@article {pmid42379395,
year = {2026},
author = {Mannila, E and Gómez-Gallego, C and Muluh, G and Nuotio, P and Koistinen, V and Erawijantari, P and Salminen, S and Lahti, L and Kolehmainen, M and Linderborg, KM},
title = {Oat-rich low-gluten diet modulates plasma short-chain fatty acids without significant changes in fecal microbiome or inflammatory markers - a randomized clinical trial in people with cardiometabolic risk.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101690},
doi = {10.1016/j.tjnut.2026.101690},
pmid = {42379395},
issn = {1541-6100},
abstract = {BACKGROUND: Increasingly popular low-gluten diets (LGDs) are generally low in fiber; however, it is possible to improve the LGD by using oat-based products.

OBJECTIVE: To investigate the changes in fecal microbiome, fasting plasma short-chain fatty acids (SCFAs), and inflammatory markers during a 6-week oat- or rice-rich LGD in individuals with increased cardiometabolic risk.

METHODS: The participants (n=69) were allocated into two parallel groups following a 6-week LGD with either oats or rice. Fasting plasma, stool, and dietary information were collected both at the baseline and at the end of the trial. Fecal microbial communities were analyzed by shotgun metagenomics (Novaseq X Plus) and characterized using MetaPhlAn4. Their functional potential was assessed with HUMAnN3 using the MetaCyc database. Plasma SCFAs were quantified by UHPLC-MS, and inflammatory markers were detected and quantified using a 45-cytokine panel (Olink Target). Diet-group differences over time were assessed with linear mixed-effects model.

RESULTS: Dietary information revealed high-oat and low-rice consumption at the baseline for both groups. Overall, the oat-rich LGD increased circulating SCFAs. Particularly, butyrate increased more during the oat-rich LGD than during the rice-rich LGD (ptimeXgroup=0.033). Regarding changes in the fecal microbiome, the rice group had a higher Shannon diversity index after the intervention than the oat group (ptimeXgroup=0.025), and more changes in the microbiome. This is possibly due to more substantial dietary changes from a low rice consumption compared to the habitual diet in the baseline. No significant differences between or changes within the groups in inflammatory markers were observed.

CONCLUSIONS: Changing to an oat-rich LGD increases fasting plasma SCFA concentrations without significant effects on the fecal microbiome and inflammatory markers in individuals with increased cardiometabolic risk. When there is a regular baseline consumption of oats, adopting a low-fiber rice-rich LGD may shift the microbiome towards potentially unfavorable direction.

NCT05526092, https://clinicaltrials.gov/study/NCT05526092.},
}

@article {pmid42379815,
year = {2026},
author = {Patel, I and Mammel, M and Gangiredla, J and Mukherjee, A},
title = {Targeted amplicon sequencing for enhanced detection of spiked Shiga toxin-producing Escherichia coli in ready-to-eat romaine lettuce: a proof-of-concept study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0102226},
doi = {10.1128/spectrum.01022-26},
pmid = {42379815},
issn = {2165-0497},
abstract = {The early and accurate detection of low-level pathogenic and indicator organisms in fresh produce is critical for preventing widespread foodborne outbreaks. Contamination of leafy greens with foodborne pathogens, such as Shiga toxin-producing Escherichia coli (STEC), is a significant public health issue, making rapid and sensitive detection methods critical for mitigating outbreaks. Although next-generation sequencing (NGS) is a powerful tool for pathogen identification, challenges remain in detecting low contamination levels in food products. Here, we demonstrate the use of a custom targeted amplicon sequencing (TAS) primer panel targeting species with food safety concerns, including known human foodborne pathogens, opportunistic pathogens, and indicator organisms related to food spoilage. Using a quasi-metagenomics approach, this proof-of-concept study demonstrates that, compared to whole-metagenomic sequencing (WMS), TAS is a rapid and sensitive NGS-based method for detecting low levels of pathogens. Ready-to-eat romaine lettuce was spiked with STEC and incubated in enrichment medium. DNA was isolated at 0.5, 5, and 6 h, and libraries were prepared for both WMS and TAS. The results indicated that TAS was more sensitive than WMS not only at detecting the pathogen at the species level but also at identifying key virulence markers stx1 and stx2. Overall, our targeted sequencing approach provides a rapid and sensitive molecular method to detect and identify foodborne pathogenic bacteria, demonstrating its potential for application in food safety.IMPORTANCEDetecting low-level pathogenic and indicator organisms is critical to prevent foodborne outbreaks. Conventional methods lack speed and sensitivity. While next-generation sequencing methods, such as whole-metagenomic sequencing (WMS), offer a broad microbial landscape view, detecting pathogens at low concentrations within complex food matrices remains challenging. To address this, a targeted amplicon sequencing (TAS) panel was designed to identify species of food safety concern and key indicator organisms. This study demonstrates that TAS is more sensitive than WMS. The application of this TAS assay provides an important bridge between qPCR and WMS by detecting and characterizing pathogens that might be present in low numbers and otherwise missed in an enrichment. TAS allows multiplexing and overcomes the critical limitation of sensitivity in complex samples, providing a robust tool for food safety surveillance. Our findings demonstrate the potential use of targeted next-generation sequencing (NGS)-based methods to mitigate the risk of foodborne illnesses.},
}

@article {pmid42379825,
year = {2026},
author = {Wang, S and Chen, M and Jiao, D},
title = {ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0410125},
doi = {10.1128/spectrum.04101-25},
pmid = {42379825},
issn = {2165-0497},
abstract = {UNLABELLED: Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe "identifiability limit" when disentangling highly similar genomes. Under high-noise conditions, sequencing errors, coverage overdispersion, and collinearity confound standard expectation-maximization algorithms, resulting in overfitting and spurious "ghost" strains. Here, we introduce zero-inflated latent allocation for strain reconstruction from metagenomes with adaptive sparsity regularization (ZILA-SRM) to overcome this barrier through three innovations. First, we integrate a zero-inflated Poisson mixture model to decouple "structural zeros" (true strain absence) from "sampling zeros" (stochastic dropout), addressing overdispersion in standard Poisson-based tools. Second, we impose a convex adaptive sparsity regularization penalty that leverages biological sparsity priors to shrink noise artifacts dynamically. Third, we implement a graph-theoretic refinement step using maximal clique enumeration to resolve haplotype collinearity. Benchmarking against StrainFinder and MixtureS on 702 synthetic data sets shows that ZILA-SRM achieves a 20% improvement in precision in high-complexity scenarios while maintaining over 80% recall for minor variants at 0.5% abundance. Re-analysis of deep-sequencing data from 195 Mycobacterium tuberculosis clinical samples reveals cryptic low-abundance drug-resistant variants in 12% of patients, including a minor clone carrying the rpoB S450L mutation. Furthermore, application to skin microbiome data sets further reveals a strong negative correlation between dominant Staphylococcus aureus and Staphylococcus epidermidis strains, providing genomic evidence for competitive exclusion. These findings establish ZILA-SRM as a robust tool for resolving strain-level diversity in complex metagenomes.

IMPORTANCE: Understanding microbial communities at the strain level is critical because closely related strains can differ dramatically in traits such as drug resistance, virulence, and ecological interactions. However, resolving individual strains from metagenomic sequencing data remains difficult, especially when strains are highly similar or present at low abundance. As a result, biologically meaningful diversity is often obscured or misinterpreted as noise. In this study, we introduce a new framework that improves the reliability of strain reconstruction from complex metagenomic data. By reducing false-positive strain detection while preserving sensitivity to rare variants, our approach enables more accurate characterization of microbial populations. This improved resolution reveals previously hidden subpopulations in clinical and microbiome datasets, providing clearer insights into microbial evolution, competition, and the emergence of clinically relevant traits such as antibiotic resistance.},
}

@article {pmid42380482,
year = {2026},
author = {Kang, X and He, P and Zhang, H and Lü, F},
title = {Virus-mediated prokaryotic community adaptation dynamics under thermal stress in municipal organic solid waste microbiomes.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10568-3},
pmid = {42380482},
issn = {2399-3642},
abstract = {Temperature influences microbial metabolic activity, which is crucial for biotechnological processes and bioproducts stabilization. However, temperature-driven responses of complex viruses and prokaryotic communities, and the modulatory role of viruses in prokaryotic community within environmental biotechnology systems, remain poorly understood. We developed a continuous thermal stress system with temperature gradients and high-resolution temporal sampling of metagenomics and metatranscriptomics, using municipal organic solid waste as a biological model. An optimized meta-omics pipeline integrating genomic potential and activity was applied to investigate the adaptive dynamics of complex prokaryotic and viral communities. Continuous thermal stress triggered stress responses in paired virus-hosts within the system. Thermal stress exerted distinct effects on temperate and virulent viruses. Viruses formed quasi-symbiotic alliances with their hosts to withstand thermal stress by integrating protein folding genes, stress response, and metabolic function genes, shaping host adaptability under thermal pressure. Equipped with multiple defense and counter-defense systems, viruses accelerated the accumulation of beneficial mutations under thermal stress, enabling them to escape host immunity and intensify competition with prokaryotic communities. This study demonstrates how viruses accelerated both the restructuring and adaptive responses of prokaryotic communities under thermal stress, advancing our understanding of phage-based therapeutic strategies in temperature-variable engineering applications.},
}

@article {pmid42381037,
year = {2026},
author = {Garcia-Castillo, L and Ferrero, G and Blaževitš, O and Francescato, G and Eliass, AT and Cortez, NE and Beltrà, M and Tarallo, S and Pardini, B and Costelli, P and Naccarati, A and Longo, VD and Penna, F},
title = {Fasting-mimicking diet counteracts gut microbial dysbiosis in experimental lynch syndrome.},
journal = {Cancer & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40170-026-00446-1},
pmid = {42381037},
issn = {2049-3002},
abstract = {The development of colorectal cancer (CRC) is largely influenced by hereditary factors, with up to one-third of cases linked to genetic predisposition. In parallel, environmental factors such as diet and intestinal microbiota play a significant role. Lynch syndrome (LS), the most common form of hereditary CRC, is due to mutations in DNA mismatch repair genes. Diet interventions such as calorie restriction (CR) can modify the course of the disease, altering nutrient supply and promoting beneficial microbial populations. Fasting-mimicking diets (FMD) are plant-based CR regimens that showed promise in modulating the gut microbiota and suppressing CRC progression in pre-clinical ectopic cancer models. In this study, Villin-Cre/Msh2-floxed (VCM) mice, modelling LS, were subjected to periodic FMD cycles for 10 months. FMD regimen influenced animal weight in a sexually dimorphic manner, stably reducing animal body weight only in males. Moreover, shotgun metagenomic sequencing revealed that FMD mitigated the dysbiotic longitudinal changes associated with cancer onset, preserving beneficial species, such as Lactobacillus johnsonii, and reducing adverse species, such as Escherichia coli. Metabolic pathway analysis also showed significant differences, with FMD preventing the upregulation of pathways involved in amino acid and nucleotide synthesis, potentially promoting tumour growth. Overall, the findings suggest that periodic FMD may result useful in a multimodal approach for LS management, counteracting gut microbiota alterations.},
}

@article {pmid42381048,
year = {2026},
author = {Porcel Sanchis, D and Pola, M and Engelberts, JP and Guerra-Font, O and Messer, L and Alberola-Mora, I and Escobar Sáez, L and Pérez Gómez, N and Portolés Campo, Á and Valero-Tebar, J and Naya Garmendia, LM and Preciado Barahona, JC and Gil García, R and Arnau, V and McIlroy, SJ and Džunková, M},
title = {Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02456-z},
pmid = {42381048},
issn = {2049-2618},
abstract = {BACKGROUND: Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in distinguishing true symbionts from contaminants. Here, we use metagenomics of museum specimens to uncover symbioses in endangered or difficult-to-collect animals, such as nudibranchs. To date, Doriopsilla is the only nudibranch demonstrated to harbor an uncultured symbiont involved in chemical defense, leaving it unclear whether comparable associations occur in other nudibranchs. We hypothesized that bona fide symbionts should belong to abundant, uncultured lineages consistently present across individuals of the same host taxon collected across space and time.

RESULTS: Using ethanol-preserved specimens archived for up to 30 years, we doubled the number of available nudibranch microbiome datasets and found that dominant uncultured symbionts are rare, with most nudibranchs likely relying on alternative chemical defense mechanisms. An exception were Polycera and Felimare that contained two previously unknown symbionts, Candidatus Polyceribacter and Candidatus Felimaribacter, from distinct uncultured orders that are globally rare in marine metagenomes. These symbionts encode diverse biosynthetic gene clusters exhibiting strain- and species-level microdiversity consistent with metabolites previously reported from their hosts. Their restricted host distribution, phylogenetic distinctiveness, and phylogenetic similarity to symbionts of sponges or corals that are not nudibranch prey, support long-term evolutionary specialization and functional convergence. Fine-scale diversification further suggests host-driven microbial adaptation following symbiosis establishment.

CONCLUSIONS: Overall, this study establishes museomics as a robust framework for symbiosis research and advances understanding of the evolutionary and chemical ecology of host-microbe interactions in rare marine invertebrates. Video Abstract.},
}

@article {pmid42381185,
year = {2026},
author = {Mouanes-Abelin, J and Pomares, C and Montoya, JG and Pondrom, M and Maria, L and Zimmer, AJ and Gomez, CA},
title = {Toxoplasmosis Beyond Transplantation: Diagnostic and Prevention Challenges in a Patient Receiving Targeted Immunomodulators.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70263},
doi = {10.1111/tid.70263},
pmid = {42381185},
issn = {1399-3062},
abstract = {Toxoplasmosis has long been recognized as a serious complication in immunocompromised host, particularly those with advanced HIV/AIDS, hematopoietic stem-cell transplantation (HSCT), solid-organ transplant (SOT), and hematological malignancies. The rapid expansion of targeted immunomodulators, including chimeric antigen receptor T-cell (CAR-T) therapies, monoclonal antibodies, and small-molecule inhibitors, is creating new at-risk populations beyond traditional transplant settings. We present a 9-year-old boy with high-risk B-cell acute lymphoblastic leukemia (B-ALL), who developed prolonged fever and macrophage activation syndrome (MAS). After an extensive unrevealing workup, disseminated acute toxoplasmosis was identified incidentally on bone marrow aspirate via morphologic identification of tachyzoites and confirmed by Toxoplasma gondii PCR. This case exemplifies the emerging threat of toxoplasmosis in non-transplant immunomodulated hosts and supports three core mitigation strategies. First, baseline Toxoplasma IgG and IgM serology should be obtained in all patients initiating targeted immunotherapy, recognizing that B-cell depletion or hypogammaglobulinemia may render IgG unreliable, and that IgM may be falsely negative, delayed, or persistently positive in immunocompromised individuals. Second, targeted PCR from clinically relevant compartments or metagenomic next-generation sequencing when conventional diagnostics is unrevealing should be applied early. Third, prevention requires a bundled approach: baseline screening, patient education for seronegative individuals, and trimethoprim-sulfamethoxazole prophylaxis with or without serial qPCR monitoring for seropositive patients. Toxoplasmosis is no longer a transplant-exclusive concern. As targeted immunomodulators reshape practice across rheumatology, oncology, neurology, and autoimmune disease, infectious diseases specialists must lead efforts to raise cross-specialty awareness, establish guidelines, and build registries to define the true burden of toxoplasmosis in these growing populations.},
}

@article {pmid42381379,
year = {2026},
author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA},
title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690687},
doi = {10.1080/19490976.2026.2690687},
pmid = {42381379},
issn = {1949-0984},
mesh = {Animals ; *Probiotics/administration & dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.},
}

Animals
*Probiotics/administration & dosage
Multiomics
*Saccharomyces boulardii/physiology
Receptors, Aryl Hydrocarbon/metabolism/agonists
Signal Transduction
*Gastrointestinal Microbiome
*Colorectal Neoplasms/immunology/microbiology/metabolism/therapy
Mice
Bacteria/classification/genetics/isolation & purification

@article {pmid42381607,
year = {2026},
author = {Lv, JL and Zhu, MQ and Gao, T and Pan, Y and Yu, HQ and Min, D and Xiong, YJ and Liu, DF},
title = {Profiling Active Low-Abundance Microbes in As/Sb-Contaminated Soils via d-Amino Acid-Based In Situ Labeling.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c07045},
pmid = {42381607},
issn = {1520-5851},
abstract = {Soil microbial communities play a pivotal ecological role in contaminated environments. However, conventional metagenomic approaches struggle to distinguish between "potential function holders" and "in situ metabolically active executors". Here, we employed a method combining fluorescent d-amino acid labeling, fluorescence-activated cell sorting, and metagenomics (FDAA-FACS-Metagenomics) to capture and profile active microbes in complex soils. The secondary addition of As(V) and Sb(V) enhanced the community's reductive activity toward these metalloids, reshaping the active assemblages. Clostridium was markedly enriched, and several low-abundance members were activated as true executors of the reduction process. MAGs recovered via FDAA-FACS revealed an active core community with functional partitioning: some taxa participated directly in As(V)/Sb(V) reduction, while others contributed to community stability through tolerance and metabolic support. Notably, a Desulfitobacteriaceae genome (MAG29) harbored both arrAB and anrAB gene clusters, a complete Wood-Ljungdahl carbon fixation pathway, and nitrogen fixation genes. These genomic features suggest the potential for a multifunctional metabolic lifestyle involving metalloid reduction, carbon fixation, and nitrogen transformation. Such metabolic versatility may enable MAG29 to contribute to coupled carbon-nitrogen cycling and metalloid transformation under contaminated environmental conditions. These findings emphasize the important ecological roles of rare, metabolically active microbes in metalloid transformation and soil ecosystem functioning.},
}

@article {pmid42381665,
year = {2026},
author = {Flach, CF and Berglund, F and Osena, G and Huijbers, PMC and Larsson, DGJ},
title = {Sewage surveillance for assessing clinical antibiotic resistance prevalence: Combining metagenomic and phenotypic data.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101485},
pmid = {42381665},
issn = {2352-7714},
abstract = {Surveillance of antibiotic resistance in clinical isolates is a cornerstone for the management of bacterial infections but is limited in large parts of the world, often due to lack of resources. Sewage surveillance has been proposed as a promising, resource-efficient complement to the traditional surveillance approach based on samples from many individual patients. Both phenotypic data on resistance in sewage isolates and abundance of antibiotic resistance genes in sewage have been shown to correlate with resistance prevalence in clinical isolates. Here, we aimed to directly compare and combine an isolate-based and a gene-based sewage surveillance approach to evaluate what best can reflect clinical resistance rates. The two approaches, based on susceptibility testing of collected E. coli isolates and metagenomic sequencing, respectively, were applied to municipal sewage samples collected in ten European countries. The data generated was related to available data on resistance to aminopenicillins, fluoroquinolones, third generation cephalosporins and aminoglycosides prevalence in clinical E. coli isolates using beta regression models. None of the tested individual predictors were superior across all four investigated classes of antibiotics. For modelling of aminopenicillin resistance, a clearly higher R[2] value was obtained when isolate-based and gene-based data was combined as predictors, also after adjusting for the number of included variables. We conclude that there could be a value of including both isolate- and gene-based sewage data for predictions of resistance rates in clinical isolates, while emphasizing the value of linking predictors to specific species and classes of antibiotics.},
}

@article {pmid42381921,
year = {2026},
author = {Salah, R and AbdElaal, KR and Ghonaim, L and Awe, OI and Moustafa, A},
title = {DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag166},
pmid = {42381921},
issn = {2635-0041},
abstract = {MOTIVATION: Accurate species-level classification of prokaryotic 16S rRNA sequences remains difficult: existing tools rely on exact alignment, k-mer heuristics, or phylogenetic placement and are limited by incomplete reference databases. Deep learning approaches in microbial genomics have focused largely on whole-genome metagenomics, leaving 16S taxonomy under-supported.

RESULTS: We present DeepTaxa, a hybrid CNN-BERT framework that pairs a multiscale CNN with a transformer trained from scratch on the DNABERT-2 BPE vocabulary, producing parallel rank-specific predictions across the seven Linnean ranks. On the Greengenes2 2024.09 test set, DeepTaxa achieves species-level accuracy of 92.96% and F1 of 0.9212 (3-seed mean; cross-seed standard deviation ≤ 0.0008 F1 at every rank), with F1 above 0.99 from domain through class and a species-level expected calibration error of 0.0242. DeepTaxa exceeds DADA2 (90.05%) and QIIME 2 (85.01%) at the species rank on the same held-out test set, with larger gains over the k-mer-based classifiers SINTAX and Kraken 2. Performance degrades smoothly with decreasing training-set similarity (species F1 from 0.95 to 0.45), and a dedicated V3-V4 amplicon checkpoint reaches 87.55% species accuracy from an approximately 420 bp window.

Source code, trained checkpoints for full-length 16S and V3-V4 amplicons, curated datasets, and reproducible workflows are publicly available at github.com/systems-genomics-lab/deeptaxa and huggingface.co/systems-genomics-lab/deeptaxa.},
}

@article {pmid42382111,
year = {2026},
author = {Sachula, W and Huimin, L and Yaxing, Z and Ding, Y and Shangxiong, Z and Shengli, L and Haizhou, S and Chunhua, Z},
title = {An integrative multi-omics investigation into the influence of forage type on the volatile flavor profile of Ujumqin sheep mutton.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1856240},
pmid = {42382111},
issn = {2297-1769},
abstract = {China ranks among the leading producers and consumers of mutton globally and the development of nutritional strategies to improve meat quality and sensory attributes. This study investigated the effect of three high-quality forages, i.e., alfalfa hay (ALFA), Leymus chinensis hay (LEYM) and oat hay (OATS) compared to corn stalks-based control diet (CORN) on rumen microbiota, metabolomics profiles, and muscle volatile flavor compounds in lambs through a multi-omics integration approach. Forty male lambs were randomly allocated into four dietary groups (n = 10/group) and fed a concentrated forage supplement for 91 days. From each group, six lambs (n = 6/group; totla 24) were slaughtered. Rumen fluid and longissimus dorsi muscle samples were collected for metagenomics, untargeted metabolomics, and volatile flavor analysis. Differential microbial taxa were identified using LEfSe analysis, followed by integrated Pearson correlation and MetoOrigin analysis to link microbiota, metabolites, and metabolic pathways. Associations with muscle volatile flavor compounds were also assessed. LEfSe analysis identified 4, 3, and 7 differentially abundant rumen microbial taxa in the ALFA, LEYM and OATS groups, respectively, compared to CORN. Integrated analysis showed these taxa correlated with 4, 9 and 11 rumen metabolites via 3, 11 and 7 microbial or host-microbial co-metabolic routes, respectively. These metabolic changes were strongly associated to alterations in muscle volatile flavor compounds. Particularly, the ALFA diet increased volatile compounds associated with fresh, grassy, floral, and citrus-like odors reduced mutton-related Pyrazine (2,5-dimethyl-). The LEYM diet reduced Pentaborane(9) and Pyrazine, which are associated with undesirable mutton like odors. The OATS diet increased 2-Nonanone and Phenylethyl Alcohol (fruity and floral smells), while suppressing n-Decanoic acid and n-Octanoic acid (associated with characteristic mutton aroma). These results showed that high-quality forages improve the mutton flavor by regulating the rumen micro-ecological network and associated metabolic pathways along the forage-microbiota-metabolites-muscle flavor axis. These findings provide a theoretical foundation for precise nutritional interventions aimed at enhancing meat quality in lambs.},
}

@article {pmid42382141,
year = {2026},
author = {Chigwada, AD and Tekere, M},
title = {Archaea-driven bioremediation of polyolefins and polyesters in extreme environments.},
journal = {Biodesign research},
volume = {8},
number = {3},
pages = {100092},
pmid = {42382141},
issn = {2693-1257},
abstract = {Global plastic production surpassed 436 million metric tonnes in 2023, with polyolefins, polyethylene and polypropylene, and polyesters, polyethylene terephthalate and polybutylene adipate terephthalate dominating the persistent fraction. In extreme environments, these recalcitrant polymers accumulate rapidly: hadal-trench sediments contain microplastic abundances of 71.1 items per kilogram dry weight, while bottom waters reach 2.06-13.51 particles per litre. Abiotic degradation is severely limited by hydrostatic pressure, hypersalinity, low temperature, and anaerobiosis. Although bacterial and fungal pathways have received primary attention, archaea adapted to polyextreme conditions represent an underexplored resource. Landmark discoveries include PET46, a lid-containing feruloyl esterase from uncultured Candidatus Bathyarchaeota in Guaymas Basin deep-sea sediments that hydrolyses semi-crystalline polyethylene terephthalate powder at rates comparable to established bacterial PETases while outperforming them on oligomers. Subsequent metagenomic prospecting identified GuaPA, a distinct Bathyarchaeia-derived PETase capable of film depolymerisation. Deep-sea plastispheres, hypersaline basins, and extraterrestrial analog sites further reveal archaeal colonisation and metabolic versatility. This review synthesises metagenomic, enzymatic, and community-level evidence, critically evaluates archaeal advantages relative to bacteria and fungi, addresses persistent gaps, including limited polyolefin mineralisation and cultivation bias, and outlines priorities for enzyme engineering and consortia design. The work advances sustainable bioremediation strategies aligned with climate-action goals and circular-economy frameworks in extreme and space environments.},
}

@article {pmid42382346,
year = {2026},
author = {He, B and Xiao, Z and Zou, L and Wei, J and Xiang, Z and Sang, F and Guo, X},
title = {Unveiling the unique gut microbial signatures in colorectal adenomas: establishment and validation of a cross-kingdom microbiome predictive model.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1854806},
pmid = {42382346},
issn = {1664-302X},
abstract = {BACKGROUND: Colorectal adenoma (CA), the main precancerous lesion of colorectal cancer (CRC), originates in approximately 85-90% of CRC cases. With increasing demands for early diagnosis and treatment, gut microbiome research has become a forefront area. While numerous studies have shown that gut bacteria are closely related to the development of colorectal adenomas and cancer, research on viruses, archaea, and fungi is limited.

METHODS: From January 2019 to January 2024, this study collected 296 fecal samples from multiple centers and performed metagenomic analysis using shotgun sequencing. Principal coordinate analysis (PCoA) was conducted based on Bray-Curtis distance at the species level, α-diversity was calculated, and LEfSe analysis identified differential microorganisms. A random forest model was developed to distinguish adenoma patients from healthy individuals, with performance evaluated through internal validation using Bootstrap sampling and external validation with an independent cohort.

FINDINGS: Significant differences in the relative abundance of certain bacteria (e.g., Phocaeicola_vulgatus and Prevotella_copri), fungi (Candida_albicans), archaea (Methanobrevibacter_oralis), and viruses (Streptococcus satellite phage Javan301) were observed in adenoma patients. Spearman correlation analysis revealed complex network relationships among these microorganisms. The prediction model achieved a mean AUC of 0.80 ± 0.05 and an external validation AUC of 0.75, demonstrating stability and generalizability.

CONCLUSION: This study shows significant cross-kingdom microbial signatures in colorectal adenoma patients, providing potential for developing new preventive and therapeutic methods. The predictive model, based on these differential microorganisms, exhibits robust and promising classification performance, offering potential for early adenoma detection.},
}

@article {pmid42382358,
year = {2026},
author = {Mengjia, C and Bujiang, W and Honghui, C and Qiying, H and Haojun, S},
title = {Biliary tract microbes and common bile duct stones: current status and prospects.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818256},
pmid = {42382358},
issn = {1664-302X},
abstract = {Common bile duct stones is a common digestive system disease, and about 5%-30% of patients with cholelithiasis are complicated with common bile duct stones. It poses significant challenges to clinical diagnosis and treatment. Although its occurrence is related to traditional factors such as abnormal bile composition and biliary dynamics disorders, the exact pathogenesis has not been fully clarified. In recent years, with the rapid development of high-throughput sequencing and metagenomics and other microbiome technologies, researchers have begun to pay attention to the role of biliary microbiota in the formation of common bile duct stones. More and more evidence indicates that the biliary tract microbes may has been associated with the occurrence and development of stones. This review firstly examines the literature implicating between biliary microorganisms and different types of common bile duct stones. We discuss the various mechanisms of action of biliary tract microorganisms in the occurrence of common bile duct stones. We also evaluated the specific value of microbial markers for diagnostic typing and prediction of recurrence.},
}

@article {pmid42382773,
year = {2026},
author = {Zhang, D and Song, Y and Bai, Y and Yan, J and Shen, R},
title = {Autoimmune GFAP astrocytopathy with eosinophils on cerebrospinal fluid cytology and isolated spinal cord lesions on MRI: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1865920},
pmid = {42382773},
issn = {1664-3224},
mesh = {Humans ; Female ; Adult ; *Glial Fibrillary Acidic Protein/immunology ; Magnetic Resonance Imaging ; *Astrocytes/immunology/pathology ; *Spinal Cord/pathology/diagnostic imaging/immunology ; *Eosinophils/immunology/pathology ; Biomarkers ; Autoantibodies/immunology ; },
abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy is an autoimmune inflammatory disorder of the central nervous system associated with GFAP-IgG. It most commonly presents as meningoencephalitis, myelitis, or meningoencephalomyelitis. Although MRI abnormalities in the brain and spinal cord are common, isolated spinal cord lesions without corresponding brain MRI abnormalities are uncommon and may pose a diagnostic challenge. Eosinophils identified on cerebrospinal fluid cytology have rarely been reported in this disorder.

CASE PRESENTATION: A 31-year-old woman presented with fever, headache, urinary retention, and meningeal irritation signs. Despite these findings, brain magnetic resonance imaging (MRI) was unremarkable, whereas spinal MRI revealed discontinuous patchy long-segment intramedullary lesions in the thoracic cord. Cerebrospinal fluid (CSF) analysis showed elevated opening pressure, pleocytosis, increased protein, and 10% eosinophils on cytological examination. Infectious studies, including CSF culture and metagenomic next-generation sequencing, were negative. Serum and CSF antibodies against aquaporin-4, myelin oligodendrocyte glycoprotein, and myelin basic protein were negative, whereas CSF GFAP-IgG was positive at a titer of 1:32, while serum GFAP-IgG was negative. Following high-dose intravenous methylprednisolone and an oral prednisone taper, the patient showed marked clinical, CSF, and radiological improvement, with complete resolution of thoracic cord lesions on follow-up MRI.

CONCLUSION: Isolated spinal cord lesions on MRI may represent an important clue to autoimmune GFAP astrocytopathy and should prompt consideration of this diagnosis even in the absence of brain MRI abnormalities. The presence of eosinophils on cerebrospinal fluid cytology may further suggest a distinct inflammatory profile and offer insight into the pathophysiology of the disease.},
}

Humans
Female
Adult
*Glial Fibrillary Acidic Protein/immunology
Magnetic Resonance Imaging
*Astrocytes/immunology/pathology
*Spinal Cord/pathology/diagnostic imaging/immunology
*Eosinophils/immunology/pathology
Biomarkers
Autoantibodies/immunology

@article {pmid42382960,
year = {2026},
author = {Zhang, WJ and Yang, Z and She, JQ and Wu, HL and Xia, ZY and Zhang, D and Suo, LG and Pan, Z and Zhang, Y and Wang, HZ and Hong, J and Zhang, C},
title = {Metagenomic analysis of ocular microbiome in aqueous humor from myopia, cataract, primary open angle glaucoma and Posner-Schlossman syndrome.},
journal = {International journal of ophthalmology},
volume = {19},
number = {7},
pages = {1235-1248},
pmid = {42382960},
issn = {2222-3959},
abstract = {AIM: To characterize the composition and functional features of the aqueous humor microbiome in common ocular diseases, including myopia, cataract, primary open angle glaucoma (POAG), and Posner-Schlossman syndrome (PSS).

METHODS: We performed metagenomic sequencing on 176 aqueous humor samples from patients with cataract (n=37), POAG (n=66), PSS (n=35), and myopia patients (n=38, as controls). Taxonomic profiling, functional annotation, and diversity analyses were conducted to characterize microbial communities, with adjustments for age and gender where appropriate. Associations between microbial features and clinical parameters were evaluated using correlation analyses.

RESULTS: We identified 6635 bacterial, 141 archaeal, 96 eukaryotic, and 108 viral operational taxonomic units (OTUs) in the aqueous humor. The microbiome was dominated by Actinomycetota and Pseudomonadota at the phylum level. Compared to myopia controls, POAG and PSS patients showed significantly reduced alpha diversity after age adjustment (P<0.05), whereas cataract patients showed no significant difference. Additionally, we identified disease-specific microbial signatures including enrichment of Cytomegalovirus (CMV) in PSS. Functional analysis revealed enrichment of distinct metabolic pathways. Finally, correlations were observed between microbiota/pathway abundance and clinical phenotype, though none remained significant after multiple testing correction.

CONCLUSION: This study provides a preliminary characterization of the aqueous humor microbiome in patients with POAG, PSS, cataract, and myopia controls. The identified microbial signatures and functional pathways offer new insights into potential microbiome-mediated mechanisms in ocular pathophysiology and may inform future diagnostic and therapeutic strategies.},
}

@article {pmid42383698,
year = {2026},
author = {Briggs, FB and Litwiler, J and Montini, F and Fereidan Esfahani, M and Sagen, J and McCauley, JL and Nelson, F and Gregory, S and Brambilla, R and Trapl, ES and Cooke Bailey, JN and Schwerdtfeger, LA and Cox, L and Weiner, H and Tobin, WO},
title = {Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261454207},
doi = {10.1177/13524585261454207},
pmid = {42383698},
issn = {1477-0970},
abstract = {BACKGROUND: Smokers with multiple sclerosis (MS) experience worse disease, yet underlying mechanisms remain unknown. Smoking disrupts bile acid and tryptophan metabolism in non-MS populations; both pathways involve host-microbiome co-metabolism and have been linked to MS.

OBJECTIVE: Determine whether smoking perturbs these metabolic pathways in MS and whether such alterations statistically mediate smoking's effect on MS severity.

METHODS: We analyzed serum bile acid, tryptophan, and tobacco-related metabolites across four independent MS cohorts (N = 266) using discovery-replication analyses. Mixed-effects regression assessed replicating associations with current smoking and nicotine exposure. Mediation analyses tested if replicating metabolites were potential mediators between smoking and MS severity. Hypothesis-generating metagenomic analyses explored smoking-associated gut-microbial shifts and metabolite correlations.

RESULTS: Current smokers and nicotine-exposed MS subjects had reductions in bile acids and tryptophan metabolites, notably indolepropionate, a neuroprotective, anti-inflammatory gut-microbial metabolite. Lower indolepropionate statistically mediated ~20% of smoking's adverse effect on MS severity. Metagenomic analyses identified potential smoking-enriched MS-linked taxa, and that indolepropionate broadly co-occurs with microbial networks (e.g. Lachnoclostridium appeared inversely associated with indolepropionate in smokers with MS).

CONCLUSION: Tobacco exposure disrupts host-microbiome tryptophan and bile acid metabolism in persons with multiple sclerosis, with indolepropionate depletion partially mediating disease severity, highlighting a potential mechanistic pathway warranting further investigation in MS smokers.},
}

@article {pmid42384485,
year = {2026},
author = {Crouch, AL and Rambeau, M and Li-Pook-Than, J and Snyder, MP and Henderson, JA and Yracheta, JM and Anderson, MZ},
title = {The gut microbiome of a Northern Plains tribe is in transition between global Indigenous and industrialized populations.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {116334},
doi = {10.1016/j.celrep.2025.116334},
pmid = {42384485},
issn = {2211-1247},
abstract = {The human gut is shaped by environmental factors, producing distinct microbial communities. Indigenous individuals practicing traditional lifestyles often harbor more diverse microbiota, with taxa often absent in industrialized people. However, little engagement has occurred with American Indian communities in North America who experienced forced relocation and dietary programs during colonization. Here, shotgun metagenomics profiled the gut microbiome of people from a Northern Plains tribe (NPT) reservation in comparison to 12 global populations engaged in traditional, agrarian, or industrialized lifestyles. Analysis of the 532 samples revealed that the NPT microbiota exhibited greater bacterial and archaeal diversity than industrialized populations but reduced diversity compared to global traditional and agrarian populations. Relative to the general United States population, NPT microbiomes encoded more virulence factor and microbial defense genes and fewer CAZyme-encoding genes. These findings suggest that the NPT gut microbiome is in transition between lifestyles associated with global Indigenous and industrialized populations.},
}

@article {pmid42384916,
year = {2026},
author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA},
title = {Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag422},
pmid = {42384916},
issn = {1367-4811},
abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13,897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on January 04, 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42384962,
year = {2026},
author = {Narayanan, AK and Philosof, A and Murali, R and Connon, SA and Wegener, G and Orphan, VJ},
title = {Viral communities from long-term anaerobic alkane-oxidizing enrichments encode predicted cell surface adhesion functions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag172},
pmid = {42384962},
issn = {1751-7370},
abstract = {The anaerobic oxidation of methane and higher C2+ alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free enrichments of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.},
}

@article {pmid42385223,
year = {2026},
author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A},
title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70359},
doi = {10.1002/mbo3.70359},
pmid = {42385223},
issn = {2045-8827},
mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; },
abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.},
}

*Rivers/microbiology/chemistry
*Metagenomics
Seasons
Bangladesh
*Bacteria/genetics/classification/drug effects/isolation & purification
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Metagenome
Water Quality
Shotgun Sequencing

@article {pmid42385456,
year = {2026},
author = {Hodžić, A and Cizek, V and Kunert, M and Berry, D and Collingro, A},
title = {Qualitative profiling of the gut-specific chlamydial population in Ixodes ricinus ticks.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {4},
pages = {102679},
doi = {10.1016/j.ttbdis.2026.102679},
pmid = {42385456},
issn = {1877-9603},
abstract = {Members of the phylum Chlamydiota are obligate intracellular bacteria increasingly recognized across a wide range of arthropod hosts, including ticks. In this study, we investigated the diversity and distribution of chlamydiae in Ixodes ricinus ticks and their potential association with Lyme borreliosis spirochetes. A total of 250 questing nymphal and female I. ricinus ticks were collected from three recreational sites in Vienna, Austria. Individual tick guts were screened for chlamydiae using pan-Chlamydiota PCR assays targeting the 16S rRNA gene, followed by sequencing for taxonomic identification. The presence and abundance of Borrelia burgdorferi sensu lato were quantified by specific qPCR to evaluate potential co-occurrence patterns. Chlamydiota DNA was detected in ticks from all investigated areas, with prevalence varying according to geography and developmental stage. Phylogenetic analyzes revealed high chlamydial diversity within the gut microbiome, predominantly comprising members of the metagenomic family MCF-D, followed by Parachlamydiaceae, Endochlamydiaceae, and Parasimkaniaceae. A positive, albeit not statistically significant, association between Chlamydiota and Borrelia was also observed. These findings indicate that the I. ricinus gut microbiome harbours a diverse assemblage of chlamydiae, suggesting potential ecological and functional relevance. Overall, our study highlights the importance of tissue-specific, single-tick analyzes for elucidating microbiome complexity and advances current understanding of Chlamydiota diversity in the tick vector. Further experimental and multi-omics studies are warranted to elucidate the biological roles of these bacteria in tick physiology and pathogen infection dynamics.},
}

@article {pmid42385542,
year = {2026},
author = {Zhong, X and Sun, Z and Wu, H and Li, E and Fang, G},
title = {Response of soil nitrogen-cycling functional genes and their associations to nitrogen enrichment in a typical subtropical estuary (Min River), Southeast China.},
journal = {Marine pollution bulletin},
volume = {232},
number = {},
pages = {120078},
doi = {10.1016/j.marpolbul.2026.120078},
pmid = {42385542},
issn = {1879-3363},
abstract = {Soil N-cycling functional genes are easily modified by environmental changes, but insufficient information is available regarding the response of their elaborate associations to nitrogen (N) enrichment in estuarine marsh ecosystem. In this study, a field experiment with four N enrichment levels (NN, 0.0 g N m[-2] yr[-1]; NL, 37.5 g N m[-2] yr[-1]; NM, 50.0 g N m[-2] yr[-1]; and NH, 100.0 g N m[-2] yr[-1]) was conducted in a typical Cyperus malaccensis marsh in the Min River estuary of southeastern China. After 28 and 40 months of sustained N additions (represented by T28 and T40 periods, respectively), the potential impacts of N enrichment on soil N-cycling functional genes and their associations were investigated by metagenomic sequencing. Results showed that although the composition of functional microbial communities showed causality with N enrichment levels, its variation was primarily driven by N-enriched duration as evidenced by the higher interpretability (64.7%). With prolonged the experiment, the diversity of soil N-cycling microbial communities dropped markedly while their richness showed no statistically significant alteration. Within each sampling period, the relative abundances of functional genes involved in organic N metabolism (ONM, glnB, GDH2 and GLT1), assimilatory nitrate reduction (ANRA, narB, nirA, NR and NIT-6), denitrification (nirS, norC and napB), N fixation (nifK/D, vnfH/K/G and anfG), dissimilatory nitrate reduction (DNRA, nrfA and nirB/D), N transport (nrtC/B) and nitrification (pmoB/C-amoB/C) significantly increased with increasing N additions. Compared with the T28 period, the relative abundances of genes involved in ONM (GDH2 and K00261_gdhA), denitrification (narI and nirS), N fixation (nifD/H and vnf/H/K) and N transport (NRT2 and nrtA/C) elevated significantly at T40 period, while those participated in DNRA (nrfH), nitrification (hao) and anammox (hzsB/C) declined markedly. Under N-enriched conditions, the network complexity of functional genes displayed decreases in the LN and MN treatments, followed by a significant increase in the HN treatment. With prolonged the experiment, the positive correlations among functional genes were weakened and the succession of functional microbial communities was driven in a more functionally specialized direction by a few dominant species. This paper found that sustained N enrichment drove the phased reconstruction of gene networks with a continuous weakening of positive associations among functional genes. The findings can guide the policymaking of targeted N load control and estuarine marsh conservation.},
}

@article {pmid42385547,
year = {2026},
author = {Paietta, EN and Lefkowitz, EJ and Van Der Pol, WJ and Hendrickson, RC and Johnston, RA and Randrianarisoa, SF and Kraberger, S and Razanamahenina, TT and Ramboninarimalala, A and Raherinirina, TG and Raveloson, L and Finley, NL and Scotch, M and Baitchman, E and Yoder, AD and Varsani, A},
title = {Divergent poxvirus identified in a non-native black rat from Madagascar.},
journal = {Virology},
volume = {623},
number = {},
pages = {111021},
doi = {10.1016/j.virol.2026.111021},
pmid = {42385547},
issn = {1096-0341},
abstract = {Non-native rodents serve as bridges between anthropogenic and natural landscapes. They have expanded across the planet alongside humans while bringing competition, predation, and pathogens, such as poxviruses, to naïve ecosystems. Although rodents serve as reservoirs for multiple zoonotic poxviruses, limited research has focused on rodents for identification of unknown poxviruses. Here, we characterized a divergent metagenome-assembled poxvirus, madamurpox virus, from the oral swab of a black rat in southeastern Madagascar. While madamurpox virus shares a phylogenetic relationship with human-infecting molluscum contagiosum virus and bat-associated Rousettus poxvirus, madamurpox virus presents extensive genetic variation and represents a putative new species and genus in the Chordopoxvirinae subfamily. Further, although madamurpox virus has a similar genome organization to molluscum contagiosum virus and Rousettus poxvirus, madamurpox virus lacks key immune modulators seen in molluscum contagiosum virus. Our findings highlight that substantial unexplored poxvirus diversity likely exists in rodents, with globally distributed, non-native rodent populations of increased interest.},
}

@article {pmid42385579,
year = {2026},
author = {Han, YH and Zou, MZ and Wei, XM and Chen, X and Tong, LC and Zhang, Y and Zhang, H and Chen, Z},
title = {Mining rare earth elements with ammonium sulfate as a leaching agent provokes a significant perturbation in soil microbial function.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142856},
doi = {10.1016/j.jhazmat.2026.142856},
pmid = {42385579},
issn = {1873-3336},
abstract = {The mining of rare earth elements (REEs), which are critical for modern technologies, frequently leads to severe soil degradation, particularly through ammonium sulfate-based in-situ leaching. This study provided a comprehensive metagenomic assessment of how REEs mining reshapes soil ecosystems. We analyzed paired samples from a mined site and an adjacent unmined control in a typical ion-adsorption REEs deposit region in China. Mining activity was associated with profound alterations in soil geochemical profiles. While soil pH decreased from 4.72 to 4.42, total carbon (TC) declined by over two-thirds (from 1.05 to 0.31 g kg[-1]), and total nitrogen (TN) exhibited a significant 22% increase (from 215.60 to 263.26 mg kg[-1]). Regarding REEs, mining caused an approximately 53% reduction in their total content (from 475.83 to 218.82 mg kg[-1]) and a restructured composition (cerium from 28% to 75%, lanthanum from 23% to 5.4%, and neodymium from 18% to 4.8%). Metagenomic analysis revealed that microbial diversity was significantly lower in the post-mining area compared to the unmined control. Bacterial communities shifted from a balanced composition to an oligotroph-dominated state, with p_Acidobacteriota increasing to 41% and the copiotrophic p_Actinomycetota declining from 23% to 10%. Fungal communities transitioned from a p_Basidiomycota-rich (31%) symbiotic state to an p_Ascomycota-dominated (77%), saprotrophic condition. Mantel tests and path analysis identified the mining-induced deterioration of soil physicochemical and nutrient properties (especially pH, TC, and Mg) as a key factor associated with microbial restructuring, rather than REEs depletion itself. Functionally, Kyoto Encyclopedia of Genes and Genomes annotation revealed a widespread suppression of metabolic pathways critical for ecosystem functioning, including C fixation, N metabolism, energy production, and environmental adaptation. The identification of key microbial taxa (e.g., declining p_Actinomycetota and p_Chloroflexota) as biomarkers for soil health, and their strong linkage to decreased C and N cycling functions, offers potential genomic targets for monitoring and guiding the recovery of soil ecosystem services in post-mining landscapes.},
}

@article {pmid42385824,
year = {2026},
author = {Zhang, W and Ran, G and Li, P and Ke, J and Ji, S and Gao, Y and Bian, R and Wang, Z},
title = {Multi-scale analysis of patterns, risks, and mechanisms of edaphic antibiotic resistance genes on the Qinghai-Tibet Plateau: Integrating regional and national perspectives.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128686},
doi = {10.1016/j.envpol.2026.128686},
pmid = {42385824},
issn = {1873-6424},
abstract = {The Qinghai-Tibet Plateau (QTP), acclaimed as the "Third Pole"," is an ecologically vulnerable region pivotal to global biogeochemical cycles. However, our knowledge of edaphic antibiotic resistance genes (ARGs) across its heterogeneous land-use regimes remains limited. Here, we systematically characterized the patterns, potential risks, and driving mechanisms of ARGs by analyzing soil samples encompassing anthropogenically disturbed soils (ADS) and pristine alpine meadows on the QTP, coupled with comparative analysis of national cropland metagenomic datasets. Metagenomic analysis identified 897 ARG subtypes, with ADS harboring significantly higher ARG abundance, diversity, and horizontal transfer potential compared to pristine alpine meadows. Source tracking analysis confirmed yak feces as the predominant source of soil ARGs, contributing 31.35%-38.33% across different land-use types. At the national scale, QTP croplands exhibited a distinct resistome profile containing 158 unique ARG subtypes, and the abundance of ARG-carrying pathogens was 1.4-fold higher than the national average, with human pathogens being the most prevalent. Non-dominant ARGs were pinpointed as pivotal biomarkers for differentiating land-use types and geographic regions. Rare microorganisms were critical drivers shaping ARG distribution, whereas mobile genetic elements and virulence factors augmented ARG transmissibility and pathogenicity. This study presents the first comprehensive characterization of the soil resistome on the QTP, highlighting that anthropogenic activities have triggered non-negligible ARG contamination in this ecologically vulnerable ecosystem. These findings underscore the urgency of implementing "One Health" strategies to mitigate the spread of antibiotic resistance in high-altitude regions, with far-reaching implications for global public health and ecological security.},
}

@article {pmid42385828,
year = {2026},
author = {Yin, Z and Zhang, Y and Song, S and Li, C and Shi, J and Yin, Y and Cai, Y},
title = {Co-contamination of antimony and arsenic reshapes resistome, virulome, and virome in poultry feces near the world's largest antimony mine.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128684},
doi = {10.1016/j.envpol.2026.128684},
pmid = {42385828},
issn = {1873-6424},
abstract = {The poultry microbiome and virome are integral to the One Health framework, with significant implications for ecosystem and human health, but their responses to arsenic (As) and antimony (Sb) exposure remain overlooked. Here, we conducted a comprehensive metagenomic characterization of the metal resistome, antibiotic resistome, virulome, and virome in poultry feces collected from the world's largest antimony mining area. We found that As and Sb co-contamination was significantly associated with elevated resistance and virulence. The abundance of metal resistance genes (MRGs) was 1.8-fold higher in the high-Sb group than in the low-Sb group (15,022.27 ± 3,538.47 vs 8,370.24 ± 4,502.07 TPM, P = 0.008), with arsR, arsB, and arsC dominating the MRG profiles. Similarly, antibiotic resistance genes (ARGs) abundance was 1.6-fold higher in the high-Sb group than in the low-Sb group (7,251.00 ± 1,844.34 vs 4,478.95 ± 2,302.69 TPM, P = 0.026), with multidrug resistance genes being the predominant class (8.09% - 58.48%). Metagenome-assembled genomes (MAGs) analysis and contig analysis suggest co-selection of MRGs, ARGs, and virulence factor genes (VFGs). We identified 100,819 viral contigs clustered into 91,004 viral operational taxonomic units (vOTUs), revealing a highly diverse viral community. Members of Enterobacteriaceae (e.g., Klebsiella) and Enterococcaceae (i.e., Enterococcus) were identified as key drivers mediating resistance and virulence dynamics, acting as resistome supercarriers, opportunistic pathogens, and viral hosts. These findings suggest that As-Sb co-contamination is an overlooked but potentially important driver of poultry antimicrobial resistance and pathogenicity, and highlight potential ecological and public health risks in mining-impacted poultry-associated environments.},
}

@article {pmid42385829,
year = {2026},
author = {Wei, C and Yun, CW and Li, XQ and Lai, LH and Gao, JP and Tang, MP and Zhou, CN and Zhang, YL and Xu, HJ},
title = {Regulatory mechanisms of N2O emissions from latosolic red soil by different ecotypes of earthworms: insights from microbial diversity and metagenomic analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128682},
doi = {10.1016/j.envpol.2026.128682},
pmid = {42385829},
issn = {1873-6424},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas pollutant, but the mechanisms by which different earthworm ecotypes regulate N2O emissions in latosolic red soils remain poorly understood. To address this issue, a microcosm incubation experiment was conducted using three earthworm ecological categories, epigeic Eisenia foetida, endogeic Pontoscolex corethrurus, and anecic Pheretima guillelmi, to investigate their effects on N2O emissions, soil nitrogen-cycling processes, microbial communities, and nitrogen-cycling functional genes in latosolic red soil. The results showed that the three earthworm ecological categories differentially affected N2O emissions by altering soil physicochemical properties, regulating related enzyme activities, and promoting inorganic nitrogen transformation, with endogeic and anecic earthworms exerting stronger stimulatory effects. Earthworm activity reshaped microbial community interactions and altered the relative abundances of key functional genes involved in nitrification, denitrification, assimilatory nitrate reduction, and dissimilatory nitrate reduction to ammonium (DNRA). Integrated analysis indicated that earthworms may jointly influence soil nitrogen transformation and N2O emissions by modifying the soil environment, promoting soil nitrogen transformation processes, and regulating microbial community structure and the relative abundance of nitrogen-cycling functional genes. Due to differences in activity patterns and disturbance intensity, the effects of different earthworm ecological categories varied substantially, with cumulative N2O emissions generally following the order: anecic > endogeic > epigeic.},
}

@article {pmid42385873,
year = {2026},
author = {Chen, P and Si, H and Wang, J and Xie, J and Gu, C and Ma, W and Liu, X and Sun, Q},
title = {Metagenomic insights into microbial responses to soil amendments and oat cultivar identity in saline-alkali soils.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125147},
doi = {10.1016/j.envres.2026.125147},
pmid = {42385873},
issn = {1096-0953},
abstract = {Host cultivar identity can influence rhizosphere microbiomes, yet its relative importance compared with soil amendment regime in saline-alkali farmland remains insufficiently resolved. Here, we compared how two oat (Avena sativa) cultivars shape soil microbial communities and functions under contrasting amendment regimes. In a field experiment, two oat cultivars, Tianyan 60 (TY60) and Musite (MST), were grown under five treatments: control, bacterial agent, organic manure, silica fume, and their combination. Soil physicochemical properties, enzyme activities, and metagenomic sequencing were used to characterize microbial taxonomic and functional profiles. Amendment regimes strongly altered soil nutrient and enzyme variables, whereas cultivar identity explained more variation than amendment regime in microbial community structure and beta diversity under the tested field conditions. Taxonomically, TY60 showed stronger amendment-associated reassembly, including enrichment of Bacteroidota, Pseudomonadota, and Ascomycota under selected treatments, whereas MST retained a comparatively more stable higher-rank backbone. Network analysis further indicated cultivar-associated differences in microbial community organization. Functionally, organic manure and the combination treatments (MIX3) produced the broadest shifts in C, N, P, and S cycling gene modules, particularly in TY60-associated soils. Null-model analyses showed that stochastic assembly dominated overall, but the dominant stochastic component differed among kingdoms, with bacteria mainly governed by drift, archaea by homogeneous dispersal, and fungi by a more balanced contribution of the drift and homogeneous dispersal. These results indicate that cultivar identity played a stronger role than amendment regime in shaping amendment-associated microbiome and functional shifts in this two-cultivar comparison, highlighting the potential value of combining cultivar choice with organic-microbial inputs to improve rhizosphere multifunctionality in saline-alkali agroecosystems.},
}

@article {pmid42385907,
year = {2026},
author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Chen, L and Zhang, X and Zhang, Y},
title = {Exogenous S[0] enhances the degradation of lignocellulose residues in anaerobic digestion: by driving the coenzyme A-dependent NAD(P)H sulforeductase pathway and persulfidation modification of cellulase.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135285},
doi = {10.1016/j.biortech.2026.135285},
pmid = {42385907},
issn = {1873-2976},
abstract = {Lignocellulose residues in food wastes are encapsulated by polysaccharide matrices, forming a "biomass barrier" that hinders their degradation during anaerobic digestion. This study demonstrates that elemental sulfur (S[0]) can serve as a low-cost in-situ enhancer, effectively breaking down this biomass barrier and significantly improving the degradation efficiency and CH4 yield of lignocellulose residues. Anaerobic fermentation experiment showed that the addition of S[0] increased cellulose and hemicellulose removal efficiencies to 94.89% and 96.78%, respectively, while VFAs concentration increased by 54.72%. Methanogenesis experiment further revealed that the optimal S[0] dosage (20 mg/L) achieved a CH4 yield of 378 mL CH4/g VS, which was 1.72 times that of the control. Microbial community analysis indicated a significant enrichment of cellulolytic bacteria, sulfur-reducing bacteria, and syntrophic acidogenic microorganisms. Metagenomic analysis further revealed that S[0] induced the sulfur reduction pathway mediated by Coenzyme A-dependent NAD(P)H Sulfide Oxidoreductase (NSR), with NSR abundance significantly increasing by 74.28%. This pathway can regenerate NAD[+] and maintain redox balance, thereby promoting the degradation of lignocellulose substrates. In addition, the sulfide generated by S[0] reduction stimulated S-persulfidation modification of cellulase active site, converting -SH to the more polar -SSH, enhancing the affinity between cellulases and lignocellulose substrates. This study demonstrates that S[0] can serve as a low-cost in-situ enhancer, effectively breaking down the biomass barrier in food wastes lignocellulosic residues and significantly improving degradation efficiency and CH4 yield.},
}

@article {pmid42374043,
year = {2026},
author = {Wu, J and Zhang, B and Ma, Y and Kuang, C and Hong, Y},
title = {Recovery of 178 metagenome-assembled genomes from sediments in subterranean estuary.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07716-z},
pmid = {42374043},
issn = {2052-4463},
support = {42476141//National Natural Science Foundation of China/ ; 42276130//National Natural Science Foundation of China/ ; 2025001//Open Fund of Hainan Xisha Marine Environment National Observation and Research Station/ ; 2024312281//Graduate Innovative Research Grant Program of Guangzhou Education Bureau/ ; 2023B1515120029//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A03J3103//Science and Technology Projects in Guangzhou/ ; },
abstract = {Subterranean estuaries (STEs), the mixing zones between terrestrial groundwater and seawater, function as critical biogeochemical reactors that buffer anthropogenic pollutants from entering the open ocean. To date, microbial diversity and community structure within STEs remain poorly characterized. Here, we reconstructed 178 metagenome-assembled genomes (MAGs) exclusively from bacteria (no archaeal MAGs identified). All MAGs met medium-quality standards (>70% completeness, <10% contamination), including 59 near-complete (>90%), 47 with completeness over 80%, and 23 over 75% complete genomes. These MAGs spanned 17 bacterial phyla, with Pseudomonadota dominating (30.9%). Crucially, 157 MAGs (88%) are unclassified at the species level based on GTDB assessment, potentially representing novel taxa, including 1 candidate family, 28 candidate genera, and 128 candidate species. This study provides a genomic resource for studying the functional roles of these unclassified taxa in STEs.},
}

@article {pmid42374196,
year = {2026},
author = {Ye, J and Mao, P and Li, B and Hao, Y and Chen, Y and Li, K},
title = {Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05346-4},
pmid = {42374196},
issn = {1471-2180},
abstract = {BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort.

METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16 S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis.

RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients.

CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.},
}

@article {pmid42374517,
year = {2026},
author = {Harvey, E and Van Brussel, K and Holmes, EC},
title = {Empowering One Health with metagenomics.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-026-00225-4},
pmid = {42374517},
issn = {2524-4655},
support = {GNT2017197//National Health and Medical Research Council/ ; },
abstract = {In an increasingly connected world a global One Health approach to the management of human, animal and ecosystem health will be critical to effective infectious disease responses. The emergence and rapid global spread of several emerging and re-emerging pathogens in the past decade has highlighted the need for rapid, sensitive and accurate diagnostics. Metagenomics, while commonly used for research purposes for almost two decades, entered the global spotlight during the COVID-19 pandemic. In this review we discuss the impacts that metagenomic studies have had on our understanding of origins, aetiology and ecology of infectious diseases within a One Health context. We also discuss the role of metagenomics in the future of diagnostics and disease surveillance, and outline the challenges and limitations of current metagenomic methods.},
}

@article {pmid42374552,
year = {2026},
author = {Wan, LY and Zou, J and Li, XM and Zhao, R and Yang, G and Zhang, MY and Xiao, QY and Wei, YD and Gao, JM and Yang, BP and Zhang, C and Jiao, YM and Wang, FS and Song, JW},
title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals pathogen spectrum and mortality predictors among patients with advanced HIV-1 disease at a tertiary hospital in China.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03234-x},
pmid = {42374552},
issn = {1743-422X},
support = {No. 20250484882//Beijing Nova Program, China/ ; No. 2025ZD01904603//National Science and Technology Major Project/ ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections remain the major causes of morbidity and mortality among people living with HIV-1 (PLWH), particularly in resource-limited settings. However, the clinical characteristics and prognostic indicators of PLWH with suspected CNS infections are not well defined. In this study, we aim to characterize the spectrum of CNS pathogens, clinical characteristics, in-hospital mortality, and factors associated with death among people with advanced HIV-1 disease (AHD) in Guangxi, China.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed to analyze types of infection in cerebrospinal fluid (CSF) from 61 treatment-naive PLWH with suspected CNS infections. Clinical data, routine laboratory tests, and biochemical tests were collected and analyzed.

RESULTS: Among the 61 CSF samples, primarily with AHD, a total of 206 pathogens were identified. Viral pathogens predominated, with Epstein-Barr virus being the most frequently identified, followed by cytomegalovirus. Compared with patients with single-pathogen infection, those with multiple infections (viral, bacterial, and fungal) exhibited significantly lower CD4 T cell counts, higher C-reactive protein levels, and markedly reduced lipid metabolism parameters. However, infection types were not significantly associated with in-hospital death. Multivariate logistic regression analysis identified plasma low density lipoprotein (LDL) and CSF lactate dehydrogenase (LDH) as independent predictors of in-hospital death.

CONCLUSION: In PLWH with AHD and suspected CNS infections, multiple pathogens frequently coexist in the CSF. Plasma LDL and CSF LDH levels were independent predictors of death, indicating their potential value as early risk stratification in AHD.},
}

@article {pmid42374590,
year = {2026},
author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB},
title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02383-z},
pmid = {42374590},
issn = {2049-2618},
support = {Heritage_2020-005_RESTOROMIC//Österreichischen Akademie der Wissenschaften/ ; },
abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.

RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.

CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.},
}

@article {pmid42375904,
year = {2026},
author = {Panagiotidi, K and Markidis, A and Karamatzanis, I and Almomani, M and Omirou, R and Kosmidou, P},
title = {The Nasopharyngeal Microbiome: A Narrative Review of the Hidden Regulator of Ear, Nose, and Throat (ENT) Inflammations.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109921},
pmid = {42375904},
issn = {2168-8184},
abstract = {The nasopharyngeal microbiome is a central regulator of respiratory health. The upper airway microbial community acts as the primary gatekeeper against respiratory pathogens and maintains homeostasis in the upper respiratory tract (URT). This community is established at birth and influenced by the delivery method and antibiotic exposure. Disruptions to this balance are recognised as a major driver of chronic inflammatory ear, nose, and throat (ENT) diseases. This review analyses the literature on the relationship between the nasopharyngeal microbiome and inflammatory ENT diseases. We searched recent literature (2015-2025) via PubMed and Scopus, focusing on 16S rRNA and metagenomic studies of the upper respiratory tract. We examined papers that linked microbial shifts to clinical outcomes in otitis media, rhinosinusitis, and allergic rhinitis, as well as studies applying machine learning to diagnostic modelling. Clinical health is associated with stable colonisation by Dolosigranulum and Corynebacterium. These commensals protect the host by maintaining the mucosal barrier and competing against pathogens. Chronic disease, in contrast, is marked by a bloom of Streptococcus, Haemophilus, or Moraxella. In chronic rhinosinusitis, loss of bacterial diversity and S. aureus biofilm formation often lead to treatment failure. Machine learning tools like Random Forest and XGBoost classifiers have been applied to nasopharyngeal microbiome data. In published cohorts, these models have achieved sensitivity and specificity values of 80-90% for identifying dysbiotic profiles associated with disease, outperforming standard culture in speed and taxonomic resolution. These findings support a shift from broad antibiotic use toward microbiome-informed treatment. Standardising sampling and sequencing methods remains the next necessary step.},
}

@article {pmid42376027,
year = {2026},
author = {Dong, X and Xiao, R and Gao, C and Huang, S and Meng, X and Yan, X and Bai, Z and Wu, S},
title = {Ruxolitinib combined with azithromycin for scrub typhus-associated hemophagocytic lymphohistiocytosis in a child: a case report and narrative literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1852110},
pmid = {42376027},
issn = {2296-2360},
abstract = {BACKGROUND: Scrub typhus-associated hemophagocytic lymphohistiocytosis (HLH) is a rare but life-threatening complication in children, with reported mortality of 11.9%-30%. Conventional immunomodulation with corticosteroids and intravenous immunoglobulin often provides insufficient control of the hyperinflammatory state, while etoposide-based chemotherapy carries significant toxicity. JAK1/2 inhibition targeting the interferon-gamma pathway represents a promising therapeutic strategy, but its application in scrub typhus-associated HLH has not been previously reported.

CASE PRESENTATION: A 5-year-11-month-old girl with no prior medical history presented with persistent fever, tachypnea, hepatosplenomegaly, and a 0.5 cm eschar in the left axilla after travel to Yunnan Province, China. Laboratory findings revealed pancytopenia (platelets 40× 10[9]/L), hyperferritinemia (>2,000 ng/mL), hypofibrinogenemia (1 g/L), and elevated interferon-gamma (135.48 pg/mL). Bone marrow aspiration demonstrated hemophagocytosis. Metagenomic next-generation sequencing confirmed Orientia tsutsugamushi infection. The patient met six of eight HLH-2004 diagnostic criteria. She was treated with oral ruxolitinib (5 mg twice daily) initiated on the day of admission, followed by intravenous azithromycin (10 mg/kg once daily) after confirmatory testing. Fever resolved within 72 h. Ruxolitinib was temporally associated with rapid clinical improvement, although causal attribution cannot be established due to concurrent therapies. By day 8, platelet count normalized to 240× 10[9]/L, ferritin declined to 1,246 ng/mL, and fibrinogen recovered to 2.4 g/L. The patient was discharged on day 13 with ruxolitinib tapered to 2.5 mg daily. At 3-month follow-up, she remained well with normal laboratory parameters.

LITERATURE REVIEW: Narrative literature review of 66 previously reported pediatric cases from Chinese and English databases (inception to May 2026) plus the present case revealed an overall mortality of 11.94% (8/67). Among these patients, 43 (64.2%) received corticosteroids, 34 (50.7%) received intravenous immunoglobulin, and only 3 (4.5%) received etoposide. The published cases suggest that absence or delay of anti-rickettsial therapy is associated with poor outcomes, though the evidence is limited by case-report bias and confounding.

CONCLUSION: This is the first report of successful JAK1/2 inhibitor therapy in scrub typhus-associated HLH. This case raises a hypothesis worth investigating further-that ruxolitinib combined with azithromycin may achieve rapid disease control with good tolerability. Prospective studies are needed to evaluate the role of targeted JAK inhibition in infection-triggered HLH.},
}

@article {pmid42376290,
year = {2026},
author = {Onumanyi, V and Ogola, HJO and Ijoma, GN and Semenya, K},
title = {PacBio HiFi sequencing datasets of culture-enriched airborne microbial cave communities from dolomitic Sudwala Caves, South Africa.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112970},
pmid = {42376290},
issn = {2352-3409},
abstract = {We present a dataset integrating physico-chemical air quality measurements with long-read PacBio HiFi shotgun metagenomic sequences from culture-enriched airborne samples collected in Sudwala Caves, one of the oldest known cave systems in South Africa. This resource provides baseline characterization of airborne microbial communities and associated environmental parameters within a subterranean karst ecosystem. A total of 106 air samples were collected across six different cave compartments and three external reference sites spanning two seasonal periods, the winter-spring transition (September-October 2024) and the summer-autumn window (February-March 2025). Environmental metadata include temperature, relative humidity, particulate matter (PM1.0, PM2.5, PM10), and formaldehyde (HCHO) concentrations, enabling direct linkage between microbial composition and air quality dynamics. Post-quality control of eighteen (18) culture-enriched metagenome datasets yielded 7.7 × 10[4] to 7.8 × 10[5] HiFi reads per sample corresponding to 0.63-6.71 Gb of high-accuracy sequence data per sample. Kaiju classification assigned 65.1-83.4% of assembled sequences to reference taxa. Domain-level profiles were dominated by Bacteria (98.7-99.9% of classified sequences), with minor representation of Eukaryota (0.06-0.15%) and extremely low abundances of Archaea (0.002-0.009%) and Viruses (0.000-0.001%). At the phylum level, airborne bacterial communities were consistently dominated by Bacillota (mean relative abundance: 46.92%), Pseudomonadota (34.28%), and Actinomycetota (15.71%) across all sampling sites and seasons, with Pseudomonadota and Actinomycetota exhibiting proportionally higher representation within cave interior environments relative to outdoor reference sites. At the genus level, Staphylococcus, Bacillus, Microbacterium, Arthrobacter, and Pseudomonas were among the most consistently detected and abundant airborne genera within cave compartments, whilst outdoor aerobiome communities were characterised by greater relative abundances of Planococcus, Sphingomonas, Stenotrophomonas, and Arthrobacter. Functional annotation using the DRAM pipeline identified 1205,651 predicted genes, with 579,682 KEGG orthologs (KO), 62,261 MEROPs peptidases, 904,193 Pfam domains, and 21,859 CAZy genes annotated. This dataset supports investigations of culturable airborne microbial composition, functional capacity, bioaerosol dynamics, and environmental health indicators in dolomitic subterranean karst systems, providing a reference framework for comparative studies of low-biomass atmospheric environments.},
}

@article {pmid42376319,
year = {2026},
author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S},
title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828012},
pmid = {42376319},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; },
abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.

METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.

RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p = 0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p = 0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p < 0.05).

CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.},
}

Humans
*Colorectal Neoplasms/microbiology
*Feces/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
Male
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Multiomics
High-Throughput Nucleotide Sequencing
Adult
Metagenome

@article {pmid42376322,
year = {2026},
author = {Qin, Q and Ning, YC and Zhu, SN and Ma, JH and Chen, W and Tian, W and Wang, CM and Wu, YF and Li, SL},
title = {Performance of metagenomic next-generation sequencing for bloodstream infections in perioperative critically ill patients- a post-hoc analysis of a prospective, multi-center cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1814969},
pmid = {42376322},
issn = {2235-2988},
mesh = {Humans ; Prospective Studies ; Female ; *Metagenomics/methods ; Critical Illness ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Intensive Care Units ; *Bacteremia/diagnosis/microbiology ; Aged ; Middle Aged ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Blood Culture ; *Sepsis/diagnosis/microbiology ; },
abstract = {BACKGROUND: Bloodstream infections (BSI) in intensive care unit (ICU) patients are associated with high morbidity and mortality, necessitating rapid and accurate pathogen identification to guide early antimicrobial therapy. However, traditional blood culture (BC) is limited by the long turnaround time and low sensitivity. Metagenomic next-generation sequencing (mNGS) has been applied in infectious disease diagnostics, but its clinical utility for perioperative ICU patients with BSI requires further evaluation.

METHODS: This post-hoc analysis included 219 perioperative ICU patients (from a prospective, multi-center cohort, July 2020-June 2023) who underwent concurrent mNGS and BC testing. The study compared pathogen detection differences between the two methods, and evaluated the diagnostic value of mNGS for clinical BSI based on mNGS-assisted clinical diagnostic criteria. Additionally, the impact of mNGS findings on clinical antimicrobial management was assessed.

RESULTS: mNGS demonstrated a higher overall pathogen detection rate than BC in the 219 enrolled patients (25.1% vs. 9.6%, p < 0.001), with significant advantages in detecting Gram-negative bacteria (13.2% vs. 5.9%, p = 0.009), anaerobes (3.6% vs. 0.5%, p = 0.018), and fungi (6.4% vs. 0.9%, p = 0.002). Mixed-pathogen infections were identified in 20% of mNGS-positive clinical BSI cases, whereas BC-positive cases exclusively had single-pathogen infections. Ultimately, 64 patients (29.2%) were diagnosed with clinical BSIs. The sensitivity and specificity of the mNGS were 85.9% (95% CI: 74.5%-93.0%), and 80.6% (95% CI: 73.4%-86.4%), respectively, and the area under the receiver operating characteristic curve was 0.833 (95% CI: 0.772-0.894). The positive predictive value and negative predictive value were 64.7% (95% CI: 53.5%-74.6%) and 93.3% (95% CI: 87.3%-96.7%), respectively. Additionally, mNGS led to a positive impact in 56 patients (25.6%), manifested by the identification of new pathogens and guidance for targeted therapy, a negative impact in 11 patients (5.0%), and no clinical impact in 152 patients (69.4%).

CONCLUSIONS: For perioperative ICU patients, mNGS demonstrated superior pathogen detection rates, broader microbial spectrum coverage, and enhanced polymicrobial infection detection capability versus BC. mNGS exhibited high diagnostic value for clinical BSI, with the potential to facilitate targeted antimicrobial therapy adjustments.},
}

Humans
Prospective Studies
Female
*Metagenomics/methods
Critical Illness
*High-Throughput Nucleotide Sequencing/methods
Male
Intensive Care Units
*Bacteremia/diagnosis/microbiology
Aged
Middle Aged
Sensitivity and Specificity
Bacteria/genetics/classification/isolation & purification
Blood Culture
*Sepsis/diagnosis/microbiology

@article {pmid42376574,
year = {2026},
author = {Biełło, K and Rodríguez-Caballero, G and Becerra-Mora, D and Dorado-Blanco, N and Sáez-Melero, LP and Moreno-Vivián, C and Luque-Almagro, VM and Olaya-Abril, A and Roldán, MD},
title = {Exploring the Tenebrio molitor gut microbiota response to LDPE and PET: putative genetic indicators and methodological insights.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746922},
pmid = {42376574},
issn = {1664-302X},
abstract = {Insect gut microbiomes are recognized as potential reservoirs of enzymatic activities relevant to plastic metabolism. Here, we investigated the taxonomic and functional dynamics of the Tenebrio molitor gut microbiota under dietary exposure to low-density polyethylene (LDPE) and polyethylene terephthalate (PET) using 16S rRNA sequencing and shotgun metagenomics. Significant compositional shifts were detected at the ASV level, with plastic-fed cohorts showing enrichment of taxa implicated in xenobiotic metabolism. Predicted functional changes suggested altered abundance of pathways related to aromatic compound processing and redox homeostasis. Metagenomic assembly and functional annotation, performed through a reproducible open-source workflow, revealed several putative proteins with distant homology to enzymes such as phthalate dioxygenases, urethanases, and polyhydroxyalkanoate depolymerases. A metagenome-assembled genome (MAG) assigned to Enterococcus accounted for most recovered protein-coding sequences. Although gene-level comparisons did not show statistically significant differences, Gene Set Enrichment Analysis (GSEA) highlighted ABC transporter signatures and stress-response ATPases under plastic-exposed conditions. Overall, this exploratory study reveals microbial shifts and putative genetic indicators of metabolic potential within the T. molitor gut, providing a reproducible analytical framework for future investigations into the microbial role in plastic bioconversion.},
}

@article {pmid42376617,
year = {2026},
author = {Lee, YS and Kuo, TF and Yang, G and Liang, YC and Yang, WC},
title = {Bidens pilosa extract and bentonite, a phytogenic formulation, as a feed additive to improve diarrhea and gut microbiota in calves: Effects on feed use and regulation of gut microbiota.},
journal = {Veterinary and animal science},
volume = {34},
number = {},
pages = {100732},
pmid = {42376617},
issn = {2451-943X},
abstract = {Phytogenics are emerging as an alternative approach to maintain animal health and productivity without using antibiotics in the livestock industry. This study investigated the function and mechanism of a phytogenic formulation composed of Bidens pilosa extract and bentonite (BPB) on diarrhea, gut microbiota and growth performance in calves. Twenty-six 15-day-old Holstein Friesian calves were fed control or 0.5% BPB diets for 4 weeks. Their diarrhea, gut microbiota, fecal IgA, and bacterial growth were analyzed using culture-based methods, 16S rRNA sequencing, and statistical analyses. BPB (0.5%) significantly reduced diarrhea, fecal scores, and fecal IgA levels, but increased body weight in calves. Furthermore, metagenomic analysis and selective agar assays indicated that 0.5% BPB decreased three bacterial genera, Campylobacter, Clostridium_sensu_stricto_1, and Escherichia/Shigella, but increased seven other bacterial genera, including Lactobacillus, Ruminococcus, and Bacteroides, in the feces of calves. Mechanistic studies suggested that BPB augmented the proliferation of bacteria associated with beneficial effects, subsequently inhibiting the growth of bacteria associated with harmful effects in the intestines of calves. In conclusion, BPB mitigated diarrhea and gut inflammation and increased body weight gain in calves by modulating the gut microbiota. This modulation involved the upregulation of bacteria with beneficial potential that antagonize the growth of bacteria with pathogenic potential.},
}

@article {pmid42376710,
year = {2026},
author = {Arguelles, EDLR and Mugikura, K and Sato, S},
title = {Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70195},
pmid = {42376710},
issn = {1529-8817},
support = {21A402//Japan Society for the Promotion of Science/ ; 23K05398//Japan Society for the Promotion of Science/ ; 26K01814//Japan Society for the Promotion of Science/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
abstract = {The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.},
}

@article {pmid42377028,
year = {2026},
author = {Lenz, C and Seel, W and Dombrowski, T and Hacker, S and Simon, M-C and Zentgraf, K and Dawczynski, C and Krüger, K},
title = {Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048926},
doi = {10.1128/msystems.00489-26},
pmid = {42377028},
issn = {2379-5077},
abstract = {Elite athletes undergo intense physical training and experience substantial physiological stress, which could affect the composition and function of their gut microbiome. This study compared the gut microbiomes of 148 German junior and senior elite athletes with those of 108 healthy adults to identify taxonomic and functional features associated with elite athletic status. Group comparisons were conducted between healthy adults, senior athletes, and junior athletes, and a matched-subgroup analysis was performed in adults only, controlling for age, sex, body mass index, and dietary pattern. Significant differences in taxonomic composition were observed between athletes and healthy adults. Healthy adults exhibited greater microbial evenness and diversity than junior athletes, whereas senior athletes displayed higher microbial richness. Principal coordinate analysis revealed distinct clustering by athletic status. Linear discriminant analysis effect size identified taxa such as Escherichia-Shigella as being enriched in athletes. Predictive metagenomic profiling (PICRUSt2) indicated differences in microbial functional potential between adult athletes and matched controls, including pathways related to amino acid metabolism, glycolysis, fatty acid β-oxidation, and quinone biosynthesis. Together, these findings demonstrate distinct taxonomic and predicted functional microbiome signatures associated with elite athletic status.IMPORTANCEElite athletic training and lifestyle are associated with the gut microbiome. Our research has revealed distinct microbial structures in elite athletes, characterized by reduced evenness in junior athletes and increased richness in senior athletes, compared to healthy adults. Matched-subgroup analyses confirmed these group-specific differences. The gut microbiomes of athletes were enriched in pathways related to amino acid biosynthesis, glycolysis, fatty acid β-oxidation, and quinone synthesis. These microbiome features may be relevant for metabolic efficiency and resilience to oxidative stress. Combining taxonomic and functional prediction data from a uniquely characterized cohort of junior and senior elite athletes provides novel insight into microbiome signatures associated with sustained physical and psychological stress, with potential implications for performance, recovery, and health.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03582020.},
}

@article {pmid42377463,
year = {2026},
author = {Brenner, T and Skarabis, A and Schaller, SJ and von Groote, T and Putensen, C and Günther, U and Sauer, M and Decker, SO and Dusse, F and Weiss, M and Suchodolski, K and Simon, TP and Rosenberger, P and Moerer, O and Unterberg, M and Schewe, JC and Bracht, H and Hutzl, S and Feißt, M and Marschall, U and Brandenburg, P and Stevens, P and Schmidt, J and Pletz, MW and Berger, MM and , },
title = {Effects of a clinical metagenomics intervention on clinical outcomes, healthcare costs, and health-related quality of life in patients with sepsis or septic shock: results of the randomized-controlled DigiSep trial.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
pmid = {42377463},
issn = {1432-1238},
support = {01NVF20013//German Innovation Fund/ ; },
abstract = {PURPOSE: Early pathogen detection is crucial in sepsis. We hypothesized that detection of microbial circulating cell-free DNA by metagenomic next-generation sequencing (mNGS) improves clinical outcomes and health-related quality of life without increasing healthcare costs.

METHODS: This randomized, controlled, interventional, open-label, multicenter trial was conducted in 24 intensive care units across Germany. The intervention group (n = 200) received mNGS diagnostics in addition to standard-of-care microbiology, compared with standard-of-care microbiology alone (control group; n = 189). The primary endpoint was the Desirability of Outcome Ranking/Response Adjusted for Duration of Antibiotic Risk (DOOR/RADAR) score.

RESULTS: The DOOR/RADAR score was not significantly improved at 28 days after sepsis onset (intervention group: 3.21 ± 1.54; control group: 3.49 ± 1.51; 95% CI - 0.58 to 0.03). However, other secondary endpoints were improved, including a reduced duration of mechanical ventilation (intervention group: 6.6 ± 9.4 days; control group: 9.3 ± 10.6 days; 95% CI - 5.03 to - 0.34) and faster shock resolution (intervention group: 6.9 ± 7.4 days; control group: 8.8 ± 8.5 days; 95% CI - 3.75 to - 0.04). Health-related quality of life at 90 days (EQ-5D-5L) was improved in the intervention group (0.312 ± 0.386) compared with the control group (0.208 ± 0.373; p = 0.047). In the subgroup with available claims data (33.2% of participating patients), healthcare costs over 180 days did not differ.

CONCLUSION: The DOOR/RADAR score as primary endpoint was not significantly improved by mNGS. Exploratory secondary analyses revealed improvements in secondary endpoints. (Funding: German Innovation Fund; ClinicalTrials.gov number, NCT04571801, registration: 25.8.2020).},
}

@article {pmid42377624,
year = {2026},
author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C},
title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42377624},
issn = {1573-0972},
mesh = {*Wastewater/microbiology ; *Microalgae/growth & development/microbiology ; Phylogeny ; *Bacteria/isolation & purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; },
abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.},
}

*Wastewater/microbiology
*Microalgae/growth & development/microbiology
Phylogeny
*Bacteria/isolation & purification/classification/genetics/metabolism
RNA, Ribosomal, 16S/genetics
Biomass
Microbial Consortia
Coculture Techniques
Biofuels
DNA, Bacterial/genetics
Metagenomics
Water Purification

@article {pmid42377631,
year = {2026},
author = {Thakur, A and Gupta, P and Sethi, S and Apreja, M and Ahmed, S and Sharma, L},
title = {Exploring the antibacterial potential of a designed peptide against Gardnerella vaginalis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42377631},
issn = {1573-4978},
mesh = {*Gardnerella vaginalis/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Antimicrobial Peptides/pharmacology ; Female ; Vaginosis, Bacterial/drug therapy/microbiology ; Hemolysis/drug effects ; Cell Survival/drug effects ; *Antimicrobial Cationic Peptides/pharmacology ; Peptides, Cyclic/pharmacology ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal dysbiosis caused by Gardnerella vaginalis, a facultative anaerobic bacillus. The failure of conventional antibiotics and recurrence of bacterial vaginosis call for alternative novel therapeutic strategies. Antimicrobial peptides (AMPs) provide a targeted, resistance-sparing alternative with their broad-spectrum activity and distinct mode of action.

METHODS: Two AMPs, i.e., TCCP-1 (cyclic) and ZMLP-2 (linear), were designed in silico from proteome sequences of Thymbra capitata and Zataria multiflora already available in NCBI. The designed peptides were chemically synthesized, evaluated for their antibacterial activity, cytotoxicity, hemolytic effects and mechanism of action against G.vaginalis.

RESULTS: TCCP-1, a cyclic peptide with an MIC of 1.95 µg/mL against G. vaginalis showed minimal cytotoxicity even at 100 µg/mL, which is much higher than its MIC value (1.95 µg/mL). TCCP-1 maintained high cell viability at lower concentrations, while a concentration-dependent reduction in viability was observed at higher concentrations. In contrast, ZMLP-2, a linear AMP, showed weak antimicrobial activity with an MIC of 100 µg/mL, exhibited a moderate reduction in cell viability (~ 70-75%) when tested at 100 µg/mL or a concentration below its MIC. Both peptides showed the disruption of bacterial membranes and, therefore, support the re-establishment of healthy vaginal flora. More significantly, TCCP-1 demonstrated efficient antimicrobial activity against G.vaginalis along with decreased cytotoxicity, making it an excellent candidate for future in vivo studies and possible clinical uses.

CONCLUSIONS: Thus, plant-derived AMPs could prove to be useful, targeted, and sustainable alternatives to BV prevention while treating both resistance and recurrence.},
}

*Gardnerella vaginalis/drug effects
Humans
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Antimicrobial Peptides/pharmacology
Female
Vaginosis, Bacterial/drug therapy/microbiology
Hemolysis/drug effects
Cell Survival/drug effects
*Antimicrobial Cationic Peptides/pharmacology
Peptides, Cyclic/pharmacology

@article {pmid42377725,
year = {2025},
author = {Yun, S and Seo, Y and Yoon, Y},
title = {Prevalence of Microorganisms and Suggestion for Potential Contribution of Microorganisms to Volatile Basic Nitrogen Production in Beef at Current Purchase Stages.},
journal = {Food science of animal resources},
volume = {45},
number = {6},
pages = {1710-1723},
doi = {10.5851/kosfa.2025.e14},
pmid = {42377725},
issn = {2636-0780},
abstract = {This study investigated the prevalence of microorganisms related to meat quality and analyzed volatile basic nitrogen (VBN) levels in beef samples to suggest potential bacteria that might contribute to VBN production at current purchase stages using metagenomic analysis. Seventy beef samples were analyzed for coliform, Escherichia coli, enterohemorrhagic E. coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, total aerobic bacteria (TAB), Enterobacteriaceae, lactic acid bacteria (LAB), Pseudomonas spp., yeast and molds (YM), and psychrotrophic bacteria (PB). VBN levels ranged from 0.69 to 22.51 mg%. Microbiota from three samples with the highest and three with the lowest VBN levels were analyzed. S. aureus was detected in only one sample at 1.2 Log CFU/g. The cell counts for TAB, coliform, Enterobacteriaceae, LAB, Pseudomonas spp., YM, and PB were 5.1, 1.7, 2.6, 4.2, 1.9, 2.9, and 5.4 Log CFU/g, respectively. Microbiota analysis revealed that samples with high VBN levels had high relative abundances of Lactobacillus and Leuconostoc. This study showed that these relatively abundant LAB were potential bacteria that might contribute to producing more VBN in beef at current purchase stages. However, the potential bacteria were suggested only by metagenomic analysis with a limited sample size without considering the endogenous meat enzymes. Therefore, further research is necessary to identify and isolate these bacteria with a larger sample size while excluding VBN produced by endogenous enzymes. Additionally, environmental factors not included due to the limited objective of this study could also be considered in further research with the different objectives from this study.},
}

@article {pmid42377908,
year = {2026},
author = {Deng, Y and Borton, MA and Nesbø, CL and Forster, MD and Konhauser, KO and Gingras, MK and Goss, GG and Wrighton, KC and Lanoil, BD and Zhong, C and Alessi, DS},
title = {Geochemistry shapes microbial diversity and selected functional traits in flowback and produced waters from hydraulically fractured formations.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag070},
pmid = {42377908},
issn = {1574-6941},
abstract = {Microbial communities inhabiting hydraulically fractured subsurface waters are increasingly recognized as important components of unconventional oil and gas systems because they can influence water quality, infrastructure integrity, and biogeochemical processes during flowback and production. However, a quantitative cross-basin understanding of their taxonomic diversity, ecological organization, and potential functional variation remains limited. In this study, we analyzed 16S rRNA gene amplicons, metagenomes, and geochemical data from flowback and produced water (FPW) from the Sichuan Basin, China, and conducted a quantitative comparison to data previously reported from the same basin and hydraulic fracturing (HF) regions in North America. Our findings revealed strong co-occurrence patterns among fermentative, sulfidogenic, and methanogenic microorganisms, which emerged as core members of microbial communities across all fractured subsurface environments. Notably, microbial diversity and selected metabolic traits differed across basins in the low-salinity systems of China, whereas high-salinity basins in North America exhibited reduced diversity and more constrained metabolic capabilities. These differences are consistent with salinity acting as an important ecological filter across the analyzed basins. Our results indicate that basin-specific geochemical context, particularly salinity, is closely associated with cross-basin differences in microbial diversity, community composition, and selected metabolic traits in fractured subsurface waters. These findings support the value of integrating geological, geochemical, and microbiological information when interpreting microbial risks and water-management strategies in hydraulic fracturing systems.},
}

@article {pmid42378511,
year = {2026},
author = {Zhang, R and Wang, B and Lu, J and Wu, J and Liu, X and Zhang, R and Marsili, E and Gong, C},
title = {The Food Additives p-Coumaric Acid Production from Corn Stalk Catalyzed by a Cold-Adapted Carboxylesterase.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c05955},
pmid = {42378511},
issn = {1520-5118},
abstract = {p-Coumaric acid is a widely utilized food additive with beneficial biological activities. A novel enzymatic catalysis strategy for the production of p-coumaric acid from lignocellulosic biomass is proposed herein. The gene encoding a carboxylesterase was identified in metagenome-assembled genome and further characterized in the isolated Glutamicibacter soli Em07. The target protein, with a molecular weight of 53 kDa, was successfully obtained through heterologous expression. The carboxylesterase exhibited cold adaptation, with optimal activity at 35 °C and pH 7.0 using 1-naphthyl acetate as substrate, and maintained over 75% of the maximum activity after incubation at 25 °C for 2 h. At 25 °C, 35.9 ± 0.4 μg of p-coumaric acid was obtained from 20 mg of corn stalk via carboxylesterase-mediated catalysis. This work achieves a high p-CA yield from lignocellulosic biomass via low-temperature enzymatic catalysis without pretreatment. The results offer valuable progress toward manufacturing high-value food additives, including p-CA.},
}

@article {pmid42378616,
year = {2026},
author = {Tyler, RS and Charles, DW and Mills, AG and Alkabab, Y},
title = {Disseminated Mycobacterium immunogenum -associated Hemophagocytic Lymphohistiocytosis after Stem Cell Transplantation.},
journal = {International journal of mycobacteriology},
volume = {15},
number = {2},
pages = {179-182},
pmid = {42378616},
issn = {2212-554X},
abstract = {Secondary hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome most commonly triggered by infection, malignancy, or transplant-related immune dysregulation. Rapidly growing mycobacteria are uncommon causes of disseminated infection and have only rarely been reported as infectious triggers of HLH. A 56-year-old immunocompromised woman with a history of allogeneic hematopoietic stem cell transplant presented with recurrent fever, progressive transaminitis, and laboratory features consistent with secondary HLH. Liver biopsy showed granulomatous hepatitis with iron overload. Initial treatment with dexamethasone and anakinra resulted in transient clinical improvement. Less than 2 weeks later, she was readmitted with worsening hepatic dysfunction and found to have acid-fast bacilli in blood and bone marrow cultures, later identified as Mycobacterium immunogenum. Despite targeted antimicrobial therapy, the patient developed progressive hepatic and renal failure and died. To our knowledge, this case represents the first reported case of disseminated M. immunogenum infection precipitating secondary HLH, expanding the recognized clinical spectrum of this rapidly growing nontuberculous mycobacterium and highlights the diagnostic challenges of atypical mycobacterial infection in immunocompromised hosts.},
}

@article {pmid42378712,
year = {2026},
author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M},
title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {6},
pages = {},
doi = {10.1093/ecco-jcc/jjag080},
pmid = {42378712},
issn = {1876-4479},
support = {//Takeda Pharmaceutical Company Ltd/ ; },
abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.

DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n = 23) or CgF (n = 17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.

RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.

CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.},
}

@article {pmid42378762,
year = {2026},
author = {Liu, J and Tan, Y and Fan, X and Xie, S and Xu, X and Zhu, L},
title = {Exogenous vitamin B12 alleviated inhibition of salinity on anaerobic dichloromethane degradation by reducing cofactor-related constraints and reshaping community functional potential.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142823},
doi = {10.1016/j.jhazmat.2026.142823},
pmid = {42378762},
issn = {1873-3336},
abstract = {Dichloromethane (DCM) frequently co-occurs with high salinity in industrial wastewater, imposing dual stress on anaerobic treatment. However, how anaerobic DCM degraders respond to salt stress and whether exogenous vitamin B12 (VB12, a key cofactor in DCM transformation) can facilitate DCM degradation remain poorly understood. Here, we established long-term enrichments (>800 days) of DCM-degrading consortia under non-saline and salt-stressed conditions (10 g/L NaCl) to investigate how VB12 affected degradation performance, community assembly, and functional potential. Salt stress significantly inhibited DCM degradation, reducing the maximum degradation rate by 71.5%, whereas VB12 substantially alleviated this inhibition and increased the degradation rate to 55.9% of the non-saline control. Metagenomic and co-occurrence network analyses indicated that salinity drove community reassembly and niche differentiation, linking DCM degraders, methanogens/homoacetogens, and fermenters within an inferred producer-cooperator-cross-feeder framework that maintained community stability under salt stress. Functional analyses showed that VB12 was associated with shifts in community functional potential toward hydrogenotrophic/acetoclastic methanogenesis and osmoadaptive metabolism, supporting stress adaptation under saline conditions. Further analysis of the mec (methylene chloride catabolism) cassette suggested that VB12 likely reduced cofactor-related constraints and reinforced downstream product-consuming functions, thereby contributing to the enhanced degradation performance. Notably, a previously uncharacterized Dehalobacteriaceae MAG, D_MAG.168, emerged as a dominant candidate DCM degrader under salt stress. Overall, these findings provide insight into the functional responses of DCM-degrading consortia to VB12 supplementation under salt stress and support the further development of VB12-assisted bioaugmentation strategies for DCM-contaminated saline industrial wastewater.},
}

@article {pmid42378793,
year = {2026},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and Jank, L and Barreto, F and Dorn, M and Cardoso, MRI and Siqueira, FM},
title = {Swine waste stabilization ponds as hotspots for antimicrobial resistance gene accumulation: a longitudinal metagenomic study.},
journal = {International journal of hygiene and environmental health},
volume = {276},
number = {},
pages = {114857},
doi = {10.1016/j.ijheh.2026.114857},
pmid = {42378793},
issn = {1618-131X},
abstract = {Using next-generation sequencing, this study provides a comprehensive longitudinal assessment of bacterial communities, antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs), and metabolic pathways in a full-scale swine waste treatment system in Brazil. Samples were collected from the first (WSP1) and final (WSP4) waste stabilization ponds of a farrow-to-finish farm during four sampling events between October 2022 and January 2023. Antibiotic molecules were additionally identified and quantified using solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry. Bacterial community composition remained remarkably stable over time. Similarly, the resistome and mobilome showed pronounced temporal stability, although a consistently higher relative abundance of ARGs and MGEs was observed in the final treatment process (WSP4). Genes encoding resistance markers of human-health relevance were detected in WSP4, including Paer_PhoP_CST, associated with polymyxin (colistin) resistance; PRC-1, linked to resistance to third-generation cephalosporins; and quinolone resistance determinants such as adeF, Paer_parE_FLO, and Mtub_gyrB_FLO. Genes encoding efflux pump complexes associated with multidrug resistance were also identified, including Paer_CpxR, PmpM, YajC, MuxB, and MexW. Supporting these findings, fluoroquinolones (ciprofloxacin and norfloxacin), lincomycin, and tetracycline molecules were detected in the waste ponds, indicating sustained selective pressure within the system. The accumulation of clinically relevant resistance determinants in the final of the waste treatment process, whose effluent is reused for agricultural irrigation, highlights waste stabilization ponds as potential hotspots for the persistence and environmental dissemination of antimicrobial resistance. These findings underscore the urgent need for improved monitoring and management of livestock waste treatment systems to mitigate antimicrobial resistance dissemination across agroecosystems.},
}

@article {pmid42378969,
year = {2026},
author = {Xing, BS and Wu, YF and Zhang, Y and Wang, XC and Li, YY and Chen, R},
title = {Carbon cloth-mediated direct interspecies electron transfer effect on the intensification mechanism of high-load codigestion dynamic membrane bioreactors.},
journal = {Water research},
volume = {304},
number = {},
pages = {126376},
doi = {10.1016/j.watres.2026.126376},
pmid = {42378969},
issn = {1879-2448},
abstract = {Acidification under high organic loading conditions and control of dynamic membrane (DM) thickness remain major challenges in the development of anaerobic dynamic membrane bioreactors (AnDMBR). In anaerobic digestion (AD), conductive materials can promote electron exchange between electron donors and acceptors, thereby accelerating electron transfer and enhancing direct interspecies electron transfer (DIET). These processes can improve methane yield and process stability at higher organic loading rates (OLRs). In this study, a carbon cloth anaerobic dynamic membrane bioreactor (CC-AnDMBR) was constructed and compared with a common nylon mesh anaerobic dynamic membrane bioreactor (NM-AnDMBR) to investigate the impact of DIET reinforcement on system performance and stability. The maximum load tolerance of the system and changes in microorganisms during this process were further evaluated to elucidate the mechanisms underlying enhanced system resilience. At a hydraulic retention time of 6.25 days (OLR of 20.13 g COD/L/day), the methane production rate of the carbon cloth reactor (313.74 ± 41.06 mL/g COD) was significantly greater than that of the nylon mesh reactor (256.02 ± 63.29 mL/g COD). Metagenomic analysis revealed that carbon cloth membranes are more conducive to the enrichment of Geobacter, which can exchange electrons with the dominant archaeal genus Methanosarcina, thereby accelerating the DIET rate within the CC-AnDMBR. The enhanced performance of the carbon cloth reactor was attributed to the higher electrical conductivity, more negative oxidation-reduction potential value, and higher electron transport system activity of the sludge. These characteristics together created a more conducive environment for conductive microorganisms and improved the system's electron transfer rate.},
}

@article {pmid42378973,
year = {2026},
author = {Min, H and Wang, Y and Wang, Q and Zhang, J and Lin, L and Li, X and Li, B},
title = {Cefpirome biodegradation by enriched bacterial consortia and isolated strain Bosea sp. MYQ: Novel insights on biodegradation pathway and bacterial interaction patterns.},
journal = {Water research},
volume = {304},
number = {},
pages = {126351},
doi = {10.1016/j.watres.2026.126351},
pmid = {42378973},
issn = {1879-2448},
abstract = {Deciphering the metabolic fate of cefpirome is essential for designing more efficient biodegradation strategies. In this study, we integrated second- and third-generation metagenomic sequencing with high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (HPLC-QTOF-MS) to unravel cefpirome biodegradation by a long-term enriched bacterial consortium and its key isolate Bosea sp. MYQ. Five biodegradation products were detected and mapped onto three cooperative pathways. Among them, four products involved in Pathways 2 and 3 were first identified in cefpirome biodegradation. Genome-scale metabolic modeling and genome-resolved metagenomics jointly revealed a pollutant-degrading network coordinated by two keystone donors, MAG2 (Variovorax) and MAG3 (Bosea sp. MYQ). They were primarily responsible for β-lactam ring-opening and the formation of downstream products, while exporting diverse metabolic intermediates to sustain pathway continuity through cross-feeding. Notably, MAG3 (Bosea sp. MYQ) encodes per-1 and bla, which likely contribute critically to cefpirome degradation by underpinning key β-lactam transformation steps. Complementary functions were provided by auxiliary and rare members, particularly MAG4 (Hyphomicrobium), MAG7 (Pandoraea), MAG10 (Methyloversatilis), and MAG21 (Phenylobacterium). These findings expand the repertoire of cefpirome-degrading microorganisms, reveal previously unrecognized biodegradation pathways, and clarify the microbial interaction network underpinning fourth-generation cephalosporin removal.},
}

@article {pmid42379260,
year = {2026},
author = {Alamri, MM and Proctor, G and Garcia-Guevara, F and Guennec, AL and Mainas, G and Shoaie, S and Nibali, L},
title = {Multiomics Analyses in Young Grade C Molar Incisor Pattern Periodontitis.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106871},
doi = {10.1016/j.jdent.2026.106871},
pmid = {42379260},
issn = {1879-176X},
abstract = {OBJECTIVE: To explore the microbial profiles in plaque and saliva and metabolic profiles in saliva and serum collected from young patients (≤25 years old) with grade C molar incisor pattern periodontitis (C/MIP), to compare them to age-matched controls and integrate both omics to elucidate C/MIP pathogenesis.

MATERIAL AND METHOD: Thirty-one young patients with C/MIP and 31 periodontally healthy age-matched controls were recruited. Bacterial profiles were investigated in unstimulated saliva and subgingival plaque using shotgun sequencing metagenomics while metabolic profiles were assessed in saliva using nuclear magnetic resonance and serum using mass spectrometry. Data from both omics analyses were integrated and visualised as interaction networks using Cytoscape software.

RESULTS: C/MIP showed significantly lower levels of several salivary (e.g., dimethylamine, proline, glycine) and serum metabolites, and higher levels of others including methyl indole-3-acetate and sulfosalicylic acid, compared to controls (P<0.001). Fifteen bacteria, of which twelve were associated with C/MIP, were differentially prevalent between groups. The plaque microbiome in C/MIP was enriched with pathogenic species such as D. oralis, C. rectus, T. denticola, and P. endodontalis, while health-associated bacteria like R. mucilaginosa and L. hongkongensis were more prevalent in controls. D. oralis and GGB10485-SGB49305 emerged as potential microbial biomarkers. Notably, metabolites such as DL-glutamine and taurine were significantly associated with periodontal pathogens.

CONCLUSION: C/MIP is marked by a distinct dysbiotic microbiome and altered metabolic profile. While key pathogens and metabolites likely contribute to disease progression, the underlying mechanisms remain only partially understood due to the complexity and incomplete characterisation of many associated factors.

CLINICAL SIGNIFICANCE: This study highlighted the multifactorial nature of C/MIP, driven by microbial dysbiosis, immune disturbances, and metabolic alterations. A comprehensive multi-omics approach offered a foundation for understanding microbial-metabolite dynamics in young patients, and highlighted candidate biomarkers for future diagnostics and therapeutics.},
}

@article {pmid42379362,
year = {2026},
author = {Piantoni, P and Sardi, MI and Aumiller, T and Khafipour, E and Roman-Garcia, Y and Chakrabarti, A and Dieho, K and Aubert, T and Schroeder, GF},
title = {Effects of increasing doses of a phytogenic product based on condensed tannins and spices on production performance and rumen microbiome of lactating dairy cows fed a low-protein diet.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28174},
pmid = {42379362},
issn = {1525-3198},
abstract = {The objective of this experiment was to determine the effect of increasing doses of a phytogenic product based on condensed tannins and spices (CTS) on production performance of lactating dairy cows fed a low protein diet. Eight rumen-cannulated Holstein Friesian dairy cows (140 ± 86 DIM; 39.0 ± 5 kg/d milk yield; mean ± SD), were used in a replicated 4 × 4 Latin Square design experiment with 4-wk periods. Treatments were: 0, 10, 20 and 30 g/d CTS (CTR, 10CTS, 20CTS, and 30CTS, respectively). The grass silage and corn silage-based diet was 55.2% forage, 38.7% NDF, 21.0% total starch, and 14.6% CP. Orthogonal contrasts were used to evaluate the linear and quadratic effect of increasing doses of CTS. Results follow the order: CTR, 10CTS, 20CTS, and 30CTS. Increasing doses of CTS quadratically increased DMI (25.4, 25.9, 26.1, and 25.1 kg/d) and milk yield (37.1, 38.5, 37.7, and 36.3 kg/d), tended to increase fat-and-protein-corrected milk (36.9, 37.6, 37.4, and 36.1 kg/d), and did not affect feed or N efficiency (1.45 ± 0.2 and 32.0 ± 2.3%, respectively). Treatments did not affect milk fat yield (1.48 ± 0.2 kg/d) but increasing doses of CTS increased milk protein yield quadratically (1.22, 1.27, 1.26, and 1.20 kg/d). Intermediate doses of CTS tended to increase de novo fatty acid yield (352, 369, 373, and 356 g/d) and decrease trans-10 C18:1 (4.31, 4.05, 4.05, and 4.24 g/d) compared with CTR and 30CTS. Treatments did not affect milk urea concentration (17.8 ± 1.7 mg/dL) or milk crude protein (3.39 ± 0.2%) or fat (4.06 ± 0.2%) content. Rumen pH and time below rumen pH of 5.8 were not affected by level of CTS supplementation. A treatment by time interaction for rumen ammonia concentration indicated that 20CTS and 30CTS increased ammonia concentration 3 h post-feeding compared with CTR and 10CTS (7.72, 7.94, 13.7, and 14.1 mg/dL). The 10CTS treatment decreased rumen propionate concentration only at 3 h post-feeding compared with the other treatments. Apparent DM and NDF total-tract digestibility were not affected by treatments. Shotgun metagenomics were used to evaluate the impact of CTS supplementation on the solid- and liquid-associated rumen microbiome. Treatment effects were only observed in the solid-associated microbiome. Supplementation of CTS linearly decreased α diversity at both the taxa and functional levels, indicating promotion of a leaner microbial community with higher doses of CTS. Differential abundance analysis identified 26 species with large fold changes, including some species with a high presence of cellulases and significant correlations with phenotypic parameters such as DMI, N efficiency, and milk production. In conclusion, a mixture of CTS affected microbiome and rumen metabolism, increasing fat-and-protein-corrected milk yield when fed at 10 and 20 g/d only. This experiment demonstrates the importance of in vivo dose response experiments with phytogenic products to determine optimum dosage for improved rumen metabolism and performance.},
}

@article {pmid42282649,
year = {2026},
author = {Boyd, AI and Quintanilla, KA and Escapa, IF and Lewis, MA and Kafer, LA and Zeng, XL and Blutt, SE and Ibberson, CB and Lemon, KP},
title = {D-alanine aminotransferase (Dat) promotes Staphylococcus aureus colonization fitness on human nasal respiratory epithelium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42282649},
issn = {2692-8205},
abstract = {Nasal colonization by Staphylococcus aureus is an established risk factor for invasive infection, yet bacterial determinants promoting fitness on human nasal mucosa remain incompletely defined. To identify genes required for early colonization of human nasal respiratory epithelium, we colonized human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) with a high-density transposon (Tn) library of the methicillin-resistant USA300 strain LAC. TnSeq analysis identified 165 genes that met our threshold for candidate colonization fitness factors. Among these, genes involved in D-alanine biosynthesis and use were enriched, including two encoding the enzymes that separately synthesize D-alanine in S. aureus: alanine racemase 1 (alr1) and D-alanine aminotransferase (dat). Disruption of dat reduced colonization fitness in competition with the parental strain by ≥ 1,000 fold across 4 different strains from clonal complexes 8, 5, and 30. In competition with the parental strain during HNO-ALI colonization, a dat::Tn mutant was 34-fold less fit than an alr1::Tn mutant. Genetic complementation with single-copy dat expressed from its native operon promoter restored parental colonization levels. Supplementation with exogenous D-alanine or L-alanine also rescued the dat::Tn colonization defect, whereas D-glutamate did not, consistent with Dat primarily producing D-alanine on nasal mucosa. Complementation with dat under control of a putative 5' intra-operon promoter substantially restored colonization but failed to support growth in chemically defined medium lacking L-alanine, suggesting a new layer of environment-specific regulation of dat transcription. Together, these findings demonstrate that Dat is a major source of D-alanine during colonization of human nasal mucosa and is required for S. aureus fitness in this environment.},
}

@article {pmid42366391,
year = {2026},
author = {Lai, T and Liu, Y and Duan, Z and Su, S and Ding, H and Dai, Y and Gao, M and Ji, M and Liao, L},
title = {Deep metagenomics uncovers functional adaptations and pathogenic risks in the gut microbiome of Antarctic fur seals (Arctocephalus gazella).},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00919-2},
pmid = {42366391},
issn = {2524-6372},
support = {2022YFC2807501//National Key Research and Development Program of China/ ; 42476264//National Natural Science Foundation of China/ ; },
abstract = {The Antarctic fur seal (Arctocephalus gazella) plays a key role in the Antarctic marine ecosystem by regulating krill, fish, and cephalopod populations through selective foraging, promoting Southern Ocean productivity via excretion, and influencing coastal island ecosystems during breeding season. Despite the importance of the gut microbiota in reflecting diet, health, and environmental adaptation, the gut microbiome of the Antarctic fur seal remains poorly characterized. To address this gap and evaluate its potential as a bioindicator of Antarctic marine environmental health, we employed shotgun metagenomics and 16S rRNA amplicon sequencing on fresh fecal samples collected from four Antarctic fur seals (designated S59, S62, S63, and S64) at King George Island, Western Antarctica. Despite inter-individual variation, both approaches identified Bacillota as the dominant phylum but showed genus-level discrepancies, with Fusobacterium prevailing in metagenomes and Clostridium in 16S amplicons. Viral communities constituted up to 5.3% of the microbiome, including an immunodeficiency-associated Lentivirus. Chitin-degrading capacity was ubiquitous, consistent with the host's krill-based diet. Metagenome-assembled genomes (MAGs) resolved distinct taxonomic contributions to discrete steps of chitin hydrolysis, suggesting that complete depolymerization requires metabolic cross-feeding among functionally complementary taxa. Notably, Helicobacter MAGs were abundant in individual S62, suggesting potential pathogenicity. Additionally, 16 antibiotic resistance gene types were detected, with bacitracin, polymyxin, and multidrug resistance dominating the resistome. These findings not only elucidate the community composition, functional potential, and ecological adaptation of the Antarctic fur seal gut microbiota but also establish a comprehensive baseline for assessing environmental change and human impacts on the Antarctic marine ecosystem, thereby offering valuable scientific data and methodological insights for the conservation of polar marine mammals.},
}

@article {pmid42366413,
year = {2026},
author = {Li, X and Li, Z and Sun, X and Guo, Y and Pang, Z and Niu, G},
title = {Honghe Bunya-like virus: a novel virus identified in mosquitoes from Yunnan, China.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13112-z},
pmid = {42366413},
issn = {1471-2164},
support = {SDYJSJGC2025059//Shandong Provincial Department of Education/ ; },
abstract = {BACKGROUND: Arboviruses represent a persistent and escalating threat to global public health, with mosquitoes serving as the principal vectors in their natural transmission cycles and geographic dissemination. Yunnan Province, southwestern China, is a recognized hotspot for arboviral diversity, yet the full spectrum of mosquito-borne viruses circulating in this region remains incompletely characterized.

RESULTS: A total of 3,300 female mosquitoes of four species across four genera were collected from rural areas of Honghe County, Yunnan Province in 2024, and subjected to viral metatranscriptomic sequencing. A previously undescribed bunya-like virus, designated Honghe Bunya-like virus, was identified in two locally dominant hematophagous mosquito species, with minimum infection rates of 0.2% and 0.3%, respectively. The viral genome comprises three single-stranded negative-sense RNA segments (L, M, and S) encoding the RdRp, glycoprotein, and nucleoprotein, respectively, consistent with the canonical architecture of the genus Orthobunyavirus. Phylogenetic analyses placed the virus within Orthobunyavirus across all three segments, though inter-segment topological incongruence was observed; amino acid identities to known orthobunyaviruses (49.7%-71.6%) fell below conspecific thresholds, suggesting a novel species.

CONCLUSIONS: This study expands the known genetic diversity of mosquito-associated virus in southwestern China and, given the phylogenetic affinity to pathogenic orthobunyaviruses and the hematophagous nature of the vector species, raises the possibility of vertebrate infection potential warranting further investigation.},
}

@article {pmid42366525,
year = {2026},
author = {Kan, J and Morales-Amador, A and Hernandez, Y and Burian, J and Ternei, MA and Brady, SF},
title = {Resistance-CONKAT-seq Guided Discovery of a ClpP Active Natural Product from a Soil Metagenome.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.6c00347},
pmid = {42366525},
issn = {1554-8937},
abstract = {The discovery of natural products with specific molecular targets from metagenomes remains challenging. To address this limitation, we developed resistance-CONKAT-seq (resistance co-occurrence network analysis of targeted sequences) which links metagenomic BGCs (biosynthetic gene clusters) to potential modes of action through the identification of colocalized molecular target-based resistance genes. Applying this approach to a soil metagenomic library, we identified the uncharacterized metagenomic azetidopyrroline (MTA) BGC associated with a potential clpP self-resistance gene. Genetic engineering and heterologous expression of the MTA BGC led to the discovery of metaze A and B, which are structurally related azetidopyrroline- and bicyclocarbamate-based natural products, respectively. Metaze B inhibited Mycobacterium tuberculosis caseinolytic protease proteolytic subunit (ClpP) with an IC50 of 1.35 μM. This study expands the chemical diversity of natural product ClpP inhibitors and further demonstrates the applicability of resistance-CONKAT-seq for target-guided discovery of natural products with specific modes of action from complex metagenomes.},
}

@article {pmid42366537,
year = {2026},
author = {Meusel, I and Manheim, D and Delaney, O and Greene, D and Tobolsky, R and Palya, H and Shapiro, N and Sharma, S},
title = {A Metagenomic Biosurveillance Network for Emerging Infectious Diseases: A Simulation-Based Model.},
journal = {Health security},
volume = {},
number = {},
pages = {23265094261453732},
doi = {10.1177/23265094261453732},
pmid = {42366537},
issn = {2326-5108},
abstract = {In this article, we propose a metagenomic next-generation sequencing (mNGS) system for symptomatic clinical respiratory disease samples in Israel to enable detection early enough to contain novel pathogen outbreaks, limit international spread and expedite countermeasure development. We built an open-source, interactive SEIR (susceptible, exposed, infectious, recovered)-based model extending the work of Sharma et al (2023) for 7 representative known respiratory pathogens with pandemic potential, aiming to estimate costs and detection time for the identification of a novel respiratory pathogen in Israel through a network of mNGS monitoring in hospitals. We find that a novel pathogen with SARS-CoV-2-like characteristics could be detected within 68 days (interquartile range [IQR]: 53 to 80) after the first 2 emergency department presentations and 213 (IQR: 94 to 429) total infections across Israel. This surveillance system would cost US$24 million annually over 10 years when implemented in Israel's 6 largest hospitals, covering 37% of the population. Our open-source interactive model allows policymakers and experts to explore different system configurations and their associated tradeoffs between cost, detection speed, and population coverage.},
}

@article {pmid42366621,
year = {2026},
author = {Tawfiq, R and Kulmanov, M and Hoehndorf, R},
title = {Evaluating completeness, coherence, and consistency of genome-scale function annotations.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
doi = {10.1093/bib/bbag336},
pmid = {42366621},
issn = {1477-4054},
support = {URF/1/5041-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5235-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/4938-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5659-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; 5932//King Abdullah University of Science and Technology (KAUST)-KAUST Center of Excellence for Smart Health (KCSH)/ ; 5940//King Abdullah University of Science and Technology (KAUST)-Center of Excellence for Generative AI/ ; //KAUST Supercomputing Laboratory/ ; },
mesh = {*Molecular Sequence Annotation/methods ; Systems Biology/methods ; *Genome ; *Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; },
abstract = {Protein function annotation traditionally follows a reductionist approach, assigning functions to individual proteins acting in isolation. This treats each annotation as an independent fact, disconnected from the broader biological system. However, proteins operate within integrated networks where their functions depend on genomic context and interacting partners. This needs to be reflected in function annotation and evaluation frameworks. We assess whether annotated protein functions could plausibly coexist within a living organism. To achieve this goal, we formalize three criteria grounded in systems biology principles: completeness (presence of essential functions), coherence (satisfaction of functional dependencies), and consistency (absence of mutually exclusive functions). We applied this framework to manually curated function annotations from six model organisms and computational function predictions from seven methods. While model organism annotations largely satisfied our constraints, computational function prediction methods systematically failed to produce biologically plausible genome-scale annotations. Our review reveals a measurable gap between the per-protein objectives of current annotation methods and the system-level criteria that an annotation set must satisfy to describe a viable organism. Our evaluation framework grounded in systems biology principles provides quantitative metrics for evaluating biological plausibility and establishes a foundation for developing system-aware annotation approaches. Augmenting protein-level annotation with system-level criteria offers a tractable path to improving annotation of the rapidly growing collection of sequenced genomes and metagenomes.},
}

*Molecular Sequence Annotation/methods
Systems Biology/methods
*Genome
*Proteins/genetics/metabolism
Genomics/methods
Computational Biology/methods

@article {pmid42366665,
year = {2026},
author = {Kuzbekov, SR},
title = {[Microbiota and microbiome of the lacrimal drainage system].},
journal = {Vestnik oftalmologii},
volume = {142},
number = {3},
pages = {91-100},
doi = {10.17116/oftalma202614203191},
pmid = {42366665},
issn = {0042-465X},
mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.},
}

Humans
*Microbiota
*Lacrimal Apparatus/microbiology/physiopathology/pathology
*Dacryocystitis/microbiology/diagnosis/physiopathology
*Lacrimal Duct Obstruction/diagnosis
Anti-Bacterial Agents/pharmacology

@article {pmid42366735,
year = {2026},
author = {Guo, X and Lai, CY and Zhao, HP},
title = {Targeted Acclimation Unlocks Adaptive Evolution of a Methanotrophic Consortium Enabling 3A5MI Elimination and Enhanced Sulfamethoxazole Biodegradation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02194},
pmid = {42366735},
issn = {1520-5851},
abstract = {Targeted pollutant exposure is widely used to acclimate microbial communities for enhanced biodegradation of recalcitrant contaminants, yet the evolutionary mechanisms underlying functional reinforcement remain poorly understood. Here, we acclimated a methanotrophic consortium achieving efficient removal of 3-amino-5-methyl-isoxazole (3A5MI) (>90%, >5 mg/L/d) and elucidated the adaptive evolutionary processes behind it. Analyses of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) revealed that dominant Methylococcaceae members served as genetic exchange hubs in the acclimation bioreactor. Integrated metagenomic and metatranscriptomic analyses showed that prolonged 3A5MI exposure activated their MGEs and promoted extensive HGT of genes related to energy generation, oxidative stress defense, and biosynthesis. This adaptive evolution enabled community-level metabolic rewiring, including optimized carbon metabolism to relieve energy limitation, niche differentiation, and specialized transcription of C-N bond catalytic functions. Furthermore, batch experiments and transformation product analyses confirmed that 3A5MI-induced functional traits (e.g., heterocycle hydroxylation and C-N bond catalysis) facilitated complete sulfamethoxazole (SMX) biodegradation. Overall, this study demonstrates the evolutionary plasticity of methanotrophic consortia under targeted acclimation and highlights MGE-driven genetic exchange and metabolic adaptation as key mechanisms that both underpin functional enhancement and support the development of methanotroph-based strategies for the biodegradation of recalcitrant isoxazole-based pollutants.},
}

@article {pmid42367190,
year = {2026},
author = {Teng, Y and Saghaï, A},
title = {Fermentative nitrite ammonifiers are abundant in soils and ecologically distinct from NrfA-dependent ammonifiers.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag144},
pmid = {42367190},
issn = {2730-6151},
abstract = {Microorganisms can use different enzymes to perform nitrite ammonification, the reduction of nitrite to ammonium, an important process to retain nitrogen in soils. Yet, the organisms mediating this process and their distribution in terrestrial ecosystems remain poorly resolved. Here, we determined the phylogenetic diversity of bacteria performing fermentative nitrite ammonification via the NAD(P)H-dependent nitrite reductase NirB, assessed their distribution across terrestrial ecosystems, and identified their environmental preferences. We found that these organisms are broadly distributed, spanning 29 phyla including Bacillota, Pseudomonadota and Actinomycetota. Screening 1587 globally distributed soil metagenomes using a phylogeny-based approach revealed that fermentative nitrite ammonifiers are ubiquitous across biomes and particularly abundant in Mediterranean forests and desert soils. In these ecosystems, they outnumbered NrfA-dependent ammonifiers, the best characterized ammonifier group to date, suggesting distinct ecological niches for the two groups. Consistent with this, random forest modelling revealed a negative relationship between fermentative nitrite ammonifiers and the carbon-to-nitrate ratio, which contrasts with a preference for high carbon-to-nitrate conditions in NrfA-dependent ammonifiers. However, moisture and salinity emerged as the strongest predictors of the abundance of fermentative nitrite ammonifiers, indicating a high tolerance to osmotic stress in this group. Overall, our results demonstrate that fermentative nitrite ammonifiers are both phylogenetically diverse and environmentally widespread, calling for future efforts to determine the conditions under which they contribute to nitrogen retention in soils.},
}

@article {pmid42367193,
year = {2026},
author = {Guo, S and McNamara, NP and Bending, GD and Mushinski, RM},
title = {Phosphorus availability mediates pathway-specific nitrogen cycling in stratified peatland microbiomes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag143},
pmid = {42367193},
issn = {2730-6151},
abstract = {Peatland microbiomes regulate nitrogen (N) cycling processes that control nutrient retention and greenhouse gas emissions in carbon-rich ecosystems. Although depth-driven redox gradients structure microbial communities, how physicochemical stratification shapes the functional versus taxonomic organization of N-cycling microorganisms remains unclear. We used shotgun metagenomics to characterize N-cycling gene distributions, taxonomic affiliations, and metagenome-assembled genomes (MAGs) across depth and vegetation gradients in a temperate blanket bog. Depth emerged as the primary structuring factor, creating functional-taxonomic decoupling. Surface peat (0-20 cm) harbored functionally diverse but taxonomically constrained communities assembled deterministically around nitrification and labile N acquisition, while subsurface peat (20-40 cm) supported taxonomically richer but functionally-simpler communities assembled stochastically and enriched in denitrification and dissimilatory nitrate reduction. Linear mixed-effects models revealed pathway-specific controls on N cycling. Denitrification increased with depth (β = 11.53, P < .05), whereas organic N transformation declined (β = -5.81, P < .05); depth effects on nitrification and N fixation became non-significant after accounting for environmental variables. Phosphorus (P) emerged as the strongest environmental predictor, regulating nitrification (β = 95.40, P < .01), N fixation (β = 128.33, P < .01), organic N transformation (β = 80.53, P < .01), and denitrification (β = -109.63, P < .05), highlighting the importance of P availability in structuring microbial N cycling. This challenges traditional N-limitation paradigms in ombrotrophic systems. MAGs revealed Pseudomonadota as the dominant N-cycling lineage, while incomplete denitrification capacity indicated genetic potential for N2O accumulation in subsurface layers. These findings demonstrate that P availability, rather than N content alone, regulates microbial N transformation capacity in peatlands, with implications for predicting nutrient dynamics under altered hydrological and nutrient deposition regimes.},
}

@article {pmid42367641,
year = {2026},
author = {Xu, C and Liu, T and Zhang, X and Feng, S},
title = {Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.},
journal = {Blood science (Baltimore, Md.)},
volume = {8},
number = {3},
pages = {e00304},
pmid = {42367641},
issn = {2543-6368},
abstract = {In patients with hematological disorders, the high risk of complex infections caused by immune dysfunction and intensive therapies poses a major challenge to the use of conventional microbiological tests (CMTs). Plasma cell-free DNA (cfDNA) metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary noninvasive tool that enables unbiased, broad-spectrum, and rapid pathogen identification directly from blood samples. This review summarizes the core applications of plasma cfDNA mNGS in patients with hematological disorders, including the diagnosis of febrile neutropenia, bloodstream infections, focal infections, and infections caused by uncommon/fastidious pathogens. It highlights the advantages of this technology in overcoming antibiotic interference, enabling early detection, and providing diagnostic value in cases without clear infection foci or when invasive sampling is not feasible. This review further discusses how China has facilitated the widespread adoption of this technology through a localized application model, cost reduction, and the development of clinically relevant interpretation models. Nevertheless, challenges remain, such as lower sensitivity than site-specific specimens in focal infections, and the difficulty in predicting antimicrobial resistance (AMR) on the basis of cfDNA mNGS. Future developmental directions should focus on technical optimization (eg, combined plasma cell-fraction testing), quality assurance and quality control management, multidimensional data integration (eg, host immune response analysis), artificial intelligence (AI)-assisted interpretation, and cost reduction through technology popularization and insurance coverage. These efforts will advance cfDNA mNGS from a pathogen detection tool toward an intelligent clinical decision-support platform, ultimately improving the diagnostic accuracy and clinical outcomes of hematological patients with infections.},
}

@article {pmid42367778,
year = {2026},
author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y},
title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1868704},
pmid = {42367778},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; },
abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.

RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P < 0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P = 0.003) and depletion of Roseburia (1.05% vs. 3.77%, P = 0.005) and Ruminococcus (5.98% vs. 7.85%, P = 0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P = 0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.

CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.},
}

Humans
*Arthritis, Rheumatoid/complications/microbiology
*Lung Diseases, Interstitial/microbiology/etiology
Female
*Metagenomics/methods
Male
*Gastrointestinal Microbiome/genetics
Middle Aged
Feces/microbiology
Aged
*Bacteria/classification/genetics
Dysbiosis/microbiology
*Metagenome

@article {pmid42367784,
year = {2026},
author = {Zheng, X and Li, D and Yao, X and Luo, X and Gao, C and Yan, X},
title = {The gut microbiota-immune-brain axis in post-traumatic stress disorder: mechanistic integration and translational prospects.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1859206},
pmid = {42367784},
issn = {1664-3224},
mesh = {Humans ; *Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Translational Research, Biomedical ; Intestinal Barrier Function ; Neuroimmunomodulation ; },
abstract = {Post-traumatic stress disorder (PTSD) is a complex mental disorder triggered by severe traumatic events. Its pathophysiology involves not only abnormalities in fear memory circuits and neuroendocrine imbalances but also immune dysregulation and alterations in gut homeostasis. In recent years, the gut microbiota, as a crucial regulatory factor connecting the periphery and the central nervous system, has garnered widespread attention for its potential role in the development and progression of PTSD, offering a new integrative perspective for understanding this disorder. This article focuses on the "gut microbiota-immune-brain axis" framework, reviewing evidence related to changes in the composition and function of the gut microbiota in PTSD. It summarizes how these changes may influence neuroplasticity abnormalities and PTSD-related behavioral phenotypes through mechanisms involving microbial metabolite production, modulation of intestinal barrier integrity, immuno-inflammatory responses, regulation of neuroendocrine homeostasis, and blood-brain barrier dysfunction. However, these mechanistic pathways remain incompletely validated in human studies. Existing research suggests that this axis holds significant value in explaining the multisystem pathological features of PTSD. Nevertheless, challenges persist, including ambiguous causal relationships in microbiota-host interactions, limited direct clinical evidence, and insufficient translational research. Current evidence primarily stems from observational studies, preclinical models, and preliminary intervention studies. The explanatory power varies across these evidence levels: population studies primarily establish correlations, animal models facilitate mechanistic validation, metagenomic and metabolic analyses yield functional insights, while clinical intervention data remain exploratory. This article aims to elucidate the key molecular and systemic mechanisms underlying this axis in PTSD and to evaluate the potential translational value and practical limitations of microbial intervention and immune modulation strategies.},
}

Humans
*Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology
Animals
*Brain/immunology/metabolism
Translational Research, Biomedical
Intestinal Barrier Function
Neuroimmunomodulation

@article {pmid42367847,
year = {2026},
author = {Sparagon, WJ and Lary, S and Ioh, MT and Lin, A and Dhungana, I and Fullmer, CR and Handel, CR and Paudel, R and Burden, J and Deubel, JN and Tayo, MAG and Rodriguez, FE and Swift, SOI and Nakayama, KK and Maaz, TM and Nguyen, NH},
title = {Soil Resistomes in a Tropical Watershed are Indirectly Structured by Bacterial Community Interactions with Soil Properties.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.18.733189},
pmid = {42367847},
issn = {2692-8205},
abstract = {Soils are recognized as reservoirs of antibiotic resistance genes (ARGs) with the potential to transfer to clinical pathogens, creating antimicrobial resistance (AMR) that poses a threat to human health. While large-scale AMR surveys have profiled how diverse biomes shape soil resistomes, less is known about the influence of specific soil properties. Here, we combined metagenomics and 16S rRNA amplicon sequencing with isolate-based approaches to investigate drivers of soil AMR across a tropical watershed from beach to mountaintop in Waimea Valley, O'ahu, Hawai□i. We leveraged functional- and taxonomic-classification of resistances to unravel how soil properties interact with bacterial taxa to structure resistomes. Metagenomic- and isolate-resistomes showed remarkable consistency, including a general gradient of increasing AMR from ridge to beach. Resistome functional composition was significantly correlated with total bacterial community structure. The relationship between resistances and soil properties was primarily dictated by taxonomic composition of each resistance. Rifampin- and Vancomycin-ARGs associated with Actinomycetes negatively correlated with soil physical properties, while resistant genes and isolates from Gammaproteobacteria positively correlated with enzymatic activity metrics. These findings indicate that soil properties structure the resistome indirectly through taxonomic filtering of microbial hosts and challenge the notion that AMR is decoupled from phylogenetic relatedness.},
}

@article {pmid42367895,
year = {2026},
author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and De Souza, ML and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH},
title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.13.732064},
pmid = {42367895},
issn = {2692-8205},
abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1 - 3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and L-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.},
}

@article {pmid42368165,
year = {2026},
author = {Tinker, KA and Ross, DE and Beebe, MN and Bagwell, CE and Smallwood, CR and Davis, RW and Gulliver, DM},
title = {Biogeochemical Assessment of Short-Term Hydrogen Storage in Methane Reservoirs with Field Sample Characterization and Reactor Experiments.},
journal = {ACS omega},
volume = {11},
number = {24},
pages = {34976-34986},
pmid = {42368165},
issn = {2470-1343},
abstract = {Hydrogen is a valuable commodity due to its high energy density and properties as a flexible energy carrier. It is possible to store hydrogen by blending it with methane and utilizing existing natural gas infrastructure. However, adapting current methane storage strategies to withstand the expected biogeochemical processes caused by H2 injection has not been fully explored. In this study, a series of experiments were designed to identify potential geochemical and microbial challenges of storing hydrogen/methane gas blends in existing methane reservoirs. First, fluid samples were collected from two methane reservoirs located in the western United States. The geochemical composition, microbial taxonomy, and metabolic potential of each fluid sample were characterized by utilizing ion chromatography (IC), inductively coupled plasma optical emission spectroscopy (ICP-OES), a Total Organic Carbon (TOC) analyzer, 16S rRNA gene amplicon sequencing, and metagenomic sequencing. Next, fluid samples from one field site (Site 2) were used to complete a series of short-term reactor experiments at reservoir conditions (80 °C and ∼1000 psi) for natural gas (100% CH4) and hydrogen blend (80% CH4/20% H2) storage environments. Both biotic and abiotic (sterilized) measurements were conducted to accurately understand and decouple abiotic and microbially driven processes, with the goal of linking these processes to storage impacts. Overall, the two reservoirs had a high, but variable, total dissolved solids (TDS) concentration, with various organic acids including acetate and propionate. The field sample was characterized by a diverse microbial community with the metabolic capacity for sulfur reduction, iron reduction, and acetogenesis. Across these reactors, there was minimal change in the fluid geochemistry and a minimal (0-5%) decrease of hydrogen gas during the initial storage event (days 1-3). This work contributes to the understanding of the complexities of hydrogen storage and demonstrates the need for additional research.},
}

@article {pmid42368245,
year = {2026},
author = {Bahr, NC and Kasibante, J and Nsangi, L and Kagimu, E and Ssebambulidde, K and Rutakingirwa, MK and Tugume, L and Ramachandran, PS and Cresswell, F and Meya, DB and Boulware, DR and Wilson, MR and Ellis, J},
title = {Central Nervous System Toxoplasmosis is an Under-Recognized Opportunistic infection in Uganda.},
journal = {Journal of tropical medicine},
volume = {2026},
number = {},
pages = {2158978},
pmid = {42368245},
issn = {1687-9686},
abstract = {In Uganda, Toxoplasma meningoencephalitis remains underdiagnosed due to the low sensitivities and specificities of available diagnostics. In our recent publication, we identified 15 cases of possible Toxoplasma gondii meningoencephalitis by cerebrospinal fluid metagenomic next-generation sequencing in patients with suspected meningitis. We herein discuss, in detail, these cases to highlight the ongoing limitations of utilizing clinical symptoms to diagnose Toxoplasma gondii meningoencephalitis, the importance of access to rapid diagnostics, and the frequency of toxoplasmosis as a possible co-infection with other opportunistic diseases among people with advanced HIV.},
}

@article {pmid42368276,
year = {2026},
author = {Zhu, H and Lin, Y and Liao, H and Li, X and Xie, Q and Zheng, Y},
title = {Infantile pulmonary abscess due to Mycobacterium abscessus subsp. massiliense identified by integrated mNGS and targeted NGS: a rare case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1828339},
pmid = {42368276},
issn = {2296-2360},
abstract = {BACKGROUND: To describe a rare case of pulmonary infection caused by Mycobacterium abscessus in an infant and to evaluate the complementary diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying non-tuberculous mycobacterial (NTM) infections when conventional testing is inconclusive.

CASE PRESENTATION: A 3-month-old male infant presented with a persistent cough and a right upper-lobe mass, initially suspected to be a congenital malformation or neoplasm. Following inconclusive routine examinations, mNGS was performed on bronchoalveolar lavage fluid (BALF). mNGS detected a single read of M. abscessus in BALF, providing an initial diagnostic clue. Subsequently, a tNGS assay was conducted on both BALF and resected lung tissue to achieve precise species identification. tNGS identified 13,272 reads of M. abscessus subsp. massiliense in BALF and 31,474 reads in lung tissue, confirming the pathogen and enabling precise molecular diagnosis. Histopathological examination revealed granulomatous inflammation with multinucleated giant cells, consistent with NTM infection. Guided by these results, the patient initially received azithromycin and was transferred to a specialized chest hospital, where a multidrug anti-NTM regimen was formulated, including azithromycin, imipenem-cilastatin, cefoxitin, and linezolid. After continued treatment at a local municipal hospital, respiratory symptoms resolved, inflammatory markers improved, follow-up CT showed progressive absorption of the right upper-lobe lesion with a small residual cavity, and the patient was discharged in stable condition without recurrent infections during available follow-up.

CONCLUSION: This case highlights the diagnostic utility of integrating mNGS and tNGS for the accurate identification of rare NTM infections in infants, particularly when routine microbiological tests and imaging findings are inconclusive.},
}

@article {pmid42368287,
year = {2026},
author = {Li, M and Sun, Z and Jia, T and Ma, M},
title = {Insights into the mechanism of intestinal flora imbalance and immune disorder in co-morbidity of pneumonia and diarrhea in children.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1836762},
pmid = {42368287},
issn = {2296-2360},
abstract = {Pneumonia and diarrhea are the two leading causes of death in children under five years of age, and these two conditions often present as a comorbidity, where the same child experiences respiratory and digestive system infection symptoms simultaneously or sequentially. Clinical data indicate that the incidence of secondary diarrhea in children hospitalized with pneumonia is high, significantly prolonging hospital stays and affecting prognosis. In recent years, the proposal of the gut-lung axis theory has provided a novel perspective for understanding this comorbidity phenomenon. The gut-lung axis refers to the bidirectional regulatory pathway between the gut microbiota and the pulmonary immune system, with the lungs and intestines sharing embryonic origin and a common mucosal immune system. This review systematically reviews the characteristics of gut microbiota dysbiosis and the mechanisms of immune disorders in the context of pediatric pneumonia-diarrhea comorbidity. Clinical studies have shown that children with comorbidity exhibit significant gut microbiota dysbiosis, characterized by a reduction in beneficial bacteria such as Bifidobacterium, an increase in opportunistic pathogens such as Escherichia coli, and decreased microbial diversity. Gut microbiota dysbiosis leads to immune disorders through multiple mechanisms, including reduced short-chain fatty acids, skewed immune cell differentiation, and dysregulated inflammatory factor networks, resulting in Th1/Th2 imbalance, decreased regulatory T cell function, and exacerbated systemic inflammatory responses. Supplementation with microecological preparations such as Saccharomyces boulardii has been shown to significantly shorten hospital stays, diarrhea duration, and fever resolution time, while improving peripheral blood immunoglobulin levels and T-cell subsets, providing evidence-based support for clinical intervention. This review also systematically reviews clinical laboratory indicators associated with comorbidity, including inflammatory markers, immune status indicators, intestinal barrier function markers, and microbiota detection methods, which have important application value in early identification, disease assessment, and treatment monitoring of comorbidity. Future research should further employ metagenomic approaches combined with longitudinal follow-up designs to elucidate the roles of specific bacterial species/strains in gut-lung axis regulation, providing new strategies for precision prevention and treatment of pediatric pneumonia-diarrhea comorbidity.},
}

@article {pmid42368316,
year = {2026},
author = {Zheng, H and Zhuang, J and Lin, Q and Wang, T and Guo, G and Huang, L and Lin, W},
title = {Study on the role and clinical relevance of gut microbiota in diabetic foot ulcers.},
journal = {3 Biotech},
volume = {16},
number = {7},
pages = {287},
pmid = {42368316},
issn = {2190-572X},
abstract = {UNLABELLED: Diabetic foot ulcers (DFU) are severe and costly complications of diabetes, predisposing to infection, amputation, and mortality, highlighting the urgent need to clarify their mechanisms for optimized clinical management. This study integrated clinical biochemistry data and multi-omics analyses (including metagenomic sequencing) from 11 patients to reveal the critical role of gut microbiota in the pathogenesis of DFU. Results showed significant host metabolic disorders in DFU patients, characterized by hypoalbuminemia (mean ± SD:32.35 ± 6.02 g/L), persistent hyperglycemia (mean ± SD:8.25 ± 3.21 mmol/L), and imbalances in trace elements such as magnesium (mean ± SD:0.84 ± 0.08 mmol/L). Concurrently, the gut microbiota composition was markedly altered, with enrichment of the phylum Bacillota_A (formerly Firmicutes; 48.7% in patients vs. 32.1% in controls) and elevated genetic potential of virulence genes (e.g., type VI secretion systems, capsular polysaccharide gene cps4J/L). Metagenomic tracing revealed that antibiotic resistance genes (ARGs) such as tet(A) and blaOXA-1 were co-localized with mobile genetic elements (MGEs) including IncF plasmids and tnpA transposases. 99.2% of key ARGs shared sequence homology with gut-derived metagenome-assembled genomes (MAGs) and co-localized with MGEs, indicating potential cross-niche transfer capacity. Furthermore, renal (mean ± SD:11.81 ± 5.75 mmol/L) and hepatic (ALT: 35.67 ± 18.22 U/L) dysfunction correlated with aggravated gut dysbiosis and ARG enrichment. In conclusion, this study confirms that host metabolic deficiencies contribute to DFU refractoriness by altering gut microbiota ecology and enhancing horizontal gene transfer of virulence and resistance determinants, providing a novel framework for precision therapies targeting the host-microbe metabolic interface.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04745-8.},
}

@article {pmid42368546,
year = {2026},
author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W},
title = {Erratum: Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1899816},
doi = {10.3389/fpls.2026.1899816},
pmid = {42368546},
issn = {1664-462X},
abstract = {[This corrects the article DOI: 10.3389/fpls.2026.1726191.].},
}

@article {pmid42368826,
year = {2026},
author = {Martínez-Noriega, M and Jean-Louis, P and Philippon, M and Sanchez-Flores, A and Gonzalez-Rizzo, S},
title = {Revealing the bacterial diversity and variation of white filamentous microbial mats in marine mangroves of Guadeloupe Island in relation to human activities.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag034},
pmid = {42368826},
issn = {2633-6685},
abstract = {White filamentous microbial mats are complex benthic communities, typically structured by sulfur-oxidizing bacteria from the Beggiatoaceae family, yet their diversity and ecological responses in mangrove ecosystems remain poorly characterized. Here, we provide a high-resolution analysis of bacterial communities associated with white microbial mats in marine mangrove sediments of Guadeloupe using 16S rRNA metabarcoding. Bacterial community composition was compared across sites with different levels of anthropogenic impact (protected, natural, and urban). While overall diversity remained stable, richness differed significantly between conditions, and beta diversity analyses revealed clear compositional structuring along the disturbance gradient. A conserved core microbiome was identified across all sites, whereas rare taxa were detected exclusively in urban sites, including Ferrimicrobium, Thermonospora, Alcanivorax, and Serratia, which has been previously associated with human-induced environmental changes. In contrast, Prosthecochloris and Chlorobaculum were highly abundant in protected sites, whereas Sulfurovum and Sulfurimonas dominated urban environments. The relative abundance of Beggiatoaceae also varied across sites, suggesting sensitivity to anthropogenic disturbance. Despite these compositional shifts, measured physicochemical parameters did not significantly correlate with the community structure, suggesting that microbial mat organization is influenced by fine-scale or unmeasured environmental gradients. Together, these findings indicate that white microbial mats respond to anthropogenic disturbance primarily through taxonomic restructuring rather than loss of diversity, highlighting their potential as sensitive indicators of environmental change in mangrove ecosystems.},
}

@article {pmid42368984,
year = {2026},
author = {Basbouss-Serhal, I and Fayad, F},
title = {Familial Mediterranean Fever and the Gut Microbiota: A Dual Perspective Review of Current Evidence.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {2},
pages = {302-308},
pmid = {42368984},
issn = {2529-198X},
abstract = {Familial Mediterranean Fever is a well-known autoinflammatory disease resulting from mutations in the MEFV gene. A recent development has linked FMF pathogenesis and mode of expression to the gut micro-biota. There may be a change in the gut microbiota profile of FMF patients, characterised by low diversity and a depletion of beneficial bacteria. Dysbiosis tends to be linked to increased gut permeability, systemic inflammation, and low response to colchicine treatment. Probiotics and prebiotics, in this case, may help restore the previous idyllic state of the microbial balance, along with a reduction in inflammatory markers, thereby demonstrating therapeutic merit. Notably, however, it did argue in some instances that changes in the microbiota were secondary to the genetic and inflammatory nature of FMF itself. It is still important to carry out longitudinal studies of naïve patients that will integrate metagenomics with immune profiling to ascertain whether microbial changes arise from causes, contributions, or coincidence in the pathogenesis of FMF.},
}

@article {pmid42369126,
year = {2026},
author = {Pang, H and Pi, C and Shen, P and Tang, Z and Bao, E and Luo, X and Zhang, Q},
title = {Case Report: pharmaceutical care in a case of complicated urinary tract infection combined with disseminated Nocardia brasiliensis infection.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1839868},
pmid = {42369126},
issn = {2296-858X},
abstract = {Given the increasing prevalence of multidrug-resistant opportunistic pathogens and the high mortality rate associated with delayed diagnosis of disseminated infections, there is an urgent need for rapid diagnostic tools and closely monitored, individualized anti-infective strategies. This study aimed to explore the critical role of comprehensive pharmaceutical care in managing disseminated Nocardia infections complicated by complicated urinary tract infection (cUTI). Through detailed documentation of a 67-year-old male patient, this study focuses on optimizing antimicrobial regimens based on pathogenetic findings and adjusting treatments for severe adverse reactions. The patient was diagnosed with disseminated Nocardia brasiliensis infection complicated by Enterococcus faecalis urinary tract infection using metagenomic next-generation sequencing (mNGS). The treatment process underwent two critical adjustments. First, during the efficacy optimization phase, the initial empirical meropenem therapy was modified to a reinforced regimen centered on trimethoprim-sulfamethoxazole (TMP-SMX), combined with linezolid and short-term amikacin, effectively controlling the spread of infection. Subsequently, during the safety optimization phase, the patient developed severe thrombocytopenia during sequential oral therapy. Prompt identification and switching to amoxicillin/clavulanate potassium resolved the adverse reactions, enabling successful continuation of subsequent treatment. Follow-up revealed a favorable patient recovery. This case demonstrates that for such complex mixed infections, rapid pathogen diagnosis represented by mNGS serves as the starting point for precision treatment, whereas the intensive combination regimen centered on TMP-SMX forms the foundation for controlling disseminated Nocardia infection. More importantly, the core insight from this case is that successful treatment relies not only on appropriate initial medication, but more critically, on proactive, dynamic pharmaceutical monitoring throughout long-term therapy. This enables early intervention for severe adverse drug reactions and timely, flexible adjustments to treatment regimens, which are essential components for ensuring ultimate therapeutic success in patients with such complex infections.},
}

@article {pmid42369553,
year = {2026},
author = {Xu, S and Jia, M and Guo, X and Liang, W and Pan, Y and Lin, Y and Li, X and Qiu, H and Hu, D and Yan, D},
title = {Metagenomics and metabolomics analyses of the mechanism of non-expression of natural mating behavior in captive male Malayan pangolins (Manis javanica).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1828282},
pmid = {42369553},
issn = {1664-302X},
abstract = {Ex situ conservation and captive breeding are important measures for conserving endangered species. However, the reproduction of some wild animals, especially males, is inhibited in captivity, but the underlying mechanism has not yet been elucidated. This study aimed to investigate the microbiota and their functions, metabolites, and their metabolic pathways impacting reproduction employing metagenomics and metabolomics analyses and using male Malayan pangolins with normal (with natural mating behavior) and abnormal (no natural mating behavior) reproduction as the research objects. The results showed that the relative abundance of Proteobacteria, Escherichia coli, and Shigella spp. was significantly higher in the abnormal reproduction (AR) group. However, the relative abundance of Firmicutes and Staphylococcus aureus was significantly higher in the normal reproduction (NR) group. Kyoto Encyclopedia of Genes and Genomes functional pathway enrichment analysis found that citrate cycle (TCA cycle, KO00020) and pyruvate metabolism (KO00620) were significantly enriched in pangolins with AR, whereas gonadotropin-releasing hormone secretion (KO04929) was significantly enriched in pangolins with NR. Metabolites such as tryptophan, arginine, and androgen were significantly enriched in pangolins with AR, whereas L-proline, taurine, choline, and spermidine were significantly enriched in pangolins with NR. Microbiota dysbiosis, energy metabolism disorder, deficiencies in key metabolic pathways and metabolites, and hormonal disturbances are all potential factors contributing to the inability of male Malayan pangolin to express natural reproductive behavior. This study provides evidence for AR of captive pangolins and offers important insights for the conservation of captive endangered species.},
}

@article {pmid42369554,
year = {2026},
author = {Zi, GR and Zhang, DJ and He, DL and Shu, F and Ou, Y and Ke, CX},
title = {Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843102},
pmid = {42369554},
issn = {1664-302X},
abstract = {Rapid and accurate detection of pathogenic microorganisms is the key to clinical diagnosis and treatment as well as public health prevention and control. As a representative of the third-generation sequencing technologies, nanopore sequencing technology has brought revolutionary potential to the field of pathogen detection by virtue of its unique advantages such as long read length, real-time sequencing and portable instruments. This paper aims to review the current application status of this technology and prospect its future development. Firstly, the basic principles and the development of mainstream platforms of nanopore sequencing are outlined. Subsequently, its specific applications in the detection of various pathogens including bacteria, viruses, fungi and parasites are systematically elaborated, with a focus on analyzing the practice and remarkable advantages of this technology in scenarios such as direct metagenomic detection without culture, rapid identification of drug resistance and virulence factors, and point-of-care rapid diagnosis. Meanwhile, this paper also objectively discusses the main technical challenges faced in the current application, including the raw read accuracy, the complexity of bioinformatics analysis and the balance between cost and benefit. Finally, the future technological optimization, standardization of data analysis workflows and the expansion of broader clinical application scenarios are prospected. Importantly, this review aims to equip clinical laboratory professionals with a balanced, evidence-based framework to evaluate the readiness, utility, and implementation pathway of nanopore sequencing for specific diagnostic use-cases (e.g., urgent meningitis/endophthalmitis, culture-negative infections, resistance gene detection) within the constraints of a clinical lab, such as cost, turnaround time, and staff expertise, in order to provide new technical perspectives and theoretical support for the precise diagnosis and active surveillance of infectious diseases.},
}

@article {pmid42369768,
year = {2026},
author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G},
title = {A foundational quantum framework for multi-pattern string matching in k-mer detection.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1802517},
pmid = {42369768},
issn = {2673-7647},
abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.

METHOD: We implement two quantum algorithms for DNA multi-pattern string matching for k-mer detection, leveraging Grover's amplitude amplification under the idealized quantum random access memory (QRAM) framework. The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O (√S) query complexity for S text positions but requiring O (m · L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O (√S · √m) in total. These asymptotic gains highlight the potential advantages that could be unlocked by future large-scale, low-noise QRAM architectures, positioning our results as a promising proof-of-concept foundation.

RESULTS: This work introduces two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.

CONCLUSION: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.

To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.},
}

@article {pmid42369969,
year = {2026},
author = {Wei, M and Xiao, Z and Du, X and Cao, J and Wu, S and Zhang, R and Yang, X and Fan, C and Lian, J and Kang, W and Wang, C and Ye, C},
title = {mNGS-Identified Mycobacterium porcinum Infection in a Newly Diagnosed Person With HIV Presenting With Recurrent Suppurative Cervical Lymphadenitis.},
journal = {Open forum infectious diseases},
volume = {13},
number = {6},
pages = {ofag373},
pmid = {42369969},
issn = {2328-8957},
abstract = {Although reports of human infection caused by Mycobacterium porcinum (M. porcinum) have gradually increased in recent years, cases occurring in people with HIV (PWH) remain rare, and the association between M. porcinum infection and suppurative cervical lymphadenitis in PWH has not been previously reported. In this case, metagenomic next-generation sequencing was used to rapidly identify M. porcinum from a pus specimen obtained from a newly diagnosed person with HIV presenting with suppurative cervical lymphadenitis as the initial manifestation. Recognition of these rare clinical features may improve understanding of non-tuberculous mycobacterial infections in PWH and their diverse clinical presentations.},
}

@article {pmid42370219,
year = {2026},
author = {Niu, X and Yu, Q and Gu, J and Lu, B and Shen, W and Tian, J},
title = {Disseminated Mycobacterium avium Complex Infection in an HIV Patient with a History of Talaromyces marneffei: Diagnostic Value of Blind Subculture and Suspected Management Challenges of Immune Reconstitution Inflammatory Syndrome.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {606947},
pmid = {42370219},
issn = {1178-6973},
abstract = {This study reported a 33-year-old male acquired immune deficiency syndrome (AIDS) patient with a 10-year human immunodeficiency virus (HIV) infection history, poor antiretroviral therapy (ART) adherence, and two previous Talaromyces marneffei infections. Self-discontinuation of ART led to severe immunosuppression and disseminated Mycobacterium avium complex (MAC) infection involving the bloodstream and bone marrow. After the restart of ART, the patient developed persistent high fever, which was clinically suspected to be MAC-associated immune reconstitution inflammatory syndrome (IRIS). However, due to the lack of serial HIV viral load and CD4[+] T lymphocyte data, a definitive diagnosis could not be established. The patient was admitted with fatigue, anorexia, and black stool as the main symptoms. MAC infection was confirmed by blood culture, bone marrow culture, and bone marrow metagenomic next-generation sequencing (mNGS) at a higher-level hospital. Notably, after transfer to our hospital, the microbiology laboratory performed blind subculture on routinely negative blood culture bottles and extended the incubation period to 15 days, successfully isolating MAC. This highlights the crucial significance of close clinical-laboratory collaboration and optimized pathogen detection for diagnosing non-tuberculous mycobacteria (NTM) infections. After initial infection control and ART restart, the patient developed recurrent fever. Given the temporal association with ART reinitiation and the dose-dependent correlation between fever and glucocorticoid adjustments, possible MAC-associated IRIS was suspected. The patient's clinical symptoms improved with glucocorticoid therapy, though this does not confirm the diagnosis. Complications including cytomegalovirus reactivation, adverse drug reactions, and human rhinovirus co-infection were managed in a standardized manner. This case suggests that the diagnosis of disseminated MAC infection in severely immunocompromised AIDS patients relies on efficient collaboration between clinicians and laboratories. However, in the absence of confirmatory immunological and virological evidence, the diagnosis of IRIS remains uncertain. Clinicians should remain vigilant for suspected IRIS when restarting ART while acknowledge that limited data may preclude a definitive diagnosis. Individualized comprehensive strategies covering anti-infection, immunomodulation, anti-inflammation, and supportive treatment are the key to managing such complex HIV-related opportunistic infections.},
}

@article {pmid42370222,
year = {2026},
author = {Chen, M and An, W and Fang, S and Zhang, M},
title = {Efficacy and Safety of Omadacycline in Patients with Mycoplasma Pneumoniae Harboring the 23S rRNA A2063G Mutation.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {601060},
pmid = {42370222},
issn = {1178-6973},
abstract = {OBJECTIVE: Mycoplasma pneumoniae is a major pathogen of community-acquired bacterial pneumonia (CABP). Macrolide-resistant Mycoplasma pneumoniae (MRMP) harboring the 23S rRNA A2063G mutation poses a global therapeutic challenge. Omadacycline, a novel aminomethylcycline approved for CABP, exhibits activity against MRMP. However, real-world data on omadacycline for A2063G-mutated MRMP pneumonia remain limited. In this study, we present our clinical experience with intravenous omadacycline in patients with genetically confirmed A2063G-mutated MRMP pneumonia.

METHODS: We retrospectively analyzed the clinical data of eight patients with MRMP pneumonia confirmed by metagenomic next-generation sequencing (mNGS). All patients had failed prior macrolide or fluoroquinolone therapy and received a 7-day course of intravenous omadacycline. Clinical symptoms, inflammatory parameters, chest CT findings, and safety were evaluated.

RESULTS: Eight patients were included. Significant reductions in inflammatory markers were observed after treatment: the neutrophil count decreased from (6.92 ± 2.13)×10[9]/L to (4.67 ± 1.03)×10[9]/L (P = 0.02), C-reactive protein decreased from (68.17 ± 50.35) mg/L to (14.77 ± 19.34) mg/L (P = 0.01), and serum amyloid A decreased from (497.28 ± 319.79) mg/L to (28.35 ± 32.28) mg/L (P < 0.01). Chest CT showed marked resolution of pulmonary lesions in seven patients. No treatment-related adverse events requiring discontinuation were reported.

CONCLUSION: Omadacycline demonstrates promising clinical efficacy and a favorable safety profile for the treatment of pneumonia caused by A2063G-mutated MRMP, promoting both clinical and radiological recovery. Larger prospective controlled studies are warranted to confirm these findings.},
}

@article {pmid42370333,
year = {2026},
author = {Mahlich, Y and Sohi, H and Veličković, M and Piehowski, PD and McDermott, JE and Gosline, SJC},
title = {spammR: an R package designed for analysis and integration of spatial multi-omic measurements.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag163},
pmid = {42370333},
issn = {2635-0041},
abstract = {MOTIVATION: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics.

RESULTS: To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with the goal of integration across multiple data types (e.g. sequencing, metabolites, proteins) within the same tissue.

spammR is implemented in R. The package is currently installable from GitHub (https://pnnl-compbio.github.io/spammR/).},
}

@article {pmid42370706,
year = {2026},
author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, MØ},
title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057726},
doi = {10.1128/msystems.00577-26},
pmid = {42370706},
issn = {2379-5077},
abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.},
}

@article {pmid42370707,
year = {2026},
author = {Victorsen, A and Knutson, TP and Bolender, L and Jung, S and Ferrieri, P and Thyagarajan, B and Hilt, EE},
title = {Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0366625},
doi = {10.1128/spectrum.03666-25},
pmid = {42370707},
issn = {2165-0497},
abstract = {UNLABELLED: Metagenomic next-generation sequencing (mNGS) in the infectious disease diagnostic space has been gaining traction and is popular for aiding in the diagnosis of central nervous system infections. However, many challenges and obstacles remain in making this technology a gold standard for infectious disease diagnostic testing. One major challenge is being able to distinguish between the clinically relevant organisms from background contamination. We performed a validation study for mNGS on cerebrospinal fluid (CSF) that utilized positive clinical samples and contrived samples that incorporated a bioinformatics pipeline that can better distinguish between background contamination and clinically relevant organisms and used a three-tiered reporting algorithm meant to decrease the inherent subjectivity that comes with interpreting and reporting data from clinical metagenomic sequencing. The validation of this assay and category-based reporting pipeline revealed an overall concordance of 91.8%, with a sensitivity of 100% and a specificity of 72.4%. In addition, we improved the detection of clinically relevant RNA viruses to almost 100% in the CSF by modifying the wet lab processing of the sample. This bioinformatics pipeline with a category-based reporting algorithm will provide more confidence in reporting microorganisms detected with this technology, mNGS, and improving patient care.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) can offer a broad, unbiased approach for the detection of infectious pathogens and has shown promise in diagnosing central nervous system infections. Despite its potential, clinical implementation remains limited by challenges in distinguishing clinically relevant organisms from background contamination. This study validated an mNGS assay for cerebrospinal fluid that incorporates an optimized bioinformatics pipeline with a three-tiered reporting algorithm designed to reduce subjectivity and enhance diagnostic confidence. The assay also has improved detection of clinically relevant RNA viruses through modified wet-lab processing. These findings support the clinical utility of a structured, category-based reporting approach for mNGS, advancing its reliability as a diagnostic tool in infectious disease testing.},
}

@article {pmid42370713,
year = {2026},
author = {Trubl, G and Roux, S and Kellom, M and Vyshenska, D and Tomatsu, A and Singh, K and Kimbrel, JA and Eloe-Fadrosh, E and Malmstrom, RR and Pett-Ridge, J and Blazewicz, SJ},
title = {Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113625},
doi = {10.1128/msystems.01136-25},
pmid = {42370713},
issn = {2379-5077},
abstract = {Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H2[18]O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant [18]O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10[10] to 6.59 × 10[10] virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H2[18]O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.},
}

@article {pmid42370731,
year = {2026},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L},
title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040726},
doi = {10.1128/msystems.00407-26},
pmid = {42370731},
issn = {2379-5077},
abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}

@article {pmid42370747,
year = {2026},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.},
journal = {mBio},
volume = {},
number = {},
pages = {e0338225},
doi = {10.1128/mbio.03382-25},
pmid = {42370747},
issn = {2150-7511},
abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}

@article {pmid42371112,
year = {2026},
author = {Tang, A and Cao, Q and Wang, M and Li, W and Xu, H and Wang, Y and Niu, H and Wang, H and Ma, G and Jia, K and Feng, X and He, C and He, J and Alballa, MM and Liao, X and Tian, T and Qin, B and Yang, N and Wei, J and Sun, J and Wang, Y and Cheng, Y and Wu, Q and Yang, J and Wang, Q and Wang, X and Liu, X},
title = {The effectiveness of a plant-based milk with fermented brown rice on constipation symptoms via gut microbiota modulation: a double-blind randomized controlled trial.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42371112},
issn = {1436-6215},
support = {DW080038K0000004//Xi'an Jiaotong University/ ; 82011530197//National Natural Science Foundation of China/ ; 202405212//Feihe Research Grant/ ; },
mesh = {Humans ; *Constipation/microbiology/diet therapy ; *Oryza ; Double-Blind Method ; Female ; *Plant-based Milk ; Adult ; *Gastrointestinal Microbiome/physiology ; Animals ; Middle Aged ; Fermentation ; Fermented Foods ; },
abstract = {PURPOSE: To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.

METHODS: This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500 ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).

RESULTS: A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all P < 0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus Blautia, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.

CONCLUSION: Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.

CLINICAL TRIAL REGISTRY: This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).},
}

Humans
*Constipation/microbiology/diet therapy
*Oryza
Double-Blind Method
Female
*Plant-based Milk
Adult
*Gastrointestinal Microbiome/physiology
Animals
Middle Aged
Fermentation
Fermented Foods

@article {pmid42371206,
year = {2026},
author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T},
title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42371206},
issn = {1573-0972},
support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; },
mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth & development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenome ; China ; Microbiota/genetics ; },
abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.},
}

*Phosphorus/metabolism
*Soil Microbiology
*Soil/chemistry
*Nitrogen/metabolism
Oryza/growth & development
*Nitrogen Cycle
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenome
China
Microbiota/genetics

@article {pmid42371248,
year = {2026},
author = {Tlaskalová-Hogenová, H and Hrnčíř, T and Štěpánková, R and Trebichavský, I and Hudcovic, T and Šplíchal, I and Šplíchalová, A and Šinkora, M and Funda, D and Sánchez, D and Kverka, M and Jirásková Zákostelská, Z and Kostovčíková, K and Coufal, Š and Procházková, P and Roubalová, R and Vannucci, L and Miler, I},
title = {Gnotobiology: from 19th-century global foundations to 21st-century omics - six decades of Czech contribution to microbiome research.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42371248},
issn = {1874-9356},
support = {22-12533S, 22-21356S, 23-05645S, 25-16094S, 26-21469S//Czech Science Foundation (GAČR)/ ; LUAUS23014//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//European Union - Next Generation EU (Operational Programme Johannes Amos Comenius)/ ; LX22NPO5102//European Union - Next Generation EU (National Institute for Cancer Research, Programme EXCELES)/ ; RVO: 61388971//Institute of Microbiology of the Czech Academy of Sciences/ ; NU21-04-00443, NU22-09-00493, NU22J-05-00056, NU23-01-00288, NU23-04-00381, NU23-05-00133, NW24-06-00509, NW24-07-00042, NW25-04-00079//Czech Health Research Council (AZV ČR)/ ; },
abstract = {Gnotobiology, from the Greek gnotos (meaning 'known') and bios (meaning 'life'), is a research discipline that uses organisms with a defined microbiological status to study the interaction between hosts and microbes. This review traces six decades of Czech gnotobiology, beginning with the launch of a dedicated gnotobiology programme at Nový Hrádek in 1962 by Jaroslav Šterzl, whose visionary aims anticipated by decades the current recognition of the microbiota as a central determinant of immune and broader physiological function. The site - originally established in 1953 as the Biological Station - was thereby transformed into one of only four gnotobiological laboratories worldwide at that time and the first in Central and Eastern Europe. The facility pioneered the rearing of germ-free piglets, rats, rabbits, and mice, establishing the experimental foundation for the laboratory's work on immune ontogeny, mucosal immunity and tolerance, and microbiota-host interactions in immune development and regulation. This review discusses the key discoveries made using these models. Among them, work at the Institute of Microbiology (Prague and Nový Hrádek) demonstrated that germ-free animals have underdeveloped lymphoid tissue and impaired adaptive immunity. The review also describes the subsequent development of gnotobiotic models of human metabolic, immune-mediated, neoplastic, and neuropsychiatric diseases. The completion of the Human Genome Project in 2001 and the emergence of microbial metagenomics in the early 2000s sparked renewed interest in host-microbe interactions and led to a rediscovery of gnotobiotic approaches as essential tools for establishing causation in microbiome research. We examine how integrating these approaches with high-throughput sequencing, metabolomics, and other omics technologies has shifted the focus from cataloguing the microbiome to mechanistically dissecting host-microbe interactions. Finally, we outline future directions, including humanized gnotobiotic models, microbiota-based therapeutics, and the convergence of gnotobiology with personalized medicine and synthetic biology.},
}

@article {pmid42371328,
year = {2026},
author = {Pattani, V and Kaneriya, J and Joshi, K and Sanghvi, G},
title = {Microbial Metabolic Strategies for Environmental Detoxification: From Enzymatic Mechanisms to Synthetic Biology and Omics.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42371328},
issn = {1559-0291},
abstract = {Microorganisms play a pivotal role in environmental detoxification by utilizing their metabolic pathways to degrade, transform, or immobilize toxic pollutants such as hydrocarbons, heavy metals, pesticides, and industrial effluents. This review explores microbial enzymatic systems, including oxidoreductases, hydrolases, and transferases, that facilitate pollutant breakdown. Various bioremediation strategies, such as bioaugmentation, biostimulation, and phytoremediation-assisted microbial degradation, are discussed alongside advances in synthetic biology and metabolic engineering, which enhance microbial efficiency for targeted detoxification. The potential of microbial consortia in tackling complex contamination scenarios is also examined. Additionally, omics-based approaches, including metagenomics, transcriptomics, and proteomics, provide deeper insights into microbial community dynamics and metabolic capabilities. Challenges such as environmental limitations, regulatory concerns, and sustainability issues are critically analyzed. By integrating microbiology with biotechnological innovations, microbial metabolism can be effectively harnessed for large-scale pollution mitigation, offering ecofriendly and cost-effective solutions to address global environmental challenges and promote sustainable industrial practices.},
}

@article {pmid42372060,
year = {2026},
author = {Jiang, H and Zhang, M and Khan, RAA and Zhao, J and Hou, J and Liu, T},
title = {Trichoderma enriches Burkholderia via cross-feeding of degradation intermediates to enhance atrazine degradation and alleviate soybean phytotoxicity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag152},
pmid = {42372060},
issn = {1751-7370},
abstract = {The widespread agricultural use of atrazine threatens soil health, and residual phytotoxicity in corn-soybean rotation systems necessitates sustainable remediation strategies. By leveraging the atrazine-degrading fungus Trichoderma lentiforme HN154, we achieved an 80.3% removal of atrazine (500 mg/kg) in non-sterilized soils from a corn planting system within 14 days, 22.1% higher degradation than in sterilized soil, while concurrently alleviating phytotoxic symptoms in soybean plants. Metagenomic analysis revealed that colonization by T. lentiforme HN154 drove restructuring of microbial networks, enriching the keystone family Burkholderiaceae, which was strongly associated with atrazine catabolism and four key catabolic enzymes (EC 3.5.4.43 (atzB), EC 3.5.1.131 (atzE), EC 3.5.1.54 (atzF), EC 3.5.4.42 (atzC)). Among 23 rhizosphere isolates, the Burkholderia strains Bur-4, Bur-5, and Bur-14 showed the highest atrazine degradation rates (26.3% - 29.4%) within 72 h. A Trichoderma-Burkholderia synthetic consortium further enhanced remediation by boosting plant antioxidant defenses (SOD, POD, CAT) and reducing oxidative damage (MDA). Mechanistically, intermediates (hydroxyatrazine and biuret) generated during T. lentiforme HN154-mediated degradation stimulated Burkholderia chemotaxis, swarming and swimming motility, while cross-feeding on these metabolites synergistically accelerated bioaugmentation (the Trichoderma-Burkholderia synthetic consortium achieved rapid atrazine degradation of 86.3% within 168 h). This study reveals tripartite interactions among exogenous microbial degraders, pollutant metabolites, and indigenous microbiota, offering a strategic foundation for microbiome-guided, precision bioaugmentation to restore soil ecological health and crop resilience.},
}