing abundance, and community structures differed significantly among groups (all P < 0.05). P. aeruginosa became increasingly dominant, accounting for up to 95.99% of the microbiota in the high abundance group. Higher P. aeruginosa abundance was associated with increased disease severity, including longer mechanical ventilation, prolonged hospital stay, and higher 28-day mortality. Sankey diagram showed a progressive decline in treatment effectiveness and an increase in mortality with increasing P. aeruginosa abundance. P. aeruginosa_RPTM showed moderate predictive value for mortality (AUC = 0.761, Sens = 69.40%, Spec = 75.30%, cutoff: 41122, grey zone: 2287-220339) and remained independently associated with 28-day mortality in multivariable analysis [2.219 (1.509 to 3.262), P < 0.001].

CONCLUSION: In patients with sCAP, higher P. aeruginosa_RPTM measured by mNGS was associated with reduced lung microbiome diversity and unfavorable clinical outcomes. RPTM-based risk stratification may help identify patients at increased risk of poor prognosis.},
}

Humans
*Community-Acquired Pneumonia/mortality/microbiology
*Pseudomonas aeruginosa/genetics/isolation & purification
Female
*Microbiota
Retrospective Studies
*Pseudomonas Infections/mortality/microbiology
Metagenomics
Male
Aged
Middle Aged
Lung/microbiology
*Community-Acquired Infections/microbiology/mortality
ROC Curve
Metagenome
High-Throughput Nucleotide Sequencing
Prognosis

@article {pmid42723101,
year = {2026},
author = {Liu, X and Yang, Z and Zhang, X and Tang, W and Wang, Y and Cao, Z and Yang, H and Wang, W and Hao, Y and Li, S},
title = {Gut microbiota-driven indole-3-propionic acid and kynurenine production is associated with improved metabolic adaptation in periparturient dairy cows.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42723101},
issn = {1674-9782},
abstract = {BACKGROUND: Gastrointestinal microbes convert tryptophan into various bioactive metabolites that influence host energy metabolism; however, these mechanisms are not well understood in periparturient dairy cows, which experience marked metabolic challenges during this period.

RESULTS: In this study, we used periparturient dairy cows with rumen and ileal cannulas as in vivo models. Blood, rumen fluid, ileal digesta, and fecal samples were collected at four time points during the periparturient period. By combining metagenome-assembled genomes (MAGs) and targeted metabolite quantification, we characterized microbial tryptophan metabolism and associated metabolite profiles during the periparturient period. The results showed that postpartum cows exhibited significantly increased serum concentrations of triglyceride (TG), aspartate aminotransferase (AST), β-hydroxybutyrate (BHBA), and total bilirubin (T-Bil) compared with prepartum cows, together with decreased levels of several tryptophan metabolites, including indole-3-propionic acid (IPA) and kynurenine (KYN), indicating that tryptophan deficiency might aggravate metabolic disturbances. Metagenomic analysis identified 578 high-quality MAGs, of which 461 contained genes involved in microbial tryptophan metabolic pathways. Among these, the ruminal taxon CAG-791 harbors acdA and contributes to IPA production, whereas the hindgut taxon Treponema_D harbors kynB and promotes KYN formation. Decreases in both taxa were consistent with the reduced levels of these metabolites observed above. In a follow-up in vivo trial with tryptophan supplementation, the abundance of CAG-791 and Treponema_D increased, along with tryptophan-derived metabolites (IPA and KYN), which further partially mitigated metabolic disturbances.

CONCLUSIONS: These findings characterize spatial and temporal changes in tryptophan metabolites and gut microbial features in periparturient dairy cows, and provide integrated evidence that alterations in tryptophan metabolism are associated with postpartum metabolic adaptation, thereby supporting the potential of tryptophan-targeted nutritional strategies to improve metabolic health in dairy cows.},
}

@article {pmid42723112,
year = {2026},
author = {Zhang, S and Zhang, N and Zhang, X and Liu, Y and Feng, Y and Xiang, J and Zhang, J and Ma, H and Lu, Y and Zhang, T},
title = {Integrated landscape of salivary metagenome and multi-biofluid metabolome characterizes a microbial-metabolic axis in upper gastrointestinal cancer progression.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42723112},
issn = {2049-2618},
mesh = {Humans ; *Saliva/microbiology ; *Metabolome ; *Gastrointestinal Neoplasms/microbiology/metabolism/pathology/diagnosis ; *Metagenome ; Disease Progression ; Metagenomics/methods ; Metabolomics/methods ; Female ; Multiomics ; Male ; Middle Aged ; Dysbiosis/microbiology ; Microbiota ; Lysine/metabolism ; },
abstract = {BACKGROUND: Upper gastrointestinal cancer (UGIC) imposes a major global health burden, yet the stage-specific molecular changes along the microbial-metabolic axis remain limited understood. We aimed to delineate this molecular landscape across UGIC progression and evaluate its potential as non-invasive methods for precision screening.

RESULTS: Derived from a multi-center population-based UGIC screening program, we enrolled 420 individuals, stratified into normal, low-grade intraepithelial neoplasia (LGIN), high-grade intraepithelial neoplasia (HGIN), and UGIC (n = 105 per group). Integrated salivary metagenomics and paired salivary/plasma metabolomics were performed to capture local and systemic dysregulation. We uncovered distinct stage-specific divergence during UGIC progression: profound remodeling of the salivary microbiota (104 differential species) and salivary metabolomics (80 differential metabolites) initiated early at the LGIN stage, whereas plasma metabolic dysregulation (40 differential metabolites) peaked significantly later at the HGIN stage. Integrative analysis revealed salivary microbiota related more closely with salivary metabolome than plasma metabolome. Moreover, statistical evidence suggested that dysbiotic salivary microbiota was associated with altered lysine- and tryptophan-related catabolic pathways converging on Acetyl-CoA-related metabolic nodes, supporting a potential metabolic mechanism in precancerous lesions. Finally, the discriminative model integrating metagenomic and metabolomic markers demonstrated promising diagnostic performance in distinguishing these precancerous lesions (LGIN: area under the curve [AUC] = 0.83; HGIN: AUC = 0.77) and UGIC (AUC = 0.76) from normal.

CONCLUSION: This study characterizes a stage-specific microbial-metabolic axis that facilitates the comprehensive understanding of UGIC pathogenesis. These multi-biofluid signatures offer a promising non-invasive triage strategy for detecting precancerous lesions and optimizing endoscopic resource allocation. Video Abstract.},
}

Humans
*Saliva/microbiology
*Metabolome
*Gastrointestinal Neoplasms/microbiology/metabolism/pathology/diagnosis
*Metagenome
Disease Progression
Metagenomics/methods
Metabolomics/methods
Female
Multiomics
Male
Middle Aged
Dysbiosis/microbiology
Microbiota
Lysine/metabolism

@article {pmid42723116,
year = {2026},
author = {Hong, X and Shen, D and Lin, C and Cao, X and Sun, Z and Liu, B and Guo, R and Liu, Z and Luo, T and Yu, Y and Yang, M and Feng, B and Zhang, W and Huang, G},
title = {Potential of plasma metagenomic next-generation sequencing to guide antibiotic therapy in acute necrotizing pancreatitis with early fever: a prospective multicenter cohort study.},
journal = {Antimicrobial resistance and infection control},
volume = {15},
number = {1},
pages = {},
pmid = {42723116},
issn = {2047-2994},
mesh = {Humans ; *Pancreatitis, Acute Necrotizing/drug therapy/microbiology/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; Male ; Female ; *Fever/drug therapy/etiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; China ; Adult ; Aged ; },
abstract = {BACKGROUND: Indiscriminate antibiotic use remains common in febrile patients with acute necrotizing pancreatitis (ANP), particularly during the early phase. Metagenomic next‑generation sequencing (mNGS) has shown diagnostic utility for infected pancreatic necrosis (IPN) and may offer a means to guide antimicrobial therapy. We aimed to explore whether mNGS could potentially improve the appropriateness of antibiotic use in ANP patients presenting with early fever.

METHODS: This prospective multicenter cohort study was conducted at five hospitals in China, enrolling ANP patients who developed fever within two weeks of symptom onset. Antibiotic susceptibility was defined per local microbiology laboratory reports. The hypothetical impact of mNGS on reducing inappropriate antibiotic use was evaluated through a retrospective simulation using predefined criteria from the BGI China antimicrobial drug usage card, as mNGS results were not disclosed to the treating teams during the actual clinical course.

RESULTS: Between May 2023 and December 2024, 125 ANP patients with early fever were enrolled. Antibiotics were administered to 91.2% (114/125) of patients, whereas only 23.2% (29/125)were eventually confirmed to have IPN, and the rate of appropriate antibiotic use was 14.5% (17/117) based on conventional culture. In our simulated model, if therapy had been guided by plasma mNGS results, the estimated rate of appropriate antibiotic use could have increased to 71.8%.

CONCLUSIONS: Plasma mNGS facilitates rapid pathogen identification and shows potential for improving antibiotic appropriateness in ANP patients with early fever.},
}

Humans
*Pancreatitis, Acute Necrotizing/drug therapy/microbiology/diagnosis
*Anti-Bacterial Agents/therapeutic use
Prospective Studies
Male
Female
*Fever/drug therapy/etiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
China
Adult
Aged

@article {pmid42723737,
year = {2026},
author = {Li, Z and Dong, Z and Jiao, L and Cai, Y and Zhang, Y and Wei, H and Fang, T and Zhang, Z and Liu, H},
title = {Real-world pathogen spectrum, clinical actionability, and host correlates of first-time mNGS testing in hospitalized patients with hematologic diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1900843},
pmid = {42723737},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Diseases/complications/microbiology ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Middle Aged ; Male ; Adult ; Hospitalization ; Viruses/isolation & purification/classification/genetics ; Aged, 80 and over ; Bacteria/isolation & purification/genetics/classification ; Fungi/genetics/isolation & purification/classification ; },
abstract = {BACKGROUND: Patients with hematologic diseases are highly susceptible to infection. Conventional tests often have low sensitivity. Metagenomic next-generation sequencing (mNGS) can detect many pathogens at once, but its clinical value depends on how the results are interpreted. It is often hard to tell true infection from colonization or contamination.

METHODS: We retrospectively studied hospitalized hematologic patients Only adult patients (≥18 years) who received mNGS for the first time. Detected organisms were reclassified using a clinical actionability system. We also analyzed the relationships between mNGS findings, host characteristics, and short-term outcomes.

RESULTS: A total of 134 patients were included. At least one organism was detected in 87.3% of patients, but only 58.2% had highly actionable results. Bacteria were the most common findings, followed by viruses and fungi. Mixed detections were frequent. Actionable results were seen more often in respiratory specimens than in blood specimens. Viral detection was associated with immune status. Pathogen read counts were only weakly related to inflammatory markers and did not independently predict adverse outcomes. Age was the only independent risk factor for adverse outcome.

CONCLUSION: mNGS had a high detection rate in hematologic patients, but not all positive findings were clinically important. Result interpretation should take specimen type and host status into account. Pathogen read counts alone were not useful for predicting short-term outcome.},
}

Humans
*Hematologic Diseases/complications/microbiology
Female
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
Aged
*Metagenomics/methods
Middle Aged
Male
Adult
Hospitalization
Viruses/isolation & purification/classification/genetics
Aged, 80 and over
Bacteria/isolation & purification/genetics/classification
Fungi/genetics/isolation & purification/classification

@article {pmid42723798,
year = {2026},
author = {Mao, X and Qu, Q and Quan, C and Lyu, H and Zhangbao, J and Wang, X and Tan, H and Li, X},
title = {Clinical features associated with cerebrospinal fluid Epstein-Barr virus positivity in autoimmune GFAP astrocytopathy: a multicenter retrospective cohort study.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1906448},
pmid = {42723798},
issn = {1664-2295},
mesh = {Humans ; Female ; Retrospective Studies ; Male ; *Glial Fibrillary Acidic Protein/immunology ; *Herpesvirus 4, Human/isolation & purification ; Middle Aged ; *Epstein-Barr Virus Infections/cerebrospinal fluid/complications ; Adult ; *Autoimmune Diseases of the Nervous System/cerebrospinal fluid/virology ; *Astrocytes/immunology ; Aged ; },
abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein astrocytopathy (GFAP-A) is an inflammatory disorder of the central nervous system. The clinical implications of Epstein-Barr virus (EBV) sequences detected in cerebrospinal fluid (CSF) by metagenomic next-generation sequencing (mNGS) remain uncertain.

METHODS: This multicenter retrospective cohort study enrolled 60 patients with GFAP-A screened from electronic medical records of two hospitals (Jan 2019-Dec 2025). Patients were stratified into CSF EBV-positive (n = 10) and CSF EBV-negative (n = 50) groups based on CSF mNGS results. Demographic characteristics, clinical manifestations, laboratory findings, MRI features, treatment, and outcomes were compared. Bonferroni correction was applied to three clinically prioritized endpoints (CSF white blood cell count, altered consciousness, CSF chloride) selected based on prior GFAP-A literature to limit multiplicity bias; the corrected two-sided significance threshold was set at α = 0.05/3 ≈ 0.0167. An exploratory Firth penalized multivariable logistic regression model fitted via R (v4.3.1, logistf package) was used to examine the adjusted associations between CSF mNGS-detectable EBV sequences and acute altered consciousness, adjusting for age and sex to mitigate small-sample bias. All other unadjusted baseline comparisons were considered exploratory and were not adjusted for multiplicity. Spearman's rank correlation was used to assess the relationships of raw EBV mNGS read counts with peak pretreatment modified Rankin Scale (mRS) score and CSF WBC count among EBV-positive patients.

RESULTS: CSF WBC count was higher in the CSF EBV-positive group than in the CSF EBV-negative group [median, 120 (interquartile range, 105-220) vs. 33 (16-97) × 10⁶/L; raw p = 0.004; Bonferroni-adjusted p = 0.012]. Altered consciousness was more frequent in the EBV-positive group (80.0% vs. 42.0%; crude odds ratio [OR] = 5.52, 95% confidence interval [CI] 1.06-28.71; raw p = 0.039), and CSF chloride was numerically lower [111.50 (104.00-117.00) vs. 115.70 (113.00-120.00) mmol/L; raw p = 0.048]; however, neither comparison met the Bonferroni-corrected criterion (adjusted p = 0.117 and 0.144, respectively). Firth penalized multivariable logistic regression fitted in R was adjusted for age and sex. CSF EBV positivity exhibited a non-significant trend toward higher odds of acute altered consciousness (OR = 4.10, 95% CI: 0.94-24.84, p = 0.060). The extremely wide confidence interval indicated high estimation uncertainty limited by the small EBV-positive subgroup (n = 10). Female sex was associated with lower estimated odds of altered consciousness (OR = 0.17, 95% CI: 0.04-0.58, p = 0.004), while age showed no independent association (OR = 0.98, 95% CI: 0.95-1.02, p = 0.312). No statistically detectable between-group differences were observed in GFAP-IgG characteristics, MRI findings, relapse, or functional outcomes. Among the 10 EBV-positive patients, raw EBV read counts were not statistically correlated with peak pretreatment mRS score (r s = 0.118, p = 0.745) or CSF WBC count (r s = -0.073, p = 0.841).

CONCLUSION: CSF WBC count was the only clinically prioritized comparison that remained statistically significant after Bonferroni correction, suggesting greater CSF pleocytosis and possibly increased intrathecal inflammatory activity in GFAP-A patients with mNGS-detectable CSF EBV. Differences in altered consciousness and CSF chloride remained inconclusive after multiplicity adjustment. Within the EBV-positive subgroup, raw EBV sequencing reads showed no correlation with inflammatory or disability measures. Current findings do not establish CSF EBV positivity as an independent pathogenic or prognostic biomarker for GFAP-A, and the biological origin of the detected EBV sequences remains uncertain.},
}

Humans
Female
Retrospective Studies
Male
*Glial Fibrillary Acidic Protein/immunology
*Herpesvirus 4, Human/isolation & purification
Middle Aged
*Epstein-Barr Virus Infections/cerebrospinal fluid/complications
Adult
*Autoimmune Diseases of the Nervous System/cerebrospinal fluid/virology
*Astrocytes/immunology
Aged

@article {pmid42723989,
year = {2026},
author = {Ma, Z and Bai, X and Tian, J and Yao, C and Yan, Z and Ma, X and Zhang, C and Ma, J and Lin, Y and Zhang, X and Wang, H},
title = {Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1914654},
pmid = {42723989},
issn = {2235-2988},
mesh = {Humans ; Female ; *Histamine/metabolism/blood ; Adult ; Male ; Cytokines/blood ; *Gastrointestinal Microbiome ; *Inflammation ; *Spondylitis/microbiology/pathology/metabolism ; Dysbiosis/microbiology ; Middle Aged ; Histidine Decarboxylase/blood ; Metagenomics ; Lipopolysaccharides/blood ; Fatty Acids, Volatile ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The pathogenesis of brucellar spondylitis (BLS) has traditionally been considered to be primarily limited to local osteoarticular lesions. With the proposal of the "gut-spine axis" concept, the role of intestinal microecological dysbiosis in inflammatory spinal diseases has attracted in an increase of attention. The overactivated inflammatory cytokine network not only mediates bone destruction and intervertebral disc damage, but also forms a bidirectional interaction with gut microbiota dysbiosis through the "gut-spine axis," collectively driving disease progression. However, the inflammatory mechanism by which gut microbiota participates in the pathological process of BLS remains largely unclear.

METHODS: This study recruited 20 BLS patients and 20 healthy donors. Multi-omics analysis including metagenomics, untargeted metabolomics, and targeted short-chain fatty acids (SCFAs) analysis, were used to compare the structural differences in gut microbiota between the two groups and screen for signature differential bacterial species. Plasma levels of histamine and histidine decarboxylase were measured by ELISA to clarify the role of differential histidine metabolic pathway in the disease. Additionally, plasma levels of lipopolysaccharide (LPS) and inflammatory cytokines (IL-1β, IL-6, IL-10, IL-17A, TNF-α) were detected by ELISA. The correlation between gut microbiota and inflammatory indicators was further analyzed.

RESULTS: Compared to the healthy control group, the α-diversity of the gut microbiota in BLS patients was significantly reduced, with the microbial community structure exhibiting increased homogeneity. Beta diversity analysis revealed significant differences, suggesting that disease progression is associated with an overall imbalance in the gut microbiota and the deterioration of its specific structural composition. At the phylum level, the abundances of Actinomycetota, unclassified_d_Viruses, and Fusobacteriota were significantly increased in the gut microbiota of BLS patients compared to the control group, while the abundances of Bacillota and Pseudomonadota were significantly decreased. Further analysis revealed that, compared to the control group, the generic abundance of Enterococcus was significantly increased, while the proportions of Blautia, Faecalibacterium, Ruminococcus, Agathobacter, Roseburia, Clostridium, Eubacterium, Alistipes and Anaerobutyricum were significantly decreased. At the species level, the abundances of Enterococcus sp and Enterococcus-faecium were increased, whereas Blautia sp, Ruminococcus sp, Faecalibacterium sp, Faecalibacterium prausnitzii, Agathobacter rectalis, Eubacterium sp, Agathobacter sp, and Roseburia sp were decreased. Furthermore, untargeted metabolomics revealed that metabolites were enriched in the histidine metabolic pathway, and the levels of SCFAs including butyrate, isobutyrate, valerate, and 4-methylvalerate in the intestinal contents were reduced in BLS. Functional KEGG profiling revealed that key KOs involved in butyrate synthesis (e.g., K00074, K00172, K01640) and transport were globally downregulated in the patient group, whereas histidine decarboxylase KOs (K01693, K11755, K19787) that convert histidine to pro-inflammatory histamine were significantly enriched. The loss of butyrate-producing symbionts led to SCFAs deficiency and mucosal barrier disruption, creating ecological niches for facultatively anaerobic Enterococcus, which further exacerbated local inflammation via proteolytic fermentation and histamine production. Compared with the control group, BLS patients showed decreased plasma levels of IL-10, while levels of IL-1β, IL-6, IL-17A, and TNF-α were increased, and LPS levels were elevated. In addition, significantly elevated plasma pro-inflammatory LPS levels in patients with BLS suggest disruption of intestinal integrity and permeability. Correlation analysis indicated a close relationship between gut microbiota and inflammation.

CONCLUSION: BLS is associated with gut microbiota dysbiosis and alterations in microbial metabolites, which may be linked to inflammatory responses and histamine metabolism. The differential microbial taxa identified in this study could be developed into a stool-based non-invasive diagnostic panel to facilitate early differentiation of BLS from other spinal disorders. Furthermore, restoring gut microbial balance through probiotic supplementation or dietary modulation may represent a promising adjunctive strategy to enhance the efficacy of standard antibiotic therapy and reduce disease recurrence.},
}

Humans
Female
*Histamine/metabolism/blood
Adult
Male
Cytokines/blood
*Gastrointestinal Microbiome
*Inflammation
*Spondylitis/microbiology/pathology/metabolism
Dysbiosis/microbiology
Middle Aged
Histidine Decarboxylase/blood
Metagenomics
Lipopolysaccharides/blood
Fatty Acids, Volatile
Metabolomics
Bacteria/classification/genetics/isolation & purification

@article {pmid42723994,
year = {2026},
author = {Ni, H and Gong, QL and Li, JM and Liu, F and Leng, X and Song, YH and Jiang, J and Li, ZY and Li, Y and Sun, YZ},
title = {Genome-resolved analysis of colonization factor repertoires reveals ecological stratification in cervid gut microbiomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1929306},
pmid = {42723994},
issn = {1664-302X},
abstract = {INTRODUCTION: Colonization factors (CFs) are important microbial traits associated with persistence and host adaptation in the gut, yet their large-scale organization in cervid gut microbiomes remains unclear.

METHODS: A total of 3,311 non-redundant high-quality metagenome-assembled genomes (MAGs), derived from 688 cervid gut metagenomic samples across 15 publicly available projects and one in-house dataset, were analyzed. CF-associated genes were identified by comparison against the GHA CF database, and CF repertoires were characterized at genome, host-species, and gastrointestinal-segment levels.

RESULTS: A total of 138,729 CF-associated genes spanning 71 CF families were identified. MAGs from Cervinae contained richer CF repertoires than those from Caprinae, and CF47 (Peptidase_C69), CF24_29 (QueH), and CF18 (Glycos_transf_2) were among the most prevalent families. CF repertoires were strongly structured by taxonomy, showed a moderate association with bacterial phylogenetic distance, and formed two recurrent genome-level configurations with distinct KEGG functional profiles. Integration of sample metadata further revealed differentiation of CF repertoires across host species and gastrointestinal segments, representing the major ecological dimensions examined in this study. Segment-associated CF variation was accompanied by redistribution of broader functional profiles, including enrichment of carbohydrate and lipid metabolism in the jejunum, membrane transport in the ileum, xenobiotics biodegradation in the cecum, and environmental adaptation in the rumen.

DISCUSSION: These findings provide a genome-resolved view of CF repertoire organization in cervid gut microbiomes and demonstrate that colonization-associated functions are structured across microbial lineages and ecological contexts. This study highlights the importance of considering microbial taxonomy and host-associated environments when interpreting the distribution of CF repertoires in mammalian gut ecosystems.},
}

@article {pmid42724308,
year = {2026},
author = {Chen, X and Gong, C},
title = {Nontuberculous mycobacterial pulmonary disease and lung cancer: a retrospective case series.},
journal = {Journal of thoracic disease},
volume = {18},
number = {8},
pages = {884},
pmid = {42724308},
issn = {2072-1439},
abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (NTM-PD) has increased worldwide. However, the clinical characteristics and optimal management of patients with concomitant lung cancer and NTM-PD remain poorly understood. This retrospective case series aimed to investigate the clinical characteristics, microbiological findings, treatment strategies, and clinical outcomes of patients with lung cancer complicated by NTM-PD.

METHODS: We retrospectively reviewed the clinical data of 13 patients with concomitant lung cancer and NTM-PD at our institution between January 2020 and January 2025. Demographic characteristics, clinical manifestations, microbiological findings, tumor stage, histological subtype, driver gene alterations, treatment strategies, and clinical outcomes were collected and analyzed. NTM species were identified by metagenomic next-generation sequencing (mNGS).

RESULTS: A total of 13 patients (8 men and 5 women) were included, with a median age of 64 years (interquartile range, 59.5-71.0 years). Adenocarcinoma was the most common histological subtype (n=7). The predominant NTM species were Mycobacterium abscessus (n=4) and the Mycobacterium avium complex (MAC) (n=5). Eleven patients received anti-NTM therapy, whereas two were managed conservatively because their respiratory symptoms improved after anticancer treatment and their pulmonary lesions remained radiologically stable. Individualized treatment sequencing enabled most patients to complete anticancer therapy. Two patients with stage I disease underwent delayed surgery following short-term anti-NTM treatment. At the last follow-up, three patients had died and ten remained alive. The mean follow-up duration was 18.69 months (range, 6-53 months).

CONCLUSIONS: Among patients with lung cancer complicated by NTM infection, the predominant species were MAC and Mycobacterium abscessus. No obvious worsening of NTM-PD was observed during concurrent treatment, but NTM infection may delay the timing of surgery for early-stage lung cancer.},
}

@article {pmid42724568,
year = {2026},
author = {Fang, Y and Wang, M and Wang, H and Xiao, S and Jie, Z and Xiong, W and Wang, X and Wang, Q and Xie, L and Li, Y and Zhu, T},
title = {Pathogens and clinical characteristics of type 2 diabetes mellitus in patients with community-acquired pneumonia via bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing: a comparative observational study.},
journal = {Journal of thoracic disease},
volume = {18},
number = {8},
pages = {870},
pmid = {42724568},
issn = {2072-1439},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers high sensitivity and specificity for pathogen detection. Type 2 diabetes mellitus (T2DM) is a key risk factor for opportunistic infections, including community-acquired pneumonia (CAP). Targeted treatment of the pathogen is beneficial to the prognosis of patients with CAP. This study aimed to explore the pathogen distribution and clinical presentation of CAP in patients with T2DM via bronchoalveolar lavage fluid (BALF) mNGS.

METHODS: In this comparative observational study, a total of 285 patients with CAP were enrolled. Ultimately, 117 CAP patients without T2DM and 96 CAP patients with T2DM were included. Demographics, clinical data, laboratory data, and BALF mNGS results were collected. Least absolute shrinkage and selection operator (LASSO) regression was performed to determine potential variables, which were subsequently included in a binary logistic regression model to identify clinical and microbiological features associated with pre-existing T2DM in CAP patients.

RESULTS: Thirteen potential T2DM-associated variables were selected by LASSO regression. Furthermore, binary logistic model identified that higher body mass index (BMI) [odds ratio (OR) =1.107, 95% confidence interval (CI): 1.004-1.221], lower rate of connective tissue disease (CTD) (OR =0.046, 95% CI: 0.002-0.935), elevated blood urea nitrogen (BUN) (OR =1.091, 95% CI: 1.003-1.187), the presence of COVID-19 (OR =6.582, 95% CI: 1.244-34.829) and Aspergillus (OR =2.909, 95% CI: 1.018-8.311) were independent variables for T2DM in CAP patients.

CONCLUSIONS: Collectively, our analysis revealed that CAP patients with T2DM had a distinct clinical profile and pathogen spectrum, characterized by a higher prevalence of COVID-19 and Aspergillus infection, a greater tendency for renal dysfunction, and a higher BMI but a lower rate of CTD. These findings underscore T2DM as a significant risk factor for COVID-19 and Aspergillus pneumonia. In clinical practice, stricter infection screening strategies should be implemented for this population, along with targeted anti-infective therapy and enhanced dynamic assessment of renal function, weight management, and blood glucose control, will help improve outcomes.},
}

@article {pmid42724691,
year = {2016},
author = {Roeselers, G and Bouwman, J and Levin, E},
title = {The human gut microbiome, diet, and health: "Post hoc non ergo propter hoc".},
journal = {Trends in food science & technology},
volume = {57},
number = {Pt B},
pages = {302-305},
pmid = {42724691},
issn = {0924-2244},
abstract = {The gastro-intestinal microbiome has become the subject of intensive research, which is beginning to elucidate its roles in human health. It is becoming increasingly recognised that gut microbiota plays a part in regulating human immune homeostasis and metabolism, which gives rise to novel opportunities for preventative and treatment strategies. The key challenge in this field is the ability to define causality in the relationship between nutrition, microbiota and host health. In this commentary we argue for an increased focus on cause-and-effect relationships within studies that relate to the human microbiome in health and predispositions to disease. With the right experimental models, data accessibility infra-structure and advanced machine learning tools, causal relationships among components of complex host-microbiome systems can be elucidated.},
}

@article {pmid42724850,
year = {2026},
author = {Li, L and Yang, X and Ning, Y and Tang, N and Chen, W and Yang, Y and Xue, Y and Pei, X and Jiang, X and Zhang, F and Chen, Z and Wei, T},
title = {Multi-omics insights into co-fermentation by Saccharomycopsis fibuligera and Bacillus velezensis enhancing the nutritional, metabolic, and aromatic quality of Pueraria thomsonii.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1938235},
pmid = {42724850},
issn = {2296-861X},
abstract = {BACKGROUND: Pueraria thomsonii is rich in isoflavonoids; however, its glycoside-dominated forms exhibit limited intestinal absorption and metabolism, and the material possesses undesirable sensory traits. This study employs a defined co-culture of Saccharomycopsis fibuligera and Bacillus velezensis to achieve coordinated starch hydrolysis, cell-wall degradation, and β-glucosidase-mediated deglycosylation. We investigate the resulting nutritional, metabolic, and volatile profiles through integrated multi-omics, establishing this consortium as a bioprocessing method for value-added P. thomsonii.

METHODS: Solid-state fermentation (SSF) was conducted at 30 °C for 72 h under microaerophilic conditions across five treatments: raw P. thomsonii (Y), natural fermentation (K), single-strain fermentation with S. fibuligera YPD01 (S) or B. velezensis NA03 (B), and co-fermentation with both strains at a 1:1 ratio (M). Nutritional components, total flavonoids, and total phenolics were quantified. Activities of α-amylase, β-glucosidase, and cellulase were assayed. The microbial community structure and functional genes were characterized through metagenomic sequencing. Untargeted metabolomics was performed using UPLC-MS, and volatile compounds were analyzed by GC-MS.

RESULTS: Co-fermentation achieved the highest nutritional quality, yielding reducing sugars (15.45 ± 0.26 mg/g), total flavonoids (9.30 ± 0.17 mg RUT/g), total phenolics (13.19 ± 0.25 mg GAE/g), total amino acids (52.11 ± 0.53 g/kg), and crude protein (12.56 ± 0.26%), all significantly surpassing other treatments. Both inoculated strains effectively colonized the substrate. Co-fermentation exhibited the highest activities of β-glucosidase (90.67 ± 2.66 U/g) and cellulase (343.77 ± 10.75 U/g). Metagenomic analysis generated approximately 659 million reads, identifying 7,737 KEGG entries, with enriched CAZy families in co-fermentation. Untargeted metabolomics identified 1,693 metabolites, with co-fermentation uniquely enriching isoflavone aglycones, peptides, and esterase-related compounds. GC-MS analysis revealed that co-fermentation produced the highest levels of fruity esters, including ethyl linoleate (1009.73 ± 32.51 μg/g) and ethyl palmitate (335.85 ± 9.76 μg/g), while hexanal was eliminated in all fermented groups.

CONCLUSION: The S. fibuligera-B. velezensis consortium enhanced the nutritional, metabolic, and aromatic quality of P. thomsonii through enzymatic biotransformation and metabolic complementarity. Co-fermentation outperformed both natural and single-strain fermentations in the release of phenolic compounds and isoflavone aglycones, amino acid enrichment, and flavor development. These findings provide a theoretical basis and technical guidance for developing high-value fermented foods and offer a reference framework for the precision microbial transformation of medicinal and edible homologous materials.},
}

@article {pmid42725043,
year = {2026},
author = {Lee, JM and Kim, HO and Kim, YJ and Singh, MK and Kim, SS and Yeo, SG},
title = {Respiratory pandemic risk in the Anthropocene: A One Health framework and GISRS+ agenda.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101553},
doi = {10.1016/j.onehlt.2026.101553},
pmid = {42725043},
issn = {2352-7714},
abstract = {Recent epidemics and pandemics caused by respiratory viruses, alongside the animal panzootic spread of highly pathogenic avian influenza A(H5Nx), have become a structural feature of the Anthropocene, yet responses remain largely reactive. This review integrates findings from WHO's Global Influenza Surveillance and Response System (GISRS) and related surveillance data (2000-2024), epidemiological studies of influenza A virus, SARS-CoV, MERS-CoV, SARS-CoV-2, and H5Nx, and One Health literature. We examine major groups of respiratory viruses and identify mismatches between risk and surveillance by focusing on spillover potential from animal hosts, human-to-human transmission and its controllability, and Anthropocene characteristics that increase epidemic risk. The analysis indicated that SARS-related coronaviruses and influenza A viruses, particularly H5Nx, are among the leading candidates based on currently available evidence because they have large reservoirs in animal hosts and spillover to humans is highly probable. The previous presymptomatic spread of SARS-CoV-2 and recent mammalian adaptation in H5N1 clade 2.3.4.4b highlight limitations of the traditional symptom-based and pathogen-specific surveillance system. Spillover events tend to occur in tropical and subtropical regions in low- and middle-income countries, but most genomic surveillance is in high-income countries. We propose interventions that address the upstream, midstream, downstream processes of epidemics. Upstream interventions are primary prevention measures related to land use, livestock, wildlife, and urban environments; midstream interventions are GISRS+-based pathogen-agnostic genomic and metagenomic early warning systems triggered by One Health; and downstream interventions include vaccines, antivirals, non-pharmaceutical interventions, and engineering with equity-centred global governance and sustainable financing.},
}

@article {pmid42725257,
year = {2026},
author = {Tahir, S and Hassan, Z and Tariq, A and Chhetri, R and Chhetri, J and Kc, M},
title = {Metagenomic sequencing in intracranial pyogenic infections: limitations in viability and implications for antimicrobial decision-making.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {9},
pages = {6213-6214},
doi = {10.1097/MS9.0000000000005586},
pmid = {42725257},
issn = {2049-0801},
}

@article {pmid42725323,
year = {2026},
author = {Weilguny, L and Probul, N and Ren, Y and Pons, N and Baumbach, J and Almeida, M},
title = {Fedflow: cloud orchestration for federated learning with the FeatureCloud platform.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag255},
doi = {10.1093/bioadv/vbag255},
pmid = {42725323},
issn = {2635-0041},
abstract = {MOTIVATION: Federated learning (FL) enables collaborative model training on geographically distributed genomic and clinical datasets while complying with data privacy laws and regulatory constraints. FeatureCloud is an existing platform for FL that provides an accessible web-based interface and a large repository of implemented methods. However, due to its graphical interface, FeatureCloud requires manual interaction of all participants, limiting automation, iteration, and reproducibility.

RESULTS: We introduce fedflow, a Python-based command-line tool for headless orchestration of FL tasks with FeatureCloud. This tool uses distributed computing resources such as virtual machines or cloud instances to automate such workflows. This allows for scalable federated computing either in local simulations or deployed in a trusted environment. Further, we demonstrate how fedflow can be used to integrate FeatureCloud in reproducible Snakemake workflows. For this, we reanalyse a metagenomic dataset with two federated algorithms and compare the results to the centralized approach with pooled data. Overall, fedflow enables automation of multi-client FL tasks, facilitates embedding of FeatureCloud in standard bioinformatics pipelines and thereby helps increase reproducibility.

AVAILABILITY: Fedflow is open-source and available at https://github.com/W-L/fedflow.},
}

@article {pmid42725563,
year = {2026},
author = {Colomer-Castell, S and Ibañez-Lligoña, M and Campos, C and Gregori, J and Garcia-Cehic, D and Rando-Segura, A and Ferrer, R and Ruzo, SP and Cortese, MF and Tabernero, D and Vico-Romero, J and Ruiz-Cobo, JC and Buti, M and Riveiro-Barciela, M and Quer, J},
title = {Whole-Genome Analysis of HEV Under Sequential Ribavirin Pressure Reveals Early Minor Variants Predicting Resistance.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71146},
doi = {10.1002/jmv.71146},
pmid = {42725563},
issn = {1096-9071},
support = {PI22/00258//Instituto de Salud Carlos III/ ; PI23/01065//Instituto de Salud Carlos III/ ; PID2021-126447OB-I00//Ministerio de Ciencia e Innovación/ ; //Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas/ ; LCF/BQ/DR23/12000020//La Caixa″ Foundation/ ; FPU21/04150//Spanish Ministry of Education/ ; Predoctoral fellowhip CC//Vall d'Hebron Institute of Research/ ; },
mesh = {*Ribavirin/therapeutic use/pharmacology ; Humans ; *Antiviral Agents/therapeutic use/pharmacology ; *Hepatitis E/virology/drug therapy ; *Hepatitis E virus/genetics/drug effects/isolation & purification ; *Drug Resistance, Viral/genetics ; *Genome, Viral ; Genotype ; *Genetic Variation ; Whole Genome Sequencing ; High-Throughput Nucleotide Sequencing ; Amino Acid Substitution ; Metagenomics ; },
abstract = {Ribavirin (RBV) failures in chronic hepatitis E virus (HEV) infection may arise from genomic adaptation, yet the contribution of minor variants remains insufficiently explored. Using a shotgun metagenomics based on next-generation sequencing to obtain the full HEV genome, we analyzed longitudinal HEV populations from sequential clinical samples collected from a patient infected by Paslahepevirus balayani genotype 3c, who underwent three different courses of RBV treatment. Viral diversity increased over time, with most amino-acid substitutions detected at sub-consensus frequencies. Several mutations linked to RBV resistance emerged under treatment pressure. Specifically, D1384N and Y1587F became fixed in the final sampling, while additional substitutions at position 1384 (including D1384T) revealed mutational hotspot. Importantly, D1384N and G1634R were already detectable at low allele frequencies after the first treatment cessation and subsequent rebound, showing that the study of minor variant populations can be early predictors for the development of RBV resistance. These findings underscore the genomic plasticity of HEV under antiviral pressure and highlight the value of deep variant profiling for anticipating RBV treatment failure.},
}

*Ribavirin/therapeutic use/pharmacology
Humans
*Antiviral Agents/therapeutic use/pharmacology
*Hepatitis E/virology/drug therapy
*Hepatitis E virus/genetics/drug effects/isolation & purification
*Drug Resistance, Viral/genetics
*Genome, Viral
Genotype
*Genetic Variation
Whole Genome Sequencing
High-Throughput Nucleotide Sequencing
Amino Acid Substitution
Metagenomics

@article {pmid42725663,
year = {2026},
author = {Furneaux, B and Roslin, T and Hardwick, B and Kerdraon, D and Autto, H and Banelyte, G and deWaard, JR and deWaard, SL and Farrell, A and Kalttopää, O and Kristensen, E and Rogers, HMK and Sones, JE and Zakharov, EV and Ovaskainen, O},
title = {Is There a Fly in My Soup? To What Extent Do Metabarcoding and Individual Barcoding Tell the Same Story?.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70195},
doi = {10.1111/1755-0998.70195},
pmid = {42725663},
issn = {1755-0998},
support = {336212//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 101059492//HORIZON-CL6-2021-BIODIV-01/ ; 856506/ERC_/European Research Council/International ; 225-20-002//Naturvårdsverket/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; MSI 42450//Canadian Foundation for Innovation/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; *Metagenomics/methods ; *Insecta/classification/genetics ; },
abstract = {Metabarcoding has become the method of choice for characterizing complex arthropod communities. The extent to which metabarcoded bulk samples will recover the same community composition as individual sequencing of all individuals in the sample remains poorly quantified. Biases such as unequal extraction of DNA from different taxa, primer mismatches and non-random PCR may cause the selective drop-out of species from metabarcoding data. At the same time, DNA metabarcoding may reveal arthropod taxa present not as individuals, but as DNA residues on the surface or in the gut of insects. To quantify the consistency in sample contents established by different means, we metabarcoded 45 bulk insect samples, then extracted all arthropods and sequenced them individually. Metabarcoding targeted 418 bp at the 3' end of the Folmer barcoding region, while individual barcodes captured the entire 658 bp Folmer region. The metabarcoding workflow, including PCR amplification, sequencing and bioinformatics, was performed in three replicates from three separate lysate aliquots per sample. For the main analyses, sequences were assigned to Barcode Index Numbers (BINs) as identical taxonomic categories across data types, thereby allowing the detection of even rare but biologically true taxa. Since such reference-based validation will be unavailable to any researcher dealing with metabarcoding data alone, we validated our key findings through an alternative workflow, i.e., de novo clustering of sequences. We found that metabarcoding is replicable, as different replicates of the same sample recover similar species richness and composition. Individual barcoding and metabarcoding provide similar impressions of relative differences in community structure: species-rich vs. species-poor samples rank similarly among data types (Spearman's ⍴ = 0.88-0.99) as do differences in relative dissimilarity between sample pairs (Spearman's ⍴ = 0.55-0.90). Dissimilarity between data types varies with BIN richness in the sample, but this relationship reflects nestedness rather than turnover: metabarcoding recovers the same set of core species as individual barcoding but adds hundreds of species on top. Any BIN recovered as an individual occurred with high probability in the metabarcoding data, and any BIN found in high read abundances by metabarcoding was likely found as an individual (p > 0.8). In terms of abundances, the number of individual insects per BIN was well predicted by the number of metabarcoding reads (R[2] > 0.68 for a model including taxonomy as a random effect). Our analysis suggests that metabarcoding data will be informative of the sample contents in terms of arthropod species richness, composition and taxon-specific abundances. Taxa recovered in low copy numbers in metabarcoding sequence data will likely represent DNA left as residues from past biotic interactions. Barring sequencing errors, both types of data yield biologically relevant insights into the taxa present in the source community.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Sequence Analysis, DNA
*Metagenomics/methods
*Insecta/classification/genetics

@article {pmid42725726,
year = {2026},
author = {Holm, JB and Maros, A and Williams, A and France, M and Ravel, J},
title = {VISTA: a classifier for metagenomic subspecies and community state typing of the vaginal microbiome.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0061226},
doi = {10.1128/mra.00612-26},
pmid = {42725726},
issn = {2576-098X},
abstract = {Metagenomic community state types (mgCSTs) capture within-species genetic and functional diversity and community structure of the vaginal microbiome, enabling precise links between microbiome composition, function, and health-related risk. VISTA, the Vaginal Inference of Subspecies and Typing Algorithm, is a two-step classifier that assigns mgCSTs to vaginal metagenomes, providing standardized, scalable classifications.},
}

@article {pmid42725772,
year = {2026},
author = {Toro, N},
title = {Landscape of retron diversity across the SPIRE microbial metagenome resource reveals candidate novel type XI-like lineages.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073226},
doi = {10.1128/msystems.00732-26},
pmid = {42725772},
issn = {2379-5077},
abstract = {Retrons are bacterial genetic elements encoding a specialized reverse transcriptase (RT) that synthesizes multicopy single-stranded DNA and are increasingly recognized as components of bacterial anti-phage defense systems. However, their diversity and ecological distribution across large-scale genomic resources remain poorly characterized. Here, we surveyed retron RTs across the SPIRE representative metagenome collection, a non-redundant, species-level data set spanning diverse microbial habitats. Using a curated panel of type-specific hidden Markov models, we identified retrons representing all canonical types together with additional divergent lineages. Retron distribution showed strong taxonomic and ecological structuring, with some groups restricted to specific bacterial phyla, whereas others were broadly distributed across environmental categories. Systematic novelty assessment identified two candidate type XI-like lineages, TXI_C2like and TXI_noncan_h, characterized by protease-independent architectures and distinct accessory modules associated with WYL- and DnaB_C-containing proteins, respectively. De novo covariance-based analyses further identified candidate msr/msd-like non-coding RNA structures in both lineages, supporting conservation of the canonical RT-ncRNA organizational framework despite extensive sequence divergence. Together, these findings expand the known diversity of retron systems and identify type XI-like retrons as a dynamic and previously underexplored evolutionary group.IMPORTANCERetrons are bacterial genetic elements that are increasingly exploited as programmable tools for genome editing, molecular recording, and biosensing in addition to their natural role in anti-phage defense. Despite this growing biotechnological interest, the true diversity of retrons across the bacterial world has remained largely unmapped. By mining a resource of over 100,000 processed microbial metagenomes, we uncovered thousands of retron sequences spanning known types as well as previously unrecognized lineages and found that their distribution is strongly shaped by both bacterial taxonomy and ecological niche. Among these, we identified two candidate new lineages related to type XI retrons that lack the protease domain typical of this group but instead carry distinct accessory proteins, expanding the known architectural diversity of these systems. These findings broaden the catalog of retron diversity available for functional characterization and biotechnological engineering and provide a framework for prioritizing candidate lineages for future experimental validation.},
}

@article {pmid42725826,
year = {2026},
author = {Chenuil, A and Bouchereau, E and Legrand, T and Calvert, V and Chemin, C and Chenesseau, S and Guillemain, D and Ortega, JMG and Haguenauer, A and Leduc, M and Legendre, F and Marschal, F and Marschal, C and Mirleau, F and Selva, M and Vanbostal, L and Zuberer, F and Mirleau, P and Plaisance, L and Rossi, V and Ruitton, S and Meglécz, E and Dubut, V},
title = {Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70188},
doi = {10.1111/1755-0998.70188},
pmid = {42725826},
issn = {1755-0998},
support = {OOB_EMBRC FR_AAP2018_n°2179//EMBRC France/ ; ANR-17-MART0001-01//Agence Nationale de la Recherche/ ; ANR-17-MART0001-02//Agence Nationale de la Recherche/ ; ANR-17-MART0001-03//Agence Nationale de la Recherche/ ; 145//ERA-Net Mar-TERA/ ; SERA-20181031//Centro para el Desarrollo Tecnológico e Industrial/ ; 4000141547/23/I-DT//European Space Agency/ ; 1166-39417//European Regional Development Fund/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; Photography/methods ; Electron Transport Complex IV/genetics ; Animals ; Mediterranean Sea ; *Metagenomics/methods ; },
abstract = {Monitoring marine biodiversity requires approaches capable of capturing its spatial and temporal complexity. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular outputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across 10 north-western Mediterranean sites to compare and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure traceability. We then conducted the first face-by-face comparison of α- and β-diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15× higher site-level richness and revealed stronger correlations with geographic distance and environmental gradients-which stemmed from its finer taxonomic resolution-whereas photography provided complementary information on macro-taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger β-diversity-distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance, weakening ecological signal. Grouping the 17 faces into five structural categories offered a more operational alternative while further increasing α-diversity and strengthening β-diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control-driven bioinformatic workflow provides a reproducible, scalable framework for long-term eDNA monitoring and early detection of biodiversity change.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Aquatic Organisms/classification/genetics
Photography/methods
Electron Transport Complex IV/genetics
Animals
Mediterranean Sea
*Metagenomics/methods

@article {pmid42726103,
year = {2026},
author = {Narayana, JK and Jaggi, TK and Dimakou, K and Ivan, FX and Mac Aogáin, M and Poh, ME and Hull, RC and Hennayake, C and Long, MB and Johnson, ED and Lind, H and Goeminne, PC and Shteinberg, M and De Soyza, A and Aliberti, S and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Shoemark, A and Ringshausen, FC and Lorent, N and Blasi, F and Chalmers, JD and Chotirmall, SH},
title = {Pseudomonas Aeruginosa Abundotypes and Interactotypes Reflect Clinical Heterogeneity in Bronchiectasis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag464},
pmid = {42726103},
issn = {1535-4970},
abstract = {INTRODUCTION: Pseudomonas aeruginosa (PA) associates with poor clinical outcomes, however, exhibits inter-individual clinical and treatment heterogeneity in bronchiectasis.

METHODS: Sputum metagenomes from n = 600 individuals with bronchiectasis from 10 countries were assessed to derive PA subgroups based on abundance (abundotypes) and/or microbial interactions (interactotypes). Longitudinal dynamics of these subgroups were assessed in two common clinical scenarios: acute exacerbation and PA eradication. Transition probabilities for each subgroup were estimated in these scenarios.

RESULTS: Four PA-abundotypes with comparable exacerbation risk were identified: PA-dominant (PD), Moderate PA-dominant (MPD), Other Microbe Dominant (OMD) and High Diversity (HD). Four separate PA-interactotypes were characterized: BC1 (PA-Neisseria interactions); BC2 (PA-S. aureus & E. coli interactions); BC3 (PA-Streptococcus interactions) and BC4 (mixed interactions). Core (conserved) interactions with commensal taxa were shared across all interactotypes while ancillary (variable) interactions remain interactotype-specific. Abundotypes correlate with bronchiectasis severity, symptoms and lung function while interactotypes stratify exacerbation risk with BC3 the lowest-risk group. BC1 and BC4 exhibit 1.45- and 1.44-higher fold rates (p = 0.037 and p = 0.048 respectively) for exacerbation while BC2 demonstrates a non-significant increase in exacerbation risk (1.32-fold; p = 0.18). In hypothesis-generating analyses using a small longitudinal cohort, PA-abundotypes remain stable through exacerbations (n = 6) while PA-interactotypes shift substantially suggesting dynamic responsiveness to acute clinical states. During PA eradication (n = 11), abundotypes exhibit structured transition with standard therapy while interactotypes demonstrate no consistent patterns.

CONCLUSION: PA-abundotypes and interactotypes represent independent traits capturing different dimensions of PA ecology and potentially contributing to observed clinical and treatment heterogeneity in bronchiectasis.},
}

@article {pmid42726321,
year = {2026},
author = {Duan, DY and Ran, J and Guo, XL and Liu, L and Liu, GH and Asada, M and Cheng, TY},
title = {Metagenomic analysis of the midgut microbiome in Dermacentor abaensis ticks at different feeding states.},
journal = {Experimental & applied acarology},
volume = {97},
number = {3},
pages = {},
pmid = {42726321},
issn = {1572-9702},
support = {No. 2025JJ50143//Natural Science Foundation of Hunan Province, China/ ; No. kq2502005//Natural Science Foundation of Changsha City, China/ ; No. 31902294//National Science Foundation of China/ ; 2024YFD1800103//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Dermacentor/microbiology/physiology ; Female ; Bacteria/classification/isolation & purification/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Feeding Behavior ; China ; *Metagenome ; },
abstract = {Ticks are blood-sucking ectoparasites of humans and animals, ranking second only to mosquitoes as vectors of diseases. Dermacentor abaensis is distributed in Sichuan, Qinghai, and Gansu, China. Because D. abaensis harbors several pathogens, it poses a threat to public health and livestock production. However, the midgut microbiota of D. abaensis at distinct feeding states remains poorly characterized. Adult D. abaensis ticks at various feeding states were collected from yaks in Gansu Province, China. Genomic DNA was extracted from midguts and midgut contents of unfed, partially fed, and fully engorged female D. abaensis. A metagenomic sequencing approach was employed to profile the midgut microflora among three groups. A total of 83 phyla, 908 genera, and 1857 species were annotated across the three groups. At the phylum level, Pseudomonadota, Mucoromycota, and Ascomycota were the most abundant. At the species level, common bacterial species such as Klebsiella pneumoniae and Anaplasma phagocytophilum, alongside viruses and eukaryotes, were detected in all three groups. Unique microorganisms were also observed in each group: unfed (n = 305), partially fed (n = 59), and fully engorged (n = 20). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the D. abaensis microbiome contains a relatively high abundance of functional genes involved in lipid and amino acid metabolism across the three different feeding states. These findings indicate that while core microbial taxa are shared in the midgut of female D. abaensis, observable trends suggest variations in microbial diversity and composition as blood-feeding progresses. The present study provides a descriptive baseline of the midgut microbial composition of D. abaensis, which may inform future studies on tick biology and the ecology of tick-borne pathogens.},
}

Animals
*Dermacentor/microbiology/physiology
Female
Bacteria/classification/isolation & purification/genetics
Metagenomics
*Gastrointestinal Microbiome
Feeding Behavior
China
*Metagenome

@article {pmid42726488,
year = {2026},
author = {Tang, L-Y and Zhang, H and Zhao, J-X and Gao, Y-Q and Zhang, X and Xie, S-C and Zheng, Z and Zhu, X-Q and Zhang, X-X and Xia, C and Liu, R and Ma, H},
title = {Toxoplasma gondii infection disrupts secondary bile acid transformation in feline gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0067426},
doi = {10.1128/aem.00674-26},
pmid = {42726488},
issn = {1098-5336},
abstract = {UNLABELLED: Bile acid (BA) transformation relies on gut microbiota and is vulnerable to Toxoplasma gondii infection, yet feline microbial BA-transforming capacity upon toxoplasmosis remains unclear. Here, we constructed a catalog of 2,474 nonredundant feline gut microbial genomes and integrated serum metabolomic data to verify BA transformation alterations. The results revealed that the feline gut microbiome harbored widespread genetic potential for BA transformation but lacked a complete 7α-dehydroxylation pathway due to the absence of the key gene baiE. The BA transformation-related genomes (2,045 in total) were predominantly from the phyla Bacillota_A and Actinomycetota, among which only 37 encoded baiB, all belonging to Bacillota_A. The distribution of BA transformation-related genes varied across intestinal regions: genes encoding 7α-HSDH were primarily enriched in the small intestine, whereas genes encoding 3α-HSDH, baiCD, and baiH were more abundant in the large intestine. Additionally, the abundance of genes encoding BSH and 3α-HSDH increased significantly in the small intestine on day 3 post-infection, accompanied by increases in the phylum Bacillota_C and genera such as Blautia_A, Enterococcus_E, and Ligilactobacillus. Serum metabolomics revealed a significant increase in cholesterol levels post-infection, supporting the impact of T. gondii infection on intestinal BA transformation. These findings illustrated that the feline gut microbiota played an important role in BA transformation and that T. gondii infection disrupted the microbial potential for secondary BA transformation. This study provided new insights into gut microbiota-associated metabolic perturbations during feline toxoplasmosis.

IMPORTANCE: Bile acid (BA) transformation plays a critical role in host metabolism and immune regulation. Although studies on BA transformation are increasing, the capacity for BA transformation within the feline gut microbiota and the impact of Toxoplasma gondii infection on this capacity remain unclear. To bridge this gap, we constructed a catalog of 2,474 nonredundant feline gut microbial genomes and integrated serum metabolomic data to verify BA transformation alterations. Our findings revealed that the feline gut microbiome lacked a complete 7α-dehydroxylation pathway, and the specific functions involved in BA transformation may differ between the small and large intestines. Furthermore, integrated metagenomic and serum metabolomic analyses suggested that T. gondii infection disrupted BA transformation capacity in the small intestine. This study provided new insights into gut microbiota-associated metabolic perturbations during feline toxoplasmosis.},
}

@article {pmid42716143,
year = {2026},
author = {Pan, Y and Wang, S and Li, B and Cao, T and Song, Y and Ou, N and Hao, X and Li, M and Liu, L and Liu, X},
title = {Chronic psychological stress impairs sperm quality via a gut-endotoxin-testis axis.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {107000},
doi = {10.1016/j.bbi.2026.107000},
pmid = {42716143},
issn = {1090-2139},
abstract = {BACKGROUND: Chronic psychological stress is increasingly recognized as a risk factor for male infertility, but the underlying mechanisms remain incompletely understood. This study aimed to investigate whether chronic stress (CS) induced-alterations of the gut microbiota and its metabolites contribute to sperm quality impairment via a gut-testis axis.

METHODS: Male C57BL/6 mice were subjected to chronic unpredictable mild stress for 10 weeks. Gut barrier integrity, systemic inflammation, and testicular phenotypes were assessed. Gut microbiota and its metabolites were profiled by 16S rRNA gene sequencing, shotgun metagenomics, and metabolomics. The contribution of the microbiota was interrogated by fecal microbiota transplantation (FMT) and probed further by oral sodium butyrate (NaB) supplementation. Intestinal barrier function was assessed by in vivo FITC‑dextran translocation and ex vivo Ussing chamber assays, blood-testis barrier (BTB) integrity by Evans blue extravasation, and the requirement for TLR4 signaling was examined pharmacologically.

RESULTS: CS induced marked gut dysbiosis, characterized by depletion of butyrate-producing taxa such as Lachnospiraceae and by reduced cecal and circulating butyrate. These changes were accompanied by impaired intestinal barrier function, endotoxemia (elevated LPS and LBP), increased BTB permeability and activation of testicular TLR4/NF-κB signaling. Fecal microbiota from CS donors was sufficient to reproduce intestinal barrier disruption, testicular inflammation and impaired sperm quality in healthy recipients, and pharmacological TLR4 blockade attenuated testicular injury in these recipients. Conversely, oral NaB restored intestinal barrier function, suppressed testicular TLR4/NF-κB signaling and pro-inflammatory cytokine levels, and rescued sperm quality in CS mice.

CONCLUSIONS: These findings delineate a gut-endotoxin-testis axis in mice, in which CS-associated depletion of butyrate‑producing taxa and consequent endotoxin exposure contribute to impaired sperm quality, and identify microbiota- or butyrate-targeted interventions as candidate strategies for psychological stress-related male infertility.},
}

@article {pmid42716389,
year = {2026},
author = {Wang, J and Wang, B and Li, W and Xing, Y and Bai, M and Zou, Y and Ji, J and Peng, Y},
title = {Sulfide-driven partial denitrification serves as a remedial strategy for suboptimal partial nitrification-anammox performance.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135813},
doi = {10.1016/j.biortech.2026.135813},
pmid = {42716389},
issn = {1873-2976},
abstract = {The partial nitrification-anammox (PNA) process applied to low C/N municipal wastewater treatment is often constrained by unstable nitrite supply and nitrate accumulation. In this study, a coupled suboptimal partial nitrification, sulfide-driven partial denitrification, and anammox (sPN-SPDA) process was developed in a step-feed sequencing batch reactor, in which sulfide was introduced as an electron donor during the second feeding stage. A high nitrogen removal efficiency of 93.2 ± 1.2 % was achieved, with effluent total inorganic nitrogen reduced to as low as 5.1 ± 0.5 mg/L. Microbial community analysis demonstrated the enrichment of sulfide-driven partial denitrification (SPD)-related denitrifiers after sulfide addition, particularly Thauera (16.3 %), which supported the conversion of NO3[-]-N to NO2[-]-N. Metagenomic analysis showed increased abundances of nitrate-reduction genes napA and napB, consistent with improved nitrite availability for anammox. Overall, this study provides a promising strategy to alleviate nitrite limitation caused by suboptimal partial nitrification and to achieve advanced nitrogen removal from low C/N municipal wastewater.},
}

@article {pmid42716393,
year = {2026},
author = {Wu, K and Yun, P and Zhou, D and Wen, G and Luo, W and Wang, W and Yan, X and Zheng, J},
title = {Decoupled sulfonamide biodegradation and resistance gene responses in leachate treatment sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135809},
doi = {10.1016/j.biortech.2026.135809},
pmid = {42716393},
issn = {1873-2976},
abstract = {Municipal solid waste leachate is an important sink of sulfonamides and resistance genes, yet the coupling between antibiotic removal and resistance-associated risks across exposure levels in leachate sludge remained unclear. Here, sludge from the primary (PNS) and secondary (SNS) nitrification units of a full-scale leachate treatment plant were exposed to a mixture of sulfadiazine (SDZ), sulfamethoxazole (SMX), and trimethoprim (TMP) at 10 and 500 µg/l for each compound in batch experiments. At 10 µg/l, PNS and SNS removed 73.4 % of SDZ and 95.0 % of SMX, while TMP concentrations decreased below the quantification limit by day 5. Their removal efficiencies decreased at 500 µg/l. Metagenomic profiles indicated greater biodegradation-related potential under low-level exposure but reduced catabolic potential under high-level exposure. Meanwhile, 10 µg/l exposure increased the relative abundances of sulfonamide resistance genes and intI1, indicating the enrichment of resistance-associated genes and increased genetic mobility potential during the 14-day incubation. Additionally, SNS exhibited stronger short-term changes in resistance-associated genes and bacterial community composition than PNS. An exploratory cross-plant comparison suggested greater dissimilarity in resistance-related than biodegradation-related profiles. Apparently,antibiotic biodegradation potential and resistance-associated risks were not coupled in leachate treatment systems. These results will shed some lights into standardized antibiotic-associated risk assessments of leachate biological treatment systems.},
}

@article {pmid42716415,
year = {2026},
author = {Kwon, H and Wang, Q and Riveros, A and Li, Y and Jiang, D},
title = {Abundance-transcription decoupling reveals functional partitioning in bioelectrochemical denitrification biofilms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125626},
doi = {10.1016/j.envres.2026.125626},
pmid = {42716415},
issn = {1096-0953},
abstract = {Bioelectrochemical denitrification (BED) is often attributed to electroactive microorganisms that access electrode-derived electrons, yet the relative functional contribution of electroactive taxa and denitrifying populations within complex BED biofilms remain unclear. Here, we integrated reactor measurements with genome-resolved metagenomics and metatranscriptomics to examine microbial community structure, functional potential, and gene transcription across contrasting BED operational regimes differing in dissolved oxygen (DO), hydraulic retention time (HRT)/loading, and poised potential. Nitrate removal exceeded 90% across all tested conditions, but nitrogen intermediate accumulation, current generation, and theoretical electron balance differed substantially. Electroactive taxa such as Geobacter dominated (>80% abundance) under longer HRT and stronger poised potential, but contributed minimally to the transcription of canonical denitrification genes. Weaker cathodic potential enriched transcriptionally active denitrifying taxa such as Stutzerimonas, Acidovorax, and MR-S7, while oxygen exposure induced redox-stress responses and reshaped nitrogen metabolism beyond being a competing electron acceptor. Together, these results reveal a decoupling between taxonomic abundance, genomic functional potential, and transcriptional contribution in BED biofilms, indicating that nitrate-removal performance cannot be inferred from current generation or electroactive-taxon abundance alone.},
}

@article {pmid42716715,
year = {2026},
author = {Verma, S and Bairoliya, S and Wang, Y and Ridley, RS and Liu, YN and Konstantinidis, KT and Yin, X and Cao, B},
title = {Global Reanalysis Reveals Recurrent Cyanobacterial Enrichment in the Aquatic Plastisphere.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c06460},
pmid = {42716715},
issn = {1520-5851},
support = {RG172/25//Ministry of Education - Singapore/ ; RT10/22//Ministry of Education - Singapore/ ; },
abstract = {The plastisphere is an emerging anthropogenic ecosystem hosting complex microbial assemblages. While heterotrophic colonizers are well studied, the role of primary producers such as cyanobacteria remains underexplored. Here, we reanalyzed 16S rRNA gene amplicon data from 3160 plastisphere samples across 62 aquatic studies to assess their role in community assembly at a global scale. Substrate type explained a significant but relatively small fraction of variation (R2 = 0.048), whereas β-diversity showed clear separation between marine and freshwater communities. Among all substrate types (plastic, microplastic, natural polymer, and nonplastic), plastic-associated communities exhibited the highest estimated contribution of deterministic assembly processes in both freshwater and marine ecosystems. Co-occurrence networks showed low modularity and high clustering, revealing recurrent community association patterns across plastisphere data sets, while several topologically central taxa exhibited frequent associations with cyanobacteria. Notably, Xenococcaceae and Phormidesmiaceae were consistently enriched on plastics relative to surrounding environments. Independent metagenomic analyses corroborate enrichment of Phormidesmiaceae. These results demonstrate recurrent cyanobacterial enrichment in plastisphere communities and identify co-occurrence patterns between cyanobacteria and heterotrophic taxa. These associations generate hypotheses regarding possible phototroph-heterotroph linkages on plastic surfaces that warrant experimental investigation.},
}

@article {pmid42716835,
year = {2026},
author = {Zhao, K and Vignolle, GA and Labus, JS and Mayer, EA and Vaughan, A and Dy, M and Vora, P and Hung, MW and Vossel, K and Gill, C and Del Rio, D and Stanton, C and Ross, RP and Cryan, JF and Kaddurah-Daouk, R and Zhang, Y and Church, A},
title = {Brain-gut crosstalk associated with brain ageing in young and mid-life adults: a multicohort cross-sectional study.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {106468},
doi = {10.1016/j.ebiom.2026.106468},
pmid = {42716835},
issn = {2352-3964},
abstract = {BACKGROUND: Brain age deviation is a promising neuroimaging biomarker of brain health, but its relevance in young and mid-life adults and its biological underpinnings remain insufficiently characterised. We aimed to test whether a functional-connectivity-derived brain ageing index (BAI) captures reproducible variability in early brain ageing and whether it is associated with cognitive-affective function and gut-derived biological signatures.

METHODS: We analysed resting-state fMRI from a discovery cohort (n = 674) with validation in a replication cohort (n = 444) and an independent cohort (n = 344). Whole-brain functional connectivity was computed using a 100-region Schaefer parcellation, and Bayesian ridge regression was used to predict chronological age; BAI was defined as the age-bias-corrected residual (predicted brain age minus chronological age). We tested associations between BAI and cognitive and affective measures across cohorts. In the independent cohort, we applied multi-view sparse partial least squares to integrate stool metagenomic and metabolomic profiles with BAI, and performed KEGG pathway enrichment analyses on features with non-zero weights.

FINDINGS: Predicted brain age correlated with chronological age across cohorts (r = 0.50-0.59). Higher BAI was consistently associated with connectivity patterns involving posterior cingulate/praecuneus and medial frontal regions, poorer cognitive performance, particularly working memory and executive function, and greater depressive symptoms. Multi-omics integration identified microbial taxa and stool metabolites, including ceramides, 24-hydroxycholesterol, dicarboxylic acids, and inverse associations with estetrol, linked to BAI. Enrichment analyses suggested involvement of neuroimmune, vascular, synaptic, and mitochondrial pathways.

INTERPRETATION: A connectivity-derived BAI captures reproducible variability in early brain ageing and links large-scale brain network organisation to gut-derived biological signatures. These findings suggest that BAI captures individual variability associated with brain health-related phenotypes and support the potential association of peripheral brain-gut biological pathways in early brain ageing.

FUNDING: National Institutes of Health, National Institute on Ageing.},
}

@article {pmid42718418,
year = {2026},
author = {Guo, Y and He, X and Zhang, L and Li, M and He, L and Lu, G},
title = {X-linked hyper-IgM syndrome presenting as severe Pneumocystis pneumonia in a 6-month-old infant: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1929323},
pmid = {42718418},
issn = {1664-3224},
mesh = {Humans ; Male ; *Pneumonia, Pneumocystis/diagnosis/etiology ; *Hyper-IgM Immunodeficiency Syndrome, Type 1/diagnosis/therapy/complications ; Infant ; *Pneumocystis carinii ; CD40 Ligand/genetics ; },
abstract = {BACKGROUND: X-linked hyper-immunoglobulin M (XHIGM) syndrome is a rare primary immunodeficiency caused by mutations in the CD40 ligand gene (CD40LG), characterized by defective T-cell-dependent B-cell class-switch recombination. Patients typically present with recurrent infections in early childhood, but diagnosis is often delayed due to heterogeneous clinical manifestations and the fact that serum IgM levels may remain within the normal range in a significant proportion of patients. Here we report a case of XHIGM in an infant whose diagnostic journey began with recurrent lymphadenitis and culminated in life-threatening Pneumocystis jirovecii pneumonia (PJP).

CASE PRESENTATION: A 6-month-old male infant was admitted with severe respiratory distress and hypoxemia. He had recurrent axillary lymphadenitis at 1 and 2 months of age and significant failure to thrive. Chest CT showed bilateral consolidative and interstitial opacities. Immunological evaluation revealed markedly decreased IgA, normal IgM and IgG, and profound T-cell lymphopenia. Sputum metagenomic sequencing identified Pneumocystis jirovecii. Whole-genome sequencing identified a hemizygous likely pathogenic CD40LG mutation (NM_000074.3:c.520C>T, p.Q174*); his mother was a carrier. He was treated with mechanical ventilation, trimethoprim-sulfamethoxazole (TMP-SMX), micafungin, corticosteroids, and intravenous immunoglobulin (IVIG), and was discharged after 36 days.

CONCLUSIONS: In infants with recurrent or opportunistic infections, persistently low IgA and declining T-cell counts-even when initial screening appears normal-should raise suspicion for underlying immunodeficiency and prompt genetic evaluation. Early aggressive management and evaluation for hematopoietic stem cell transplantation are essential to improve outcomes.Serial immunological evaluation is essential in infants with recurrent or opportunistic infections, as persistently low IgA and declining T-cell counts-even when initial screening appears normal-should prompt genetic evaluation for underlying immunodeficiency. Early aggressive management and evaluation for hematopoietic stem cell transplantation are essential to improve outcomes.},
}

Humans
Male
*Pneumonia, Pneumocystis/diagnosis/etiology
*Hyper-IgM Immunodeficiency Syndrome, Type 1/diagnosis/therapy/complications
Infant
*Pneumocystis carinii
CD40 Ligand/genetics

@article {pmid42718506,
year = {2026},
author = {Huang, X and Zhang, Q and Huang, L and Xu, J},
title = {Diagnostic challenge of GAD65-associated autoimmune encephalitis mimicking post-traumatic complications in an older adult: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1929756},
pmid = {42718506},
issn = {2296-858X},
abstract = {INTRODUCTION: Glutamic acid decarboxylase 65 (GAD65) antibody-associated autoimmune encephalitis is an uncommon immune-mediated neurological disorder with heterogeneous neuropsychiatric manifestations. Diagnosis is particularly challenging in older adults when symptoms of recent traumatic brain injury (TBI) overlap with structural or metabolic conditions.

CASE PRESENTATION: We report a 79-year-old man who developed recurrent headache, progressive confusion, abnormal behavior, poor oral intake, intermittent myoclonic jerks, and low-grade fever after TBI complicated by chronic subdural hematoma. Initial laboratory testing revealed hyponatremia, and the working diagnosis was post-traumatic brain syndrome with syndrome of inappropriate antidiuretic hormone secretion (SIADH). Although serum sodium was corrected and nocturnal agitation partially improved, persistent daytime confusion, cognitive impairment, behavioral abnormalities, and low-grade fever prompted further investigation. Cerebrospinal fluid (CSF) analysis showed mild inflammatory changes with pleocytosis and elevated protein. CSF metagenomic next-generation sequencing (mNGS) and paraneoplastic antibody testing were negative, whereas the autoimmune encephalitis panel was positive for GAD65 antibody at a titer of 1:32. Whole-body positron emission tomography-computed tomography (PET-CT) did not reveal malignancy. The diagnosis was therefore revised to GAD65 antibody-associated autoimmune encephalitis. Because high-dose corticosteroids were considered unsuitable owing to his history of gastric ulcer and previous gastrointestinal bleeding, he was treated with intravenous immunoglobulin (IVIG) at a total dose of 2 g/kg divided over 3 consecutive days followed by oral azathioprine 50 mg daily. His fever resolved within 1 week, and his mental status and responsiveness gradually improved. At 6-month follow-up, he had achieved near-baseline mental status, was able to walk with a cane, and was almost fully independent in daily activities, without relapse or serious treatment-related adverse events.

DISCUSSION: This case highlights the diagnostic difficulty of recognizing autoimmune encephalitis after TBI. The clinical overlap between post- traumatic syndrome and immune-mediated brain injury often delays diagnosis, emphasizing the value of targeted CSF autoantibody testing in atypical cases.

CONCLUSION: Traumatic brain injury may obscure the onset of GAD65-associated autoimmune encephalitis. Early recognition and a corticosteroid-sparing immunotherapy strategy (IVIG and azathioprine) can yield favorable outcomes in elderly patients with medical comorbidities.},
}

@article {pmid42718697,
year = {2026},
author = {Liu, X and Hu, D and Tan, J and Yu, Y},
title = {Non-invasive management of severe chlamydia psittaci pneumonia presenting with hypoxemia and diarrhea: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1855281},
pmid = {42718697},
issn = {2296-858X},
abstract = {This case report describes a rare presentation of severe Chlamydia psittaci pneumonia in a 43-year-old female patient with prominent hypoxemia and gastrointestinal symptoms, and evaluates the efficacy of standardized non-invasive integrated management for critically ill patients with this atypical phenotype. The patient was admitted with lumbago, persistent high fever, progressive dyspnea, severe hypoxemia, and intractable non-bloody watery diarrhea. Chest computed tomography (CT) revealed extensive bilateral pulmonary ground-glass opacities and consolidation. Rapid and precise etiological diagnosis was achieved via targeted metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF), which identified high-load Chlamydia psittaci infection, with 227,155 normalized reads and a genomic coverage of 98.6%. Comprehensive non-invasive multidisciplinary management was implemented throughout the disease course, including high-flow nasal cannula (HFNC) oxygen therapy, dual anti-infective therapy with omadacycline combined with levofloxacin, symptomatic supportive care, and standardized stepwise early rehabilitation training. Dynamic monitoring of clinical and laboratory indicators showed a gradual and sustained decline in inflammatory biomarkers (C-reactive protein,procalcitonin, interleukin-6),accompanied by progressive absorption of pulmonary lesions and recovery of respiratory function. The patient avoided invasive mechanical ventilation throughout hospitalization, was successfully weaned from HFNC on day 14 of admission, and achieved completeclinical, laboratory and radiological recovery at the 1-month follow-up. This case conforms to the CARE (CAse REports) reporting guidelines. It highlights that severe psittacosis pneumonia can present with atypical dominant manifestations of combined hypoxemia and severe gastrointestinal diarrhea, which is easily misdiagnosed clinically. Targeted mNGS enables rapid etiological confirmation of atypical severe psittacosis, and individualized non-invasive integrated management can achieve favorable prognosis in eligible critically ill patients, providing a valuable clinical reference for the standardized diagnosis and treatment of similar rare cases.},
}

@article {pmid42719063,
year = {2026},
author = {Li, X and Wang, J and Liu, FW and Yang, TT and Ma, C and Liu, Q and Wei, J and Ling, B and Jiang, YH and Zhou, TC},
title = {Metagenomic next-generation sequencing contributes to the diagnosis of Gardnerella vaginalis bacteremia associated with a rare extragenital infection and diagnostic challenges in a 13-year-old female patient: A case report.},
journal = {Biomedical reports},
volume = {25},
number = {4},
pages = {117},
pmid = {42719063},
issn = {2049-9442},
abstract = {Gardnerella vaginalis (G. vaginalis) is a well-recognized cause of bacterial vaginosis but is rarely associated with extragenital infections, particularly in individuals without a history of sexual activity. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of pathogens and has emerged as a valuable diagnostic approach for challenging infectious diseases. The current report outlines a case of G. vaginalis bacteremia in a 13-year-old female patient presenting with fever and acute bronchitis. Peripheral blood mNGS, combined with conventional microbiological investigations, was performed to identify the causative pathogen. Initial empirical treatment with piperacillin-tazobactam and azithromycin failed to control the recurrent fever. Traditional cultures of blood, cerebrospinal fluid and bone marrow aspirate all returned negative results, whereas peripheral blood mNGS identified G. vaginalis as the potential pathogen. Following targeted therapy with metronidazole for 3 days, the patient's body temperature returned to normal, and follow-up blood mNGS at discharge was negative for the pathogen. Due to its fastidious growth requirements, G. vaginalis is difficult to detect using conventional culture methods, which may lead to delayed diagnosis and false-negative results. The present case highlights the utility of mNGS for timely and accurate pathogen identification in diagnostically challenging infections. The current case also broadens the recognized clinical spectrum of G. vaginalis infections by demonstrating its potential to cause bloodstream infection with persistent fever in an adolescent without a reported history of sexual activity.},
}

@article {pmid42719094,
year = {2026},
author = {Guo, C and An, Y and Ye, J and Ma, Y and Zhao, Q and Wang, L and Ma, W and Zhang, M and Wang, M and Wang, Y and Yang, J and Ye, L and Yang, L},
title = {Clinical characteristics and prognostic factors in non-HIV patients with Pneumocystis jirovecii pneumonia and BALF cytomegalovirus co-detection: a retrospective cohort study.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1921801},
pmid = {42719094},
issn = {2296-2565},
mesh = {Humans ; Retrospective Studies ; *Pneumonia, Pneumocystis/mortality/diagnosis ; *Bronchoalveolar Lavage Fluid/virology/microbiology ; Prognosis ; *Pneumocystis carinii/isolation & purification ; *Cytomegalovirus Infections/diagnosis ; Male ; Female ; *Cytomegalovirus/isolation & purification ; Middle Aged ; *Coinfection ; },
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection in immunocompromised patients. BALF cytomegalovirus (CMV) co-detection is frequently observed in PJP patients, but its clinical characteristics and prognostic impact in non-HIV populations remain unclear.

METHODS: In this single-center retrospective cohort study, we enrolled 62 non-HIV patients with confirmed PJP between 2019 and 2023. BALF CMV co-detection was defined as detectable CMV DNA in bronchoalveolar lavage fluid via metagenomic next-generation sequencing (mNGS), combined with compatible respiratory symptoms and chest computed tomography abnormalities. The Benjamini-Hochberg false discovery rate (FDR) correction was applied for multiple comparisons.

RESULTS: Overall, 31 patients (50.0%) had BALF CMV co-detection. The 28-day all-cause mortality was significantly higher in the CMV co-detection group than in the PJP-only group (54.84% vs. 19.35%, p = 0.008), and dyspnea was more prevalent (p = 0.024). After FDR correction for 39 laboratory parameters, only fibrinogen remained significantly lower in the co-detection group (q = 0.039), while (1,3)-β-D-glucan (BDG) and D-dimer showed independent associations with CMV co-detection in multivariable analyses. mNGS revealed more concurrent viral and fungal pathogens in the co-detection group, and multiple co-pathogens were more frequent in non-survivors within this subgroup. Interleukin-6 (IL-6), procalcitonin (PCT) and D-dimer were identified as independent prognostic factors for 28-day mortality in the CMV co-detection subgroup.

CONCLUSION: In this single-center retrospective cohort, BALF CMV co-detection is associated with substantially elevated unadjusted 28-day mortality in non-HIV patients with PJP. These findings are hypothesis-generating; IL-6, PCT and D-dimer show potential as exploratory prognostic markers. Comprehensive mNGS-based pathogen screening combined with biomarker monitoring may facilitate risk stratification in this high-risk population, pending validation in larger prospective cohorts.},
}

Humans
Retrospective Studies
*Pneumonia, Pneumocystis/mortality/diagnosis
*Bronchoalveolar Lavage Fluid/virology/microbiology
Prognosis
*Pneumocystis carinii/isolation & purification
*Cytomegalovirus Infections/diagnosis
Male
Female
*Cytomegalovirus/isolation & purification
Middle Aged
*Coinfection

@article {pmid42719130,
year = {2026},
author = {Dai, Y and Li, H and Wang, H and He, Y and Cai, K and Wu, X and Zou, H and Wang, Y and Cai, L and Wu, X and Shamsi, IH},
title = {Insights into the changes of soil microorganism communities and carbon cycle metabolic functions caused by the application of L-glufosinate-ammonium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1920057},
pmid = {42719130},
issn = {1664-302X},
abstract = {L-glufosinate-ammonium (L-GLA), a widely used herbicide, exerts detrimental non-target effects on crops, soil microorganisms, and ecosystems. However, its impacts on soil microbial communities and metabolic functions remain poorly understood. In this study, we applied L-GLA at two concentrations-600 g a.i. hm[-2] (low, L) and 3,000 g a.i. hm[-2] (high, H)-to yellow-brown soil and investigated its effects on microbial community composition, carbon cycle-related metabolic functions, and soil metabolites using integrated metagenomics and soil environmental pseudotargeted metabolomics at 30 and 60 days post-application. The degradation rate of L-GLA was concentration-dependent, with half-lives of 18.8 days (L) and 29.7 days (H). Both doses significantly reduced soil organic matter (SOM) and available potassium (AK) content, and markedly altered microbial community richness, structure, and composition. L-GLA exposure also disrupted the complexity of soil microbial co-occurrence networks and the activities of carbon-cycle-related enzymes. Metabolomic analysis further revealed significant (p < 0.05) and dose-dependent alterations in the soil metabolite profile. Correlation analysis indicated strong associations between characteristic microbial taxa and differential metabolites. Our findings provided critical insights into how L-GLA influences the soil microecological environment and contributed to a deeper understanding of soil microbial ecology in the context of modern agricultural practices.},
}

@article {pmid42719200,
year = {2026},
author = {Fan, L and Wang, M and Zeng, Q and Xu, H and Wei, Y and Zhao, C},
title = {Enhanced corn straw decomposition and wheat growth promotion by filamentous consortium comprising Trichoderma reesei, Aspergillus niger and Neurospora crassa.},
journal = {3 Biotech},
volume = {16},
number = {10},
pages = {415},
pmid = {42719200},
issn = {2190-572X},
abstract = {UNLABELLED: The effects of Trichoderma reesei, Aspergillus niger, and Neurospora crassa on corn straw decomposition and wheat growth were evaluated in this study. Hydroponic experiments showed that the dual combination TA (T. reesei + A. niger) and the triple combination TAN (TA + N. crassa) increased cellulase activity and wheat germination ratios (TA: 1.5 ± 0.06; TAN: 1.4 ± 0.17). Pot experiments confirmed that both TA and TAN enhanced germination (TA: 1.77 ± 0.39; TAN: 1.83 ± 0.34), as well as the height, fresh weight and dry weight of wheat seedlings. The optimal amount of straw addition was 4500 kg/ha. Analysis of soil components during the decomposition process indicated that the addition of TA and TAN enhanced the activities of cellulase, sucrase, urease and catalase, while increasing soil organic matter content. Metagenomic analysis after TA addition indicated shifts in microbial community: at the phylum level, Proteobacteria and Acidobacteria increased, while Actinobacteria decreased; at the genus level, lignocellulose degraders (Pseudoxanthomonas) and nitrifiers (Nitrospira) were enriched, whereas oligotrophic Actinobacteria (Nocardioides) and aromatic degraders (Devosia) declined. This microbiome restructuring accelerated straw decomposition and improved soil nutrient transformation. Overall, TA and TAN consortia showed synergistic performance, supporting their potential application in straw return practices.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05057-7.},
}

@article {pmid42719226,
year = {2026},
author = {Luo, L and Guo, Y and Nie, Z},
title = {A case report of Emergomyces orientalis infection in the lung of HIV infected in patient and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1874569},
pmid = {42719226},
issn = {2296-858X},
abstract = {OBJECTIVE: This study reports a rare case of pulmonary Emergomyces orientalis infection with clinical characteristics, diagnostic approaches and therapeutic regimens of this rare fungal infection, aiming to provide evidence for clinical diagnosis and management.

METHODS: We retrospectively analyzed the patient's clinical symptoms, imaging manifestations, laboratory examinations including metagenomic next-generation sequencing (mNGS), diagnostic and therapeutic procedures, as well as prognosis. Related published literature was searched, reviewed and summarized.

RESULTS: The patient presented with a 3-day cough and expectoration. Conventional pathogen examinations showed the patient is infected with the HIV virus and definite diagnosis of Emergomyces orientalis infection was finally confirmed by mNGS of lung biopsy specimens. He received liposomal amphotericin B combined with symptomatic supportive therapy. Clinical symptoms were alleviated and pulmonary lesions were absorbed after treatment.

CONCLUSION: Pulmonary Emergomyces orientalis infection is uncommon and prone to missed diagnosis and misdiagnosis with high mortality. Routine pathogen culture yields a low positive rate. mNGS serves as a critical tool for early and accurate diagnosis. Individualized antifungal treatment, strict drug interaction assessment and therapeutic monitoring are essential to optimize clinical prognosis.},
}

@article {pmid42719363,
year = {2026},
author = {Batool, M and Hussain, S and Shar, AG and Rehman, HU and Waraich, EA and Haidar, A and Zulfiqar, U and Shao, R and Alghafri, JSK and Gururani, MA},
title = {Unveiling diverse interactions between soil microbiota and host plants for sustainable agriculture: current limitations and prospects.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841614},
pmid = {42719363},
issn = {1664-302X},
abstract = {The intricate relationship between soil microbiota and host plants plays a pivotal role in maintaining soil health and sustaining agricultural productivity. In this review, we examined current knowledge of these interactions, highlighting both their significance and the limitations in existing research. Although substantial progress has been made in elucidating the roles of diverse microbial communities in nutrient cycling, plant growth promotion, and disease suppression, several challenges remain. These include the complexity and diversity of microbial communities, as well as the dynamic nature of soil-plant interactions under varying environmental conditions. Furthermore, there is a need for greater integration of interdisciplinary approaches, encompassing molecular biology, microbiology, ecology, and agronomy, to effectively address these challenges. In this context, this study proposes future research directions aimed at advancing our understanding of soil microbiota-plant interactions and their implications for sustainable agriculture. These include the development and application of advanced omics techniques, such as metagenomics and metatranscriptomics, to comprehensively characterize microbial communities and their functional attributes. Furthermore, harnessing the potential of microbial inoculants and biofertilizers tailored to specific crops, soils, and environmental conditions represents a promising strategy for improving soil health, enhancing nutrient use efficiency, and ensuring sustainable crop production. Overall, addressing these research gaps and leveraging emerging technologies will deepen our understanding of soil microbiota-plant interactions and facilitate the development of innovative, science-based strategies to promote resilient and sustainable agricultural systems.},
}

@article {pmid42719838,
year = {2026},
author = {Li, Y and Hu, Y and Yang, Y and Li, WY and Fan, M and Zhang, W and Wang, Y},
title = {Antimicrobial Decision-Making in Culture-Negative Bacterial Meningitis with mNGS-Detected Prevotella-Dominant Anaerobic Signals: Two Case Reports and a Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {635205},
pmid = {42719838},
issn = {1178-6973},
abstract = {Anaerobic meningitis is uncommon and may be underrecognized when cerebrospinal fluid (CSF) culture is non-diagnostic, particularly after antimicrobial exposure or when anaerobic collection, transport, and incubation conditions are suboptimal. Metagenomic next-generation sequencing (mNGS) can provide complementary microbiological evidence in selected culture-negative central nervous system (CNS) infections, but low-biomass CSF results require explicit quality-control reporting and careful assessment of contamination and clinical plausibility. We report two culture-negative bacterial meningitis cases in which CSF mNGS showed a Prevotella-dominant anaerobic signal. Prevotella oris was the predominant species-level detection in both cases, accompanied by lower-abundance anaerobic co-detections. Because P. oris was not recovered by culture or independently confirmed by species-specific PCR, the results were classified as mNGS-supported Prevotella-dominant signals rather than confirmed monomicrobial P. oris meningitis. Both patients received case-specific antimicrobial therapy adjusted according to clinical status, serial CSF findings, neuroimaging evolution, and adverse-event monitoring. Case 1 required meropenem re-escalation after radiological progression and recurrent intracranial hypertension, whereas Case 2 improved after escalation to meropenem followed by the documented de-escalation to metronidazole. Both patients achieved favorable functional outcomes. These cases illustrate how CSF mNGS may be used as an adjunct when conventional microbiology is non-diagnostic, while emphasizing that sequencing signals, serial CSF changes, imaging, and treatment response must be interpreted together. The two observations do not establish P. oris causality or a standardized escalation/de-escalation regimen.},
}

@article {pmid42719848,
year = {2026},
author = {Chen, Y and Zou, X and Zhong, Y and Luo, W and Zou, X and Zeng, H and Liu, X},
title = {Complementary Utility of Metagenomic Next-Generation Sequencing and Blood Culture for Bloodstream Infections: Insights into Pathogen-Specific Inflammatory and Coagulation Profiles.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {637436},
pmid = {42719848},
issn = {1178-6973},
abstract = {BACKGROUND: Bloodstream infections (BSIs) are a major cause of sepsis and mortality in critically ill patients, yet accurate pathogen identification remains challenging because blood culture has limited sensitivity and delayed turnaround time. This study aimed to evaluate the complementary diagnostic value of blood culture and mNGS for BSIs patients, and to identify distinct inflammatory and coagulation signatures across bacterial, viral, fungal and polymicrobial infections to facilitate rapid early pathogen discrimination.

METHODS: In this retrospective study, 18,803 patients with suspected BSI admitted between December 2017 and December 2024 were included. Baseline clinical characteristics and blood culture results were collected. Blood culture was performed as first-line testing, whereas mNGS was selectively applied to patients with negative blood cultures or persistent clinically suspected infection to assess its incremental pathogen detection. Differences in pathogen distribution and inflammatory/coagulation biomarkers across pathogen types were analyzed. Receiver operating characteristic (ROC) curve analysis was conducted to evaluate the predictive performance of these biomarkers for viral and fungal infections.

RESULTS: Compared with blood culture, mNGS provided additional pathogen detection, with newly identified pathogens comprising viruses (33.5%, 184/550), polymicrobial infections (34.9%, 192/550), and fungal pathogens, whereas single bacterial infections accounted for only 14.5% (80/550). Compared with bacterial infections (n=80), viral infections (n=184) were associated with significantly lower procalcitonin (PCT), C-reactive protein (CRP), and fibrinogen (FIB), but higher prognostic nutritional index (PNI) (all p<0.05). Fungal infections (n=57) showed significantly lower PNI and FIB levels (p<0.05) than bacterial infections (n=1098). ROC analysis demonstrated moderate discriminatory performance of PCT, CRP, and FIB for viral infections, while PNI and FIB showed comparable predictive value for fungal infections.

CONCLUSION: mNGS complements conventional blood culture by expanding pathogen detection in clinically selected patients, while inflammatory and coagulation biomarkers may assist early etiological assessment and support clinical assessment and antimicrobial decision-making.},
}

@article {pmid42719862,
year = {2026},
author = {Zhao, W and Feng, C and Zhang, Y and Wang, L},
title = {Gut-Lung Axis Microbiome Dysbiosis and Cross-Domain Network Analysis in Bronchiectasis Complicated by Invasive Pulmonary Aspergillosis.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {612147},
pmid = {42719862},
issn = {1178-6973},
abstract = {PURPOSE: To explore the clinical significance of pulmonary and gut microbiota in patients with bronchiectasis (BE) with invasive pulmonary aspergillosis (BE-IPA). By analyzing cross-domain microbial networks, we aimed to elucidate the bidirectional interaction mechanisms of the gut-lung axis, provide a theoretical basis for clinical diagnosis, and to identify potential candidate biomarkers and inform future mechanistic studies from a microbiomic perspective.

PATIENTS AND METHODS: We retrospectively examined 78 patients with BE, divided into BE without IPA (n = 37) and BE-IPA (n = 41) groups. Bronchoalveolar lavage fluid and anal swabs were collected. Metagenomic next-generation sequencing was used to analyze microbiota diversity, species composition, and metabolic pathways between the groups. Clinical data were evaluated for correlations with specific taxa, and a cross-domain microbial co-occurrence network was constructed.

RESULTS: Compared to the BE group, the BE-IPA group exhibited significant differences in pulmonary microbiota β-diversity (P < 0.05) and increased gut microbiota evenness (Shannon and Simpson indices, P < 0.05). Aspergillus and species-level Aspergillus fumigatus were significantly enriched in the BE-IPA group lungs, whereas Parabacteroides and Hoylesella were enriched in the gut. The relative abundance of core gut commensals such as Bacteroides dorei was negatively correlated with Acute Physiology and Chronic Health Evaluation II score. The BE-IPA group showed 17 upregulated gut metabolic pathways (P < 0.05), primarily involving lipopolysaccharide biosynthesis and carbohydrate metabolism. Pulmonary A. fumigatus exhibited negative correlations with gut B. dorei and pulmonary Rothia mucilaginosa.

CONCLUSION: The pulmonary microbiota in the BE-IPA group showed a fungal-bacterial symbiotic network centered on A. fumigatus, whereas gut microbiota presented a bacterial co-occurrence network enriched with Parabacteroides. In patients with BE-IPA, pulmonary and gut microbes were associated with multiple clinical indicators and metabolic pathways. These microbiota signatures may aid in the assessment of disease severity in BE-IPA, with the gut commensal B. dorei emerging as a candidate biomarker and a potential subject for future interventional studies.},
}

@article {pmid42709883,
year = {2026},
author = {Liu, Y and Yan, S and Zhang, J and Chen, Y and Zhou, Y and Huang, C and Jiang, T and Gao, Y and Zhu, H and Shi, H and Han, C and Li, F and Zhang, J and Zhao, J and Cao, M},
title = {Curvularia lunata drives biodeterioration of PVC secondary cable insulation involving surface colonization, moisture retention and chemical deterioration.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357774},
pmid = {42709883},
issn = {1932-6203},
mesh = {*Ascomycota/metabolism/isolation & purification/genetics ; *Polyvinyl Chloride/chemistry ; Surface Properties ; Biodegradation, Environmental ; Water/chemistry ; },
abstract = {Microbial degradation of cable insulation materials is a critical issue affecting the reliability of power systems. In this study, metagenomic analysis was employed to reveal the microbial community structure on contaminated substation cables, identifying Curvularia lunata as a dominant fungal species in high-voltage environments. Subsequently, a specific strain, Curvularia lunata B3, was isolated and identified for further investigation. To assess its specific impact on insulation performance, artificial inoculation experiments were conducted on secondary cable samples. Multi-dimensional characterization techniques, including SEM, WCA measurements, halogen moisture analysis, FTIR, XPS, and LCR digital bridge testing, were utilized to evaluate material degradation. The results demonstrated that C. lunata colonization caused significant surface erosion, characterized by the formation of holes and furrows. This physical damage was accompanied by a marked decrease in hydrophobicity, with the water contact angle dropping from 88.30 ± 0.79° to 78.27 ± 1.27°, and a gradual increase in water content to approximately 1.2% over 60 days. Chemical analysis revealed that microbial activity induced oxidation and dechlorination of the PVC insulation, evidenced by the reduction of C-Cl bonds and the emergence of oxygen-containing functional groups. These physicochemical alterations significantly compromised the electrical insulation of the cables, as evidenced by a marked decrease in series resistance (Rs) and an increase in series capacitance (Cs). This study elucidates the mechanisms of fungal erosion on cable insulation and provides a scientific basis for developing targeted protective strategies in power systems.},
}

*Ascomycota/metabolism/isolation & purification/genetics
*Polyvinyl Chloride/chemistry
Surface Properties
Biodegradation, Environmental
Water/chemistry

@article {pmid42710124,
year = {2026},
author = {Yin, G and Shen, Z and Zhao, Y and Liu, X and He, X and Shen, W and Liu, Y and Guo, R and Shang, J and Chen, J and Liao, Q},
title = {Identification of functional microorganisms and genes mediating ciprofloxacin degradation in dynamic habitats of algal bloom decomposition.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143501},
doi = {10.1016/j.jhazmat.2026.143501},
pmid = {42710124},
issn = {1873-3336},
abstract = {Decay of algal blooms in eutrophic lakes generates detritus-rich, redox-dynamic microhabitats that modulate the degradation of emerging pollutants as antibiotics. The degradation pathways of antibiotics within algal-detritus accumulation zones and the associated microbial assimilators remain insufficiently understood. In this study, localized algal bloom decay zones were simulated using static lake microcosms, and DNA-stable isotope probing (DNA-SIP) combined with metagenomic analysis were employed to elucidate ciprofloxacin (CIP) degradation pathways and to identify microorganisms potentially involved in CIP assimilation under elevated CIP exposure. Results demonstrate that ecological succession linked to algal decomposition was closely synchronized with CIP degradation, which primarily proceeded via defluorination, decarboxylation, and piperazine ring modification. The bottom detritus layer showed enrichment of aromatic compound-degrading bacteria, including Hydrogenophaga, Reyranella, and Rhodoblastus, in heavy DNA fractions, indicating their potential role in CIP assimilation. This layer also contained functional genes associated with benzoate, halogenated aromatic compounds, and polycyclic aromatic hydrocarbon degradation pathways. In addition, enrichment of the AAC(6')-Ib-cr gene family in the bottom layer coincided with detection of N-acetylated CIP products, suggesting a possible acetylation-mediated inactivation mechanism. Collectively, the study identified candidate microorganisms and genes linked to CIP-derived assimilation and degradation in algal-detritus-rich microhabitats, providing mechanistic insights into antibiotic degradation in polluted algal decay hotspots.},
}

@article {pmid42710127,
year = {2026},
author = {Liu, S and Ji, Y and Hu, X and Qu, S and Peng, X and Yin, Z and Zhou, S and Tsang, YF},
title = {Microalgal-bacterial sludge enhances dimethyl phthalate (DMP) biodegradation beyond adsorption: Metabolic pathways, microbial responses, and adaptive mechanisms.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143497},
doi = {10.1016/j.jhazmat.2026.143497},
pmid = {42710127},
issn = {1873-3336},
abstract = {Phthalate acid esters (PAEs), as typical environmental endocrine disruptors, pose severe threats to ecosystems and human health due to their persistence in aquatic environments, while conventional wastewater treatment processes exhibit low removal efficiency and risk secondary pollution. This study constructed microalgal-bacterial sludge (MABS) to systematically investigate its removal efficiency and the degradation mechanisms of dimethyl phthalate (DMP). The results demonstrate that, compared to conventional activated sludge (AS), DMP MABS exhibited greater tolerance to DMP and higher DMP removal efficiency, reaching 96.9%, with biodegradation rather than adsorption becoming the dominant removal route, improved settling performance (SVI decreased to 51.19 mL/g), increased biomass, and stimulated secretion of extracellular polymeric substances (EPS, up to 40.00 mg/g VSS) to form a protective barrier against toxicity. Microbial analysis revealed that Pseudomonadota dominated the microbial community and was strongly associated with metabolic functions, while MAG-based metagenomic binning identified Burkholderiales as the largest order-level contributor to DMP-related functional genes. Integrating EPS characterization with metagenomic evidence, we further hypothesize an EPS-mediated microalgal-bacterial interaction model in which LB-EPS enriches DMP at the aggregate interface, TB-EPS stabilizes oxic-anoxic microzones, and microalgal-derived oxygen and carbon sources, signaling, chemotaxis, biofilm formation, and vitamin-associated functions collectively support bacterial DMP catabolism. Qualitatively assigned intermediates together with metagenomic annotations proposing a putative DMP biodegradation pathway involve de-esterification to monomethyl phthalate and phthalic acid (lip, gnl, and pgl, etc.), followed by aerobic dioxygenase-catalyzed or anaerobic decarboxylation to protocatechuic acid (pht3, pht4, and pht5, etc.) or benzoic acid (benA-xylX and benB-xylY), ultimately entering the tricarboxylic acid cycle (pcaG, pcaF, ligK, and galD, etc.). This technology integrates high-efficiency degradation, energy conservation, and resource recovery potential, providing theoretical and technical foundations for wastewater treatment plants to address emerging pollutants.},
}

@article {pmid42710166,
year = {2026},
author = {Podosokorskaya, OA and Merkel, AY and Novikov, AA and Klyukina, AA and Elcheninov, AG},
title = {Melioribacter sulfuriphilus sp. nov., facultatively anaerobic thermophilic sulfur- and thiosulfate-respiring bacterium from Karmadon hot springs of North Ossetia (Russian Federation).},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126768},
doi = {10.1016/j.syapm.2026.126768},
pmid = {42710166},
issn = {1618-0984},
abstract = {Novel facultatively anaerobic moderately thermophilic bacteria, strains OK-6-Me[T] and OK-1-Me, were isolated from the hot springs of Karmadon (North Ossetia, Russian Federation). Gram-stain-negative, motile rods were present singly, in rosettes, and formed biofilms. Both strains grew optimally at 55 °C, pH 7.0 and did not require sodium chloride. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, xylan, lichenan, xyloglucan, mannan, locust bean gum, pectin) as well as proteinaceous substrates (gelatin, casein). Growth under anaerobic conditions was observed both in the presence and absence of external electron acceptors (sulfur, thiosulfate, nitrite, arsenate, Fe-citrate, ferrihydrite). Major cellular fatty acids of both strains were iso-C15:0, anteiso-C15:0, and anteiso-C17:0. The size of the genomes were 3.3 and 3.2 Mb for strain OK-6-Me[T] and OK-1-Me, respectively. Genomic DNA G + C content was 37% for both strains. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, the strains represented a new species of the genus Melioribacter of family Melioribacteraceae within the class Ignavibacteria, for which the name Melioribacter sulfuriphilus sp. nov. is proposed, with type strain OK-6-Me[T] (= B-3972[T] = CGMCC 1.18264 [T] = BIM B-2154[T] = UQM 41932[T]). Analysis of OK-1 and OK-6 metagenomes revealed presence of various genes involved in carbon (CO2 fixation, carbohydrate hydrolysis, hydrocarbons degradation, fermentation), nitrogen (nitrate, nitrite, NO and N2O reduction) and sulfur cycles (sulfate reduction, sulfur or thiosulfate reduction, oxidation of sulfur compounds). MAGs OK-1-035 and OK-6-024 almost identical to genomes of strain OK-1-Me and OK-6-Me[T] presumably are integral part of these complex trophic chains.},
}

@article {pmid42710654,
year = {2026},
author = {Chen, Y and Li, Y and Chen, Y and Gou, C and Li, H and He, X and Zeng, N and Du, E and Chen, X and Gui, F},
title = {Host detoxification and gut microbiota are associated with chlorantraniliprole resistance in Spodoptera frugiperda.},
journal = {Journal of insect physiology},
volume = {},
number = {},
pages = {105062},
doi = {10.1016/j.jinsphys.2026.105062},
pmid = {42710654},
issn = {1879-1611},
abstract = {Spodoptera frugiperda is a major agricultural pest that causes severe damage in China. Chlorantraniliprole (CAP) is the primary insecticide used for control; however, it is yet unknown how much the intrinsic detoxification system and gut microbiota of the host contribute to resistance. In this study, we used a resistant strain (CR) with a 71.85-fold resistance ratio after 10 generations of CAP selection. The molecular and microbial changes associated with CAP resistance in S. frugiperda were systematically analyzed by integrating phenotypic and multi-omics data. Results demonstrated that detoxification enzyme activities were markedly increased in the CR strain. Host-mediated metabolic pathways driven by Cytochrome P450 and glutathione S-transferase were significantly upregulated. Furthermore, transcriptome evidence indicated that CAP-induced calcium dysregulation was mitigated via enhanced calcium sequestration and endoplasmic reticulum chaperone responses, suggesting physiological tolerance of insects to this insecticide.. Continuous CAP stress also significantly reshaped the gut microbial community structure of S. frugiperda, with Enterococcus emerging as the dominant genus. According to metagenomic annotation, the gut microbiome was enriched in candidate genes associated with CAP degradation, including dehalogenases and amidases, that could potentially break the chemical bonds in CAP and thereby contribute to resistance. Enterococcus mundtii was the most prominently contributor in terms of gene abundance. Phylogenetic analysis revealed sequence similarities and conserved domains between candidate microbial degradation genes and host metabolic detoxification genes, suggesting potential functional similarity. The integrative analyses suggested that S. frugiperda resistance may arise from correlated changes in host endogenous metabolism, calcium homeostasis, and gut-microbiota-mediated degradation potential. The gut microbiota may form a coordinated adaptive regulatory system by encoding candidate degrading enzymes and exhibiting correlative coupling with host genes, which requires further functional validation. These findings highlight the potential synergy between host detoxification and gut microbiota as a contributing factor to CAP resistance in S. frugiperda.},
}

@article {pmid42710694,
year = {2026},
author = {Tian, J and Wang, Y and Lu, L and Hu, X and Zhou, Y and Tian, S and Liu, Y and Yang, H and Fang, H and Zhou, Q and Qiu, Z and Zhu, J and Zhang, C and Wang, W},
title = {Gut microbiota correlating with glycerophospholipid metabolism dysregulation is associated with brain functional alterations in adolescent depression.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {107005},
doi = {10.1016/j.bbi.2026.107005},
pmid = {42710694},
issn = {1090-2139},
abstract = {Gut microbiota dysbiosis has been linked to depression; however, evidence regarding this association in adolescents remains scarce, and the underlying molecular and neuropathological mechanisms are poorly understood. We conducted an integrative multi-omics study combining fecal metagenomic sequencing, serum untargeted metabolomics, resting-state fMRI, and spatial brain transcriptomics in 160 adolescents with depression (PT) recruited from multicenter cohort and 90 local healthy controls (HC) during the same period. Multimodal neuroimaging assessed spontaneous activity, functional connectivity, and structure-function coupling. Cross-omics association, mediation analyses, and machine learning were applied to identify mechanistic pathways and robust biomarkers. Adolescents with depression exhibited distinct gut microbial dysbiosis and pronounced disruption of glycerophospholipid metabolism. Multiple phospholipids and their metabolites were significantly altered and closely associated with differential microbial taxa. Neuroimaging revealed abnormal functional reorganization and regional structure-function decoupling, prominently involving the precuneus and precentral gyrus. Transcriptomic mapping demonstrated that brain regions showing the greatest functional alterations were enriched for genes related to phospholipid metabolism. Mediation analyses indicated that gut microbiota may influence depressive symptoms through glycerophospholipid metabolites and precentral gyrus dysfunction. A cross-validated multi-omics biomarker panel showed strong predictive performance for identifying patients with depression. These findings suggested glycerophospholipid metabolism may be as a key molecular interface linking gut microbial dysbiosis to brain network dysfunction in adolescents with depression, providing a multiscale framework for microbiota-informed stratification and prevention.},
}

@article {pmid42711294,
year = {2026},
author = {Peng, Y and Woods, LC and Perlaza-Jimenez, L and Lappan, R and Jespersen, M and Dong, X and Holland, SR and Chown, SL and Leung, PM and Greening, C},
title = {Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42711294},
issn = {2041-1723},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; MGS and MITS//Monash University (MU)/ ; },
mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Soil Microbiology ; Phylogeny ; *Selection, Genetic ; Hydrogenase/genetics ; *Adaptation, Physiological/genetics ; Metagenome ; Aldehyde Oxidoreductases/genetics ; Bacteria/genetics/classification ; Multienzyme Complexes ; },
abstract = {Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the eco-evolutionary processes underlying adaptation to Antarctica's polyextreme conditions remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence microbial adaptation in 16 Antarctic soils using combined short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show frequent HGT across communities. While transferred genes span diverse functional categories, those involved in energy metabolism are exchanged at higher frequency. Genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently disseminated. Approximately a quarter of carbon monoxide dehydrogenases and [NiFe]-hydrogenases are predicted to be horizontally acquired and are often associated with mobile genetic elements. Analysis of polymorphisms suggests widespread purifying selection, particularly for aerotrophy genes, providing further evidence that aerotrophy is critical for microbial survival in Antarctica. Genetic variation in hydrogenases is tightly associated with predicted protein structures, with intense selection acting on critical sites preserving stability and function. Together, these findings show that previously unrecognized eco-evolutionary dynamics shape the composition and function of Antarctic microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.},
}

Antarctic Regions
*Gene Transfer, Horizontal
*Soil Microbiology
Phylogeny
*Selection, Genetic
Hydrogenase/genetics
*Adaptation, Physiological/genetics
Metagenome
Aldehyde Oxidoreductases/genetics
Bacteria/genetics/classification
Multienzyme Complexes

@article {pmid42711738,
year = {2026},
author = {Gao, X and Qin, R and He, J},
title = {Analysis of the pulmonary microbiome in ARDS patients using bronchoalveolar lavage fluid metagenomic next-generation sequencing: a retrospective observational study.},
journal = {Journal of intensive care},
volume = {14},
number = {1},
pages = {},
pmid = {42711738},
issn = {2052-0492},
support = {KJQN202300410//Science and technology research project of Chongqing Education Commission/ ; kryc-yq-2127//Kuanren Talents Program of the second affiliated hospital of Chongqing Medical University/ ; },
abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) exhibits significant clinical heterogeneity, with inflammatory subphenotypes (hypoinflammatory and hyperinflammatory) representing a key axis for precision medicine. The role of the pulmonary microbiome in these subphenotypes remains poorly understood.

METHODS: This retrospective study enrolled 159 ARDS patients. Using a validated machine-learning classifier, patients were stratified into hypoinflammatory (n=92) and hyperinflammatory (n=67) groups. Bronchoalveolar lavage fluid (BALF) was analyzed by metagenomic next-generation sequencing (mNGS) and conventional microbiological testing (CMT). Clinical characteristics, pathogen profiles, and pulmonary microbiome composition were compared between groups.

RESULTS: Patients in the hyperinflammatory phenotype had more severe disease, with significantly higher in-hospital mortality (65.7% vs. 30.4%, P < 0.001) and 28-day mortality (53.7% vs. 22.8%, P < 0.001). mNGS demonstrated superior diagnostic performance, identifying pathogens in 18.2% of cases that were negative by conventional microbiological testing (CMT), whereas CMT alone detected pathogens in only 2.5% of mNGS-negative cases. mNGS showed significant advantages in viral detection (74.5% vs. 28.2%, P < 0.001) and in the identification of mixed infections (74.5% vs. 41.1%, P < 0.001). Acinetobacter baumannii was the most prevalent species in both phenotypes; however, the hyperinflammatory phenotype was enriched for Klebsiella pneumoniae, Legionella pneumophila, and influenza A (H1N1), whereas Stenotrophomonas maltophilia and herpesviruses were more prevalent in the hypoinflammatory phenotype. Species richness was significantly reduced in the hyperinflammatory phenotype (Chao1, P < 0.001; ACE, P = 0.001). In adjusted analyses, this association remained virtually unchanged after adjustment for ARDS etiological category and pulmonary vs. extrapulmonary ARDS, and remained significant in the fully adjusted model additionally accounting for age, sex, and immunosuppression (Chao1: P = 0.002; ACE: P = 0.003). Evenness indices (Shannon/Simpson) and overall community structure (β-diversity; PERMANOVA, P = 0.156) did not differ between phenotypes, suggesting a selective depletion of rare, low-abundance taxa rather than a global restructuring of the pulmonary microbiota. Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa of exploratory significance: the hyperinflammatory phenotype was enriched for Bifidobacterium dentium and Gemella sanguinis, whereas the hypoinflammatory phenotype was enriched for commensals such as Streptococcus mitis. Network analysis revealed well-defined positive and negative correlations between pathogens and commensal taxa.

CONCLUSIONS: The hyperinflammatory phenotype of ARDS is characterized by greater clinical severity and a distinct pulmonary microbiome signature. Metagenomic next-generation sequencing (mNGS) substantially outperforms conventional methods for etiological diagnosis. LEfSe analysis identified differentially enriched taxa, with the hyperinflammatory phenotype enriched for microorganisms that typically colonize the oral cavity or gut (e.g., Bifidobacterium dentium), suggesting potential microbial translocation along the oral-lung or gut-lung axis. These findings provide a novel microbiome dimension for the precision subphenotyping of ARDS.},
}

@article {pmid42711823,
year = {2026},
author = {Saragiotto, GK and de Oliveira, LFV and Geciana Tomaz Dos Santos, B and Nunes Sanches, R and Merizzi de Oliveira, M and Campos Freire, F and Dias de Oliveira Carvalho, R and Sivieri, K and Sartoratto, A and Cabral, L and Azevedo, V and Belli, T and Costa Antunes, AE},
title = {Exploratory case comparison of gut microbiome functional potential in ultramarathoners differing in adiposity and finish time.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2725874},
doi = {10.1080/15502783.2026.2725874},
pmid = {42711823},
issn = {1550-2783},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Feces/chemistry/microbiology ; *Adiposity/physiology ; *Obesity/microbiology/physiopathology ; *Marathon Running/physiology ; Fatty Acids, Volatile/analysis/metabolism ; Male ; Body Mass Index ; *Physical Endurance/physiology ; *Running/physiology ; },
abstract = {Understanding variations in gut microbial functional potential among endurance athletes may inform future personalized nutritional strategies. This exploratory case-comparison study aimed to investigate predicted microbial functional potential using shotgun metagenomic sequencing and fecal metabolites, in two post hoc-selected runners who represented extreme and contrasting outcomes from the same single-stage 217 km mountain ultramarathon: a normal-BMI fast-finisher and an obese slow-finisher. The main descriptive findings suggest that the normal-BMI fast finisher exhibited smaller observed differences among the analyzed enzyme-coding functions and pathways in the sample collected after race completion, with a predominance of enzyme-coding functions associated with nucleic acid-related processes and protein biosynthesis. In contrast, the obese slow-finisher showed larger observed differences in predicted functional potential between the pre- and post-race samples. Distinct fecal metabolite patterns were also observed, with selective short-chain fatty acid (SCFA) changes in the normal-BMI fast-finisher and reductions across all analyzed SCFAs in the obese slow finisher. Given the limitations of this study, including the confounding effects of adiposity, unmeasured dietary intake, and post hoc selection bias, these descriptive observations provide hypothesis-generating data rather than establishing causal relationships with performance. Taken together, these findings encourage further investigation in larger cohorts.},
}

Humans
*Gastrointestinal Microbiome/physiology
Feces/chemistry/microbiology
*Adiposity/physiology
*Obesity/microbiology/physiopathology
*Marathon Running/physiology
Fatty Acids, Volatile/analysis/metabolism
Male
Body Mass Index
*Physical Endurance/physiology
*Running/physiology

@article {pmid42711910,
year = {2026},
author = {Bai, J and You, Q and Si, G and Hu, D and Sun, A and Su, S and Wang, R and Fan, J and Gao, S and Zhu, T and Song, CL and Zhou, F and Lv, Y},
title = {Gut Microbiota-Derived Indole-3-Propionic Acid Alleviates Diabetic Osteoporosis Through Nrf2-Mediated Ferroptosis Suppression.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77649},
doi = {10.1002/advs.77649},
pmid = {42711910},
issn = {2198-3844},
support = {12474461//National Natural Science Foundation of China/ ; 82402806//National Natural Science Foundation of China/ ; 81971160//National Natural Science Foundation of China/ ; 7202222//Beijing Municipality Natural Science Foundation/ ; 2022-2-4096//Capital Health Development Research Special Project/ ; },
abstract = {Diabetic osteoporosis combines impaired bone formation with disproportionate skeletal fragility, yet the microbial metabolites linking diabetes-associated dysbiosis to bone dysfunction remain unclear. This study implicates indole-3-propionic acid (IPA), a gut microbiota-derived tryptophan metabolite, in the maintenance of skeletal homeostasis under diabetic conditions. Circulating IPA was lower in diabetic mice and in a small exploratory cohort of patients with diabetic osteoporosis. IPA concentrations were positively associated with bone mass. Metagenomic profiling linked lower IPA to impaired microbial tryptophan metabolism and reduced Clostridium abundance. In diabetic mice, IPA supplementation improved trabecular microarchitecture and bone formation. In bone marrow mesenchymal stem cells subjected to high glucose and palmitate, IPA also restored GPX4 and SLC7A11 expression and was associated with recovery of Nrf2-mediated antioxidant signaling. Pharmacological inhibition of Nrf2 substantially attenuated these anti-ferroptosis and pro-osteogenic effects. Together, these findings support a gut microbiota-IPA-Nrf2-ferroptosis pathway linking altered microbial tryptophan metabolism to impaired osteogenesis. They provide a rationale for evaluating IPA as a potential therapeutic strategy for diabetic osteoporosis.},
}

@article {pmid42711968,
year = {2026},
author = {Liang, G and Wang, C and Liu, R and Ji, Q and Zhang, X and Zhao, L and Liu, X and Zhang, H and Zhuang, G and Zheng, J},
title = {Assembly Dynamics and Functional Divergence of Anaerobic Communities Driven by Iron Oxides.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70412},
doi = {10.1111/1462-2920.70412},
pmid = {42711968},
issn = {1462-2920},
support = {GYY-NYHJ-2023-WT-002//the Weiqiao-UCAS Innovation Research Projects on Carbon Neutrality Technology/ ; },
mesh = {*Ferric Compounds/metabolism/chemistry ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Sewage/microbiology ; Anaerobiosis ; Minerals/metabolism ; Ferrosoferric Oxide/metabolism ; Methane/metabolism ; Iron Compounds ; },
abstract = {Iron oxides play an important role in regulating global biogeochemical cycles, yet how their physicochemical properties influence community structure, function, and assembly remains poorly understood. Here, we investigated the effects of four representative iron oxides-ferrihydrite (Fh), goethite (Gt), haematite (Ht), and magnetite (Mt)-serving as terminal electron acceptors on microbial communities enriched from activated sludge. Metagenomic profiling revealed mineral-dependent divergence in community composition and functional potential. The communities developed on amorphous Fh demonstrated low microbial diversity and were heavily dominated by Pseudomonas_A. In contrast, the communities associated with crystalline oxides (Gt and Ht) maintained intermediate diversity. Notably, the Mt. communities exhibited a more polycentric structure, possessing the highest richness and evenness, alongside a significant enrichment of Geobacter. Methane was detected in crystalline-oxide systems but remained below detection in Fh systems. Mineralogical analyses revealed substantial Fe(III) reduction and secondary mineral formation across treatments. Null-model analysis of pairwise turnover supports mineral-associated community turnover while highlighting that the relative contributions of selection versus undominated processes vary among minerals. Overall, these findings demonstrate that iron oxide identity is associated with differences in anaerobic community structure and biogeochemical outcomes.},
}

*Ferric Compounds/metabolism/chemistry
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Sewage/microbiology
Anaerobiosis
Minerals/metabolism
Ferrosoferric Oxide/metabolism
Methane/metabolism
Iron Compounds

@article {pmid42711992,
year = {2026},
author = {Farese, M and Moraitou, M and Jin, C and Forsythe, A and Micarelli, I and van der Valk, T and Manzi, G and Parducci, L and Tafuri, MA and Guschanski, K},
title = {Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70357},
doi = {10.1002/ajpa.70357},
pmid = {42711992},
issn = {2692-7691},
support = {//Bertil Lundman Foundation for Anthropological Studies (Swedish Phytogeographical Society)/ ; DOT1326JZS//Italian Ministry of University and Research (MUR)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Italy ; History, Ancient ; *Life Style/history ; Dental Calculus/microbiology ; DNA, Ancient/analysis ; *Mouth/microbiology ; Roman World/history ; },
abstract = {OBJECTIVES: The fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social élite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall.

MATERIAL AND METHODS: We analyzed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries (I-III century CE, Lucus Feroniae and Isola Sacra) and one post-Classical cemetery (IV-VIII century CE, Selvicciola), all located in proximity to the city of Rome, Italy.

RESULTS: We detect significant differences in the taxonomic and functional composition of the oral microbiome between the three sites, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible.

DISCUSSION: The distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices, in line with previously published isotopic and morphological data. Its rural position may have mitigated the cyclical food crises that affected the contemporary Isola Sacra and the later community of Selvicciola, buffering it against the nutritional stress observed in these two locations. This finding supports the temporal stability of the dental calculus microbiome while highlighting the impact of lifestyle on the oral microbial communities.},
}

Humans
*Microbiota/genetics
Italy
History, Ancient
*Life Style/history
Dental Calculus/microbiology
DNA, Ancient/analysis
*Mouth/microbiology
Roman World/history

@article {pmid42712102,
year = {2026},
author = {Pellegrini, C and Ravaioli, F and De Fanti, S and Siliquini, A and Sala, C and Rochat, M and Pollarini, V and Polischi, B and Pasti, A and Grasso, M and Rambaldi, M and Cardoni, F and Grotteschi, N and Caraci, F and Cortelli, P and Provini, F and Lodi, R and Morandi, L and Parchi, P and Pirazzoli, GL and Sambati, L and Tonon, C and Bacalini, MG},
title = {Alterations of gut microbiota in Down syndrome and their association with Alzheimer's disease.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {9},
pages = {e71815},
doi = {10.1002/alz.71815},
pmid = {42712102},
issn = {1552-5279},
support = {PNC0000002//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; B53C22006330001//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; GR-2019-12369983-Theory-enhancing//Italian Ministry of Health/ ; //Italian Ministry of Health - "Ricerca Corrente" funding/ ; },
mesh = {Humans ; *Down Syndrome/microbiology/blood/complications ; *Alzheimer Disease/blood/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Aged ; Adult ; Biomarkers/blood ; Aged, 80 and over ; tau Proteins/blood ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Neurofilament Proteins/blood ; Glial Fibrillary Acidic Protein/blood ; },
abstract = {INTRODUCTION: Adults with Down syndrome (DS) have a higher risk of Alzheimer's disease (AD). As gut microbiota (GM) alterations have been reported in AD, we investigated their association with cognitive decline and plasma AD biomarkers in DS.

METHODS: Fecal and plasma samples were collected from 58 adults with DS (21-75 years) and 30 euploid controls (CTRL; 25-83 years). GM was profiled using 16S rRNA sequencing, filtering low prevalent taxa. Major neurocognitive disorder (NcD) was diagnosed with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) criteria. Plasma levels of phosphorylated tau 181 (p-tau181), neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were measured using Simoa.

RESULTS: DS showed no changes in overall microbial diversity compared to CTRL, but genera including UBA1819 and Intestinibacter were altered. Specific genera showed changes in DS with NcD, like Alistipes (increased) and Roseburia (decreased), with the latter negatively associated with plasma AD biomarkers.

DISCUSSION: Adults with DS display AD-associated changes in GM partially resembling those reported previously in euploid AD patients.},
}

Humans
*Down Syndrome/microbiology/blood/complications
*Alzheimer Disease/blood/microbiology
Female
Male
*Gastrointestinal Microbiome/physiology
Middle Aged
Aged
Adult
Biomarkers/blood
Aged, 80 and over
tau Proteins/blood
Feces/microbiology
Young Adult
RNA, Ribosomal, 16S/genetics
Neurofilament Proteins/blood
Glial Fibrillary Acidic Protein/blood

@article {pmid42712403,
year = {2026},
author = {Kariithi, HM and Carabetta, VJ and Leyson, CL and Goraichuk, IV},
title = {Editorial: Sequencing technologies in advancing veterinary and zoonotic infection research.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1950388},
pmid = {42712403},
issn = {2235-2988},
}

@article {pmid42712443,
year = {2026},
author = {Weng, X and Zhang, H and Liu, P and Gao, W and Li, H},
title = {A case report of a patient with chronic granulomatous disease complicated by invasive aspergillosis and disseminated Burkholderia multivorans infection.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1915139},
pmid = {42712443},
issn = {2296-858X},
abstract = {BACKGROUND: Chronic granulomatous disease (CGD) is a rare inborn error of immunity characterized by defective phagocyte oxidative burst, leading to recurrent, life-threatening infections with catalase-positive bacteria and fungi. Co-infections with Aspergillus and Burkholderia species in CGD are exceedingly rare and often fatal due to synergistic pathogenic mechanisms and limited therapeutic options.

CASE PRESENTATION: We report a fatal case of X-linked CGD in a 14-year-old male with a history of recurrent infections, who presented with severe pneumonia, respiratory failure, and profound growth retardation. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified Aspergillus flavus complex, Burkholderia multivorans, and subsequent cultures confirmed disseminated B. multivorans infection and invasive aspergillosis. Whole-exome sequencing revealed a novel missense mutation, c.1514T>A (p.Leu505Gln), in the CYBB gene, predicted to result in loss of NADPH oxidase function, which is consistent with the severe infectious phenotype observed. Despite aggressive antimicrobial therapy and intensive supportive care, the patient developed refractory septic shock and multiorgan failure, and died on day 14 of hospitalization.

CONCLUSIONS: This case underscores the lethal potential of concurrent Aspergillus and Burkholderia infections in X-linked CGD and highlights the critical importance of early diagnosis, which can be achieved through functional assays such as the DHR test or NBT test, followed by genetic confirmation when available. The novel CYBB mutation expands the known genotype-phenotype spectrum of severe X-CGD. Prompt recognition of primary immunodeficiencies in children with recurrent infections caused by typical pathogens is essential to enable timely prophylaxis and curative interventions such as hematopoietic stem cell transplantation before irreversible infectious complications occur.},
}

@article {pmid42712642,
year = {2026},
author = {Li, T and Zhou, X and Xiong, F and Zhao, T and Jiang, N and Cai, Y and Hu, Y and Lu, C and Xuan, Y and Gai, X},
title = {Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1924993},
pmid = {42712642},
issn = {1664-302X},
abstract = {BACKGROUND: Tobacco root rot, caused by Fusarium species, is a persistent soil-borne disease that threatens tobacco production. To identify endophytic contributors to disease suppression, this study compared the root endophytic microbiomes of healthy and diseased tobacco plants using metagenomic sequencing and isolated functional bacteria from healthy roots.

RESULTS: Metagenomic analysis of 30 root samples (223 Gb) generated 2.9 million non-redundant genes and identified 1,953 core genera. Healthy plants contained distinct endophytic microbial communities enriched in bacterial taxa and pathways associated with secondary metabolite biosynthesis, siderophore production, chemotaxis, biofilm formation, and carbohydrate metabolism. This microbiome-guided approach identified TM-1, an endophytic Enterobacter strain that significantly inhibited Fusarium solani by 62.29% in a dual-culture assay. Transcriptome profiling revealed that TM-1 treatment broadly altered F. solani gene expression, with prominent effects on ribosome function, amino acid biosynthesis, carbon metabolism, and glycolysis. TM-1 disrupted sugar transporter-related gene expression, and deletion of five representative genes significantly restricted fungal mycelial growth, with the strongest inhibition (66.47%) observed for the hexose transporter homolog MRS44_010803.

CONCLUSION: These results indicate that healthy tobacco roots harbor disease-suppressive endophytic microorganisms and suggest that TM-1 may suppress F. solani by interfering with sugar transport and carbon acquisition. These findings provide a potential biocontrol resource for the sustainable management of tobacco root rot.},
}

@article {pmid42712652,
year = {2026},
author = {Yasir, M and Klena, JD and Abd El Ghany, M},
title = {Editorial: Infectious disease control in the microbial functional genomics era.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934262},
doi = {10.3389/fmicb.2026.1934262},
pmid = {42712652},
issn = {1664-302X},
}

@article {pmid42712876,
year = {2026},
author = {Tsuda, Y and Tanizawa, Y and Vu, TMH and Nishimura, Y and Shintani, M and Abe, H and Hasebe, F and Kasuga, I and Nagao, M and Suzuki, M},
title = {VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag109},
pmid = {42712876},
issn = {2631-9268},
mesh = {*Metagenome ; *Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; Virulence/genetics ; *Bacteria/genetics/pathogenicity ; *Software ; *Metagenomics/methods ; Virulence Factors/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Bacterial pathogens spread in clinical and environmental settings, and mobile genetic elements (MGEs), such as plasmids and phages, mediate the transfer of virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) among bacterial communities. Metagenomic analysis of environmental and wastewater samples using highly accurate long-read sequencing technologies, such as Pacific Biosciences (PacBio) HiFi sequencing, provides valuable insights into monitoring the regional spread of VFGs and ARGs, including dissemination mediated by MGEs. No visualization tool is currently available for the comprehensive display of numerous resulting circular metagenome-assembled genomes (cMAGs) with functional gene annotations. Here, we developed visualization of circular metagenome-assembled genome (VicMAG), a visualization tool for highly complex cMAGs derived from long-read metagenome assemblies annotated using updated databases of VFGs, ARGs, and MGEs. Using 353 cMAGs from PacBio HiFi sequencing of a wastewater sample, we demonstrated the utility of VicMAG for metagenome visualization. VicMAG provides comprehensive, size-aware visualization of cMAGs representing bacterial chromosomes and plasmids, annotated with VFGs, ARGs, and phages. By simultaneously visualizing all cMAGs in a framework, VicMAG facilitates a holistic understanding of the distribution and genomic context of VFGs and ARGs across complex microbial communities. This tool supports integrated surveillance of bacteria associated with virulence and antimicrobial resistance across clinical, environmental, and One Health contexts.},
}

*Metagenome
*Drug Resistance, Bacterial/genetics
*Genome, Bacterial
Virulence/genetics
*Bacteria/genetics/pathogenicity
*Software
*Metagenomics/methods
Virulence Factors/genetics
Interspersed Repetitive Sequences

@article {pmid42712939,
year = {2026},
author = {Tiwari, SK and Telatin, A and Singh, D},
title = {Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag110},
pmid = {42712939},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Molecular Sequence Annotation ; },
abstract = {Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.},
}

Humans
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Molecular Sequence Annotation