@article {pmid41680579,
year = {2026},
author = {López-Guzmán, SF and Sánchez-Jasso, DE and Hernández-Sánchez, J and Oviedo, N and Bermudez-Cruz, RM},
title = {Molecular Characterization of the Murine Catsper4 Promoter and its Regulation by CREMτ.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {41680579},
issn = {1933-7205},
support = {IMSS R-2023-785-056//Instituto Mexicano del Seguro Social/ ; },
abstract = {Cation channel sperm-associated protein 4 (CATSPER4) is a subunit of the sperm-specific cation/calcium channel, CatSper, located in the principal piece of the sperm flagellum. It is expressed during the late stages of spermatogenesis, and disruption of the gene encoding this protein leads to male infertility. Mutations in Catsper4 are linked to asthenozoospermia. However, the molecular mechanisms regulating Catsper4 expression remain unclear. Here, we present a detailed molecular characterization of the Catsper4 promoter in mice, focusing on the role of the cAMP-responsive element modulator isoform τ (CREMτ) in its transcriptional regulation. Analysis of publicly available metagenomic chromatin immunoprecipitation-sequencing (ChIP-seq) data revealed the presence of activation histone marks-H3K4me3, H3K4me1, and H3K27ac-within a region corresponding to the 631 bp predicted promoter, suggesting an active promoter region. Although the predicted Catsper4 promoter showed minimal activity, a 65 bp deletion at the 3'-end of the promoter significantly enhanced the transcription. Moreover, removal of the 239 bp in the 5'-flanking region also increased the transcriptional activity, indicating that the core promoter region spans the region from - 99 to + 63 bp relative to the transcription start site (TSS). Notably, a cAMP-responsive element was predicted at + 91, a relevant site in the regulation of other Catsper family genes. To explore its function, we mutated this site and overexpressed CREMτ. Electrophoretic mobility shift assays (EMSA) and ChIP assays confirmed that CREMτ binds to the murine Catsper4 promoter both in vitro and in vivo. This study provides the first functional analysis of the Catsper4 promoter, shedding light on the mechanisms regulating its expression and highlighting the key role of CREMτ in this process.},
}

@article {pmid41680567,
year = {2026},
author = {Chen, L and Hong, C and Xie, Y},
title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.},
journal = {Aging clinical and experimental research},
volume = {38},
number = {1},
pages = {76},
pmid = {41680567},
issn = {1720-8319},
mesh = {Humans ; *Sarcopenia/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; Aged ; Muscle Strength ; },
abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.},
}

Humans
*Sarcopenia/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
Probiotics/therapeutic use
Aged
Muscle Strength

@article {pmid41680318,
year = {2026},
author = {Choudhary, S and Kanaujia, R and Bahadur, R and Angrup, A},
title = {The role of metagenomic next-generation sequencing in spinal infections: a systematic review and meta-analysis.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41680318},
issn = {1432-0932},
}

@article {pmid41680314,
year = {2026},
author = {Alrasheed, AS and Zawawi, AM and Alsulami, LM and Alghirash, FA and Alsalmi, SO and Alhalal, IA},
title = {Clinical utility of metagenomic next-generation sequencing in diagnosing spinal infections: a systematic review and meta-analysis.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41680314},
issn = {1432-0932},
}

@article {pmid41679837,
year = {2026},
author = {Sacco, O and Johansen, EL and Tian, Y and Holck, J and Kirkensgaard, JJK and Blennow, A and De Lise, F and Shaikh-Ibrahim, A and Moracci, M and Curci, N and Svensson, B and Cobucci-Ponzano, B and Wang, Y},
title = {Biochemical characterisation of the 4-α-glucanotransferase from the hyperthermophilic archaeon Pyrobaculum arsenaticum and its formation of high-amylose resistant starch.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124919},
doi = {10.1016/j.carbpol.2026.124919},
pmid = {41679837},
issn = {1879-1344},
mesh = {*Glycogen Debranching Enzyme System/metabolism/chemistry ; *Amylose/chemistry/metabolism ; *Pyrobaculum/enzymology ; *Starch/chemistry ; Hot Temperature ; Hydrolysis ; Hydrogen-Ion Concentration ; },
abstract = {High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85 °C, pH 5.5; Naples, Italy), showed highest activity at 100 °C and pH 5.5, and specific activity of maltotriose disproportionation at 75 °C of 1170 U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75 °C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.},
}

*Glycogen Debranching Enzyme System/metabolism/chemistry
*Amylose/chemistry/metabolism
*Pyrobaculum/enzymology
*Starch/chemistry
Hot Temperature
Hydrolysis
Hydrogen-Ion Concentration

@article {pmid41679819,
year = {2026},
author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M},
title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124886},
doi = {10.1016/j.carbpol.2026.124886},
pmid = {41679819},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation & purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.},
}

*Gastrointestinal Microbiome/drug effects
*Galactans/chemistry/pharmacology/isolation & purification
Fermentation
*Agaricales/chemistry
Molecular Docking Simulation
Fatty Acids, Volatile/metabolism
Prebiotics

@article {pmid41679750,
year = {2026},
author = {Lamont, RF and Jørgensen, JS},
title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.70173},
pmid = {41679750},
issn = {1471-0528},
abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.

METHODOLOGY: A narrative review.

RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.},
}

@article {pmid41679688,
year = {2026},
author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM},
title = {Modulation of Host Proteostasis by Prevotella corporis via Induction of the Heat Shock Response.},
journal = {Cell stress & chaperones},
volume = {},
number = {},
pages = {100150},
doi = {10.1016/j.cstres.2026.100150},
pmid = {41679688},
issn = {1466-1268},
abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, but the mechanisms by which commensal microbes confer proteoprotection remain largely unexplored. We have previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to P. corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ1-42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.},
}

@article {pmid41679496,
year = {2026},
author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y},
title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123973},
doi = {10.1016/j.envres.2026.123973},
pmid = {41679496},
issn = {1096-0953},
abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.},
}

@article {pmid41679417,
year = {2026},
author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J},
title = {Female reproductive microbiome in fertility care.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2026.02.015},
pmid = {41679417},
issn = {1556-5653},
abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. While conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads versus relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches based on clinical context and discuss emerging technologies, including multi-omics integration for implementing microbiome assessment in fertility care.},
}

@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}

@article {pmid41678593,
year = {2026},
author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH},
title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.},
journal = {Circulation research},
volume = {138},
number = {4},
pages = {e326978},
doi = {10.1161/CIRCRESAHA.125.326978},
pmid = {41678593},
issn = {1524-4571},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; },
abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Myocardium/metabolism/pathology
*Regeneration
*Heart/physiology

@article {pmid41678126,
year = {2026},
author = {Yao, Y and Lai, Y and Wu, Q and Xu, W},
title = {Targeted next-generation sequencing improves diagnosis and antimicrobial stewardship in Chlamydia psittaci pneumonia.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41678126},
issn = {1435-4373},
support = {20231001//Changning District Medical Key Specialty/ ; 20231001//Changning District Medical Key Specialty/ ; },
abstract = {UNLABELLED: PURPOSE : Chlamydia psittaci pneumonia (CPP) remains underdiagnosed due to nonspecific clinical manifestations. This study assessed the clinical utility of targeted next-generation sequencing (tNGS) in optimizing CPP diagnosis and antimicrobial stewardship, with a focus on empirical quinolone efficacy.

METHODS: We conducted a retrospective cohort study of 35 CPP patients (November 2022-October 2023) diagnosed by tNGS of respiratory specimens (8 sputum/27 bronchoalveolar lavage fluid [BALF]). Data included epidemiological history, laboratory findings, imaging features, therapeutic interventions, and clinical outcomes. Statistical comparisons between severe and non-severe CPP were performed using Student's t-test and Mann-Whitney U tests.

RESULTS: Median diagnostic delay post-admission was 4 days (IQR:3-5). Fever predominated as initial presentation (97.1%), with 45.7% reporting avian contact. Leukocyte counts were normal/mildly elevated,, yet neutrophil ratio (83.86 ± 6.17%) and D-dimer (1.31 ± 0.86 mg/L) were notably increased. All patients showed elevated CRP (175.52 ± 87.62 mg/L) and ESR (70.00 ± 22.62 mm/h). Severe CPP cases (n = 8) exhibited higher CRP (p = 0.041) and procalcitonin (p = 0.013) than non-severe cases. Common comorbidities included hepatic dysfunction (68.6%) and pleural effusion (34.3%). Polymicrobial co-infections occurred more frequently in severe CPP cases than in non-severe cases (OR = 21.07, 95% CI:1.11-402.30). tNGS-guided diagnosis prompted antibiotic adjustment in 60.0% of patients (21/35) to targeted quinolone, tetracycline, or combination therapy. Clinical recovery was achieved in 97.1%, with 2.9% mortality.

CONCLUSIONS: tNGS enhances early CPP diagnosis and targeted antimicrobial adjustment. Quinolones demonstrate high efficacy as empirical treatment. The strong association between severe CPP and polymicrobial co-infections necessitates comprehensive pathogen screening. Study limitations include a single-center design and a small sample size, warranting validation through prospective multicenter studies.},
}

@article {pmid41678125,
year = {2026},
author = {Hou, Y and Sun, H and Meng, S and Xu, W and Yu, Y and Wang, W and Liu, D and Jia, H and Wang, Y and Chu, H and Sun, Z},
title = {Deciphering the different Mycobacterium avium complex infections of HIV and non-HIV patients by bacterial GWAS and immune cells flow cytometry.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41678125},
issn = {1435-4373},
support = {82272347//National Natural Science Foundation of China/ ; 2022-1G-2161//Capital Health Research and Development of Special Fund/ ; },
abstract = {PURPOSE: Pulmonary diseases caused by Mycobacterium avium complex (MAC) show species-specific epidemiology: M. avium predominates in HIV-positive patients, while M. intracellulare mainly affects immunocompetent hosts. This study aimed to elucidate the bacterial and host mechanisms underlying these differences.

METHODS: We integrated clinical metagenomic next-generation sequencing (mNGS), k-mer-based bacterial genome-wide association study (GWAS) of clinical isolates, peripheral blood immunophenotyping of 175 patients, and mouse infection models with or without CD4 depletion.

RESULTS: K-mer GWAS identified lipid metabolism and transport genes (notably mce) enriched in isolates from hosts with different HIV statuses. Immunophenotyping showed that in HIV-negative patients, M. intracellulare infection elicited higher NKT cell frequencies than M. avium, a difference absent in HIV-positive hosts. In mice, anti-CD4[-]/M. intracellulare infection showed steadily increasing bacterial burden with time (ρ = 0.824), whereas M. avium exhibited no such trend. Early after infection (weeks 1-2), anti-CD4[-]/M. avium group had higher bacterial burden and NKT levels than anti-CD4[-]/M. intracellulare, but by week 4 the pattern reversed (all p < 0.05). CD4 depletion eliminated species-specific differences in NKT activation, and at both weeks 2 (p < 0.05) and 4 post-infection (p > 0.05), the anti-CD4[+]/M. avium groups carried a higher bacterial burden than the anti-CD4[+]/M. intracellulare groups.

CONCLUSION: MAC species exhibit fundamentally divergent infection dynamics driven by differential NKT cell activation, likely shaped by species-specific lipid antigens. This lipid-NKT axis explains contrasting clinical patterns of M. avium and M. intracellulare and highlights a potential target for host-directed interventions.},
}

@article {pmid41677732,
year = {2026},
author = {Dos Santos, LCRM and de Almeida, JDR and de Sousa, NSO and Fernandes, FDS and Ennes, JFV and Frickmann, H and de Souza, JVB and de Souza, ÉS},
title = {Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677732},
issn = {2079-7737},
support = {EDITAL N. 020/2024 - PRODUTIVIDADE EM CT&I//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; CNPq/MCTI Universal Call No. 10/2023//National Council for Scientific and Technological Development/ ; },
abstract = {The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches-culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses-discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota.},
}

@article {pmid41677194,
year = {2026},
author = {Simm, NM and Williams, GM and Fowler, S and Barlow, K and Carter, B and Talley, NJ and Keely, S and Duncanson, K and Hoedt, EC},
title = {A Scoping Review of Methods Used to Investigate Relationships between Dietary Intake and the Gastrointestinal Microbiome.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf306},
pmid = {41677194},
issn = {1753-4887},
support = {//Australian Government Research Training Program Scholarship/ ; //Australian NSW Health Round 5 Early-Mid Career Grant/ ; },
abstract = {The gastrointestinal (GI) microbiome is intrinsically linked to human health and disease, with dietary intake being a major modifiable variable contributing to microbial colonization and fermentation. Diet-microbiome studies are heterogeneous in the methods used to assess and record dietary intake, to sequence the microbiome data, and to analyze associations. To capture the extent of these inconsistencies, we performed a systematic scoping review to synthesize the information on methods used to assess and compare relationships between diet and the GI microbiome in human studies. Our search identified papers with metrics of both dietary intake and the GI microbiome (using either 16S rRNA or metagenomic shotgun sequencing) and specific diet-microbiome associative analysis. The databases searched were MEDLINE, EMBASE, CINAHL, Cochrane, and Google Scholar, and the search produced 22, 228 unique records after de-duplication. After full-text screening, 1,262 articles were selected for full extraction. A subset of 295 studies captured whole dietary intake and investigated associations with the GI microbiome. This subset assessed diet using 84 different food frequency questionnaires, 12 alternative surveys, and 4 types of diet recalls or diaries ranging from 1 to 14 days. Fifty-five percent (n = 163) of studies investigated habitual dietary intake, 35% (n = 101) investigated recent dietary intake, and 10% (n = 30) used methods to assess both. Eighty-one percent of studies employed 16S rRNA sequencing, with wide variation in extraction, sequencing, pre-processing, and annotation methods. Gaps in the reporting of the methods for each step of the sequencing and analysis process were evident, limiting future comparison of study outcomes. Microbiome-specific statistical methods were used in 11% of the subset-predominantly correlational methods that are not recommended for microbiome data. In conclusion, this review revealed extensive inconsistencies within the exploratory diet-microbiome studies, despite the existence of recommendations to assist researchers. Collaborative efforts to develop consensus in methods and reporting are needed to substantially progress the obtaining of high-quality evidence and meta-analysis in the diet-microbiome research field.},
}

@article {pmid41676497,
year = {2026},
author = {Lindstedt, K and Wheelock, A and Samutela, M and Kabir, W and Chasaya, M and Namuziya, N and Marsden, EJ and Kapasa, M and Mumba, C and Mulenga, B and Nkole, L and Pieciak, R and Mudenda, V and Chikoti, C and Ngoma, B and Chimoga, C and Chirwa, S and Pemba, L and Nzara, D and Lungu, J and Forman, L and Simulundu, E and MacLeod, W and Moyo, C and Somwe, SW and Holt, KE and Sundsfjord, A and Gill, CJ},
title = {Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.703236},
pmid = {41676497},
issn = {2692-8205},
abstract = {UNLABELLED: Klebsiella pneumoniae (Kp) is a leading cause of neonatal and infant deaths in sub-Saharan Africa and frequently associated with antimicrobial resistance. Previously, we identified Kp as a major cause of fatal community-associated lower respiratory infections among infants and children under five years in Lusaka, Zambia, using postmortem tissue sampling and pathogen specific multiplex qPCR. In this follow-up study, we employed a novel culture-independent RNA-probe hybridization-capture metagenomic sequencing approach, targeting Kp pan-genome core and accessory genes, to perform in-depth genomic analysis of Kp from eleven post-mortem lung biopsy samples from seven of these children. Analysis detected Kp in all cases except one, which identified Klebsiella quasipneumoniae subspecies similipneumoniae . Core-genome multi-locus sequence typing (cgMLST) revealed six clonal groups (CG607, CG1123, CG10072, CG280, CG3648, and CG10344) belonging to five sublineages (SL607, SL17, SL280, SL37, and SL10072), with perfect concordance between paired samples from the same case. Two infants sampled the same month harbored SL607 lineages sharing 621 out of 629 cgMLST alleles, suggesting clonal spread. Kp capsule (K) loci were detected in all but one case and included potential vaccine targets KL25, KL23, and KL122. Antimicrobial resistance genes were widespread among samples, particularly encoding resistance toward aminoglycosides, β-lactams, sulphonamides, tetracyclines, and trimethoprim. Extended spectrum β-lactamases were identified in four cases, three of which were bla CTX-M-15 . The acquired Kp sideophore yersiniabactin (lineage ybt14) was identified in both cases associated with SL607, and the acquired siderophore aerobactin (lineage iuc5) was identified in one of these, suggesting possible convergence of antimicrobial resistance and hypervirulence. The detection of Kp with extensive antimicrobial resistance causing fatal community acquired pneumonia signals a deeply concerning epidemiologic shift from a largely nosocomial pathogen. This calls for urgent epidemiological investigations to better understand the burden, transmission dynamics, antimicrobial resistances, and potential vaccine targets for Kp in other community settings across sub-Saharan Africa.

AUTHOR SUMMARY: Klebsiella pneumoniae is a major cause of infections and death among newborns and young children, particularly in low-income countries, where it is frequently resistant to antibiotics. While well-known as a hospital-associated pathogen, we previously showed K. pneumoniae is also a leading cause of fatal community lung infections among infants and children in Lusaka, Zambia. In this follow-on analysis, we performed deeper genetic analysis of K. pneumoniae detected from the cluster of community pneumonia deaths using lung tissue samples from seven of these children. Since traditional bacterial cultures were unavailable, we instead used a novel approach that enriched and sequenced specific regions of the K. pneumoniae genome directly from the biopsy samples without culturing bacterial isolates. We identified five different K. pneumoniae genetic subtypes, known as sublineages. Two sublineages, which came from children sampled the same month, were highly similar, suggesting clonal spread. Multiple acquired antimicrobial resistance genes were detected across all sublineages. Acquired virulence factors, which may cause more aggressive infections, were also detected in two cases. We also identified capsule types previously suggested as potential vaccine targets. This study underscores the urgent need to better understand and address the emerging burden of antibiotic-resistant K. pneumoniae pneumonia and other invasive infections among infants and children in community settings in sub-Saharan Africa.},
}

@article {pmid41676450,
year = {2025},
author = {Zhang, L and Liu, Y and Wang, S and Ching, JY and Tam, WH and Leung, TF and Leung, TY and Chan, PKS and Mak, JWY and Cheung, CP and Tun, HM and Chang, EB and DeLeon, O and Huang, Q and Chen, X and Huo, H and Miao, Y and Cheong, PK and Ip, KL and Yeung, YL and Chang, MK and Lyu, C and Yang, H and Li, B and Fan, Y and Sun, Y and Jiang, S and Ng, SC and Chan, FKL},
title = {MOMMY study profile: An integrative early-life multi-omics cohort in China.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70068},
pmid = {41676450},
issn = {2996-9514},
abstract = {Large-scale, prospective birth cohorts capturing the complex interplay between the gut microbiome, host biology, and environmental exposures are crucial to understanding early-life health but remain scarce, particularly within Asian populations. To address this gap, we established the MOMMY cohort (The MOther-infant Microbiota transmission and its link to long terM health of babY), a large, prospective birth cohort uniquely designed to investigate maternal-paternal-infant microbiota transmission and its impact on child health within the understudied Chinese population. MOMMY aims to recruit 20,000 families from three geographically and economically diverse regions across China. This cohort prospectively follows pregnant mothers, fathers, and their infants, with children up to 7 years of age. Since September 2019, we have systematically collected a comprehensive repository of longitudinal biospecimens-including maternal and infant stool, breast milk, cord blood, and parental blood-stored in an accredited biobank. This is complemented by extensive data on environmental exposures, diet, and health outcomes gathered through validated questionnaires and physician assessments. The MOMMY cohort's unique value lies in its unprecedented scale, geographic diversity, and its integrative multi-omics design, which will combine metagenomic, metabolomic, immunologic, and epigenetic data. By creating this unique resource, MOMMY will elucidate how early-life microbial and molecular trajectories, shaped by genetic and environmental factors, influence child development and disease risk, thereby filling a critical gap in global microbiome research.},
}

@article {pmid41676447,
year = {2025},
author = {Deng, F and Han, Y and Li, M and Peng, Y and Chai, J and Yang, G and Li, Y and Zhao, J},
title = {HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70041},
pmid = {41676447},
issn = {2996-9514},
abstract = {Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively compares PacBio High-Fidelity (HiFi) sequencing-based metagenome-assembled genomes (MAGs) against Illumina MAGs, Oxford Nanopore Technologies (ONT) MAGs, and isolate whole-genome sequencing genomes from the same sample. HiFi sequencing yielded 31 high-quality MAGs, including 10 complete circular genomes. HiFi MAGs demonstrated significantly higher completeness, continuity, and lower contamination than Illumina or ONT MAGs (p-adj < 0.05). Crucially, HiFi MAGs exhibited closer genomic proximity to corresponding isolates at both single-nucleotide polymorphism and gene presence/absence levels. This benchmarking establishes HiFi as a robust approach for generating MAGs rivaling isolated genome quality, providing critical insights for accurate microbial genomic studies.},
}

@article {pmid41676442,
year = {2025},
author = {Chaboy-Cansado, R and Talavera-Marcos, S and Gallego-Simón, R and Cobeta, P and Roscales, G and Rastrojo, A and de Cárcer, DA},
title = {Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70037},
pmid = {41676442},
issn = {2996-9514},
abstract = {Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research.},
}

@article {pmid41676438,
year = {2025},
author = {Liu, Y and Ise, Y and Takami, H and Urakawa, R and Tateno, R and Toyoda, A and Ohte, N and Shi, W and Jiang, L and Isobe, K},
title = {Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70054},
pmid = {41676438},
issn = {2996-9514},
abstract = {Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene- or taxon-specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium-related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and [[15]]N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation-that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower-pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher-pH range but diminished within the lower-pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher-pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower-pH soils were enriched in stress-adaptive functions, which promoted ammonium retention and limited N transformations-thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium-related N cycling processes across forests under varying environmental conditions.},
}

@article {pmid41676216,
year = {2026},
author = {Dang, Y and Deng, Z and Wang, K and Luo, J and Wang, C and Long, F and Kong, J},
title = {Cystic fibrosis complicated by allergic bronchopulmonary aspergillosis in a Chinese adolescent: a case report and literature review.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {43},
pmid = {41676216},
issn = {2523-1995},
abstract = {BACKGROUND: Cystic fibrosis (CF) predisposes patients to allergic bronchopulmonary aspergillosis (ABPA). The objective of this study is to enhance the recognition of CF-related ABPA (CF-ABPA) in adolescents through a detailed case study. A multidisciplinary management approach is essential. Early diagnosis and intervention could substantially improve outcomes, warranting further longitudinal research on optimized treatment protocols.

CASE DESCRIPTION: A 15-year-old patient presenting with persistent respiratory symptoms underwent a series of diagnostic tests, including serum immunoglobulin E (IgE) testing, chest computed tomography (CT), bronchoscopy, bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), and whole-exome sequencing to identify CFTR mutations. The diagnostic findings revealed markedly elevated serum IgE levels (2,359.0 IU/mL), the presence of bronchiectasis with mucus plugging on CT imaging, and mNGS detection of Aspergillus fumigatus with an abundance of 97.28%. The diagnosis of CF-ABPA was confirmed by identification of a pathogenic CFTR mutation. Later antifungal therapy and corticosteroids produced notable clinical improvement.

CONCLUSIONS: CF was under-recognized historically, but this case shows that it is a clinically important cause of bronchiectasis and ABPA in Chinese adolescents. The identification of Aspergillus was accurate with the mNGS. Genetic test confirmed that the subject is a CF patient with compound heterozygous mutations in CFTR gene. The finding urges the clinician to have a high index of suspicion for the CF-ABPA in those with asthma-like refractory symptoms with structural lung disease. When diagnosed early and accurately, antifungal therapy and inhaled corticosteroids can be administered timely. The patient experienced a notable improvement both clinically and radiologically, as well as functionally. The future work should promote awareness of this clinical entity and systematic screening of similar patients in China. Further multicenter studies are necessary to formulate diagnostic and therapeutic guides for CF-ABPA in Asia.},
}

@article {pmid41676189,
year = {2026},
author = {Zhang, G and Fang, X and Yang, H and Zhu, Y},
title = {Severe empyema caused by mixed oral anaerobic bacterial infection: a case report.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {28},
pmid = {41676189},
issn = {2523-1995},
abstract = {BACKGROUND: Empyema is a life-threatening pleural infection that can result from various bacterial sources. While oral anaerobic bacteria are recognized as potential pathogens, severe empyema caused by mixed oral anaerobic bacterial infection remains clinically rare. Recent advances in metagenomic next-generation sequencing (NGS) have improved the etiological diagnosis of complex infections. This case demonstrates the clinical significance of NGS technology and oral health in preventing systemic infections.

CASE DESCRIPTION: An 80-year-old male with poor oral hygiene and multiple dental caries presented with acute onset of left-sided chest pain, chills, and fever. Physical examination revealed diminished breath sounds over the left lung. Imaging studies confirmed left-sided empyema. Pleural fluid NGS identified mixed oral anaerobic bacteria including Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Finegoldia magna. The patient underwent thoracoscopic empyema debridement, with postoperative tissue pathology showing suppurative inflammation with fibrinous necrosis. Surgically excised tissue NGS additionally detected Finegoldia magna along with Epstein-Barr virus and human herpesvirus 6. Following targeted anti-infective therapy with meropenem and metronidazole, the patient recovered successfully.

CONCLUSIONS: This case highlights the critical role of NGS technology in identifying mixed oral anaerobic pathogens and guiding precision-targeted treatment of empyema. The atypical presentation of empyema caused by oral anaerobic bacteria warrants early surgical intervention combined with appropriate antimicrobial therapy. Our findings emphasize the importance of oral health maintenance in preventing life-threatening systemic infections and broaden our understanding of oral-systemic disease relationships.},
}

@article {pmid41676099,
year = {2026},
author = {Zheng, H and QuBie, X and Wang, J and Liu, P and Zhang, W},
title = {Clinical features and chest CT findings of Chlamydia pneumoniae pneumonia.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1717744},
pmid = {41676099},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aimed to investigate the clinical features and chest computed tomography (CT) findings in 42 patients with Chlamydia pneumoniae pneumonia, as confirmed by metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective analysis of clinical data and chest CT findings (both at disease onset and within 1 month thereafter) in 42 patients diagnosed with Chlamydia pneumoniae pneumonia by mNGS at our hospital between August 2022 and August 2025.

RESULTS: Of the 42 patients, 25 (59.5%) presented with fever, 26 (61.9%) with sore throat, 30 (71.4%) with cough, 27 (64.3%) with expectoration, 11 (26.2%) with myalgia, 10 (23.8%) with general fatigue, and 10 (23.8%) with neurological symptoms such as headache and dizziness. Laboratory tests revealed that 12 patients (28.6%) showed a mild increase in white blood cell count, 10 (23.8%) had elevated neutrophil counts, 21 (50.0%) exhibited elevated C-reactive protein (CRP) levels, and 6 (14.3%) had CRP levels exceeding 100 mg/L. In the early stage, chest CT demonstrated a lobular pneumonia pattern in 16 patients (55.2%), involvement of a single lung lobe in 20 (69.0%), predominant lower-lung distribution in 19 (65.5%), and a nodular-patchy pattern in 8 patients (27.6%) with a nodular-patchy pattern. The main accompanying features included a halo sign in 25 patients (86.2%), centrilobular nodules in 23 (79.3%), and bronchial wall thickening in 20 (69.0%). In the mid-to-late stage, chest CT revealed a lobular pneumonia pattern in 23 patients (76.7%), single-lobe involvement in 23 (76.7%), and predominant lower-lung distribution in 20 (66.7%). The major concomitant features were a halo sign in 21 patients (70.0%), centrilobular nodules in 20 (66.7%), and bronchial wall thickening in 24 (80.0%).

CONCLUSION: Chest CT findings of Chlamydia pneumoniae pneumonia are predominantly characterized by a lobular pneumonia pattern, lower-lobe distribution, and associated features such as bronchial wall thickening, centrilobular nodules, and a peripheral halo sign. Certain imaging differences exist between early and middle-to-late stages, with the nodular-patchy pattern potentially representing an ultra-early imaging marker, which may provide clues for early clinical intervention.},
}

@article {pmid41676059,
year = {2026},
author = {Li, X and Yi, H and Wu, G and He, A and Li, R and Long, Y and Lin, C and Jiang, Z},
title = {Neutrophil CD64 index for rapid diagnosis of Pneumocystis jirovecii pneumonia in malignancy patients requiring mechanical ventilation: a retrospective analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1706786},
pmid = {41676059},
issn = {1664-302X},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) incidence and associated mortality have risen significantly in non-HIV immunocompromised patients, highlighting the urgent need for rapid, non-invasive diagnostics. Current methods face limitations including invasiveness, prolonged processing, or inadequate specificity. The neutrophil CD64 (nCD64) index emerges as a promising novel biomarker. Here, we conducted this study to evaluate the diagnostic performance of nCD64 index for PJP and further assess the predictive value of its longitudinal changes for 28-day mortality.

METHODS: This retrospective cohort study (July 2022-March 2025) analyzed mechanically ventilated malignancy patients with unexplained diffuse pulmonary infiltrates at a tertiary intensive care unit (ICU). PJP diagnosis required predefined clinical, radiological, and bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF mNGS) criteria. The nCD64 index was measured via flow cytometry at ICU admission and serially after ≥3 days of anti-PJP therapy. Diagnostic performance for PJP and prognostic value for 28-day mortality were assessed.

RESULTS: Among 28 PJP and 38 non-PJP patients, nCD64 index was significantly higher in PJP (13.33 vs. 2.84, p < 0.001). Receiver operating characteristic (ROC) curve analysis showed an area under the curve (AUC) of 0.846 (95% CI: 0.736-0.932) for PJP diagnosis, with sensitivity 89.3% and specificity 71.1% at cutoff ≥7. Multivariate analysis confirmed nCD64 index as an independent PJP predictor (OR = 1.097, 95% CI: 1.026-1.173; p = 0.007). Post-therapy nCD64 index elevation predicted 28-day mortality with high sensitivity (81.8%) and specificity (86.7%).

CONCLUSION: The nCD64 index functions as a dual-purpose biomarker for malignancy patients with respiratory failure requiring mechanical ventilation: it provides a rapid, non-invasive diagnostic tool for PJP and dynamically stratifies mortality risk. Moreover, dynamic tracking offers a real-time window into treatment response, guiding therapeutic decisions.},
}

@article {pmid41675707,
year = {2025},
author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L},
title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e62},
pmid = {41675707},
issn = {2996-9514},
abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.},
}

@article {pmid41675165,
year = {2025},
author = {Liu, S and Ye, Y and Guo, B and Hu, Y and Jiang, K and Liang, C and Xia, S and Wang, H},
title = {ViOTUcluster: A high-speed, All-in-one pipeline for viromic analysis of metagenomic data.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70023},
pmid = {41675165},
issn = {2996-9514},
abstract = {ViOTUcluster is a user-friendly, high-speed, accurate, All-in-one solution that streamlines the entire viromic analysis workflow-from raw reads to the generation of viral operational taxonomic units tables, as well as other key viromic analysis tasks.},
}

@article {pmid41675153,
year = {2025},
author = {Ye, L and Hu, Q and Zang, T and Wang, Y and Heng, H and Chan, EWC and Chen, S},
title = {Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70004},
pmid = {41675153},
issn = {2996-9514},
abstract = {The pork microbiome was investigated using an integrated approach combining isolation and metagenomic sequencing methods to comprehensively analyze the pathogens and resistome on pork surfaces. The study revealed a large number and diversity of pathogens and resistance genes, potentially originating from air, transportation, water, or cross-contamination. These findings underscore the importance of implementing multifaceted food surveillance strategies to monitor and mitigate these risks effectively.},
}

@article {pmid41675151,
year = {2025},
author = {Skoog, EJ and Kebabonye, K and Klempay, B and Gondwe, M and Makati, K and Babayani, N and Jongman, M and Bowman, J and Aluwihare, L},
title = {Viral metagenomics of Okavango Delta water pans reveal novel insights into wildlife disease potential.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70018},
pmid = {41675151},
issn = {2996-9514},
abstract = {Botswana's Seronga region saw a mass elephant die-off potentially linked to water sources. This study analyzes Okavango Delta metagenomes, uncovering a diversity of viruses and harmful pathogens. Findings highlight the importance of understanding viral ecology in these waters and support One Health's objective in protecting human, animal, and ecosystem health.},
}

@article {pmid41675149,
year = {2025},
author = {Shen, H and Du, C and Jiang, S and Dong, W and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Native synthetic microbial communities enhance zha-chili by boosting the fermentation capacity of indigenous microorganisms.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70009},
pmid = {41675149},
issn = {2996-9514},
abstract = {Fermented foods are a crucial part of the global diet, accounting for one-third of global food intake. Traditional fermented foods often rely on natural fermentation, leading to safety risks. The construction of synthetic microbial communities (SynComs) tailored for fermented foods is a key strategy to solve these issues. Here, we designed and constructed SynComs consisting of two bacterial and three fungal species, utilizing the study model of zha-chili. Using various high-throughput sequencing technologies, the dynamic alternations of microorganisms during the fermentation process were investigated, and the impact of SynComs on the fermentation process was evaluated. SynComs reduced fermentation time by approximately 15 d, increased flavor yields (8% for ethyl lactate and ethyl acetate), and greatly improved the quality of the zha-chili. Meanwhile, SynComs altered the succession of the fungal community so that Pichia became the dominant microorganism throughout the fermentation process, and the pattern of fungal community succession was brought closer to the null model. Metagenomic annotation results showed notable changes in functional genes, especially in glycoside hydrolases family. SynComs enhanced the positive correlations between indigenous microorganisms and flavor compounds while increasing other community microorganisms' contribution to flavor production. These findings provide a new approach to improve the quality of zha-chili and other traditional fermented foods through natural fermentations. We proposed that SynComs enhanced fermented foods by boosting the fermentation capacity of indigenous microorganisms.},
}

@article {pmid41674905,
year = {2025},
author = {Díaz-Santiago, E and Sadio, TD and Diéme, JS and Hurtado-Martínez, M and Kindler, C and Manrique, E and Pugnaire, FI},
title = {Soil microbial communities in contrasting environments show a common core of species linked to Maytenus senegalensis shrubs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699694},
pmid = {41674905},
issn = {1664-302X},
abstract = {INTRODUCTION: The existence of a core microbiota specific to a plant species, or the set of microorganisms shared by all plant individuals of the species, is of utmost importance because of its many conceptual and practical consequences. The core microbiota is assumed to gather the most ecologically and functionally relevant microorganisms associated to a plant in a given environment, presumably establishing positive feedbacks that support its persistence and performance in a plant community.

METHODS: We tested the existence of a potential core microbiota in Maytenus senegalensis shrubs in two contrasted, distant ecosystems; a dry environment (Almeria, Spain) and a relatively wetter ecosystem (Dakar, Senegal).

RESULTS: Soil microbial community structure widely differed between sites influenced by soil and climate. However, a subset of microbial phylotypes appeared consistently associated to all M. senegalensis plants across our two disparate ecosystems while they were absent in the surrounding soil, suggesting the presence of a core microbiota in M. senegalensis.

DISCUSSION: Microbiota had an effect on germination that differed between sites, perhaps due to climatic constrains. We show that the assembly of understory microbial communities depends on the plant's sorting effect on the surrounding soil microbiota, plus some other taxa likely transferred by seeds; this assembly mechanism is relevant for the coevolution of plants and microorganisms, and critical for potential community responses to environmental changes.},
}

@article {pmid41674903,
year = {2025},
author = {Ding, Z and Ren, K and Xu, Y and Feng, T and Cui, K and Liu, Q and Liao, C},
title = {Disease-driven restructuring of the gut microbiome underlies inflammatory bowel disease dysbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1744574},
pmid = {41674903},
issn = {1664-302X},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent intestinal disorder with rising global incidence, yet its complex pathogenesis remains poorly understood, underscoring the need to clarify the microbial mechanisms underlying intestinal inflammation. IBD is associated with a profound imbalance of the gut microbial ecosystem. However, the ecological and functional remodeling of the gut microbiota during IBD progression remains unclear. This study used metagenomic sequencing to investigate microbial composition, functional capacity, and ecological interactions in the gut microbiota of IBD patients compared with healthy individuals.

RESULTS: The IBD group exhibited significantly reduced microbial diversity and a distinct community structure compared with healthy controls. Pro-inflammatory genera such as g_Fusobacterium (p < 0.001) and g_Morganella (p < 0.001) were enriched, whereas short-chain fatty acid producing bacteria, including g_Ruminococcus (p < 0.0001) and g_Agathobacter (p < 0.0001), were markedly depleted. Functional annotation revealed decreased abundance of carbohydrate-active enzymes (GH3, GH44, GH53, and GH77; all p < 0.05) associated with polysaccharide degradation, together with enrichment of pathways related to immune activation and inflammation, such as the JAK-STAT and chemokine signaling pathways (p < 0.05). Co-occurrence network analysis further showed that IBD-associated microbes formed positively correlated clusters dominated by inflammatory taxa, whereas healthy microbiota were organized around SCFA-producing commensals.

CONCLUSION: Compared with healthy individuals, the gut microbiota of IBD patients undergoes functional reprogramming characterized by loss of metabolic versatility and enrichment of inflammation-related pathways. These findings provide new insights into the ecological and metabolic mechanisms through which the gut microbiota contribute to intestinal inflammation and disease progression.},
}

@article {pmid41674838,
year = {2026},
author = {Berta, J and Rowe, L and Garry, B},
title = {Catching the Mardi Gras fever: Quantifying the impact of mass gathering tourism on local bacterial prevalence and community diversity in municipal wastewater.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8681977/v1},
pmid = {41674838},
issn = {2693-5015},
abstract = {We employed 16S metagenomic analysis to measure the impact of Mardi Gras tourism on the bacterial ecology found in New Orleans' municipal wastewater. Throughout the peak of the 2023 Carnivale season, species turnover was significantly higher in New Orleans than it was in our control site. Alpha diversity metrics peaked 2-to-3 weeks after Mardi Gras Day, increasing between 65% and 1967% over Carnivale. We also found that human pathogens and microbiota had significantly stronger, more positive correlations with the rise in Mardi Gras tourism than did environmental control species. These changes in wastewater abundance for two species - S. enterica and E. coli - mirrored the concurrent clinical isolate data from the same region for Salmonella spp. and STEC. We also found that multiple alpha and beta diversity measures correlated strongly with increases in tourism during the peak of Carnivale season.},
}

@article {pmid41674736,
year = {2026},
author = {Mukenschnabl, K and Humpel, O and Abdalla, TE and Wood, E},
title = {An Unusual Case of Unexplained Infertility: Co-colonization of the Uterus and Seminal Fluid.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e101251},
pmid = {41674736},
issn = {2168-8184},
abstract = {Chronic endometritis (CE) is defined as a persistent, mild inflammation of the endometrium induced by intrauterine bacterial infection. CE has been associated with infertility in patients with recurrent in vitro fertilization (IVF) failure. We report an unusual case of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility. A 35-year-old woman presented to the office for infertility evaluation after 16 months of inability to conceive naturally using ovulation kits. Initial workup revealed adequate ovarian reserve with an anti-Müllerian hormone (AMH) level of 4.8 ng/mL, tubal patency on hysterosalpingogram, and normal semen analysis. The patient and her partner failed to conceive following three cycles of ovulation induction with intrauterine insemination (IUI). In preparation for IVF, an endometrial biopsy (EMB) was performed, and five CD138+ plasma cells per 10 high-power fields suggested CE. The patient underwent antibiotic therapy, yet EMB remained positive. At this time, the partner's semen culture was positive for Enterococcus faecalis and Escherichia coli. Endometrial microbiome metagenomic analysis (EMMA) and analysis of infectious chronic endometritis (ALICE) demonstrated co-colonization with the same bacteria seen on her partner's semen culture. Both the patient and her partner required multiple rounds of antibiotic therapy before successful conception via IVF. This case demonstrates an unusual occurrence of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility, suggesting a potential pathway for CE development from bacteriospermia. The patient's EMMA/ALICE tests and the partner's semen cultures revealed the presence of the same bacteria. While current literature does not identify the development of CE from the bacteria in a partner's semen, there is an association between bacteria in semen and infertility. In couples with unexplained infertility, thorough evaluation for CE with EMB and EMMA/ALICE can be performed in conjunction with a semen culture on the partner to explore potential co-colonization and guide dual-partner treatment.},
}

@article {pmid41674628,
year = {2026},
author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA},
title = {Plant-based whole-food diets are feasible during autologous stem cell transplantation and are associated with dose-dependent microbiome modulation: Results from a pilot clinical trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.26345403},
pmid = {41674628},
abstract = {Plant-based dietary strategies may offer a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked to infectious complications and inferior survival. We conducted a single-arm study to test the feasibility and biological activity of a high-fiber, plant-based, whole-food meal delivery intervention during the peri-transplant period. Adults with multiple myeloma (n = 22) received fully prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting consumption of nutrient-dense, high-fiber foods despite transplant-related symptoms that often limit oral intake. The primary endpoints were feasibility and tolerability, defined by successful enrollment, adherence to study procedures, and patient-reported intake of study meals; diet was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming at least some proportion of delivered meals and with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. Larger randomized trials are warranted to determine whether microbiome-targeted nutrition can reduce transplant-related toxicities, enhance immune recovery, and improve disease control in multiple myeloma. The trial is registered at ClinicalTrials.gov (NCT06559709).},
}

@article {pmid41674603,
year = {2026},
author = {Agudelo, C and Nsereko, M and Ainebyona, A and Andama, A and Castro, R and Leung, SRM and Nakafeero, J and Nannyonga, G and Nolan, K and Teran, L and Wambi, P and Young, MG and Kato-Maeda, M and Cattamanchi, A and Jaganath, D and Wobudeya, E and Wolf, AR},
title = {Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.29.26345155},
pmid = {41674603},
abstract = {BACKGROUND: Stool-based molecular tests are a noninvasive option for pediatric tuberculosis (TB) diagnosis, but have lower sensitivity compared to sputum-based tests. Untargeted metagenomic sequencing (mNGS) on stool could improve sensitivity and identify new gene targets for molecular testing.

METHODS: We performed shotgun mNGS on DNA isolated from stool samples of children undergoing assessment for pulmonary TB in Uganda. We defined the performance of mNGS to identify Mycobacterium tuberculosis (Mtb) against a microbiological reference standard (MRS, TB if sputum Xpert Ultra or culture positive) and a composite reference standard (TB if confirmed or unconfirmed TB). We also compared accuracy of mNGS against the stool-based Xpert Ultra test. Finally, we identified enriched genomic loci among Mtb classified reads.

RESULTS: We analyzed 176 stool samples of children with a median age of 3.6 years (IQR, 1-6 years). !"#$%&'(')*(+,-. (')*(&*%&$'$/$'$*&(01(234-(5$')(60&$'$/*(78(9*1$%*9(as ≥ 1, 2, or 5 sequence fragments were 35.5% (95% CI 19%:;;<=.(>;?@<(AB>< : 45%), and 19.4% (13%-25%) respectively, and specificities 92.64% (87%-96%), 97% (93%-99%), and 99.3% (96%-100%). Stool Xpert Ultra had similar sensitivity (22.6%) to stool mNGS considering all samples tested. In a head-to-head comparison, stool mNGS had lower sensitivity than stool Xpert Ultra (38.5% vs. 53.8%, difference -15.3%, 95% CI 14-68 to 25-81). mNGS utilized rRNA, virulence proteins and membrane proteins not targeted in current PCR-based platforms.

CONCLUSIONS: Metagenomic sequencing of stool DNA did not increase sensitivity of TB detection, but identified novel targets for molecular testing that may support development of more sensitive tests.},
}

@article {pmid41674575,
year = {2025},
author = {Zhang, Z and Xu, Y and Pang, K and Wu, C and Zhao, C and Lei, T and Zhang, J and Hai, T and Zhao, F and Zhao, Y},
title = {Microbiota humanization drives human-like metabolic and immune transcriptomic shifts in pigs.},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70034},
pmid = {41674575},
issn = {2996-9514},
abstract = {Pigs are increasingly recognized as promising candidates for clinical xenotransplantation and as large-animal models for biomedical research; however, interspecies differences in gut microbiota, immune function, and metabolism remain major barriers. To address this, we established gut microbiota-humanized (GMH) pigs by transplanting human fecal microbiota into antibiotic-treated pigs. We systemically evaluated alterations in microbiota composition, serum metabolites, and immune cell profiles using integrated metagenomic, quasi-targeted metabolomic and single-cell transcriptomic (scRNA-seq) analyses. Metagenomic profiling revealed a shift in the intestinal microbiota of GMH pigs toward a human-like composition, characterized by enrichment of Bacteroidia and depletion of Bacilli. Metabolomic analysis showed that GMH pigs exhibited serum metabolite profiles more closely resembling those of humans. Among 423 detected serum metabolites, 136 that were lower in control pigs than in humans were upregulated in GMH pigs, whereas 79 that were elevated in control pigs decreased post-transplantation. Notably, pathways related to tryptophan metabolism, bile acid biosynthesis, and fatty acid metabolism were enhanced in GMT pigs, while carbon-related and glycolytic pathways were attenuated, indicating partial convergence toward human metabolic phenotype. Integration of microbial and metabolite data identified 20 and 33 metabolites associated with Bacteroidia and Bacilli, respectively. scRNA-seq profiling of peripheral blood mononuclear cells demonstrated transcriptional and compositional remodeling of T cells, monocytes, and B cell subsets in GMH pigs. These findings demonstrated that human fecal microbiota can reshape both systemic metabolic and immune artitecture in pigs, offering a robust large-animal platform for studying host-microbiota interactions and advancing translational application in xenotransplantation and microbiome-based therapeutics.},
}

@article {pmid41674563,
year = {2025},
author = {Lyu, W and Chen, L and Li, DF and Li, SY and Dai, Q and Zhou, HL and Liu, YY and Zhou, JY and Liang, XJ and Wang, L},
title = {Lactobacillus johnsonii-FM1 modulates gut microbiota and secretes anticancer metabolite vanillic acid to inhibit colorectal tumorigenesis.},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70050},
pmid = {41674563},
issn = {2996-9514},
abstract = {During colorectal cancer (CRC) progression, probiotics support gut microbial balance, enhance intestinal barrier integrity, and exert antioxidant and anti-inflammatory effects. Such supplementation may slow tumor growth and serve as an adjunctive therapy for CRC. In this study, we evaluated the impact of Lactobacillus johnsonii-FM1 in Apc [Min/+] and azoxymethane/dextran sulfate sodium-induced CRC mouse models. Our results demonstrate that L. johnsonii-FM1 markedly reduces tumor number, size, and volume in both models. Shotgun metagenomic sequencing showed that L. johnsonii-FM1 increases the abundance of potentially beneficial taxa while decreasing opportunistic pathogens, thereby preserving gut barrier function. Moreover, untargeted metabolomics paired with liquid chromatography-tandem mass spectrometry identified vanillic acid (VCA) as a key bioactive metabolite produced by L. johnsonii-FM1. In vitro, VCA inhibits CRC cell line proliferation, diminishes colony formation, induces cell-cycle arrest, and promotes apoptosis. Mechanistically, VCA attenuates CRC progression by suppressing Wnt/β-catenin signaling. Our findings suggest a promising probiotic-based adjunctive strategy for CRC prevention and treatment.},
}

@article {pmid41674474,
year = {2026},
author = {Sun, Y and Shuai, X and Sheng, Q and Lu, Y and Wu, Z and Sun, Y and Wu, D and Guo, X},
title = {Torque Teno Virus or Herpesviruses Detection By Metagenomic Next-Generation Sequencing Predicts In-Hospital Major Adverse Events in Critically Ill Patients With Severe Infections.},
journal = {Journal of medical virology},
volume = {98},
number = {2},
pages = {e70840},
pmid = {41674474},
issn = {1096-9071},
support = {//Zhongguancun Precision Medicine Foundation/ ; },
mesh = {Humans ; Critical Illness ; *Torque teno virus/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Aged ; *Herpesviridae/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; *Cross Infection/virology/epidemiology ; *Metagenomics/methods ; Adult ; *DNA Virus Infections/virology ; Risk Factors ; *Herpesviridae Infections/virology/diagnosis ; China/epidemiology ; Intensive Care Units ; },
abstract = {Viral detection occurs frequently in critically ill patients. Patients with multiple viremic events had a higher ICU mortality. The highly sensitive mNGS technology has significantly enhanced viral pathogen detection rates. We enrolled 134 critically ill patients with severe infections who underwent mNGS testing during January 2019 to December 2021, at Qilu Hospital (Qingdao) of Shandong University. Viral pathogens were identified in 78 cases (58.2%). Torque teno virus (TTV) or herpesviruses (HVs) showed the highest detection rates (23.1% and 29.9%, respectively). The incidence of major adverse events (MAEs) in the hospital was 53.0%. Patients with TTV or HVs detection had more secondary nosocomial infections and stress ulcers, and the incidence of MAEs showed an increasing trend. Multivariate Logistic regression analysis showed that APACHE II score (OR: 1.10, 95%CI: 1.02-1.19, p = 0.018) and TTV or HVs detection by mNGS (OR: 2.40, 95% CI: 1.05-5.50, p = 0.038) were independent risk factors for MAEs. This study advocates the use of mNGS for detecting viruses in critically ill patients with severe infections, as it serves as a predictor for heightened risk of in-hospital MAE.},
}

Humans
Critical Illness
*Torque teno virus/genetics/isolation & purification
Male
Female
Middle Aged
Aged
*Herpesviridae/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
*Cross Infection/virology/epidemiology
*Metagenomics/methods
Adult
*DNA Virus Infections/virology
Risk Factors
*Herpesviridae Infections/virology/diagnosis
China/epidemiology
Intensive Care Units

@article {pmid41674272,
year = {2026},
author = {Macey, MC and Mahnert, A and Stephens, BP and Kucukkilic-Stephens, E and Olsson-Francis, K},
title = {An ensemble binning approach to identify functional diversity in cleanroom environments.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {384},
number = {2314},
pages = {},
doi = {10.1098/rsta.2024.0438},
pmid = {41674272},
issn = {1471-2962},
support = {//UK Space Agency/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Metagenome ; *Environment, Controlled ; Spacecraft ; },
abstract = {Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilization protocols to minimize microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high-quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity, temperature and alkalinity. Growth rate index (GRiD) analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.},
}

*Microbiota/genetics
*Bacteria/genetics/classification/metabolism
Metagenomics/methods
Metagenome
*Environment, Controlled
Spacecraft

@article {pmid41674268,
year = {2026},
author = {Zaccaria, T and Beblo-Vranesevic, K and de Jonge, MI and Netea, MG and Rettberg, P},
title = {Survival limits of psychrotolerant microorganisms with relevance for planetary protection of the icy moons.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {384},
number = {2314},
pages = {},
doi = {10.1098/rsta.2024.0435},
pmid = {41674268},
issn = {1471-2962},
support = {//Deutsches Zentrum für Luft- und Raumfahrt/ ; //Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; /ERC_/European Research Council/International ; },
mesh = {*Extraterrestrial Environment ; *Moon ; Spacecraft ; *Microbial Viability ; Arctic Regions ; },
abstract = {Investigating the survival limits of extremophilic microorganisms exposed to simulated space conditions can shed light on the ability of terrestrial microorganisms to survive and propagate on other planetary bodies. Although microbes can be found in all environmental niches on Earth, this study focuses on psychrophilic and psychrotolerant microorganisms (prokaryotes and eukaryotes) which have been isolated from locations of interest such as icy moon analogue environments (e.g. Canadian high arctic, Antarctica) and cleanrooms, which might be relevant for forward planetary protection. Our research aimed to reproduce conditions for microorganisms on spacecraft travelling to the outer solar system which could contaminate the icy moon's subsurface oceans. The microorganisms were grown under oligotrophic conditions in minimal media supplemented with only a single carbon source and exposing them to extreme conditions, in terms of temperature fluctuations, in terms of freeze and thaw cycles, and radiation, as they occur during the space travel to the outer solar system. Our results in combination with future metagenome data and phenotype prediction tools will allow the identification of planetary protection relevant microorganisms in spacecraft assembly cleanrooms and on spacecraft and support the development of a target-oriented planetary protection constraints for missions to the icy moons. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.},
}

*Extraterrestrial Environment
*Moon
Spacecraft
*Microbial Viability
Arctic Regions

@article {pmid41674105,
year = {2026},
author = {Song, B and Zeb, J},
title = {The midgut of Aedes albopictus shapes its bacteriome but not its mycobiome.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70505},
pmid = {41674105},
issn = {1526-4998},
support = {//City University of Hong Kong/ ; },
abstract = {BACKGROUND: Midgut microbiota consists mainly of bacteria and fungi and can interact directly or indirectly with ingested pathogens. However, both the specific microbes that stably colonize the mosquito midgut and how the midgut shapes their microbiome remain poorly understood. In this study, we analyzed the midgut microbiome of the insect vector Aedes albopictus at three different developmental stages collected from the field. Additionally, we reared field-collected larvae under laboratory conditions, using either field water from the breeding habitat or sterilized water, to track the linear evolution of the microbiome from larvae to adulthood.

RESULTS: Our metagenomic analysis revealed that the mosquito host selected specific bacterial species, while the mycobiome remained virtually identical to that of the surrounding water. We identified 42 core bacterial species that form a highly interactive network, as well as two core fungal species, both of which were consistently more abundant in the mosquito gut than in the surrounding water across all life stages in both laboratory and field conditions. Furthermore, we successfully assembled 271 bacterial genomes de novo, 14 of which belonged to core species. These 14 bacterial genomes were enriched in genes associated with antioxidant function and cAMP metabolism.

CONCLUSION: This study uncovers fluctuating bacterial dynamics alongside conserved fungal communities in the mosquito gut, suggesting distinct mechanisms that shape the bacteriome and mycobiome. This study highlights the antioxidant function in stabilizing bacteria in Aedes albopictus. © 2026 Society of Chemical Industry.},
}

@article {pmid41674065,
year = {2026},
author = {Jo, S and Seo, H and Lee, KA and Kim, S and Rahim, MA and Barman, TI and Kim, HS and Song, HY},
title = {Skin Microbiome Profiling in Patients with Primary Sjögren Disease Compared to Healthy Individuals.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510010},
doi = {10.4014/jmb.2510.10010},
pmid = {41674065},
issn = {1738-8872},
mesh = {Humans ; *Sjogren's Syndrome/microbiology ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Female ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification ; Adult ; DNA, Bacterial/genetics ; Aged ; Biodiversity ; Case-Control Studies ; Sequence Analysis, DNA ; Skin Microbiome ; },
abstract = {Primary Sjögren disease (SjD) is a systemic autoimmune disease characterized by inflammation of exocrine glands, most commonly leading to dry mouth and dry eyes. Although the etiology of SjD remains unclear, emerging evidence suggests that the microbiome modulates immune homeostasis. This study aimed to compare the skin microbiomes of SjD patients with those of healthy controls (HCs) using 16S rRNA gene sequencing. Taxonomic composition, alpha and beta diversity, and predicted functional profiles were evaluated. We observed a significant depletion of Cutibacterium and a marked reduction in microbial diversity in SjD patients. Beta diversity analyses revealed distinct clustering among groups. Functional prediction suggested the downregulation of metabolic pathways associated with microbial homeostasis. Our findings propose that alterations in the skin microbiota may contribute to SjD pathogenesis and serve as potential biomarkers or therapeutic targets.},
}

Humans
*Sjogren's Syndrome/microbiology
*Skin/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Female
Middle Aged
Male
*Bacteria/classification/genetics/isolation & purification
Adult
DNA, Bacterial/genetics
Aged
Biodiversity
Case-Control Studies
Sequence Analysis, DNA
Skin Microbiome

@article {pmid41673994,
year = {2026},
author = {Lin, C and Wang, J and Chai, S and Yan, Y and Cao, D and Guo, Y and Xu, M and Zhang, Y and Yuan, Z and Shi, Y and Liu, GR and Luo, LJ and Deng, S and Zhao, Y and Zhang, XH and Kang, X and Wei, J and Zhang, Z and Yang, J and Liu, SL and Liu, H},
title = {Enterolactone and THBS1-3TSR synergistically inhibit ovarian cancer and suppress angiogenesis in the tumour microenvironment.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70327},
pmid = {41673994},
issn = {1476-5381},
support = {CYCX24017//Heilongjiang CHUNYAN Innovation Team Program/ ; 82104217//National Natural Science Foundation of China/ ; 82020108022//National Natural Science Foundation of China/ ; LH2024H028//Heilongjiang Provincial Natural Science Foundation/ ; YJSCX2025-18HYD//Postgraduate Research & Practice Innovation Program of Harbin Medical University/ ; 2018M630380//China Postdoctoral Science Foundation/ ; LBH-Q21139//Heilongjiang Postdoctoral Financial Assistance/ ; LBH-Z18198//Heilongjiang Postdoctoral Financial Assistance/ ; 2019QD0026//Merit-based Funding for Returned Oversea Students in Heilongjiang Province/ ; 2019-YQ-08//Harbin Medical University Excellent Young Talents Funding/ ; 6101020101//Special Fund of Harbin Medical University/ ; XSTS2025164//Academic Enhancement Support Program of Hainan Medical University/ ; },
abstract = {BACKGROUND AND PURPOSE: Ovarian cancer is a highly malignant disease with poor prognosis due to its insidious occurrence, early metastasis and high rate of recurrence after treatment. Enterolactone (ENL) has previously been reported to inhibit ovarian cancer in positive correlation with THBS1 expression, but the involved molecular events remain unknown. In this study, we looked into interactions between ENL and THBS1 to elucidate the mechanisms underlining their joint inhibitory effects on ovarian cancer.

EXPERIMENTAL APPROACH: We observed the suppressive effect of ENL on ovarian cancer cells by cell counting kit-8, wound healing, transwell, western blot and immunohistochemistry assays. The binding of ENL to THSB1 was assessed by molecular docking and microscale thermophoresis assays. Inhibition of malignant angiogenesis by ENL was inspected by tube formation assay and zebrafish experiment. The in vivo anticancer abilities of ENL were investigated by xenograft and allograft ovarian cancer animal models, and the fecal microbiota was analysed by metagenomics.

KEY RESULTS: This study demonstrated potent inhibitory effects of ENL on ovarian cancer by both in vitro and in vivo experiments. Analysis of 61 clinical samples showed a correlation between poor prognosis and low THBS1 expression. ENL affected the expression of THBS1 and other proteins such as CD36. ENL through binding with the 3TSR domain of THBS1 inhibited malignant angiogenesis and suppressed cancer progression. ENL administration could also ameliorate gut dysbacteriosis.

CONCLUSIONS AND IMPLICATIONS: ENL has potent inhibitory effects on ovarian cancer and suppresses malignant angiogenesis by binding to THBS1-3TSR. ENL ameliorates gut dysbacteriosis.},
}

@article {pmid41673851,
year = {2026},
author = {Zhu, Z and Kang, J and Song, M and Liu, Y and Dong, H and Wang, L and Fu, M and Ma, C and Guo, Q and Liu, Q},
title = {Early diagnosis of extranodal NK/T lymphoma presenting with oral ulcer and lip swelling by metagenomics next-generation sequencing: a case report.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-07866-x},
pmid = {41673851},
issn = {1472-6831},
abstract = {BACKGROUND: Extranodal natural killer/T-cell lymphoma, is a rare, aggressive lymphoma strongly associated with Epstein-Barr virus infection. Its clinical manifestations are often non-specific, and atypical presentations outside the nasal cavity, such as lip swelling or oral ulcers, can mimic benign oral conditions, leading to delayed diagnosis. Histological variability and tissue necrosis further hinder early diagnosis. Metagenomic next-generation sequencing (mNGS) has emerged as a useful adjunct for detecting pathogen-specific nucleic acids when conventional pathology is inconclusive.

CASE PRESENTATION: A 39-year-old man presented with a one-month history of recurrent upper lip swelling and a persistent labial and hard palate ulcer. Examination revealed firm swelling of the upper lip, a U-shaped ulcer on the upper labial mucosa, and an ulcer on the right hard palate. Laboratory tests were normal. Considering the patient's recollection of a prior fish bone injury to the oral mucosa, we performed mNGS on biopsy tissue in addition to routine histopathology. mNGS revealed a high load of Epstein-Barr virus DNA, prompting targeted immunohistochemistry and in situ hybridization, which confirmed the presence of Epstein-Barr virus-encoded RNA in atypical lymphocytes, establishing the diagnosis of extranodal NK/T-cell lymphoma. PET/CT showed a hypermetabolic upper-lip mass without systemic spread. The patient was classified as Ann Arbor stage IE, group A. Treatment with two cycles of pegaspargase, gemcitabine, and oxaliplatin resulted in complete healing of oral lesions, followed by localized radiotherapy. No recurrence was observed at the eight-month follow-up.

CONCLUSIONS: This case illustrates that extranodal NK/T-cell lymphoma can present with isolated oral lesions, posing significant diagnostic challenges. Incorporating mNGS into the evaluation of suspicious or infection-like oral lesions expedite Epstein-Barr virus detection, guide targeted pathological workup, and reduce diagnostic delays, ultimately improving patient outcomes.},
}

@article {pmid41673713,
year = {2026},
author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ},
title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {65},
pmid = {41673713},
issn = {2049-2618},
support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Biofilms/growth & development ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Droughts ; *Microbiota ; *Rivers/microbiology ; Metagenomics/methods ; Metagenome ; Switzerland ; Diatoms/genetics ; Viruses/classification/genetics/isolation & purification ; Cyanobacteria/genetics/classification ; },
abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.

RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.

CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.},
}

*Biofilms/growth & development
*Bacteria/classification/genetics/isolation & purification/metabolism
*Droughts
*Microbiota
*Rivers/microbiology
Metagenomics/methods
Metagenome
Switzerland
Diatoms/genetics
Viruses/classification/genetics/isolation & purification
Cyanobacteria/genetics/classification

@article {pmid41673414,
year = {2026},
author = {Salokas, J and Sofieva-Rios, S and Paatero, J and Asmi, E and Karppinen, A and Sofiev, M},
title = {Evaluation of commercial kits and purification approaches for DNA extraction from atmospheric samples for 3rd generation sequencing without amplification.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38534-3},
pmid = {41673414},
issn = {2045-2322},
support = {101086109//HORIZON EUROPE Research Infrastructures/ ; 101086109//HORIZON EUROPE Research Infrastructures/ ; 479507//Research Council of Finland/ ; 479507//Research Council of Finland/ ; 337552//Research Council of Finland/ ; 318194//Research Council of Finland/ ; },
abstract = {We present a DNA extraction protocol for atmospheric bioaerosol samples collected on glass-fiber filters widely used in air quality monitoring. The protocol produces high-quality molecules suitable for third-generation sequencing and other applications. The initial protocol was developed and applied in a Bioaerosol campaign performed in Finland and Lithuania in 2021 using low-volume air samplers, which posed stringent requirements to the method sensitivity. The protocol included a phenol-chloroform step for DNA purification, thus involving aggressive reagents; it was also quite time consuming and laborious. The present study advances this protocol to exclude the use of hazardous chemicals by using the SPRI paramagnetic bead technology for DNA purification and compares it to several commercial extraction methods. Despite trailing in efficiency to the initial method, the new development proved to be more efficient than several column-based commercial kits. The updated protocol was effective for a relatively high mass ratio of biological material to filter material: 70 nanograms of potential DNA on the filter to one milligram of filter fiber, as detected with the initial phenol-chloroform-based method. However, the new approach was not effective for a mass ratio lower than 15 nanograms of potential DNA per milligram of the filter material. The applicability of the new protocol for preparation of samples for the 3rd generation sequencing was confirmed by subsequent processing of the samples with the Oxford Nanopore (ONT) GridION sequencer.},
}

@article {pmid41673333,
year = {2026},
author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z},
title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02705-6},
pmid = {41673333},
issn = {1432-184X},
support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; },
abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.},
}

@article {pmid41673107,
year = {2026},
author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG},
title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39378-7},
pmid = {41673107},
issn = {2045-2322},
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.},
}

@article {pmid41673004,
year = {2026},
author = {Niu, M and Fu, L and Yan, Q and He, Z and Li, D and Zhen, Y and Wang, M and Li, C},
title = {35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06812-4},
pmid = {41673004},
issn = {2052-4463},
abstract = {The hadal trench is the deepest part of the global ocean and harbors highly abundant microbial cells. However, the diversity and function of the majority of microbial communities in this part of the ocean are still unclear. Here, we collected 35 metagenomes from three push cores across different sites in both the northern and southern Yap trench to construct a comprehensive gene and genome dataset. A total of 32 million non-redundant genes were predicted from the whole metagenome datasets, with 63% assigned to known functional groups based on currently available databases. A total of 404 metagenome-assembled genomes (MAGs) with completeness >50% and contamination <10% were retrieved, and their taxonomy was highly diverse across 26 phyla. Alpha- and Gammaproteobacteria, Phycisphaerae, Nitrospiria, and Dehalococcoidia were dominant classes across all samples. The nonredundant gene and MAG datasets are valuable resources for advancing our understanding of the diversity, composition, and functions of microbiota in the sediment of the hadal trench.},
}

@article {pmid41672513,
year = {2026},
author = {Nishijima, S and Hattori, M and Nagata, N},
title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {102},
number = {2},
pages = {82-103},
doi = {10.2183/pjab.102.006},
pmid = {41672513},
issn = {1349-2896},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Japan ; *Health ; *Disease ; East Asian People ; },
abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.},
}

Humans
*Gastrointestinal Microbiome/genetics
Japan
*Health
*Disease
East Asian People

@article {pmid41672407,
year = {2026},
author = {Furst, AJ and Johnson, KE and Nagel, EM and Yerabandi, N and Kats, AM and Gallagher, TT and Gale, CA and Palmsten, K and Pierce, S and Hoffman, S and Jacobs, K and Fields, DA and Isganaitis, EM and Bode, L and Demerath, EW},
title = {Gestational diabetes, human milk oligosaccharide (HMO) concentrations, and their links to infant weight gain and the gut microbiome in a United States observational cohort.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101235},
doi = {10.1016/j.ajcnut.2026.101235},
pmid = {41672407},
issn = {1938-3207},
abstract = {BACKGROUND: Gestational Diabetes Mellitus (GDM) increases offspring obesity risk, but whether this occurs via changes in human milk composition, including alterations in human milk oligosaccharides (HMOs), is unknown.

OBJECTIVE: To identify differences in HMO concentrations in mothers with and without GDM and test whether GDM-associated HMOs are associated with infant growth, body composition, and fecal microbiome characteristics over the first 6-months of life.

METHODS: Human milk was collected at 1- month postpartum from 337 females (49 with GDM) who fed their infants breastmilk exclusively. HMOs were quantified by high performance liquid chromatography and multivariate regression models were used to test differences in HMO concentrations by GDM status (false discovery rate adjustment for multiple testing set at q<0.05). HMOs associated with GDM were then tested for associations with infant growth, body composition, and 1 and 6-months infant fecal microbial abundances measured by metagenomic whole-genome sequencing.

RESULTS: Participants with GDM had approximately 1 standard deviation higher milk 6'SL (β (95% Confidence interval): 0.58 (0.20, 0.96)) and LNFP III (0.55 (0.16, 0.94) compared to those without GDM and 6'SL concentration was also positively associated with weight and length gain. While infants of mothers with GDM had lower 1-month fecal alpha-diversity and altered abundances of 6/56 microbial species detected compared to those without GDM, microbial features were not associated with the concentration of either 6'SL or LNFP III and evidence for mediation of GDM-growth and GDM-microbiome by HMOs was not found.

CONCLUSIONS: Mothers with a GDM diagnosis had higher milk concentrations of LNFP III and 6'SL, and 6'SL was in turn associated with increased infant growth rate, but neither HMO was associated with differential infant gut microbial abundances. The results suggest that the link between 6'SL and faster infant growth, if causal, occurs via mechanisms independent of the infant gut microbiome.

CLINICAL TRIALS REGISTRATION: The study is registered with ClinicalTrials.gov under NCT03301753.},
}

@article {pmid41672331,
year = {2026},
author = {Yu, J and Allela, OQB and Alkhazali, WH and Bishoyi, AK and Oweis, R and Varma, P and Kashyap, A and Panigrahi, R and Chauhan, AS and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M},
title = {The Gut Microbiome as a Modulator of Antibiotic Resistance: Mechanisms, Dynamics, and Therapeutic Interventions.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108357},
doi = {10.1016/j.micpath.2026.108357},
pmid = {41672331},
issn = {1096-1208},
abstract = {The gut microbiome is increasingly recognized as a critical factor in the dynamics of antibiotic resistance, influencing the acquisition, persistence, and dissemination of antibiotic resistance genes (ARGs) among both commensal and pathogenic bacteria. This research focuses on elucidating the mechanisms by which the gut microbiome modulates the horizontal gene transfer (HGT) of ARGs, a key driver of the global antibiotic resistance crisis. By employing advanced metagenomic sequencing and functional assays, this study aims to identify specific microbial species, genetic elements, and metabolic pathways that either facilitate or inhibit the transfer of ARGs within the gut environment. Particular attention is given to the role of microbial metabolites, interspecies interactions, and environmental factors that shape the resistome the collection of all resistance genes within the microbiome. Additionally, this research explores innovative microbiome-based interventions, such as the use of probiotics, prebiotics, and bacteriophage therapy, to disrupt the transmission of ARGs and restore microbial balance. These interventions are designed to target the gut microbiome as a reservoir of resistance genes, offering a novel approach to curbing the spread of antibiotic resistance. The significance of this work lies in its potential to provide actionable insights into microbiome-mediated resistance mechanisms and to develop targeted strategies that complement traditional antibiotic therapies. By addressing the gut microbiome as a modifiable factor in the resistance landscape, this research could contribute to mitigating the global burden of antibiotic resistance, preserving the efficacy of existing treatments, and improving public health outcomes in the face of this pressing challenge.},
}

@article {pmid41672322,
year = {2026},
author = {Gu, JJ and Mao, BD and Dou, XX and Zhang, BX and Xu, JW and Fu, CW and Lan, BJ and Zhang, XJ and Xu, Z and Gao, F},
title = {Unveiling the mechanisms of mechanical stirring for enhanced performance and stability of algal-bacterial flocs treating low C/N synthetic wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134175},
doi = {10.1016/j.biortech.2026.134175},
pmid = {41672322},
issn = {1873-2976},
abstract = {Algal-bacterial symbiotic systems (ABS) represent an environmentally sustainable wastewater treatment technology with significant application potential, though achieving stable and efficient operation remains a critical research challenge. This 180-day comparative study systematically investigated the performance differences and underlying mechanisms between mechanically stirred and aerated algal-bacterial symbiotic flocs (ABF) cultured in low C/N ratio wastewater. The results demonstrate that mechanical stirring enhances symbiotic interactions between microalgae and bacteria, leading to significantly improved performance metrics including higher biomass concentration (3.5 g/L), elevated dissolved oxygen levels (10.3 mg/L), increased lipid content (58.4%) and lipid productivity (9.3 mg/L/d), along with superior settling characteristics as evidenced by the reduced sludge volume index (80.7 mL/g). During Phase Ⅳ, the stirred ABFs exhibited exceptional contaminant removal efficiencies, achieving 98.2% ammonium nitrogen, 83.2% total nitrogen, and 89.7% chemical oxygen demand removal. Extracellular polymeric substance (EPS) analysis revealed stimulated secretion under stirring conditions (222.3 mg/g), with tight-bound EPS (TB-EPS) predominating, significantly enhancing floc structural stability. Metagenomic analysis demonstrated that stirring enriched functional genera like Thauera and Rubrivivax, strengthening denitrification and organic degradation capacities, while activating key pathways such as the TCA cycle and nitrogen metabolism, upregulating the abundance of EPS synthesis-related genes (e.g., galU), elucidating the molecular mechanisms underlying efficient nutrient removal and floc stability. This study presents an optimized strategy for establishing high-performance ABS in low C/N ratio wastewater treatment, offering both environmental sustainability and economic viability.},
}

@article {pmid41672314,
year = {2026},
author = {Gao, C and Sui, Q and Tang, Q and Zhang, J and Yan, B and Yu, D and Zuo, F and Gui, S and Liu, Z and Hu, X and Wei, Y},
title = {Integration of real-time NH4[+]-N control and spatial microbial engineering achieves high removals of nitrogen and carbon in a sequence anoxic-oxic-anoxic (SAOA) system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134189},
doi = {10.1016/j.biortech.2026.134189},
pmid = {41672314},
issn = {1873-2976},
abstract = {The imbalance among nitrite supply, nitrate accumulation and aeration demand poses significant challenges in single-stage partial nitrification-anammox (PN/A) systems for stably treating high-strength anaerobically digested swine wastewater (ADSW) at low C/N ratio. Here, we propose a novel process that integrates real-time NH4[+]-N control with a floc-granule partitioned biomass architecture in a sequence anoxic-oxic-anoxic (SAOA) system to dynamically modulate free ammonia (FA) concentration while preventing free nitrous acid (FNA) inhibition. By maintaining an NH4[+]-N endpoint of 50 mg/L, FA was stabilized at 5.2 mg N/L, and FNA was effectively suppressed. Thus, the SAOA system achieved 94.14% TN removal at a loading rate of 0.24 kg N/(m[3]·d) and 92.71% COD at low influent COD/TN ratio of 1.71, respectively. Metagenomic and enzymatic profiling revealed a distinct ecological stratification: floccular biomass was enriched with Candidatus Kuenenia, whereas granular microenvironments favored ammonia-oxidizing bacteria (AOB), accompanied by the upregulation of key nitrification and anammox genes. Kinetic analysis of COD and NH4[+]-N removals revealed a stage-specific metabolic transition from carbon-driven to autotrophic nitrogen-dominated removal. This study provides mechanistically robust and scalable control paradigm for advancing simultaneous, high-efficiency nitrogen and carbon removal from nitrogen-rich and carbon-limited wastewater.},
}

@article {pmid41672081,
year = {2026},
author = {Miller, KJ and Wolff, IM and Montes de Oca Valeriano, LA and Soto-Giron, MJ and Jangi, S and Schott, EM and Charbonneau, MR and Ballok, AE and Toledo, GV},
title = {Targeted detection of microbes in synbiotic medical foods SBD111 and SBD121 to evaluate gut persistence: a randomised, open label trial.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-13},
doi = {10.1163/18762891-bja00109},
pmid = {41672081},
issn = {1876-2891},
abstract = {The viability and persistence of orally administered microbes in the human gut are essential to their biological function. We previously described the development of two synbiotic medical foods, SBD111 and SBD121, each comprising four food-derived microbial strains and prebiotic fibres for the dietary management of postmenopausal bone loss and rheumatoid arthritis, respectively. Here, we report a randomised, open-label clinical study examining gut persistence of SBD111 and SBD121 microbes by testing faecal samples from healthy adults following administration for seven days. Thirty-eight participants, aged 18-64 years with a body mass index (BMI) of 18.5-35 kg/m2, were randomised to receive one of the two synbiotic medical foods daily for one week, followed by a four-week monitoring period. Employing quantitative PCR (qPCR), shotgun metagenomics, and culture-based assays, we evaluated the presence and viability of the microbial strains comprising each synbiotic medical food during and after administration. SBD111 and SBD121 were well-tolerated with minimal adverse events reported. Strains were detected in over 80% of participants during the administration period, with strain abundance peaking in the first week. Persistence in the follow-up period varied by strain and detection method. The microbial strains were detected by qPCR and metagenomic sequencing for a median of seven days and three days during the follow-up period, respectively. However, Bacillus amyloliquefaciens was consistently detected for seven days by both methods. Culture-based assays confirmed the presence of viable strains from both synbiotic medical foods in stool samples up to one-week post-consumption. Faecal metagenome diversity and metabolic functional potential remained stable throughout the administration and follow-up periods. Collectively, these results establish that SBD111 and SBD121 deliver viable microbes that transiently persist in the gut, reinforcing their promise for safe and targeted dietary interventions and highlighting the value of multi-platform detection strategies for comprehensive microbial persistence assessment. This trial, funded by Sōlarea biō, is registered at ClinicalTrials.gov (NCT06614166).},
}

@article {pmid41671969,
year = {2026},
author = {Fan, B and Peng, H and Ran, J and Yao, H and Luo, W and Hong, B},
title = {Environmental and microbial regulation of multi-temporal scale methane flux dynamics in a shallow karst lake.},
journal = {Water research},
volume = {294},
number = {},
pages = {125511},
doi = {10.1016/j.watres.2026.125511},
pmid = {41671969},
issn = {1879-2448},
abstract = {Lakes are increasingly recognized as hotspots for methane (CH4) emissions, yet high-frequency (hourly-scale) measurements of CH4 fluxes throughout all seasons and a clear understanding of their underlying environmental control mechanisms are still lacking. Here, we explore the dynamics of CH4 flux and its hydrological and biogeochemical mechanisms in a karst shallow lake ecosystem, based on eddy covariance (EC), stable carbon isotope, and metagenomic sequencing techniques. Our 13-month EC monitoring shows that the lake was a CH4 source to the atmosphere, with average emission rate being 2.07 ± 1.20 mmol CH4 m[-2] d[-1], with the highest emissions in autumn (3.63 ± 0.5 mmol m[-2] d[-1]), accounting for more than twice those of winter. Seasonal CH4 flux variations were primarily driven by water temperature, water level, and electrical conductivity. Elevated temperature stimulated methanogenesis, water level changes altered redox gradients shaping methanogen activity, and electrical conductivity regulated substrate availability favoring acetoclastic methanogens. At the diurnal scale, CH4 emissions were higher at night than during the day, with diel flux variations were mainly controlled by water temperature, which enhanced methanogenesis while suppressing oxidation. These environmental controls on CH4 flux are consistent with the structure of the methanogenic community and support the dominance of acetoclastic methanogenesis. Methanothrix was found to be the dominant (∼65%) methanogenic microbe in this carbonate-rich alkaline karst lake. Additionally, the dominant pathway of CH4 production in the lake was acetoclastic methanogenesis, with the apparent fractionation factor of δ[13]C-CH4 being 1.041 ± 0.002. We emphasize the importance of integrating physicochemical variability with microbial functional potential to advance understanding of biogeochemical feedbacks in carbonate-rich karst systems and improve the accuracy of CH4 emission estimates across scales.},
}

@article {pmid41671965,
year = {2026},
author = {Niu, L and Pan, Y and Li, Y and Chen, X and Liu, X and Chen, Y and Wang, L and Zhang, W},
title = {WWTP effluents influence prokaryotic viral diversity and interaction with hosts: Regulating the virus-mediated nitrogen-cycling processes in river sediments.},
journal = {Water research},
volume = {294},
number = {},
pages = {125519},
doi = {10.1016/j.watres.2026.125519},
pmid = {41671965},
issn = {1879-2448},
abstract = {As an important water replenishment measure for urban rivers, the input of wastewater treatment plant (WWTP) effluents can change both the nutrient loading and the microbial community diversity of receiving rivers. However, our knowledge of the characteristics of viral communities and virus-mediated nitrogen-cycling processes in WWTP effluents-receiving rivers remains very limited. In this study, the prokaryotic virus, host and non-host communities in sediments were detected via metagenome and virome methods, to explore the variation characteristics of viral communities, interactions with hosts and virus-mediated nitrogen-cycling processes along the upper reference reach (UR), middle receiving reach (MR) and lower recovery reach (LR) of a typical WWTP effluents-receiving river. The results showed that compared to the non-hosts, viruses and hosts were much more sensitive to the influence of WWTP effluents. Among the three reaches, viruses and hosts showed more obvious spatial variability in community diversity and structures than those of non-hosts. Compared to UR, viruses in MR displayed the highest community diversity and virus-to-host abundance ratio, while viruses in LR maintained the high abundance ratio. Co-occurrence network analysis indicated the more important central roles of viruses than those of prokaryotes in bridging species or groups within the virus-host-prokaryote communities, especially in MR and LR. Functional gene analyses revealed that viral communities might potentially regulate nitrogen cycles in MR and LR via two pathways: directly carrying more abundant nitrogen-related auxiliary metabolic genes (N-vAMGs) and indirectly regulating hosts involved in nitrogen transformations (N-hosts) via enriched viruses, which showed strong responses to nitrogen loadings (TN and NO3[-]-N) in rivers. Both N-vAMGs and virus-enrichment N-hosts, dominantly involved in denitrification, dissimilatory nitrate reduction to ammonium, and organic degradation and synthesis processes, significantly increased in MR and LR, which highlighted a long-term regulation potential of viral communities to WWTP effluents-receiving rivers. Together, these findings provided a new insight into the nonnegligible ecological role of viruses in influencing biogeochemical cycles in WWTP effluents-receiving urban rivers.},
}

@article {pmid41671964,
year = {2026},
author = {Zhao, G and Chen, W and Zhang, W and Zhang, R and Huang, X},
title = {Unveiling the environmental fate and risks of non-heterocyclic sulfacetamide: From a novel degradation mechanism to microecological effects.},
journal = {Water research},
volume = {294},
number = {},
pages = {125520},
doi = {10.1016/j.watres.2026.125520},
pmid = {41671964},
issn = {1879-2448},
abstract = {The presence of sulfonamides (SAs) in the environment has been demonstrated to be a significant factor in pollution. Despite extensive research on heterocyclic SAs, the degradation mechanisms and ecological effects of non-heterocyclic sulfacetamide (SA) remain poorly understood. Our previous study isolated a challenging-to-culture strain, Leucobacter sp. HA-1, known for its SAs-degrading capacity, contains the conserved gene sadA. However, SA was not detected within the degradation spectrum linked to monooxygenase SadA activity. This indicates that other genes may be involved in SA degradation in strain HA-1. In this study, two adjacent and functionally similar amidohydrolases, SamA1 and SamA2, were identified from strain HA-1 as initiators of SA degradation to sulfanilamide (SN). The amino acid sequence similarities of SamA1 and SamA2 with reported enzymes were 39.44% and 34.54%, respectively. The combined expression of SamA1 and SmaA2 had a synergistic effect in enhancing the degradation and resistance of SA. The molecular mechanism behind strain HA-1's SA degradation was elucidated through microscopic analysis combining enzyme characterization with toxicological assessments and comparative genomics. An artificial bioremediation microecosystem targeting SA was established, notably, adding HA-1 enhanced bioaugmentation efficacy for SA elimination significantly. Metagenomic analyses revealed dynamic changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and potential functional enzymes related to SA biodegradation within these microecosystems. Under our experimental conditions, bioaugmentation with HA-1 showed potential as a strategy for SA removal and reduced the accumulation or spread risk of ARGs and MGEs. This study revealed the fate mechanisms and microecological effects of non-heterocyclic sulfacetamide SA, which are different from typical SAs, and contributes to the further promotion of the elimination of the negative environmental and ecological impacts of antibiotics.},
}

@article {pmid41671957,
year = {2026},
author = {Wu, J and He, C and Wu, K and Feng, W and Yang, Y and Zhou, Q and Mao, P and Xiao, X},
title = {Silver sulfide nanoparticles amplify earthworm gut denitrification and elevate N2O emissions in subtropical forest soils under nitrogen deposition.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119853},
doi = {10.1016/j.ecoenv.2026.119853},
pmid = {41671957},
issn = {1090-2414},
abstract = {Silver sulfide nanoparticles (Ag2S-NPs), commonly introduced into forest soils via sewage sludge, may disrupt nitrogen (N) cycling under elevated N deposition. This study examined how Ag2S-NPs and earthworms (Eisenia fetida) interact to influence N2O emissions in subtropical forest soils subjected to long-term simulated N deposition. A 60-day incubation was conducted using soils treated with low (1 mg Ag kg[-1]) and high (30 mg Ag kg[-1]) Ag2S-NP doses. Nitrogen deposition alone suppressed N2O emissions by acidifying soil and inhibiting nitrification. In contrast, earthworm activity enhanced emissions by stimulating organic matter turnover and N-cycling gene expression. Under N deposition, Ag2S-NPs significantly increased N2O emissions in a dose-dependent manner, with the high dose raising emissions by 68 % compared to earthworm-only treatments. Metagenomic analysis revealed that this effect was driven by increased gut-associated denitrification, with notable enrichment of narG/H/I and nirK/S genes, and denitrifiers such as Microbacterium and Bacillus. Conversely, soil nitrification declined, as reflected by reduced NO3[-] levels and amoA gene abundance. Multivariate models identified gut denitrification genes as key predictors of N2O flux. These findings highlight the synergistic impact of Ag2S-NPs and earthworms on greenhouse gas emissions in N-deposited soils and underscore the importance of considering nanomaterial-fauna-microbe interactions in forest ecosystems.},
}

@article {pmid41671864,
year = {2026},
author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H},
title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141429},
doi = {10.1016/j.jhazmat.2026.141429},
pmid = {41671864},
issn = {1873-3336},
abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.},
}

@article {pmid41671813,
year = {2026},
author = {Wang, N and Jin, M and Zhu, Z and Wang, Y and Li, X and Xu, J and Cheng, S and Zhu, Y and Wang, R and Xu, T and Yin, F and Li, X and Ke, Y and Yue, H},
title = {Ecological distribution and functional characterization of polyethylene-degrading enzymes from diverse metagenomes.},
journal = {The Science of the total environment},
volume = {1018},
number = {},
pages = {181486},
doi = {10.1016/j.scitotenv.2026.181486},
pmid = {41671813},
issn = {1879-1026},
abstract = {Polyethylene (PE), the most widely produced synthetic polymer, is highly resistant to degradation and poses long-term ecological risks due to its accumulation in terrestrial and aquatic ecosystems. Although biological degradation pathways have been investigated, research has primarily concentrated on heavily polluted environments, leaving the ecological distribution of PE-degrading enzymes largely unknown. In this study, we systematically screened more than 4.57 billion metagenomic sequences from diverse ecological sources-including farmland soils, Przewalski's horse gut microbiota, insect symbionts, and human oral microbiomes-for homologs of known PE-degrading enzymes. A total of 701 candidate sequences were identified using an integrated pipeline combining sequence homology, structural modeling, and molecular docking. Thirty-two representative enzymes were heterologously expressed and tested on pristine PE films and microspheres, among which 25 exhibited measurable activity, inducing surface erosion, up to ∼1.5% mass loss (w/w) of PE films over 30 days, and oxidative modifications. These degradative effects were validated by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), and stable carbon isotope (δ[13]C) analysis, collectively supporting molecular-level oxidation and early-stage carbon turnover associated with enzymatic PE degradation. Notably, PE-degrading activity was observed in microbiomes from relatively minimally disturbed environments, suggesting that microbial communities may adaptively evolve plastic-degrading capabilities in response to chronic, low-level exposure. These findings expand our understanding of plastic pollution's ecological footprint and highlight naturally occurring enzymes as promising candidates for sustainable bioremediation.},
}

@article {pmid41671795,
year = {2026},
author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B},
title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134181},
doi = {10.1016/j.biortech.2026.134181},
pmid = {41671795},
issn = {1873-2976},
abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.},
}

@article {pmid41671170,
year = {2026},
author = {Chettleburgh, C and Chiappe, C and Davidson, H and Taggar, G and Zhao, A and Habash, M and Landgraff, C and Parreira, VR and Lévesque, RC and Goodridge, L},
title = {Coffee Cartridge Filtration: A Rapid, Inexpensive, and Easy Method to Concentrate Nucleic Acids from Pathogens and Fecal Biomarkers in Wastewater.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag037},
pmid = {41671170},
issn = {1365-2672},
abstract = {AIMS: We propose coffee cartridge filtration as an alternative method for the concentration of nucleic acids from microorganisms in wastewater.

METHODS AND RESULTS: In this study, coffee cartridge filtration was directly compared with PEG precipitation through mass balance analysis. The utility of coffee cartridge filtration was further demonstrated through a 10-month longitudinal analysis of Giardia, human norovirus genogroup I and II, and hepatitis A virus in 45 wastewater samples from Guelph, Ontario, Canada. Fourteen of these wastewater samples were enriched with the Illumina Viral Surveillance Panel v2 and sequenced with the Illumina NextSeq 1000. PEG precipitation was more efficient at concentrating nucleic acids from all microorganisms and viruses, but all endogenous targets were detected following coffee cartridge filtration. Hepatitis A was detected in four wastewater samples and best correlated with four clinical cases when a one-week wastewater lead time was applied. HuNoV-GI and HuNoV-GII were detected within the RT-qPCR linear dynamic range in 44/45 samples. Nucleic acids from the Polyomaviridae, Astroviridae, and Calciviridae families were most identified in coffee cartridge-filtered wastewater samples.

CONCLUSIONS: Coffee cartridge filtration is an effective method to concentrate nucleic acids from microorganisms in wastewater in resource-limited settings.},
}

@article {pmid41671148,
year = {2026},
author = {Buczek, DJ and Kabir, W and Lindstedt, K and Mäklin, T and Thorpe, HA and Suzuki, Y and Corander, J and Samuelsen, Ø and Sundsfjord, A},
title = {Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
pmid = {41671148},
issn = {2057-5858},
mesh = {*Klebsiella pneumoniae/genetics/classification/isolation & purification ; *Computational Biology/methods ; *Metagenome ; Humans ; Whole Genome Sequencing ; Phylogeny ; Klebsiella Infections/microbiology ; Genome, Bacterial ; },
abstract = {Klebsiella pneumoniae is a major cause of human infections and is frequently associated with antimicrobial resistance (AMR). Carriage of K. pneumoniae in the gut is a major risk factor for infection and a reservoir for the spread of high-risk clonal lineages and associated AMR determinants. Accurate detection of K. pneumoniae at the subspecies level is therefore essential to better understand K. pneumoniae gut colonization ecology and clonal dissemination. We analysed two recently developed bioinformatic tools, mSWEEP and StrainGE, for sequence type (ST) detection of K. pneumoniae in culture-enriched sweep metagenomes compared to single-colony whole-genome sequencing (WGS). We show that both mSWEEP and StrainGE perform highly accurate ST detection, concordant with culture in 46/49 and 44/49 samples with WGS-detected single STs, respectively, as well as in 2/3 samples with two WGS-detected STs. Within-sample ST diversity was detected in 19 and 15 samples by mSWEEP and StrainGE, respectively, highlighting a major advantage of these tools over conventional single-colony WGS. StrainGE could also reconstruct accurate phylogenetic relationships between strains of the same ST for 2/3 different STs tested. Additionally, assembly of the genomes provides better resolution of ST detection by mSWEEP. Together, our results show that both mSWEEP and StrainGE are accurate tools for the detection and analysis of K. pneumoniae STs from mixed bacterial samples.},
}

*Klebsiella pneumoniae/genetics/classification/isolation & purification
*Computational Biology/methods
*Metagenome
Humans
Whole Genome Sequencing
Phylogeny
Klebsiella Infections/microbiology
Genome, Bacterial

@article {pmid41670507,
year = {2026},
author = {Xing, Y and Chen, M and Shen, M and Zhong, Q},
title = {A Case of Rare Facial Infection Caused by Mycobacterium scrofulaceum.},
journal = {Clinical laboratory},
volume = {72},
number = {2},
pages = {},
doi = {10.7754/Clin.Lab.2025.250549},
pmid = {41670507},
issn = {1433-6510},
mesh = {Humans ; Male ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Tomography, X-Ray Computed ; Face/microbiology ; },
abstract = {BACKGROUND: In July 2024, our hospital confirmed a rare case of facial infection with Mycobacterium scrofulaceum. The patient visited our hospital due to pain and pus discharge from the right orbital incision for one month. The patient suffered multiple facial fractures due to trauma three months ago. He underwent systemic anti infection treatment and open reduction and internal fixation surgery at an external hospital. After the surgery, there was repeated swelling around the orbit, and the patient did not fully recover. One month ago, the infraorbital area was swollen again, locally ruptured, and purulent discharge was visible. After self-flushing and dressing change, the condition improved. Recently, there has been swelling around the eye socket again. In order to seek further treatment, he came to our hospital for treatment. Outpatient diagnosis: 1. Multiple space infections in the right orbit, temporal region, and skull base; 2. Postoperative open facial bone fracture.

METHODS: CT (skull and neck), facial wound pus: bacterial culture and identification, acid fast staining, Gram staining, T-SPOT tuberculosis infection detection, identification of Mycobacterium species (DNA microarray chip method), Metagenomic Next-generation Sequencing (mNGS). Other related auxiliary examinations included blood routine, urine routine, liver function, kidney function, electrocardiogram, etc. Results: CT (skull and neck) results: 1. After multiple fractures of the maxillofacial bone and anterior skull base, there is abnormal enhancement density shadow in the right maxillofacial region, indicating infection. Clinical laboratory tests: blood routine + high-sensitivity CRP (whole blood): white blood cell count 9.66 x 109/L, total neutrophil count 6.87 x 109/L, whole blood high-sensitivity C-reactive protein 46.21 mg/L, coagulation function: fibrinogen detection 6.61 g/L, D-dimer determination 1,231.52 FEU/L, inflammatory markers: interleukin-6 15.48 pg/mL, procalcitonin 0.037 ng/ml; Liver function test: total protein 85.2 g/L, globulin 44.4 g/L, aspartate aminotransferase 12.8 U/L. Facial wound pus examination: T-SPOT tuberculosis infection test: positive, with 40 antigen stimulated pore spots. Bacterial Gram staining: A small amount of Gram positive bacilli were found. Acid fast staining: acid fast bacilli detected ++: bacterial culture + identification: growth of mycobacteria ++, identification of mycobacterial species (DNA microarray method): Mycobacterium scrofulaceum, identification of Metagenomic Next-generation Sequencing (mNGS): Mycobacterium scrofulaceum. Clinical treatment plan: Chlorpheniramine 200 mg/d, Clarithromycin 0.5 g/d; Moxifloxacin 0.4 g/d, locally applied with 3% boric acid solution wet compress to enhance local wound dressing change. After 2 months of hospitalization, the patient's orbital swelling significantly improved, no obvious purulent discharge was observed locally, and the infection indicators significantly decreased. The patient improved and was discharged from the hospital.

CONCLUSIONS: This article reports a rare case of facial infection caused by Mycobacterium scrofulaceum. Mycobacterium scrofulaceum was quickly and accurately identified through mycobacterial strain identification (DNA microarray chip method) and mNGS. Reasonable treatment measures were adopted clinically, and the patient improved and was discharged. We hope that in the future, this study can provide assistance for the clinical diagnosis and treatment of Mycobacterium scrofulaceum infection.},
}

Humans
Male
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
Tomography, X-Ray Computed
Face/microbiology

@article {pmid41670415,
year = {2026},
author = {Hasegawa, T and Iwai, S and Ikeda, HO and Miyaoka, D and Sato, N and Fujimoto, K and Wei, X and Kusaka, M and Miyata, M and Numa, S and Otsuka, Y and Imoto, S and Uematsu, S and Tsujikawa, A},
title = {Increased Gut Microbiota Diversity in Patients With Retinitis Pigmentosa and Implications for Disease Phenotypes and Progression.},
journal = {Investigative ophthalmology & visual science},
volume = {67},
number = {2},
pages = {27},
doi = {10.1167/iovs.67.2.27},
pmid = {41670415},
issn = {1552-5783},
mesh = {*Gastrointestinal Microbiome/genetics/physiology ; Animals ; Humans ; *Retinitis Pigmentosa/microbiology/physiopathology ; Mice ; Female ; Male ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Disease Models, Animal ; Phenotype ; Adult ; Feces/microbiology ; Electroretinography ; Anti-Bacterial Agents/pharmacology ; Tomography, Optical Coherence ; Aged ; Mice, Inbred C57BL ; *Bacteria/genetics/isolation & purification ; },
abstract = {PURPOSE: Inflammation is often present in retinitis pigmentosa (RP) and is reported to affect visual outcome. Gut microbiota plays a crucial role in inflammatory diseases. This study aimed to elucidate the relationship between the gut microbiota and RP.

METHODS: The 16S rRNA gene sequencing analysis was performed on stool samples collected from 103 patients with RP and 64 healthy individuals. The α and β diversities of gut microbiota, along with relative abundances, were compared between patients and healthy individuals, as well as between patients with or without cystoid macular edema (CME). The RP model rd10 mice were treated with or without antibiotics starting at 7 days of age. Retinal structure and function were evaluated.

RESULTS: Gut microbiota diversity was higher in patients with RP than in healthy individuals (P < 0.001). Moreover, patients with CME had greater diversity than did those without CME and showed a higher abundance of Romboutsia and Ruminococcus (P < 0.05). Antibiotics-treated rd10 mice showed suppressed apoptosis, attenuated decrease of photoreceptors, and a significantly lower incidence of retinal detachment. Retinal function was significantly preserved in mice treated with antibiotics. In antibiotics-treated mice, the expression of Il-1β, Nlrp3, Caspase-1, pNFkb, pJNK, and pCREB1 was downregulated, suggesting suppression of the NLRP3 inflammasome.

CONCLUSIONS: Patients with RP exhibited distinct gut microbiota characteristics compared to that of healthy individuals. Treatment with antibiotics attenuated disease progression in the RP model mouse. Modifying the gut microbiota may be a potential therapeutic strategy for modifying disease progression in RP in future investigations.},
}

*Gastrointestinal Microbiome/genetics/physiology
Animals
Humans
*Retinitis Pigmentosa/microbiology/physiopathology
Mice
Female
Male
Disease Progression
RNA, Ribosomal, 16S/genetics
Middle Aged
Disease Models, Animal
Phenotype
Adult
Feces/microbiology
Electroretinography
Anti-Bacterial Agents/pharmacology
Tomography, Optical Coherence
Aged
Mice, Inbred C57BL
*Bacteria/genetics/isolation & purification

@article {pmid41670373,
year = {2026},
author = {Pham, S and Sharma, N and Sankaran, B and Nguyen, J and Estes, MK and Hyser, JM and Prasad, BVV},
title = {Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0217625},
doi = {10.1128/jvi.02176-25},
pmid = {41670373},
issn = {1098-5514},
abstract = {Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.IMPORTANCEHuman noroviruses (HuNoVs) are a significant cause of sporadic and epidemic gastroenteritis worldwide. There are no vaccines or antiviral drugs currently available to treat infections. Our work here demonstrates the potential of the Tulane virus cell culture system as a surrogate for screening small-molecule inhibitors of the human norovirus proteases.},
}

@article {pmid41675709,
year = {2025},
author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y},
title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e51},
pmid = {41675709},
issn = {2996-9514},
abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.},
}

@article {pmid41676130,
year = {2024},
author = {Yousuf, S and Luo, H and Zeng, M and Chen, L and Ma, T and Li, X and Zheng, M and Zhou, X and Chen, L and Xi, J and Lu, H and Cao, H and Ma, X and Bian, B and Zhang, P and Wu, J and Gan, R and Jia, B and Sun, L and Ju, Z and Gao, Y and Malik, WA and Ma, C and Lyu, H and Li, Y and Hou, H and Zhou, Y and Bai, D and Wang, Y and Yang, H and Xun, J and Du, S and Zhang, T and Wan, X and Peng, K and Xu, S and Wen, T and Chen, T and Liu, YX},
title = {Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e42},
pmid = {41676130},
issn = {2996-9514},
abstract = {The advent of next-generation sequencing has revolutionized microbiome research, enabling in-depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high-throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user-friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon).},
}

@article {pmid41676120,
year = {2024},
author = {Ling, Y and Liu, Z and Han, S and Wu, H and Mu, C and Zhu, W},
title = {Integrated omics revealed the altered colonic microenvironment after inhibition of peripheral serotonin synthesis by LP533401.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e34},
pmid = {41676120},
issn = {2996-9514},
abstract = {Gut-derived 5-hydroxytryptamine (5-HT), known as serotonin, plays a crucial role in regulating gastrointestinal functions. However, the impact of disruptions in gut-derived 5-HT synthesis on the early gut microbiome and intestinal microenvironment remains unclear. In this study, LP533401, an inhibitor targeting peripheral 5-HT synthesis, was administered orally to neonatal rats starting at 4 days post-birth. By day 11, inhibition of gut-derived 5-HT resulted in altered colonic morphology, characterized by increased crypt depth and reduced myenteric thickness. To investigate the mechanisms underlying these alterations, we employed a combination of metagenomics, mucosal transcriptome, and untargeted metabolomics on colonic samples. Metagenome profiling revealed an upregulation in the microbial two-component system (ko02020) and tyrosine metabolism (ko00350), with minimal effects on taxa abundances. Transcriptome profiling analysis indicated the discriminant expression of genes enriched in pathogen infection-responsive signaling (e.g., Salmonella and Yersinia infection) and the Wnt signaling pathway that affected stem cell proliferation. Consistent with increased crypt depth, marker genes related to cell proliferation were excessively activated. Metabolomics analysis indicated lower ascorbate level and higher succinic acid level, correlating with 5-HT concentrations and increased crypt depth. Additionally, altered metabolic pathways (e.g., nucleotide metabolism, signal transduction, metabolism of cofactors and vitamins) suggested an impact on the colonic function. In summary, early inhibition of gut-derived 5-HT may unfavorably reshape the colonic microenvironment, affecting gut morphology, microbial function, stem cell proliferation, and mucosal metabolism.},
}

@article {pmid41676124,
year = {2024},
author = {Xie, Y and Xu, S and Xi, Y and Li, Z and Zuo, E and Xing, K and Bai, L and Li, K},
title = {Global meta-analysis reveals the drivers of gut microbiome variation across vertebrates.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e35},
pmid = {41676124},
issn = {2996-9514},
abstract = {Shifts in gut microbial diversity and structure are one route by which vertebrate hosts adapt to local environmental conditions. However, recent studies have mostly been limited to a single species, small sample sizes, or restricted geographic ranges. Therefore, drawing a global picture of vertebrate gut microbiome diversity, community structure, and determinants for their adaptive shifts remains to be elucidated. We here collected 6508 samples from 113 vertebrate species covering diverse classes, feeding behaviors, and host habitats based on 16S rRNA gene sequencing. The results showed that host diet pattern had a significant impact on gut microbiome variation, which might drive taxonomic and functional contents of gut microbiome across vertebrates. Of note, the phylum Fusobacteria were enriched in carnivorous vertebrate gut while herbivorous vertebrate gut selectively increased the abundance of Verrucomicrobia. Also, climate factors were strongly associated with gut microbiome variation across vertebrates. Interestingly, we found that the abundance of microbiota belonging to Bacteroidetes increased gradually while the members from Proteobacteria showed a decreasing trend from high- to low-latitude zones, potentially contributing to vertebrate adaptation to local climate condition. Additionally, we comprehensively deciphered the common antibiotic resistomes and their potential mobility between terrestrial vertebrate gut microbiome (n = 487) and their sympatric soil biological environment samples (n = 203) by integrating metagenomic sequencing datasets. Particularly, potential horizontal antibiotic resistance genes (e.g., bacA) transfers were detected between vertebrates gut microbiome and their sympatric soil biological environment. Together, our findings provide new evidence of how external environmental factors affect vertebrate gut microbiome variation.},
}

@article {pmid41676117,
year = {2024},
author = {Shi, P and Xu, S and Yang, Z and Wang, L and Wu, Y and Li, Y and Zhu, Z},
title = {Harnessing gut microbiota for longevity: Insights into mechanisms and genetic manipulation.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e36},
pmid = {41676117},
issn = {2996-9514},
abstract = {The gut microbiota is pivotal in maintaining health, with most microorganisms being beneficial, except for a few pathogens. Emerging evidence suggests a link between the gut microbiome and aging, hinting at its potential role in longevity. However, understanding the relationship is challenging due to the microbiota's complexity. This perspective summarizes the mechanisms by which gut microbes regulate host lifespan and explores genetic manipulation strategies to promote healthy aging in the elderly.},
}

@article {pmid41676115,
year = {2024},
author = {Zhou, Y and Zheng, J and Song, W and Yan, X and Du, L and Ma, Z and Fu, Y and Ouyang, Z and Xiao, Y and Liu, Z and Tian, F and Wong, JWH and Shih, JHD and Liang, S and Tian, H and Liu, L and Wei, K and Zhang, C and Li, J and Wang, X},
title = {OUTPOST: A comprehensive analysis software for whole-metagenome shotgun sequencing incorporating group stratification.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e29},
pmid = {41676115},
issn = {2996-9514},
abstract = {The whole metagenOme shotgun seqUencing sTream Pipeline that is cOmprehensive and uSeful for mulTi groups experiments (OUTPOST) is a comprehensive analysis software for whole-metagenome shotgun sequencing incorporating group stratification, which encompasses 14 modules and boasts over 50 functions, distinguishing itself for its comprehensiveness when compared with 17 existing whole-metagenome shotgun sequencing (WMGS) tools. OUTPOST introduces innovative methods for multi-group experimental designs and meta-analysis-based biomarker identification.},
}

@article {pmid41676125,
year = {2024},
author = {Xia, JJ and Zhong, Q and Li, ZM and Wei, QZ and Jiang, LY and Duan, C and Jia, HJ and Tan, YM and Han, LY and Krutmann, J and Wang, J and Liu, X},
title = {Culture dependent and independent approaches reveal the role of specific bacteria in human skin aging.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e26},
pmid = {41676125},
issn = {2996-9514},
abstract = {Skin aging is a dynamic process involving a spectrum of phenotypic changes, making it an attractive model for studying microbiome-phenotype interactions. Therefore, 822 facial microbial samples and 14 skin phenotypes from corresponding areas were assessed in a Chinese cohort. Porphyrins and the chronological age exhibited the most significant microbial variability. We further profiled the dynamics of the skin microbiome associated with age and aging phenotypes. Using a multiple linear regression model, we predicted premature/delayed aging-related microbial species, mainly Moraxella osloensis and Cutibacterium acnes. We also validated the biological functions of the host-microbe interactions in vitro. Moraxella osloensis isolated from healthy skin regulates collagen metabolism and extracellular matrix assembly, and promotes cell senescence in human keratinocytes and fibroblasts, making it potentially applicable in the development of antiaging interventions.},
}

@article {pmid41675545,
year = {2024},
author = {Huang, L and Luo, S and Liu, S and Jin, M and Wang, Y and Zong, X},
title = {Comparative multiomics analyses reveal the breed effect on the colonic host-microbe interactions in pig.},
journal = {iMetaOmics},
volume = {1},
number = {1},
pages = {e8},
pmid = {41675545},
issn = {2996-9514},
abstract = {Dysregulation of the gut microbiota often leads to immune-related disorders, indigestion, or diarrhea. Here, Jiaxing Black (JXB) pig, a local Chinese pig breed known for its great tolerance and digestibility of nutrients, was employed for a metagenomic and transcriptomic integrative analysis to reveal the gut microbiota-genes and gut microbiota-pathway interactions. A total of 452 differentially expressed genes, and 174 phyla were found between the JXB and the Duroc × Landrace × Yorkshire (DLY) pigs. Detailed analysis revealed that the differences in colon gene expression signatures between the JXB and DLY are mainly enriched in metabolic and inflammatory responses, with Lactobacillus and Lachnospiraceae enriched in DLY and JXB, respectively. Notably, Pacebacteria, Streptophyta, and Aerophobetes were found to participate in the PI3K-Akt mediated immune response in both pig breeds; however, they only accelerated the metabolism in the intestines of JXB pigs. Moreover, the host could regulate microbe metabolism and immune response by Ig-like domain-containing protein and ITIH2, PAEP, and TDRD9, respectively. Taken together, our results revealed both common and breed-specific regulations of host genes by gut microbiota in two pig breeds.},
}

@article {pmid41670185,
year = {2026},
author = {Sampara, P and Tomatsu, A and Malmstrom, RR and Ziels, RM},
title = {Quantitative DNA Stable Isotope Probing Identifies Active Microorganisms Assimilating Volatile Fatty Acids in Full-Scale Enhanced Biological Phosphorus Removal Processes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c14266},
pmid = {41670185},
issn = {1520-5851},
abstract = {Enhanced biological phosphorus removal (EBPR) systems often rely on exogenous carbon sources, such as volatile fatty acids (VFAs), to achieve higher P removal. Here, we employed DNA quantitative stable isotope probing (qSIP) using two VFAs, acetate and propionate, in cyclic anaerobic/aerobic incubations to assess their effects on P cycling and microbial activity with biomass from two full-scale EBPR water resource-recovery facilities that utilize VFA addition. We found that anaerobic VFA uptake preferences differed within known groups of PAOs, such as Candidatus Accumulibacter and Tetrasphaera-affiliated members (e.g., Ca. Phosphoribacter), between the two biomasses. The combination of qSIP with metagenomics identified isotopically labeled phages that were linked to active PAOs, highlighting their potential roles in modulating EBPR community composition and activity. The highest levels of anaerobic labeling from acetate were in genomes belonging to Saccharimonadales and Rickettsiales, which are generally host-associated with bacteria and eukaryotes, respectively. This finding highlights the possibility of cross-feeding between PAO hosts and their parasites or predators, as well as the role of so-far uncharacterized organisms participating in carbon cycling under EBPR conditions. Collectively, these results expand our understanding of the ecological interactions involved in communities anaerobically uptaking VFAs and cycling P that are central to EBPR.},
}

@article {pmid41669888,
year = {2026},
author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004254},
pmid = {41669888},
issn = {1473-5598},
abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.

AIM: This study assessed the association between gut microbiome and incident hypertension.

METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74  years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.

RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster, Bariatricus, CAG-317-146760, and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.

CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.},
}

@article {pmid41669552,
year = {2026},
author = {Hearne, G and S Refahi, M and Duan, HN and Brown, JR and Rosen, GL},
title = {Normalized compression distance for DNA classification.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20677},
pmid = {41669552},
issn = {2167-8359},
mesh = {Humans ; *Data Compression/methods ; Algorithms ; *Genomics/methods ; *Sequence Analysis, DNA/methods ; Open Reading Frames ; Neural Networks, Computer ; *DNA/classification/genetics ; },
abstract = {Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.},
}

Humans
*Data Compression/methods
Algorithms
*Genomics/methods
*Sequence Analysis, DNA/methods
Open Reading Frames
Neural Networks, Computer
*DNA/classification/genetics

@article {pmid41669550,
year = {2026},
author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A},
title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20648},
pmid = {41669550},
issn = {2167-8359},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Nutrients ; *Stress, Physiological ; Phylogeny ; Biodegradation, Environmental ; },
abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Araceae/microbiology
*Bacteria/genetics/classification
*Nutrients
*Stress, Physiological
Phylogeny
Biodegradation, Environmental

@article {pmid41669395,
year = {2025},
author = {Criollo Delgado, L and Zewude, D and Karzhaev, DS and Polev, DE and Potokina, EК},
title = {Identification of CtE1 gene nucleotide polymorphisms and development of SNP-based KASP markers in guar (Cyamopsis tetragonoloba (L.) Taub.).},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {25},
number = {8},
pages = {1246-1254},
doi = {10.18699/vjgb-25-134},
pmid = {41669395},
issn = {2500-0462},
abstract = {Guar (Cyamopsis tetragonoloba (L.) Taub), is an important short-day legume crop, whose cultivation is limited at high latitudes due its photoperiod sensitivity, that negatively impacts flowering and maturation of this industrial-oriented crop. In its close relative, soybean, the E1 gene has been highly associated with the regulation of flowering time under long-day conditions. In this study we investigated the natural diversity of the E1 homologue gene (CtE1) in a panel of 144 guar accessions. For this purpose, the CtE1 gene was amplified and sequenced using Illumina. As a result, five novel SNPs were identified in the 5'-untranslated region, coding region, and 3'-untranslated region of the CtE1 gene. One non-synonymous SNP was located in the coding region causing a conservative Arg→Lys substitution. Based on the identified SNP, five KASP markers linked to polymorphism in the target gene were developed and tested in the guar collection. No significant associations were detected between discovered SNPs and available data on variability in flowering time or vegetation period length in the cohort of 144 accessions. These findings suggest that natural variation of the CtE1 gene in the studied germplasm collection has minimal effect on flowering or maturation. The limited functional allelic diversity observed in the CtE1 gene of guar compared to the E1 gene in soybean likely reflects differences in their evolutionary histories, domestication bottlenecks, and selection pressures.},
}

@article {pmid41668736,
year = {2025},
author = {Wang, Q and Ding, H and Hao, Z and Liao, G},
title = {Metagenomic next-generation sequencing enhances diagnosis of fungal infections in kidney transplant recipients: a retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1667475},
pmid = {41668736},
issn = {2235-2988},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Female ; Male ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Transplant Recipients ; *Fungi/genetics/classification/isolation & purification ; Adult ; *Mycoses/diagnosis/microbiology ; Aged ; },
abstract = {BACKGROUND: Although fungal infections are relatively rare, they have low detection rates and high mortality rates. The value of metagenomic next-generation sequencing (mNGS) in kidney transplant patients with fungal infections remains insufficiently explored, especially regarding diagnosis and antimicrobial stewardship.

METHODS: From September 2021 to August 2023, 234 kidney transplant patients were enrolled, with detailed data collected on 66 patients suspected of fungal infections. The pathogen detection performance of mNGS and conventional microbiological tests (CMTs) was compared. The impacts of mNGS and CMTs on treatment adjustment were also assessed. Finally, the value of mNGS in detecting donor-derived infections was investigated.

RESULTS: Among 66 patients, 21 fungal species were identified: 18 species detected by mNGS and 10 by CMTs. The overall positive rate of mNGS was significantly higher than culture (90.67% vs. 26.67%), especially for multiple fungal infections (9vs0). mNGS identified more Candida (26vs12), Pneumocystis jirovecii (14vs0), Aspergillus (10vs4), Mucor (6vs2) organisms compared with CMTs. Donor-derived fungi were identified in 11 (6.7%) patients, including 10 cases of Candida spp. and 1 case of Mucor spp. Anti-infection therapies were adjusted in 28 (24.4%) cases based on mNGS.

CONCLUSION: The mNGS technique showed distinct advantages in detecting fungal infections in kidney transplant patients, facilitating informed anti-infection strategies and enhanced graft protection. Moreover, it provides effective identification of fungal infections originating from donor sources.},
}

Humans
*Kidney Transplantation/adverse effects
Female
Male
Middle Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Transplant Recipients
*Fungi/genetics/classification/isolation & purification
Adult
*Mycoses/diagnosis/microbiology
Aged

@article {pmid41668735,
year = {2025},
author = {Cao, Y and Wang, C and Yin, H and Xu, D and Li, W and Yuan, Z and Xu, W and Song, Z and Pang, F and Wang, D},
title = {Establishing hospital-specific background microbial libraries to reduce false positives in mNGS diagnosis of periprosthetic joint infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1668697},
pmid = {41668735},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Hospitals ; False Positive Reactions ; *Bacteria/genetics/classification/isolation & purification ; Computational Biology ; },
abstract = {BACKGROUND: Due to the high sensitivity of metagenomic next-generation sequencing (mNGS), trace amounts of nucleic acid contamination can lead to false positives, posing challenges for result interpretation. This study is the first to experimentally identify and establish background microbial libraries (BML) related to periprosthetic joint infection (PJI) across different medical institutions, aiming to demonstrate the necessity of institution-specific BMLs to improve mNGS diagnostic accuracy.

METHODS: Samples were taken from 3 different acetabular reamer for hip arthroplasty in 7 different hospitals. The whole process was strictly aseptic, mNGS was performed according to standard operating procedures. The sterility of instruments was confirmed by culture method. The sequencing results of specimens from different hospitals were compared to analyze the difference of background bacteria. Bioinformatics analysis and visualization were presented through R language.

RESULTS: A total of 26 samples (24 instrument swabs and 2 negative controls) generated 254 million reads, of which 1.13% matched microbial genomes. The proportion of microbial reads (1.13%) falls within ranges typically observed for contamination in low-biomass metagenomic sequencing studies. Among these, bacteria accounted for 87.48%, fungi 11.18%, parasites 1.26%, and viruses 0.06%. The most abundant bacterial genera included Cutibacterium, Staphylococcus, and Acinetobacter. Principal component analysis revealed distinct bacterial compositions among the seven hospitals, and clustering analysis showed significant inter-hospital variation (p < 0.05). Liaocheng People's Hospital exhibited the highest species richness (340 species), followed by Guanxian County People's Hospital (169 species).

CONCLUSIONS: The composition and abundance of residual bacterial DNA vary markedly among institutions, underscoring the necessity of establishing hospital-specific BMLs. Incorporating such libraries into clinical mNGS interpretation can effectively reduce false positives and enhance the diagnostic accuracy of PJI. arthroplasty, bacterial culture, next-generation sequencing, joint replacement, periprosthetic joint infection, background microbial libraries.},
}

Humans
*Prosthesis-Related Infections/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Hospitals
False Positive Reactions
*Bacteria/genetics/classification/isolation & purification
Computational Biology

@article {pmid41668733,
year = {2025},
author = {Sui, Q and Yu, J and Cui, S},
title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1707599},
pmid = {41668733},
issn = {2235-2988},
mesh = {Humans ; Middle Aged ; Male ; Female ; Aged ; Retrospective Studies ; *Atherosclerosis/microbiology/diagnosis ; *Microbiota ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Risk Factors ; Bacteria/classification/genetics/isolation & purification ; *Cardiovascular Diseases/microbiology/diagnosis ; Metagenomics ; },
abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.

METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).

RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.

CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.},
}

Humans
Middle Aged
Male
Female
Aged
Retrospective Studies
*Atherosclerosis/microbiology/diagnosis
*Microbiota
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
ROC Curve
Risk Factors
Bacteria/classification/genetics/isolation & purification
*Cardiovascular Diseases/microbiology/diagnosis
Metagenomics

@article {pmid41668731,
year = {2025},
author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C},
title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1745848},
pmid = {41668731},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Culex/microbiology/genetics/physiology ; Metagenomics ; *Smell/genetics ; Gene Expression Profiling ; Arthropod Antennae/metabolism ; Transcriptome ; Computational Biology ; Multiomics ; },
abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.

METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.

RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that the gut microbial richness of male individuals was significantly higher than that of females, and the β-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.

DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.},
}

Animals
*Gastrointestinal Microbiome/genetics
Female
Male
*Culex/microbiology/genetics/physiology
Metagenomics
*Smell/genetics
Gene Expression Profiling
Arthropod Antennae/metabolism
Transcriptome
Computational Biology
Multiomics

@article {pmid41668536,
year = {2026},
author = {Wei, H and Guo, S and Ding, W and Yang, Y and Hu, X and Aili, A and Chen, X and Xue, X and Pan, L},
title = {Altered gut microbial dynamics and the antivascular remodeling effect of carnosine in hypobaric hypoxic pulmonary hypertension rats.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2025237},
pmid = {41668536},
issn = {1745-7270},
abstract = {Exposure to chronic hypobaric hypoxia provokes marked alterations in the gut microbiota and its metabolome, yet the functional significance of histidine-derived metabolites in hypobaric hypoxic pulmonary hypertension (PH) remains underexplored. Here, we employ 16S rDNA, metagenomic, and untargeted metabolomic sequencing to characterize longitudinal shifts in the fecal microbiota and metabolites during hypobaric hypoxic PH development in Sprague-Dawley rats. Fecal carnosine levels and the abundance of its producer, Ruminococcus bromii, both decrease significantly over 28 days of hypobaric hypoxia (P < 0.05). Spearman correlation shows that carnosine is inversely correlated with the percentage of pulmonary arteriole media thickness (MT%; r = -0.8741, P < 0.001). Therapeutic supplementation with carnosine restores systemic and pulmonary antioxidant defenses and attenuates vascular remodeling without altering right ventricular pressures. In vitro, carnosine inhibits hypoxia-induced pulmonary artery smooth muscle cell (PASMC) proliferation and migration and suppresses nuclear factor erythroid 2-related factor 2 (Nrf2) accumulation. These findings reveal dynamic gut-lung crosstalk in hypobaric hypoxic PH and nominate carnosine as a metabolite-based intervention to mitigate hypoxia-driven pulmonary vascular remodeling.},
}

@article {pmid41668418,
year = {2026},
author = {Moguel, B and Olivas, LC and Guerrero-Osornio, MG and Herrera Paredes, S},
title = {Recent microbial evolutionary insights from metagenomics.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag029},
pmid = {41668418},
issn = {1759-6653},
abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics -through its ability to recover genomic information directly from environmental samples- has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA (aDNA) has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain -including improving bioinformatic tools for degraded aDNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.},
}

@article {pmid41668124,
year = {2026},
author = {Zhang, R and Debeljak, P and Gadegaonkar, SS and Baudet, C and Ringard, A and Blain, S and Obernosterer, I},
title = {Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02293-6},
pmid = {41668124},
issn = {2049-2618},
support = {202006220057//China Scholarship Council/ ; ANR19-CE01-0012//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean.

RESULTS: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses.

CONCLUSIONS: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.},
}

@article {pmid41668110,
year = {2026},
author = {Fujii, H and Sato, M and Nguyen, HAT and Vu, HTT and Kakiuchi, S and Dhoubhadel, BG and Nakamura, S and Motooka, D and Ogura, Y and Nakano, S and Parry, CM and Morimoto, K and Yoshida, LM and Anh, DD and Hayashi, T and Iida, T and Ariyoshi, K},
title = {Genomic analysis of the genetic background underlying Streptococcus pneumoniae beta-lactam nonsusceptibility in central Vietnam: increased beta-lactam nonsusceptibility and dynamics of the pbp2x gene.},
journal = {Tropical medicine and health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s41182-025-00889-0},
pmid = {41668110},
issn = {1348-8945},
support = {2014-Ippan-10, 2015-Ippan-25//Institute of Tropical Medicine, Nagasaki University/ ; },
abstract = {BACKGROUND: We previously reported alarmingly high carriage rates of Streptococcus pneumoniae (SP) serotype 19F and serogroup 6 isolates, which were not susceptible to multiple beta-lactams among children under five years of age in Vietnam. Multilocus sequence typing analysis revealed the predominance of two major lineages, ST320 and ST13223, among serotype 19F and serogroup 6 isolates, respectively. Investigating the association between nonsusceptible genotypes and clinical outcomes could help optimize patient care or lead to the development of new diagnostic tests.

METHODS: We performed WGS on SP isolates randomly selected from the two major lineages and their related strains. FASTQ quality control and de novo assembly were performed using CLC Genomics Workbench ver. 7.5.1. Draft genome sequences were annotated using DFAST (DDBJ Fast Annotation and Submission Tool), which revealed the serogroups/serotypes and the sequences of the three major penicillin-binding protein genes and the sequence types. Draft sequences were aligned using MUMmer ver. 3.23, and putative recombination events and phylogenetic relationships excluding recombination regions were identified using Gubbins ver. 2.4.1. Finally, the association between a detected nonsusceptible genotype and the duration of hospital stay was evaluated in patients with acute respiratory infection.

RESULTS: WGS analysis (serotype 19F/ST320, n = 22; serogroup 6/ST13223, n = 13; and isolates closely related to ST13223, n = 4) revealed substantial differences in genomic diversity and antimicrobial susceptibility between serogroup 6/ST13223 and serotype 19F/ST320 isolates, particularly the recombination-prone nature of serogroup 6/ST13223. Among the 23 recombination events observed in serogroup 6/ST13223, only those spanning the pbp2x region (15.5 kb and 6.4 kb) were associated with high MICs for multiple beta-lactams. A subset of ST13223 isolates and all ST320 isolates carried the identical pbp2x allele 16, which was significantly associated with a lack of susceptibility to the combination of penicillin, cefotaxime, and meropenem (p < 0.0001; odds ratio 11.5; 95% confidence interval [CI] 3.35-39.3). No significant association was demonstrated between the presence of this pbp2x allele and prolonged hospitalization (p = 0.6123).

CONCLUSIONS: We revealed that the widespread nonsusceptibility to multiple beta-lactams among SP isolates circulating in central Vietnam was primarily driven by the dynamics of the pbp2x gene. However, the nonsusceptible pbp2x allele had little effect on clinical outcome.},
}

@article {pmid41667950,
year = {2026},
author = {Rodrigues, GVP and Ferreira, LYM and Aguiar, ERGR},
title = {ViralQuest: a user-friendly interactive pipeline for viral-sequences analysis and curation.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06391-6},
pmid = {41667950},
issn = {1471-2105},
support = {Financial Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
}

@article {pmid41667397,
year = {2026},
author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E},
title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2627692},
doi = {10.1080/19490976.2026.2627692},
pmid = {41667397},
issn = {1949-0984},
mesh = {Humans ; *Ceftriaxone/therapeutic use/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy ; Aged ; *Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification ; Genetic Variation ; Adult ; Rectum/microbiology ; },
abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.},
}

Humans
*Ceftriaxone/therapeutic use/pharmacology
*beta-Lactamases/genetics/metabolism
*Anti-Bacterial Agents/therapeutic use/pharmacology
Male
Female
Middle Aged
Prospective Studies
*Gastrointestinal Microbiome/drug effects
*Enterobacteriaceae Infections/microbiology/drug therapy
Aged
*Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification
Genetic Variation
Adult
Rectum/microbiology

@article {pmid41667306,
year = {2026},
author = {Tong, Y and Chen, Y and Dong, Y and Chen, K and Yang, J and Dong, X and Wan, X and Luo, Z and Fang, J and Liu, Y and Li, W and Wang, Z and Gu, X},
title = {Characterization of the oral microbiota of Kawasaki disease patients by metagenomic analysis: A pilot study.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2026.01.007},
pmid = {41667306},
issn = {1995-9133},
abstract = {BACKGROUND: Kawasaki disease (KD) is an acute febrile systemic vasculitis characterized by vascular inflammation. Its pathogenesis has been linked to the infiltration of IgA[+] plasma cells within the respiratory tract, suggesting the upper airway may act as a potential portal of entry. However, evidence connecting respiratory infections to KD remains limited. This study aimed to explore the relationship between oral microbiota and KD development.

METHODS: Oral swab samples were collected from 25 KD patients before and after intravenous immunoglobulin (IVIG) treatment, as well as from 25 healthy controls. Metagenomic sequencing was performed to characterize overall microbial composition and identify potential microbial markers associated with KD.

RESULTS: Significant alterations in oral microbiota composition were observed between KD patients and healthy controls. The diversity of oral microbiota in KD patients was markedly lower than that in healthy controls, and exhibited an upward trend following IVIG treatment. Elevated levels of Streptococcus, Prevotella, and Veillonella, along with reduced levels of Haemophilus, Neisseria, and Rothia, were closely associated with KD development. Putative novel pathogen Abiotrophia defectiva was significantly enriched in patients with KD. Correlation analysis revealed that the relative abundances of several Haemophilus species were positively correlated with albumin levels in KD patients before IVIG treatment. Additionally, the anti-inflammatory bacterium Rothia mucilaginosa may play a protective role against the development of coronary artery lesions in KD.

CONCLUSION: These findings provide new evidence that distinct alterations in the oral microbiome are associated with KD development. Oral microbiota-based biomarkers may represent a potential strategy for KD therapy.},
}

@article {pmid41667136,
year = {2026},
author = {Tarrant, E and Cormack, IG and Hunter, CE and Werbowy, O and Dorawa, S and Wang, L and Steen, IH and Sandaa, RA and Guðmundsdóttir, EE and Ketelsen-Striberny, B and Kaczorowska, AK and Kaczorowski, T and Pohl, E and Freitag-Pohl, S},
title = {Structure, function, and applications of two novel phage recombinases from extreme environments.},
journal = {Nucleic acids research},
volume = {54},
number = {4},
pages = {},
doi = {10.1093/nar/gkag069},
pmid = {41667136},
issn = {1362-4962},
support = {//European Union's Horizon 2020 Research/ ; 685778//Innovation Programme Virus-X project: Viral Metagenomics for Innovation Value/ ; EP/S022791/1//Engineering and Physical Sciences Research Council/ ; UMO-2019/34/H/NZ2/00584//Norway Financial Mechanism through the National Science Center/ ; A/SP/453344/202//Ministry of Education and Science/ ; },
mesh = {Rec A Recombinases/chemistry/genetics/metabolism ; *Bacteriophages/enzymology/genetics ; *Viral Proteins/chemistry/metabolism/genetics ; Models, Molecular ; DNA, Single-Stranded/metabolism ; Escherichia coli/genetics ; Crystallography, X-Ray ; *Recombinases/chemistry/metabolism/genetics ; Escherichia coli Proteins/chemistry/genetics ; DNA-Binding Proteins ; },
abstract = {This study describes the identification and characterization of two new extremophilic phage recombinases, UvsXt and UvsXp, discovered through metagenomic analysis within the Virus-X project, and explores their potential applications in biotechnology. DNA recombinases are essential for maintaining genome integrity across all kingdoms of life by facilitating homologous recombination and repairing double-stranded DNA breaks. Their capacity to bind and stabilize single-stranded DNA (ssDNA) has led to wide-ranging applications in molecular biology. UvsXt and UvsXp show homology with known bacterial RecA and viral UvsX recombinases, including conservation of key catalytic residues and DNA-binding motifs. Biochemical assays reveal that both enzymes exhibit superior DNA strand-exchange activity compared to Escherichia coli RecA. High-resolution crystal structures of UvsXt (2.0 Å) and UvsXp (2.6 Å) confirm a conserved RecA-like core fold, with distinct structural variation at the N-terminus responsible for oligomerization. However, in spite of their similarities, we show that neither enzyme is capable to functionally replace RecA in E. coli. Their remarkable thermostability and functionality across diverse chemical environments highlights their robustness for biotechnological use. Notably, UvsXt enhances loop-mediated isothermal amplification of viral RNA by stabilizing ssDNA intermediates. These findings expand the repertoire of thermostable recombinases with potential utility in diagnostic applications.},
}

Rec A Recombinases/chemistry/genetics/metabolism
*Bacteriophages/enzymology/genetics
*Viral Proteins/chemistry/metabolism/genetics
Models, Molecular
DNA, Single-Stranded/metabolism
Escherichia coli/genetics
Crystallography, X-Ray
*Recombinases/chemistry/metabolism/genetics
Escherichia coli Proteins/chemistry/genetics
DNA-Binding Proteins

@article {pmid41667040,
year = {2026},
author = {Liu, J and Guan, H and Hu, S and Lu, H and Tang, X and Tang, CJ},
title = {Dialysis-controlled sulfur substrate delivery enhances Sulfur-Autotrophic denitrification under oxygen stress.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134158},
doi = {10.1016/j.biortech.2026.134158},
pmid = {41667040},
issn = {1873-2976},
abstract = {Sulfur autotrophic denitrification (SAD) is a low-carbon nitrogen removal process using reduced sulfur compounds as electron donors. However, dissolved oxygen (DO) disrupts SAD by promoting unproductive sulfur oxidation and electron loss. Here, dialysis membranes (1000 and 100 Da) were applied to regulate thiosulfate release and establish controlled substrate gradients under engineering-relevant inhibitory DO conditions (0.5-3.5 mg L[-1]). Compared with direct dosing (Rck), the 100 Da reactor (R100) achieved 19% higher nitrate removal efficiency and greater fraction of electrons allocated to denitrification (EDUden ≈ 76%), accompanied by pronounced zero-valent sulfur accumulation, indicating pathway-level reallocation. Microbial analyzes revealed enrichment of Thiobacillus-like sulfur-oxidizing denitrifiers and increased prevalence of oxygen tolerant nitrate reductase (napA), confirmed by metagenomic and qPCR. These results demonstrate that controlled sulfur release creates an electron-buffered microenvironment that enhances SAD resilience to DO, offering a donor-efficient strategy for nitrogen removal in oxygen-fluctuating wastewater systems.},
}

@article {pmid41667020,
year = {2026},
author = {Lawal, MS and Hayashida, K and Sugi, T and Omoare, AA and Bile, N and Maikudi, HI and James, POI and Villeng, F and Babatunde, O and Idris, J and Yamagishi, J},
title = {Detection of Novel Pegivirus C Genome in an Unexplained Febrile Outbreak, Gombe State, Nigeria, 2024 by Enhanced mNGS Approach.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108470},
doi = {10.1016/j.ijid.2026.108470},
pmid = {41667020},
issn = {1878-3511},
abstract = {OBJECTIVES: In July 2024, an outbreak of acute febrile illness occurred in Chassi village, Gombe State, Nigeria, affecting over 30 individuals, primarily children, with symptoms including fever, jaundice, abdominal pain, and mucosal bleeding. The cause remained unidentified after conventional diagnostics excluded known viral hemorrhagic fevers, malaria, and bacterial infections. This study aimed to investigate the potential etiologic agent behind the outbreak using unbiased genomic techniques.

METHODS: We employed a metagenomic next-generation sequencing (mNGS) strategy with viral enrichment to analyze serum samples from 22 symptomatic patients. A novel complete 9.3 kb genome of Pegivirus C (GOMBE-017-2025) was reconstructed and phylogenetically compared to global sequences. Detection was validated using targeted PCR and Sanger sequencing. Environmental and microbial testing were conducted on local water sources.

RESULTS: Pegivirus C was consistently detected in all 22 samples. The reconstructed genome showed 92.7% identity to a 2018 Nigerian strain and clustered with West African isolates. PCR and sequencing confirmed its presence. Environmental and bacterial sources were ruled out as causative agents.

CONCLUSIONS: The uniform detection of Pegivirus C in this localized outbreak raises concern over its potential pathogenic or co-pathogenic role. These findings support the need for further investigation into its transmission dynamics, tropism, and clinical relevance.},
}

@article {pmid41666926,
year = {2026},
author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P},
title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.12.051},
pmid = {41666926},
issn = {1097-4172},
abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.},
}

@article {pmid41666920,
year = {2026},
author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A},
title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.01.013},
pmid = {41666920},
issn = {1934-6069},
abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.},
}

@article {pmid41666847,
year = {2026},
author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110114},
doi = {10.1016/j.envint.2026.110114},
pmid = {41666847},
issn = {1873-6750},
abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.},
}

@article {pmid41666834,
year = {2026},
author = {S, H and A, P},
title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107903},
doi = {10.1016/j.marenvres.2026.107903},
pmid = {41666834},
issn = {1879-0291},
abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.},
}

@article {pmid41666744,
year = {2026},
author = {Kelly, LT and Beach, DG and Blaszczak, JR and Bouma-Gregson, K and Brown, SM and Cheng, H and Davidson, JL and Fastner, J and Francis, M and Jimenez, AG and Genzoli, L and Goel, R and Gonzalez, D and Handley, KM and Hilt, S and Humbert, JF and Jamieson, R and Johnston, L and Junier, P and Lawrence, J and McCarron, P and Meissner, S and Mormando, J and Puddick, J and Quiblier, C and Rajpirathap, N and Schampera, C and Selwood, A and Shearer, K and Sohrab, A and Stancheva, R and Valadez-Cano, C and Zabrecky, JM and Wood, SA},
title = {The global proliferation of aquatic, benthic Microcoleus: Taxonomy, distribution, toxin production, ecology, and future directions.},
journal = {Water research},
volume = {294},
number = {},
pages = {125441},
doi = {10.1016/j.watres.2026.125441},
pmid = {41666744},
issn = {1879-2448},
abstract = {There have been sporadic reports of aquatic, benthic Microcoleus proliferations in freshwater rivers, lakes, and reservoirs for four decades, with reports increasing in frequency over the last twenty years, suggesting a possible rise in their global distribution, frequency, and intensity. Microcoleus can produce anatoxins which are neurotoxic, and ingestion of toxic mats has caused hundreds of dog fatalities and raised serious human and ecological health concerns. This review synthesizes and evaluates current knowledge on Microcoleus distribution, taxonomy, toxin production, toxicity, ecology, environmental drivers, and biotic interactions. Toxin-producing Microcoleus have been reported in at least 18 countries, though many regions have not conducted toxin testing, suggesting a broader but under-reported distribution. Proliferations occur across diverse habitats, including cobble-bedded streams, large sandy rivers, reservoirs, and lakes. Microcoleus proliferations also occur on macrophytes, both in lakes and rivers. Genomic analyses currently classify anatoxin-producing Microcoleus into distinct species, with all known anatoxin-producers isolated from freshwater ecosystems. Anatoxin concentrations vary widely over space and time, within and among waterbodies. While studies on environmental drivers remain limited, research in cobble-bedded rivers suggests that moderate enrichment of dissolved inorganic nitrogen and low dissolved reactive phosphorus concentrations in the water column promote proliferation. Metagenomic approaches have revealed unique nutrient acquisition and storage strategies used by Microcoleus. Key knowledge gaps remain around the environmental and ecological triggers of proliferation, toxin production, genomic diversity and microbial interactions. Addressing these gaps through coordinated, global studies using robust datasets and consistent methods is critical to improve prediction, monitoring, and mitigation of this increasingly widespread public and ecological health threat.},
}