@article {pmid41551460,
year = {2026},
author = {Cornman, RS and Hepner, MJ and Otto, CRV},
title = {The Appalbees menu: a multiyear, multilocus metagenetic assessment of pollen foraging by Appalachian Bombus affinis workers.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20284},
pmid = {41551460},
issn = {2167-8359},
mesh = {Animals ; Bees/physiology ; *Pollen/genetics/classification ; Virginia ; West Virginia ; DNA Barcoding, Taxonomic ; Appalachian Region ; *Feeding Behavior ; Metagenomics ; Pollination ; },
abstract = {BACKGROUND: Detailed studies of foraging behavior are needed for scientific management of the endangered rusty-patched bumblebee (Bombus affinis) in the disjunct and ecologically differentiated habitats it presently occupies. Current knowledge gaps hinder recovery planning but are challenging to redress through direct observation of rare interactions in the field.

METHODS: We used genetic metabarcoding to characterize the taxonomic composition of pollen collected by B. affinis workers in the Appalachian mountains of Virginia and West Virginia from 2021-2023. We developed a custom sequence database of the regional flora and compared results for two independent genetic loci, internal transcribed spacer 1 and internal transcribed spacer 2 (ITS1 and ITS2).

RESULTS: While ITS2 consistently detected more plant diversity, results from the two loci were broadly concordant with a few notable exceptions. The plant genera Hydrangea, Actaea, Rhododendron, Tilia, and (unexpectedly) Laportea were prominent in midsummer samples, with Rubus a consistent contributor in late spring and early summer. Pea flowers (family Fabaceae) were relatively infrequent but the genera Securigera and Trifolium were detected before the Hydrangea bloom and again in late summer afterwards. The diversity of forage plants was highest in late summer, driven primarily by various genera of Asteraceae. Comparing the current data with previous work indicates regional differentiation in forage plants between Appalachia and the upper Midwest, but also allows 'consensus' forage sources that are supported by multiple lines of evidence and shared between regions to be tabulated. These results should help managers focus survey efforts for this endangered species and plan habitat enhancements.},
}

Animals
Bees/physiology
*Pollen/genetics/classification
Virginia
West Virginia
DNA Barcoding, Taxonomic
Appalachian Region
*Feeding Behavior
Metagenomics
Pollination

@article {pmid42012700,
year = {2026},
author = {Chen, J and Xi, M and Hu, W and He, R and Zhang, W and Zhang, Y and Chen, X and Chen, J},
title = {Adult Onset of MSMD Caused by IL-12Rβ1 Variants: Report of a Young Woman with NTM Infection Lacking Bacille Calmette-Guérin (BCG)-induced Diseases.},
journal = {Journal of clinical immunology},
volume = {46},
number = {1},
pages = {},
pmid = {42012700},
issn = {1573-2592},
support = {23141901900//the Shanghai Science and Technology Innovation Action Plan，experimental animal research project/ ; 23PJD073//the Shanghai Pujiang Program/ ; ynms202306//Basic Research Project of the Sixth People's Hospital of Shanghai/ ; },
abstract = {UNLABELLED: Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by increased susceptibility to infections caused by weakly virulent mycobacteria (such as nontuberculous mycobacteria (NTM) or the Bacillus Calmette–Guérin (BCG) vaccine) in otherwise healthy individuals. In this study, we described a 29-year-old patient with MSMD due to NTM infection identified using metagenomic next-generation sequencing (mNGS) testing. The patient showed a poor response to standard antimycobacterial treatment. Therefore, we performed whole-exome sequencing (WES) and identified three heterozygous variants in IL-12Rβ1 (Ala131Thr, Arg323* and Arg561*). The two deleterious IL-12RB1 variants, Arg323* and Arg561*,were shown to be in trans (paternal and maternal, respectively). Further investigation revealed that two of these variants (Arg323* and Arg561*) could affect the binding between IL-12Rβ1 and IL-12Rβ2, leading to a weakened response of CD4[+] T cells to stimulation with IL-12 plus tuberculosis antigen (TbAg), with reduced expression levels of IFN-γ and its downstream target p-STAT4. However, these variants did not affect the CD4[+] T-cell response to glucan stimulation, as the three heterozygous variant loci do not interfere with the aggregation of IL-12Rβ1 and IL-23R. This autosomal recessive, partial IL-12Rβ1 deficiency ultimately resulted in the patient developing disseminated NTM infection. In clinical treatment, we combined IFN-γ with standard antimycobacterial therapy. The patient showed only a partial response to therapy. Therefore, as detection techniques continue to advance, it is important for clinicians to increase their understanding of MSMD to enable faster and more accurate diagnosis and treatment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10875-026-02009-x.},
}

@article {pmid42235671,
year = {2026},
author = {Peng, D and Liu, X and Wang, L and Pan, Y and Kang, B and Liu, X and Xu, R and Cheng, Y},
title = {A multi-omics signature of microplastic exposure and its clinical, metabolic, and microbial correlates in colorectal cancer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128426},
doi = {10.1016/j.envpol.2026.128426},
pmid = {42235671},
issn = {1873-6424},
abstract = {Microplastics (MPs) are emerging environmental contaminants with potential human health implications, yet their distribution and biological effects in colorectal cancer (CRC) remain unclear. Here, we investigate the presence of MPs in blood, tumor, and peri-tumor tissues from CRC patients using a multi-omics approach. We find that MPs, particularly polyvinyl chloride (PVC) and polyethylene (PE), are more abundant in tumor and peri-tumor tissues than in blood. Tissue-specific MPs were associated with clinical traits, serum metabolites, and gut microbes. Functional analysis suggested MP-related alterations in microbial pathways involving carbohydrate metabolism, fatty acid degradation, and bile acid biosynthesis. Our findings provide the first integrative evidence suggesting potential links between MPs exposure to metabolic and microbial dysregulation in CRC patients.},
}

@article {pmid42235696,
year = {2026},
author = {Tang, P and Shuai, H and Yang, Z and Cen, Q and Mao, Y and Wang, J and Zhou, Y},
title = {Contributions and mechanisms of bioclogging-induced oxygen-limited microsites to nitrogen removal in porous media.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135059},
doi = {10.1016/j.biortech.2026.135059},
pmid = {42235696},
issn = {1873-2976},
abstract = {Nitrate (NO3[-]-N) in wastewater treatment plant (WWTP) effluents has become a contributing factor to the increasing eutrophication risk in receiving waters, whereas the relatively high dissolved oxygen (DO, approximately 7-8 mg L[-1]) in effluents constrains NO3[-]-N removal. Constructed wetland systems based on porous media are major technologies for advanced treatment of WWTP effluents. Although bioclogging in such systems is usually regarded as a negative phenomenon, it may create favorable anoxic microenvironments for denitrification through transport confinement. In this study, vertical saturated flow-through porous-media columns were established to systematically elucidate how bioclogging reshapes oxygen transport and drives microbial functional reorganization under bulk-oxic conditions. The results showed that hydraulic conductivity (k) decreased from 27.5 and 18.1 cm s[-1] in Groups A and B, respectively, to < 0.03 cm s[-1], while NO3[-]-N removal increased from 61 to 64% during start-up to 88-91% at day 24. The two-dimensional plate experiment directly captured the full evolution of pore-scale oxygen-limited microenvironments from discrete patches to connected structures. DO heatmaps further showed that bioclogging-induced transport confinement generated nested confined oxygen-limited microsites within an otherwise bulk-oxic flow field. Denitrification-related genes were enriched in the clogging-affected upper and intermediate layers, indicating that efficient denitrification was more likely associated with bioclogging-induced confined oxygen-limited microsites than simply with medium depth. Metagenomic analysis further revealed a metabolic division of labor within the microbial community, with Ectobacillus mainly associated with upstream nitrate reduction, Nitrospira and Chitinophagaceae playing complementary roles in downstream steps, and Ignavibacterium exhibiting genomic signatures consistent with enhanced organic-carbon metabolism and potential reducing-equivalent generation. Overall, bioclogging coupled bulk-oxic and locally oxygen-limited functions through transport confinement and community-level metabolic partitioning, providing new mechanistic insights into stable nitrogen removal under high-DO effluent conditions.},
}

@article {pmid42235698,
year = {2026},
author = {Zhou, X and Yu, Z and Liao, H and Wang, Y and Zhuang, L and Zhou, S},
title = {Bacteria and viruses associated with antibiotic resistome in hyperthermophilic co-composting of cow manure and mushroom residue.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135075},
doi = {10.1016/j.biortech.2026.135075},
pmid = {42235698},
issn = {1873-2976},
abstract = {Antibiotic resistance in livestock-derived wastes represents a critical environmental and public health concern. Here, we applied genome-resolved metagenomic analysis to characterize antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and associated viral communities during co-composting of cow manure and mushroom residue. By day 20, hyperthermophilic composting (HTC) achieved markedly higher ARG removal (93%) than conventional thermophilic composting (TC, 84%). This enhanced performance was associated with the enrichment of thermophilic taxa (e.g., Bacillaceae and Sporolactobacillaceae) and the suppression of mesophilic ARG reservoirs (e.g., Enterobacteriaceae and Pseudomonadaceae). Genome-resolved analysis further revealed that a majority of multidrug-resistant ARB were eliminated during HTC, particularly Klebsiella pneumoniae and Escherichia coli harboring diverse ARGs and virulence factor genes. These high-risk pathogens were predicted to be targeted by a subset of lytic phages, including those affiliated with Autographiviridae and Schitoviridae, suggesting a potential role of lytic phages in suppressing resistance- and virulence-associated ARB. Collectively, these findings provide genome-resolved insights into the coordinated roles of thermophile-driven suppression and phage-mediated predation of ARB in ARG removal, highlighting HTC as a promising strategy for safer manure recycling and resistance risk mitigation.},
}

@article {pmid42235960,
year = {2026},
author = {Chongdar, N and Goyal, A and Damare, SR},
title = {Genomic Survey of Carbon Monoxide Dehydrogenases Reveals Their Widespread Distribution in Marine Habitats.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70375},
doi = {10.1111/1758-2229.70375},
pmid = {42235960},
issn = {1758-2229},
support = {DST/INSPIRE/04/2021/002518//Department of Science and Technology, Govenrnment of India/ ; },
abstract = {Most carbon monoxide (CO) produced in the ocean is consumed by microorganisms encoding carbon monoxide dehydrogenases (CODHs), thereby significantly reducing the flux of CO from the ocean to the atmosphere. CODHs are of two types based on the metal content of their active sites: the oxygen-sensitive, nickel-containing Ni-CODH and the oxygen-tolerant, molybdenum-copper-containing Mo-CODH. Although CODHs have been reported from specific marine environments, their combined distribution across ocean ecosystems remains unclear. Here, we analyzed the NCBI non-redundant protein database and identified 1969 Ni-CODH and 864 Mo-CODH genes from marine prokaryotes spanning diverse oceanic ecosystems. Using metagenomic analyses across three marine biomes, we showed that oxygen availability selectively constrains Ni-CODH gene abundance, but not Mo-CODHs. Thus, Ni-CODHs are restricted to oxygen-limited niches, while Mo-CODHs occur across both oxygenated and oxygen-limited marine environments. Phylogenetic analyses indicated that all previously described CODH clades are represented in the marine ecosphere, highlighting their evolutionary diversity. Genome context analyses suggest that approximately 50% of the marine Ni-CODH potentially participate in carbon fixation via the Wood-Ljungdahl pathway, whereas most marine Mo-CODH likely contribute to the supplementary energy conservation. Together, these results provide an integrated view of CODH distribution and potential function in marine ecosystems.},
}

@article {pmid42236101,
year = {2026},
author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A},
title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).},
journal = {BMJ open},
volume = {16},
number = {6},
pages = {e111607},
doi = {10.1136/bmjopen-2025-111607},
pmid = {42236101},
issn = {2044-6055},
abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.

METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-naïve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.

ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.},
}

@article {pmid42236489,
year = {2026},
author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, LM and Yeow, C and Valentin-Alvarado, L and Adams, PD and Banfield, JF and Siegel, JB and Prywes, N and Shih, PM},
title = {Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73982-5},
pmid = {42236489},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sample and synthesize a library of diverse rubisco sequences with an emphasis on clades that are sparsely represented in the biochemical literature. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily - in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize an unusually large catalytic subunit among characterized rubiscos, originating from a early-branching subclade with secondary structural elements not present in canonical rubisco architectures.},
}

@article {pmid42236734,
year = {2026},
author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L},
title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07581-w},
pmid = {42236734},
issn = {2052-4463},
support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.},
}

@article {pmid42237168,
year = {2026},
author = {Hou, X and Fu, Y and Jia, Z and Hou, L and Yin, Y and Xu, K},
title = {Multi-omics elucidates the regulatory mechanisms of tryptophan in gut health of weaned piglets.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00586-1},
pmid = {42237168},
issn = {2524-4671},
support = {CARS-35//China Agriculture Research System of MOF and MARA/ ; 2023JJ20043//Natural Science Foundation of Hunan Province Project/ ; 32372913//National Natural Science Foundation of China/ ; 2023RC3204//Science and Technology Innovation Program of Hunan Province/ ; },
abstract = {Tryptophan (Trp), an essential amino acid (AA) implicated in diverse physiological and pathological processes, remains incompletely characterized in its mechanisms regulating intestinal health in weaned piglets. In this study, 27 weaned Bama miniature pigs with highly homogeneous genetic characteristics (6.200 ± 0.242 kg) were randomly divided into three groups and fed a basal diet, a diet supplemented with 0.5-fold Trp, or a diet supplemented with 1.5-fold Trp for 21 days. We used multi-omics approaches to investigate the mechanisms by which Trp regulates intestinal health through dietary interventions with different concentrations. Both Trp-supplemented groups exhibited significantly reduced diarrhea incidence (P = 0.012) and improved intestinal morphology compared to the control group (P < 0.05). While Trp-targeted metabolomics showed no statistically significant alterations, metagenomic analysis revealed Trp-driven microbial remodeling, characterized by increased α-diversity, elevated abundances of Deferribacteres, Turicibacter, Clostridials_Bacteria, and Turicibacter_Sanguinis, alongside decreased Tenericutes and Chryseobacterium. Transcriptome analysis further identified immune-related pathways as central targets of Trp action. Subsequent cytokine quantification confirmed Trp's immunomodulatory effects: pro-inflammatory cytokines (IL-1β, IL-6, IL-17) decreased, while anti-inflammatory IL-10 increased. Collectively, our findings demonstrate that Trp alleviates weaning-associated intestinal dysfunction by reshaping microbial ecosystems and regulating immune homeostasis.},
}

@article {pmid42237383,
year = {2026},
author = {Zhang, J and Shi, X and Peng, S and Zhang, C and Qiao, S and Yu, H},
title = {Icariin shapes post-withdrawal fecal resistome dynamics in layer hens.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42237383},
issn = {1674-9782},
support = {B2024064//Hubei Provincial Department of Education Scientific Research Project/ ; 2025RZ026//Research and Innovation Initiatives of Wuhan Polytechnic University/ ; 202409//Open Fund of Hubei Province Key Laboratory of Animal Nutrition and Feed Science/ ; 32402807//Young Scientists Fund of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: While the livestock industry actively seeks alternatives to antibiotics, residual low-dose exposures continue to drive the spread of antibiotic resistance genes (ARGs). Icariin, a plant-derived compound, is recognized for improving poultry growth and immunity. However, it remains unclear how this compound influences the environmental persistence of ARGs, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) during the vulnerable recovery phase after antibiotic withdrawal.

RESULTS: We designed a two-phase feeding trial with laying hens, using longitudinal metagenomic sequencing to track post-withdrawal resistance dynamics. Following initial exposure to a low-dose antibiotic mixture that established a baseline of elevated resistance, hens received either a basal diet, an icariin-supplemented diet, or a copper sulfate-supplemented diet. The data indicate that icariin supplementation consistently reduced the burdens of both ARGs and MGEs. It also suppressed the potential for HGT and restricted the diversity of microbial hosts harboring these resistance elements. Conversely, copper sulfate-a traditional metal-based additive-exacerbated resistance risks by expanding both the abundance and the host range of ARGs and MGEs. Across all treatments, the population of Escherichia and the prevalent ARG subtype bacA correlated strongly with total resistance loads, tracking the overall resistome burden.

CONCLUSIONS: Compared to conventional copper sulfate treatments, icariin facilitates a safer ecological recovery in the poultry gut by actively lowering ARG and MGE reservoirs after antibiotic withdrawal. These genomic insights, combined with its known physiological benefits, support icariin as a sustainable feed additive. Furthermore, the Escherichia-bacA correlation provides a reliable, streamlined indicator for monitoring resistance risks in farm environments. However, as these findings rely on short-term fecal metagenomic tracking, further validation through multi-environment studies is warranted.},
}

@article {pmid42237400,
year = {2026},
author = {Liu, J and Huang, W and Wu, X and Ma, Y},
title = {Coronavirus disease 2019-associated encephalitis and concomitant subdural hematoma: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-026-06148-y},
pmid = {42237400},
issn = {1752-1947},
support = {82171350//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents a global pandemic with evolving viral variants. In addition to respiratory symptoms, a growing trend of reports indicates that the central nervous system could also be affected in COVID-19 patients.

CASE PRESENTATION: Herein, we reported a case of a 61-year-old Chinese male with fever, psychiatric symptoms, and concomitant subdural hemorrhage. Although naso-oropharyngeal swab tests for SARS-CoV-2 ribonucleic acid detections were negative, the metagenomic next-generation sequencing from cerebrospinal fluid (CSF) samples showed the exclusive positive finding of SARS-CoV-2. The patient was diagnosed with probable COVID-19-associated encephalitis, and was recovered after receiving anti-infection medications, high-dose methylprednisolone pulses (1 g/day for 5 days), and subsequent intravenous immunoglobulin (0.4 g/kg body weight for 5 days) therapies.

CONCLUSION: Our case underscores the importance that for patients with fever and unexplained neuropsychiatric symptoms, it is recommended to conduct CSF testing to screen for possible pathogen infections, and to perform cranial imaging promptly to detect concomitant lesions.},
}

@article {pmid42237409,
year = {2026},
author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X},
title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02433-6},
pmid = {42237409},
issn = {2049-2618},
support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; },
abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.

RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.

CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.},
}

@article {pmid42237424,
year = {2026},
author = {Yang, L and Chen, J},
title = {mPower: a real data-based power analysis tool for microbiome study design.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02427-4},
pmid = {42237424},
issn = {2049-2618},
support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; },
abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.},
}

@article {pmid42237575,
year = {2026},
author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT},
title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwag119},
pmid = {42237575},
issn = {1476-6256},
abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.},
}

@article {pmid42237904,
year = {2026},
author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH},
title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01505},
pmid = {42237904},
issn = {1520-5851},
abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.},
}

@article {pmid42237982,
year = {2026},
author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC},
title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.},
journal = {Journal of nutritional science},
volume = {15},
number = {},
pages = {e37},
pmid = {42237982},
issn = {2048-6790},
abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.},
}

@article {pmid42238272,
year = {2026},
author = {Gallina, G and Pizzi, C},
title = {Reference-free k-mer based dissimilarity measures for metagenomes comparison.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1788907},
pmid = {42238272},
issn = {2673-7647},
abstract = {MOTIVATION: Metagenomics plays a crucial role in unraveling the relationship between microbial communities and the environment in which they live, allowing the development of food and environmental control techniques. Similarly, the study of microbial environments within the human body plays a crucial role towards precision medicine. In these contexts, the problem of metagenomic samples comparison is among the most challenging from the computational point of view due to the size of the datasets and to the incompleteness of microbial databases. Thus, the ability to define and efficiently compute reference-free dissimilarity measures is key to the development of effective and practical tools for metagenomes comparison.

RESULTS: In this work, we present a systematic experimental validation of reference-free k -mer-based dissimilarity measures. To this purpose, we investigate the correlation between two popular ecological dissimilarity measures, Bray-Curtis and Jaccard, computed using reference-free and reference-based k -mer approaches, for 12 ≤ k ≤ 31 . Our experiments cover both simulated and real metagenomics settings (samples from the human body and the oceans), and consider both linear and ranking correlation between the computed values. Our results support the hypothesis that the two definitions are indeed correlated for a wide range of values of k , and promote the development of efficient reference-free computational tools based on k -mer statistics for metagenomes comparison.},
}

@article {pmid42238651,
year = {2026},
author = {Zhang, Q and Zhang, X and Cao, M and Ma, J and Yan, R and Wang, H and Jia, S},
title = {Study on the Role and Mechanism of γδ T Cells in Atherosclerosis Under a High-Fat Diet.},
journal = {Reviews in cardiovascular medicine},
volume = {27},
number = {5},
pages = {48002},
pmid = {42238651},
issn = {2153-8174},
abstract = {BACKGROUND: This study aimed to investigate the effects of γδ T cell inhibition under a high-fat diet (HFD) on metabolic function, immune inflammation, gut microbiota, and atherosclerosis (AS) progression in ApoE [-/-] mice.

METHODS: ApoE [-/-] mice were assigned to three groups: a control group (normal diet), a model group (HFD), and an intervention group (HFD + γδ T cell receptor (TCR) monoclonal antibody). After 12 weeks, flow cytometry was used to assess γδ T cell levels, and cytokines (interferon-gamma (IFN-γ), IL-17A) were measured. Inflammatory markers in blood and adipose tissue were quantified, gut microbiota composition was analyzed via fecal metagenomics, and atherosclerosis was evaluated using Oil Red O, Masson's trichrome, and hematoxylin and eosin (HE) staining methods.

RESULTS: The HFD activated γδ T cells and increased pro-inflammatory cytokines in ApoE [-/-] mice. Treatment with the γδ TCR monoclonal antibody suppressed γδ T cells, reduced IFN-γ and IL-17A expression, improved lipid profiles, and decreased tumor necrosis factor-alpha (TNF-α), IL-1β, and IL-6 levels. Gut microbiota analysis showed an increase in beneficial bacteria, and histological staining (Oil Red O, HE, and Masson's trichrome) confirmed a reduction in atherosclerotic lesion burden.

CONCLUSION: The γδ T cells contribute to AS development under the HFD. Inhibition of γδ T cells reduces inflammation, improves gut microbiota composition, and attenuates atherosclerosis progression.},
}

@article {pmid42238901,
year = {2026},
author = {Zhao, T and Chen, Y and Sun, H},
title = {A case of severe Legionella pneumonia treated with omadacycline and nemonoxacin.},
journal = {Respiratory medicine case reports},
volume = {62},
number = {},
pages = {102437},
pmid = {42238901},
issn = {2213-0071},
abstract = {Severe Legionella pneumophila pneumonia carries high mortality, and treatment is challenged by emerging resistance to conventional fluoroquinolones/macrolides and diagnostic delays. Novel agents such as omadacycline and nemonoxacin show theoretical promise, yet robust clinical evidence in legionellosis is lacking. We report a 59-year-old man with severe community-acquired pneumonia(sCAP) who initially received empiric ceftazidime-avibactam plus nemonoxacin. Respiratory failure did not improve, and the inflammatory markers did not decline. Subsequent bronchoalveolar lavage fluid metagenomic next-generation sequencing(BALF-mNGS) and urinary Legionella antigen confirmed Legionella pneumonia. We then switched to dual therapy with omadacycline and nemonoxacin. The combination led to rapid improvements in inflammatory markers, hypoxemia, and creatine kinase levels. This case provides a clinical rationale for using omadacycline plus nemonoxacin as salvage therapy in severe Legionella pneumonia when conventional regimens fail.},
}

@article {pmid42239023,
year = {2026},
author = {Tang, F and Liu, H and Xi, L and Li, C and Wang, X and Wang, B},
title = {Solid-phase enrichment uncovers a hidden Salmonella transmission chain in a recurrent pediatric household cluster: a case report.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1820049},
pmid = {42239023},
issn = {2296-2565},
abstract = {OBJECTIVES: To describe a household cluster of recurrent pediatric non-typhoidal Salmonella (NTS) infection and compare the yield of conventional culture, solid-phase enrichment, and shotgun metagenomic sequencing across symptomatic children and household contacts.

METHODS: Longitudinal fecal specimens from a 4-year-old boy (Mo) with three discrete NTS episodes in 2 months, his monozygotic twin (TB), and three adult co-residents were processed by conventional culture; specimens from Episode 2 onwards and all contact specimens additionally received solid-phase enrichment, and a subset shotgun metagenomics. Isolates were characterized by VITEK 2, XbaI-PFGE, and whole-genome sequencing.

RESULTS: None of Mo's episodes met sepsis criteria (peak WBC 12.52 × 10?/L, CRP 5.46 mg/L, PCT 1.14 ng/mL); TB had one self-limited episode, both parents had brief symptomatic periods, and the grandmother was asymptomatic. Conventional culture was positive only at Mo's first episode, whereas solid-phase enrichment recovered Salmonella from three culture-negative pediatric acute-phase specimens (Mo 4.12, TB 4.16, Mo 5.1). Adult contacts were negative by both culture-based methods, but metagenomic sequencing detected Salmonella reads in all three. Mo_0412 and TB_0416 were S. enterica serovar Enteritidis ST11, with identical cgMLST, 99.9966% ANI, and 97% PFGE similarity, indicating a clonal household source. Mo received antibiotics across four classes during his recurrences, vs. two sequential agents in TB.

CONCLUSION: Conventional culture, solid-phase enrichment, and metagenomic sequencing functioned as complementary modalities, each recovering Salmonella the others missed, supporting a tiered diagnostic strategy for household NTS investigation. Cumulative antibiotic exposure may have contributed to Mo's differential susceptibility, a hypothesis warranting prospective study.},
}

@article {pmid42239051,
year = {2026},
author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H},
title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.22.727306},
pmid = {42239051},
issn = {2692-8205},
abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.},
}

@article {pmid42239166,
year = {2026},
author = {Ghadermazi, P and Emerson, JB and Olm, MR},
title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726564},
pmid = {42239166},
issn = {2692-8205},
abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain .},
}

@article {pmid42239183,
year = {2026},
author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A},
title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.21.727052},
pmid = {42239183},
issn = {2692-8205},
abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.},
}

@article {pmid42239221,
year = {2026},
author = {Keown, RA and Sikkema, AP and Barbone, VA and Ferrell, BD and Donnelly, OB and Iredell, SC and Zatopek, KM and Brumm, PJ and Mead, DA and Lohman, GJS and Wommack, KE and Polson, SW},
title = {Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726624},
pmid = {42239221},
issn = {2692-8205},
abstract = {UNLABELLED: Viruses constitute a significant proportion of Earth's genetic diversity, yet most remain uncharacterized beyond their sequences in viral metagenomes. Linking viral genotypes to phenotypes-especially enzyme function to phage infection dynamics-is challenging due to the lack of cultured virus-host systems. DNA polymerase I (PolA), essential for genome replication in ∼25% of dsDNA phages, provides an opportunity to explore these connections. In phage T7, residue 526 is critical for nucleotide incorporation, with previous in vitro evidence indicating impacts on enzyme efficiency and fidelity. Previous analyses identified three substitutions at this position (Tyr/Y, Phe/F, Leu/L) linked with deeply rooted viral PolA clades. Mutation impacts at residue 526 were tested in vitro and in vivo . The Y526F protein exhibited a 50% reduction in specific activity, and when introduced via High Complexity Golden Gate Assembly into T7 demonstrated a 53% decrease in burst size and significantly longer latent period compared to wild type. The Y526L protein exhibited a 97% decrease in activity, and the Y526L phage was incapable of completing its lifecycle. These findings confirm historical biochemical data, provide in vivo context for these mutations in the T7- E. coli system, and offer experimental support for genotype-to-phenotype associations in viral PolA, informing viral metagenomics studies.

GRAPHICAL ABSTRACT: Created in BioRender. Keown, R. (2026) https://BioRender.com/mhrmup3.},
}

@article {pmid42239239,
year = {2026},
author = {Cho, Y and Tsuboyama, K and Litberg, TJ and Jung, MD and Obisesan, A and Wang, Q and Phoumyvong, CM and Thibeault, J and Ovchinnikov, S and Rocklin, GJ},
title = {Accurate protein stability prediction for small domains using mega-scale experiments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.19.726285},
pmid = {42239239},
issn = {2692-8205},
abstract = {Predicting absolute protein folding stability is a long-standing challenge in biophysics, with broad applications in protein design and in understanding genetic variation and evolution. Physics-based simulations have shown limited success at predicting stability and are often computationally intractable, and machine learning methods have been constrained by the lack of sufficiently large experimental datasets. We recently introduced cDNA display proteolysis, a cell-free approach that can measure folding stability for nearly one million protein domains in parallel. Here, we applied this method to measure stability for 1.8 million diverse protein domains 60-80 amino acids in length primarily taken from the MGnify metagenomic database and spanning over 200,000 sequence families. Using this new "MGnify Stability dataset", we developed the predictive models SaProtΔG and ESM3ΔG, which accurately predict absolute folding stability for small domains with root mean squared error of 0.8 kcal/mol over a 6 kcal/mol range (Spearman rank correlation of 0.88). These predictors show high accuracy at predicting effects of substitutions, insertions, and deletions, successfully identify global trends toward higher stability in thermophilic organisms, and improve discrimination of stable and unstable computationally designed proteins. Our results illustrate how megascale biophysical measurements can complement existing evolutionary and structural data to enable accurate absolute stability prediction for small domains.},
}

@article {pmid42239480,
year = {2026},
author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR},
title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.19.726352},
pmid = {42239480},
issn = {2692-8205},
abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.

RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .

CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.},
}

@article {pmid42239539,
year = {2026},
author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L},
title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1765801},
pmid = {42239539},
issn = {2235-2988},
abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.

METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.

RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.

DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.},
}

@article {pmid42239987,
year = {2026},
author = {Zhao, C and Zhang, L and Wang, Y and Yang, G and Ren, C and Cao, X and Yu, Q and Jin, B and Men, Y and Liu, H and Zhang, J},
title = {Microbial Dehalogenation of 3,5,6-Trichlorooctafluorohexanoic Acid under Different Reducing Conditions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17496},
pmid = {42239987},
issn = {1520-5851},
abstract = {Chlorinated polyfluoroalkyl substances (Cl-PFAS) have emerged as promising alternatives to legacy PFAS due to their enhanced microbial reactivity and improved environmental degradability. However, their transformation mechanisms under environmentally relevant reducing conditions remain poorly characterized. This study investigated the microbial dehalogenation of 3,5,6-trichlorooctafluorohexanoic acid (CTFE3), a representative Cl-PFAS, under nitrate-, sulfate-, iron-reducing, and methanogenic conditions. Microbial defluorination was observed across all reducing environments, with higher total defluorination efficiencies (∼60%) under nitrate- and sulfate-reducing conditions compared to iron-reducing and methanogenic conditions (∼30%) under the tested experimental conditions. Proposed biotransformation pathway analysis suggested that CTFE3 underwent more diverse and sequential hydrolytic dechlorination under nitrate- and sulfate-reducing conditions, which was associated with more extensive defluorination. Genes associated with hydrolytic dechlorination were consistently enriched under these conditions, but not in iron-reducing or methanogenic environments. Metagenomic binning further identified key taxa (e.g., Methyloversatilis discipulorum, Herbaspirillum seropedicae, Paracoccaceae, and Rhodobacteraceae-related bacteria) harboring both hydrolytic dechlorination and nitrate/sulfate-reduction genes, suggesting their involvement in CTFE3 hydrolytic dechlorination and subsequent defluorination. This study demonstrates that reducing conditions play an important role in shaping CTFE3 transformation patterns and highlight hydrolytic dechlorination as a viable pathway associated with extensive microbial defluorination, thereby offering insights for sustainable Cl-PFAS remediation.},
}

@article {pmid42240391,
year = {2026},
author = {de Sousa, LP and Calderon Fajardo, AA and Brandão, MM and Maia de Oliveira, V and Romero, GQ},
title = {Metagenome-assembled genomes of four novel bacterial species from Atlantic rainforest stream sediments in Brazil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0033626},
doi = {10.1128/mra.00336-26},
pmid = {42240391},
issn = {2576-098X},
abstract = {Here, we report draft genome sequences of four novel bacterial species from Atlantic rainforest stream sediments in southeastern Brazil. The genomes represent distinct lineages within Nitrospirota and Pseudomonadota (average nucleotide identity <95% to known species) and encode diverse metabolic capabilities, including nitrification, denitrification, and aromatic compound degradation.},
}

@article {pmid42240519,
year = {2026},
author = {Gharbi, M and Abbassi, MS},
title = {Bacteria as anticancer agents: bioactive metabolites, engineered platforms, and translational mechanisms.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag050},
pmid = {42240519},
issn = {1472-765X},
abstract = {Bacteria represent a vast and underexplored reservoir of bioactive compounds with significant anticancer potential. Numerous bacterial taxa, particularly actinomycetes, Bacillus, Pseudomonas, and marine-derived species, produce structurally diverse metabolites exhibiting cytotoxic, cytostatic, pro-apoptotic, immunomodulatory, and anti-angiogenic activities against cancer cells. Clinically established agents such as actinomycin D and bleomycin highlight the therapeutic relevance of bacterial natural products, while recent discoveries continue to expand the repertoire of bioactive polyketides, peptides, alkaloids, and proteins. These compounds act through multiple mechanisms, including DNA intercalation, induction of apoptosis, cell cycle arrest, metabolic disruption, and modulation of the tumor microenvironment. Advances in metagenomics, genome mining, and synthetic biology have enabled the identification and activation of previously silent biosynthetic gene clusters, significantly enhancing drug discovery potential. In addition to metabolite-based anticancer agents, advances in synthetic biology have enabled the development of engineered bacterial platforms capable of selectively colonizing tumors, delivering therapeutic molecules, and activating prodrug therapies within the tumor microenvironment. Despite ongoing challenges related to toxicity, limited yield, selectivity, and clinical translation, bacterial-derived compounds remain a promising frontier in oncology. This review summarizes bacterial sources, bioactive metabolites, molecular mechanisms, preclinical and clinical applications, and future prospects for developing effective and safe anticancer strategies.},
}

@article {pmid42240631,
year = {2026},
author = {Hernández-Velázquez, R and Hernández-Avilés, JS},
title = {Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {6},
pages = {},
pmid = {42240631},
issn = {1465-2080},
abstract = {Warm monomictic maar lakes in tropical regions represent dynamic systems where thermal stratification generates strong vertical gradients in oxygen availability and redox conditions, shaping microbial community structure and function. Lake Atexcac (Puebla, Mexico) undergoes seasonal stratification and episodic whiting events that provide a framework to examine microbial responses to changing hydrodynamic conditions. In this study, we applied deep shotgun metagenomic sequencing to characterize the taxonomic composition and functional potential of microbial communities across the epilimnion, metalimnion and hypolimnion during two contrasting stratification phases: early stratification associated with a whiting event and a later, well-established stratification period.Metagenomic profiles revealed a clear vertical organization of microbial communities, with samples clustering primarily according to thermal strata and the metalimnion displaying the highest genetic differentiation. Genome-resolved analyses enabled the recovery of a large number of metagenome-assembled genomes, with marked differences in their vertical distribution between hydrodynamic phases. The recovered genomes encompassed diverse metabolic pathways related to carbon, nitrogen and sulphur transformations, reflecting the heterogeneous redox conditions along the water column. Notably, sulphur-related metabolisms were widespread across strata, and Chlorobiota-affiliated genomes and metagenomic reads were consistently detected in suboxic layers. These organisms were found to harbour diverse thiosulphate disproportionation pathways and are thought to play an important role in the sulphur cycle that has not previously been reported in this type of lacustrine system.Overall, this study provides a genome-resolved perspective on microbial diversity and metabolic potential in a stratified tropical maar lake and establishes a baseline for future comparative and process-oriented studies integrating water column and sediment microbial communities.},
}

@article {pmid42241759,
year = {2026},
author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R},
title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107151},
doi = {10.1016/j.psj.2026.107151},
pmid = {42241759},
issn = {1525-3171},
abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.},
}

@article {pmid42241815,
year = {2026},
author = {Zhang, S and Liu, X and Cheng, R and Huang, C and Zhang, Z and Long, S and Yang, Q},
title = {Elucidating the Feammox nitrogen transformation pathway: Key intermediates and putative multi-species metabolic cooperation in a long-term Feammox-dominant system.},
journal = {Water research},
volume = {303},
number = {},
pages = {126223},
doi = {10.1016/j.watres.2026.126223},
pmid = {42241815},
issn = {1879-2448},
abstract = {The emerging Fe(Ⅲ) reduction coupled to anaerobic ammonia oxidation (Feammox) process offers a promising approach toward carbon neutrality in wastewater treatment. However, its nitrogen transformation pathway and metabolic mechanism remain unclear. This study established a Feammox-dominant sequencing batch reactor (Fe-SBR) and operated it for 515 days, achieving an ammonia removal efficiency of 97.9 ± 4.5% during the stable phase. Feammox was confirmed as the dominant process for NH4[+]-N conversion, accounting for 83.2% of ammonia transformation. NH2OH, NO, and N2O were identified as key intermediates in the Feammox nitrogen transformation pathway. By integrating metagenomic analysis of functional gene dynamics with metagenome-assembled genomes (MAGs), a potential coupled iron-nitrogen (Fe-N) metabolic pathway was proposed. This pathway suggested that the Feammox process might be accomplished through multi-species metabolic cooperation, with MtrC-mediated extracellular electron transfer potentially serving as the key link coupling nitrogen transformation to the iron redox cycle. These findings provide novel insights into the Feammox metabolic pathway and lay a theoretical foundation for the future precise control and optimization of this process.},
}

@article {pmid42241861,
year = {2026},
author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L},
title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130128},
doi = {10.1016/j.jenvman.2026.130128},
pmid = {42241861},
issn = {1095-8630},
abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.},
}

@article {pmid42241983,
year = {2026},
author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M},
title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.},
journal = {International journal of food microbiology},
volume = {459},
number = {},
pages = {111881},
doi = {10.1016/j.ijfoodmicro.2026.111881},
pmid = {42241983},
issn = {1879-3460},
abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.},
}

@article {pmid42242027,
year = {2026},
author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M},
title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128569},
doi = {10.1016/j.micres.2026.128569},
pmid = {42242027},
issn = {1618-0623},
abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.},
}

@article {pmid42242076,
year = {2026},
author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG},
title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142602},
doi = {10.1016/j.jhazmat.2026.142602},
pmid = {42242076},
issn = {1873-3336},
abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.},
}

@article {pmid42229597,
year = {2026},
author = {Fard, MB and Kwon, S and Vrieze, J and Wu, D},
title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135056},
doi = {10.1016/j.biortech.2026.135056},
pmid = {42229597},
issn = {1873-2976},
abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.},
}

@article {pmid42229598,
year = {2026},
author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y},
title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135043},
doi = {10.1016/j.biortech.2026.135043},
pmid = {42229598},
issn = {1873-2976},
abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.},
}

@article {pmid42229914,
year = {2026},
author = {Li, H and Yang, L and Chen, B and Zhang, L and Zhu, J and Zhang, H and Lin, L},
title = {Pneumococcal Rib Osteomyelitis With Concurrent Lung and Chest Wall Abscess in an Infant.},
journal = {Pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1542/peds.2025-073077},
pmid = {42229914},
issn = {1098-4275},
abstract = {We present a rare case of a 7-month-old infant with a complex invasive Streptococcus pneumoniae infection involving rib osteomyelitis, a pulmonary abscess, and a chest wall abscess. The patient presented with persistent fever and no respiratory symptoms. On day 9, chest radiography was performed because of persistent fever and marked leukocytosis, consistent with the American College of Radiology Appropriateness Criteria that recommend imaging in febrile infants with high fever (≥39°C) or elevated white blood cell counts (≥20 000/mm3). On day 14, the emergence of a chest wall mass prompted escalation to ultrasonography, which provided noninvasive assessment of soft tissue involvement. Subsequent contrast-enhanced computed tomography scans were undertaken to delineate the extent of contiguous spread, evaluate rib destruction, and exclude alternative diagnoses. Microbiological cultures of sputum and aspirated pus, along with metagenomic sequencing, confirmed the presence of macrolide-resistant S. pneumoniae. Because of benzylpenicillin and cephalosporin allergy, intravenous linezolid was selected, resulting in rapid clinical improvement. A 6-week course (intravenous infusion followed by oral) led to complete resolution on imaging, with no recurrence over 5 years. This case underscores the importance of appropriate imaging modalities in febrile infants without respiratory symptoms and the need to consider extrapulmonary spread in chest wall masses. It highlights the diagnostic value of metagenomic sequencing and susceptibility testing in guiding individualized antimicrobial therapy, particularly in macrolide-resistant settings.},
}

@article {pmid42230119,
year = {2026},
author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G},
title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338252},
pmid = {42230119},
issn = {1468-3288},
abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.},
}

@article {pmid42230654,
year = {2026},
author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F},
title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01029-0},
pmid = {42230654},
issn = {2055-5008},
abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.},
}

@article {pmid42230804,
year = {2026},
author = {Linh, LTK and My, TN and Thi Tran, N and Song, LH and Nurjadi, D and Boutin, S and Velavan, TP},
title = {Metagenomic profiling reveals shared resistome signatures between humans and pigs in Vietnamese smallholder farms.},
journal = {npj antimicrobials and resistance},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44259-026-00223-6},
pmid = {42230804},
issn = {2731-8745},
support = {PACE-UP; DAAD Project ID: 57592343//Deutscher Akademischer Austauschdienst/ ; },
abstract = {Antimicrobial resistance (AMR) is a global health concern, yet the extent of resistant genes and microbial exchange between humans and livestock in low- and middle-income countries remains underexplored. Vietnam, an AMR hotspot, was studied using shotgun metagenomic sequencing of paired faecal samples from pigs and caretakers across 50 small-scale farms. Results revealed 10,270 antimicrobial resistance genes (ARGs) representing 550 unique types, including clinically relevant mcr, blaOXA-58, and optrA genes. Pigs showed higher total AMR abundance, while workers harboured richer resistomes. Approximately 52% (288/550) of ARGs were shared between hosts, dominated by aminoglycoside, β-lactam, and tetracycline resistance genes, often co-located with mobile genetic elements, indicating horizontal transfer potential. Closely related Escherichia coli strains were identified in both hosts, consistent with strain sharing or exposure to common sources beyond individual farms. These findings highlight the human-pig interface as an important setting for shared AMR signatures and support the need for integrated One Health surveillance and antimicrobial stewardship.},
}

@article {pmid42231385,
year = {2026},
author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N},
title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01343-5},
pmid = {42231385},
issn = {1475-2891},
support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; },
abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.

METHODS: A total of 102 male Han participants was randomized to curcumin (812 mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.

RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P = 0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P < 0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P < 0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P < 0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.

CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.

TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.},
}

@article {pmid42231497,
year = {2026},
author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I},
title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02443-4},
pmid = {42231497},
issn = {2049-2618},
abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.

RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.

CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.},
}

@article {pmid42231509,
year = {2026},
author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F},
title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42231509},
issn = {2049-2618},
support = {FESR1078-MummyLabs//European Regional Development Fund/ ; },
abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.

RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.

CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.},
}

@article {pmid42231528,
year = {2026},
author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA},
title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2679516},
doi = {10.1080/19490976.2026.2679516},
pmid = {42231528},
issn = {1949-0984},
abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.},
}

@article {pmid42232316,
year = {2026},
author = {Webster, NS and Bell, SC and Luter, HM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {211},
pmid = {42232316},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).},
}

@article {pmid42232360,
year = {2026},
author = {Li, Y and Yi, G and Han, Z and Fu, J and Xu, L},
title = {Comparison of mNGS microbial detection profiles between percutaneous lung aspiration biopsy and bronchoalveolar lavage fluid in infective pneumonia.},
journal = {Open medicine (Warsaw, Poland)},
volume = {21},
number = {1},
pages = {20261445},
pmid = {42232360},
issn = {2391-5463},
abstract = {OBJECTIVES: To compare the mNGS-based microbial detection profiles of percutaneous lung aspiration biopsy (PLAB) and bronchoalveolar lavage fluid (BALF) in patients with infective pneumonia under real-world clinical sampling strategies.

METHODS: The study included 166 patients with infective pneumonia, of whom 54 underwent PLAB to obtain unfixed fresh lung tissue from the lesion site, while 112 underwent fiberoptic bronchoscopy to obtain BALF.

RESULTS: In the BALF group, 3 pathogens of high concern and 5 suspected pathogens, totaling 8 types of pathogens, were detected. In contrast, in the PLAB group, 1 pathogen of high concern and 1 suspected pathogen, totaling 2 types of pathogens were detected. Cumulatively, 348 pathogens were identified in the BALF group. In the PLAB group, 96 pathogens were identified cumulatively, p<0.001. In the BALF group, the most frequently detected pathogen was Streptococcus pneumoniae, with 19 strains of Mycobacterium tuberculosis among the special pathogens. In the PLAB group, the most frequently detected pathogen was Epstein-Barr virus (EBV) (14.58 %).

CONCLUSIONS: BALF and PLAB showed different mNGS microbial detection patterns under different clinical sampling strategies. Because of the retrospective non-paired design, these findings should be interpreted as descriptive comparative data rather than proof of the superior diagnostic performance of either sampling method.},
}

@article {pmid42232489,
year = {2026},
author = {Huang, Y and Yang, M and Liu, J and Zhang, M and Penttinen, P and Zhang, L and Ge, L and Zhang, X and Zhao, N},
title = {Phage succession and putative mechanisms of microbial community regulation in Sichuan radish paocai (traditional Chinese fermented vegetable).},
journal = {Food chemistry: X},
volume = {36},
number = {},
pages = {103997},
pmid = {42232489},
issn = {2590-1575},
abstract = {Spontaneous fermentation of Sichuan paocai is shaped by complex microbial and environmental factors, yet phage communities remain understudied. This study presents integrated viromic and metagenomic analysis of radish paocai combined with metabolite profiling to elucidate phage diversity, dynamics, ecological roles, and sources. Time-series metagenomics revealed Lactiplantibacillus increasing from 11% to 71%, while viromics showed phages comprising 78% of viral contigs, with Uroviricota reaching 88% by day 5. Host prediction indicated that 89% of phages targeted Lactiplantibacillus, mainly L. plantarum. Correlation analysis suggested that core phages were associated with fermentation-related metabolites, including volatile compounds (e.g., decanal), implicating that phages might influence metabolism by modulating host activity. Functional annotation showed phage encoded amino acid and carbohydrate metabolism genes, suggesting auxiliary metabolic roles. Source analysis suggested that most phages in radish paocai may be derived from bacterial prophages. This work advances understanding of phage diversity and ecological function in fermented vegetable ecosystems.},
}

@article {pmid42232626,
year = {2026},
author = {Han, X and Zhang, L and Zhang, R and Liu, W},
title = {Case Report: Multiple organ dysfunction syndrome in a preterm infant secondary to respiratory syncytial virus and bacterial co-infection.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1825002},
pmid = {42232626},
issn = {2296-2360},
abstract = {This article reports a case of a 1-month 11-day-old preterm infant, born at 36 + 6 weeks gestation, who presented to an outside hospital emergency department with a persistent cough that had not improved over four days. During this period, the infant progressively developed respiratory distress and lethargy. The infant subsequently developed cardiopulmonary arrest, underwent cardiopulmonary resuscitation, and was transferred to our hospital under endotracheal intubation with positive pressure ventilation. Respiratory pathogen polymerase chain reaction testing of a throat swab was positive for respiratory syncytial virus (RSV), while sputum and bronchoalveolar lavage fluid culture and blood metagenomic next-generation sequencing (mNGS) detected Haemophilus influenzae and S. pneumoniae. After 22 days of hospitalization and treatment including invasive mechanical ventilation, antibiotic adjustment, intravenous immunoglobulin (IVIG), and dexamethasone, the infant was discharged without further complications. Metagenomic next-generation sequencing provides rapid diagnostic evidence for mixed infections, while integrated interventions, including IVIG, short-course corticosteroids, and nutritional support, effectively modulate immune responses.},
}

@article {pmid42232631,
year = {2026},
author = {Gao, L and Wen, Y and Jing, X},
title = {Case Report: Cervical lymphadenitis resulting from Pseudomonas aeruginosa diagnosed by metagenomic next-generation sequencing.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1795457},
pmid = {42232631},
issn = {2296-2360},
abstract = {Pediatric cervical lymphadenitis is usually caused by Staphylococcus aureus and Streptococcus pyogenes. Cases resulting from Gram-negative bacteria are rare. Herein, we report the case of an 11-year-old boy who developed cervical lymphadenitis. He was diagnosed with a Pseudomonas aeruginosa infection through metagenomics next-generation sequencing of blood and biopsy. After treatment with meropenem, the patient's condition improved and he was discharged. Lymphadenitis may be caused by Gram-negative opportunistic pathogens. Metagenomic next-generation sequencing can help identify the underlying cause.},
}

@article {pmid42232653,
year = {2026},
author = {Fan, F and Wang, B and Jia, R and Lyu, J and Han, F},
title = {Amelioration of tic disorder by Jujuboside A via gut microbiota remodeling and intestinal 5-HT signaling.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1760647},
pmid = {42232653},
issn = {1662-4548},
abstract = {BACKGROUND: Tic disorder (TD) is a common chronic neuropsychiatric condition manifesting during childhood and adolescence. Jujuboside A (JuA) may alleviate TD symptoms; however, the mechanisms underlying its therapeutic effects remain unclear.

METHODS: We established a rat model of TD and used histological techniques to evaluate the effects of JuA on pathological changes. We also measured 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels and assessed tryptophan hydroxylase 1 (TPH1) mRNA expression. Finally, we analyzed the gut microbiota composition in fecal samples using 16S rRNA metagenomic sequencing.

RESULTS: JuA administration alleviated pathological changes in rats with TD, increased 5-HT and 5-HIAA levels, and upregulated TPH1 mRNA expression. Compared with no treatment, JuA treatment increased the proportion of Bacteroidia, Muribaculaceae, Bacteroidales, and Bacteroidota, while reducing that of Bacilli, Lactobacillaceae, Lactobacillus, Lactobacillales, and Firmicutes.

CONCLUSION: These findings indicate that JuA mitigates TD progression, potentially by remodeling the gut microbiota and regulating 5-HT levels.},
}

@article {pmid42232910,
year = {2026},
author = {Oskolkov, N},
title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1603339},
pmid = {42232910},
issn = {1664-302X},
abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.},
}

@article {pmid42232914,
year = {2026},
author = {Chamberlain, EJ and Boulton, W and Connors, E and Calianos, T and Bowman, JS and Creamean, JM and Mock, T and Kim, HH},
title = {From microbial diversity to functional potential using dimensionality reduction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786397},
pmid = {42232914},
issn = {1664-302X},
abstract = {The high dimensionality of microbial diversity data from 'omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide 'omics informed ecotype diversity to leverage in mechanistic biogeochemical models.},
}

@article {pmid42233252,
year = {2026},
author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR},
title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
doi = {10.1093/database/baag029},
pmid = {42233252},
issn = {1758-0463},
support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; },
abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.},
}

@article {pmid42233644,
year = {2026},
author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M},
title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149825},
doi = {10.1128/msystems.01498-25},
pmid = {42233644},
issn = {2379-5077},
abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.},
}

@article {pmid42233648,
year = {2026},
author = {Hu, J and Zhang, H and Miao, H and Chang, W and Zheng, J and Hu, F and Zhang, D and Guo, W and Hu, P and Han, R and Wang, J and Li, L and Wang, X},
title = {Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0399325},
doi = {10.1128/spectrum.03993-25},
pmid = {42233648},
issn = {2165-0497},
abstract = {UNLABELLED: This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1-M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18-20 h and 14-19 h, respectively, whereas the ONT workflow was completed within 4-6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios.

IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies-established short-read platforms and newer long-read nanopore sequencing-using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.},
}

@article {pmid42233650,
year = {2026},
author = {Kane, M and Moukaha Doukanda, SF and Sankhé, S and Sow, B and Ndione, MHD and Mhamadi, M and Dieng, M and Diop, SMBS and Seye, S and Mbanne, M and Faye, O and Barry, MA and Sembene, PM and Loucoubar, C and Fall, G and Diallo, A and Diagne, CT and Dia, N and Diagne, MM},
title = {Evaluating myxovirus resistance protein A-based rapid testing combined with pathogen sequencing for arboviral and incidental viral infection surveillance in Senegal.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0339225},
doi = {10.1128/spectrum.03392-25},
pmid = {42233650},
issn = {2165-0497},
abstract = {Accurate differentiation between viral and bacterial infections remains challenging in resource-limited, arbovirus-endemic settings, leading to antibiotic misuse and diagnostic uncertainty. Myxovirus resistance protein A (MxA), an interferon-induced host biomarker, may offer a pathogen-agnostic approach to improve rapid diagnosis and clinical triage. We evaluated the performance of an MxA rapid diagnostic test (RDT) using archived samples from febrile patients collected during dengue virus (DENV) and chikungunya virus (CHIKV) outbreaks in Senegal. We tested 171 blood samples from patients with acute febrile illness using an MxA RDT and RT-qPCR for DENV and CHIKV. Samples with discordant results (MxA-positive and RT-qPCR-negative) underwent metagenomic and hybrid-capture Illumina-based sequencing to detect missed infections. Sequencing data were analyzed using maximum-likelihood phylogenetics to assess viral lineage placement. The MxA RDT demonstrated moderate-to-high sensitivity (70.0%-85.1%, depending on virus) and moderate specificity (70.2%) for detecting primary arboviral infections. Among discordant samples, sequencing revealed previously missed pathogens, including DENV serotype 3 (genotype III), Parvovirus B19 (B19V), and Torque teno virus (TTV). Detection of B19V and TTV highlights the broader clinical utility of host-response biomarkers to uncover unexpected viral pathogens in high-diversity settings. MxA's longer persistence than viral RNA enables detection of recent infections missed by PCR. Combined with sequencing, this broadens the diagnostic window, improves clinical triage, and supports identification of underdiagnosed viruses. Future research should integrate MxA testing into routine clinical care and surveillance protocols to enhance outbreak responses in resource-limited regions.IMPORTANCETimely and equitable viral diagnosis is vital in outbreak-prone regions where advanced laboratories are scarce. This study shows how a simple, rapid test for the host biomarker myxovirus resistance protein A can provide real-time detection of viral infections such as dengue and chikungunya, even in remote or frontline health centers. When paired with pathogen sequencing, the test also uncovers infections that standard PCR may miss. This integrated approach demonstrates how field-deployable diagnostics can operate both during and between epidemics, strengthening outbreak preparedness, improving patient triage, and advancing laboratory equity worldwide.},
}

@article {pmid42233654,
year = {2026},
author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H},
title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0318325},
doi = {10.1128/spectrum.03183-25},
pmid = {42233654},
issn = {2165-0497},
abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.

IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.},
}

@article {pmid42233680,
year = {2026},
author = {Grettenberger, CL and Macalady, JL and Hamilton, TL},
title = {Metabolic diversity of Ferrovaceae and potential contributions to iron oxidation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0070026},
doi = {10.1128/aem.00700-26},
pmid = {42233680},
issn = {1098-5336},
abstract = {Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.},
}

@article {pmid42233768,
year = {2026},
author = {Éles, ZB and Rahmani, L and Gyöngyösi, E and Szarka, K and Rebenku, I and Veress, G and Major, T and Kónya, J and Szalmás, A},
title = {Sublineage-Specific A45S Polymorphism Alters the Biological Function of the Human Papillomavirus 11 E7 Protein.},
journal = {Journal of medical virology},
volume = {98},
number = {6},
pages = {e70997},
doi = {10.1002/jmv.70997},
pmid = {42233768},
issn = {1096-9071},
support = {FK125038//National Research, Development and Innovation Office/ ; //Hungarian Academy of Sciences/ ; //Faculty of Medicine, University of Debrecen/ ; //Richter Gedeon Talentum Foundation/ ; },
abstract = {The E7 oncoprotein of human papillomavirus (HPV) plays a crucial role in viral pathogenesis and replication. Although it is generally highly conserved across HPV genotypes, naturally occurring E7 variants can display functional differences that may affect viral persistence, oncogenic potential, and host cellular responses. The prevalent HPV11 A2 sublineage is characterized by a distinctive amino acid substitution at position 45 (A45S) within the E7 protein. In comparative analyses of transfected primary keratinocytes and HPV-negative cancer cells, we here demonstrate that the A45S substitution enhances the interaction of HPV11 E7 with key cellular targets, including pRb family proteins and PTPN14. A further consequence is an increased ability to target both PTPN14 and pRb family proteins for degradation. Functionally, these differences are exemplified by the S45 variant's enhanced ability to activate E2F-driven gene expression, particularly resulting in elevated mRNA levels of key factors involved in homologous recombination-mediated repair of DNA double-strand breaks, a pathway critical for preserving genomic integrity. Together, these findings indicate that the A45S substitution imparts high-risk-like molecular properties to the low-risk HPV11 E7 oncoprotein. To our knowledge, this is the first report to identify a functionally significant alteration in HPV11 E7 activity resulting from a naturally occurring sequence variation. Understanding the underlying mechanisms could provide new strategies for targeting the therapeutically challenging HPV-associated conditions, such as recurrent respiratory papillomatosis.},
}

@article {pmid42234268,
year = {2026},
author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M},
title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42234268},
issn = {1573-4978},
abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.},
}

@article {pmid42234577,
year = {2026},
author = {Faure, R and Faure, U and Truong, T and Derzelle, A and Lavenier, D and Flot, JF and Quince, C},
title = {SNooPy: a statistical framework for long-read metagenomic variant calling.},
journal = {Nucleic acids research},
volume = {54},
number = {10},
pages = {},
doi = {10.1093/nar/gkag556},
pmid = {42234577},
issn = {1362-4962},
support = {101088572//ERC/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; },
abstract = {Current long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a single nucleotide polymorphism (SNP)-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant-calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.},
}

@article {pmid42234710,
year = {2026},
author = {Liu, F and Lai, T and Xu, W and Li, G},
title = {ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0349393},
doi = {10.1371/journal.pone.0349393},
pmid = {42234710},
issn = {1932-6203},
abstract = {Accurate functional annotation of viral proteins is essential for genomic surveillance, yet rapid viral evolution causes "functional drift" that challenges conventional sequence-only models. These models often lack interpretability and struggle with fragmented sequences from complex environmental samples such as wastewater. We developed ViralMultiNet, a structure-aware multimodal framework that integrates multi-scale k-mer encodings (4-7-mers) with functional semantic embeddings derived from UniProt annotations. Using a curated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) dataset of 66,011 samples from wastewater metagenomics (NCBI SRA: SRX28474964), we implemented gated multimodal fusion and triple knowledge distillation to transfer structural insights from a teacher to a student model. Model performance was evaluated via 5-fold cross-validation and external validation on emerging variants. Training efficiency was optimized using Low-Rank Adaptation and Flash Attention. ViralMultiNet achieved robust classification performance with a macro F1 score of 0.921 ± 0.004, accuracy of 0.928 ± 0.003, and AUC of 0.983 in cross-validation. The distilled student model matched teacher performance within a negligible margin (<0.003 F1 difference) while reducing training time by 40.4% (from 94.3 to 56.2 minutes per epoch). Interpretability analysis revealed that model attention peaks consistently aligned with experimentally validated functional domains of the SARS-CoV-2 Spike protein, including the receptor-binding domain (residues 319-541), S1/S2 cleavage site (681-685), and fusion peptide (816-835). ViralMultiNet offers a scalable, interpretable solution for viral protein function prediction. Its ability to generalize across variants and map attention to critical biological regions supports deployment in wastewater-based early warning systems, enhancing global pandemic preparedness.},
}

@article {pmid42235107,
year = {2026},
author = {Candia-Herrera, D and Guerra, M and Carrasco-Fernández, J and Campos-Quiroz, C and Garcia-Gomez, M and Igual, JM and Carro, L and Castro, JF},
title = {Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126734},
doi = {10.1016/j.syapm.2026.126734},
pmid = {42235107},
issn = {1618-0984},
abstract = {Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250[T], was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250[T] (=RGM 3146[T] = IMI 507634[T]).},
}

@article {pmid42235155,
year = {2026},
author = {Zhang, YF and Li, MY and Zhang, Y and Ding, H and Yun, L and Li, ZY},
title = {Genome-resolved analysis reveals successional dynamics and functional transitions in chicken gut archaea across the broiler growth cycle.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107186},
doi = {10.1016/j.psj.2026.107186},
pmid = {42235155},
issn = {1525-3171},
abstract = {Archaea are indispensable members of the gut microbiota, playing important roles in host metabolism and gut homeostasis. Despite their ecological significance, the archaeal community within the chicken gut remains poorly understood, particularly regarding its taxonomic diversity, functional potential, and successional dynamics throughout the broiler growth cycle. In this study, we employed a metagenome-assembled genome (MAG) approach to systematically characterize the composition, phylogeny, and functional shifts of the chicken gut archaea. We constructed a genome catalog comprising 172 non-redundant archaeal MAGs, encompassing 11,796 protein clusters. Community analysis revealed that alpha diversity indices differed significantly across growth stages, suggesting that the archaeal community becomes increasingly robust and functionally complex as the host matures. Functional annotation further demonstrated broad metabolic versatility, with distinct metabolic profiles emerging across multiple functional modules at different ages. This study reveals the dynamics of chicken gut archaeal communities and their potential functional characteristics across different production stages, providing a basis for future research into their ecological roles and possible associations with host gut ecosystem stability.},
}

@article {pmid42235160,
year = {2026},
author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X},
title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107187},
doi = {10.1016/j.psj.2026.107187},
pmid = {42235160},
issn = {1525-3171},
abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.},
}

@article {pmid42235395,
year = {2026},
author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W},
title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142574},
doi = {10.1016/j.jhazmat.2026.142574},
pmid = {42235395},
issn = {1873-3336},
abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.},
}

@article {pmid42235463,
year = {2026},
author = {Lin, Q and Mei, X and Zheng, H and Meng, J and He, F and Yang, B and Ru, X and Su, M and Wang, D and Tan, N and Fang, J and Fu, S and Ouyang, N and Yang, Z and Jiang, S and Zhang, Y},
title = {Optimisation and validation of capture mNGS for predicting antimicrobial resistance.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106319},
doi = {10.1016/j.ebiom.2026.106319},
pmid = {42235463},
issn = {2352-3964},
abstract = {BACKGROUND: Antibiotic resistance critically compromises bacterial infection treatment. While antimicrobial susceptibility testing (AST) remains the standard for resistance assessment, its culture dependence is time-consuming. Clinical metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection and antibiotic resistance gene (ARG) profiling. However, low ARG detection sensitivity and unclear genotype-phenotype correlations limit its clinical utility.

METHODS: We developed capture mNGS approach with probe-based ARG enrichment and a host-attribution algorithm for precise ARG-bacteria linkage. Its ARG detection sensitivity was comparatively analysed against standard mNGS. Using phenotypic AST as reference, we then evaluated the clinical predictive value of capture mNGS-detected ARGs in a retrospective cohort from Sun Yat-sen Memorial Hospital (SYSMH) and an external cohort from Liuzhou Worker's Hospital (LWH). In addition, a prospective cohort from SYSMH was used to explore the clinical utility of ARG detection by mNGS.

FINDINGS: Compared to standard mNGS, capture mNGS significantly enhanced ARG detection sensitivity, achieving a 44-fold increase in sequencing depth. In our retrospective cohort, key resistance genes detected by capture mNGS accurately predicted phenotypic resistance: blaCTX-M achieved a sensitivity of 1.00 (95% CI: 0.86, 1.00) and specificity of 1.00 (95% CI: 0.59, 1.00) for ceftriaxone resistance prediction, with an area under the receiver operating characteristic curve (AUC) of 0.93 (95% CI: 0.87, 0.99). BlaKPC demonstrated a sensitivity of 0.94 (95% CI: 0.73, 1.00) and specificity of 1.00 (95% CI: 0.95, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.92, 1.00). Similarly, blaOXA-23 exhibited a sensitivity of 0.95 (95% CI: 0.82, 0.99) and specificity of 1.00 (95% CI: 0.69, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.94, 1.00), which was externally validated in the LWH cohort. In addition, mecA showed a sensitivity of 0.94 (95% CI: 0.71, 1.00) and specificity of 0.94 (95% CI: 0.81, 0.99) for oxacillin resistance (AUC = 0.94, 95% CI: 0.87, 1.00). Whereas blaTEM/blaSHV showed higher false-positive rates for cephalosporin resistance and ErmB/ErmC showed lower sensitivity (0.6, 95% CI: 0.32, 0.84) for macrolide-lincosamide-streptogramin (MLS) resistance. Capture mNGS reported results (median turnaround time (TAT): 24.71 h (IQR 22.74-41.00)) were shorter than AST (median TAT: 73.16 h (IQR 54.19-93.42)). In a prospective cohort, the time to guide antibiotic therapy based on reported positive ARGs was significantly shorter than that based on reported resistant phenotypes from AST.

INTERPRETATION: These results highlight that ARGs can be leveraged to rapidly and accurately predict bacterial resistance phenotypes with high sensitivity and specificity, thereby guiding antibiotic management in clinical practice.

FUNDING: The National Natural Science Foundation of China, the Guangdong Science and Technology Department, Science and Technology Projects in Guangzhou.},
}

@article {pmid42224761,
year = {2026},
author = {Ma, S and Zhao, B and Jing, G and Han, M and Wang, M and Shan, X and Wang, Z and Lu, S and Liu, X and Wu, F},
title = {Vertical stratification and distribution patterns of the ARG resistome in Fuxian Lake: Insights from a global baseline.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142528},
doi = {10.1016/j.jhazmat.2026.142528},
pmid = {42224761},
issn = {1873-3336},
abstract = {Deep lakes are critical reservoirs for antibiotic resistance genes (ARGs), yet global ARG dynamics and vertical mechanisms remain poorly constrained. By combining metagenomics with a global comparative analysis across 17 plateau lakes and 83 Fuxian Lake samples, this study investigates ARG distribution from macro- to micro-scales. The macro-scale analysis identified Longitude, Latitude, and Temperature (all p-values < 0.05) as dominant constraints on ARG abundance. A distinct, synergistic mechanism drives vertical stratification: ARG enrichment occurs in the deep layer (50-150 m) at the lake center, but enrichment shifts to the shallow layer (0-40 m) in the tourism area. This complex pattern is governed by a biotic-abiotic synergy. Specifically, ARG dynamics in the deep layer are jointly regulated by biotic factors and physicochemical constraints such as pH and ORP. Differences observed at the local scale, including the increase in ARG abundance and rare-to-core conversion, contrast with broader patterns observed across plateau lakes. This study provides the first global distribution spectrum of ARGs in plateau lakes and reveals crucial interactive patterns. The persistent presence of high-risk ARGs and critical priority pathogens necessitates heightened vigilance. We propose controlling anthropogenic inputs and mitigating the risk of deep sediment pollutant release as crucial strategies for these vital freshwater resources.},
}

@article {pmid42224764,
year = {2026},
author = {Sun, Y and Yu, Z and Wu, C and Wang, J and Feng, X},
title = {First insights into agricultural practice-driven mobilization and methylation of arsenic and mercury in soil with implications for groundwater risk mitigation.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142530},
doi = {10.1016/j.jhazmat.2026.142530},
pmid = {42224764},
issn = {1873-3336},
abstract = {The migration of heavy metals from soils to groundwater via karst conduits (e.g., dolines) in karst terrains threatens the safety of anthropogenic water supplies. Despite widespread recognition of contamination risks, the underlying mechanisms governing the transformation and mobilization of heavy metals, particularly those mediated by agricultural activities, remain inadequately characterized. Here, we systematically studied the impact of rice straw return (RS) on the biogeochemical transformation processes of both arsenic (As) and mercury (Hg) from a co-polluted soil in karst regions using a combination of geochemical, microbial, and spectroscopic approaches. The results indicated that RS enhanced the desorption of As from Fe(III)oxyhydroxides and methylation of As(III). Metagenomic sequencing analyses revealed that RS increased the abundance of Fe-reducing bacteria (FeRB) and As-methylating microorganisms, which collectively drive As mobilization and transformation. Furthermore, RS promoted the release of Hg from Fe(III)oxyhydroxides and stimulated methylmercury (MeHg) formation, primarily due to the increased abundance of Hg-methylating microbes and hgcAB genes, as well as enhanced Hg availability through the transformation of HgS into organic matter bound Hg and nano-HgS. These findings are essential for predicting As and Hg leaching risks from soils to groundwater under the influence of agricultural practices in karst regions worldwide.},
}

@article {pmid42224874,
year = {2026},
author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF},
title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.},
journal = {The Science of the total environment},
volume = {1042},
number = {},
pages = {181905},
doi = {10.1016/j.scitotenv.2026.181905},
pmid = {42224874},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.},
}

@article {pmid42225156,
year = {2026},
author = {Feng, S and Bao, Y and Zhu, X and Wu, J and Chen, W and Huang, D and Zhou, T and Meng, L and Lee, CH and Li, D and Huang, M},
title = {Biodegradable versus persistent nanoplastics reshape nitrogen metabolism and biofilm architecture in denitrifying biofilters.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135048},
doi = {10.1016/j.biortech.2026.135048},
pmid = {42225156},
issn = {1873-2976},
abstract = {The presence of nanoplastics (NPs) in biological wastewater treatment systems is an emerging concern. Nevertheless, their differential influence on critical biofilm-mediated processes has yet to be fully elucidated. In this study, denitrifying biofilters were exposed to biodegradable polylactic acid nanoplastics (PLA-NPs) and non-biodegradable polystyrene nanoplastics (PS-NPs) to simulate both typical and cumulative high-exposure scenarios. Results showed that long-term NP stress significantly reduced the denitrification performance, with a maximum inhibition of 35% in total nitrogen (TN) removal. Mechanistically, PLA and PS induced distinct biofilm remodeling strategies. PLA exposure enhanced nitrate assimilation pathways, promoting nitrogen sequestration into microbial biomass. In contrast, PS-NPs elicited concentration-dependent stress responses. Low PS exposure was associated with reduced extracellular polymeric substances (EPS) and enhanced carbohydrate degradation potential, whereas high PS concentrations were linked to altered EPS composition, decreased microbial diversity, and directional succession toward stress-tolerant genera. Metagenomic analysis revealed shifts in central carbon metabolic strategies, including enhanced gluconeogenesis and EPS precursor synthesis under NP exposure. Differences in substrate bioavailability between PLA and PS treatments further contributed to distinct carbon utilization patterns within the biofilms. Overall, this study demonstrates that NP biodegradability governs biofilm functional stability, nitrogen transformation, and denitrification performance, providing mechanistic insight into NP-biofilm interactions in engineered systems.},
}

@article {pmid42225158,
year = {2026},
author = {Wang, M and Wang, H and Liang, X and Li, J and Wang, C and Cui, L and Yang, S and Lin, J and Yang, Q and Yang, Z},
title = {Enhanced phenanthrene degradation in microalgae-bacteria systems: Mechanistic roles of exogenous and indigenous degraders.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135034},
doi = {10.1016/j.biortech.2026.135034},
pmid = {42225158},
issn = {1873-2976},
abstract = {This study investigates the synergistic mechanisms of phenanthrene (PHE) biodegradation using Chlorella vulgaris consortia with exogenous (EB) and indigenous (IB) bacteria. Results showed that both cooperative systems significantly enhanced algal growth and PHE removal, with biomass increasing by 17.2% (C.v-EB) and 75.0% (C.v-IB), and biodegradation rates reaching 75.3%-78.4%. Mechanistically, C.v-EB relied on enzymatic antioxidant responses (SOD and CAT) and a protein-rich extracellular polymeric substance (EPS) shield to mitigate oxidative stress. In contrast, C.v-IB exhibited superior resilience through non-enzymatic redox regulation (glutathione/thioredoxin systems) and the formation of a dense, biofilm-like EPS matrix supported by active transport genes (wzm/wzt). Metagenomic analysis revealed that C.v-IB possessed higher metabolic redundancy and energy production efficiency, organized into a coordinated "Degradation-Defense-Communication" genomic architecture via quorum sensing. Furthermore, both consortia expanded the metabolic landscape of PHE, effectively eliminating intermediate toxicity through divergent pathways. These findings provide a systematic framework for developing robust algal-bacterial biotechnologies for the remediation of polycyclic aromatic hydrocarbons in wastewater.},
}

@article {pmid42225249,
year = {2026},
author = {Nie, X and Qin, J and Liu, M and Wang, H and Hou, K and Duan, Y},
title = {Process-Level Design of Engineered Microalgal-Bacterial Systems for Carbon-Efficient Nitrogen Removal from Low C/N Wastewater: Carbon/Electron Redistribution Revealed by Metabolic Network Analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124883},
doi = {10.1016/j.envres.2026.124883},
pmid = {42225249},
issn = {1096-0953},
abstract = {Carbon scarcity in low carbon-to-nitrogen (C/N) wastewater limits electron donor availability and constrains biological nitrogen removal. Although microalgal-bacterial symbiosis (MBS) is a promising low-input alternative, the mechanisms that sustain nitrogen removal under carbon-limited conditions remain unclear. Here, process-level characterization and metagenomic analysis were combined to investigate community assembly and carbon/electron redistribution in engineered MBS systems. Under the tested conditions, a balanced algae-to-bacteria ratio (1:1) created the most stable niche and achieved >97% NH4[+]-N removal with minimal nitrate accumulation, indicating effective coupling of nitrification, denitrification, and assimilation. EPS dynamics showed a shift from accumulation to reutilization during prolonged carbon limitation: polysaccharides decreased in the later stage as external COD was depleted, suggesting mobilization of EPS as an internal carbon source. Consistently, TCA-cycle genes (e.g., IDH, OGDH, mdh) were enriched whereas glycolysis-related genes (e.g., GAPDH, PGK) declined, indicating a shift in metabolic potential toward greater generation of reducing equivalents. Overall, the results suggest that EPS functions as a dynamic carbon reservoir and that algae-bacteria interactions promote carbon/electron redistribution under carbon-limited conditions. This study provides a process-level basis for designing carbon-efficient wastewater treatment systems.},
}

@article {pmid42226305,
year = {2026},
author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R},
title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42226305},
issn = {1756-994X},
support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; },
abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.

METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.

RESULTS: MFP participants (n = 32) experienced weight loss compared to controls (- 0.52 ± 0.03 kg vs. - 0.03 ± 0.02 kg, p < 0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56 ± 0.12 mmHg vs. - 0.16 ± 0.12 mmHg, p < 0.05 and diastolic: -0.36 ± 0.08 mmHg vs. - 0.01 ± 0.08 mmHg, p < 0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.

CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.

CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.},
}

@article {pmid42226423,
year = {2026},
author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W},
title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260317},
pmid = {42226423},
issn = {2765-0189},
abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.

METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.

RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.

CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.},
}

@article {pmid42227278,
year = {2026},
author = {Li, W and Wang, Z and Fu, H and Ma, YR and Gu, Y and Zhuang, JL and Zhao, YX and Liu, YD and Yang, Q and Shapleigh, JP and Jin, RC and Guo, J and Kartal, B and Rittmann, BE},
title = {A Novel Freshwater Anammox Species of Candidatus Loosdrechtia Thriving Under Dual Salinity and Sulfate Stresses.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c03295},
pmid = {42227278},
issn = {1520-5851},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are key players in the global nitrogen cycle and are widely applied in energy-efficient nitrogen removal processes. However, their activity is often inhibited in saline and sulfate-rich environments. Here, we report the discovery and characterization of Candidatus Loostrechtia thiotolerans (HSAMX1), a novel nonmarine anammox species that became dominant under combined high salinity (3% by weight) and high sulfate concentrations (∼86 mM). Through integrated metagenomic and metatranscriptomic analyses, we reveal the physiological and molecular strategies enabling HSAMX1 to thrive under dual-stress conditions. In response to osmotic stress, HSAMX1 activated ion export systems and subsequently synthesized organic osmoprotectant solutes to maintain cellular homeostasis. It also encoded and strongly expressed the sulfide:quinone oxidoreductase (SQR) gene, which accounted for over 90% of the total community SQR transcription. Intriguingly, HSAMX1 did not emerge under either salinity or sulfate stress alone, suggesting a previously unrecognized niche shaped by the interactions of these two stressors. These findings expand our understanding of nonmarine anammox diversity and identify a promising candidate for nitrogen removal in sulfate-laden, saline wastewater.},
}

@article {pmid42227352,
year = {2026},
author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT},
title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70190},
pmid = {42227352},
issn = {1365-2591},
support = {//European Society of Endodontology/ ; },
abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.

METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (< 3 mm) or large (> 7 mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p < 0.05 was considered as significant.

RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p = 0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.

CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.},
}

@article {pmid42227741,
year = {2026},
author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD},
title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0018826},
doi = {10.1128/msystems.00188-26},
pmid = {42227741},
issn = {2379-5077},
abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.},
}

@article {pmid42227750,
year = {2026},
author = {Becker, DJ and Dyer, KE and Olbrys, BL and Hightower, MG and Allira, M and Demory, B and Lock, LR and Taylor, KN and Bhata, NN and Hernandez, SM and Lawson, PA and Youssef, NH and Miller, SL and Elshahed, MS and Verrett, TB and Clark, KL},
title = {Molecular detection of relapsing fever Borrelia puertoricensis in migratory Mexican free-tailed bats.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0008526},
doi = {10.1128/msphere.00085-26},
pmid = {42227750},
issn = {2379-5042},
abstract = {UNLABELLED: Bats have been increasingly recognized to host relapsing fever borreliae as well as borreliae that form novel clades adjacent to the Lyme borreliosis group. However, the genetic diversity and zoonotic potential of bat-borne borreliae remain poorly understood, in part because most work to date has focused on bats in the tropics. Fewer bat-borne Borrelia surveys have been conducted in temperate zones, where many bats undertake seasonal migrations that may facilitate pathogen dispersal. We surveyed blood from nearly 400 Mexican free-tailed bats (Tadarida brasiliensis) during their seasonal occupancy in Oklahoma, USA, during 2022 and 2023, for Borrelia spp. Targeted PCR of the 16S rRNA and flaB genes revealed high nucleotide identity to Borrelia puertoricensis, and shotgun metagenomics further demonstrated high amino acid identity to strains isolated from argasid ticks and human blood. This represents the first detection of Borrelia puertoricensis in bats and only the second detection within wild vertebrate hosts. Infection prevalence was low but comparable to that of other borreliae in bats. Our findings suggest that Mexican free-tailed bats may contribute to the dispersal of this emerging tick-borne bacterial pathogen in North America.

IMPORTANCE: Bacteria in the genus Borrelia are primarily spread by ticks and cause either Lyme borreliosis or relapsing fever. Substantial work has demonstrated the degree to which rodents and songbirds can contribute to the enzootic cycles and dispersal of these human diseases, but comparatively less attention has been paid to the role of wild bats, particularly in temperate regions. We here report human-relevant findings from a two-year, seasonal survey of migratory Mexican free-tailed bats (Tadarida brasiliensis) in Oklahoma, USA. We tested nearly 400 bats and identified Borrelia puertoricensis, a relapsing fever species that could infect humans. Importantly, this represents the first detection of Borrelia puertoricensis in bats and only the second detection in wild vertebrate hosts, expanding the known host range of this emerging tick-borne pathogen. Given the known migratory routes of Mexican free-tailed bats, our results have implications for the role that bats may play in tick-borne pathogen dispersal in North America.},
}

@article {pmid42227946,
year = {2026},
author = {Wang, H and Wang, X and Xiu, Z and Wei, H and Cai, H and Chen, J and Zhang, T and Yang, Y},
title = {Substrate-driven microbial specialization and cooperative dechlorination of chlorinated pollutants in estuarine ecosystems.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0023526},
doi = {10.1128/aem.00235-26},
pmid = {42227946},
issn = {1098-5336},
abstract = {Organohalide-respiring bacteria (OHRB) are globally distributed, yet their ecological roles in marine environments remain poorly understood, with few isolates characterized from these systems. Here, we describe a stable anaerobic consortium from estuarine sediments that performs sustained dechlorination of 1,1,2-trichloroethane (1,1,2-TCA) to vinyl chloride (VC) at a rate of 126.3 ± 0.9 µM d[-1]. This activity was associated with the stable co-enrichment of two key populations, Dehalogenimonas and Desulfitobacterium, which increased to dominate the community at 49.7% and 32.5%, respectively. Metagenome-assembled genomes confirmed both populations represent novel species with distinct genomic adaptations. Dehalogenimonas sp. strain H harbors 24 putative reductive dehalogenase genes and complete ectoine biosynthesis pathways (ectABC) essential for osmotolerance, while Desulfitobacterium sp. strain Y represents the first cultivated marine-associated member of this genus. Proteomic analysis confirmed active expression of multiple reductive dehalogenases from strain H, strongly supporting its role as the primary dechlorinator. Concurrently, physiological and genomic data suggest that strain Y is strongly co-selected under 1,1,2-TCA-amended conditions and likely occupies a crucial supportive niche. Alongside its extensive metabolic versatility that likely buffers the consortium against environmental fluctuations, its complete de novo corrinoid biosynthesis pathway implies a complementary role as a vitamin B12 provider for the extreme corrinoid-auxotrophic strain H. This study provides evidence for a stable co-enrichment consistent with nutritional niche differentiation within native microbial communities and suggests a potential cooperative interaction between novel Dehalogenimonas and Desulfitobacterium species, advancing our understanding of halogen cycling in coastal ecosystems.IMPORTANCEEstuaries serve as critical interfaces between terrestrial and marine ecosystems, yet the microbial processes governing chlorinated pollutant fate in these vulnerable zones remain largely unexplored. Our discovery of a novel partnership between Dehalogenimonas and Desulfitobacterium species challenges the conventional understanding that Desulfitobacterium is restricted to terrestrial habitats. Integrative multi-omic and physiological analyses reveal that Dehalogenimonas strain H serves as the highly specialized primary dechlorinator, while Desulfitobacterium strain Y is stably co-enriched and exhibits genomic potential to sustain the consortium by providing essential corrinoid cofactors. The identification of genomic determinants underlying salt tolerance in Dehalogenimonas, including ectoine and mannosylglycerate biosynthesis pathways, provides mechanistic insights into OHRB adaptation to fluctuating salinity. These findings have direct implications for developing bioremediation strategies for contaminated coastal sites and highlight the importance of characterizing microbial diversity in transitional ecosystems.},
}

@article {pmid42228562,
year = {2026},
author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N},
title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117478},
doi = {10.1016/j.celrep.2026.117478},
pmid = {42228562},
issn = {2211-1247},
abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.},
}

@article {pmid42229136,
year = {2026},
author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E},
title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142560},
doi = {10.1016/j.jhazmat.2026.142560},
pmid = {42229136},
issn = {1873-3336},
abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.},
}

@article {pmid42229568,
year = {2026},
author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G},
title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124851},
doi = {10.1016/j.envres.2026.124851},
pmid = {42229568},
issn = {1096-0953},
abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (± 40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.},
}

@article {pmid42229596,
year = {2026},
author = {Lou, D and Duan, J and Zhou, B and Zhou, H and Wang, Y and Yang, J and Cui, J and Ma, X and Tan, J and Duan, H},
title = {Characterization and activity enhancement of a novel thermostable 3-quinuclidinone reductase through modulating the microenvironment of catalytic residues.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135058},
doi = {10.1016/j.biortech.2026.135058},
pmid = {42229596},
issn = {1873-2976},
abstract = {The biocatalytic synthesis of chiral alcohols offers a sustainable alternative to traditional chemical catalysis, yet the lack of robust, high-efficiency enzymes remains an industrial bottleneck. Here, a novel thermostable 3-quinuclidinone reductase (SdQR) was discovered via metagenomic mining of hot spring environments and biochemically characterized. Among the candidates, the H161Q variant, situated proximal to the conserved catalytic triad, emerged as a high-potential lead. Experimental validation revealed that the H161Q mutation yielded a 16-fold increase in catalytic efficiency (kcat/Km) over the wild-type enzyme while preserving its exceptional thermostability. Molecular dynamics (MD) simulations and MM-PBSA calculations elucidated the mechanistic basis for this enhancement: the mutation establishes a "structurally rigid yet physicochemically fluid" microenvironment. This subtle shift optimizes the hydrophobic landscape within the active pocket and modulates cofactor binding thermodynamics, lowering the desolvation energy barrier without compromising the robust structural scaffold. This study provides a highly potent biocatalyst for the asymmetric synthesis of (R)-3-quinuclidinol, and highlights a sophisticated engineering paradigm for the precise physicochemical fine-tuning of catalytic microenvironments in industrial enzymes.},
}

@article {pmid42218514,
year = {2026},
author = {Fabre, V and Robinson, ML and Martino, F and Monge, R and Forastiero, A and Corso, A and Pasteran, F and Karyakarte, R and Randive, B and Singh, S and Naik, M and Prasad, HB and Schwab, KJ and Simner, PJ and Berman, Y and Foy, WI and Salinas, AB and Gupta, A and Lu, J and Vasquez, AM and Noble-Wang, J and Moser, KA and Perry-Dow, KA and Patrick, M and Rock, C},
title = {Environmental reservoirs of carbapenem-resistant organisms in the intensive care unit: a multicenter longitudinal study in two middle-income country hospitals.},
journal = {Antimicrobial resistance and infection control},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13756-026-01768-x},
pmid = {42218514},
issn = {2047-2994},
support = {75D30121D12750/CC/CDC HHS/United States ; },
abstract = {BACKGROUND: There is limited data regarding environmental reservoirs of carbapenem-resistant organisms (CRO) during non-outbreak settings in resource-limited hospitals, or the role of these reservoirs in healthcare transmission.

METHODS: Prospective longitudinal study in which sinks and high-touch surfaces (HTS) were sampled prior to room cleaning in intensive care units (ICUs) in two hospitals (hospital A, Argentina, and hospital B, India), July 2023-February 2024. Selective media was used to recover CROs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) pairwise analysis were performed on environmental and clinical isolates to evaluate bacterial transmission dynamics. Metagenomic sequencing was performed to evaluate bacterial diversity of environmental samples.

RESULTS: Of 541 environmental samples collected, 47.9% in hospital A and 97.5% in hospital B grew at least one CRO. Most CROs tested for the presence of a carbapenemase were positive (63.9-91.0% for hospital A and B isolates, respectively). Carbapenemase producer (CP)-Acinetobacter baumannii and CP-Pseudomonas spp. predominated in HTS and sinks samples, respectively, in hospital A; while CP-Klebsiella pneumoniae predominated in hospital B samples. WGS of 113 CRO isolates and SNP analysis demonstrated certain lineages established enduring reservoirs in the ICUs environment (e.g., blaVIM-36 P. aeruginosa ST395 isolates with 2-9 SNP difference were detected in sinks over 7 months). Several clusters involving environmental and clinical isolates that shared an epidemiological link and displayed ≤ 10 SNP difference were identified (e.g., blaOXA-23 A. baumannii ST195 isolated from three unique patients who stayed in the same private room on sampling months 4, 5, 6 and 7, and from HTS of that room on sampling month 5 displayed 0-3 SNP difference). Metagenomic analysis identified additional AMR genes of clinical importance.

CONCLUSIONS: CROs were abundant and persisted in the ICU environment in countries with high prevalence of MDROs. Our data suggests movement of clones between the environment and patients.},
}

@article {pmid42218533,
year = {2026},
author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY},
title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01680-4},
pmid = {42218533},
issn = {1756-994X},
support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; },
abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.

METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.

RESULTS: Durable disease control (PFS ≥ 24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.

CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).},
}

@article {pmid42218921,
year = {2026},
author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X},
title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108650},
doi = {10.1016/j.ympev.2026.108650},
pmid = {42218921},
issn = {1095-9513},
abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.

METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.

PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.

CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.},
}

@article {pmid42219044,
year = {2026},
author = {Shil, S and Dutta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A},
title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107565},
doi = {10.1016/j.mimet.2026.107565},
pmid = {42219044},
issn = {1872-8359},
abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.},
}

@article {pmid42219122,
year = {2026},
author = {Wang, X and Huang, Y and Xu, J and Lin, B and Chen, X and Li, ZH},
title = {Exogenous floc-granule replacement stabilizes aerobic granular sludge via quorum sensing/quorum quenching-mediated ecological reorganization.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135039},
doi = {10.1016/j.biortech.2026.135039},
pmid = {42219122},
issn = {1873-2976},
abstract = {Aerobic granular sludge (AGS) operation remains constrained by excessive granule enlargement, particle-size redistribution, and structural instability. In this study, exogenous floc-granule replacement was evaluated as a chemical-free, in situ particle-size management strategy for AGS. A conventional granulation reactor (R1) and an exogenous floc-granule replacement reactor (R2) were operated in parallel to compare granulation dynamics, reactor performance, extracellular polymeric substances (EPS), extracellular acyl-homoserine lactones (AHLs), respiration, bacterial partitioning, metagenomic functional gene profiles, and microbial co-occurrence patterns. During the first replacement window, R2 maintained smaller and more uniform granules than R1, with mean particle size of 220 μm on Day 83 compared with 378 μm in R1. R2 also maintained comparable chemical oxygen demand and NH4[+]-N removal performance and showed lower nitrite accumulation during rapid granulation. Particle-size regulation was accompanied by lower extracellular AHL accumulation, altered EPS composition, and distinct respiratory allocation, reflecting higher autotrophic-to-heterotrophic respiration ratio in R2 than in R1 on Day 82 (0.10 vs. 0.07). Comparative characterization indicated that exogenous flocs represented a distinct biomass fraction with smaller particle size, lower protein-to-polysaccharide ratio, and lower extracellular AHL accumulation than endogenous flocs and mature granules. Metagenomic and co-occurrence network analyses showed higher abundance of quorum quenching (QQ)-related genes and greater representation of QQ- or combined quorum sensing /QQ-associated taxa in R2. Overall, exogenous floc-granule replacement represents a tunable structure-based strategy for regulating AGS particle-size distribution, but its effectiveness should be further evaluated according to application scenario.},
}

@article {pmid42219517,
year = {2026},
author = {Velando, F and Molina, L and Hurtado, I and van Dillewijn, P and Segura, A},
title = {Aeonium decorum as a microbial recruitment platform for atmospheric polycyclic aromatic hydrocarbons mitigation in urban gardens.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00914-7},
pmid = {42219517},
issn = {2524-6372},
abstract = {BACKGROUND: In the context of the Sustainable Architecture, green roofs, green walls, green belts or urban farms are becoming popular infrastructures in cities and have been proposed as promising elements to ameliorate air pollution. Atmospheric contaminants are deposited not only on the foliar surface of plants, but also in soils. Plants may interact with pollutants, but their associated microbiomes (epiphytic, endophytic and rhizospheric) may harbor contaminant-degrading bacteria which could play an important role in pollutant mitigation. Therefore, we explored the effects of atmospheric contaminants, using naphthalene as a model compound, on some of the living elements of urban gardens (plants and microbiomes).

RESULTS: Exposure to gaseous naphthalene had weak effects on Aeonium decorum and Trifolium repens plants (measured as efficiency of photosystem II), and on soil bacterial diversity. Although the presence of naphthalene is not the major driver of soil bacterial community structure, metagenomic and qPCR analysis revealed an increase in polycyclic aromatic hydrocarbon (PAH)-ring hydroxylating dioxygenases in Aeonium planted soils, suggesting a positive effect of this plant species for the selection of potential contaminant-degrading microbes. We have also observed an increment in Pseudomonas (known for their capacity to degrade contaminants) and Solimonas in response to naphthalene. Validation of tools designed to evaluate the exposure of plants to atmospheric contaminants was performed creating urban gardens planted with A. decorum plants and exposed to environmental conditions.

CONCLUSIONS: Our results suggest that Pseudomonas and Solimonas could be used as markers for biodegradation. A. decorum is proposed as a good candidate for amelioration of atmospheric contaminants and gardens constructed with these plants carried PAH degrading bacteria on leaf surfaces indicating that they have the capacity to respond to the presence of contaminants.},
}

@article {pmid42219665,
year = {2026},
author = {Recio, MI and de la Torre, J and Rocha-Martin, J and de la Mata, I and Ramos, JL},
title = {A Biotechnological Approach to Enzyme-Based Fertilisers: Immobilisation of Acid Phosphatases.},
journal = {Microbial biotechnology},
volume = {19},
number = {6},
pages = {e70385},
doi = {10.1111/1751-7915.70385},
pmid = {42219665},
issn = {1751-7915},
support = {PID2021-123469OB-IOO//Agencia Estatal de Investigación/ ; MICIU/AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; PREDOC_01447//Consejería de Conocimiento, Investigación y Universidad, Junta de Andalucía/ ; },
mesh = {*Acid Phosphatase/metabolism/chemistry ; *Enzymes, Immobilized/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Clay ; *Fertilizers/analysis ; Aluminum Silicates/chemistry ; *Biotechnology/methods ; Temperature ; Soil/chemistry ; },
abstract = {We explore enzyme-based technologies as sustainable alternatives to conventional chemical fertilisers, addressing the challenges associated with using enzymes in free or immobilised form for agricultural applications. We use the metagenome-derived Class A acid phosphatase M2-32, selected for its high activity, broad pH tolerance and thermophilic properties, and evaluated its immobilisation on clay minerals to enhance stability and applicability in soils. Several clays were tested as immobilisation supports. Bentonite caused complete enzyme inactivation, while kaolin formed aggregates and was unsuitable. In contrast, palygorskite, sepiolite and agrozeolite adsorbed more than 99% of the added enzyme. However, only a fraction of the immobilised enzyme retained catalytic activity, with optimal performance observed at moderate protein loading (40-80 μg protein). Among the tested supports, palygorskite consistently provided the highest specific activity (22,000 ± 2200 U/mg), followed by sepiolite (11,000 ± 730 U/mg), whereas agrozeolite (2250 ± 40 U/mg) showed comparatively low activity. ATR-FTIR spectroscopy confirmed successful enzyme immobilisation without significant alteration of the clay structures. Immobilised M2-32 preserved a broad pH range (between 4 and 8.5) and thermophilic behaviour similar to the free enzyme, remaining active up to 50°C. Immobilisation increased substrate affinity while reducing Vmax relative to the free enzyme. To assess environmental compatibility, the effects of free and palygorskite-immobilised M2-32 on soil microbial communities were evaluated using corn rhizosphere microcosms with different organic matter contents. Metabarcoding high-throughput sequencing revealed that microbial diversity and community structure were primarily shaped by soil type, plant presence and incubation time. Enzyme application, whether free or immobilised, did not significantly alter microbial diversity or composition. Overall, these results support palygorskite-immobilised M2-32 as a promising, environmentally compatible candidate for enzyme-based fertiliser development.},
}

*Acid Phosphatase/metabolism/chemistry
*Enzymes, Immobilized/metabolism/chemistry
Hydrogen-Ion Concentration
Enzyme Stability
Clay
*Fertilizers/analysis
Aluminum Silicates/chemistry
*Biotechnology/methods
Temperature
Soil/chemistry

@article {pmid42219690,
year = {2026},
author = {Zhu, P and Yuan, X and Wang, X and Shi, Y},
title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70343},
doi = {10.1111/1462-2920.70343},
pmid = {42219690},
issn = {1462-2920},
support = {SDAIT0107//Shandong Modern Agricultural Technology & Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; },
mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention & control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; },
abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.},
}

*Triticum/microbiology
*Fusarium/physiology
*Soil Microbiology
*Silicon Dioxide/pharmacology
Metabolic Networks and Pathways/drug effects
*Microbiota/drug effects
*Plant Diseases/microbiology/prevention & control
*Disease Resistance/drug effects
Lignin/metabolism
*Nanoparticles

@article {pmid42219901,
year = {2026},
author = {Yang, J and Shi, T and Du, Z and Wang, Y and Shen, J and Wu, C and Fu, B},
title = {Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {6},
pages = {},
doi = {10.1093/jac/dkag190},
pmid = {42219901},
issn = {1460-2091},
support = {32141002//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ionophores/pharmacology/administration & dosage ; *Plasmids/genetics ; Chickens/microbiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; Polyether Compounds ; Cecum/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Bacteria/drug effects/genetics ; Polyether Polyketides ; Conjugation, Genetic/drug effects ; Pyrans ; },
abstract = {BACKGROUND: Chronic sub-inhibitory antimicrobial exposures may shape antibiotic resistance (AMR) dissemination at the animal, food and environment interface. Polyether ionophore coccidiostats remain widely used in poultry production, yet their influence on AMR dissemination at sub-inhibitory exposure is unclear.

OBJECTIVES: To determine whether sub-minimum inhibitory concentration (MIC) polyether ionophores enhance resistance plasmid transfer in vitro and to characterize their effects on gut microbiota and resistome dynamics in vivo during and after administration.

METHODS: We investigated the effects of representative polyether ionophores at sub-MICs on resistance spreading phenotypes in vitro and gut resistome dynamics in VREfm-challenged broilers. In vitro plasmid conjugation and related phenotypes were quantified, and in vivo caecal microbiota and resistome were profiled by 16S rRNA gene sequencing and shotgun metagenomics.

RESULTS: Sub-MIC polyether ionophores increased plasmid conjugation, copy number and biofilm formation in Enterococcus spp., whereas no comparable effects were observed in Escherichia coli. In vivo, salinomycin temporarily disrupted caecal microbiota development and, at Day 20, suppression of indigenous taxa (e.g. Faecalibacterium) was accompanied by a transient surge in VREfm colonization and vanA abundance; resistome expansion was non-persistent. After salinomycin cessation, recovery of beneficial genera like Akkermansia was associated with reduction of the total resistance gene burden towards pre-treatment baseline by Day 42.

CONCLUSIONS: Polyether ionophores can promote resistance dissemination phenotypes in vitro, but gut ecological resilience may limit long-term impacts after cessation of exposure under recommended dosing conditions. The transient resistome surge during the treatment suggests increased shedding and potential environmental dissemination via manure, warranting surveillance and risk assessment.},
}

Animals
*Ionophores/pharmacology/administration & dosage
*Plasmids/genetics
Chickens/microbiology
Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/drug effects
*Drug Resistance, Bacterial/genetics/drug effects
Polyether Compounds
Cecum/microbiology
*Gene Transfer, Horizontal/drug effects
*Bacteria/drug effects/genetics
Polyether Polyketides
Conjugation, Genetic/drug effects
Pyrans

@article {pmid42221085,
year = {2026},
author = {Liu, F and Yang, K and Wu, M and Li, P and Luo, L},
title = {Case Report: Basal ganglia brain abscess caused by Nocardia farcinica.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1798434},
pmid = {42221085},
issn = {2296-858X},
abstract = {We report a rare case of Nocardia farcinica brain abscess in the basal ganglia, detailing its diagnosis, management, and rehabilitation. Diagnosing brain abscess based solely on clinical and imaging findings remains extremely challenging. Fortunately, metagenomic next-generation sequencing (mNGS) proved valuable in this case by rapidly identifying the pathogen, thereby facilitating targeted antibiotic therapy. This case highlights the importance of differentiating brain abscess from ischemic stroke and intracranial tumors. After completing a full course of anti-infective therapy and comprehensive rehabilitation, the patient achieved significant recovery in activities of daily living (ADL).},
}

@article {pmid42221483,
year = {2026},
author = {Yang, H and Liu, S and Chen, X and Yin, C and Xiao, L and Xu, W and Lv, S and Xie, L and Yin, C},
title = {Gut microbiota-associated immunomodulation contributes to the protective effects of fluvastatin against endometriosis in a mouse model, accompanied by increased Akkermansia muciniphila abundance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762444},
pmid = {42221483},
issn = {1664-302X},
abstract = {BACKGROUND: Endometriosis (EMs) is a chronic inflammatory disease characterized by tumor-like growth behavior and limited therapeutic options. Increasing evidence suggests that gut microbiota may contribute to EMs progression by promoting chronic inflammation and immune dysregulation. Fluvastatin, a lipid-lowering agent, exhibits anti-inflammatory, anti-tumor, and immunomodulatory effects and has also been reported to influence microbial homeostasis. However, the relationship among fluvastatin treatment, gut microbiota, and EMs progression remains unclear. This study aimed to investigate this relationship.

MATERIALS AND METHODS: A mouse model of EMs was established by autologous uterine tissue transplantation, followed by oral fluvastatin administration for 3 weeks. Lesion growth, inflammatory responses, and immune characteristics were evaluated by histology, quantitative PCR, flow cytometry, immunofluorescence, and immunohistochemistry. Gut microbiota involvement was assessed using antibiotic-mediated microbiota depletion and fecal microbiota transplantation (FMT). Microbial composition was analyzed by metagenomic sequencing. The role of Akkermansia muciniphila was evaluated by direct oral supplementation.

RESULTS: Fluvastatin significantly reduced the volume and mass of ectopic lesions and decreased the mRNA expression of pro-inflammatory cytokines. It was also associated with changes in macrophage polarization-related markers and reduced abnormal activation of splenic immune cells. Antibiotic-induced gut microbiota depletion attenuated the protective effects associated with fluvastatin treatment, whereas FMT from fluvastatin-treated mice partially transferred similar protective changes. Metagenomic analysis revealed that fluvastatin reshaped gut microbiota composition and increased the abundance of Akkermansia muciniphila. Moreover, oral supplementation with Akkermansia muciniphila attenuated EMs progression and was associated with anti-inflammatory and immune-related changes similar to those observed after fluvastatin treatment.

CONCLUSION: These findings suggest that the protective effects associated with fluvastatin treatment are accompanied by changes in gut microbiota composition, including increased abundance of Akkermansia muciniphila. Gut microbiota may contribute to the beneficial effects of fluvastatin in EMs. These results support the potential value of microbiota-informed therapeutic strategies for EMs.},
}

@article {pmid42221497,
year = {2026},
author = {Taussig, R and Peralta, R and Bustamante, JP},
title = {A pilot proof-of-concept study of microbial and botanical diversity in honey samples from Necochea, Argentina.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1833002},
pmid = {42221497},
issn = {1664-302X},
abstract = {INTRODUCTION: Honey is a complex biological matrix containing plant-derived, microbial, and viral components that reflect both environmental and hive-associated processes. Traditional methods for determining botanical origin, such as melissopalynology, have limitations in resolution and scope. In this context, untargeted shotgun metagenomics emerges as a promising integrative approach for comprehensive honey characterization.

METHODS: This pilot study explored the feasibility of applying an untargeted shotgun metagenomic approach to honey samples from Necochea, Buenos Aires province, Argentina. Two honey samples and a pollen control sample from Rosa chinensis were subjected to DNA extraction, shotgun library preparation, and sequencing on an Illumina NextSeq 500 platform.

RESULTS: The control sample showed exclusive assignment to Rosa chinensis, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to Helianthus annuus (common sunflower) and Eucalyptus grandis (rose gum), consistent with the regional flora. Key bacterial taxa included Paenibacillus larvae in one sample, Acinetobacter johnsonii in the other, and Apilactobacillus kunkeei, Bradyrhizobium sp., Sphingobium yanoikuyae, and Stutzerimonas stutzeri in both. Apis mellifera filamentous virus was detected in both samples.

DISCUSSION: Given the limited sample size, these findings should be interpreted as exploratory and hypothesis-generating. Nevertheless, this proof-of-concept supports the potential of untargeted metagenomics as an integrated tool for the simultaneous characterization of botanical origin, microbial communities, and viral content in honey, offering advantages over targeted amplicon-based approaches. Future studies with larger and systematically designed cohorts will be necessary to validate and extend these observations.},
}