@article {pmid42308338,
year = {2026},
author = {Ong, CJN and Nazari, R and Cabuhat, KSP and Ogaya, JB and Ahmed, MM and Shomuyiwa, DO and Musa, SS and Daberechi, OJ and Abdi, YH and Dulay, RMR and Lucero-Prisno, DE},
title = {The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag064},
pmid = {42308338},
issn = {1574-6941},
abstract = {The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes present in pathogenic and non-pathogenic microorganisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water-soil-air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.},
}

@article {pmid42308739,
year = {2026},
author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Hoerr, FJ and Robinson, K and Hauck, R},
title = {Jejunal histopathology, metagenome, and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107215},
doi = {10.1016/j.psj.2026.107215},
pmid = {42308739},
issn = {1525-3171},
abstract = {This study investigated the efficacy of various dietary fiber sources and combinations in mitigating subclinical enteric infection in broilers. Using a randomized complete block design, 2,160 d-old YP x Ross 708 male broilers were assigned to eight treatments. These included an unchallenged control and a challenged control, followed by six dietary treatments applied to challenged broilers. The dietary treatments consisted of fiber supplementation with oat hulls (OH) or soy hulls (SH), either alone or in combination with wheat middlings (WM) or sugar beet pulp (SBP). Birds were challenged with Eimeria spp. followed by Clostridium perfringens, and a multi-omics approach was employed to analyze jejunal histopathology, microbiome, and host mucosal transcriptome. While the enteric challenge induced significant histopathological changes, fiber combinations including OH-WM and OH-SBP significantly (P < 0.05) reduced cumulative pathology scores. The challenge caused a shift toward Lactobacillus crispatus dominance in the microbiome. Each fiber source altered the microbiome distinctively: OH increased Romboutsia sp., OH-SBP enriched beneficial Limosilactobacillus spp., and SH combinations enhanced butyrate-producing Dysosmobacter welbionis. Transcriptome analysis revealed that fiber supplementation suppressed inflammatory pathways while upregulating cell cycle progression and DNA repair pathways. Integration of bacteriome with host gene expression data revealed coordinated associations, including a link between Glutamicibacter protophormiae, Spirosoma, Eggerthella, and Blautia through host genes APOB, DSEL, and ENPP7, indicating a correlation of fiber-degrading bacteria with host lipid metabolism and extracellular matrix remodeling. These findings suggest that combining insoluble and soluble fibers may create a more resilient gut environment against enteric challenges through complementary mechanisms, with OH based combinations notably exhibiting reduced pathology, stronger anti-inflammatory response and suppression of opportunistic species.},
}

@article {pmid42308920,
year = {2026},
author = {Xu, Z and Zhu, W and Xia, Q and Huang, W and Chi, Y and Qi, H and Chan, OYP and Ching, JY and Chan, FK and Chan, NN and Ng, SC},
title = {Synbiotics and antioxidants synergistically attenuate disease progression in metabolic dysfunction-associated steatotic liver disease.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {201},
number = {},
pages = {119656},
doi = {10.1016/j.biopha.2026.119656},
pmid = {42308920},
issn = {1950-6007},
abstract = {BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to gut dysbiosis, highlighting gut microbiome modulation as a promising therapeutic strategy. This study investigated the synergistic effects of synbiotics and antioxidants in MASLD.

METHODS: We evaluated the effects of synbiotics, antioxidants, and their combination (SLD07) on metabolic and histopathological parameters and energy balance (Promethion system) in high-fat diet-fed mice. Plasma metabolome and faecal microbiome were analysed. In a 3-month pilot study of patients with MASLD (n = 27), we examined the safety and efficacy of SLD07 (20 billion CFU/day), with microbiome alterations assessed by metagenomic sequencing.

RESULTS: In mice, SLD07 significantly attenuated metabolic and hepatic parameters, including body weight gain, white adipose tissue, serum triglycerides, low-density lipoprotein, liver histology (p < 0.05), and increased the respiratory exchange ratio (p < 0.001). Synbiotics enhanced glucose tolerance and insulin sensitivity (p < 0.05), while antioxidants primarily reduced adipose tissue (p < 0.05). Liver tissue MDA levels were reduced only in the combination group, whereas GSSG levels were reduced in the combination and antioxidants alone groups (p < 0.05). Liver transcriptomics revealed that all treatments reversed HFD-upregulated inflammation and oxidative pathways, with the combination showing the broadest effect. Gut microbiota was mainly modulated by synbiotics, while systemic metabolome changes were driven by antioxidants. In the clinical pilot study, treatment reduced liver fat and stiffness (p < 0.01), increased Bifidobacterium, and upregulated the L-glutamine pathway, with no serious adverse events.

CONCLUSION: This integrated translational investigation demonstrates that the synbiotic-antioxidant combination alleviates MASLD through dual modulation of gut microbiota and systemic oxidative stress.},
}

@article {pmid42309017,
year = {2026},
author = {Yang, X and Liu, W and Mao, Y and Wang, H},
title = {Correlation analysis of lead stress-induced alterations in root metabolome and rhizosphere microbiome of Cuminum cyminum L.},
journal = {Ecotoxicology and environmental safety},
volume = {320},
number = {},
pages = {120390},
doi = {10.1016/j.ecoenv.2026.120390},
pmid = {42309017},
issn = {1090-2414},
abstract = {Lead (Pb) contamination in agricultural soils poses serious threats to crop production and food safety. Cuminum cyminum L. is an important spice crop widely cultivated in arid regions, but its rhizosphere responses to Pb stress remain poorly understood. Here we conducted a field plot experiment with four Pb treatment levels (0, 400, 800, and 1200 mg/kg) and employed an integrated approach combining soil physicochemical and enzymatic analyses, metagenomics, and root metabolomics to characterize the rhizosphere of C. cyminum after 40 days of Pb exposure. Pb significantly decreased soil pH, organic matter, nitrogen availability, and available phosphorus and potassium, while altering soil enzyme activities by suppressing urease and acid phosphatase and enhancing catalase activity. Pb stress reshaped rhizosphere microbial communities by increasing microbial richness at low and moderate Pb levels but reducing community evenness under high Pb stress. Metal-tolerant taxa, including Sphingomonas, Arenimonas, and Gemmatimonas, were selectively enriched. Functional analyses revealed a broad enhancement of microbial metabolic potential, particularly in amino acid, carbohydrate, and energy metabolism pathways. Concurrently, Pb exposure correlated with extensive root metabolic reprogramming, characterized by accumulation of amino acids, organic acids, and flavonoids. The random forest results indicated that soil physicochemical properties had a stronger correlation with plant growth than root metabolites or rhizosphere microorganisms under Pb stress conditions. Overall, this study reveals a coordinated rhizosphere strategy of C. cyminum to Pb stress, providing new insights into heavy metal adaptation mechanisms in spice crops and informing sustainable cultivation in Pb-contaminated soils.},
}

@article {pmid42309163,
year = {2026},
author = {Sutthiboonyapan, P and Jungpraditphol, I and Krasaesin, A and Khamwachirapitak, C and Choi, Y and Porntaveetus, T and Wiriyakijja, P},
title = {Supragingival Plaque Microbiome Composition Associated with Oral Lichen Planus Activity and Desquamative Gingivitis Severity: An Exploratory, Cross-Sectional, Shotgun Metagenomic Study.},
journal = {European journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0046-1824444},
pmid = {42309163},
issn = {1305-7456},
abstract = {OBJECTIVES: The microbial contribution to desquamative gingivitis (DG), a frequent and debilitating form of immune-mediated oral lichen planus (OLP), remains undefined. This study employed shotgun metagenomic sequencing to investigate the role of the oral microbiome in DG site involvement and severity, as well as OLP disease activity.

MATERIALS AND METHODS: In this exploratory, cross-sectional study, supragingival plaque samples were collected from nine OLP patients at desquamative gingivitis-affected sites (DG sites), sites not affected by desquamative gingivitis (non-DG sites), and pooled full-mouth samples. Shotgun metagenomic sequencing was performed to reveal oral microbial profiles and their functional pathways. Disease severity was assessed using the Oral Lichen Planus Disease Activity Scale (OLP-DAS) and the Desquamative Gingivitis Clinical Score (DGCS).

STATISTICAL ANALYSIS: Associations between microbial profiles and disease severity were assessed using Spearman's correlation. Microbial and functional pathway profiles were compared between DG and non-DG sites using the paired Wilcoxon signed-rank test. A p-value <0.05 was considered statistically significant.

RESULTS: Significant differences in microbial composition between DG and non-DG sites were identified, including 6 genera and 17 species (p < 0.05). Several taxa showed notable correlations with disease severity (r ≥ 0.7), according to DGCS, with 10 genera and 16 species positively associated with DGCS, and 5 genera and 8 species associated with OLP-DAS. Notably, the fructan biosynthesis pathway showed a significant inverse correlation with DG severity (r = - 0.70, p < 0.05) and was linked to Actinomyces sp. oral taxon 448, which was enriched in DG sites. This suggested that increasing disease severity may be associated with reduced microbial polysaccharide-production potential.

CONCLUSIONS: The DG microbiome shows distinct functional and taxonomic changes. Fructan biosynthesis was more abundant in DG sites than in non-DG sites, but showed an inverse correlation with DG severity, highlighting candidate biomarkers and potential therapeutic targets.},
}

@article {pmid42309238,
year = {2026},
author = {R, K and Chandra, A and Pal, S and Tiwari, H and Shekhar, A and Agarwal, R},
title = {Microbial Dysbiosis in Oral Potentially Malignant Disorders: A Systematic Review.},
journal = {Journal of stomatology, oral and maxillofacial surgery},
volume = {},
number = {},
pages = {102876},
doi = {10.1016/j.jormas.2026.102876},
pmid = {42309238},
issn = {2468-7855},
abstract = {BACKGROUND: Oral potentially malignant disorders (OPMDs) including oral leukoplakia (OLK), proliferative verrucous leukoplakia (PVL), and oral verrucous hyperplasia (OVH) pose variable malignant transformation risk to oral squamous cell carcinoma (OSCC), yet the role of microbial dysbiosis in their progression remains ambiguous.

OBJECTIVES: To elucidate microbial shifts in OPMDs, their association with dysplasia progression and malignant transformation, highlighting prospects for early detection and risk stratification.

MATERIAL AND METHODS: A comprehensive literature search was conducted across scientific databases up to May 2025. Studies investigating microbial dysbiosis in OLK, PVL, or OVH using 16S rRNA sequencing, metagenomic, or transcriptomic analyses were included. Risk of bias was assessed using the modified Newcastle-Ottawa scale.

RESULTS: OPMDs showed inconsistent alpha diversity and distinct beta diversity compared to controls. Microbial composition differed by lesion type: OLK was enriched with Fusobacterium periodonticum, Porphyromonas pasteri, Streptococcus, and Haemophilus; PVL with Campylobacter concisus, Leptotrichia, and Haemophilus parainfluenzae; and OVH with Porphyromonas gingivalis, Tannerella forsythia, and Saccharibacteria TM7. High-risk OLK showed reduced diversity and enrichment of Fusobacterium nucleatum, Parvimonas, and Streptococcus infantis. Malignant transformation revealed lesion-specific shifts, including increased Fusobacterium, Capnocytophaga and Porphyromonas in OLK-OSCC, while Neisseria was specifically enriched in progressive OLK lesions, Treponema and Campylobacter in PVL-OSCC, and Capnocytophaga sputigena and Prevotella oris in OVH-OSCC.

CONCLUSION: This review highlights the pivotal role of microbial dysbiosis in the evolution of OPMDs to malignancy. Distinct microbial signatures across OLK, PVL, and OVH may serve as biomarkers for disease stratification and early detection of high-risk lesions.},
}

@article {pmid42309478,
year = {2026},
author = {Maya, MA and Raboni, SM and Giamberardino, HIG and Nogueira, MB and Giamberardino, ALG and Ferreira, LH and Torrecilha, VT and Pereira, LA and Usuga, J and Aristizabal-Valencia, M and Vasquez, A and Berg, MG and Rebolledo, PA and Averhoff, F and Cloherty, GA and Hernandez-Ortiz, JP and Osorio, JE},
title = {Clinical and Genomic Characterization of Pediatric Adenovirus-Associated Severe Acute Respiratory Infection: A Binational Study from Brazil and Colombia, 2022-2023.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108893},
doi = {10.1016/j.ijid.2026.108893},
pmid = {42309478},
issn = {1878-3511},
abstract = {BACKGROUND: Human adenovirus (HAdV) is detected in fewer than 10% of hospitalized children with acute respiratory infections, yet several regions reported unusual increases in 2021-2022. We investigated an HAdV outbreak detected through surveillance in Curitiba, Brazil, and Antioquia, Colombia, comparing clinical and genomic characteristics before and during the outbreak.

METHODS: We conducted a multicenter observational study of HAdV-associated severe acute respiratory infection in hospitalized children. Respiratory samples collected between February 2022 and April 2023 underwent metagenomic sequencing and hexon gene analysis. Clinical and phylogenetic analyses evaluated viral dynamics and genetic diversity.

RESULTS: A HAdV outbreak occurred in both regions during late 2022. HAdV-C predominated before the outbreak, whereas HAdV-B3 became the dominant genotype at both sites during the outbreak. During the outbreak, bronchiolitis/asthma exacerbation was most common in Antioquia, whereas pneumonia predominated in Curitiba. Phylogenetic analysis of the hexon gene identified two distinct HAdV-B3 clades that diverged from a shared ancestor but expanded independently in Brazil and Colombia.

CONCLUSION: Following relaxation of non-pharmacological measures, both regions experienced a substantial rise in HAdV-B3-associated disease. Despite increased case numbers, clinical patterns remained stable within sites but differed between regions. Integrated genomic and clinical surveillance provides important insights into adenovirus lineage expansion and outbreak dynamics.},
}

@article {pmid42309606,
year = {2026},
author = {Silverstein, J and Chapman, A},
title = {Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {2},
pages = {100702},
pmid = {42309606},
issn = {2090-5920},
abstract = {Ancient DNA (aDNA) research has revolutionised archaeology and forensic science by enabling genomic recovery from highly degraded remains. This review explores the biochemical and environmental factors influencing aDNA preservation, alongside methodological advances that have improved data yield and authenticity. Techniques such as next-generation sequencing (NGS), single-stranded library preparation, and hybridisation capture have transformed the field, allowing recovery from ultrashort fragments and challenging contexts such as warm climates. Authentication strategies-including cytosine deamination profiling, fragment length analysis, and rigorous contamination controls-remain essential to ensure reliability. Applications of aDNA extend beyond ancestry reconstruction and population genetics to include forensic identification, kinship analysis, and pathogen detection. Lessons from forensic genetics, such as stringent validation and contamination mitigation, have informed best practices in archaeological contexts. However, ethical considerations are central to both domains. Issues of Indigenous data sovereignty, consent, repatriation, and culturally sensitive interpretation demand transparent, community-led research frameworks. These principles align with international agreements such as the Nagoya Protocol and emerging guidelines for equitable benefit-sharing. Despite significant progress, challenges persist, including geographic sampling bias, interpretive uncertainty, and the need for interdisciplinary integration. Future directions emphasise long-read sequencing, metagenomic approaches, and artificial intelligence-driven analytics, alongside robust ethical governance. By combining technological innovation with culturally responsible practices, aDNA research continues to advance our understanding of human history while reinforcing the importance of ethical stewardship in forensic and archaeological science.},
}

@article {pmid42309718,
year = {2026},
author = {Sakiyama, Y},
title = {[Metagenomic analysis for central nervous system infections: clinical utility and future directions].},
journal = {Rinsho shinkeigaku = Clinical neurology},
volume = {},
number = {},
pages = {},
doi = {10.5692/clinicalneurol.cn-002248},
pmid = {42309718},
issn = {1882-0654},
abstract = {Encephalitis and meningitis are neurological emergencies in which delayed diagnosis may lead to severe neurological sequelae, necessitating accurate and rapid etiological identification. In recent years, metagenomic next-generation sequencing (mNGS), which enables comprehensive analysis of microbial genomes without prespecified hypotheses, has attracted increasing attention. Its clinical application in neuroinfectious diseases has contributed to improved diagnostic yield and the detection of rare pathogens. In particular, mNGS has been shown to be useful in clinically challenging situations such as culture-negative cases, anaerobic infections, mixed infections, and immunocompromised hosts. However, the technology also has inherent limitations, including enormous data volume, challenges in interpreting pathogenic relevance, limited turnaround time, high cost, and a lack of standardized analytical pipelines. Thus, although mNGS represents a valuable complementary tool to conventional diagnostic methods, it is not universally applicable, and its results must be carefully interpreted within appropriate clinical contexts.},
}

@article {pmid42311379,
year = {2026},
author = {Saito, Y and Sato, S and Sasanami, Y and Yamashita, T and Yamada, M},
title = {Heterologous expression and structural characterization of polyamide 4-degrading enzyme from a soil bacterium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811100},
pmid = {42311379},
issn = {1664-302X},
abstract = {Polyamide 4 (PA4) is a bio-based plastic with thermal stability, excellent mechanical properties, and good biodegradability in various environments. To understand the biodegradation of PA4 under natural environments, PA4-degrading microorganisms and enzymes have been investigated. Although our previous research identified the amino acid sequence and predicted the three-dimensional (3D) structure of a PA4-degrading enzyme from a marine environment (Nyl4A pa), those of an enzyme from terrestrial environments have remained unidentified. In this study, we identified the PA4-degrading enzyme gene (nyl4Apx) from the PA4-degrading soil bacterium Pseudoxanthomonas sp. TN-N1. In addition, nyl4Apx was successfully expressed in Escherichia coli BL21(DE3) and Brevibacillus choshinensis HPD31-SP3. The PA4-degrading activity of the enzyme secreted by recombinant B. choshinensis HPD31-SP3 reached 68.8 Δ655 nm/h/100 mL broth, representing a 2.4-fold increase compared with that produced by recombinant E. coli BL21(DE3). Based on a homology search using the amino acid sequence and predicted 3D structure of the enzyme, Nyl4A px was predicted to be composed of a substrate-binding domain, a middle domain, and a catalytic domain. Among these domains, the substrate-binding and catalytic domains of Nyl4A px are sequentially and structurally similar to those of Nyl4A pa . Furthermore, putative homologs of Nyl4A px and Nyl4A pa were found in marine-associated environmental metagenomes through BLAST searches. To our knowledge, this is the first report describing the structural properties of a PA4-degrading enzyme from a soil bacterium.},
}

@article {pmid42311675,
year = {2026},
author = {Zhang, H and Fan, B and Ma, R and Jiang, R and Qin, Z and Qu, X and Wang, J and Xue, J and Wang, C and Liu, X and Guo, L},
title = {Gut microbiota and sepsis-associated acute kidney injury: a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1724266},
pmid = {42311675},
issn = {1664-3224},
mesh = {Humans ; *Acute Kidney Injury/microbiology/etiology/therapy/immunology ; *Sepsis/complications/microbiology/immunology ; Animals ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Intestinal Barrier Function ; Signal Transduction ; },
abstract = {BACKGROUND: Sepsis-associated acute kidney injury (SA-AKI) carries high morbidity and mortality, yet its pathogenesis remains incompletely understood. Emerging evidence underscores the gut-kidney axis as a critical pathway in SA-AKI development.

OBJECTIVE: This review aims to synthesize current knowledge on how sepsis-driven gut dysbiosis compromises intestinal barrier integrity and contributes to SA-AKI, and to explore potential therapeutic strategies targeting the gut microbiota.

METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, and Scopus databases for publications between 2005 and 2026. Studies focusing on gut-kidney crosstalk mechanisms in sepsis/AKI were included. Key findings from human and animal studies were summarized.

RESULTS: Sepsis induces marked gut dysbiosis characterized by loss of microbial diversity and expansion of pathobionts. This dysbiosis compromises intestinal barrier integrity, facilitating translocation of bacterial products such as lipopolysaccharide (LPS). Upon entering circulation, these mediators activate systemic inflammation and renal signaling cascades, including the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-κB) pathway, leading to tubular injury and impaired renal function. Recent human metagenomic studies have identified specific microbial signatures associated with AKI, such as increased Clostridium asparagiforme and decreased Roseburia spp., alongside elevated uremic toxin-producing bacteria like Gordonibacter pamelaeae. Additionally, gut-derived metabolites including indoxyl sulfate, p-cresol sulfate, and trimethylamine N-oxide (TMAO) have been implicated in promoting renal inflammation and fibrosis. Importantly, renal dysfunction further disrupts gut homeostasis, establishing a pathological gut-kidney feedback loop. Targeting the gut-kidney axis via fecal microbiota transplantation, probiotic supplementation, or short-chain fatty acid administration may offer novel therapeutic avenues.

CONCLUSIONS: Sepsis induces gut microbiota dysregulation play an important role in the development of SA-AKI. The intestine-kidney crosstalk may provide a basis for the treatment of sepsis-induced organ injury and also provide new ideas for the treatment of SA-AKI.},
}

Humans
*Acute Kidney Injury/microbiology/etiology/therapy/immunology
*Sepsis/complications/microbiology/immunology
Animals
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Intestinal Barrier Function
Signal Transduction

@article {pmid42311883,
year = {2026},
author = {Tan, S and Liao, Q and Wen, Y and Zhu, Y},
title = {Case Report: Invasive pulmonary aspergillosis caused by Aspergillus lentulus in a boy with chronic granulomatous disease.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1813957},
pmid = {42311883},
issn = {2296-858X},
abstract = {Aspergillus lentulus is a slow-growing and drug-resistant fungus, which has been primarily reported in adults, usually immunocompromised ones, suffering from invasive pulmonary aspergillosis (IPA). This condition is rare in children. Here, we report a case of invasive pulmonary aspergillosis due to Aspergillus lentulus in a boy with no history of recurrent infections who presented with a prolonged fever of unknown origin. Based on chest CT scan findings showing typical halo signs, a fungal infection was strongly suspected. Empirical antifungal therapy was initiated at early admission but failed to resolve the persistent fever in this case. The causative pathogen was confirmed by blood metagenomic next-generation sequencing (mNGS). Subsequent genetic analysis identified a pathogenic mutation in the X-linked CYBB gene, confirming chronic granulomatous disease (CGD). Eventually, following a combination therapy of voriconazole and micafungin, the boy became afebrile and was discharged, pending hematopoietic stem cell transplantation (HSCT). To our knowledge, no previous cases of Aspergillus lentulus infection in children with CGD have been reported in the literature. This case underscores the critical importance of identifying the causative microorganism. It also highlights the value of emerging detection methods, such as mNGS. At present, there is no consensus for the optimal antifungal regimen against pediatric Aspergillus lentulus infections. Clinical improvement was achieved in this patient following combination therapy with voriconazole and micafungin, offering a practical therapeutic reference for managing this refractory fungal infection.},
}

@article {pmid42312035,
year = {2026},
author = {Radzieta, M and Malone, M and Schwarzer, S and Bergamin, E and Whitely, G and Jensen, S},
title = {Anaerobe-associated microbial shifts at infection onset in diabetes-related foot ulcers revealed by longitudinal metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1812721},
pmid = {42312035},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Bacteria, Anaerobic/classification/genetics/isolation & purification ; *Microbiota ; Longitudinal Studies ; Male ; Female ; Aged ; Middle Aged ; Metagenome ; },
abstract = {INTRODUCTION: Diabetes-related foot infections (DRFIs) are a major cause of hospitalisation and carry a significantly increased risk of lower extremity amputation. To date there is a lack of longitudinal studies examining within-patient microbiome dynamics during the transition from non-infected to infected diabetes-related foot ulcers (DRFUs).

METHODS: We used shotgun metagenomic sequencing to longitudinally profile the wound microbiome of 6 patients with DRFUs who developed clinical infections, utilising taxonomic profiling, metagenome assembly and binning and strain level analysis to characterise within-patient microbial shifts.

RESULTS: DRFUs with no signs of clinical infection were colonised by virulent pathogens including Staphylococcus aureus, Streptococcus agalactiae, Enterococcus faecalis, Enterobacter hormaechei and Pseudomonas aeruginosa. In most patients, infection onset was associated with a decrease in pathogen abundance and a significant increase in obligate anaerobes including Prevotella spp, Peptoniphilus spp, Porphyromonas spp and Anaerococcus spp.

CONCLUSION: These findings highlight the potential importance of anaerobes and hypoxia in DRFIs and may support monitoring of tissue oxygen saturation as a predictor of infection onset.},
}

Humans
*Diabetic Foot/microbiology
*Metagenomics/methods
*Bacteria, Anaerobic/classification/genetics/isolation & purification
*Microbiota
Longitudinal Studies
Male
Female
Aged
Middle Aged
Metagenome

@article {pmid42312150,
year = {2026},
author = {Sabogal-Rodriguez, D and Caro-Quintero, A},
title = {PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag150},
pmid = {42312150},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) are routinely recovered from metagenomic studies, yet the population genetic information embedded within these datasets remains largely underutilized. Analyzing within-species genetic variation can reveal adaptive evolution, selection pressures, and ecological dynamics that are hidden when MAGs are treated as homogeneous entities. Existing tools address individual analysis steps in isolation, requiring manual integration and creating barriers for researchers without extensive bioinformatics expertise.

RESULTS: Here we present PopMAG, a Nextflow pipeline and interactive Shiny application that automates population genetics analysis of MAGs. PopMAG integrates quality control, community profiling, competitive read mapping, functional annotation, and microdiversity estimation into a single reproducible workflow. The pipeline calculates key population genetics metrics including nucleotide diversity (π), p N / p S ratios, fixation index (F S T), Levins' index and SNVs counts with results consolidated into an interactive visualization platform for metadata-driven exploration. We demonstrate PopMAG's utility through analysis of longitudinal cystic fibrosis lung metagenomes, where we identify patterns consistent with antibiotic-driven selection in Pseudomonas aeruginosa efflux pump genes coinciding with treatment intervention.

PopMAG and corresponding documentation are publicly available at https://github.com/daasabogalro/PopMAG.},
}

@article {pmid42312179,
year = {2026},
author = {Chen, X and Xue, CX and Wang, J and Wang, S and Su, M and Liu, R and Zhu, XY and Liu, J and Yao, P and Fu, L and Yang, Z and Greening, C and Todd, JD and Zhang, XH},
title = {Metagenomic expansion of Joyebacterota identifies Cavimicrobium, a dominant sulfide-producing lineage in anoxic marine ecosystems.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag137},
pmid = {42312179},
issn = {2730-6151},
abstract = {Extreme anoxic environments are hotspots of sulfur cycling and harbor numerous novel uncharacterized microbial lineages. Although the phylum Joyebacterota was recently proposed, its internal phylogenetic architecture and evolutionary adaptations remain poorly understood. Here, we significantly expand the genomic diversity and metabolic framework of this phylum by integrating recovered metagenome-assembled genomes, and propose a novel genus, Cavimicrobium. Phylogenomic analysis placed Cavimicrobium as a distinct clade and further divided into four species-level subgroups associated with diverse anoxic sources, including sediments from the Salton Sea, the Eastern Gotland Basin, and the anoxic waters of the Sansha Yongle Blue Hole (SYBH). Unlike previous broad surveys, our study revealed that this lineage evolved from a facultatively anaerobic ancestor and underwent adaptive gene gain and loss through phylogenetic reconstruction. Genomic evidence suggested that this lineage harbored a previously overlooked anaerobic sulfite reduction (asrABC) pathway that likely mediating thiosulfate uptake and conversion to sulfite and sulfide. Notably, Cavimicrobium was particularly abundant in the anoxic waters of SYBH, comprising up to one-third of the bacterial community in particle-associated fraction below 100 m, where it is likely a major contributor to sulfide accumulation. Analysis of MAGs and global amplicon datasets revealed that Cavimicrobium is widespread across anoxic environments, comprising up to 0.32% of the bacterial community in 354 200 publicly available 16S rRNA gene amplicon samples. Together, these findings reveal a new lineage dominant in certain anoxic environments where they are likely important mediators of sulfur cycling, and broaden our understanding of biogeochemical potential of Joyebacterota.},
}

@article {pmid42312182,
year = {2026},
author = {Wang, Z and Zhu, Y and Liu, X and Li, Z and Bai, J and Zou, M and Zhang, C and Liu, Y and Li, F and He, K},
title = {iSymBase: an integrative functional-genomic platform for ecological exploration of insect symbionts.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag128},
pmid = {42312182},
issn = {2730-6151},
abstract = {Insect symbionts play essential roles in host biology, influencing nutrition, immunity, reproduction, and environmental adaptation, ultimately shaping insect physiology, ecology, and evolution. With the rapid growth of functional and genomic datasets on insect symbionts, there remains a critical need for a dedicated platform to systematically compile, organize, and analyze these datasets from an integrative ecological perspective. Here, we developed an insect Symbiont database, named as iSymBase, by manually curating functional records and genomic datasets of insect symbionts from published academic literature. Currently, iSymBase contains over 2657 insect symbiont functional records spanning 795 host species, along with 1494 metagenomes, 14 992 amplicon datasets, and standardized genome and gene catalogs, providing a comprehensive resource for ecological and comparative insect symbiont researches. iSymBase offers standardized query functionalities, such as data browsing, keyword associative search, sequence alignment, data download, and submission. Beyond conventional database functionalities, iSymBase provides several innovative tools: insect-symbiont interaction network for host-symbiont ecological relationships, a batch annotation tool for detecting ecologically functional symbionts from microbiome profiles, and an artificial intelligence (AI)-powered chatbot iSymSeek designed to assist researchers with related knowledge queries. Taken together, iSymBase will serve as an open-access and continually updated platform for storing, querying, and analyzing insect symbiont data, supporting ecological exploration of host-symbiont interactions, symbiont functional diversity, and microbiome-driven adaptation. Database URL: http://symbiont.insect-genome.com/.},
}

@article {pmid42312183,
year = {2026},
author = {Zheng, YL and Guo, YS and Ren, XY and Wang, YF and Cui, HL and Zhang, LM and Ding, LJ and Zhu, YG},
title = {Unveiling the role of soil microorganisms in indicating paddy soil health via metagenomics combined with machine learning.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag133},
pmid = {42312183},
issn = {2730-6151},
abstract = {The soil microbiome performs various ecological functions, making it a potentially vital component of soil health assessment; however, the indicator taxa of soil health remain unidentified. This study explored these taxa in paddy soils of the black soil region in Northeast China. First, the soil health index (SHI) was evaluated using representative physicochemical and biological parameters, revealing that approximately one-third of the soils had a low health level. A Random Forest model was then developed based on microbial species' relative abundance to predict the SHI, achieving an R [2] value greater than 0.6. Based on the SHapley Additive exPlanations values of this model, 40 microbial species were identified as potential indicator taxa of soil health, with 39 of these taxa occurring in more than 50% of the samples. Specifically, paddy soils with more abundant carbon (C)- and nitrogen (N)-fixing bacteria exhibited higher soil organic matter and total N contents, along with higher health levels. Conversely, soils rich in denitrifying bacteria exhibited lower SHI values because of increased N loss. Furthermore, C-fixing, N-fixing, and denitrifying genes showed functional relationships with the corresponding soil properties and SHI. In addition, halophilic, halotolerant, and eutrophic bacteria indicated soil health by reflecting salinity and nutrient status. The potential of these indicator taxa was validated at multidecadal and regional spatial scales. These results highlight the practical value of such indicator taxa, which elucidate the ecological processes associated with soil health and respond predictably to changes in soil health, thereby serving as rapid diagnostic tools for assessing soil health.},
}

@article {pmid42312244,
year = {2026},
author = {Heidrich, V and Fackelmann, G and Ricci, L and Spadazzi, R and Baldanzi, G and Punčochář, M and Catassi, G and Marchi, P and Modesto, M and Piccinno, G and Porcari, S and Rondinella, D and Asnicar, F and Valles-Colomer, M and Mattarelli, P and Ianiro, G and Segata, N},
title = {Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals.},
journal = {Cell press blue},
volume = {1},
number = {3},
pages = {None},
pmid = {42312244},
issn = {3051-3839},
abstract = {Interpersonal strain transmission shapes the human microbiome, yet a comparative understanding of the transmission dynamics across body sites is lacking. We analyzed 1,644 paired oral and fecal metagenomes to investigate microbiome transmission among healthy cohabitants and intra-individual oral-gut overlap. Cohabitants shared significantly more oral and gut strains than non-cohabitants. Romantic partners exhibited the highest oral strain-sharing rates, exceeding their gut strain sharing. Higher oral transmissibility was associated with increased longitudinal strain replacement, while the most transmissible gut species were linked to poorer cardiometabolic health. Within individuals, 74.5% of cases of species detected in both sites involved the same strains, primarily related to abundant oral species such as Streptococcus salivarius, suggesting saliva-mediated transmission. Conversely, Bifidobacterium longum strains never overlapped between sites, with the recently proposed B. longum subsp. nexti uniquely colonizing the oral cavity. These findings extend our understanding of microbiome spread and its potential consequences for human health.},
}

@article {pmid42312840,
year = {2026},
author = {Peterson, LF and Wang, J and Gow, NAR and LeibundGut-Landmann, S and Brewer, MG},
title = {Influence of fungi on epithelial homeostasis and role in inflammatory diseases.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0031925},
doi = {10.1128/cmr.00319-25},
pmid = {42312840},
issn = {1098-6618},
abstract = {SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera Malassezia and Candida. We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.},
}

@article {pmid42312855,
year = {2026},
author = {Lim, SJ and Thompson, LR and Goodwin, K},
title = {Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0079926},
doi = {10.1128/aem.00799-26},
pmid = {42312855},
issn = {1098-5336},
abstract = {UNLABELLED: The Gulf of Mexico/Gulf of America provides ecosystem services derived from marine biodiversity and oil and gas resources. Threats posed by unintended releases of oil and gas can be attenuated by microbial processes, necessitating the documentation of baseline microbial diversity to better understand spill dynamics and to inform bioremediation strategies. Here, we analyze metagenomic sequencing of 10 water column samples collected from the Green Canyon 233 (GC233) lease block near the mussel-fringed brine lake, Brine Pool NR-1. Bioinformatics processing produced 60 bacterial metagenome-assembled genomes (MAGs), 11 archaeal MAGs, 149 microbial taxa predicted from assembled full-length small subunit (SSU) rRNA genes, and 389 microbial genera predicted from single-copy marker genes. Abundant taxa classified from these analyses included archaeal Nitrosopumilaceae, Nitrosopelagicus, and Thalassarchaeaceae and the bacterial taxa Pelagibacteraceae and SAR324. The MAGs revealed genes that degrade gaseous and non-gaseous hydrocarbons, including methane, other alkanes, and aromatic compounds. These samples were collected in 2009, fortuitously prior to the 2010 Deepwater Horizon (DWH) oil spill. Therefore, we searched for members of the rare biosphere that dominated the DWH plume during the early phase of microbial succession. Sequences related to Bermanella spp. were not detected initially. The search was expanded by mapping reads from ours and an additional 55 metagenomic libraries to two Bermanella MAGs. Read recruitment to Bermanella sp913054445 enriched in DWH plume samples was low (<1%) for our samples, those collected after the spill, and most experimental samples compared to samples collected outside (3%) and inside the DWH plume (19%-23%) during the spill.

IMPORTANCE: Microbes execute oil spill biodegradation through complex interactions involving whole microbiome communities by harnessing genes distributed across multiple taxa. Therefore, metagenomic data sets provide taxonomic and functional annotations to aid in understanding spill dynamics. Although the Deepwater Horizon oil spill provided opportunities to observe ecosystem recovery, data about the microbiome prior to the spill are scarce and limited to amplicon sequencing. Our metagenomic libraries, although not derived from the same lease block as the blowout, contribute linkages between microbial taxonomy and function in an area of active oil and gas production. This analysis can aid microbial indicator development, machine learning, and modeling efforts to bioremediate hydrocarbon influxes in marine environments.},
}

@article {pmid42313157,
year = {2026},
author = {Cardenas Alegria, OV and Torres, MC and Breyer, GM and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Ramos, RTJ and Dorn, M and Kich, JD and Siqueira, FM},
title = {Dynamics of Bacterial Communities and Resistomes Across Swine Waste Stabilization Ponds and Fertilized Soils.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42313157},
issn = {1432-0991},
mesh = {Animals ; Swine ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Soil Microbiology ; *Manure/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ponds/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Soil/chemistry ; Metagenomics ; Genes, Bacterial ; *Microbiota ; },
abstract = {The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota, Bacteroidota, and Pseudomonadota, whereas soils were enriched in Actinomycetota, particularly Streptomyces. WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF. Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes (ermB and mefA). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.},
}

Animals
Swine
*Bacteria/genetics/classification/drug effects/isolation & purification
*Soil Microbiology
*Manure/microbiology
*Drug Resistance, Bacterial/genetics
*Ponds/microbiology
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
Fertilizers/analysis
Soil/chemistry
Metagenomics
Genes, Bacterial
*Microbiota

@article {pmid42313166,
year = {2026},
author = {Taguchi, R and Ebihara, A and Tsunematsu, Y and Jeelani, G and Suzuki, R and Nozaki, T and Suenaga, K and Iwasaki, A},
title = {Discovery, Genome-Guided Structure Elucidation, and Total Synthesis of Terukufazoline A, a Macrocyclic Docosapeptide, from a Marine Cyanobacterium.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.6c06625},
pmid = {42313166},
issn = {1520-5126},
abstract = {The structure elucidation of large molecules remains a central challenge in natural products chemistry. This challenge has been addressed through spectroscopic methods as well as degradative and synthetic approaches, which have provided effective solutions. Recent advances in genome analysis have enabled an orthogonal approach to structure elucidation based on biosynthetic gene information. In this study, we report the structure elucidation of an unprecedentedly large cyanobactin, terukufazoline A (1), through integration of spectroscopic analysis, metagenome-guided biosynthetic information, chemical degradation, and total synthesis. Terukufazolines A (1) and B (2) were discovered from an undescribed marine cyanobacterium, and the intractable NMR and tandem MS data for 1 prompted us to incorporate biosynthetic gene information. Metagenomic analysis identified the cyanobactin biosynthetic gene cluster, whose core peptide sequence enabled the assignment of the amino acid sequence of 1. The absolute configuration was established by degradation-based analyses, and the proposed structures were verified by convergent total syntheses of 1 and 2.},
}

@article {pmid42313402,
year = {2026},
author = {Louine, M and Dandekar, R and Reddy, SP and Karalius, MC and Waldrop, G and Wang, S and Gakuru, J and Kimuda, S and Mugabi, T and Musubire, AK and Kagimu, E and Abassi, M and Kabahubya, M and Williams, DA and Phan, HV and Dai, B and Zia, M and Zorn, KC and Fouassier, C and Gerungan, C and Marra, PS and Skipper, CP and Bahr, NC and Langelier, CR and Creswell, FV and Boulware, DR and Meya, DB and Wilson, MR},
title = {Cerebrospinal fluid transcriptional immune pathways linked to survival in HIV-associated tuberculous meningitis.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag313},
pmid = {42313402},
issn = {1537-6613},
abstract = {BACKGROUND: TB meningitis (TBM) has up to 50% mortality in people living with HIV. We investigated differences in cerebrospinal fluid (CSF) host immune responses associated with short-term mortality.

METHODS: We enrolled a prospective cohort of adults with definite, probable and possible HIV-related TBM in Kampala, Uganda. Metagenomic next-generation sequencing (mNGS) of bulk CSF RNA was used to detect co-infecting or alternate CNS pathogens and refine cohort diagnosis. Host transcriptomic profiles from the refined cohort were then compared between 14-day survivors and non-survivors.

RESULTS: CSF mNGS reclassified or excluded 14% of participants based on pathogen detection, yielding 110 participants for transcriptomic analysis, of whom 23% (n=25) died within 14 days. More than 2000 genes were differentially expressed in the CSF based on 14-day mortality (adjusted p-value <0.05). Survivors upregulated T-cell receptor signaling (LCK, FYN, LAT), T-cell survival and differentiation (IL7, CD27, IL12RB1), B-cell receptor signaling (CD81, PLCG2, TNFRSF13C), cytotoxic lymphocyte and NK cell genes (KLRD1, ULBP1), TNF signaling, and class I MHC antigen processing pathways, while downregulating neutrophil chemoattractant CXCL1 and classical complement genes C4A and C4B. Unsupervised clustering identified a hypoinflammatory subgroup with significantly elevated mortality.

CONCLUSIONS: Short-term TBM survival was associated with upregulation of adaptive immunity - including T-cell, B-cell, NK cell, and cytotoxic lymphocyte signaling - alongside TNF signaling and IFN-γ-driven class I MHC antigen processing pathways, with concurrent restraint of complement and neutrophil pathways. This supports investigation of targeted immunomodulatory agents that preserve protective responses while selectively dampening injurious innate pathways, rather than broad immunosuppression with corticosteroids.},
}

@article {pmid42313512,
year = {2026},
author = {Han, M and Zhao, H and Lai, J and Zhao, S and Dong, B and Xi, H},
title = {Succession and Functional Adaptation of Bacterial and Fungal Communities in Biological Soil Crusts Responding to Uranium Stress.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70359},
doi = {10.1111/1462-2920.70359},
pmid = {42313512},
issn = {1462-2920},
support = {22106182//National Natural Science Foundation of China/ ; 2022YFC3702500//National Key Research and Development Program of China/ ; SKLNBC2023-03//State Key Laboratory of NBC Protection for Civilian/ ; },
mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Fungi/metabolism/classification/genetics ; Adaptation, Physiological ; Biodegradation, Environmental ; *Soil Pollutants, Radioactive/metabolism ; *Microbiota ; Stress, Physiological ; },
abstract = {Uranium (U) mining causes severe radioactive contamination threatening ecosystems. Biological soil crusts (BSCs), as pioneer communities in degraded habitats, show strong heavy metal accumulation potential, yet their adaptive mechanisms under U stress remain unclear. In this study, BSCs from a uranium tailings dam in Hunan Province were exposed to simulated U stress. Results showed that BSCs exhibited exceptionally high U accumulation capacity (up to 4131 mg/kg), and effectively immobilised U by converting it into residual and organic-bound fractions (collectively > 70%) via carboxyl complexation and microbial mineralisation, thus significantly reducing environmental mobility. U stress caused damage to the photosynthetic and antioxidant systems of the BSCs. Microbial community complexity decreased, with tolerant taxa including Proteobacteria and Bacilli significantly enriched. Metagenomics revealed distinct cross-kingdom functional adaptation strategies: bacteria upregulated energy metabolism and acetaldehyde metabolism to facilitate efflux detoxification, while fungi strengthened lipid homeostasis and antioxidant metabolism. Several U-tolerant strains (Bacillus, Aspergillus and Penicillium) closely associated with U immobilisation were further isolated and verified. This study systematically reveals the synergistic tolerance mechanisms of BSCs under U stress and provides key microbial resources and theoretical support for the in situ bioremediation of U-contaminated sites.},
}

*Uranium/metabolism
*Soil Microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
*Fungi/metabolism/classification/genetics
Adaptation, Physiological
Biodegradation, Environmental
*Soil Pollutants, Radioactive/metabolism
*Microbiota
Stress, Physiological

@article {pmid42301563,
year = {2026},
author = {Xiao, Q and Chen, B and Xu, Z and Cui, Z},
title = {Endophthalmitis caused by Shinella species: the first case report.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12348-026-00610-0},
pmid = {42301563},
issn = {1869-5760},
abstract = {BACKGROUND: Endophthalmitis is a severe intraocular infection associated with potentially devastating visual outcomes. Shinella, a Gram-negative bacillus commonly found in water and soil, has never been reported as a cause of human disease.

CASE PRESENTATION: A 49-year-old female farmer presented with a 7-day history of vision loss, ocular irritation, and ophthalmalgia in her right eye. She had been previously misdiagnosed and treated with high-dose systemic corticosteroids at another institution. She underwent emergent pars plana vitrectomy. Vitreous samples were analyzed using conventional culture and metagenomic next-generation sequencing (mNGS), which identified Shinella species as the predominant pathogen. Intravitreal amikacin and systemic ceftazidime were initiated on postoperative day 3 after culture confirmed Gram-negative bacilli. Two weeks of targeted antibiotic therapy resulted in complete resolution of intraocular inflammation and near-full visual recovery.

CONCLUSION: To our knowledge, this is the first reported case of intraocular infection caused by Shinella species. This case highlights Shinella as a potential ocular pathogen and demonstrates the utility of pars plana vitrectomy combined with mNGS for diagnosing atypical intraocular infections.},
}

@article {pmid42302013,
year = {2026},
author = {Nayak, AR and Shukla, J and Kulkarni, S and Biswas, R and Kurkure, N and Kaore, M and Chaudhari, S and Bajpai, U and Kannan, K and Sivanesan, S and Sontakke, SD and Husain, A and Kulurkar, PM and Bafna, A and Kashyap, RS},
title = {Study protocol on antimicrobial resistance burden, transmission dynamics, and therapeutic bacteriophages in livestock and exposed farming populations in Nagpur, India: An integrated One Health approach.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350919},
doi = {10.1371/journal.pone.0350919},
pmid = {42302013},
issn = {1932-6203},
mesh = {Animals ; India/epidemiology ; Humans ; *Bacteriophages/isolation & purification/physiology ; *One Health ; *Livestock/microbiology/virology ; Anti-Bacterial Agents/pharmacology ; Longitudinal Studies ; Prospective Studies ; Drug Resistance, Multiple, Bacterial ; *Drug Resistance, Bacterial ; },
abstract = {The rise in antimicrobial resistance (AMR) is a severe public health threat worldwide. India bears a disproportionately heavy burden of this problem due to ample antimicrobial usage in both humans and animals and scarce integrated surveillance. Since humans, animals, and environmental reservoirs which can harbour resistant microorganisms interact very closely on farms livestock, these are considered critical hotspots for the emergence and dissemination of antimicrobial-resistant bacteria and resistance genes. This work presents a 36-month prospective longitudinal observational study protocol aimed at quantifying the burden and characterizing the transmission dynamics of a selected set of key bacteria, that are clinically significant and hence, pathogenic-Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa-alongside their AMRprofiles in livestock, farm-exposed human populations, and environmental reservoirs in Nagpur, India, within the framework of One Health. Seasonal sampling of milk, animal faeces, human stool, soil, wastewater, drinking water, and animal feed will be carried out on dairy farms located in urban, peri-urban, and rural areas. Pathogens will be isolated using standard microbiological techniques and characterized based on antimicrobial susceptibility by employing VITEK®2 and disc diffusion methods. At the same time, bacteriophages against multidrug-resistant isolates will be isolated, purified, and characterized through plaque assays, host-range analysis, electron microscopy, and whole-genome sequencing for their therapeutic potential evaluation. Additionally, metagenomic next-generation sequencing will be utilized on a select number of samples to comprehensively characterize the resistomes and diversity of phages. The research will provide detailed longitudinal data on the frequency and spread of AMR among human, animal, and environmental compartments, create a biobank of AMR isolates and lytic bacteriophages, and offer genomic clues to delineate phage-based treatments and well-informed mitigation strategies of AMR within the framework of One Health in India. The results will be made public through peer-reviewed articles, presentations at scientific meetings, and deposition of sequence data in open-access databases.},
}

Animals
India/epidemiology
Humans
*Bacteriophages/isolation & purification/physiology
*One Health
*Livestock/microbiology/virology
Anti-Bacterial Agents/pharmacology
Longitudinal Studies
Prospective Studies
Drug Resistance, Multiple, Bacterial
*Drug Resistance, Bacterial

@article {pmid42302279,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Rachid, D},
title = {From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
doi = {10.1093/bib/bbag316},
pmid = {42302279},
issn = {1477-4054},
support = {//University Mohammed VI Polytechnic (UM6P), Morocco/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Biomarkers ; *Colorectal Neoplasms/microbiology/genetics ; Machine Learning ; *Precision Medicine ; Causality ; Mendelian Randomization Analysis ; Metagenomics ; },
abstract = {Human gut microbiome research has generated many disease associations, yet few translate into clinical applications. A central obstacle is not a lack of data, but the limited integration of causal reasoning, as most studies report correlations without establishing directionality, confounding control, or mechanistic evidence. We propose a unified causal inference framework that integrates directed acyclic graphs, Mendelian randomization, double machine learning, mediation analysis, and tests of causal reversibility into a single decision-aware workflow. Unlike prior applications of these tools in isolation, our framework explicitly separates assumption mapping, causal identification, effect estimation, and mechanistic interpretation, introducing "assumption guardrails" that constrain interpretation at each stage and prevent overinterpretation of observational findings. Using a colorectal cancer case study with public metagenomic data, we demonstrate how the framework operates under real-world constraints, transforming observational associations into testable, mechanism-based hypotheses. The contribution is architectural in that it organizes existing tools into a disciplined, integrated pipeline that clarifies the strength of evidence at each stage. This operational blueprint provides a reproducible path from correlation to causation in microbiome research and toward precision interventions.},
}

Humans
*Gastrointestinal Microbiome
*Biomarkers
*Colorectal Neoplasms/microbiology/genetics
Machine Learning
*Precision Medicine
Causality
Mendelian Randomization Analysis
Metagenomics

@article {pmid42302398,
year = {2026},
author = {Xie, S and Ding, L and Liu, L and Ong, YS and Li, J and Zhu, Z},
title = {NanoSimFormer: an end-to-end Transformer-based nanopore signal simulator with basecaller guidance.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag402},
pmid = {42302398},
issn = {1367-4811},
abstract = {MOTIVATION: High-fidelity simulation of nanopore sequencing signals is critical for rigorous benchmarking and validation of the nanopore signal processing pipeline. However, existing signal simulators often fail to capture the non-linear dynamics of nanopore current signals, relying on static pore models or lacking optimization objectives tied to basecalling, resulting in synthetic signals with low basecalling accuracy and fidelity.

RESULTS: We introduce NanoSimFormer, an end-to-end Transformer-based signal simulator that integrates basecaller guidance during training to generate high-fidelity nanopore signals. NanoSimFormer achieves a median basecalling accuracy exceeding 99% and Q-scores above 22.8 for Oxford Nanopore Technologies' latest DNA R10.4.1 and direct RNA sequencing, closely mirroring real experimental baselines. It faithfully recapitulates experimental variant calling performance across the five human samples, achieving F1-scores of 0.9953-0.9973 and 0.7862-0.8612 for single-nucleotide polymorphisms and small indels detections, respectively. Compared with previous simulators, NanoSimFormer also substantially reduces false positives in homopolymer and short tandem repeat regions. NanoSimFormer-derived reads enable high-quality de novo bacterial assembly with consensus error rates below one mismatch per 100 kbp and maintain high correlations with experimental abundance in metagenomic and transcriptomic datasets.

NanoSimFormer is freely available on GitHub at: https://github.com/BioinfoSZU/NanoSimFormer.

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

@article {pmid42302503,
year = {2026},
author = {Chen, Y and Yoo, S and Ahn, S and Imran, HZB and Reyes, YA and Nguyen, DV and Soltani, T and Wu, D},
title = {Mesospace-domain biochar regulates electron transfer to enhance elemental sulfur-driven autotrophic denitrification for low-carbon mariculture wastewater treatment.},
journal = {Water research},
volume = {303},
number = {},
pages = {126268},
doi = {10.1016/j.watres.2026.126268},
pmid = {42302503},
issn = {1879-2448},
abstract = {Elemental sulfur-driven autotrophic denitrification (S[0]AD) offers a promising approach for nitrate removal from recirculating aquaculture system (RAS) wastewater. However, it is constrained by the low bioavailability and restricted electron-donating kinetics of elemental sulfur (S[0]). This study developed an enhanced S[0]AD system based on mesospace-domain biochar-embedded hydrogel scaffolds (S[0]AD-BCgel) that modulated electron transfer to promote denitrification and enabled sulfur recovery. Biochar (pyrolyzed at 800 °C; charBC800) increased denitrification efficiency and kinetics by 1.5-fold and 18.1-fold, respectively, compared to the biochar-free control. The improved S[0]AD was attributed to its three synergistic roles in regulating electron transfer: (i) a biopseudocapacitor with abundant quinone functionalities and high electron exchange capacity that facilitated electron relaying; (ii) a bioconductor with graphite-like structures that stimulated interfacial electron transfer; and (iii) a biomodulator that stimulated intracellular electron transfer and promoted extracellular electron transfer in extracellular polymeric substances by enriching cytochrome c and flavin-like compounds. These coordinated properties optimized S[0] utilization and interspecific microbial interactions. Metagenome-assembled genomes (MAGs) further unveiled a shift in the denitrifying microbiota toward modularized consortia characterized by robust metabolic cross-feeding, underpinning improved S[0]AD stability. Moreover, spent hydrogels after S° consumption enable in-situ and ex-situ recovery of biogenic sulfur, supporting material reusability. These findings shed light on the mechanisms by which immobilized biochar regulated electron transfer and microbial interactions during S[0]AD within hydrogel matrices, providing valuable references for sustainable mariculture wastewater treatment and resource recovery.},
}

@article {pmid42302690,
year = {2026},
author = {Li, X and Wen, S and Yu, C and Zhang, J and Xu, W and Yue, Z and Zhang, J},
title = {Dynamic evolution of the antibiotic resistome and mobilome on the microplastics of hospital wastewater.},
journal = {Journal of environmental management},
volume = {412},
number = {},
pages = {130243},
doi = {10.1016/j.jenvman.2026.130243},
pmid = {42302690},
issn = {1095-8630},
abstract = {Antimicrobial resistance is a major global health threat. Hospital wastewater serves as a significant reservoir for both microplastics (MPs) and antibiotic resistance genes (ARGs). MPs have recently been recognized not only as persistent pollutants but also as novel ecological niches for microbial colonization. However, the underlying mechanisms and key biological carriers driving MPs - mediated antimicrobial resistance transmission in hospital wastewater remain unclear. Here, we quantified the occurrence and characteristics of MPs in hospital wastewater and combined an incubation experiment with metagenomic sequencing to resolve the temporal dynamics of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) on MPs surfaces. MPs reached an abundance of 9.5 particles/L, with polyethylene (PE) dominating. Across the 28-day colonization period, with samples collected at 7, 14, 21, and 28 days, 68 ARGs, 443 MGEs and 414 VFs were detected, along with 129 prophage, highlighting the potential for enhanced horizontal gene transfer (HGT) in the plastisphere. We further reconstructed 360 metagenome-assembled genome (MAGs) spanning 16 phyla, and identified Pseudomonadota and Bacteroidota as core hosts of ARGs on MPs. Variance partitioning analysis revealed that MGEs were the major drivers of ARGs variation, independently explaining 44.4% of the dynamics. Our findings provide new insights into the ecological processes of antibiotic resistome of the MPs in the hospital wastewater.},
}

@article {pmid42302785,
year = {2026},
author = {Zhou, Q and Lu, Y and Wang, L and Zhou, W and Oba, H and Zhou, Y and Shen, M and Qu, X and De Souza, C and Rayner, A and Chen, Y and Cheng, TY and Ling, Z and Li, L and Liu, C and Voigt, AY and Xiong, R and Oh, J and Spakowicz, D and Dravillas, C and Tian, AW and Nicolls, MR and Huynh, AT and Chen, X and Hu, J and He, M and He, F and Snyder, MP and Yang, J and Zhou, X},
title = {Power and sample-size estimation in human microbiome research.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {101174},
doi = {10.1016/j.medj.2026.101174},
pmid = {42302785},
issn = {2666-6340},
abstract = {Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.},
}

@article {pmid42302870,
year = {2026},
author = {Zhao, J and Wang, J and Li, S and Lu, Q and Zhang, P and Qi, Y and Xu, X and Fan, J and Chen, C and Zhang, W},
title = {Chlorella pyrenoidosa reduces fecal heavy metal concentrations and antibiotic resistance gene abundance in lambs by modulating the gastrointestinal microbiota.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135186},
doi = {10.1016/j.biortech.2026.135186},
pmid = {42302870},
issn = {1873-2976},
abstract = {Using feed additives and their residues leads to the accumulation of heavy metals and antibiotics in the feces of fattening sheep, thereby posing a threat to the surrounding soil and ecological cycle. Chlorella, a novel feed raw material or additive widely applied in aquaculture, has the potential to mitigate such ecological risks. In this study, we investigated the potential of Chlorella pyrenoidosa as a dietary supplement for fattening lambs to mitigate multi-pollutant emissions from manure via gastrointestinal microbiome modulation. The results demonstrated that dietary supplementation with 3% Chlorella pyrenoidosa (W3) markedly reduced fecal concentrations of several heavy metals (Fe, Cu, Zn, Cr, As, Pb) and total phosphorus, while shifting phosphorus speciation toward more stable forms. Metagenomic analysis revealed that W3 reshaped the metabolic functional profile of the gastrointestinal microbiota and drove the succession of key microbial taxa, particularly promoting the proliferation of Clostridium and other genera in feces. Furthermore, Chlorella pyrenoidosa reduced the abundance of high-risk antibiotic resistance genes (ARGs, e.g., macB). It simplified the ARG-metal resistance gene co-occurrence network and was associated with an attenuated potential for vertical transmission of resistance genes along the digestive tract. Structural equation modeling further confirmed that pollutant reduction was closely associated with the functional remodeling of the microbiome. Thus, this study suggests that Chlorella pyrenoidosa may mitigate the environmental risks associated with heavy metals, bioavailable phosphorus, and ARGs in manure by regulating the gastrointestinal microbial ecosystem. This provides a novel strategy and theoretical basis for reducing source pollution in animal husbandry.},
}

@article {pmid42302872,
year = {2026},
author = {Wang, Y and Kang, Y and Dong, J and Cheng, C and Wu, H and Guo, Z and Zhang, J},
title = {Iron-based anodes facilitate concurrent mercury removal and bioenergy generation in constructed wetland-microbial fuel cells.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135193},
doi = {10.1016/j.biortech.2026.135193},
pmid = {42302872},
issn = {1873-2976},
abstract = {Constructed wetland-microbial fuel cell (CW-MFC) is a promising technology for wastewater treatment with concurrent resource and energy recovery. However, its power generation capacity and mercury (Hg) removal efficiency are significantly limited by the insufficient electron transfer of anode materials. In this study, CW-MFCs were developed using zero-valent iron and siderite as anode materials. The incorporation of iron-based substrates significantly enhanced Hg removal, with total Hg removal efficiencies increasing by 22.9 % and 18.4 %, respectively, compared to conventional CW-MFCs. The integration of iron-based materials increased the availability of organic/inorganic electron donors by 9.1-350.0 %, thereby enhancing power generation performance by 17.9-34.9 %. This enhancement promoted the reduction of Hg(II) and inhibited the formation of methylmercury. Additionally, the electricity generated by the MFC facilitated Fe(III)/ Fe(II) redox cycling, which supported continuous corrosion and electron release from the iron anode. Metagenomic and electrochemical analyses demonstrated that the use of iron-based materials in CW-MFCs improved both extracellular and intracellular electron transfer efficiencies, and strengthened the synergistic interaction between the iron-based anode and electroactive bacteria. The genes that related to Hg(II) reduction, including merA, were also improved. Generally, this study highlights the potential of iron-based anodes to enhance Hg removal and power generation in CW-MFCs, providing a sustainable and energy-recovering strategy for wastewater treatment.},
}

@article {pmid42304204,
year = {2026},
author = {Ai, X and Ren, Z and Liu, C and Zhang, C and Li, H and Ding, H and Yu, Y and Luo, W and Bi, Y},
title = {Unveiling microbial communities and biogeochemical cycles in Antarctic colored snow.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05306-y},
pmid = {42304204},
issn = {1471-2180},
support = {2022YFC2807605//National Key Research and Development Program of China/ ; KP202101//the Key Laboratory of Polar Science, MNR, Polar Research Institute of China/ ; MEEST-2022-03//the MNR Key Laboratory of Marine Eco-Environmental Science and Technology, China/ ; 91851201//National Natural Science Foundation of China/ ; 31971477//National Natural Science Foundation of China/ ; },
abstract = {Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. β-Diversity differed significantly between RS and GS across these three domains (P < 0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P < 0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.},
}

@article {pmid42304206,
year = {2026},
author = {Pfeifer, D and Graf, M and Rurik, C},
title = {Genestrip: exact and efficient read classification for selected groups of organisms.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42304206},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; Databases, Genetic ; *Software ; },
abstract = {BACKGROUND: The consumption of main memory resources is a significant burden in k-mer-based metagenomic analysis when creating related databases but also when performing (unique) k-mer-counting and read classification. Genestrip addresses this issue by focusing on small but freely configurable groups of organisms. Regarding the selected organisms, Genestrip produces k-mer databases and results comparable to those of KrakenUniq but at a fraction of its required memory resources. Our tool ensures that during database generation, the most suitable lowest common ancestor taxon is assigned for each stored k-mer by also considering genomes of organisms whose k-mers are not included in the database. This enables read analysis with high precision and recall for the organisms of interest.

RESULTS: We assess the correctness, usefulness and performance of Genestrip in different contexts and show that it indeed ascertains high quality read classifications for organisms whose genomes are included in a corresponding database. Our example databases comprise millions to a few billions of k-mers covering a dozen to a few thousands of species and lend themselves to usage in tick surveillance, medical diagnostics or agriculture. All databases were generated on a regular PC within hours, and related analysis performance was competitive to highly favorable. The deliberate focus on a particular set of genera or species allows for more genomes to be included from related organisms while the resulting databases remain small. Since k-mer compression becomes unnecessary, false positives emerging from related information loss are entirely avoided. We exemplify that such small but deep databases tend to improve recall during read classification while sustaining high precision.

CONCLUSIONS: Due to Genestrip's particular way of updating the k-mers' lowest common ancestor taxa, both database creation and fastq file analysis can be realized with little memory and with favorable runtimes as well as high classification quality. So both, database creation and read classification may be performed even on regular PCs. Genestrip's qualities empower users to flexibly design, build and use small k-mer databases for their own needs with potentially deep genomic coverage.},
}

*Metagenomics/methods
Databases, Genetic
*Software

@article {pmid42304260,
year = {2026},
author = {Yang, X and Jing, S and Li, S and Zhang, Y and Dong, L and Zou, T},
title = {Chronic non-bacterial osteomyelitis presenting as fever of unknown origin in a child: a diagnostic pitfall.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-07002-2},
pmid = {42304260},
issn = {1471-2431},
abstract = {BACKGROUND: Chronic non-bacterial osteomyelitis (CNO), also referred to as chronic recurrent multifocal osteomyelitis (CRMO), is a rare autoinflammatory bone disorder in children and adolescents. Bone pain is the most common presenting symptom, whereas prolonged recurrent fever of unknown origin is uncommon and may mimic infection or malignancy, leading to extensive diagnostic evaluations, including invasive procedures.

CASE PRESENTATION: We report a 12-year-old girl who presented with recurrent fever as the predominant symptom, accompanied by delayed and intermittent musculoskeletal pain. Extensive infectious, rheumatologic, and oncologic investigations, including repeated cultures, metagenomic next-generation sequencing, and bone marrow examination, were unrevealing. Magnetic resonance imaging demonstrated multifocal bone marrow edema, and positron emission tomography-computed tomography showed multifocal FDG-avid skeletal lesions, with a maximum SUV of 6.85 among the focal skeletal lesions, raising concern for malignancy. Histopathological examination of a femoral bone biopsy revealed lymphoplasmacytic infiltration with focal fibrosis and no evidence of infection, granulomatous inflammation, necrosis, or malignancy. Based on the clinical course, imaging findings, exclusion of infection and malignancy, and histopathological findings, a diagnosis of CNO/CRMO was established. The patient improved after stepwise treatment with naproxen, methotrexate, and prednisone.

CONCLUSION: This case illustrates an uncommon fever-dominant presentation of pediatric CNO/CRMO with multifocal skeletal lesions mimicking malignancy. CNO/CRMO should be considered in children with fever of unknown origin accompanied by delayed musculoskeletal symptoms or multifocal bone marrow lesions. In typical cases, biopsy may be avoided when clinical and imaging findings are characteristic; however, in atypical presentations with systemic symptoms and malignancy-like imaging findings, bone biopsy may remain necessary to exclude infection and neoplastic disease.},
}

@article {pmid42304541,
year = {2026},
author = {Dutta, R and Obayomi, O and Yosef, AF and Ghazaryan, L and Chalifa-Caspi, V and Lapidot, M and Gillor, O},
title = {A cooperative cobalamide biosynthesis guild in the endosphere of the edible aquatic plant Wolffia globosa Mankai.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00917-4},
pmid = {42304541},
issn = {2524-6372},
support = {16-38-0038//Ministry of Agriculture and Rural Development/ ; },
abstract = {BACKGROUND: Cobalamin (vitamin B12) is synthesized only by certain bacteria and archaea and is rarely found in plant-derived foods because plants neither synthesize nor require this cofactor. The edible duckweed Wolffia globosa Mankai is unusual in containing bioavailable cobalamin, suggesting a microbial origin. However, how cobalamin biosynthetic capacity is organized within angiosperm-associated microbiomes remains largely unresolved. Here, we investigated bacterial community structure and cobamide biosynthetic potential across the cultivation medium, plant surface, and internal tissues of Mankai to determine how cobalamin production is maintained in this aquatic plant microbiome.

RESULTS: Bacterial communities differed significantly among compartments, with the endosphere forming a low-diversity, host-filtered microbiome enriched in specialized taxa. Genome-resolved metagenomics showed that only a minority of endophytic bacteria encoded near-complete cobamide biosynthesis pathways consistent with de novo synthesis. In contrast, many co-occurring taxa lacked multiple biosynthetic steps but were enriched in genes associated with cobamide precursor salvage and remodeling. Network analysis identified putative producer taxa as highly connected hubs linked to salvager populations, consistent with metabolite cross-feeding. Comparative genomic analysis demonstrated reduced cobamide biosynthetic gene complements in endophytic genomes relative to closely related free-living strains, supporting adaptive pathway reduction in the host-associated niche.

CONCLUSIONS: Cobalamin production in the Mankai endosphere appears to arise from a metabolically interdependent bacterial consortium rather than from single autonomous producers. These findings identify cooperative micronutrient biosynthesis as an organizing principle in plant-associated microbiomes and position Mankai as a tractable model for studying cobamide-mediated microbial cooperation in aquatic crops. Understanding these interactions may support microbiome-informed strategies to stabilize micronutrient production and functional resilience in controlled aquatic plant cultivation systems.},
}

@article {pmid42305251,
year = {2026},
author = {Zicos, MH and Barnes, I and Frantz, L and Brace, S},
title = {Megaherbivore coprolite DNA: yields and comparison of three ancient DNA extraction protocols on coprolites of giant ground sloth Mylodon darwinii.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21009},
pmid = {42305251},
issn = {2167-8359},
mesh = {Animals ; *DNA, Ancient/isolation & purification/analysis ; *Sloths/genetics ; },
abstract = {Coprolites offer rich potential for palaeodietary studies as snapshots of past dietary behaviour and environment. They require adapted laboratory methods to retrieve the DNA of the depositor, its microbiome, diet and environmental taxa. Here we compare the performance of three common ancient DNA (aDNA) extraction methods to recover metagenomes from coprolites of Darwin's ground sloth Mylodon darwinii from Cueva del Milodón (Chile). The Qiagen PowerSoil Kit outperformed the other two methods in terms of DNA recovery and library complexity, but the communities inferred from the DNA extracted by the three methods were similar. We were able to recover signatures of local Patagonian flora, as well as sloth mitochondrial genomes, confirming the taxonomic identity of the coprolite depositors.},
}

Animals
*DNA, Ancient/isolation & purification/analysis
*Sloths/genetics

@article {pmid42305671,
year = {2026},
author = {Wu, C and Lou, Y and Wang, L and Wang, F and Wang, X and Liu, Y and Uwaremwe, C and Li, Z and Zhang, Z and Zhu, Y and Su, X and Tian, Y},
title = {Biocontrol mechanisms of two Paenibacillus strains against Astragalus membranaceus root rot and their effects on soil microecological structure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1827299},
pmid = {42305671},
issn = {1664-302X},
abstract = {Astragalus membranaceus is an important medicinal herb in China, yet its yield and quality are severely constrained by root rot disease. In this study, two efficient antagonistic strains, HQ-1 and HQT-2, were isolated and identified as Paenibacillus polymyxa and Paenibacillus terrae, respectively. Both strains exhibited multiple plant growth-promoting traits and strong inhibitory activity against Fusarium solani (syn. Neocosmospora solani) GF-3. In vitro assays confirmed that their sterile fermentation filtrates effectively inhibited pathogen growth and damaged fungal hyphae. GFP labeling further verified their colonization potential on plant roots, while greenhouse experiments indicated preventive efficacies of 86.046% for HQ-1 and 80.619% for HQT-2. In addition, they significantly promoted the growth of A. membranaceus. Metagenomic analysis showed that biocontrol bacterium-treated soils had significantly increased relative abundance of beneficial microorganisms, alongside a reduction in phytopathogenic taxa. Notably, despite the scarcity of biocontrol reports for P. terrae, our study introduces strains HQ-1 and HQT-2 as highly effective, multifunctional resources for sustainable control of A. membranaceus root rot. This study provides much-needed systematic evidence on the efficacy of P. terrae in biocontrol, thereby addressing a notable lack of comprehensive data in the current literature.},
}

@article {pmid42306533,
year = {2026},
author = {Zhang, S and Li, L and Niu, Z and Liu, M and Mao, J and Min, J and Xu, S and Li, R and Zhang, H and Yin, J and Wu, X},
title = {A large-scale retrospective analysis reveals the fungal pathogen spectrum across diverse clinical specimens using metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779223},
pmid = {42306533},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification/pathogenicity ; Aged ; Adult ; Child ; Adolescent ; Young Adult ; *Mycoses/microbiology/diagnosis ; *Invasive Fungal Infections/microbiology/diagnosis ; Child, Preschool ; Aged, 80 and over ; Infant ; },
abstract = {INTRODUCTION: Early diagnosis of invasive fungal diseases (IFD) remains a major clinical challenge due to pathogen diversity and nonspecific symptoms. This study used metagenomic next-generation sequencing (mNGS) technology to comprehensively characterize fungal profiles across various clinical specimens and the demographic characteristics (sex and age) of the patient population. The results provide laboratory evidence to support the diagnosis and treatment of fungal infections.

METHODS: A total of 11,161 mNGS reports from clinical specimens collected at the Renmin Hospital of Wuhan University between March 2022 to August 2024 were retrospectively analyzed. Fungal spectra and patient demographics were comprehensively profiled and compared across different specimen types.

RESULTS: The highest fungal detection rate was observed in bronchoalveolar lavage fluid (36.85%, 1,985/5,387), followed by urine (22.76%, 264/1,160), blood (13.38%, 380/2,840), pleural and peritoneal fluid (12.91%, 174/1,348), cerebrospinal fluid (CSF) (13.82%, 17/123), and wound exudates (12.87%, 39/303). Candida species were the most frequently detected fungi across all specimen types except CSF, wherein Aspergillus predominated. Overall fungal detection rates were significantly higher in male patients than in female patients (26.76% vs. 23.84%, P < 0.01) and in individuals aged > 60 years compared with those aged ≤ 60 years (33.04% vs. 20.02%, P < 0.001), although this trend varied by specimen type. Multivariate logistic regression analysis confirmed that male sex (adjusted odds ratio [aOR]=0.893,95% confidence interval: 0.824-0.967, P = 0.006) and advanced age (≥80 years: aOR=14.77,95% confidence interval: 12.08-18.06, compared with minors) were independent risk factors for fungal detection. Among fungal-positive specimens, 68.28% (1,952/2,859) were co-detected with bacteria, and 15.63% (447/2,859) showed polyfungal detection (≥ 2 fungal species).

CONCLUSION: In conclusion, our findings highlight the predominance of Candida and Aspergillus, identify elderly male patients as a high-risk population, and underscore the high frequency of bacterial-fungal co-detection. Overall, Clinicians should combine mNGS results with imaging, conventional fungal tests (G/GM assays, culture), and clinical presentation for a more accurate diagnosis of IFD.},
}

Humans
Male
Female
Retrospective Studies
*High-Throughput Nucleotide Sequencing
Middle Aged
*Metagenomics/methods
*Fungi/genetics/classification/isolation & purification/pathogenicity
Aged
Adult
Child
Adolescent
Young Adult
*Mycoses/microbiology/diagnosis
*Invasive Fungal Infections/microbiology/diagnosis
Child, Preschool
Aged, 80 and over
Infant

@article {pmid42306745,
year = {2026},
author = {Hang, M and Liu, Y and Shen, X and Zhao, Y and Xu, Y and Gong, X and Xu, L and Li, N and Dong, L},
title = {The clinical and translational perspectives on the lung microbiome in interstitial lung diseases: a bibliometric review.},
journal = {Journal of thoracic disease},
volume = {18},
number = {5},
pages = {478},
pmid = {42306745},
issn = {2072-1439},
abstract = {BACKGROUND: Increasing evidence suggests that microbiota plays important roles in the pathogenesis and progression of interstitial lung diseases (ILDs). However, the global research landscape and emerging trends in this field remain insufficiently characterized. This study aimed to systematically characterize the research landscape, evolving hotspots, and future trends in the field of host microbiota and ILDs using bibliometric and visualization approaches, and to further explore the progress of related clinical studies.

METHODS: Publications up to November 8, 2025 were retrieved from the Web of Science Core Collection. Concurrently, clinical trials within the same timeframe were extracted from PubMed to assess advancements in the field. Bibliometric and visual analyses were conducted using VOSviewer, CiteSpace, SCImago Graphica, and Microsoft Excel.

RESULTS: A total of 295 publications were included, showing a marked increase in research output since 2012. China and the United States were the leading contributors, with the United States demonstrating higher academic impact and stronger international collaboration. Core institutions and authors were mainly concentrated in North America and Europe. Keyword analysis revealed a clear evolution of research focus, shifting from early exposure-related studies and hypersensitivity pneumonitis to lung microbiome dysbiosis, the gut-lung axis, and metagenomic approaches. Recent hotspots emphasize microbiome-based clinical applications, with increasing attention to host-microbiome interactions and immune regulatory mechanisms.

CONCLUSIONS: Research on microbiota and ILDs has expanded rapidly and shows increasing interdisciplinary integration. Future studies should enhance international collaboration, clarify underlying mechanisms, and promote clinical translation of microbiome-based biomarkers and personalized therapeutic strategies.},
}

@article {pmid42306944,
year = {2026},
author = {Abaeva, IS and Pestova, TV and Hellen, CUT},
title = {Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites.},
journal = {Nucleic acids research},
volume = {54},
number = {11},
pages = {},
doi = {10.1093/nar/gkag629},
pmid = {42306944},
issn = {1362-4962},
support = {R01 GM097014/NH/NIH HHS/United States ; R21 AI188505/NH/NIH HHS/United States ; R35 GM122602/NH/NIH HHS/United States ; },
mesh = {*Internal Ribosome Entry Sites ; *RNA, Viral/chemistry/metabolism ; Nucleic Acid Conformation ; Ribosomes/metabolism ; *Dicistroviridae/genetics ; Genome, Viral ; Base Sequence ; *Peptide Chain Initiation, Translational ; },
abstract = {Viral internal ribosomal entry sites (IRESs) are highly structured cis-acting RNAs that mediate end-independent initiation of translation. Their origin remains obscure. The simplest IRESs (type 6) occur in the intergenic region of Dicistroviridae genomes (order Picornavirales), consist of two pseudoknots, and initiate translation by factor-independent binding to ribosomes. Larger variants contain a third pseudoknot that modifies the mechanism of IRES function by engaging with the ribosomal head and promoting binding to the ribosomal aminoacyl site. Metagenomic analyses undertaken to identify structurally distinct type 6 IRESs identified subsets ranging from ∼120-260 nt in length. They differ by the cumulative addition of structural elements, suggesting an accretion mechanism for the structural elaboration of IRESs. Insertions occurred at specific loci, possibly reflecting non-templated nucleotide insertion during replication, and form additional subdomains. Biochemical analysis showed that these novel classes of type 6 IRES all bound directly to the ribosomal peptidyl site. Identification of chimeric IRESs implicates recombinational exchange of domains as a second mechanism for the diversification of IRES structure. Recombination likely also accounts for the presence of type 6 IRESs at the 5'-end of dicistrovirus-like genomes and in families other than Dicistroviridae, including Marnaviridae (order Picornavirales) and Tombusviridae (order Tolivirales).},
}

*Internal Ribosome Entry Sites
*RNA, Viral/chemistry/metabolism
Nucleic Acid Conformation
Ribosomes/metabolism
*Dicistroviridae/genetics
Genome, Viral
Base Sequence
*Peptide Chain Initiation, Translational

@article {pmid42306954,
year = {2026},
author = {Lee, D and Norton, NJ and Dale, AP},
title = {Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
pmid = {42306954},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Conventional microbiological tests have limitations in the microbial diagnosis of immunocompromised patients. Next-generation sequencing (NGS) technologies have the potential to overcome some of these challenges by enabling rapid, comprehensive, and hypothesis-free pathogen detection, potentially improving the speed and accuracy of microbial diagnosis and subsequent clinical outcomes. This review summarizes current evidence for the use of NGS technologies in immunocompromised populations, highlights areas of demonstrated clinical impact, and identifies key priorities for broader clinical integration.

RECENT FINDINGS: Case reports and series have demonstrated the utility of NGS in diagnosing unusual or atypical infections amongst immunocompromised patients that were initially missed by conventional methods. Retrospective observational studies indicate that NGS can achieve higher sensitivity and greater pathogen detection rates than conventional diagnostics, although performance may be limited for certain pathogens, such as Aspergillus and Mycobacterial species. The clinical impact of NGS-guided interventions varies, reflecting both differences in study design and challenges in interpreting metagenomic data.

SUMMARY: NGS technologies have the potential to enhance microbial diagnosis in immunocompromised patients, particularly in complex, polymicrobial, or atypical infections where conventional methods fail. However, widespread clinical adoption is limited by high costs, complex workflows, and the need for advanced bioinformatics infrastructure and expertise. Further research is required to define clinical impact, cost-effectiveness, and to standardize workflows and guide optimal time for implementation, in order to inform evidence-based integration of NGS into routine clinical practice.},
}

@article {pmid42307633,
year = {2026},
author = {Carasso, S and Kasher-Dvora, M and Gefen, T and Geva-Zatorsky, N},
title = {Phase variation-mediated bacterial functional plasticity as a lens for understanding microbe‒host interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2687913},
doi = {10.1080/19490976.2026.2687913},
pmid = {42307633},
issn = {1949-0984},
mesh = {Humans ; *Host Microbial Interactions ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/physiology ; *Bacterial Physiological Phenomena ; Animals ; },
abstract = {The human gut microbiome represents a dynamic microbial ecosystem profoundly influencing host physiology, immune development, and disease susceptibility. While metagenomic approaches have advanced our understanding of microbial composition and functional potential, they remain insufficient to capture the real-time molecular events governing host‒microbe interactions. Taxonomic abundance and genomic content alone do not reflect active gene expression or phenotypic output, and functional roles cannot be reliably inferred from phylogenetic identity, given the substantial heterogeneity observed even within species. Central to bridging this gap is the concept of bacterial functional plasticity, with a focus on phase-mediated functional plasticity, the intrinsic capacity of microbes to rapidly remodel their activity and phenotype in response to environmental and host-derived cues. This review highlights phase variation as a prominent and evolutionarily conserved mechanism underlying plasticity, encompassing DNA inversions, short-sequence repeat modifications, and broader structural genomic variation. Emerging evidence demonstrates not only the prevalence of phase-variable mechanisms across diverse gut taxa but also their significant regulatory, ecological, and immunological consequences. These findings reframe the microbiome from a static consortium of species to a functionally dynamic system capable of rapid rewiring in response to environmental pressures. By integrating genomic, ecological, and host-response data, this review lays the groundwork for mechanistic frameworks that could explain how flexible microbial strategies influence bacterial behavior and host outcomes. Moving beyond cataloging microbial composition toward deciphering the logic of functional adaptation will be essential for translating microbiome research into predictive, diagnostic, and therapeutic applications.},
}

Humans
*Host Microbial Interactions
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/physiology
*Bacterial Physiological Phenomena
Animals

@article {pmid42307846,
year = {2026},
author = {Gomes, RF and García, GJY and Cardoso, MS and Dutra, JDCF and de Abreu Waldow, V and Akamine, RN and de Sousa, MP and Groposo, C and Brenig, B and Figueiredo, H and de Carvalho Azevedo, VA and Góes-Neto, A},
title = {Metagenomics and metatranscriptomics of prokaryotic and fungal microbiomes in produced water associated with petroleum degradation and pipeline corrosion from an oil terminal in Brazil.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42307846},
issn = {1573-0972},
mesh = {*Fungi/genetics/classification/metabolism/isolation & purification ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Petroleum/metabolism/microbiology ; *Metagenomics ; Biodegradation, Environmental ; Corrosion ; Oil and Gas Fields/microbiology ; *Microbiota/genetics ; *Water Microbiology ; Hydrocarbons/metabolism ; Phylogeny ; },
abstract = {The prokaryotic microbial communities involved in hydrocarbon degradation and associated with oil pipeline corrosion have been extensively studied. Nonetheless, fungi can perform significant metabolic activities in these environments. Studies evaluating metabolically active microbial communities in oil reservoirs are limited. Our study investigated the total/DNA and active/RNA communities of Archaea, Bacteria, and Fungi in produced water samples from an onshore terminal in Brazil. DNA and RNA were sequenced using the Illumina HiSeq 2500 platform, and the meta-omics sequences were analyzed. Shannon alpha diversity (taxonomic and functional) revealed that total communities were more diverse than metabolically active ones, with Bacteria showing higher diversity than Archaea and Fungi. The bacterial genera Syntrophotalea (sulfur reducer) and Pseudodesulfovibrio (sulfate reducer) were most prominent in total communities, while Halanaerobium (acid producing) dominated active communities. These results confirm the presence of Microbially Influenced Corrosion (MIC); however, the aprAB and dsrABC genes showed very low expression. Methanogenic Archaea Methanocalculus, Methanoplanus, and Methanothrix were frequent in both total and active communities, and mcrABDG genes were significantly expressed in metatranscriptomic sequences. Fungal genera Absidia, Penicillium, and Rhizopus were dominant in DNA samples, whereas Saccharomycodes, Pichia, Coemansia, and Schizosaccharomyces dominated RNA samples. These fungi can remediate environments contaminated with recalcitrant hydrocarbons. Despite the limited information obtained from fungal functional profile, an in-depth investigation of their activities and interrelation with Archaea and Bacteria in oil reservoirs is crucial for monitoring and mitigating oil biodegradation and pipeline biocorrosion processes.},
}

*Fungi/genetics/classification/metabolism/isolation & purification
Brazil
*Bacteria/genetics/classification/metabolism/isolation & purification
*Archaea/genetics/classification/metabolism/isolation & purification
*Petroleum/metabolism/microbiology
*Metagenomics
Biodegradation, Environmental
Corrosion
Oil and Gas Fields/microbiology
*Microbiota/genetics
*Water Microbiology
Hydrocarbons/metabolism
Phylogeny

@article {pmid42307995,
year = {2026},
author = {Laiton, L and Acevedo, FE},
title = {Gut microbiome of the grape berry moth, Paralobesia viteana (Lepidoptera: Tortricidae) larvae through the grape ripening process revealed by high-throughput 16S and 18S rRNA sequencing.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
pmid = {42307995},
issn = {2057-5858},
mesh = {Animals ; *Vitis/parasitology/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; *Moths/microbiology ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Fungi/classification/genetics/isolation & purification ; },
abstract = {The grape berry moth (GBM) Paralobesia viteana (Lepidoptera: Tortricidae) is an important pest of grapes in eastern North America. The larvae damage grape clusters by direct feeding and by increasing susceptibility to fungal and bacterial pathogens. In this study, we sequenced the V3-V4 region of the 16S rRNA gene and the V4 region of the 18S rRNA gene to characterize the composition and diversity of GBM larval gut bacterial and fungal communities when fed on immature and mature 'Concord' grapes. The data were analysed with QIIME 2, and downstream analyses included taxonomic composition, differential abundance, phylogenetic, functional and alpha/beta diversity analyses. While overall bacterial community diversity did not differ significantly between treatments, differential abundance analysis identified specific bacterial taxa enriched in each larval group. Ninety-three per cent of the bacterial communities belonged to the phylum Proteobacteria, and some may play roles in amino acid and carbohydrate metabolism in the insect gut. Analyses of the 18S rRNA region showed significant taxon-level compositional differences in fungal communities between larvae grown on grapes at different ripening stages. Ascomycota was the dominant phylum (98%) present in the guts of larvae fed on mature grapes, while larvae fed on immature grapes mainly contained fungi within the Cryptomycota (51%). Larvae fed on ripe grapes had a 10-fold higher fungal abundance and were enriched in Saccharomycetales yeasts. Several of the identified microbial taxa in larval guts are commonly found in grapes, which suggests they might be transient insect residents that are ingested with the diet. In conclusion, diet strongly shaped GBM gut-associated fungal communities; specific bacterial taxa also differed between larval groups despite similar overall bacterial diversity. These results contribute to basic knowledge of gut-associated microbes in fruit-feeding insects.},
}

Animals
*Vitis/parasitology/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Larva/microbiology
RNA, Ribosomal, 18S/genetics
Phylogeny
*Gastrointestinal Microbiome/genetics
*Moths/microbiology
Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Fungi/classification/genetics/isolation & purification

@article {pmid42308045,
year = {2026},
author = {Cornman, A and Tranzillo, M and Zulaybar, NG and Bouzit, I and Hwang, Y},
title = {Linear-time prediction of proteome-scale microbial protein interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {25},
pages = {e2610619123},
doi = {10.1073/pnas.2610619123},
pmid = {42308045},
issn = {1091-6490},
support = {GBMF13344//Gordon and Betty Moore Foundation (GBMF)/ ; G-24-67500//Schmidt Futures (Schmidt Futures Projects, LLC)/ ; },
mesh = {*Proteome/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; *Protein Interaction Mapping/methods ; Prediction Algorithms ; Computational Biology/methods ; Protein Interaction Maps ; },
abstract = {Protein-protein interactions (PPIs) underpin biological function, yet proteome-scale interaction prediction remains bottlenecked by the quadratic computational complexity of all-vs.-all pairwise comparisons. Here, we present FlashPPI, a contrastive learning framework, grounded in residue-level interactions, that enables linear-time prediction of physical protein interfaces across a microbial proteome. By leveraging a genomic language model that captures cross-protein coevolutionary signals from metagenomic sequences, FlashPPI aligns interacting partners in a shared latent space. We demonstrate a four-fold performance increase over existing sequence-based methods, while reducing proteome-wide screening time from days to minutes. Crucially, FlashPPI achieves comparable screening performance to state-of-the-art structure-folding models at a fraction of the computational cost. Finally, we integrate FlashPPI into an interactive web platform that combines predicted networks with functional annotations and genomic context, making proteome-wide network analysis rapid and accessible for microbial discovery.},
}

*Proteome/metabolism/genetics
*Bacterial Proteins/metabolism/genetics
*Protein Interaction Mapping/methods
Prediction Algorithms
Computational Biology/methods
Protein Interaction Maps

@article {pmid42308105,
year = {2026},
author = {Zuffa, S and Allaband, C and Charron-Lamoureux, V and Caraballo-Rodriguez, AM and Patan, A and Mohanty, I and Agongo, J and Bostick, JW and Connerly, TJ and Thron, T and Needam, BD and de Castro Fonseca, M and Benitez, RS and Hansen, L and Tubb, H and Cao, J and Kalecký, K and Bottiglieri, T and MahmoudianDehkordi, S and Schimmel, L and Kueider-Paisley, A and Graham, SF and Siegel, D and Wang, M and Knight, R and Kaddurah-Daouk, R and Dorrestein, PC and Mazmanian, SK and , },
title = {A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117499},
doi = {10.1016/j.celrep.2026.117499},
pmid = {42308105},
issn = {2211-1247},
abstract = {The etiology of Alzheimer's disease (AD) remains unclear but is likely driven by gene-environment interactions. We present a multi-organ untargeted metabolomics atlas (n = 2,271) paired with metagenomics data (n = 666) from two AD transgenic mouse models (3xTg and 5xFAD) under colonized and germ-free conditions. Systems-level analyses revealed clusters of dysregulated molecules across tissues, including carnitines, bile acids, B vitamins, neurotransmitters, and N-acyl lipids. Metabolic shifts were associated with the depletion of Akkermansia muciniphila and enrichment of Mucispirillum schaedleri in the 3xTg model. We identify previously unexplored carnitines linked to microbial metabolism of phenylalanine. Using tissueMASST-a mass spectrometry search tool we developed to translate animal-model findings into a human clinical context-we trace phenylacetyl-carnitine in human plasma and serum samples (n = 1,470) from independent cohorts, revealing associations with aging, cognitive impairment, and diminished memory performance. This public resource and associated tools will aid future research in AD etiology.},
}

@article {pmid42308119,
year = {2026},
author = {Holman, DB and Gzyl, KE and Kommadath, A and Määttänen, P},
title = {Multi-omic characterization of the sow colostrum and milk microbiome and proteome.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001726},
pmid = {42308119},
issn = {2057-5858},
mesh = {Animals ; *Colostrum/microbiology ; *Milk/microbiology ; Female ; *Proteome/genetics ; Multiomics ; *Microbiota/genetics ; Swine ; *Bacteria/classification/isolation & purification/genetics ; Metagenomics/methods ; Proteomics ; },
abstract = {Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as Sarcina perfringens and Streptococcus suis, and potentially beneficial bacterial species like Lactobacillus amylovorus and Lactiplantibacillus plantarum. The microbial composition and functional potential shifted significantly as the milk matured, with L. amylovorus, Limosilactobacillus reuteri and Rothia spp. among the most relatively abundant taxa. Several antimicrobial resistance genes, including erm(C), tet(K), tet(M), lnu(A), poxtA and fexB, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including Rothia spp. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.},
}

Animals
*Colostrum/microbiology
*Milk/microbiology
Female
*Proteome/genetics
Multiomics
*Microbiota/genetics
Swine
*Bacteria/classification/isolation & purification/genetics
Metagenomics/methods
Proteomics

@article {pmid42297107,
year = {2026},
author = {Cr, P and Krishna, V and Sethuraman, N and Nambi P, S and Ramasubramanian, V and Balaguru, P and Gopalakrishnan, R},
title = {Diagnostic utility of 16S rRNA meta genomic next-generation sequencing in clinical Infectious Diseases practice: a retrospective study from South India.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101166},
doi = {10.1016/j.ijmmb.2026.101166},
pmid = {42297107},
issn = {1998-3646},
abstract = {OBJECTIVES: 16S rRNA sequencing is an emerging diagnostic tool for bacterial syndromes caused by fastidious pathogens and in culture negative infections. However, it can pose significant challenges from pre-analytic to post-analytic phase due to sampling issues, lack of an approved platform and test characteristics. We aimed to evaluate the diagnostic performance of 16S rRNA sequencing in sterile site samples compared to conventional microbiological techniques [CMT] and a composite reference standard [CRS] METHODS: We conducted a retrospective study at a tertiary hospital from January 2022 to July 2024. We included clinical data of patients with sterile site samples processed for both CMT and 16S rRNA sequencing. Sequencing used the Credence Genomics pipeline.

RESULTS: 166 samples met the inclusion criteria: 97 tissue, 35 pus, and 34 fluid samples. Pathogen detection rate was 42.8% [71/166] by CMT and 58.4% [97/166] by 16S rRNA. Concordance between methods was 50.6%. Sensitivity and specificity of 16S rRNA against CMT was 60.6% and 43.2%; and 69.4% and 66.7% against CRS respectively. CMT showed 54% sensitivity and 92.9% specificity against CRS. Combined testing improved sensitivity to 84.7% and accuracy was 78.9%.

CONCLUSION: 16S rRNA sequencing provides incremental diagnostic sensitivity over conventional microbiological techniques but at the cost of reduced specificity. Its routine frontline use as a standalone diagnostic tool is not supported by our findings. Instead, it may be best reserved for selected culture-negative cases with high clinical suspicion, where results can be interpreted in conjunction with clinical, radiological, and microbiological data by experienced clinicians.},
}

@article {pmid42297247,
year = {2026},
author = {Yang, S and Xing, KY and Tao, YF and Wang, JY and Liu, KH and Zhang, M and Xu, XR and Zhu, L and Wei, W},
title = {Metagenomics-guided targeted isolation and mechanistic elucidation of haloalkaliphilic bisphenol A-degrading microorganisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135172},
doi = {10.1016/j.biortech.2026.135172},
pmid = {42297247},
issn = {1873-2976},
abstract = {Bisphenol A (BPA), a typical endocrine-disrupting compound, poses significant environmental risks. Efficient bioremediation in high-salinity and alkaline environments, such as saline-alkaline industrial wastewater and landfill leachate, remains challenging due to the lack of microorganisms capable of maintaining activity under extreme conditions. Here, this study developed a strategy integrating metagenomic functional prediction with targeted enrichment and isolation. Soil microcosm experiments combined with metagenomic analyses identified soda saline-alkaline soils with high BPA degradation potential, and predicted microbial degradation predominantly via hydroxylation, with archaeal involvement also suggested. Guided by these predictions, 14 saline-alkaline-tolerant BPA-degrading bacterial strains (13 genera) and 20 haloalkaliphilic archaeal strains (16 genera) were successfully isolated. The proportion of BPA-degrading archaea (95.24%) was higher than bacteria (58.33%), challenging the view that this function is restricted to bacteria and fungi. Genomic analyses revealed bacterium Pseudomonas reidholzensis SAS-B12 and archaeon Natronomonas gomsonensis SR-A11 degrade BPA via hydroxylation, with differing downstream ring-cleavage pathways. SR-A11 also exhibited high laccase activity, suggesting multi-enzyme synergistic degradation. Response surface methodology optimization showed SAS-B12 achieved ∼50% BPA degradation under simulated saline-alkaline wastewater (pH 8.3, salinity 2.3%), and SR-A11 achieved similar efficiency under extreme conditions (pH 9.8, salinity 23.6%). This study expands the phylogenetic diversity of BPA-degrading microorganisms and provides microbial resources, enzymatic insights, and methodological support for targeted bioremediation in saline-alkaline wastewater.},
}

@article {pmid42297252,
year = {2026},
author = {Li, Q and Zhang, Q and Huang, D and Chen, S and Zhang, B},
title = {Electrically enhanced, Nature-Driven microbial attenuation of chromate and dichloromethane in groundwater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135175},
doi = {10.1016/j.biortech.2026.135175},
pmid = {42297252},
issn = {1873-2976},
abstract = {Natural attenuation is a nature-based approach that relies on intrinsic biogeochemical and microbial processes to mitigate mixed heavy metals and organic pollutants in aquifer, yet its efficiency is limited by electron donor scarcity and suppressed microbial activity. Here, a low-energy bioelectrochemical strategy that uses a mild electric field (0.6 V) was introduced to sustainably stimulate the attenuation of chromate [Cr(VI)] and dichloromethane (DCM) co-contamination in groundwater. With minimal electrical input, Cr(VI) and DCM removal reached 95.0 ± 2.6% and 95.2 ± 0.5%, substantially outperforming the no-voltage and single-pollutant systems. The electric field alleviated electron-donor limitations and metabolic inhibition, enabling efficient and energy-conserving bioremediation. Mineralogical and spectroscopic analyses (SEM-EDS, XPS, XRD) confirmed the reduction of Cr(VI) to Cr(III) precipitates (e.g., Cr2O3) and the progressive dechlorination and mineralization of DCM. Integrated metagenomic and metatranscriptomic profiling revealed active functional guilds (e.g., Sphingopyxis, Pseudomonas, Hyphomicrobium) expressing key genes for chromate reduction (yieF, chrA), dehalogenation (dhlA, dcmA), and electron-shuttling metabolism (ribE). This work demonstrates an applicable remediation technology that can be powered by renewable electricity and integrated into secure groundwater management systems. It offers a pathway for environmentally safe pollutant mitigation by harnessing nature-based microbial processes, supporting the transition toward enhanced natural attenuation.},
}

@article {pmid42297258,
year = {2026},
author = {Wei, S and Wang, L and Li, Y and Wang, B and Wang, T and Li, J},
title = {Cometabolic degradation of ofloxacin by aerobic methane oxidation coupled with denitrification: Identification of degraders, helper bacteria, and metabolic networks.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135168},
doi = {10.1016/j.biortech.2026.135168},
pmid = {42297258},
issn = {1873-2976},
abstract = {The aerobic methane oxidation coupled with denitrification (AME-D) system enables simultaneous nitrogen removal and antibiotics cometabolic degradation, yet the underlying microbial ecological mechanisms remain poorly understood. This work took ofloxacin (OFL) as a typical antibiotic pollutant and established long-term stable sequencing-batch AME-D reactors to explore their nitrogen removal efficiency and OFL degradation sustainability under antibiotic stress. A multi-omics approach combining metagenomics, metaproteomics, and metabolomics was adopted to identify the core degraders and functional helper bacteria, and unravel the synergistic metabolic interactions sustaining the system's performance. Results indicate that the AME-D cometabolic system maintains high-efficiency nitrogen removal capacity and achieves effective OFL degradation under OFL stress. The piperazine ring is the primary reactive site of OFL, undergoing ring cleavage to form intermediate products. Multi-omics results demonstrate that microbial community structure is significantly reshaped by OFL pressure. Aerobic methane-oxidizing bacteria (MOB) are identified as core degraders, which mediate OFL cometabolism via methane monooxygenase (pMMO/sMMO) and supply available electron donors. Denitrifiers and stress-tolerant auxiliary bacteria form synergistic networks by optimizing nitrogen metabolism, activating efflux pumps and regulating antioxidant defenses, which maintains system functional stability under high OFL stress. Fluorescence in situ hybridization (FISH) verification confirms that MOB, nitrifiers and denitrifiers form compact spatial interaction structures in sludge, which provide favorable conditions for interspecific substance exchange and electron transfer. This study clarifies the multi-scale functional maintenance mechanism of AME-D cometabolic system, offering theoretical support for the treatment of antibiotic-laden wastewater and ecological risk control of antibiotic resistance.},
}

@article {pmid42297276,
year = {2026},
author = {Maas, MAM and Rutjes, SA and Bossers, A and Stege, PB and van der Plaats, RQJ and Kuiper, I and van der Ark, KCH and Husman, AMR},
title = {Use of metagenomics for the detection of pathogens in the environment: A scoping review.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125050},
doi = {10.1016/j.envres.2026.125050},
pmid = {42297276},
issn = {1096-0953},
abstract = {Pathogens in the environment may pose a threat to our ecosystem and public health by causing infectious disease outbreaks. Early detection and identification are crucial for effective surveillance, outbreak prevention, and source attribution. However, analyzing environmental samples (e.g., air, soil, water, biowaste) is challenging due to their complex composition. Testing for each pathogen, known and undiscovered ones, is not possible yet. Metagenomic shotgun sequencing offers a promising approach for pathogen-agnostic DNA detection in these matrices. This review provides guidance and recommendations for experimental design, DNA extraction, library preparation, sequencing, and bioinformatics, and underscores the need for standardized protocols and inter-laboratory studies. This scoping review addresses metagenomic methodologies for pathogen detection in environmental matrices by highlighting current practices, challenges and limitations, and provides guidance for researchers and practitioners. Following the PRISMA guidelines, we identified 81 relevant studies from 6,034 initial records. Most studies utilized Illumina short-read sequencing, with fewer using long-read platforms like Oxford Nanopore Technologies or Pacific Biosciences. DNA extraction protocols varied, with a trade-off between DNA yield and preserving community structure. Few studies reported inter-laboratory comparisons or standardized workflows. Selection of bioinformatics tools and reference databases significantly influenced taxonomic classification, yet reporting of analytical parameters was often incomplete. This review highlights the need for appropriate controls and increased transparency in reporting applied methods and settings. Methodological diversity and unreported gaps hinder reproducibility and comparability, while a systematic approach in environmental metagenomics holds great promise for pathogen and ecosystem monitoring.},
}

@article {pmid42297323,
year = {2026},
author = {Li, Y and Hu, Y and Cheng, S and Fang, H and Guo, Y},
title = {Compound-specific effects of phthalate esters on nitrogen cycling and N2O emissions in paddy soils under contrasting moisture regimes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128593},
doi = {10.1016/j.envpol.2026.128593},
pmid = {42297323},
issn = {1873-6424},
abstract = {Phthalates (PAEs) are commonly used as plasticizers and agrochemical additives, easily released and accumulated in soils. As emerging organic pollutants, how PAEs affect soil nitrogen (N) cycling remains unclear. Here, a 91-day microcosm experiment was conducted to investigate the response of functional microorganisms and nitrous oxide (N2O) emissions to dimethyl phthalate (DMP) and di(2-ethylhexyl) phthalate (DEHP) enrichment under different moisture regimes. Metagenomic analysis showed that PAE type, rather than concentration, predominantly shaped microbial community structure and N-cycling functional profiles. Under unflooded conditions, DEHP increased cumulative N2O emissions by 42%, accompanied by enhanced nitrification potential, higher abundances of amoA and hao, and enrichment of Nitrosospira. Conversely, DMP and co-exposure treatments reduced cumulative N2O emissions by 49.24-67.86%, together with suppressed autotrophic nitrification and increased denitrification module abundance. Under flooded conditions, DMP and co-exposure increased nosZ abundance and enriched Telmatospirillum, indicating a greater potential for N2O reduction. In addition, PAE exposure increased the complexity of microbial co-occurrence networks and strengthened associations between functional taxa and N-cycling genes. Structural equation modelling showed that PAE-induced shifts in soil pH, dissolved organic carbon, and inorganic N pools jointly regulated nitrification and denitrification pathways, thereby determining N2O emission patterns. These findings highlight the potential for plasticizer contamination to reshape nitrogen transformation and nitrogen loss pathways in paddy soils under contrasting moisture regimes.},
}

@article {pmid42297331,
year = {2026},
author = {Fan, S and Li, Y and Zhang, L and Xie, S},
title = {Experimental evidence for the role of phages in mitigating antibiotic resistance genes in mangrove sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {405},
number = {},
pages = {128589},
doi = {10.1016/j.envpol.2026.128589},
pmid = {42297331},
issn = {1873-6424},
abstract = {The ecological role of bacteriophages (phages) in mitigating or proliferating antibiotic resistance genes (ARGs) in mangroves remains elusive due to the lack of direct experimental validation. Climate change-driven seawater encroachment introduces non-native phages into mangrove ecosystems, yet the potential impacts of this process on ARG spread have not been elucidated. Here, we established flooded microcosms inoculated with phage suspensions derived from native and non-native mangrove sediments, thus simulating phage input disturbance caused by climate change. Our results revealed distinct phage-host interaction patterns: non-native phages exerted short-term disturbances on bacterial communities, but neither phage source altered the bacterial or resistome structure. Nevertheless, phages specifically influenced the composition and dynamics of ARGs, with non-native phages showing stronger regulatory effects. Furthermore, 77 ± 2.1% of viral operational taxonomic units (vOTUs) were lytic, and 154 out of 185 phage-antibiotic-resistant bacteria (ARB) links were lytic, indicating that lytic phages played a dominant role in controlling ARB abundance and promoting ARG mitigation, whereas 0.68 ± 0.46% of host-infecting lysogenic phages carried ARGs, contributing little to ARG proliferation. Moreover, only 3.2 ± 0.56% vOTUs carried ARGs, resulting in negligible phage-mediated transduction for ARG dissemination. This study provides the first direct experimental evidence for the impacts of phages from different sources on the fate of ARGs in mangrove ecosystems, and offers novel insights into the ecological mechanisms underlying the spread of ARGs in the context of global climate change.},
}

@article {pmid42297767,
year = {2026},
author = {Song, YC and Shi, C and Stratton, KG and Ayala-Ortiz, C and Stohel, I and Freire-Zapata, V and Tfaily, MM and Eloe-Fadrosh, E and Graham, EB},
title = {Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42297767},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/chemistry ; *Metagenome ; *Bacteria/metabolism/genetics/classification ; Archaea/metabolism/genetics/classification ; *Organic Chemicals/metabolism/chemistry ; },
abstract = {Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon-atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of complex SOM through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism/chemistry
*Metagenome
*Bacteria/metabolism/genetics/classification
Archaea/metabolism/genetics/classification
*Organic Chemicals/metabolism/chemistry

@article {pmid42298252,
year = {2026},
author = {Biter, R and Regney, M and Schmidt, AE and Swanson, N and Elrod, M and Lescroël, A and Burnham, C and Jongsomjit, D and Winquist, S and Pennycook, J and Ainley, DG and Dugger, KM and Ballard, G and Kraberger, S and Varsani, A},
title = {Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica.},
journal = {Archives of virology},
volume = {171},
number = {7},
pages = {},
pmid = {42298252},
issn = {1432-8798},
support = {1935870//National Science Foundation/ ; },
mesh = {Animals ; Antarctic Regions ; Phylogeny ; Genome, Viral ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/veterinary/virology ; *Charadriiformes/virology ; *Bird Diseases/virology ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua (Stercorarius maccormicki) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake (Rissa tridactyla), Larus smithsonianus papillomavirus 1 from American herring gull (Larus smithsonianus) and Fratercula arctica papillomavirus 1 from Atlantic puffin (Fratercula arctica), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp. and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins (Pygoscelis adeliae), Weddell seals (Leptonychotes weddellii), Antarctic fur seals (Arctocephalus gazella), leopard seals (Hydrurga leptonyx) and emerald notothen (Trematomus bernacchii).},
}

Animals
Antarctic Regions
Phylogeny
Genome, Viral
*Papillomaviridae/genetics/isolation & purification/classification
*Papillomavirus Infections/veterinary/virology
*Charadriiformes/virology
*Bird Diseases/virology
DNA, Viral/genetics

@article {pmid42298353,
year = {2026},
author = {Strokach, A and Zakharevich, N and Aginova, V and Grigoryevskaya, Z and Petukhova, I and Bagirova, N and Romanov, M and Dyachkova, M and Morozov, M and Veselovsky, V and Kanaeva, V and Kalinin, D and Larin, A and Shitikov, E and Klimina, K},
title = {Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681788},
doi = {10.1080/19490976.2026.2681788},
pmid = {42298353},
issn = {1949-0984},
mesh = {Humans ; *Immunotherapy ; *Melanoma/therapy/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome ; Female ; Cohort Studies ; *Bacteria/classification/genetics/isolation & purification ; Male ; Russia ; Metagenomics ; Metagenome ; *Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Aged ; Treatment Outcome ; Adult ; },
abstract = {Melanoma is an aggressive malignancy with a significant risk of mortality. In recent years, treatment strategies have undergone a paradigm shift with the advent of immunotherapy, particularly immune checkpoint inhibitors (ICIs). Despite notable clinical success, a substantial proportion of patients fail to respond or eventually develop resistance to ICIs. Emerging evidence highlights the gut microbiota as a critical modulator of host immune responses and is one of the potential determinants of immunotherapy efficacy. We performed a cross-cohort analysis of gut microbiome profiles from melanoma patients treated with ICIs. The study integrated the first Russian cohort (62 patients) with six previously published international datasets, comprising a total of 490 patients across seven cohorts. In all cases, metagenomic sequencing was performed using various Illumina platforms, and raw sequencing data were processed using a unified bioinformatic pipeline. Analysis revealed 527 metagenome-assembled genomes (MAGs) significantly associated with treatment outcome: 239 with response and 288 with non-response. Notably, the species Faecalibacterium sp900539945, Phocaeicola vulgatus, Bifidobacterium adolescentis, Faecalibacterium taiwanense, and Gemmiger qucibialis were consistently associated with response, while Enterobacter ludwigii was linked to non-response. Analysis of the Russian cohort revealed both conserved and population-specific microbial signatures, highlighting the coexistence of globally shared and region-dependent microbiome features. Our results also show that species-level annotations may obscure opposing response associations within the same taxa, highlighting the need for MAGs or strain profiling. Together, this study demonstrates that cross-cohort analysis enables the identification of robust and reproducible bacterial markers of immunotherapy response, providing a foundation for microbiome-based prediction and modulation strategies in melanoma.},
}

Humans
*Immunotherapy
*Melanoma/therapy/microbiology/immunology/drug therapy
*Gastrointestinal Microbiome
Female
Cohort Studies
*Bacteria/classification/genetics/isolation & purification
Male
Russia
Metagenomics
Metagenome
*Immune Checkpoint Inhibitors/therapeutic use
Middle Aged
Aged
Treatment Outcome
Adult

@article {pmid42298382,
year = {2026},
author = {Raj, K and Sharma, P and Riyaz, M and Shouche, YS and Multani, K and Sharma, M and Dhaliwal, M},
title = {Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05248-5},
pmid = {42298382},
issn = {1471-2180},
support = {S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; },
abstract = {BACKGROUND: The human gut microbiome consists of a complex and diverse community of commensal microorganisms and has been under extensive research consideration in the past few decades. Although several recent studies have targeted the determination of bacterial composition of the ecosystem, the knowledge about the mycobiome, virome, and functional attributes of the same remains scarce. The aim of the present study was to investigate the functional and resistome profile of the gut microbiome in the Pangwala tribal community of India using a combined Whole Metagenome Shotgun (WMS) sequencing and bioinformatics approach.

RESULTS: The findings revealed a remarkable diversity of microorganisms inhabiting the gut of both groups, with similar level of diversity among the dominant genera like Prevotella, Bifidobacterium and Succinivibrionaceae. The mycobiome was dominated by the subkingdom Dikarya (74%), while Fungi incertae sedis accounted for 23% of the total fungal species in both groups. The virome analysis showed the dominance of the Caudoviricetes class, with bacteriophages being the most dominant. Moreover, functional analysis identified the prominent metabolic pathways and the key gene families involved in the pathways, highlighting Prevotella copri as the major contributor. Additionally, the study identified the resistome and showed that there were more than 100 potential antibiotic-resistant genes (ARGs) and high levels of resistance to vancomycin in both groups.

CONCLUSION: This study presents a comprehensive overview of the gut microbiome in the Pangi population, detailing both in its taxonomic structure and functional traits. The results show that, despite the high degree of diversity in the gut microbiome, there seems to be evident functional redundancy, which underlines a core stable microbiome. The resistome profile offers complete exploratory picture of the resistome and establishes a valuable baseline for future studies. Furthermore, we anticipate that these findings will add valuable insights to understand the Antimicrobial resistance (AMR) stewardship in the light of one health aspect.},
}

@article {pmid42298622,
year = {2026},
author = {Wang, F and Sang, Y and Guo, J and Fu, Y and Yang, M and Shan, F and Chen, Y and Zhang, S and Li, X and Li, J and Zhang, L},
title = {Dietary glycyrrhizic acid improves growth performance and modulates upper respiratory microbiota in weaned piglets.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05622-5},
pmid = {42298622},
issn = {1746-6148},
support = {231111111600//Henan Province Key Research and Development Plan Project/ ; 251111113300//Henan Province Key Research and Development Plan Project/ ; CARS-35//the National Pig Industry Technology System/ ; },
abstract = {BACKGROUND: Natural products with dual immunomodulatory and antimicrobial functions offer promising strategies to reduce antibiotic use in livestock. Glycyrrhizic acid (GA), the principal bioactive component of licorice, has demonstrated anti-inflammatory and antiviral properties, yet its translational potential in swine health remains underexplored. This study evaluated the efficacy of GA in weaned piglets under commercial nursery conditions as an antibiotic alternative. A total of 225 weaned piglets were assigned to five groups: negative control (CON, basal diet), farm routine (FA, conventional antibiotics), and three GA-supplemented groups (GLL, 0.65 g/kg; GLM, 1.3 g/kg; GLH, 2.6 g/kg).

RESULTS: The result showed that dietary GA supplementation (2.6 g/kg) numerically improved growth performance and reduced cough scores, although not statistically significant. GA significantly decreased the diarrhea index and improved skin scores. GA also significantly increased serum IgG and IgM levels in piglets and showed a trend toward higher IgA levels. Furthermore, GA exhibited a trend toward lowering serum IL‑1β levels while upregulating IFN‑γ and IL‑10 levels. Regarding antioxidant parameters, GA significantly upregulated T‑SOD, GSH‑PX, and CAT activities and downregulated LDH activity. Metagenomic analysis revealed that high‑dose glycyrrhizic acid (GA) significantly increased the abundance of Alloprevotella, while decreasing the abundances of Moraxella pluranimalium and 11 other pathogenic species associated with respiratory diseases and lung injury, including Glaesserella parasuis, Mesomycoplasma hyorhinis, Mesomycoplasma hyopneumoniae, Streptococcus suis, among others, thereby reshaping the upper respiratory tract microbiota of pigs.

CONCLUSIONS: Collectively, these findings support GA as a viable non-antibiotic strategy for improving immune function, antioxidant capacity, and respiratory health in weaned piglets.},
}

@article {pmid42298631,
year = {2026},
author = {Yan, Q and Li, M and Wang, G and Zhang, A and Li, Y and Guo, R and Zhang, Y and Yang, W and Zhang, Y and Liu, X and Li, X and Zheng, N and Wang, L and Fan, S and Ma, R and Lu, T and Zhou, S and Guan, T and Xing, G and Li, S and Wang, L and Li, Y},
title = {Cross-kingdom microbial associations characterize responsiveness to fecal microbiota transplantation in patients with irritable bowel syndrome.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08269-w},
pmid = {42298631},
issn = {1479-5876},
abstract = {BACKGROUND: Precise outcome prediction for fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) remains a clinical challenge. The roles of the gut virome and its interplay with bacteria in FMT efficacy are particularly underexplored. This secondary analysis aimed to conduct an exploratory, hypothesis-generating investigation into these cross-kingdom dynamics.

METHODS: We conducted a secondary, integrative analysis of a published cohort, performing longitudinal, cross-kingdom metagenomic profiling on 83 samples from 22 IBS patients and healthy donors. We integrative approach combined microbial diversity, species-specific biomarker identification, bacterial-viral associated networks, and exploratory random forest modeling to identify microbial features associated with FMT outcomes.

RESULTS: IBS patients showed higher bacterial and viral alpha diversity than donors. Cross-kingdom profiling identified 223 bacterial and 724 viral biomarkers. Donor-enriched biomarkers were predominantly health-associated Bacteroidetes (e.g., B. ovatus, B. faecis), whereas pre-FMT-enriched biomarkers were largely Firmicutes (e.g., B. obeum) with potential pathobiont roles. The Effect and No effect groups displayed different microbial trajectories. Although both groups shifted toward a donor-like composition initially, only responders maintained a stable donor-like ecology throughout the 12-month follow-up, supported by more resilient bacterial-viral association networks. Exploratory random forest modeling highlighted microbial features, such as R. pickettii, with high relative importance for outcome discrimination. However, permutation testing (p = 0.548-0.616) confirmed that model performance on this small cohort did not exceed chance level, underscoring the risk of overfitting and the exploratory nature of these computational findings.

CONCLUSIONS: This integrative re-analysis provides preliminary evidence that cross-kingdom gut microbiome profiles are strongly associated with FMT outcomes in IBS. Successful outcomes appear linked to sustained donor-like remodeling and stable bacterial-viral networks. Our findings are primarily hypothesis-generating and offer a framework of candidate biomarkers for future validation in larger cohorts. This work underscores the necessity of external validation to develop robust, microbiome-based tools for personalized FMT therapy.},
}

@article {pmid42298685,
year = {2026},
author = {Yanagawa, Y and Yoshida, N and Makiuchi, T and Kawashima, A and Uemura, H and Aoki, T and Mizushima, D and Gatanaga, H and Watanabe, K},
title = {Multi-omics profiling and bile-acid exposure assays implicate a gut microbiome-parasite axis linked to persistent Entamoeba histolytica carriage.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00845-1},
pmid = {42298685},
issn = {1757-4749},
support = {IN-JP-380-5724//Gilead Sciences/ ; JP26K10011//Japan Society for the Promotion of Science/ ; JP23fk0108680h0001//Japan Agency for Medical Research and Development/ ; },
abstract = {Asymptomatic Entamoeba histolytica (Eh) carriage is a major transmission reservoir, yet how the gut ecosystem-particularly microbiota-derived metabolites such as secondary bile acids-supports persistent colonization remains unclear. We investigated whether gut microbiome-metabolite features are associated with Eh carriage and could influence parasite phenotypes METHODS: We integrated shotgun metagenomics from a prospectively screened outpatient cohort (n=36) with functional in vitro assays. An ordinal stepwise model across detection states (Eh-, Eh_qPCR, Eh_Cyst) was used to identify candidate microbial features, followed by bile-acid exposure assays and transcriptomic profiling to evaluate impacts on parasite fitness and metronidazole susceptibility in vitro RESULTS: Microbiome profiling suggested taxon-specific shifts rather than wholesale dysbiosis. Community-level beta diversity showed no significant separation, whereas genus richness was higher in Eh_Cyst (unadjusted p=0.046). Multivariable modeling yielded concordant directional but non-significant trends (all q>0.9), highlighting Firmicutes genera including Coprococcus, Ruminococcus, and Catenibacterium as candidate taxa. We then evaluated deoxycholic acid (DCA), a microbiota-modified secondary bile acid. In vitro, 100 μM DCA extended Eh survival under nutrient-limited conditions and reduced metronidazole susceptibility after pretreatment. Transcriptomic profiling showed that DCA induced a distinct response, including an 8.34-fold induction of the ABC transporter P-glycoprotein-2 and upregulation of lipid remodeling and stress-response genes, supporting a bile acid-driven adaptive program consistent with intestinal persistence CONCLUSIONS: Our findings suggest that secondary bile acids, exemplified by DCA, can reprogram Eh gene expression and attenuate metronidazole susceptibility in vitro. In the context of cyst-associated microbiome signatures, this supports the plausibility of a microbiome-bile acid-parasite axis that may promote persistence in asymptomatic carriers and could influence treatment efficacy.},
}

@article {pmid42298736,
year = {2026},
author = {Amat, S and Holman, DB and Luecke, SM and Gzyl, KE and Anas, M and Stokka, G},
title = {The bovine ocular microbiome: a multi-approach study of composition and antimicrobial activity.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00587-0},
pmid = {42298736},
issn = {2524-4671},
support = {20-21-2022; 22-14-0231; 24-30-0265//North Dakota State Board of Agricultural Research and Education/ ; },
abstract = {BACKGROUND: Despite widespread use of antimicrobials and vaccines, the incidence of infectious bovine keratoconjunctivitis (IBK), or pinkeye, continues to increase in North American beef cow-calf operations. Recent research suggests that there is potential for the commensal ocular microbiome to help mitigate IBK. Therefore, this study characterized the ocular microbiome of cattle with and without IBK using culture-based methods and shotgun metagenomic sequencing and assessed the ability of commensal bacteria to inhibit Moraxella spp. in vitro. Ocular swabs (n = 143) were collected from IBK-affected (n = 102) and healthy cattle (n = 41) before antimicrobial treatment from North Dakota herds. Bacteria were cultured aerobically and anaerobically on five different media and the isolates were identified. A subset of swabs (37 IBK-affected; 12 healthy) underwent shotgun metagenomic sequencing. The genomes of 31 isolates, including Moraxella bovoculi, Moraxella bovis, and commensal bacteria, were also sequenced. Fifty-two commensal isolates were screened for inhibition of Moraxella spp. using an agar slab method, with five isolates further tested by qPCR for inhibition in the presence of the culturable ocular microbiome.

RESULTS: The 351 bacterial isolates taxonomically identified represented 61 genera from three phyla. The majority of isolates belonged to Bacillus (25.9%), Streptococcus (11.1%), Staphylococcus (10.1%), and Moraxella (9.4%) genera. Shotgun metagenomic analysis revealed significant differences in ocular microbial species composition between IBK-affected and healthy cattle (R² = 0.05; P = 0.015) based on Bray-Curtis dissimilarity. Dominant bacterial species included Cutibacterium acnes, Mannheimia pernigra, Mesomycoplasma bovoculi, Moraxella bovis, and Moraxella bovoculi. Eight bacterial species, including Bifidobacterium globosum and Bacillus licheniformis, were more abundant in healthy cattle, while Arthrobacter luteus was enriched in IBK cases. Thirty-seven high-quality metagenome-assembled genomes were also recovered, with 27% classified as Mesomycoplasma bovoculi. Moraxella spp. genomes exhibited strain-specific antimicrobial resistance and virulence gene diversity. Seventeen commensal isolates inhibited Moraxella, with Weizmannia coagulans, Lentilactobacillus buchneri, and Paenibacillus polymyxa showing strong activity. Selected isolates maintained inhibitory effects in co-culture with the ocular microbiome.

CONCLUSION: The ocular surface of beef cattle is inhabited by a diverse microbiome that includes several bacterial strains that have the potential to be used as therapeutics to inhibit IBK pathogens.},
}

@article {pmid42298774,
year = {2026},
author = {Chen, X and Ding, S and Tang, H and Yang, Q and Yuan, L and Zhang, A and Li, Y and Wang, Q and Yan, X and Wang, Z and Wang, M and Zheng, Z},
title = {Monochromatic light reprograms transcription, metabolism, and rhizosphere microbial communities in Salvia miltiorrhiza.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2686334},
doi = {10.1080/15592324.2026.2686334},
pmid = {42298774},
issn = {1559-2324},
mesh = {*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics ; *Rhizosphere ; *Light ; *Microbiota/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; *Transcription, Genetic/radiation effects ; },
abstract = {Salvia miltiorrhiza is a valuable medicinal plant with diverse pharmacological applications and high market demand. Light quality is a critical environmental factor regulating plant growth, secondary metabolism, and interactions with rhizosphere microorganisms. However, the effects of short-term, pure monochromatic light exposure on S. miltiorrhiza remain largely unexplored. In this study, we employed integrated transcriptomic, metabolomic, and rhizosphere metagenomic analyzes to investigate the responses of S. miltiorrhiza under different monochromatic light conditions: ultraviolet (UV), blue (B), red (R), and far-red (FR), with white light (WL) as the control. GO enrichment analysis indicated that all monochromatic light treatments activated defense responses, while specific pathways related to light stimulus, wounding, and reactive oxygen species were uniquely enriched under B, R, and FR light. Metabolomic analysis showed a general decrease in metabolite abundance under monochromatic light compared to WL, with the R treatment inducing the highest number of significantly upregulated metabolites. Integrated KEGG pathway analysis of differential transcripts and metabolites highlighted the enrichment of secondary metabolic pathways, including diterpenoid, monoterpenoid, and phenylpropanoid biosynthesis. Notably, quantitative HPLC analysis confirmed that UV, R, and FR light significantly promoted the accumulation of dihydrotanshinone I and tanshinone IIA, while decreasing salvianolic acid A content. Metagenomic analysis revealed that monochromatic light, especially B light, reduced rhizosphere microbial alpha diversity and altered the abundance of specific bacterial families and species. Functional gene annotation also showed treatment-specific shifts in microbial metabolic potential and virulence factors. In conclusion, short-term monochromatic light culture, particularly R and FR, effectively modulates the transcriptome and metabolome of S. miltiorrhiza, enhancing the accumulation of key bioactive tanshinones, while simultaneously reshaping its rhizosphere microbial community. These findings offer a potential light-based strategy for improving the quality of S. miltiorrhiza.},
}

*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics
*Rhizosphere
*Light
*Microbiota/radiation effects
Gene Expression Regulation, Plant/radiation effects
*Transcription, Genetic/radiation effects

@article {pmid42299582,
year = {2026},
author = {Yu, Y and Wang, C and Pan, X and Ding, C and Chen, J},
title = {Metagenomic profiling of biliary microbiota reveals distinct microbial and functional features in cholelithiasis and cholecystic polyps.},
journal = {Medicine},
volume = {105},
number = {24},
pages = {e49251},
doi = {10.1097/MD.0000000000049251},
pmid = {42299582},
issn = {1536-5964},
support = {2022YFC2804205//National key research and development program of China/ ; },
mesh = {Humans ; *Cholelithiasis/microbiology ; *Metagenomics/methods ; *Polyps/microbiology ; *Microbiota/genetics ; Female ; *Bile/microbiology ; Male ; *Metagenome ; Middle Aged ; Aged ; },
abstract = {Cholelithiasis and cholecystic polyps are common gastrointestinal conditions, and recent studies suggest that biliary microbiota dysbiosis may be closely associated with their pathogenesis. In this small cohort (n = 11), bile samples were aseptically collected during surgery from 6 patients with cholelithiasis and 5 patients with cholecystic polyps. Metagenomic sequencing was performed to investigate differences in the microbial composition and functional profiles between the 2 groups. The results revealed that the microbial α diversity of bile from patients with cholelithiasis was significantly greater than that of the polyp group, with significant differences in the Richness, Chao1, ACE, and Shannon indices (P < .05). β-diversity analysis further revealed distinct differences in microbial community composition across the groups. Linear discriminant analysis effect size analysis revealed Pseudomonadota as the only phylum enriched in the polyp group, whereas the cholelithiasis group was enriched with multiple phyla, such as Campylobacterota, Bacillota, and Fusobacteriota, and 35 genera, such as Bacteroides, Mucilaginibacter, and Pedobacter. Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis indicated that the microbial community in the cholelithiasis group was significantly associated with neurodegenerative disease-related pathways, while the microbial community in the polyp group was enriched in pathways related to ribosomes and fluid shear stress. This study highlights the potential role of biliary microecological imbalances in the development of biliary diseases and provides a theoretical basis for exploring pathogenesis and microbiota-based therapeutic strategies.},
}

Humans
*Cholelithiasis/microbiology
*Metagenomics/methods
*Polyps/microbiology
*Microbiota/genetics
Female
*Bile/microbiology
Male
*Metagenome
Middle Aged
Aged

@article {pmid42299645,
year = {2026},
author = {Paulsen, J and Sharrett, ST and Mumey, D and Larsen, EM and Nguyen, NK and Lendemer, J and Calabria, LM and Hoffman, JR and Magori, K and Allen, JL},
title = {Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag153},
pmid = {42299645},
issn = {2160-1836},
abstract = {Transposable elements (TEs) have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e., dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of TEs using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradicts previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of TEs in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater TE activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving TE proliferation in rare species' genomes, and if TE content is predictive of increased extinction risk.},
}

@article {pmid42299860,
year = {2026},
author = {Barandouzi, ZA and Eng, T and Khanna, N and Shelton, J and Scott, I and Patel, P and Remick, J and Jin, R and Meador, R and Bruner, DW},
title = {Gut Microbiome Associations With Depressive Symptoms in Women With Gynecologic Cancer: A Longitudinal Study.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {10998004261461549},
doi = {10.1177/10998004261461549},
pmid = {42299860},
issn = {1552-4175},
abstract = {About one-quarter of women diagnosed with gynecologic cancer experience depressive symptoms. While the precise mechanism remains unclear, little is known about the association between gut microbiota and depressive symptoms in gynecologic cancer. Thus, this study aimed to evaluate the associations between gut microbiota and depressive symptoms in women with gynecologic cancer over cancer treatment. Thirty-seven women with cervical or endometrial cancer were followed at pre-treatment (T0), 6-8 weeks (T1), and 6 months post-radiation (T2). Depressive symptoms were assessed using the Patient Health Questionnaire-9 (PHQ-9). Rectal swabs were collected at each visit and sequenced for the V4 region of the 16S rRNA gene. MaAsLin2 models evaluated cross-sectional associations between gut microbial taxa and depressive symptoms at each time point, whereas GEE models assessed longitudinal associations over the course of cancer treatment. The patients had an average age of 60 years, and 43% were Black. At baseline (T0), 24% of patients exhibited depressive symptoms, which decreased to 21% at T1 and further to 13% at T2. GEE models showed that lower α-diversity (Shannon index, p = 0.05), dissimilar β-diversity (Bray-Curtis distance, p = 0.02), and reduced abundance of the genus Ruminococcus (p = 0.02) were predictive factors associated with depressive symptoms throughout cancer treatment. Higher depressive symptoms were longitudinally associated with lower gut microbial Shannon diversity, dissimilar microbial community composition, and lower abundance of the genus Ruminococcus. Larger longitudinal studies using shotgun metagenomic sequencing are needed to validate these findings and further elucidate the microbial mechanisms underlying depressive symptoms in women with gynecologic cancers.},
}

@article {pmid42300105,
year = {2026},
author = {Wilson, SMG and Oliver, A and Alkan, Z and Patil, BS and Kable, ME and Lemay, DG},
title = {Association between dietary polyphenol intake and polyphenol-utilizing bacteria in healthy adults.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00158k},
pmid = {42300105},
issn = {2042-650X},
abstract = {Dietary polyphenols are bioactive compounds with a bidirectional impact on the gut microbiome; they shape the microbial community and are transformed through bacterial metabolism. However, there are limited studies pairing metagenomic and dietary data to investigate the relationship between polyphenol intake and the taxonomic and functional profiles of the human gut microbiome. We examined if dietary polyphenol intake associates with microbial composition and polyphenol utilization capacity. Healthy adults participated in a cross-sectional study balanced for age, sex, and BMI. Polyphenol intake was previously estimated by mapping multiple 24 h dietary recalls to the Food Database (FooDB). We coupled intake with microbial taxonomic and functional profiles from shotgun-sequenced fecal metagenomes (n = 313). Microbial reads were mapped to dbPUP, a database with 60 experimentally characterized, gut-associated polyphenol utilization proteins (PUPs). We assessed the relationship of polyphenol intake on microbial diversity, abundance of microbes with PUP genes, PUP gene counts, and select lipopolysaccharide (LPS) producers, accounting for age, sex, BMI, fiber intake, and diet quality. Specific polyphenols associated with an increased abundance of nine PUP-containing genera. We found 117 associations between polyphenol intake and microbial PUP genes, with 85 associations involving hydrolysis PUPs. Diversity in polyphenol intake was positively associated with diversity in PUP genes but not with microbial diversity. Lastly, we detected a positive relationship between intake of olive-related polyphenol classes and abundance of order Bacteroidales, a producer of immunoinhibitory LPS. Dietary polyphenol intake may influence the gut microbiome's capacity for polyphenol utilization, particularly its hydrolytic activity, without impacting taxonomic diversity or composition.},
}

@article {pmid42300247,
year = {2026},
author = {Götze, S and Beemelmanns, C},
title = {Advances in the discovery and functional analysis of Anti-infective and immunomodulatory natural products from host-associated microbiomes.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6np00003g},
pmid = {42300247},
issn = {1460-4752},
abstract = {Covering: 2018 to 2025Over recent years, metagenomic-driven studies have revealed an enormous encoded repertoire for the biosynthesis of secondary metabolite scaffolds within host-associated microbiota, yet only a small fraction of these chemical scaffolds has been characterized. This review focuses on recent discoveries of natural products with anti-infective and immunomodulatory properties derived from diverse host-associated microbiomes, covering the period from 2018 to 2025. The selected examples span a wide range of anti-infective and immunomodulatory activities, underscoring the deep integration of microbial secondary metabolism with host physiology, while also highlighting the need for more targeted and efficient combined approaches to fully exploit the predicted biosynthetic capacity of microbiomes for anti-infective research and beyond.},
}

@article {pmid42300737,
year = {2026},
author = {Bueno de Mesquita, CP and Stallard-Olivera, E and Fierer, N},
title = {Predicting oxygen levels in microbial habitats using a metagenome-based approach.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0054526},
doi = {10.1128/msystems.00545-26},
pmid = {42300737},
issn = {2379-5077},
abstract = {Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ, one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate aerobes to obligate anaerobes, quantification of bacterial community oxygen preferences could be used to infer variation in oxygen levels and bacterial metabolic strategies. After using ensemble machine learning to select the 20 most important genes that predict oxygen tolerances in individual bacteria, we established a relationship between the abundance ratio of aerobic:anaerobic indicator genes and the proportional abundance of aerobic bacteria using simulated metagenomes with varying ratios of known aerobes and anaerobes. We developed a tool, OxyMetaG, that takes metagenomic reads as input, extracts bacterial reads, maps reads to the 20 genes, and predicts oxygen availability in any sample on a scale from 0% to 100% (completely anoxic to completely oxic). We tested OxyMetaG on a suite of metagenomes with measured or inferred oxygen levels across a variety of environmental and host-associated samples. To demonstrate its utility, we applied OxyMetaG to 540 surface soils, showing that surface soils are predominantly oxic, but wetter sites with finer textures have relatively less oxygen. Finally, we applied OxyMetaG to 73 human gut samples, showing that in the first 3 years of life, human guts progress from oxygen levels as high as 61% down to 0%. We expect OxyMetaG to have broad utility for characterizing oxygen levels in both modern and ancient microbial habitats.IMPORTANCEOxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.},
}

@article {pmid42300757,
year = {2026},
author = {Li, B and Li, S and Pei, Y and Sun, X and Ding, C and Yu, J and Zhou, M and Han, J and Yang, H and Wan, Y},
title = {Tibetan kefir grain-fermented milk attenuates DSS-induced colitis through coordinated regulation of intestinal barrier function, inflammation, and gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01565d},
pmid = {42300757},
issn = {2042-650X},
abstract = {This study evaluated the prophylactic efficacy of Tibetan kefir grain-fermented milk (Kefir-milk) in a dextran sulfate sodium (DSS)-induced colitis model and examined host- and fermentation-related changes associated with the intervention. Kefir-milk pretreatment attenuated disease activity, reduced colon shortening, and alleviated histopathological injury. These changes were accompanied by improved intestinal barrier-related readouts, including higher expression of ZO-1, Occludin, and MUC2, together with lower colonic MPO, TNF-α, IL-1β, and IL-6 levels. 16S rRNA profiling showed improved α-diversity, partial restoration of overall community structure, enrichment of Muribaculaceae and other genera commonly linked to intestinal homeostasis, and suppression of Escherichia-Shigella. Shotgun metagenomics indicated that the final Kefir-milk matrix was dominated by Lactobacillus-related taxa, while untargeted UPLC-HRMS/MS metabolomics revealed broad fermentation-associated remodeling of the milk metabolome, including altered relative abundances of features annotated as hippuric acid, p-cresyl sulfate, leucic acid, and phenyllactic acid. In LPS-challenged RAW264.7 macrophages, sterile filtered water-soluble extracts from Kefir-milk modulated polarization-associated marker expression and reduced pro-inflammatory cytokine responses at both transcript and protein levels. Collectively, these findings indicate that Kefir-milk attenuated DSS-induced colitis under the present experimental conditions and was associated with concurrent changes in barrier-related markers, gut microbiota, and the milk metabolome.},
}

@article {pmid42300775,
year = {2026},
author = {Hawkes, CG and Carroll, BO and Moylan, AD and Stiker, MEJ and Wang, T and Serrano, MG and Ridlon, JM and Miller, DP},
title = {Genomic and phenotypic insights into the novel species Selenomonas lamontii type strain ATCC 33150, currently described as Selenomonas sputigena.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0034126},
doi = {10.1128/spectrum.00341-26},
pmid = {42300775},
issn = {2165-0497},
abstract = {Selenomonas sputigena is an anaerobic, gram-negative bacterium found in the human mouth and upper respiratory tract. This organism is emerging as an important contributor to human health and disease. In the oral cavity, S. sputigena contributes to periodontitis and is associated with early childhood caries. Much of our current understanding of the genus Selenomonas and its relation to human health derives from studies of a single species, S. sputigena, and is further limited to the type strain, ATCC 35185. As S. sputigena is emerging as a significant contributor to human health, we sought to characterize the S. sputigena ATCC 33150 strain. Genomic analyses revealed that ATCC 33150, previously described as S. sputigena, is a novel Selenomonas sp., and we propose the name Selenomonas lamontii. Phenotypic comparison to S. sputigena reveals that S. lamontii grows more slowly and to a lower density in vitro. S. lamontii is more motile than S. sputigena and does not form surface-attached biofilms. Re-analysis of existing metagenomic data revealed the consistent presence of ATCC 33150 across all samples, with significantly elevated relative abundance in periodontitis-associated saliva compared to healthy donor controls. Collectively, we have identified ATCC 33150 as a new Selenomonas sp. and conducted one of the first direct comparative studies of traits relevant to colonization and persistence among Selenomonas spp.IMPORTANCERecognizing that strain ATCC 33150, historically described as Selenomonas sputigena, is a previously undescribed species has important implications for microbial systematics, physiology, and pathogenesis. Accurate taxonomic assignment underpins all downstream biological interpretation (e.g., comparative genomics, microbiome composition studies, virulence studies, and metabolic modeling). The identification of a novel species, therefore, refines the phylogenetic framework of the genus Selenomonas, enables more precise genotype-phenotype correlations, and may uncover previously unrecognized adaptations relevant to oral biofilm ecology and host interactions. Beyond taxonomy, this discovery strengthens the foundation and rigor of future mechanistic studies and provides context for discrepancies in previous studies involving this strain and ATCC 35185.},
}

@article {pmid42300931,
year = {2026},
author = {Medouni-Haroune, L and Medouni-Adrar, S and Messaoudene, L and Negrichi, S and Bouiche, C and Sahraoui-Remini, Y and Allam, A and Meghlaoui, Z and Mouhoubi, K and Abbou, A and Brahimi, N and Mellal, MK and Sari, Z and Madani, K},
title = {Animal-based diets and the human gut microbiota: an integrative review combining metagenomic profiling and graphical synthesis of diet-microbiota associations.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00371k},
pmid = {42300931},
issn = {2042-650X},
abstract = {This review examines the relationships between animal-based diets, gut microbiota architecture, and human health by integrating insights from metagenomic studies and literature-based graphical representations. The gut microbiota is a complex microbial ecosystem, whose organization is closely linked to intestinal homeostasis and host health. Drawing on published metagenomic datasets, the review synthesizes patterns of dominant microbial groups and their organization within the gut, providing a framework for interpreting diet-related microbial variations across different geographic and cultural contexts. Evidence from the literature on animal-derived foods is integrated through graphical visualization to illustrate associations between specific foods and gut microbial taxa. These visualizations highlight distinct association patterns and microbial responses to various animal-based dietary components. The review discusses these patterns in relation to intestinal health, disease susceptibility, and potential dietary interventions. Overall, this work provides a structured, integrative perspective on the impact of animal-based diets on gut microbiota architecture, emphasizing the relevance of combining metagenomic insights with literature-based synthesis to inform nutritional science and public health strategies.},
}

@article {pmid42301021,
year = {2026},
author = {Echeverry-Pérez, JS and Castelli, M and Muñoz-Leal, S and Nava, S and Sassera, D and Sánchez-Vialas, A and Olmeda, AS and Valcárcel, F and Uribe, JE},
title = {Genomic evolution of Francisella: metabolic innovation, endosymbiotic transitions to ticks, and biogeographic history.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag135},
pmid = {42301021},
issn = {1759-6653},
abstract = {Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. Beyond vector roles, they maintain mutualistic associations with bacteria, including endosymbionts that provide essential B vitamins lacking in their blood-based diet. The most extensively studied endosymbionts belong to the genera Coxiella, Midichloria, and Francisella. The genus Francisella encompasses endosymbionts (FE), pathogens (FP), opportunistic pathogens (FO) and free-living environmental strains (FL), making it a powerful system for evolutionary and comparative genomic analyses. In this study, total DNA from six adult female ticks of the genera Hyalomma and Amblyomma was sequenced to generate new FE genomes. Seven deeply sequenced public metagenomes were also assembled, yielding 71 Francisella and three Allofrancisella strains. This dataset supported phylogenomic reconstruction and comparison of genomic features, including vitamin biosynthesis and virulence pathways, with a focus on transitions to tick endosymbiosis. A densely sampled MLST phylogeny was constructed to explore biogeographic patterns. Our results show that, except for FE, no ecological trait is monophyletic, supporting an origin of Francisella diversity from free-living ancestors. Biogeography suggests Palearctic and Afrotropical FE strains are derived and may involve horizontal transfers. Francisella comparative genomics reveals two contrasting profiles: environmental generalists and host-restricted specialists. These findings reinforce the role of tick FEs as nutritional mutualists, retaining key pathways such as riboflavin, shikimate, and biotin biosynthesis. In contrast, virulence is not ancestrally conserved but an innovation in pathogenic lineages, largely degraded in tick FEs. These results advance understanding of endosymbiont evolution and provide genomic insights with potential for disease control.},
}

@article {pmid42301089,
year = {2026},
author = {Wang, H and Liang, Y and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y},
title = {Dietary High Fiber and N-Carbamylglutamate Enhance Sow Reproductive Performance via Modulating Lactobacilli, Lipid Metabolites, and the PI3K-Akt Signaling Pathway.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {12},
pages = {e72059},
doi = {10.1096/fj.202601343R},
pmid = {42301089},
issn = {1530-6860},
support = {2025M780240//China Postdoctoral Science Foundation/ ; 2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; },
mesh = {Animals ; *Glutamates/pharmacology/administration & dosage ; Female ; *Lactobacillus/drug effects/metabolism ; Signal Transduction/drug effects ; Swine ; *Proto-Oncogene Proteins c-akt/metabolism ; *Reproduction/drug effects ; *Dietary Fiber/pharmacology/administration & dosage ; *Phosphatidylinositol 3-Kinases/metabolism ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; },
abstract = {The aim of this study was to investigate the combined effects of a high-fiber diet supplemented with N-carbamylglutamate (NCG) (H + N) on the gut microbiota, metabolites, and transcriptome in Landrace × Yorkshire sows using a multi-omics approach. Sows were allocated to four groups in a 2 × 2 design: Low-fiber or high-fiber diets, each with or without 0.05% NCG supplementation. The H + N treatment significantly increased litter weight at weaning. Metagenomic analysis revealed H + N significantly altered gut microbiota composition and function, particularly enriching Lactobacillus at multiple taxonomic levels from order to species (including Lactobacillus sp. 910 589 175). Plasma metabolomics identified two key lipid mediators, L-α-glycerylphosphorylcholine and taurocholic acid, whose abundances were significantly elevated by H + N and positively correlated with the enriched Lactobacillus. Transcriptomic profiling showed activation of the PI3K-Akt signaling pathway in response to H + N, which was associated with observed improvement in litter weight at weaning. Collectively, the multi-omics study uncovered a novel synergistic axis wherein H + N modulated the gut microbiome (specifically Lactobacillus enrichment), which in turn shaped the lipid metabolome to activate the PI3K-Akt pathway, ultimately enhancing sow reproductive efficiency.},
}

Animals
*Glutamates/pharmacology/administration & dosage
Female
*Lactobacillus/drug effects/metabolism
Signal Transduction/drug effects
Swine
*Proto-Oncogene Proteins c-akt/metabolism
*Reproduction/drug effects
*Dietary Fiber/pharmacology/administration & dosage
*Phosphatidylinositol 3-Kinases/metabolism
*Lipid Metabolism/drug effects
Gastrointestinal Microbiome/drug effects
Animal Feed/analysis

@article {pmid42301310,
year = {2026},
author = {Cosoveanu, A and González-Carracedo, MA and Sopena Lasala, J and Pérez Pérez, JA and Cabrera, R},
title = {Shaping Fungal Communities in Cenchrus setaceus: Host Condition and Habitat Filtering.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02805-3},
pmid = {42301310},
issn = {1432-184X},
abstract = {We investigated the leaf-associated fungal communities of Cenchrus setaceus across a host condition gradient (high- vs. low-condition plants) and environmental zones (coast vs. hill; trade-wind exposure) on Tenerife (TF) and La Palma (LP). We hypothesized that community assembly reflects both host-driven deterministic filtering and abiotic promotion of richness in favourable environments via two mechanisms: (i) high-condition plants promote stable, guild-structured communities; (ii) humid, topographically buffered zones enhance fungal richness, especially for endophytes and saprotrophs. Nanopore sequencing and functional guild annotation revealed island- and zone-specific fungal assemblages. In TF, low-condition plants were associated with genera linked to stressed or exposed conditions whereas high-condition plants, especially in humid northern hills, supported more recurrent yeast-like and niche-associated taxa. In LP, high-condition plants in eastern hill zones were associated with distinct taxa, while drier western coastal low-condition plants were enriched in stress-related fungi. Fungal genera richness (Hill0) was consistently higher in low-condition plants (TF: 146 vs. 95; LP: 94 vs. 76; p < 0.05), while Shannon diversity diverged: greater in high-condition plants on LP (3.29 vs. 2.98), but lower on TF (3.10 vs. 3.28; p < 0.05). Community structure was shaped primarily by host condition in TF (PERMANOVA R[2] = 8.6%, p < 0.05), and by zone in LP (R[2] = 15.0%, p < 0.05). On TF, low-condition plants hosted significantly higher richness of saprotrophic, endophytic and plant-pathogenic genera (all p ≤ 0.001), whereas in LP zone × condition effects shaped guild richness patterns, with saprotroph richness increasing 2.66-fold in high condition plants from eastern hills relative to the eastern coast. Overall, high-condition plants supported less diverse but compositionally more stable fungal communities, while favourable environments enhanced guild richness independently of host condition.},
}

@article {pmid42301501,
year = {2026},
author = {Öz, M and Üstüner, E},
title = {Omics technologies in aquafeed: unlocking the black box towards systems biology.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42301501},
issn = {1438-7948},
mesh = {Animals ; *Systems Biology/methods ; *Aquaculture/methods ; Multiomics ; Metabolomics ; *Fishes/genetics/metabolism/growth & development ; Animal Feed ; Proteomics/methods ; Nutrigenomics ; },
abstract = {The aquaculture industry is undergoing a critical transition from marine-based to plant-based and novel protein sources. However, the physiological impacts of these dietary shifts remain largely obscured when evaluated solely by traditional performance metrics such as Feed Conversion Ratio (FCR) and Specific Growth Rate (SGR). This 'Black Box' approach fails to detect sub-clinical metabolic disorders, gut dysbiosis, and molecular stress responses until phenotypic losses occur. This review provides a comprehensive synthesis of how omics technologies - nutrigenomics, proteomics, metabolomics, and metagenomics - are elucidating the molecular mechanisms underlying fish nutrition. We examine the capacity of transcriptomics to identify early markers of soybean meal-induced enteritis and the role of proteomics in assessing muscle quality beyond mere gene expression. Furthermore, we highlight the integration of these layers into a 'Systems Biology' approach, utilizing multi-omics and bioinformatics to unravel the complex diet-microbiota-host axis. Finally, the review discusses the transition towards 'Precision Aquafeed.' It identifies the current challenges in cost, data standardization, and bioinformatics that must be overcome to implement these high-throughput tools in commercial feed formulation.},
}

Animals
*Systems Biology/methods
*Aquaculture/methods
Multiomics
Metabolomics
*Fishes/genetics/metabolism/growth & development
Animal Feed
Proteomics/methods
Nutrigenomics

@article {pmid42301503,
year = {2026},
author = {Bao, W and Li, X and Pan, H and Gao, Y and Zhao, L and Liu, J and Wang, S and Zhang, Y},
title = {Detoxification mechanisms of black soldier fly larvae against microcystin-LR.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42301503},
issn = {1438-7948},
mesh = {Animals ; *Microcystins/toxicity/metabolism ; Marine Toxins ; Larva/microbiology/metabolism/growth & development/drug effects/genetics ; *Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; Inactivation, Metabolic ; *Simuliidae/microbiology/metabolism/genetics/growth & development/drug effects ; },
abstract = {This study aimed to elucidate the detoxification mechanisms of black soldier fly larvae (BSFL) against microcystin-LR (MC-LR). Using concentration-gradient exposure (0 - 400 µg/L) and integrated metagenomic and transcriptomic analyses, we investigated the growth responses, gut microbiota alterations, and synergistic detoxification mechanisms of BSFL. The results revealed that the growth performance of BSFL was not significantly affected even at high MC-LR concentrations (400 µg/L). However, significant alterations occurred in the gut microbial composition, with increased relative abundances of Actinobacteria and Firmicutes, along with increased species richness and diversity, which correlated with increasing exposure concentrations. Functional analysis revealed that functions related to carbohydrate metabolism, energy metabolism, and substrate transport were significantly enriched in the exposed groups. Transcriptomic data further indicated that MC-LR induced intestinal oxidative stress, with significant upregulation of antioxidant-related genes (superoxide dismutase, isocitrate dehydrogenase, and peroxiredoxin 6) as well as key xenobiotic metabolism genes (carboxylesterase, glutathione S-transferase, and UDP-glucuronosyltransferase). Additionally, heat shock proteins and the Toll signaling pathway were activated. We speculate that BSFL maintains gut microbial homeostasis against MC-LR toxicity through the coordinated regulation of gut microbial communities, host antioxidant systems, xenobiotic metabolism pathways, and immune responses, providing a theoretical foundation for safe resource utilization of cyanobacteria.},
}

Animals
*Microcystins/toxicity/metabolism
Marine Toxins
Larva/microbiology/metabolism/growth & development/drug effects/genetics
*Gastrointestinal Microbiome/drug effects
Oxidative Stress
Inactivation, Metabolic
*Simuliidae/microbiology/metabolism/genetics/growth & development/drug effects

@article {pmid40608175,
year = {2025},
author = {Ye, Z and Yu, Y and Cao, Z and Ye, Z and Gu, X and Shen, X and Cai, B and Lin, B and Ji, C and Qiao, N and Wu, Z and Chen, Z and Ma, Z and Chen, L and Liang, B and Liao, Y and He, W and Shen, Q and Han, J and Cao, X and Zhou, X and Shou, X and Shen, M and Wang, Y and Zhang, Z and Ye, H and Zhang, Q and Gao, R and Zhang, Y},
title = {Microbiome and metabolic disorder in prolactinoma: intrinsic gender differences and extrinsic therapy effects.},
journal = {Pituitary},
volume = {28},
number = {4},
pages = {83},
pmid = {40608175},
issn = {1573-7403},
support = {24ZR1408900//Natural Science Foundation of Shanghai Municipality/ ; 320.6750.2023-13-11//Wu Jieping Medical Foundation/ ; 2023ZD0506800//National Major Science and Technology Projects of China/ ; 82202906//National Natural Science Foundation of China/ ; },
abstract = {PURPOSE: Prolactinoma is the most common functional pituitary adenoma. As for gender disparity in the metabolic state, males tended to have higher rates of metabolic disorders, while treatment with dopamine agonists enabled partial improvement in metabolic disorders. Oral medication used to be the first-line treatment option; thus, the efficacy of dopamine receptor agonists is linked to the intestinal microenvironment. The gut microbiome is known to interact with host physiology and metabolic profile. Therefore, it is necessary to uncover the linkages between the alteration of gut microbiota and prolactinoma. METHODS: 28 Patients diagnosed with prolactinoma and 31 healthy controls were included. Fecal samples were collected for 16 S rRNA gene sequencing and metagenomic sequencing to identify featured intestinal microflora between patients and healthy individuals, as well as to examine how gender and dopamine agonists affect the gut microbiome’s structure. RESULTS: Agathobacter, Blautia, Dorea, Fusicatenibacter, and Mediterraneibacter were prominent in the PRLoma group. Bilophila wadsworthia, Clostridium sp. CAG:7, Megasphaera elsdenii, and Mycoplasma sp. CAG:472 were independently associated with metabolic disorders in male patients. This metabolic regulatory effect may result from the levels of Xylose, the glycine to serine ratio, N2-acetyl, N6, N6-dimethyllysine levels, and the cholesterol to oleoyl-linoleoyl-glycerol (18:1 to 18:2) ratio in plasma. Furthermore, administering dopamine agonists reduced harmful species such as Fusobacterium mortiferum, Bacteroides fragilis, and Ruminococcus biciculans, potentially contributing to an improved metabolic status. CONCLUSIONS: Patients with prolactinoma have different intestinal flora than healthy individuals. In addition to the occurrence of prolactinoma and concomitant serum prolactin excess, the gender effect and administration of dopamine agonists are also involved in regulating intestinal microbiota and the metabolic status of the host.},
}

@article {pmid40608216,
year = {2025},
author = {Kamruzzaman, M and Goo, T and Park, T},
title = {Hierarchical structural component model for pathway analysis of multinomial phenotypes.},
journal = {Genes & genomics},
volume = {47},
number = {8},
pages = {923-933},
pmid = {40608216},
issn = {2092-9293},
support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Many statistical methods for pathway analysis have been used to identify novel pathways from biomarkers associated with a certain disease. However, most of these methods are based on single pathway analysis and do not consider multiple pathways simultaneously. To address this issue, a hierarchical structural component model (HisCoM) was developed, which takes into account all pathways at the same time, as well as takes into consideration the correlations among them. HisCoM has been successfully applied to the analysis of continuous, count, and binary phenotypes. OBJECTIVE: In this study, our goal is to propose HisCoM-Categ by extending HisCoM for pathway analysis for both nominal or ordinal multinomial phenotypes, when the phenotypes have more than two possible unordered or ordered discrete categories. METHODS: The foundation of the proposed HisCoM-Categ is the multivariate extension of generalized linear models. Specifically, HisCoM-Categ accounts for the hierarchical structure of biomarkers and pathways, as well as the correlations that exist among pathways. RESULTS: Through the simulation study, HisCoM-Categ was shown to have higher power compared to the other existing methods. In addition, HisCoM-Categ was illustrated with two different omics datasets, including metabolomic, and metagenomic datasets. HisCoM-Categ for ordinal multinomial phenotypes was illustrated by the metabolomic and metagenomic datasets. Those applications demonstrated that HisCoM-Categ successfully identified the well-known pathways that are associated with multinomial phenotypes. CONCLUSIONS: The current study proposes a novel pathway analysis method HisCoM-Categ to identify pathways that have been associated with multinomial phenotypes.},
}

@article {pmid41182402,
year = {2025},
author = {Tekgül, ZB and Adıgüzel, A},
title = {Microbial viability assessment with PMA-qPCR: challenges, opportunities, and future directions.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {343},
pmid = {41182402},
issn = {1432-072X},
abstract = {Since molecular analyzes are insufficient to distinguish living and non-living cells, lead to misleading results, and dead cells also multiply their DNA/RNA, a method that can give more sensitive results was needed. PMA (propidium monoazide), which is used to prevent the DNA of dead cells from negatively affecting the experimental results, is a viability indicator that binds only to the DNA of damaged cells and prevents them from being multiplied by PCR, and was first introduced in 2006. Recently the interest in the use of PMA in many fields such as microbiome and metagenomic studies, environmental microbiology, food microbiology, antibiotic and disinfectant effectiveness tests, clinical microbiology and diagnosis, and cell culture and biotechnology has increased considerably. Therefore, the purposes of use, principles, applications in various fields and limitations of PMA have been investigated. The current review of this vitality marker, which has a history of less than 20 years, will lead to its use of many new scientific studies and will provide convenience to scientists by bringing together studies on the use of this dye.},
}

@article {pmid41661326,
year = {2026},
author = {Umemura, A and Sasaki, A and Sasaki, D and Iizuka, A and Chiba, M and Aihara, K and Ubukata, N and Kumagai, H and Tanahashi, Y and Iwasaki, T and Ando, T and Nitta, H},
title = {Impact of laparoscopic sleeve gastrectomy on gut and oral microbiota diversity, weight loss, and the metabolic outcomes.},
journal = {Surgery today},
volume = {},
number = {},
pages = {},
pmid = {41661326},
issn = {1436-2813},
abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) alters the gut microbiota (GM). Changes in oral microbiota (OM) after MBS have not yet been thoroughly investigated. In this study, we evaluated the changes in GM and OM before and after laparoscopic sleeve gastrectomy (LSG) in patients with severe obesity and investigated the relationship between improvements in GM/OM, weight loss, and the metabolic effects. METHODS: Thirty-seven severely obese patients who underwent LSG were enrolled in this study. We retrieved samples from the feces and oral mucosa from baseline to 1-year after LSG. These samples were subjected to a 16 S rRNA metagenomic analysis using a next-generation sequencer. We evaluated the significant changes in GM/OM and compared the results with clinical outcomes. RESULTS: Regarding OM diversity, g_Actinomyces (p = 0.003), o_Rothia (p = 0.020), and g_Streptococcus (p = 0.004) increased. With regard to GM, g_Slackia (p = 0.039), g_Bacillus (p = 0.030), g_Roseburia (p = 0.027), and g_Faecalibacterium (P = 0.003) increased, the proportion of p_ Firmicutes increased, and p_Bacteroidetes decreased in both groups. Changes in g_Akkermansia did not contribute to GM/OM diversity. The weight loss and remission rates of type 2 diabetes were higher in patients with increased normal oral flora and a recovery of g_Faecalibacterium in GM. CONCLUSIONS: We clarified that the LSG reconstructs GM/OM as weight loss and the metabolic effects are enhanced.},
}

@article {pmid41764137,
year = {2026},
author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J},
title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.},
journal = {Obesity surgery},
volume = {36},
number = {4},
pages = {1607-1620},
pmid = {41764137},
issn = {1708-0428},
abstract = {OBJECTIVE: To identify predictive biomarkers from the perspectives of gut microbiota and bile acid metabolites for polycystic ovary syndrome (PCOS) remission following metabolic bariatric surgery in patients with PCOS and obesity. METHODS: We conducted a one-year follow-up of patients with obesity and PCOS who underwent sleeve gastrectomy (SG) to assess their PCOS remission status. Metagenomics and bile acid metabolomics were performed and compared between the remission and non-remission groups to identify differential microbial species and bile acid metabolites. The associations between these biomarkers and PCOS remission was then evaluated using Generalized Estimating Equations (GEE) models and Receiver Operating Characteristic (ROC) analysis. RESULTS: SG led to marked improvements in metabolic parameters and hyperandrogenemia. These changes were accompanied by substantial shifts in the gut microbiome, which correlated with alterations in gonadal hormone levels. Based on PCOS outcomes, patients were categorized into remission and non-remission groups. The remission group showed a higher abundance of A. equolifaciens and Clostridium sp CAG 299, along with lower baseline circulating levels of ursodeoxycholic acid (UDCA). These factors were positively associated with PCOS remission. ROC analysis demonstrated that the combination of A. equolifaciens, Clostridium sp CAG 299, UDCA, and average follicle number yielded an AUC of 0.93 for predicting remission. CONCLUSION: A composite biomarker signature incorporating specific gut microbiota profiles, circulating UDCA levels, and ovarian follicle count shows strong potential as an effective predictor of PCOS remission after SG.},
}

@article {pmid41851512,
year = {2026},
author = {Zhang, S and Yang, B and Xie, Z and Jiang, F and Liu, K},
title = {Occurrence of Antibiotics at a Typical Livestock Farm in Northwest China: Emergence Characteristics and Ecological Risk Assessment.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {116},
number = {4},
pages = {},
pmid = {41851512},
issn = {1432-0800},
support = {2024TCYCQNBS03//"Tianchi Talents" Young Doctors Recruitment Program/ ; 252102321066//Key Research & Development and Promotion of Special Project (Scientific Problem Tackling) of Henan Province/ ; },
abstract = {This study analyzed veterinary antibiotics (VAs) and resistance genes (ARGs) in manure and soil at a typcial livestock farm in Northwest China using LC-MS and metagenomics. Sulfonamides (SAs) were highest in chicken manure, while quinolones (QNs) dominated cattle manure and adjacent soil (172.784 ng g−1 total QNs). Transfer rates of QNs and tetracyclines from manure to soil exceeded 100%, indicating significant ecological risk via the food chain. Metagenomics revealed the tetracycline resistance gene tetA (58) dominated the soil ARG pool. Significant positive correlations (p < 0.05) existed between QN concentrations (including ciprofloxacin, lomefloxacin) and quinolone resistance genes (flu), and between soil tetracyclines and multidrug resistance genes (mul). Ecological risk modeling confirmed a high mixed contamination risk for QNs (RQ = 2.36 > 1).},
}

@article {pmid41866595,
year = {2026},
author = {Taha, MME and Abdelwahab, SI and Binjomah, AZ and Memish, Z and Sahli, KA and Qadri, M and Alarifi, A and Khardali, A and Farasani, A and Madkhali, F and Moshi, JM and Alsaadi, KH and Alshahrani, S},
title = {Mapping the genomic frontier: a comprehensive bibliometric analysis and thematic evolution of whole-genome sequencing for Mycobacterium tuberculosis (1994-2025).},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866595},
issn = {1573-0972},
abstract = {Whole-genome sequencing of Mycobacterium tuberculosis (WGS-TB) has revolutionized tuberculosis research by providing high-resolution insights into drug resistance, transmission dynamics, and evolutionary pathways. However, the global research landscape, collaboration networks, and thematic evolution of WGS-TB remain underexplored. A comprehensive dataset of WGS-TB publications was retrieved from Scopus. Analyses were conducted using Bibliometrix for productivity trends, Lotka’s and Bradford’s Laws, normalized word cloud, and thematic mapping; VOSviewer for co-authorship, co-occurrence, bibliographic coupling, and unsupervised term clustering; and CiteSpace for reference co-citation analysis (RCCA) and thematic evolution. Between 1994 and 2025, WGS-TB publications exhibited exponential growth, particularly after 2015. The United States, China, and the United Kingdom were leading contributors, supported by globally connected institutions. Collaboration networks revealed strong North–South partnerships, with South Africa acting as a critical bridge. Keyword and thematic analyses identified dominant themes such as drug resistance, genomics, and epidemiology, with emerging areas including metagenomic sequencing and mutation dynamics. Bradford’s Law identified 12 core journals, while RCCA delineated clusters in drug resistance surveillance and molecular epidemiology. This study offers the first integrative mapping of WGS-TB research, illuminating its thematic evolution, global collaboration structure, and emerging directions in genomic surveillance and precision medicine.},
}

@article {pmid41903015,
year = {2026},
author = {Ma, N and Zhang, H and Yuan, L and Lian, P and Yang, W and Huang, Y},
title = {Bioremediation of enrofloxacin and modulation of nitrogen cycling in a simulated aquaculture system by the fungus Cladosporium cladosporioides 11.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41903015},
issn = {1573-0972},
support = {NO. 2025A005//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {While microbial bioremediation is a promising strategy for antibiotic removal, the potential of fungi in mitigating antibiotic contamination and its associated ecological impacts in aquaculture systems remains largely unexplored. This study evaluated the bioremediation efficacy of the fungus Cladosporium cladosporioides 11 (CC11) in a simulated aquaculture ecosystem. The introduction of CC11 significantly accelerated enrofloxacin (ENR) removal in the aquaculture system and mitigated ENR bioaccumulation in crucian carp. Meanwhile, CC11 application notably lowered the accumulation of total nitrogen and ammonium nitrogen in the water column. Metagenomic analysis revealed that CC11 helped maintain a more active nitrogen-cycling microbial community, sustaining higher abundances of key genes involved in nitrogen fixation (nifB/K/T/Z) and assimilatory nitrate reduction (nasA/C/E/B/D) under ENR stress. Furthermore, CC11 restored specific bacterial taxa correlated with these functional genes, including methylotrophs associated with nif genes and Comamonadaceae members linked to nas genes, thereby reinforcing the functional network for nitrogen transformation. These findings demonstrate that CC11 acts as a multifunctional bioremediation agent, capable of simultaneously enhancing antibiotic removal and regulating nitrogen dynamics, offering a sustainable strategy for managing ENR pollution in aquaculture environments.},
}

@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.},
}

@article {pmid41944841,
year = {2026},
author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME},
title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41944841},
issn = {1432-072X},
abstract = {Tapping Panel Dryness (TPD) is a complex physiological disorder in Hevea brasiliensis that leads to the cessation of latex flow, causing significant economic loss, yet its underlying cause remains unclear. Anatomical investigation of bark samples collected from TPD-affected samples exhibited deformed latex vessels, blocked sieve tubes, and DNA-containing bodies within phloem elements. Metagenomic profiling indicated largely similar microbial composition and diversity between healthy and TPD-affected bark samples, except for the presence of low-abundance taxa such as phytoplasma only in affected samples. However, predicted metabolic pathways differed significantly between healthy and TPD samples. The combined anatomical, cytological, and molecular evidences in the current study supports the potential involvement of a biotic factor in the etiology of TPD.},
}

@article {pmid41981555,
year = {2026},
author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C},
title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08193-x},
pmid = {41981555},
issn = {1472-6831},
support = {P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Human papillomavirus (HPV) is a major cause of oropharyngeal and other cancers, occurs more frequently among people with HIV (PWH). Despite antiretroviral therapy, HPV-related cancer incidence remains elevated in this group. Oral dysbiosis in PWH may impair mucosal immunity, promoting HPV persistence and inflammation. Periodontal disease, frequently observed in PWH, further contributes to microbial imbalance and immune dysregulation, increasing susceptibility to oral HPV infection. This study investigates the relationship among oral microbiome composition, periodontal disease and oral HPV infection behavior in PWH, considering immunologic and social determinants of health. METHODS: The characterizing oral microbiome and periodontal disease in oral HPV-positive individuals (COMP-HPV), an observational longitudinal study will enroll 500 PWH and follow them up for two years. Oral rinse for HPV testing and periodontal assessment will be collected every six months; saliva for inflammatory markers, oral rinse for microbiome and oral cytobrush for immunological profiling will be collected annually. Immune profiling will include high-dimensional flow cytometry and 10X RNA-sequencing to characterize innate and adaptive immune subsets, with emphasis on HLA-DR–positive populations, enabling evaluation of oral immune modulation during HPV infection. The study has four specific aims such as to examine associations between oral microbiome composition (16S and metagenomics) and oral HPV infection, including prevalence, incidence, persistence, and clearance; to assess the impact of periodontal disease on oral HPV infection and investigate whether the oral microbiome mediates this relationship; to determine how oral microbiome composition influences immunological responses in HPV-positive PWH and to evaluate the role of social determinants on oral microbiome composition and HPV infection. Data from this longitudinal study will be used to understand the natural history of oral HPV infection, the interplay with periodontal disease, microbial alterations, and immunological changes, providing evidence to guide interventions for reducing HPV-associated disease in PWH. TRIAL REGISTRATION NUMBER: Not applicable. DISCUSSION: The COMP-HPV study aims to contribute to the body of research designed to investigate mechanisms underlying oral HPV infection among PWH to improve immune responses to reduce HPV infection and relevant carcinoma.},
}

@article {pmid41986587,
year = {2026},
author = {Ishibashi, N and Akase, Y and Ito, A and Kishimoto, K and Watanabe, S and Yokoyama, H and Mekata, T},
title = {Genome characterization and environmental DNA-based detection of a novel adenovirus from red seabream (Pagrus major).},
journal = {Archives of virology},
volume = {171},
number = {5},
pages = {},
pmid = {41986587},
issn = {1432-8798},
support = {25K09243//JSPS KAKENHI/ ; },
abstract = {A novel piscine adenovirus, Pagrus major adenovirus 1 (PmAdV-1), was identified in red seabream (Pagrus major) by metagenomic sequencing. The 29,519 bp genome encodes 22 predicted open reading frames and exhibits a unique organization, with the fiber gene positioned upstream of the conserved adenovirus gene cluster. Phylogenetic analyses indicate that PmAdV-1 forms a sister lineage to red-eared slider adenovirus 1 within a clade of fish and reptilian adenoviruses, but its assignment to the genus Testadenovirus remains uncertain. A virus-specific qPCR assay was developed to monitor PmAdV-1 in environmental DNA from rearing seawater. Viral loads transiently increased in some juvenile tanks without marked mortality. These findings expand current knowledge of fish adenovirus diversity.},
}

@article {pmid41991788,
year = {2026},
author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T},
title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41991788},
issn = {1573-0972},
abstract = {Increasing water scarcity poses significant threats to crop production and agricultural sustainability. Water deficit and the environmental impacts of synthetic nitrogen fertilization necessitate the development of sustainable cropping systems that enhance resource use efficiency while mitigating climate and economic risks. This study investigates the effects of Mesorhizobium ciceri inoculation (CMG6 strain (SI-DP 40653)), varying water–nitrogen regimes, and a potato-chickpea intercropping system (IC) on plant performance, metabolic responses, rhizospheric microbial diversity. Field trials, located in northeastern Tunisia, showed that IC combined with efficient M. ciceri inoculation significantly outperformed sole cropping (SC) across all physiological parameters. Under standard conditions, this synergy bolstered chickpea biomass and photosynthetic capacity. Notably, under reduced nitrogen input, inoculated intercropping (IC) boosted chickpea shoot biomass by more than twofold compared with sole cropping (SC). Intercropping also improved drought resilience, reducing stress-induced metabolic decline by approximately 40% relative to monocropping systems. Secondary metabolite production was stimulated, with higher accumulation of polyphenols and tannins observed particularly under reduced nitrogen conditions in inoculated systems. Additionally, intercropping improved potato productivity under low-nitrogen conditions while maintaining stable yields under drought stress. Metagenomic analysis showed that water stress accounted for approximately 22% of microbial community variation. However, intercropping and inoculation reshaped rhizosphere communities by enhancing the abundance and diversity of beneficial bacterial groups, particularly Bacilli, and buffering drought-induced shifts. These results emphasized the synergistic benefits of IC and Rhizobium inoculation in improving crop productivity, stress resilience, and soil health while reducing reliance on synthetic inputs.},
}

@article {pmid42020676,
year = {2026},
author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR},
title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020676},
issn = {1867-1314},
abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.},
}

@article {pmid42043563,
year = {2026},
author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W},
title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043563},
issn = {1432-072X},
support = {Intramural Faculty Grant//Bose Institute/ ; },
abstract = {A Trans-Himalayan lake-desert ecosystem was explored for the low-to-high temperature adaptations of copiotrophic psychrophiles having potentials for substantive carbon remineralization under natural and/or anthropogenically-influenced conditions of high organic matter delivery to the environment. Overall 27 bacterial species were isolated from the brackish-water and sediment-surface of Tso Moriri (a massive lake on the Changthang plateau that remains frozen for approximately one third of the year), and the fine talus covering a lake-side rocky mountain. In Luria broth (LB), all isolates grew at 4 °C and 15 °C; at -10 °C, 13 could grow while others remained only metabolically-active. Catabolizing different complex-organic-compounds, all isolates achieved considerable growth at 4 °C; 20 accomplished low growth at -10 °C. LB-based growth dwindled with rising temperature: 23, 11, and none of the isolates grew at 28 °C, 37 °C, and 42 °C respectively. In agar-overlay assays, most actinobacterial isolates inhibited other mesophilic bacteria. The isolates’ genomes, and their habitats’ metagenomes, encompassed diverse genes for extreme-temperature adaptation, carbohydrate catabolism, antibiosis and antibiotic-resistance. All in-vitro findings collectively engender the following hypothesis, via contextual inferences pending field-study-based validations. Warming-induced cessation of organotrophic growth, within high-altitude cryospheres, would curb the production of simple-fatty-acids, CO2 and N2O. Short-supply of acetate and CO2 would, in turn, cut-back methanogenesis. Such negative-feedback control of greenhouse gas production at the micro-habitat level can add-up in the biome-scale to mitigate broader environmental warming; it, however, endangers the ecosystem from thermally-better-adapted foreign microbes that can usher positive-feedback cycles of warming. In the latter scenario, antibiosis potentials of native actinobacteria become pivotal to microbiome protection.},
}

@article {pmid42046064,
year = {2026},
author = {Tang, S and Cai, L and Hao, Y and Jiang, Q and Luan, X and Fang, X and Li, Z and Zhu, J},
title = {SCFAs inhibited NETosis to alleviate lung inflammation in COPD: a potential role for GPR43.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03688-1},
pmid = {42046064},
issn = {1465-993X},
support = {82575021//the National Natural Science Foundation of China/ ; 2408085MH230//Anhui Provincial Natural Science Foundation/ ; 2022AH020044//the Science Fund for Distinguished Young Scholars in Universities of Anhui Province/ ; 2024AKLCMF04//the Foundation of Anhui Provincial Key Laboratory of Chinese Medicinal Formula/ ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, and poses a significant socioeconomic burden attributable to its high mortality and morbidity. Short-chain fatty acids (SCFAs), as the key metabolites produced by gut microbiota, have been considered to be involved in the regulation of pulmonary inflammation. However, the underlying bridging mechanisms through the gut-lung axis remain elusive. METHODS: To delineate cellular heterogeneity during COPD progression, we profiled lung tissues from rats at distinct stages (Days 0, 7, 14, and 28) using scRNA-seq, followed by bulk transcriptomic analysis to pinpoint critical dysregulated pathways. Gas chromatography-mass spectrometry (GC-MS) was employed to quantify the differential SCFA levels. The protective effects of SCFAs against pulmonary inflammation in COPD were evaluated via pulmonary function testing, HE staining, and ELISA. Flow cytometry, Western blotting, immunofluorescence and scanning electron microscopy were employed to explore the mechanism of SCFAs regulating neutrophil extracellular trap (NET) formation in vitro and in vivo. Finally, metagenomic sequencing was applied to investigate the impact of SCFAs on gut microbial communities. RESULTS: ScRNA-seq demonstrated the intense immune activation during the progress of COPD, characterized by neutrophil accumulation exceeding 50% of cellular composition on the 14th day in the lung tissue. Transcriptomic analysis further pinpointed neutrophil-driven NETosis as the key pathogenic pathway. The results of GC-MS showed the significant downregulation of SCFAs represented by acetic acid and propionic acid in COPD. Exogenous supplementation with SCFAs (acetic acid and propionic acid) activated the key receptor GPR43, suppressed the expression of NETs marker proteins (NE, MPO, and CitH3) and attenuated inflammatory cytokine levels in COPD rats. Rescue experiments with NETs inducers/inhibitors and GPR43 agonists/antagonists further elucidated the regulatory mechanisms of SCFAs/GPR43 axis in COPD inflammation. Furthermore, metagenomic sequencing revealed that SCFAs reshaped the intestinal flora in COPD by enriching the abundance of beneficial bacteria. CONCLUSION: As one of the key receptors for gut microbiota-derived SCFAs, GPR43 may be involved in the process by which SCFAs alleviate pulmonary inflammation in COPD through regulating NET formation. These findings provide valuable experimental evidence for promoting the clinical translation of therapeutic strategies characterized by gut microbiota and their metabolites.},
}

@article {pmid42057016,
year = {2026},
author = {Chen, H and Shi, X and Huang, Z and Li, X and Zhou, Y and Tan, D and Xie, Z and Wu, X and Zhou, M and Hong, D},
title = {Co-occurrence of viral encephalitis and autoimmune encephalitis: overlapping peaks encephalitis or coincidence condition?.},
journal = {BMC neurology},
volume = {26},
number = {1},
pages = {},
pmid = {42057016},
issn = {1471-2377},
support = {No.82101419//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Many studies have shown that autoimmune encephalitis (AE) can occur after viral encephalitis. However, no reports have focused on the interval between viral infection peaks and probable AE peaks. OBJECTIVES: To assess the possibility that viral infection and neuronal autoantibodies are concomitantly present within a 72-hour interval in patients diagnosed with encephalitis. METHODS: We retrospectively analyzed encephalitis patients admitted to our institution between 2018 and 2025. The inclusion criteria were as follows: the interval from the initial onset of symptoms to serum and cerebrospinal fluid (CSF) sampling was less than 72 h, with concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies. Viral detection was performed using metagenomic next-generation sequencing (mNGS), whereas neuronal autoantibodies were measured by cytometric bead array (CBA). RESULTS: Among 347 patients with encephalitis, fifteen patients had concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies within 72 h after the initial onset of symptoms.These fifteen patients presented with prominent clinical manifestations including headache, seizures, psychosis and memory disorders. Cerebrospinal fluid (CSF) analysis revealed features consistent with aseptic or viral encephalitis. A variety of neuronal autoantibodies were identified, namely NMDA-R-IgG, CASPR2-IgG, LGI1-IgG, LON5-IgG, GFAP-IgG, GAD65-IgG and mGluR5-IgG.Metagenomic next-generation sequencing (mNGS) assays demonstrated that 5 patients were infected with Human Herpesvirus Type 1 (HSV-1) and 10 patients with Epstein-Barr Virus (EBV). CONCLUSIONS: The concomitant detection of viral infection and neuronal autoantibodies in serum or cerebrospinal fluid (CSF) within a short time window (≤ 72 h) after the initial onset of symptoms was defined in this study as Overlapping Peak Encephalitis (OPE) or coincidence condition, which suggests that it represents a distinct clinical entity. This finding underscores the importance of simultaneously performing both metagenomic next-generation sequencing (mNGS) and neuronal autoantibody assays in patients with suspected viral encephalitis. Early identification of such comorbid conditions is of paramount importance; timely diagnosis combined with antiviral therapy and immunomodulatory intervention may significantly improve clinical outcomes.},
}

@article {pmid42285959,
year = {2026},
author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X},
title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04161-9},
pmid = {42285959},
issn = {2158-3188},
abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.},
}

@article {pmid42286003,
year = {2026},
author = {Hensen, ADO and Harmanus, C and Verbeek-Menken, PH and Koopman, JPR and Lamers, OAC and Roozen, GVT and Janse, JJ and Balke-Buijs, M and van der Stoep, MYEC and Meij, P and van Amerongen-Westra, IM and Schipper, P and Crul, C and Pattacini, L and Rox, K and Farowski, F and Tsakmaklis, A and Vehreschild, MJGT and Kuijper, EJ and Smits, WK and Roestenberg, M},
title = {Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74327-y},
pmid = {42286003},
issn = {2041-1723},
support = {101007799//Innovative Medicines Initiative (IMI)/ ; },
abstract = {Clostridioides difficile infections remain a major global healthcare burden, underscoring the need for novel therapies. Human colonisation models provide mechanistic insight into C. difficile colonisation and facilitate identification of novel intervention targets. We conducted a placebo-controlled, randomised clinical trial (NCT05693077) administering non-toxigenic C. difficile (NTCD) capsules to healthy participants to assess safety and colonisation as primary endpoints, and microbiota susceptibility as a secondary endpoint. A total of 69 healthy participants (18-45 years), not previously colonised with C. difficile and without recent antibiotic use, were enrolled following a health assessment. NTCD capsules administered for five consecutive days at low or high dose, was safe with no dose-response relationship in colonisation outcomes. Vancomycin pretreatment induced colonisation success: with 5% colonisation without, 32% after one day, and 84% after five days vancomycin pretreatment. Some participants that cleared vancomycin rapidly acquired non-challenge C. difficile strains prior to NTCD challenge. Microbiota profiling (using shotgun metagenomics) revealed reduced α-diversity and pronounced community restructuring. These findings highlight the impact of antibiotic-mediated microbiota disruption, the widespread environmental presence of C. difficile, and the feasibility of meaningful microbiota assessment in small-scale intervention trials, thereby providing a robust tool to investigate this globally impactful infection.},
}

@article {pmid42286360,
year = {2026},
author = {Morelli, S and Romano, S and Cosenza, G and Abate, S and Lombardi, L and Pilli, E},
title = {A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {42286360},
issn = {1618-2650},
abstract = {Species identification from highly degraded DNA remains a major challenge across ecology, conservation genetics, wildlife forensics, and museum science, where samples are often scarce, contaminated, and embedded in complex matrices. Under these conditions, standard reference-based and metagenomic classifiers are prone to false-positive assignments, particularly when ultra-fragmented DNA and conserved genomic regions are not explicitly accounted for. Here, we present a damage-aware next-generation sequencing (NGS) workflow for conservative species identification from minute quantities of highly degraded DNA, designed to minimize misclassification in low-input and damage-rich datasets. The workflow integrates micro-sampling, half-uracil-DNA-glycosylase (half-UDG) library preparation, PCR duplicate removal, multi-genome mapping against a curated reference panel, and a post-mapping read-ubiquity classifier that distinguishes species-specific reads from those shared across conserved loci. Using collagen-rich substrates as a proof-of-concept, we demonstrated accurate species attribution from samples as small as 1 mm[2], including mixtures and mineral-containing matrices. The workflow reliably identifies dominant biological sources, reduces false-positive assignments driven by conserved genomic regions, and remains robust to common physical and chemical treatments such as swelling, heating, and plaster addition. Overall, this study provides a proof-of-concept framework for conservative species identification in challenging degraded DNA contexts. The workflow may be adaptable to a broader range of degraded DNA contexts-including wildlife monitoring, regulatory enforcement, forensic investigations, and the analysis of processed biological materials-although further validation across diverse matrices will be required.},
}

@article {pmid42286394,
year = {2026},
author = {Shen, Q and Chen, J and Chen, Y and Liu, J and Mao, L and Shi, W and Ndjekadom, A and Wang, J and Wang, X and Liu, Y and Yang, S and Ji, L and Wu, P and Tong, F and Yang, H and Zhang, W},
title = {Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {42286394},
issn = {1572-994X},
support = {22KJA320001//Jiangsu Province Higher Education Basic Science (Natural Science) Research Project/ ; No. 2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; },
abstract = {Aedes albopictus is a globally important mosquito species capable of transmitting a variety of viruses. In this study, a total of 440 Ae. albopictus individuals were collected from Fanchang, Anhui Province, and 22 tissue libraries were constructed for metagenomic sequencing. A total of 649,930,614 reads were obtained and assembled into 209,335 contigs, of which 18,339 showed similarity to known viral proteins, spanning 13 viral families including both DNA and RNA viruses. Because several DNA virus-related sequences were recovered from the dataset, we further focussed on CRESS-DNA virus-related sequences and members of the family Parvoviridae. Phylogenetic analysis showed that three CRESS-DNA virus-related sequences clustered within Smacoviridae and Genomoviridae, while two Parvoviridae genomes were assigned to Brevihamaparvovirus and Protoparvovirus. These findings provide a metagenomic overview of the Ae. albopictus-associated virome in Anhui Province and provide baseline information on mosquito-associated DNA virus-related sequences in this region.},
}