@article {pmid42166402,
year = {2026},
author = {Peta Martinez, NA and Reinoso Arnaldi, M and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in <italic>Drosophila</italic> with Kdm5 Deficiency.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-21},
pmid = {42166402},
issn = {1421-9859},
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B, or KDM5C are found in patients with intellectual disability and ASD. Here, we use a genetically tractable Drosophila model of loss-of-function of the ASD-associated chromatin regulator Kdm5 to investigate how host genetic disruption influences gut microbial composition and social behavior. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5LOF) revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.

METHODS: We evaluated multiple microbiota-based interventions, including probiotic supplementation with L. plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in adult Kdm5LOF flies. Gut bacterial abundance was quantified using colony-forming unit assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.

RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5LOF and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5LOF flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5LOF mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5LOF recipient flies.

CONCLUSION: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships in the context of disruption of an ASD-associated gene and for studying microbiota-based modulation of host physiology and behavior. All experiments were conducted in adult flies, and thus, these findings reflect post-developmental effects of Kdm5 disruption.},
}

@article {pmid42508343,
year = {2026},
author = {Singh, CK and Sodhi, KK and Seth, R and Seth, RK},
title = {Gamma radiation-induced changes in the male adult gut bacterial community composition of a serious pest, Spodoptera litura (Noctuidae: Lepidoptera) and its F1 progeny.},
journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine},
volume = {237},
number = {},
pages = {112830},
doi = {10.1016/j.apradiso.2026.112830},
pmid = {42508343},
issn = {1872-9800},
abstract = {Spodoptera litura (Fabr), a noctuid Lepidopteran pest, can be effectively controlled using Inherited Sterility Technique (IS), a modified version of the Sterile Insect Technique (SIT). To ensure its operational success, the role of the gut microbiome in irradiation-induced fitness effects needs to be characterized. The role of gut bacteriome of the irradiated (130Gy) male adult moth and their F1 progeny was systematically examined. The current study aims to assess the effect of irradiation on bacterial diversity and relate with the reproductive performance of radio-sterilized moths. A culture-independent, high-throughput amplicon sequencing approach targeting bacterial 16S rRNA gene regions was employed to profile microbiome composition and diversity. Three experimental regimens were established: (i) unirradiated control males (N), (ii) partially sterilized males exposed to 130Gy (130Gy P1), and (iii) male F1 progeny derived from irradiated male parent (130Gy F1). Bacterial diversity and richness were reduced in gut of both the irradiated male parent and its F1 progeny compared with control (N). The Proteobacteria abundance was increased in the gut of 130 Gy P as compared to the control, whereas in the 130Gy F1 gut, its abundance was decreased significantly. The Firmicutes dominated the gut microbiome of the 130Gy F1 male moths. Further, the principal component analysis plot showed that the normal male moths were more closely related to 130 Gy P male moths in terms of gut bacterial diversity than to 130Gy F1 male moths. The functional pathways involved in the chitin and chloramphenicol were enriched in the guts of irradiated parent moths, whereas lignin degradation was enriched in 130Gy F1 progeny with respect to the control. This study might indicate the relevance of microbiome in reproductive fitness of irradiated moths and help in the optimization of this radio-genetic technique by validating the proposed gamma dose of 130Gy, towards pest control operations.},
}

@article {pmid42508663,
year = {2026},
author = {Wang, Z and Gu, Z and Yan, C and Zhou, J and Dai, B and Luo, L and Wang, X and Shi, P and Xia, S},
title = {Sulfur vacancies enhance pyrite-driven autotrophic denitrification: mechanistic insights into electron-supplying pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135508},
doi = {10.1016/j.biortech.2026.135508},
pmid = {42508663},
issn = {1873-2976},
abstract = {Pyrite-driven autotrophic denitrification (PAD) is a promising carbon-free strategy for nitrate-contaminated wastewater treatment, yet the role of sulfur vacancies (SVs) remains poorly understood. Herein, we investigated the effects of SVs on denitrification activity, interfacial reactivity, and microbial mechanisms in PAD. Electrochemical characterization and batch tests indicated that SVs introduction boosted electron release from pyrite, achieving 98.1% nitrate removal, 1.59-fold higher than pristine pyrite. By integrating X-ray photoelectron spectroscopy, density functional theory calculations, and metagenomic results, we propose a mechanistic framework in which SVs enhance the electron-supplying capacity of pyrite via two routes: (i) SVs strengthen interactions between pyrite and microbial electron shuttles (e.g., riboflavin and methyl-naphthoquinone), supporting the potential involvement of extracellular electron transfer in enhancing electron availability to denitrifiers; and (ii) SVs are expected to weaken local Fe-S bonding and promote Fe(III)-mediated pyrite oxidation, thereby favoring Fe(II) mobilization and the potential involvement of sulfur intermediates (S[0], S2O3[2-]) during PAD. These changes were accompanied by altered surface Fe/S speciation and enrichment of sulfur-oxidizing denitrifiers, particularly Thiobacillus. Additionally, SV-enriched PAD system also exhibited superior resistance to antibiotic and metal stress and achieved continuous nitrogen polishing from real secondary effluent, confirming its strong potential for engineering scalability and practical implementation.},
}

@article {pmid42509323,
year = {2026},
author = {Spazzapan, M and Raison, N and Steves, C and Sahai, A},
title = {The urinary microbiome, overactive bladder and bladder pain syndrome/interstitial cystitis - mechanisms, diagnostics and therapeutic opportunities.},
journal = {Nature reviews. Urology},
volume = {},
number = {},
pages = {},
pmid = {42509323},
issn = {1759-4820},
abstract = {Overactive bladder and bladder pain syndrome/interstitial cystitis are prevalent, multifactorial disorders with poorly understood pathophysiology. The discovery of the urinary microbiome has overturned the sterile urine paradigm and created new opportunities for mechanistic and translational research. Increasing evidence suggests that bladder microbial communities are associated with urothelial signalling, immune tone and neural pathways that influence urgency, pain and treatment response. In overactive bladder, Lactobacillus-predominant profiles are associated with lower symptom burden and improved response to pharmacotherapy, whereas Gardnerella-enriched and Pseudomonadota-enriched communities positively correlate with refractory disease. In bladder pain syndrome/interstitial cystitis, microbial alterations are not based on a single pathogenic signature but converge on metabolic and immune dysregulation. Multi-omics studies integrating metagenomics, metabolomics and host immune data are beginning to define functional pathways linking microbial metabolites, epithelial barrier function and nociceptor sensitization. Results from emerging clinical trials suggest that urinary microbiome profiling might enable patient stratification and inform treatment selection, whereas interventions, such as probiotics, oestrogen therapy or dietary modulation, hold potential as adjunctive strategies. Together, these advances position the urinary microbiome as a promising contributor to lower urinary tract health and a potential target for precision urology, although the functional importance and causal role of the low-biomass urinary microbiome in disease remain crucial unresolved questions.},
}

@article {pmid42509522,
year = {2026},
author = {Chen, PY and Hsu, TW and Chiang, TY and Huang, CL},
title = {Comparative analysis of root microbiomes in four Swertia species from Taiwan.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {42509522},
issn = {1618-0860},
support = {NSTC 103-2621-B-006-002-//National Science and Technology Council/ ; },
abstract = {Swertia (Gentianaceae) comprises four species endemic to Taiwan that possess significant medicinal potential. While root microbiomes are known to promote plant adaptation, the microbial ecology of Taiwanese Swertia remains largely unexplored. We investigated the rhizosphere and root endosphere microbiomes of these species using 16S rRNA gene sequencing and predictive functional profiling, integrated with host phylogenetic data. Our results revealed that rhizosphere bacterial communities were significantly more diverse than those in the root endosphere. PERMANOVA indicated that host species and plant compartment significantly influenced bacterial communities, but the high residual variance suggests that much of the community variation remains unexplained by the variables measured in this study. Phylogenetic analysis indicated that the root endosphere is more strongly influenced by host phylogeny, with closely related species harboring more similar communities. Functional profiling further demonstrated that the rhizosphere is predicted to be enriched in pathways related to nitrogen fixation and organic matter degradation, whereas the endosphere harbors bacterial taxa potentially associated with pathogen suppression. These findings underscore the multifaceted roles of the root microbiome in supporting the development, stress adaptation, and ecosystem sustainability of Swertia species in Taiwan's unique altitudinal gradients.},
}

@article {pmid42509999,
year = {2026},
author = {Hazan, S and Spradling-Reeves, KD and Papoutsis, A and Walker, SJ},
title = {Correction: Hazan et al. Shotgun Metagenomic Sequencing of Gut Microbiota in Triplet Sibling with ASD and Gastrointestinal Symptoms: A Descriptive Case Report. Children 2020, 7, 255.},
journal = {Children (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/children13070863},
pmid = {42509999},
issn = {2227-9067},
abstract = {The title of this publication [...].},
}

@article {pmid42510718,
year = {2026},
author = {Liu, J and Liu, S and Zhou, X and Zhong, Z and Hu, Q and Li, Q and Lin, Z and Huang, X and Zheng, B},
title = {Protective Effects of Fructus mume Extract Against Deoxynivalenol-Induced Intestinal and Liver Injury in Mice.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141172},
pmid = {42510718},
issn = {2079-7737},
support = {JZ230013//the Key Project of Fujian Provincial Education and Scientific Research Program for Young and Middle-aged Teachers/ ; KLY24109XA//Fujian Provincial Department of Finance/ ; },
abstract = {Deoxynivalenol (DON), a prevalent mycotoxin, induces intestinal and hepatic injury. Fructus mume extract (FME) possesses bioactive properties, yet its protective role against DON remains unclear. This study aimed to investigate the protective mechanisms of FME in DON-challenged mice. Male C57BL/6 mice were divided into control, DON (3 mg/kg), and DON with low-, medium-, or high-dose FME groups for 4 weeks. Analyses included histopathology, UPLC-Q-TOF-MS, network pharmacology, biochemistry, qRT-PCR, immunohistochemistry, a TUNEL assay, metagenomics, and metabolomics. FME significantly alleviated growth inhibition and tissue damage. Among the 38 components identified by UPLC-Q-TOF-MS, all 38 acted on 156 genes, including IL-1β, caspase3, and BAX, to alleviate DON-induced intestinal and hepatic injury. FME enhanced hepatic antioxidant capacity and reduced inflammation by suppressing NF-κB signaling. FME upregulated tight junction proteins, inhibited apoptosis, and restored microbial diversity by enriching beneficial bacteria. Metabolomics revealed FME reversed DON-induced metabolic disruptions in the liver. Correlation analysis indicated FME remodeled the microbiota-liver metabolite network. In conclusion, FME attenuates DON-induced intestinal injury by modulating the gut-liver axis through antioxidant, anti-inflammatory, and anti-apoptotic activities.},
}

@article {pmid42510727,
year = {2026},
author = {Meng, X and Xue, Y and Shen, M and Shen, Y},
title = {UV Aging Strengthens the Effects of Polyvinyl Chloride Microplastics on Soil Bacterial Community Structure and Predicted Functional Profiles.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141181},
pmid = {42510727},
issn = {2079-7737},
support = {42507354//National Natural Science Foundation of China/ ; 24KJB610005//Jiangsu Provincial Fundamental Science Research Program for Higher Education Institutions/ ; },
abstract = {Soil microplastics undergo aging, but how aging modifies their effects on soil bacterial communities remains unclear. Here, we conducted a 180-day incubation experiment with no PVC (CK), pristine PVC microplastics (IP), and UV-aged PVC microplastics (AP, 0.5%, w/w). UV aging markedly altered PVC surface properties: roughness increased from approximately 12.9 to 21.8 nm, water contact angle decreased from 91.44° to 82.38°, and the O/C ratio increased from 0.37 to 0.43. Bacterial richness indices were largely unchanged, whereas Shannon diversity decreased under AP, indicating reduced community evenness. Bray-Curtis analysis showed significant community separation among treatments (PERMANOVA: R[2] = 0.364, p = 0.003), with UV aging further altering the trajectory of PVC-induced community reorganization. At the genus level, AP was associated with enrichment of Methylobacillus and lower robustness in exploratory co-occurrence network analysis, suggesting a distinct bulk-soil bacterial response compared with IP. Functional prediction further suggested that AP and IP were associated with different predicted pathway profiles, with AP showing higher predicted representation of pathways related to carbon metabolism, respiratory energy metabolism, potential prokaryotic carbon fixation, environmental sensing, cellular maintenance, and antimicrobial-resistance-associated categories, whereas IP was mainly associated with transport- and communication-related predicted functions. These predicted functional patterns require further validation using metagenomic, qPCR, transcriptomic, biochemical, or chemical approaches. Overall, these findings highlight the need to consider the UV aging status of PVC microplastics when evaluating their effects on soil bacterial communities.},
}

@article {pmid42510739,
year = {2026},
author = {Liu, X and Zhao, X and Li, H and Wu, Y and Yao, Y and Wang, Z},
title = {Comparative Study on Blood Gas Indicators, Antioxidant Capacity, Intestinal Metabolome, and Microbiome in High- and Low-Performance Tumbler Pigeons.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141193},
pmid = {42510739},
issn = {2079-7737},
support = {2023B02036//The Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; },
abstract = {The purpose of this experiment is to investigate the differences in blood gas indicators, antioxidant indicators, and lactate content between high- and low-performance tumbler pigeons after exercise, and to use metabolomics and metagenomics techniques to screen for differential metabolites and bacteria related to tumbler pigeon exercise. This experiment selected 12 high-performing (HP) and 12 low-performing (LP) tumbler pigeons, half male and half female, and all pigeons were raised under the same conditions. Three experimental pigeons were grouped for exercise training, with a 20 min training session. The results showed significant differences (p < 0.05) in multiple blood gas parameters related to acid-base balance and gas exchange between the HP and LP groups after tumbler pigeon exercise. In addition, the content of glutathione peroxidase (GSH Px), superoxide dismutase (SOD), and catalase (CAT) in the liver of the HP group of tumbler pigeons was significantly lower than that of the LP group (p < 0.05). In comparison, the content of malondialdehyde (MDA) was significantly higher than that of the LP group (p < 0.05). The content of lactate (Lac) was significantly higher than that of the LP group (p < 0.05). Non-targeted metabolomics analysis revealed that differential metabolites were mainly enriched in pathways such as biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and fatty acid synthesis. Intestinal metagenomics analysis revealed that the Corynebacteriaceae, Bacillus, Pseudomonad phylum and Corynebacterium were significant biomarkers with significant differences in the gut microbiota of the HP group of tumbler pigeons (p < 0.05). In summary, there are significant differences in blood physiological parameters, antioxidant capacity, lactate content, intestinal metabolites, and gut microbiota between high- and low-performance tumbler pigeons after exercise. This result provides theoretical guidance and data support for cultivating high-performance tumbler pigeons.},
}

@article {pmid42511030,
year = {2026},
author = {Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z and Li, M},
title = {Integrated Rumen Metabolomics and Metagenomics Reveal Microbe-Metabolite Signatures Associated with Heat Tolerance in Dairy Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142152},
pmid = {42511030},
issn = {2076-2615},
support = {BK20241934//Natural Science Foundation of Jiangsu Province/ ; 2022YFF1001200//National Key Research and Development Program of China/ ; },
abstract = {Heat stress impairs dairy cow productivity and rumen function, but rumen metabolic features associated with natural heat tolerance remain unclear. This study generated rumen fluid metabolomic data and integrated them with previously generated metagenomic abundance data from the same heat-tolerant (HT) and heat-sensitive (HS) Holstein cows selected from a cohort of 120 cows using an entropy-weighted TOPSIS model. Untargeted LC-MS identified 116 differential metabolites, including 66 enriched in HS cows and 50 enriched in HT cows. The HS cows showed higher levels of nucleotide-related metabolites, whereas HT cows were enriched in thiamine, L-malate, and argininosuccinic acid. Pathway enrichment mainly involved nucleotide metabolism, pyrimidine metabolism, pyruvate metabolism, and thiamine metabolism. Reanalysis of metagenomic data identified 12 differential microbial taxa, including HT-enriched Prevotella and Ruminococcus flavefaciens. Spearman correlation analysis revealed phenotype-associated microbe-metabolite associations, and ROC analysis based on the discovery dataset suggested that uridine 5'-monophosphate, thiamine, L-malate, and argininosuccinic acid had exploratory potential to distinguish HT and HS cows. These findings provide exploratory evidence that rumen microbe-metabolite associations are related to natural heat tolerance in dairy cows.},
}

@article {pmid42511119,
year = {2026},
author = {Zhang, B and Ma, X and He, Z and Liu, J and Chen, P and Wang, F and Xie, J and Lv, C and Pan, F},
title = {Effects of Perilla Seed Extract Dietary Supplementation on Meat Quality, Rumen Fermentation, and Rumen Microbiome-Metabolome of Tan Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142242},
pmid = {42511119},
issn = {2076-2615},
support = {2023GAAS42//Gansu Academy of Agricultural Sciences/ ; },
abstract = {Perilla seed extract (PSE), a natural resource rich in α-linolenic acid and flavonoids, represents a promising dietary strategy to sustainably optimize rumen fermentation and improve the nutritional profile of ruminant meat. This study evaluated the effects of dietary PSE supplementation on rumen fermentation, microbiome-metabolome profiles, and subsequent meat quality in Tan lambs. Sixty 3-month-old male Tan lambs were randomly assigned to four dietary treatments (n = 15 per treatment) containing 0% (CON), 0.01% (LPSE), 0.03% (MPSE), or 0.05% (HPSE) PSE on a dry matter (DM) basis. In the rumen, the 0.03% PSE inclusion increased the propionate proportion from 20.50% to 23.80% (P-linear = 0.004) and carboxymethyl cellulase activity from 12.45 to 14.85 U/mL (P-linear = 0.007; P-quadratic = 0.045). Exploratory metagenomics showed that 0.03% PSE enriched Prevotella (18.67% to 21.06%) and Ruminococcus_E (1.20% to 2.13%), while decreasing the biohydrogenating genus Butyrivibrio compared with CON (LDA > 2, p < 0.05). These microbial shifts were accompanied by the accumulation of beneficial metabolites (e.g., small peptides and itaconic acid) and up-regulation of the pantothenate and CoA biosynthesis pathway. Consequently, the 0.03% PSE diet optimized meat quality, decreasing shear force by 12.7% (from 45.65 to 39.85 N; P-linear = 0.005, P-quadratic = 0.018) and drip loss (from 4.82% to 3.85%; P-linear = 0.022, P-quadratic = 0.015), while increasing redness (P-linear = 0.012, P-quadratic = 0.045). Furthermore, it increased meat C18:3n-3 (from 0.62% to 0.91%) and total n-3 PUFA (from 1.12% to 1.52%), while decreasing the n-6/n-3 ratio from 6.76 to 5.13 (P-linear ≤ 0.005 for all). Flavor amino acids also increased (P-linear = 0.008). These findings suggest that 0.03% PSE supplementation potentially improves lamb meat quality by favorably modulating rumen fermentation and microbe-metabolite interactions, highlighting its promise as a natural feed additive, though further validation is warranted.},
}

@article {pmid42511143,
year = {2026},
author = {Di Martino, B and Carnevale, M and Corsi, L and Sarchese, V and Pellegrini, F and Smoglica, C and Petrini, A and Martella, V and Marsilio, F and Di Profio, F},
title = {Emerging Mammarenaviruses in Wildlife: Expanding Host Range and Implications.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142263},
pmid = {42511143},
issn = {2076-2615},
abstract = {Mammarenaviruses are enveloped, ambisense, single-stranded RNA viruses capable of causing fatal hemorrhagic fevers and severe neurological disorders in humans. Although muroid rodents have historically been recognized as the primary reservoirs for major pathogens like Lassa virus, recent surveillance has revealed a significant expansion of their host range. This review aims to synthesize current global data regarding the epidemiology of mammarenaviruses in conventional reservoirs and the emergence of novel arenaviruses in non-traditional mammalian hosts. To achieve this, we comprehensively analyzed recent molecular and metagenomic surveillance data, evolutionary studies, and epidemiological reports published worldwide. Key discoveries include Wenzhou virus in Asian house shrews, Plateau Pika virus in plateau pikas, and an independent, geographically clustered of hedgehog-associated arenaviruses across Europe. Ultimately, this review underscores the global distribution of these pathogens and the critical need for continued, multi-host surveillance worldwide.},
}

@article {pmid42511188,
year = {2026},
author = {Meanti, F and Bellassi, P and Fontana, A and Dall'Asta, M and Rebecchi, A},
title = {Unveiling Microbial Dynamics in the Spontaneous Fermentation of Oat and Rice Okara Sourdoughs.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {42511188},
issn = {2304-8158},
support = {F/310136/01-05/X56//Ministry of Enterprises and Made in Italy/ ; },
abstract = {Sourdough fermentation is increasingly explored as a sustainable strategy for the valorisation of cereal-based by-products, although okara from oat- and rice-based beverage production remains largely underexplored. This study investigates the microbial evolution and nutritional characteristics of oat and rice okara sourdoughs obtained by spontaneous fermentation using the back-slopping technique. High-throughput sequencing revealed dynamic but matrix-dependent microbial composition. At the beginning of fermentation, oat okara was dominated by the Bacillus genus, while the Streptococcus genus was the most abundant in rice okara. After 30 days of back-slopping, the bacterial communities of both matrices were dominated by Lactobacillus, accounting for 80.1% and 73.3% of the relative abundance in oat and rice okara sourdoughs, respectively. Secondary bacterial taxa differed between matrices, with Weissella prevailing in oat okara (7.0%) and Acetobacter in rice okara (11.2%). Yeast communities showed a substrate-dependent temporal succession, being initially dominated by Pichia in both oat and rice okara sourdoughs (96.6% and 97.1%, respectively), whereas Saccharomyces became predominant at later fermentation stages, reaching 54.8% in oat okara and 83.5% in rice okara. From a nutritional perspective, okara sourdoughs exhibited promising characteristics, being rich in proteins and free amino acids, particularly glutamic acid, aspartic acid and leucine. The fatty acid profile was marked by oleic, linoleic and stearic acids, while nutritionally important minerals associated with musculoskeletal and immune function, such as calcium, zinc and selenium, were present in relevant quantities in the sourdoughs. These findings provide new insights into oat and rice okara sourdoughs and support the use of fermented okara as a sustainable ingredient with potential functional relevance.},
}

@article {pmid42511198,
year = {2026},
author = {Zhang, S and Wu, Y and Wang, F and Li, H and Zheng, N and Chen, H and Zhao, Y},
title = {Camel Milk Alleviates Chronic Fatigue Syndrome-like Symptoms in Mice by Modulating the Small Intestinal Microbiota and Inflammation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {42511198},
issn = {2304-8158},
support = {2025D01B138//Science and Technology Department of Xinjiang Uyghur Autonomous Region/ ; },
abstract = {This study aimed to investigate the therapeutic effects of camel milk (CM) on chronic fatigue syndrome (CFS) and elucidate the mechanisms underlying the microbiota-gut-brain axis. Using a murine model of CFS induced by chronic restraint and forced swimming stress, we administered lyophilized CM (1500 mg/kg/day, equivalent to approximately 121.5 mg/kg/day in humans based on body surface area conversion using the standard allometric scaling formula) orally. CM supplementation was significantly associated with ameliorated fatigue-like behaviors, as evidenced by prolonged swimming endurance and reduced immobility time. Metagenomic analysis revealed that CM was associated with reshaping of the small intestinal microbiota, including enrichment of beneficial Lactococcus lactis and suppression of pathobionts (H. hepaticus and H. typhlonius). These microbial shifts correlated with increased luminal lactic acid, improved intestinal barrier integrity (increased villus height, reduced crypt depth), and attenuated local inflammation (reduced TNF-α and IL-6, elevated IL-10). Consequently, CM was associated with reduced bacterial translocation and systemic inflammation, and normalization of hypothalamic-pituitary-adrenal (HPA) axis hyperactivity. We conclude that CM is associated with prevention of CFS-like symptoms through modulation of the gut ecosystem and strengthening of the intestinal barrier, potentially breaking the vicious cycle of gut inflammation and HPA axis dysfunction, although causality remains to be established through fecal microbiota transplantation or similar mechanistic studies.},
}

@article {pmid42511274,
year = {2026},
author = {Huang, H and Li, X and Zhang, K and Liang, B and Bai, S and Dong, X and Yan, D},
title = {Dietary Green Alfalfa Supplementation Reduces Backfat Thickness and Improves Muscle Water-Holding Capacity in Diqing Tibetan Pigs.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {42511274},
issn = {2304-8158},
support = {XDYC-QNRC-2023-0394//Young Talent Project of the Yunnan Province Xing Dian Ying Talent Support Program/ ; 202305AF150128//Yunnan Provincial Academician Expert Workstation Project/ ; 202202AE090005, 202302AE090015//Major Science and Technology Special Projects of Yunnan Province/ ; },
abstract = {Feed scarcity constrains livestock production, particularly on the Qinghai-Tibet Plateau. The effects of green alfalfa (GA) on Diqing Tibetan pig performance remain unclear. This study aimed to evaluate GA effects on Diqing Tibetan pig performance and to explore the potential underlying mechanisms through integrated metagenomic, transcriptomic, and metabolomic analyses. Thirty-six Diqing Tibetan pigs were randomly assigned to two groups and fed either a basal diet or a diet containing 90% basal diet and 10% GA. GA did not adversely affect growth performance but reduced 6-7 rib backfat thickness and muscle water loss rate by 19.79% (FDR = 0.027) and 17.80% (FDR = 0.036), while increasing muscle moisture content by 3.51% (FDR = 0.036). GA increased cecal microbial alpha diversity, Bacteroidota-related taxa, and functional genes related to lipid and vitamin metabolism, while decreasing Bacillota and Lactobacillus johnsonii. In the longissimus dorsi, TNNI1, MYL2 and MYL3 were upregulated, whereas FOS and FOSB were downregulated; GA increased vanillyl alcohol, L-histidine, LPE (0:0/22:5), and licochalcone B, but decreased glyceryl monostearate, benzaldehyde, cortisol, tryptamine, 4-ethyloctanoic acid, 8-methylnonanoic acid, and purine. Overall, 10% GA reshaped gut microbial, muscle transcriptomic, metabolomic profiles and collectively influenced 6-7 rib backfat thickness and muscle water-holding capacity in Diqing Tibetan pigs.},
}

@article {pmid42511774,
year = {2026},
author = {Nappo, A and Abbasi, AM and Berno, G and Rueca, M and Smoquina, F and Gruber, CEM and Fabeni, L and Spezia, PG and Carletti, F and Pietrucci, D and Petricciuolo, M and Carnevali, A and Sanna, N and Talarico, C and Federici, E and Chillemi, G and Maggi, F},
title = {Comparative Analysis of Viral Communities in Hospital, University and Urban Wastewater by Shotgun Metagenomic Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511774},
issn = {1422-0067},
support = {CUP F53C24001620001//European Union Next-GenerationEU/ ; Ricerca Corrente-Linea 1 on emerging and re-emerging infections//Ministry of Health/ ; },
abstract = {Wastewater-based surveillance has emerged as a powerful approach for population-level monitoring of pathogen circulation in a timely and non-invasive manner. In this study, shotgun metagenomic sequencing was applied to wastewater samples collected from a hospital (HP), a university campus (UN), and a wastewater treatment plant (WTP). Viral sequences were taxonomically classified using Kraken2. Specifically, HP samples showed the highest viral richness, followed by WTP and UN samples (HP vs. UN, p = 0.0003; WTP vs. UN, p = 0.0018). Using Jaccard distance, significant differences were observed between WTP and UN (R[2] = 0.181, p < 0.001), WTP and HP (R[2] = 0.159, p < 0.001), and UN and HP (R[2] = 0.223, p < 0.001), and similarly, for Sørensen-Dice dissimilarity: WTP vs. UN (R[2] = 0.238, p < 0.001), WTP vs. HP (R[2] = 0.212, p < 0.001), and UN vs. HP (R[2] = 0.307, p < 0.001). Human-associated viral families were detected across all sources, predominantly Poxviridae, Orthoherpesviridae, Polyomaviridae and Circoviridae. Furthermore, the taxonomic composition of indirectly associated viruses, mainly Anelloviridae and Crassvirales, was examined. Overall, these findings support the potential of wastewater metagenomics as a reliable tool for monitoring viral diversity within environmental and public health contexts, although further research is needed to establish its operational utility for routine surveillance applications within a One Health framework.},
}

@article {pmid42511982,
year = {2026},
author = {Xu, Y and Li, C and Zhao, Y and Lei, S and Yang, W and Yao, S and Wu, K and Huang, J and Yu, Z and Chen, S},
title = {Tracking Gut Homeostasis: Key Taxa Transitions and Core Network Hyper-Connectivity as Early Signals of Dysbiosis.},
journal = {Biomedicines},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/biomedicines14071508},
pmid = {42511982},
issn = {2227-9059},
support = {2022JJ30916//Hunan Provincial Natural Science Foundation/ ; 82270564//National Natural Science Foundation of China/ ; 82470564//National Natural Science Foundation of China/ ; 2022M713521//China Postdoctoral Science Foundation/ ; },
abstract = {Background: Although the gut microbiota is generally recognized to remain relatively stable in healthy individuals, its taxonomic composition still undergoes subtle temporal fluctuations. To systematically characterize these dynamic variations, we adopted "enterotypes" as a macroscopic and practical metric to evaluate the structural dynamics of the intestinal microbial community. Methods: We longitudinally recruited a cohort of healthy adults and collected a total of 72 shotgun metagenomic fecal samples across approximately 40 days. All samples underwent metagenomic sequencing, and subjects were grouped by their predominant enterotypes and longitudinal fluctuation patterns. We evaluated the microbial markers and the longitudinal co-occurrence network topologies of different groups to clarify the potential factors causing gut microbial fluctuations. Results: Longitudinal tracking revealed that those undergoing persistent alterations in microbial communities exhibited diarrhea symptoms, accompanied by markedly greater variability in gut microbiota. The reduction in Alistipes shahii is a potential predictive marker for community instability, exhibiting a cross-validated AUC of 0.824 (95% CI: 0.760-0.888). Furthermore, the co-occurrence network and correlation analysis indicated that fluctuating communities exhibited significantly higher clustering coefficients and denser connectivity among core taxa. Rather than indicating robustness, this dense architecture reflected an increased degree of microbial interdependence within the unstable gut microbial community. Conclusions: This preliminary study discovered candidate bacteria taxa that may serve as indicators of disturbances in the gut microbiota. Furthermore, the hyper-connectivity during continuous fluctuations suggested that increased interdependent microbial relationships meant diminished gut resilience. These results offer a new perspective for detecting early signals of dysbiosis and understanding mechanisms underlying stability of gut microbiota.},
}

@article {pmid42512542,
year = {2026},
author = {Liu, L and Zhang, J and Ma, Q and Wang, J},
title = {Herpesvirus-Associated Visual Impairment: Clinical Features, Etiological Spectrum, and Treatment Outcomes in Consecutive Patients from a Tertiary Neurological Clinic.},
journal = {Brain sciences},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/brainsci16070768},
pmid = {42512542},
issn = {2076-3425},
abstract = {[Background] Herpesvirus infections can induce diverse visual impairments with permanent sequelae, yet systematic data on their clinical spectrum and outcomes remain scarce. [Methods] We conducted a single-center retrospective cohort study at the Department of Neurology, Beijing Tongren Hospital, Capital Medical University. Thirteen consecutive patients (19 affected eyes) with herpesvirus-related visual impairment admitted between January 2016 and January 2025 were enrolled. Demographic data, clinical manifestations, etiological tests (polymerase chain reaction [PCR], metagenomic next-generation sequencing [mNGS], serology), neuroimaging, treatment regimens, and visual outcomes were analyzed. [Results] The cohort had a mean age of 50.4 years (range 31-66), with male predominance (84.6%, 11/13). Varicella zoster virus (VZV) was the leading pathogen (76.9%, 10/13), followed by herpes simplex virus type 1 (HSV-1), Epstein-Barr virus (EBV), and pseudorabies virus (PRV). Eight patients (61.5%) developed optic neuritis (ON) secondary to VZV infection, and five patients (38.5%) suffered from acute retinal necrosis (ARN), which was caused by VZV (n = 2), HSV-1 (n = 2), and PRV (n = 1). Bilateral involvement occurred in 46.2% (6/13) of patients. ARN was associated with the most severe visual loss. At the disease nadir, 46.2% of patients (6/13) presented with no light perception (NLP). Notably, five of these six NLP cases were diagnosed with ARN. Etiological confirmation was achieved in only 38.5% (5/13) of cases. mNGS of cerebrospinal and vitreous fluid, alongside aqueous humor PCR, are pivotal for diagnosing HSV-1/EBV mixed infections and rare PRV infection. All patients received antiviral therapy, 11 of whom (84.6%) were treated with intravenous antiviral agents. Glucocorticoids were administered as combination therapy to all patients. However, only one of eight VZV-ON eyes showed genuine visual improvement. In VZV-ARN, the initially involved eyes stayed NLP at final follow-up, while the fellow eyes recovered vision. Still, all non-VZV ARN patients had persistent bilateral NLP during follow-up. [Conclusions] Herpesvirus-associated visual impairment is dominated by VZV, manifests as ON or ARN, and carries a high risk of severe permanent vision loss-particularly in ARN. The emergence of zoonotic PRV underscores the need for heightened clinical vigilance. Diagnostic delays and insufficient interdisciplinary collaboration contribute substantially to poor outcomes.},
}

@article {pmid42513364,
year = {2026},
author = {Zheng, L and Wang, X and Li, J and He, H and Chen, X},
title = {Metagenomic Next-Generation Sequencing Versus Conventional Microbiological Tests for Pathogen Identification and Prognostic Evaluation in Pediatric Patients with Post-Cardiac Surgery Infections: A Retrospective Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/jcm15145450},
pmid = {42513364},
issn = {2077-0383},
support = {Chinese Academy of Medical Sciences Fuwai Hospital high-level Hospital Research Fund（2025-GSP-QN-40,2025-GSP-QN-7 and 2025-GSP-GG-19）//Fu Wai Hospital/ ; },
abstract = {Object: Postoperative infection is a severe complication after pediatric cardiac surgery, which is closely associated with sepsis, multiple organ dysfunction, prolonged mechanical ventilation, extended ICU stay and increased mortality. Conventional microbiological tests (CMT) are limited by low sensitivity, long turnaround time, and poor capacity for detecting viruses and polymicrobial infections. This study aimed to compare the diagnostic efficacy of mNGS with that of CMT, and to explore the impact of polymicrobial infection on clinical outcomes in this high-risk pediatric population. Methods: A retrospective cohort study was conducted on 4889 pediatric patients admitted to the PICU after cardiac surgery from January 2025 to March 2026. A total of 510 patients were diagnosed with postoperative infections, including 879 CMT specimens and 86 mNGS specimens enrolled for analysis. Pathogen detection rates, pathogen spectrum and antimicrobial resistance profiles were compared between the two detection methods. Clinical prognostic indicators including mechanical ventilation duration, PICU length of stay and the requirement for continuous renal replacement therapy (CRRT) were further compared between patients with polymicrobial infection and monomicrobial infection. Results: Respiratory tract infection accounted for 87.8% of all postoperative infections, and Gram-negative bacteria were the predominant pathogens, accounting for 65.9%. The overall pathogen detection rate of mNGS was significantly higher than that of CMT (79.1% vs. 56.5%, p < 0.001). Notably, mNGS exhibited significantly better performance in detecting viruses (37.2% vs. 5.8%, p < 0.001), anaerobic pathogens and polymicrobial infections (38.2% vs. 5.4%, p < 0.001). Patients with polymicrobial infections had significantly longer mechanical ventilation time, longer PICU stay, and higher CRRT utilization rate (all p < 0.05), indicating a poorer clinical prognosis. Gram-negative bacteria showed high resistance to penicillins and early-generation cephalosporins, but remained susceptible to carbapenems and β-lactamase inhibitor combination agents. Gram-positive bacteria showed a high resistance rate to penicillin, while maintaining 100% susceptibility to vancomycin and linezolid. Conclusions: mNGS serves as a more sensitive and comprehensive tool for pathogen detection in children with post-cardiac surgery infections, especially for viral and polymicrobial infections. Polymicrobial infection is an independent risk factor for adverse clinical outcomes. Routine application of mNGS in critically ill children may help guide targeted antimicrobial therapy and improve prognosis.},
}

@article {pmid42513896,
year = {2026},
author = {Ma, P and Ma, F and Hu, Q and Zhang, W and Gu, H and Wei, D and An, Z},
title = {Study on Gut Microbiota Adaptation of Plateau Zokor (Eospalax baileyi) to High-Altitude Environments.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071390},
pmid = {42513896},
issn = {2076-2607},
abstract = {To further investigate altitude-associated variations in gut microbiota and serum metabolites of plateau zokors (Eospalax baileyi) and elucidate their adaptive mechanisms to high-altitude environments, we performed fecal metagenomic sequencing and serum metabolomic profiling (Q200 platform) on individuals from high (3700 m, n = 6) and low (2700 m, n = 6) elevations, followed by integrated analysis of microbial and metabolomic datasets. Results indicated that in high-altitude plateau zokors, the relative abundance of Firmicutes decreased, while that of Bacteroidota increased. The dominant genera within this group were identified as Bacteroides and unclassified members of the Lachnospiraceae family. Moreover, the abundances of Bacteroides and unclassified members of the Muribaculaceae family increased with elevation. At the species level, seven fully annotated differentially abundant taxa were identified: Candidatus Amulumruptor caecigallinarius, Schaedlerella arabinosiphila, Muribaculum gordoncarteri, Heminiphilus faecis, Prevotellamassilia timonensis, Staphylococcus aureus, and Bacteroides graminisolvens. KEGG enrichment analysis indicated significant upregulation (p < 0.05) of energy supply pathways, such as oxidative phosphorylation, and antioxidant-related pathways, including β-alanine and lysine metabolism, in the high-altitude group. Conversely, cysteine and methionine metabolism pathways were markedly downregulated (p < 0.05). Serum levels of ursodeoxycholic acid and tauroursodeoxycholic acid (TUDCA) were significantly elevated (p < 0.05), while deoxycholic acid (DCA) levels decreased (p < 0.05). In conclusion, the composition and function of gut microbiota, along with serum metabolite profiles, differ significantly (p < 0.05) between plateau zokors from different altitudes. Through synergistic interactions between gut microbiota and host metabolites, plateau zokors develop adaptive mechanisms that integrate energy metabolism, oxidative stress response, intestinal barrier integrity, and mucosal immunity. This ultimately facilitates their acclimatization to high-altitude extreme environments characterized by hypoxia and low temperatures.},
}

@article {pmid42513908,
year = {2026},
author = {Carvalho, APA and Almada, MS and Leal, CD and Fernandes, J and Costa, MC and Fonseca, VS and Giovanetti, M and Alcantara, LCJ and Araújo, JC},
title = {International Airport Wastewater as a Sentinel Site for Genomic Surveillance of Human Viruses and Bacteriophages.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071402},
pmid = {42513908},
issn = {2076-2607},
support = {424004/2021-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 01779-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 306899/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 0000000-X//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
abstract = {Airports are strategic targets for wastewater-based epidemiology because they concentrate highly mobile populations and may provide early signals of pathogen circulation. However, metagenomic investigations of airport wastewater remain limited, particularly in South America. Here, we present one of the first hybrid-capture target-enriched metagenomic investigations of airport wastewater in Brazil, integrating the detection of human-associated viruses and bacteriophage-derived host signatures to evaluate airports as sentinel surveillance sites. Seven untreated wastewater samples collected from a major Brazilian airport between December 2021 and March 2023 were concentrated, subjected to nucleic acid extraction, and analyzed using hybrid-capture target-enriched next-generation sequencing. Taxonomic analysis identified 615 viral and bacteriophage-associated taxa, including 440 viruses and 175 bacteriophages. Among the viral fraction, 21 human-associated viral taxa representing eight viral families were selected for detailed analysis. Norovirus GII was detected in all samples, while Mamastrovirus 1 and JC polyomavirus were detected in six of seven samples. SARS-CoV-2 and dengue virus type 1 were simultaneously detected in the March, 2023 sample. The bacteriophage fraction comprised 47 host-associated phage groups, with Streptococcus-associated phages predominating across samples. These findings demonstrate that airport wastewater can capture diverse human viral and bacteriophage-derived signatures associated with population mobility, supporting its application in environmental genomic surveillance and early-warning systems for emerging and circulating pathogens.},
}

@article {pmid42513909,
year = {2026},
author = {Luo, D and Ponsero, AJ and Wright, K and Baker, DJ and Telatin, A and Townsley, C and Giotis, ES},
title = {Microbiome Stability in Wild and Rehabilitated Insectivorous Bats Revealed by Shotgun Metagenomics.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071403},
pmid = {42513909},
issn = {2076-2607},
support = {MR/Z506242/1/MRC_/Medical Research Council/United Kingdom ; RGS\R2\242527//Royal Society/ ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG2260/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation-associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.},
}

@article {pmid42513924,
year = {2026},
author = {Li, F and Suo, L and Bian, K and Sun, K and Yang, C and Tang, J},
title = {First Report of Bergeyella zoohelcum Associated with Hemorrhagic Pneumonia in Forest Musk Deer (Moschus berezovskii): Evidence from Bacterial Culture, 16S rRNA Sequencing, and Metagenomic Analysis.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071418},
pmid = {42513924},
issn = {2076-2607},
support = {2025NC-YBXM-120//Shaanxi Key Research and Development Program/ ; 2024k-08//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025k-26//Science and Technology Projects of Shaanxi Academy of Science/ ; },
abstract = {Hemorrhagic pneumonia is a severe and often fatal disease in captive forest musk deer (Moschus berezovskii), but the pathogen remains incompletely understood. Based on incomplete statistics, the estimated incidence in captive populations ranges from 20% to 80%, with the disease occurring mainly in autumn, winter, and early spring. The disease has an acute onset and rapid progression. Due to the species' strong stress response, affected animals rarely show behavioral changes, making early detection difficult. In this study, we investigated a mortality case presenting with oral bleeding and hematemesis on a forest musk deer farm. Postmortem examination revealed diffuse hemorrhagic pneumonia, and lung tissue samples were collected for histopathology, bacterial isolation, full-length 16S rRNA gene sequencing, and DNA/RNA virome sequencing. Histological examination showed extensive alveolar hemorrhage, fibrinous exudate, and macrophage infiltration. Bacterial culture and 16S rRNA gene sequencing identified Bergeyella zoohelcum as the predominant bacterium, accounting for 100% of the bacterial community in the lung tissue. Virome analysis revealed predominantly DNA bacteriophages (e.g., Cirlivirales, Cremevirales, Microviridae) and no known pathogenic RNA viruses; only seven low-abundance, unclassified RNA viral contigs of low completeness were detected. These results indicate that B. zoohelcum is the likely causative agent of hemorrhagic pneumonia in this case, with no evidence of viral involvement. This study provides the first direct association of B. zoohelcum with hemorrhagic pneumonia in forest musk deer, highlighting its pathogenic potential and the importance of monitoring this bacterium in captive populations.},
}

@article {pmid42513986,
year = {2026},
author = {Gan, L and Fang, S and Wu, H and Yao, T and Chen, W and Li, Y and Han, Y and Zhou, L},
title = {Metagenomic Insights into the Seasonal Distribution and Dissemination Risks of Biocide and Metal Resistance Genes in a Subtropical Coastal Ecosystem.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071480},
pmid = {42513986},
issn = {2076-2607},
support = {No. GXKEYLA-2023-01-1//Ministry of Agriculture and Rural Affairs/ ; },
abstract = {The widespread use of antimicrobial biocides and metals has led to the continuous accumulation of biocide and metal resistance genes (BMRGs) in the environment. The issue is of growing concern, as it reduces the efficacy of these agents and poses a potential threat to coastal ecological security. However, the extent of coastal BMRG pollution, its transmission mechanisms, and the influence of seasonal variations on its assembly remain poorly understood. In this study, metagenomic sequencing was employed to investigate BMRGs, microbiomes, and mobile genetic elements (MGEs) within the subtropical nearshore ecosystem of the Beibu Gulf during the autumn and winter seasons. A total of 33 BMRG types and 457 subtypes were detected, with higher subtype diversity in winter than in autumn (440 vs. 326 subtypes). Notably, genes resistant to multi-biocides exhibited the highest diversity, whereas those resistant to both biocides and metals were the most abundant. Co-occurrence network analysis showed that 22 of the 23 detected BMRGs in the winter network were associated with MGEs, especially transposase-related elements such as tnpA. Path modeling indicated that BMRG abundance was more strongly associated with bacterial community composition in autumn, whereas MGE-related variables showed stronger associations in winter. These findings suggest a pronounced seasonal shift in the underlying mechanisms shaping BMRG dynamics, with bacterial communities playing a dominant role in autumn and MGEs playing a more critical role in winter. This seasonal shift highlights the need for season-specific monitoring of BMRGs, coastal pollution control, and resistance-risk management in subtropical coastal ecosystems.},
}

@article {pmid42513994,
year = {2026},
author = {Duan, C and Wang, D and Tan, L and Wang, Q and Tan, Z and Cheng, Y},
title = {Habitat-Dependent Ecological Differentiation of Soil and Water Microbiomes in High-Altitude Alpine Meadow Ecosystems on the Qinghai-Tibetan Plateau.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071489},
pmid = {42513994},
issn = {2076-2607},
support = {2023-NK-147//Science and Technology Department of Qinghai Province/ ; },
abstract = {High-altitude ecosystems are characterized by extreme environmental conditions that strongly influence microbial community structure and function. However, whether soil and water microbiomes exhibit similar ecological responses to environmental variation in alpine meadow ecosystems on the Qinghai-Tibetan Plateau remains poorly understood. Here, we combined 16S rRNA gene amplicon sequencing and metagenomic sequencing to compare soil and water microbiomes across two regions (LZ and NQ) with distinct physicochemical profiles. Environmental heterogeneity was more pronounced in water habitats, where all measured parameters (pH, total nitrogen, total organic carbon, and chemical oxygen demand) varied significantly between sites (p < 0.001). Correspondingly, water microbiomes exhibited greater regional differentiation than soil microbiomes, evidenced by stronger beta-diversity separation (PERMANOVA, R[2] = 0.667 vs. 0.376) and a lower proportion of shared ASVs (65.3% vs. 97.2%). Ecological assembly analysis revealed a sharp contrast: water communities were primarily governed by deterministic processes (accounting for >80% of assembly, with heterogeneous selection as the dominant driver), whereas soil microbiomes were dominated by stochastic processes (>50%). Furthermore, water microbiomes underwent more intense network restructuring, with interaction complexity increasing significantly from 70 nodes and 268 edges in the LZ region to 130 nodes and 577 edges in the NQ region, whereas soil networks remained relatively stable (146 nodes/368 edges to 128 nodes/391 edges). Functional profiling further indicated broader regional redistribution in water compared to the relatively conserved functional framework of soil communities. Resistome analysis identified distinct ARG structures between habitats while revealing 25 overlapping categories, suggesting potential ecological connectivity. Collectively, our findings demonstrate that water microbiomes are more sensitive to regional environmental variation than soil microbiomes, with aquatic communities responding through deterministic restructuring and heightened interaction complexity. These results provide quantitative evidence that high-altitude soil and water microbiomes adopt distinct ecological strategies, offering new insights into the mechanisms governing microbial adaptation and antibiotic resistance distribution.},
}

@article {pmid42514009,
year = {2026},
author = {Zheng, H and Zhang, Y and Wang, Z and Li, D},
title = {Bacterial Diversity, Structure, and Function in Rhizosphere and Bulk Soils of Grapevines: Comparing Gravelly, Calcareous, and Aeolian Sandy Textures.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071504},
pmid = {42514009},
issn = {2076-2607},
support = {U20A2042//Key Project of the National Natural Science Foundation of China Regional Innovation and Devel-opment Joint Fund/ ; 2025QN03197//National Natural Science Foundation of Inner Mongolia Autonomous Region/ ; CARS-29-zp-03//Water Physiology and Water-saving Cultivation in the National Grape Industry Technology System/ ; },
abstract = {Soil texture is a key determinant shaping bacterial communities in vineyard ecosystems, yet how different soil textures modulate bacterial characteristics in rhizosphere versus bulk soils during grapevine growth remains poorly understood. This study collected rhizosphere and bulk soil samples from five commercial Vitis vinifera cv. Cabernet Sauvignon vineyards in the eastern piedmont of Helan Mountain, Ningxia, China, spanning three distinct textures (gravelly, calcareous, and aeolian sandy soils). Shotgun metagenomic sequencing, soil physicochemical analysis, and four soil enzyme activity (alkaline phosphatase, urease, catalase, and invertase) measurements were conducted, using PERMANOVA and RDA to identify dominant driving factors. The results showed that bacteria accounted for 97.6% of all annotated sequences, representing the dominant group in soil microbial communities. Significant differences in bacterial abundance and alpha diversity (Chao1, ACE, Shannon, and Simpson) were observed in bulk soils across textures, whereas rhizosphere soils showed significant abundance differences but similar diversity levels. However, the 50 cm bulk soil sampling distance may have attenuated the true rhizosphere effect, and these findings should be interpreted with this methodological constraint in mind. Notably, bacterial community structure differed significantly between soils of the same pedogenic type but different textures, confirming that soil texture, rather than pedogenic classification, is the primary driver. Thirteen dominant bacterial phyla (>1% relative abundance) were identified, with Proteobacteria (47.7%), Actinobacteriota (22.9%), and Acidobacteriota (6.5%) as the main taxa. Mantel tests revealed significant correlations between nitrogen, phosphorus, organic matter contents and enzyme activities in rhizosphere soils (r ≥ 0.4, p < 0.01). RDA indicated that total phosphorus (TP), organic matter (OM), alkali-hydrolyzable nitrogen (AN), Mg, pH, available K (AK), and enzyme activities were key drivers of bacterial community structure (p < 0.05). Annotated metabolic functions based on KEGG orthology indicated lower overall metabolic pathway abundances in gravelly soils compared to calcareous and aeolian sandy soils. In conclusion, soil texture, rather than broad pedogenic classification, primarily shapes vineyard bacterial communities, providing a theoretical basis for precision viticulture and sustainable soil management.},
}

@article {pmid42514018,
year = {2026},
author = {Yin, Y and Zhao, B and Li, R and Wang, R and Peng, J and Xia, B and Tian, J},
title = {Identification of Leptotrichia hofstadii as a Post-Treatment Recurrence Biomarker in Severe Early Childhood Caries.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071513},
pmid = {42514018},
issn = {2076-2607},
support = {82301078//National Natural Science Foundation of China/ ; L232110//Beijing Natural Science Foundation/ ; },
abstract = {Recurrence remains a significant challenge following the treatment of Severe Early Childhood Caries (S-ECC). This study aimed to identify candidate recurrence-related biomarkers for S-ECC and elucidate their potential pathogenic mechanisms. Through metagenomic sequencing of supragingival plaque from 32 children at one month post-treatment, we identified Leptotrichia hofstadii as one of the potential biomarkers for S-ECC recurrence (AUC = 0.8438 for the sequencing set and AUC = 0.75 for the validation set). In vitro dual-species biofilm assays using crystal violet staining and Confocal Laser Scanning Microscopy (CLSM) demonstrated that L. hofstadii promotes early-stage S. mutans colonization and extracellular polysaccharide (EPS) formation through contact-dependent synergistic interactions. Scanning electron microscopy revealed that L. hofstadii may function as a spatial scaffold within dual-species biofilm. Furthermore, this synergy significantly accelerates environmental acidification, leading to earlier attainment of the critical demineralization threshold (pH 5.5). At the transcriptional level, carbohydrate metabolism-related pathways were upregulated in dual-species biofilm, including starch and sucrose metabolism, PTS and ABC transporters. Additionally, the fruA gene, which degrades fructan in EPS was downregulated in the dual-species biofilm compared with S. mutans monoculture. These findings suggest that L. hofstadii facilitates a cariogenic microenvironment by enhancing the metabolic activity of S. mutans biofilms. Collectively, this study identifies L. hofstadii as a potential biomarker for S-ECC recurrence prediction and provides preliminary insights into possible interspecies mechanisms, offering valuable clues for future research into targeted preventive strategies.},
}

@article {pmid42514045,
year = {2026},
author = {Wang, M and He, Q and Qiu, Y and Huang, L and Zhang, Y and Ye, D and He, Z and Wen, C},
title = {High Humidity Exacerbates Rheumatoid Arthritis in Mice via Prevotella stercorea-Mediated Chondroitin Sulfate Degradation.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071540},
pmid = {42514045},
issn = {2076-2607},
support = {82405212//National Natural Science Foundation of China/ ; 82274382//National Natural Science Foundation of China/ ; 82474147//National Natural Science Foundation of China/ ; },
abstract = {Background: Rheumatoid arthritis (RA) is influenced by environmental exposures. High humidity has been clinically associated with worsened joint symptoms, but the microbial and metabolic mechanisms remain unclear. We investigated whether a gut microbiota-metabolism axis contributes to humidity-associated aggravation of collagen-induced arthritis (CIA). Methods: CIA mice were maintained under normal or high relative humidity. We integrated 16S rRNA and metagenomic sequencing, liquid chromatography-tandem mass spectrometry metabolomics, and intestinal barrier assessments. Fecal microbiota transplantation (FMT) was performed to evaluate microbiota dependency. Based on multi-omics findings, we quantified chondroitin sulfate (CS) and conducted functional experiments involving Prevotella stercorea (P. stercorea) supplementation, CS administration, and in vitro degradation assays. Results: High humidity aggravated arthritis severity and systemic inflammation, including increased interleukin-6, interleukin-17A, and granulocyte colony-stimulating factor, and was accompanied by impaired intestinal barrier integrity. FMT supported a microbiota-dependent contribution. Metagenomic analysis identified enrichment of P. stercorea and glycosaminoglycan degradation pathways under high humidity. CS abundance was reduced in articular cartilage, P. stercorea degraded CS in vitro and was associated with cartilage CS loss in vivo, and CS supplementation attenuated arthritis under high humidity and reduced the arthritis-promoting effects associated with P. stercorea. Conclusions: High humidity is associated with microbiota-dependent functional remodeling, enhanced CS degradation, and aggravated arthritis in CIA mice. These findings suggest that humidity-associated alterations in microbial CS metabolism may link environmental exposure to cartilage disruption and joint inflammation.},
}

@article {pmid42514066,
year = {2026},
author = {Nawaz, MA and Nawaz, MZ and Haider, SZ and Alghamdi, HA and Yan, W},
title = {Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071561},
pmid = {42514066},
issn = {2076-2607},
support = {RGP2/665/46//King Khalid University/ ; },
abstract = {Small non-coding RNAs (sRNAs) are ubiquitous post-transcriptional regulators that enable rapid bacterial adaptation to fluctuating environments. Previous reviews have largely focused on sRNA mechanisms in model organisms. This review integrates computational prediction, meta-omics-based discovery, and synthetic biology applications of small regulatory RNAs in marine and environmental prokaryotes, providing a multi-layered perspective from identification to functional and engineering applications. The current landscape of sRNA identification tools is critically evaluated, with emphasis on strategies to overcome challenges such as false-positive predictions. Recent advances in mapping the RNA interactome and emerging evidence of previously underappreciated roles of sRNAs in environmental adaptation are discussed. Additionally, metagenomic and metatranscriptomic studies revealing the diversity of environmental sRNAs in uncultured microbial communities are summarized, highlighting their ecological significance. Finally, a curated overview of synthetic sRNA applications in metabolic engineering, including target genes and enhanced product yields, is provided as a resource for strain engineering. Collectively, this review provides a holistic view of prokaryotic sRNA biology, distinguishing it from more narrowly focused studies. Overall, sRNAs are highlighted as key regulatory elements linking microbial environmental adaptation with emerging biotechnological applications through advances in meta-omics guided discovery and synthetic RNA engineering.},
}

@article {pmid42514075,
year = {2026},
author = {Ferreira, NE and Mendes-Correa, MC and Costa, ACD},
title = {Editorial for the Special Issue "Advances in Viral Metagenomics".},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071570},
pmid = {42514075},
issn = {2076-2607},
abstract = {Viral metagenomics has fundamentally transformed how we investigate the virosphere [...].},
}

@article {pmid42514080,
year = {2026},
author = {Chang, Y and Liu, X and Song, L and Xu, F and Zhang, Z and Yu, M and Wu, G and Zhang, D and Xu, C},
title = {Cold Exposure Shifts Gut Microbial Butyrate Synthesis Toward the Lysine-Dependent and But-Mediated Terminal Pathways to Enhance Cold Tolerance in Min Pigs.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071575},
pmid = {42514080},
issn = {2076-2607},
support = {32302709//National Natural Science Foundation of China/ ; ZL2024C012//Heilongjiang Provincial Natural Science Foundation/ ; LH2023C013//Heilongjiang Provincial Natural Science Foundation/ ; },
abstract = {This study combined seasonal observation in Min pigs and acute cold challenge experiments in Min pigs and Large White pigs to analyze changes in gut butyrate synthesis under cold exposure and its association with thermogenesis. Compared with summer, Min pigs in winter showed significantly higher Bacteroidota abundance (p = 0.006), lysine-pathway genes (p < 0.05), and relative gene abundance of the but terminal pathway (p < 0.05). Fecal (47.96 vs. 40.24 µmol/L, p = 0.020) and serum (4.64 vs. 2.17 µmol/L, p = 0.046) butyrate were also elevated and correlated with 10 thermogenesis-related genes (p < 0.05). Acute cold challenge increased serum butyrate (p = 0.017) and SLC16A1 expression (adjusted p = 0.027) only in Min pigs. Min pigs exhibited higher lysine pathway abundance and greater but terminal contribution than Large White pigs. Metagenomic binning recovered 40 lysine-pathway MAGs (27 unique to Min pigs) and 15 dual-pathway MAGs (11 unique to Min pigs), with Bacteroidota MAGs harboring complete lysine and dual terminal pathways. Collectively, cold exposure correlates with enrichment of lysine-dependent and but terminal butyrate synthesis pathways, highlighting butyrate-producing bacteria as candidate taxa for further investigation of cold-induced gut metabolic remodeling in pigs.},
}

@article {pmid42514086,
year = {2026},
author = {Zheng, Y and Ma, N and Zhao, B and Li, Y and Tian, Y and Liu, J and Quan, Y},
title = {Wastewater Metagenomics for Antimicrobial Resistance and Pathogen Surveillance: A Bibliometric Analysis.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071583},
pmid = {42514086},
issn = {2076-2607},
support = {YDZJ202601ZYTS183//Jilin Province Science and Technology Department/ ; },
abstract = {Wastewater systems are critical reservoirs where antibiotic resistance genes, antibiotic-resistant bacteria, and pathogens converge and disseminate into receiving waters, posing risks to ecosystems and public health. Metagenomics enables culture-independent surveillance of resistome and pathogens in wastewater. After the COVID-19 pandemic, the rapid expansion of wastewater-based epidemiological surveillance, together with growing emphasis on the One Health framework, has further promoted the integration of wastewater metagenomic monitoring with public-health surveillance strategies. However, no bibliometric study has systematically mapped the global research landscape at the intersection of metagenomics, wastewater systems, antimicrobial resistance, and pathogen surveillance. This study retrieved 1161 publications from the Web of Science Core Collection and used CiteSpace to conduct bibliometric analyses. From 2010 to 2025, annual publications increased from 1 to 219, with 72.7% of the total output concentrated between 2021 and 2025. China led in publication output but showed low betweenness centrality, whereas Australia and Sweden served as key intermediaries. Keyword analysis revealed a gradual thematic evolution from the basic detection of antibiotic resistance genes in activated sludge, through studies of dissemination mechanisms, to recent work on One Health and wastewater surveillance. Literature co-citation analysis showed that integration between environmental monitoring and public health literature remains limited, suggesting that the translation of metagenomic surveillance data into health risk assessment frameworks is still at an early stage. By mapping the field's knowledge structure and gaps, this review highlights priorities for advancing wastewater-based Antimicrobial Resistance surveillance, including standardizing analytical methods, developing artificial intelligence-assisted resistome analysis, promoting equitable participation from underrepresented regions, and operationalizing One Health surveillance, thereby supporting the translation of wastewater monitoring into actionable public-health solutions.},
}

@article {pmid42514091,
year = {2026},
author = {Valiakhmetov, EE and Frolov, M and Sukhanov, AY and Miftakhov, AK and Validov, SZ},
title = {Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071587},
pmid = {42514091},
issn = {2076-2607},
support = {FMEG-2027-0007//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, Bacillus, and Pseudomonas). The pipeline applies a two-round specificity-filtering strategy combining whole-genome comparison and high-sensitivity BLASTn validation of revealed strain-specific loci (SSL) against the NCBI nucleotide database. SSL count decreased with increasing Average nucleotide identity (ANIb) of the strains used for the analysis, ranging from one locus in B. halotolerans (ANIb = 98.91%) to 15 loci in S. rhizophila (ANIb = 86.49%). All 25 SSL were universally AT-rich, mainly accessory-genome-associated, with flanking regions enriched in genes of unknown function (34.6%) and mobile genetic elements (19.2%). TaqMan qPCR assays targeting SSL demonstrated high specificity-no target sequences were detected across ten geographically distinct soil samples, nor in a native rhizosphere metagenome-and sensitivity, with limits of detection of 0.01-0.1 pg of genomic DNA. Spike-in experiments in soil yielded method detection limits (MDL) of 850-15,000 CFU/g. All four strains were detected in the wheat rhizosphere seven days after consortium application in a field experiment, validating the pipeline for multi-strain field monitoring.},
}

@article {pmid42514099,
year = {2026},
author = {Flores-Fernández, CN and Hiron, TK and Dobrijevic, D and Zavaleta, AI and Jeffries, JWE and O'Callaghan, CA and Lye, GJ and Ward, JM and Cárdenas-Fernández, M},
title = {Taxonomic and Functional Comparative Metagenomics of Peruvian Salterns: Insights into Microbial Communities and Aminotransferase Potential.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071595},
pmid = {42514099},
issn = {2076-2607},
support = {BB/M027864/1//UK Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/R021627/1//BBSRC ERA CoBioTech/ ; EP/S024883/1//Engineering and Physical Sciences Research Council/ ; 007-2014-FONDECYT//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; EP/S01778X/1//Future Biomanufacturing Research Hub/ ; },
abstract = {Metagenomic analysis of extreme environments is essential in biotechnological research. This work aimed to determine and compare the microbial diversity of two Peruvian saline environments and characterise their functional profiles. Soil metagenomic DNA (mDNA) was analysed from Maras and Pilluana salterns, both with a thalassohaline origin but with different geographical and environmental conditions. Maras samples exhibited more diversity and a remarkably higher abundance of archaea (phylum Euryarchaeota). The most dominant bacterial phyla across all the samples were Pseudomonadota and Actinomycetota. Multiple pathways specific to archaea were more abundant in Maras, as were pathway-related synthesis and degradation of compatible osmolytes such as glycine betaine and ectoine. The most abundant pathways in Pilluana were associated with fatty acid biosynthesis and oxidation. A total of 49 and 47 metagenomic-assembled genomes (MAGs) were retrieved from Maras and Pilluana samples, respectively. Bacterial MAGs were mainly classified within the phyla Psudomonadota, Actinomycetota, Planctomycetota, and Gemmatimonadota. Additionally, a total of 20 putative aminotransferases class III (ATs, PF00202) from Maras3 were cloned and expressed in E. coli Rosetta, and their substrate scoping was assayed against several aldehyde and ketone substrates; AT pQR3082 and pQR3090 showed unique broad substrate acceptance for aromatic and aliphatic substrates. Our study provides new insights into the microorganisms and metabolic pathways of these unique extreme environments, highlighting the promising biotechnological potential of metagenomic ATs.},
}

@article {pmid42514486,
year = {2026},
author = {Chen, X and Wang, J and Tang, L and Zeng, Z and Gao, D and Yi, Y and Qin, L and Xiao, Y and Yang, H and Yang, B},
title = {From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/plants15142118},
pmid = {42514486},
issn = {2223-7747},
support = {Grant No. YLS-2025-ZY02030//Yuelushan Laboratory Breeding Program/ ; No. 22A0151//the Scientific Research Fund of Hunan Provincial Education Department/ ; No. CX20251060//the Hunan Province Graduate Student Scientific Research Innovation Project/ ; No. 31800076//the National Natural Science Foundation of China/ ; No. 2019JJ50245//Natural Science Foundation of Hunan province, China/ ; 2024RC2052//Joint Talent Introduction Program of Yuelushan Laboratory/ ; },
abstract = {Plant endophytes can regulate host plant growth, improve stress resistance, and facilitate the biosynthesis of secondary metabolites, with great research value and application potential. However, traditional approaches for the isolation, cultivation and identification of plant endophytes are constrained by low culturability, limited species diversity, and loss of their original ecological functions inside host tissues. In recent years, integrated multi-omics strategies combining metagenomics, metatranscriptomics, and metaproteomics have exhibited the greatest potential to mitigate culturability limitations by enabling genome-guided targeted strain isolation and in situ functional activity profiling, among which the cultivation and targeted isolation of endophytes benefit most from omics integration. These approaches drive a paradigm shift from conventional blind screening to precise targeted isolation, and from generic medium culture to omics-guided rational cultivation, greatly improving the accuracy of strain identification and functional characterization. Nevertheless, current omics-based strategies still face inherent limitations including high experimental costs, complex operational procedures, and challenging data interpretation. The most critical future direction lies in establishing standardized experimental protocols and shared resource databases, combined with microfluidic platforms and artificial intelligence-assisted bioinformatics analysis, to address the core bottlenecks restricting endophyte isolation, cultivation and identification. This review is the first to systematically summarize research progress on traditional approaches, omics technologies and emerging strategies for plant endophyte isolation, cultivation and identification, highlights prevailing challenges and developmental trends in this field, and provides methodological references for the efficient exploitation and sustainable utilization of plant endophyte resources.},
}

@article {pmid42514595,
year = {2026},
author = {Wang, LJ and Ji, F and Qi, SY and Li, QF and Zhao, M and Xu, CJ and Li, YT and Zhang, AL},
title = {Pine-Extracted Volatile Oils Suppress Root Rot in Psammosilene tunicoides Through Direct Antifungal Activity and Rhizosphere Microbiome Modulation.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/plants15142228},
pmid = {42514595},
issn = {2223-7747},
support = {No.20254916CE340047//Yunnan Key Laboratory of Chinese Medicine Processing/ ; },
abstract = {Frequent outbreaks of root rot in Psammosilene tunicoides W. C. Wu & C. Y. Wu severely compromise the quality of its medicinal materials and hinder its large-scale cultivation. Interestingly, wild P. tunicoides growing under pine trees rarely experience this disease. To explore the potential basis of root rot suppression, we evaluated the direct antifungal activity of pine-derived volatile oils and the associated changes in the rhizosphere microbiome. GC-MS showed that pine turpentine was dominated by α-pinene (45.50%) and longifolene (28.20%). In vitro assays confirmed its highly efficient inhibition (81.65-94.71%) against major root rot pathogens in P. tunicoides. Beyond direct antifungal effects, metagenomic analysis indicated that volatile oil (SYR) treatment was associated with shifts in the rhizosphere microbiome, including increased relative abundances of potentially beneficial taxa, such as Paenibacillus, Trichoderma, and Geosiphon. Pine volatiles might be associated with shifts in the rhizosphere microbial community of P. tunicoides, potentially involving plant-mediated changes in root exudation and the enrichment of certain beneficial microbes. However, it remains to be further elucidated regarding the specific mechanisms underlying these community changes. Functional prediction of the microbial community suggested a predominance of metabolic pathways, secondary metabolite biosynthesis, and flagellar assembly in the SYR group. Conclusively, pine volatiles may contribute to root rot suppression through two potential processes: direct pathogen inhibition and beneficial microbiome enrichment. This study provides a theoretical basis for establishing sustainable agroforestry co-planting systems for P. tunicoides.},
}

@article {pmid42514670,
year = {2026},
author = {Ericsson, AC},
title = {A Comprehensive Review of the Equine Gut Microbiome in Health and Disease.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070659},
pmid = {42514670},
issn = {2306-7381},
abstract = {Molecular microbiology has revolutionized our understanding of the complex host-associated microbiomes required for normative development and physiology. Horses and other members of the family Equidae are particularly reliant on the early maturation and lifelong maintenance of an unusually rich hindgut microbiome for optimal digestion and overall health and performance. Research on the equine gut microbiome has accelerated in the past several years, necessitating a renewed appraisal of the field. The present work is a comprehensive and critical review of the literature regarding the bacterial gastrointestinal microbiome of horses. First, the developmental trajectory of the foal gut microbiome is discussed, followed by descriptions of the taxonomic membership of the core equine gut microbiome, its primary functions and effects on host physiology, and intrinsic and extrinsic factors that shape the equine microbiome during health, with a focus on diet and supplements. Next, evidence supporting adverse effects on the equine gut microbiome of gastrointestinal conditions including colic and colitis, extraintestinal conditions including obesity and laminitis, and pharmacological interventions including antibiotics and non-steroidal anti-inflammatory drugs is summarized. Lastly, clinical and experimental research investigating the effects of treatments targeting the gut microbiome of horses, including probiotics, prebiotics, and fecal microbiome transfer, is critically examined. Conclusions summarize the connection between natural (i.e., wild) equine behavior and the health of the equine gut microbiome and the impacts of human management.},
}

@article {pmid42514689,
year = {2026},
author = {Abi, K and Xia, Z and Gou, L and Zhang, W and Ji'e, K and Li, S and Gao, T and Banma, W and Yang, F},
title = {Integrated 16S rRNA and Metagenomic Analysis of Pulmonary Microbiota in Sheep with Pneumonia.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070679},
pmid = {42514689},
issn = {2306-7381},
support = {SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Mutton Goat & Sheep/ ; 2024CXTD08//Scientific and Technological Innovation Team for Qinghai-Tibetan Plateau Research in Southwest Minzu University/ ; },
abstract = {Sheep are a major livestock species in China, yet pneumonia-related mortality poses a significant obstacle to intensive farming. In this study, 115 sheep lung samples were collected and classified into different pneumonia severity groups based on lung lesion scoring. Subsequently, this study employed 16S rRNA sequencing to systematically investigate the structure and diversity of the pulmonary microbiota in sheep, including alpha diversity, beta diversity, and LEfSe analyses. Metagenomic techniques were also applied to analyze the abundance of metabolic pathways, exploring the associations between functional gene differences and pneumonia severity, as well as putative antibiotic resistance genes, virulence factors, and the species contributions of functional genes in severe pneumonia cases. Microbial richness and diversity were significantly higher in the severe pneumonia group than in the healthy/mild lesion group (p < 0.05). While the dominant microbial structures were similar across the groups, notable differences were observed in the abundance of respiratory disease-associated genera, with Pasteurella, Mannheimia, Mycoplasma, Bibersteinia, and Moraxella identified as significantly enriched in severe cases. Moreover, several genera originating from the gut and oral cavity were also associated with pneumonia, suggesting a potential gut-lung axis. Carbohydrate metabolism was the most prevalent pathway in all groups, whereas amino acid metabolism was significantly enriched in the severe pneumonia group. Putative antibiotic resistance genes were differentially enriched; the severe pneumonia group showed significant enrichment of genes conferring resistance to aminoglycosides, tetracyclines, and polymyxins. Virulence factor analysis identified nutritional/metabolic factors and adhesion as the predominant virulence mechanisms. Species contribution analysis further revealed that Mannheimia, Mycoplasma, Pasteurella, and Moraxella were the predominant species associated with functional gene enrichment. In conclusion, the current study reveals associations between changes in the pulmonary microbiota structure and function and the severity of pneumonia in sheep, aiming to provide a foundation for future hypothesis-driven research on the role of the pulmonary microbiota in pneumonia progression.},
}

@article {pmid42514698,
year = {2026},
author = {Sun, Y and Xu, S and Luo, Z and Fan, T and Zhou, X},
title = {Analysis of Bacterial Diversity in Fresh Milk from Commercial Dairy Farms in Xinjiang Based on Metagenomic Sequencing.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070688},
pmid = {42514698},
issn = {2306-7381},
support = {2023NY03-1//Xinjiang Production and Construction Corps/ ; 2024AB035//Xinjiang Production and Construction Corps/ ; },
abstract = {To investigate the biological characteristics of microbes in fresh milk, this study gathered fresh milk from seven large-scale dairy farms in the southern and northern regions of Xinjiang, analyzing the composition and abundance of bacterial communities in these samples through metagenomic sequencing technology. Firmicutes, Proteobacteria, and Actinobacteria were consistently identified as the dominant phyla across all samples, with stable relative abundance patterns across regions. At the genus level, the genera with the highest relative abundances were Sporosarcina, Streptococcus, and Escherichia, with relative abundances of 2.51-2.58%, 2.23-2.27%, and 1.93-1.97%, respectively. While exploring species richness, it was observed that the XN group had the most OTUs, the DR group had the fewest, and there were significant differences in community structure between the ND group and the other six groups. Further Alpha diversity analysis revealed no significant variation in Chao1 indices across the seven sample groups, highlighting a significant difference in Shannon index for ND samples, and no significant differences in Shannon indices between the CJ, JY, KT, DR, and TR samples. Shifting focus to functional potential, the top three relative abundances in the microbial metagenome KEGG functional library are biological systems, human diseases, and environmental information processing; additionally, within the CAZy (Carbohydrate-Active enZymes) database, the three most abundant categories are glycosyltransferases (GT), glycoside hydrolases (GH), and carbohydrate-binding modules (CBM). By delineating these patterns, this study demonstrates the microbial spectrum characteristics of fresh milk from southern and northern Xinjiang, China, offering a theoretical foundation for enhancing the quality of fresh milk in the area.},
}

@article {pmid42514990,
year = {2026},
author = {Kumar, M and Suleimenova, S and Nuralibekov, S and Kasymbekov, Y and Sabyrzhan, T and Isbekov, K and Assylbekova, S and Fefelov, V and Pangereyev, B and Karamendin, K and Kydyrmanov, A},
title = {Metagenomic Characterization and Molecular Screening of Pathogens in Freshwater Amphipods (Gammarus lacustris) from Kazakhstan: Implications for Aquaculture Biosecurity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070663},
pmid = {42514990},
issn = {2076-0817},
support = {BR23591095//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
abstract = {Freshwater amphipods of the genus Gammarus are important trophic components of aquatic ecosystems and are increasingly considered a potential bioresource for aquaculture. However, their role in the maintenance and transmission of infectious agents remains poorly understood. This study evaluated the presence of major crustacean and fish pathogens in Gammarus lacustris populations from Kazakhstan and characterized associated viral communities using metagenomic sequencing. Six pooled samples collected from freshwater ecosystems across Kazakhstan were screened using PCR and RT-PCR assays targeting World Organisation for Animal Health (WOAH)-listed pathogens, including White Spot Syndrome Virus, Taura Syndrome Virus, Infectious Myonecrosis Virus, Aphanomyces astaci, and Aphanomyces invadans. In parallel, high-throughput sequencing (Illumina NovaSeq) was performed to assess virome composition and structure. No WOAH-listed pathogens were detected, suggesting a low detectable occurrence of major notifiable agents under the conditions of the present study. Metagenomic analysis revealed a virome dominated by RNA viruses, particularly picorna-like viruses (Picornaviridae), Dicistroviridae, and Marnaviridae. Phylogenetic and genome organization analyses identified potentially novel or highly divergent viral lineages within Picornavirales. Collectively, these findings suggest a favorable epizootiological profile of G. lacustris populations while highlighting freshwater amphipods as hosts of diverse and partially uncharacterized viral communities relevant to aquatic disease surveillance and aquaculture biosecurity.},
}

@article {pmid42515020,
year = {2026},
author = {Dalle Carbonare, L and Vareschi, A and Dervishi, K and Deiana, M and Locatelli, E and Minoia, A and Piritore, FC and Ruggiero, A and Barbu, IC and Zipeto, D and Piubelli, C and Valenti, MT},
title = {High-Touch, High-Risk: An Exploratory Microbiome Analysis of Hospital Wheelchairs.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070693},
pmid = {42515020},
issn = {2076-0817},
support = {FUR LDC//University of Verona/ ; FUR MTV//University of Verona/ ; Fondi Ricerca Corrente" - L3P6//Ministry of Health/ ; },
abstract = {In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric wheelchairs to characterize microbial DNA recovered from wheelchair surfaces under routine clinical conditions. Microbial DNA and biomass were detected on all sampled surfaces, with median DNA concentrations of approximately 0.015 ng/µL, median cell counts of approximately 4.8 × 10[5] cells/mL, and median OD600 values of approximately 0.038, although variability among wheelchairs was observed. NGS analysis revealed heterogeneous microbial communities composed mainly of taxa associated with human skin microbiota and environmental sources. Opportunistic taxa including Escherichia coli, Staphylococcus haemolyticus, Achromobacter xylosoxidans, and Clostridioides difficile DNA were detected. Differences in microbial composition were observed between the pooled fabric and leather samples, with fabric samples characterized by the dominance of specific taxa and leather samples exhibiting a more heterogeneous microbial profile. In addition, median DNA concentration, cell counts, and OD600 values were reduced by approximately 98-100% on the protective barrier compared with uncovered wheelchair surfaces, with statistically significant differences between conditions. Overall, these findings suggest that hospital wheelchairs may harbor measurable levels of microbial biomass and microbial DNA despite routine sanitation procedures. Lower contamination levels were observed on the protective barrier under the conditions tested. Due to the exploratory nature of the study, the small sample size, and the use of pooled samples for metagenomic analyses, these observations should be interpreted with caution and require confirmation in larger studies.},
}

@article {pmid42515023,
year = {2026},
author = {Montoya, JG and Cho, SM and Smith, S and Gomez, CA and Contopoulos-Ioannidis, DG},
title = {The Hidden Risk of Toxoplasmosis in the Expanding Immunomodulated Host Population: A Call for Guidelines and Registries in Patients on Biologics, Small Molecules, and Cellular Therapies.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070696},
pmid = {42515023},
issn = {2076-0817},
abstract = {Targeted immunotherapies with biologics, small molecules, and CAR T-cell therapies have revolutionized treatment across autoimmune, chronic inflammatory, oncologic, and transplant-related conditions. However, they have also expanded the population of patients susceptible to opportunistic infections. Toxoplasma gondii (T. gondii), a globally prevalent parasite, has emerged as an underrecognized pathogen in this immunomodulated host population. Toxoplasmosis, in such patients, can occur either through reactivation of a chronic/latent/past infection or from an acute/primary infection and may be severe and even fatal. We present here the recommendations for such patients from the Remington Lab, the National Reference Center for Toxoplasmosis in the US. Screening for Toxoplasma infections is needed at baseline prior to starting targeted immunotherapy to identify seropositive patients who would benefit from prophylaxis or pre-emptive strategies and seronegative patients who would benefit from measures to prevent primary/acute infections. Prompt diagnosis of Toxoplasma disease (toxoplasmosis) with molecular tools (T. gondii PCR and/or agnostic metagenomics next-generation sequencing), and prompt initiation of anti-Toxoplasma therapy, can be lifesaving and prevent permanent neurocognitive sequelae and vision loss. The immunomodulatory effects of these therapies persist for several months after discontinuation, thereby extending the window of vulnerability. T. gondii-seropositive women are at increased risk of vertical transmission, even if targeted immunotherapy was discontinued several months before conception. We make a call for education, guidelines, prospective registries, targeted research, and addition of toxoplasmosis risk in the Warnings section of drug leaflets (and particularly so for T. gondii-seropositive women who intend to conceive after having been on targeted immunotherapies).},
}

@article {pmid42515101,
year = {2026},
author = {Weng, M and Zhou, G and Wu, Q and Chen, Q and Li, J and Wang, Z and Li, W},
title = {Mycobacterium tuberculosis and Mycobacterium avium Complex Cutaneous Co-Infection: Diagnostic and Therapeutic Challenges.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070774},
pmid = {42515101},
issn = {2076-0817},
abstract = {Cutaneous co-infection with Mycobacterium tuberculosis (MTB) and Mycobacterium avium complex (MAC) is extremely rare and easily missed due to overlapping histopathological features. We report a previously healthy, HIV-negative middle-aged woman who presented with a progressive destructive mass in the left inguinal-perineal region. Imaging revealed sinus tract formation, osteolytic bone lesions, and chronic inflammation in the right middle lobe of the lung. Initial metagenomic next-generation sequencing (mNGS) detected 3756 reads of the Mycobacterium tuberculosis complex (MTBC) and 111 reads of Mycobacterium intracellulare (M. intracellulare); the latter was interpreted as possible colonization or contamination because of its low abundance. Empirical anti-tuberculosis therapy produced only transient partial improvement, followed by paradoxical worsening, local recurrence, and new bone destruction. After a high suspicion of mixed infection, a MAC-directed combination regimen (including azithromycin and a short course of amikacin) was added, leading to complete clinical cure; subsequent repeat cultures confirmed the presence of MAC. This is the first report of cutaneous MTB-MAC co-infection in the inguinal-perineal region of an adult without overt immune abnormalities, accompanied by disseminated bone lesions. This case highlights that in regions where nontuberculous mycobacteria (NTM) are co-endemic, atypical destructive skin lesions with paradoxical worsening despite initial response to anti-tuberculosis therapy should raise suspicion of MAC co-infection. The combination of mNGS and conventional culture facilitates identification of mixed infections and guides precision therapy, but mNGS results must be interpreted cautiously in the clinical context.},
}

@article {pmid42515556,
year = {2026},
author = {Martino, F and Panmei, K and Duchen, D and Thomas, DL and Kandathil, AJ and Clipman, SJ},
title = {Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070704},
pmid = {42515556},
issn = {1999-4915},
support = {1DP2DA056130-01/NH/NIH HHS/United States ; R01DA058567/NH/NIH HHS/United States ; },
abstract = {Oxford Nanopore technology enables cost-effective, portable, long-read analyses of pathogen genomes. Accurate detection and interpretation of small circular viral genomes, including Anelloviridae, remain challenging due to limited base-level error quantification in rolling-circle amplification (RCA)-derived datasets. Here, we characterized read-level sequencing error profiles using M13mp18, a 7.2 kb circular phage genome, subjected to 1X and 3X shearing during library preparation. M13mp18 DNA was serially diluted into pooled anellovirus-positive plasma DNA extracts. Using custom error-analysis pipelines, we quantified mismatch, insertion, and deletion rates and evaluated consensus reconstruction accuracy across simulated sequencing depths. Since metagenomic viromes contain mixtures of related genomes and uneven coverage across taxa, depth-normalized subsampling was used to assess the precision of read-level error estimates under heterogeneous coverage. Across four benchmarked datasets, per-base error rates ranged from 0.018 to 0.022 errors per aligned base. Complete M13mp18 reference reconstruction was achieved at input levels ≥ 4.6 log10 copies, and consensus sequences reached 100% identity at depths ≥ 15X when sufficient reads were available. Below 4.6 log10 input copies, recovery was inconsistent. These findings provide a controlled empirical characterization of read-level error behavior in RCA-derived nanopore sequencing and support the interpretation of circular DNA virome data generated in complex metagenomic backgrounds.},
}

@article {pmid42515578,
year = {2026},
author = {Meyer, C and Jackson, VLN and de Haan, F and Bolhuis, H and Allen, MJ and Monier, A and Brussaard, CPD},
title = {Infection Dynamics and Coexistence of Two Novel Arctic Phytoplankton Viruses.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070726},
pmid = {42515578},
issn = {1999-4915},
support = {na//University of Amsterdam/ ; na//Royal Netherlands Institute for Sea Research/ ; },
abstract = {Marine algal viruses exhibit a high level of diversity, and closely related viruses targeting the same algal host species can stably coexist. Here we report an example of a single virus-host system concealing hidden complexity. We discovered two double stranded (ds) DNA viruses infecting the Arctic picophytoplankter Micromonas polaris coexisting in culture for over a decade. Genomic sequencing of the lysate originally characterized as MpoV-44T revealed that it comprises two distinct prasinoviruses with ~203-204 kb genomes (MpoV-44T.A and MpoV-44T.B), of which conserved regions only accounted for 36% (the nucleotide level). The viruses were subsequently separated and compared at both genomic and phenotypic levels. In dual infection studies using a single host strain under nutrient-replete conditions, MpoV-44T.A outcompeted MpoV-44T.B. Yet MpoV-44T.B-like viruses were more abundant than MpoV-44T.A-like ones in natural Arctic metagenomes. This apparent paradox may be explained by differences in host strain specificity and/or possible resilience to nutrient stress by MpoV-44T.B, which we hypothesize based on genomic data. This work unveils hidden virus diversity, illustrating that the dynamics of viral coexistence are not always easily predictable, and underscores the importance of studying the underlying mechanisms at play.},
}

@article {pmid42515580,
year = {2026},
author = {Yin, L and Huang, P and Xu, Y and Peng, O and Zhu, K and Xie, E and Yang, S and Liu, J and Li, X and Yan, Z and Qin, J and Lin, W},
title = {Avian Orthoreovirus in China: Molecular Evolution, Transmission Ecology, Immune Modulation, and Integrated Control in the Genomic Era.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070728},
pmid = {42515580},
issn = {1999-4915},
support = {2023YFD1301800//the National Key R&D Program of China/ ; 2024090301, YF2025NYRC03 and 2024020101//the Science and Technology Plan Program of Yunfu city/ ; 2024CXTD15//the Fourth Round of Guangdong Provincial Modern Agricultural Industry Technology System Innovation Team Construction Project/ ; 2023B1212070018//the Science and Technology Plan Program of Guangdong Province/ ; },
abstract = {Avian orthoreovirus (ARV) has re-emerged as one of the most important viral pathogens affecting modern poultry production worldwide. In China, the epidemiological landscape of ARV has undergone a substantial transformation over the past decade, characterized by increasing genotypic diversity, frequent genome reassortment, an expanding host range, and recurrent vaccine-breakthrough outbreaks. Growing evidence indicates that contemporary ARV populations evolve within a dynamic multispecies transmission network shaped by intensive poultry production, host adaptation, and vaccine-associated selective pressures. Recent molecular studies have revealed extensive genetic heterogeneity among circulating strains and highlighted the limitations of conventional σC-based classification systems for accurately describing viral evolution, pathogenicity, and antigenic diversity. Whole-genome analyses further demonstrate that reassortment among chicken-origin, duck-origin, and goose-origin orthoreoviruses plays a pivotal role in generating novel viral variants with altered biological properties. In parallel, accumulating evidence suggests that ARV exerts broad immunomodulatory effects through the disruption of innate antiviral signaling, impairment of lymphoid organ function, interference with vaccine responsiveness, and the enhancement of susceptibility to secondary infections. These findings indicate that ARV should be regarded not only as an arthrotropic pathogen but also as an important immunopathological agent influencing flock health and productivity. This review summarizes current knowledge of ARV in China, with an emphasis on molecular epidemiology, genomic evolution, reassortment mechanisms, transmission ecology, immune interference, vaccine escape, and integrated prevention strategies. Particular attention is given to the increasing importance of whole-genome surveillance, phylodynamic analysis, and multispecies epidemiological monitoring for understanding contemporary ARV evolution. Future perspectives involving structural vaccinology, precision immunization, metagenomics-assisted surveillance, and predictive evolutionary modeling are also discussed. Collectively, sustainable ARV control will likely require genome-informed and adaptive prevention frameworks integrating virology, immunology, epidemiology, and precision poultry management.},
}

@article {pmid42515587,
year = {2026},
author = {Yuan, L and Zhang, N and Yuan, M and Xu, J and Liu, Z and Li, Z},
title = {Novel Species Diversity in China's Northeastern Border Region.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070735},
pmid = {42515587},
issn = {1999-4915},
support = {No. 2025ZD01900100//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; },
abstract = {The northeastern region of China is characterized by complex ecosystems, including forests and wetlands, and borders North Korea, Russia, and Mongolia. It serves not only as a natural reservoir for various microorganisms but also as a critical geographical and ecological hub for cross-border exchanges in Northeast Asia. Based on metagenomics and meta-transcriptomics investigations, this study systematically reviews the current research status of novel pathogens in the northeastern border region of China. It systematically organizes the newly discovered species, their classifications, and geographical distributions, with a focus on analyzing novel viruses that have potential pathogenicity to humans. The novel viruses identified in the northeastern border region belong to 11 viral families, including 9 from the Nairoviridae, 4 from the Rhabdoviridae, 3 each from the Astroviridae, Picornaviridae, and Parvoviridae, and 1-2 from other viral families, indicating a broad diversity of newly discovered viruses. These novel viruses are found in a wide range of hosts, including humans, ticks, minks, Marmota sibirica, and Myodes rufocanus, underscoring the significant public health risks these viruses pose. Geographically, the novel viruses discovered in the northeastern border region show a clustering pattern, with new species primarily concentrated in areas bordering Russia and North Korea. This highlights the unique role of the region as a hotspot for cross-border pathogen transmission and risk. The findings provide a systematic scientific reference for understanding the spectrum of unknown novel pathogens and their geographical distribution in the northeastern border region, assessing the risk of emerging infectious diseases, and optimizing active surveillance systems.},
}

@article {pmid42515641,
year = {2026},
author = {Liu, W and Wang, Y and Ma, J and Liang, X and Yang, L},
title = {Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070789},
pmid = {42515641},
issn = {1999-4915},
support = {42407182//National Natural Science Foundation of China/ ; },
abstract = {Composting is widely used to reduce biological risks during manure recycling, but changes in viral communities and virus-associated antibiotic resistance genes (ARGs) remain poorly resolved. This study aimed to assess changes in DNA viral communities, eukaryotic viral protein signals, virus-associated ARGs, and predicted virus-host linkages during chicken manure composting using paired analyses of total-community metagenomes and viral-particle-enriched viromes. Both approaches recovered viral assemblages dominated by Uroviricota and lytic viruses but produced distinct profiles. Viromes yielded more taxonomically assigned viral operational taxonomic units and a higher proportion of relatively complete viral genomes, whereas metagenomes produced a larger predicted virus-host network. Composting restructured viral communities, reducing manure-associated genera and enriching stage-specific groups. Eukaryotic viral protein signals declined during composting. Virus-associated ARGs accounted for 24.83-38.76% of ARG abundance in metagenomes and 5.38-45.09% in viromes, with lower abundance and richness in viromes. Selected virus-associated ARGs showed transient early enrichment, particularly in the virome. By maturity, both overall virus-associated ARG signals and higher-risk ARG signals had declined. Predicted virus-host associations included bacterial groups containing potential opportunistic pathogens. These results show that composting restructures viral communities and attenuates virus-associated ARG signals, while metagenomes and viromes provide complementary but non-interchangeable views of viral ecology and ARG risk.},
}

@article {pmid42515794,
year = {2026},
author = {Frăsinariu, OE and Ștreangă, V and Rugină, AL and Mîndru, DE and Vintilă, TC and Bădulescu, OV and Bararu-Bojan, I and Lupu, VV and Lupu, A and Mihai, A and Loghin, II and Popescu, DE and Teșoi, DF},
title = {Gut Microbiota and Metabolic Dysfunction-Associated Steatotic Liver Disease: From Dysbiosis to Metagenomic Insights and Therapeutic Perspectives.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {7},
pages = {},
doi = {10.3390/ph19071113},
pmid = {42515794},
issn = {1424-8247},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as the most common chronic liver disorder in the pediatric population, closely paralleling the global rise in childhood obesity. Increasing evidence highlights the gut-liver axis as a key contributor to MASLD pathogenesis, with gut microbiota dysbiosis influencing hepatic steatosis through multiple interconnected mechanisms, including increased intestinal permeability, endotoxemia, altered bile acid metabolism, and modulation of host energy homeostasis. In children, the characterization of microbiota signatures associated with MASLD remains challenging due to heterogeneity across studies, age-related microbial dynamics, and methodological variability. This review synthesizes current evidence regarding the role of the gut microbiota in pediatric MASLD, focusing on pathogenetic pathways, reported microbial patterns, and microbiota-targeted therapeutic strategies, while incorporating relevant mechanistic evidence from adult studies where pediatric data remain limited. Although several taxa have been repeatedly associated with pediatric MASLD, findings are not yet sufficiently consistent for clinical application. Interventions such as probiotics, prebiotics, and dietary modulation show promising but still preliminary results, with limited high-quality pediatric trials available. A deeper mechanistic understanding and standardized study designs are needed to clarify causality and to support microbiota-based precision approaches in pediatric MASLD management.},
}

@article {pmid42515825,
year = {2026},
author = {Kean, K and Mayne, RM and Reid, K and Secret, S and Singleton, BK and Rockett, R and Rajendra, P and Harvala, H and Breuer, J and Azim Ansari, M and Lythgoe, K and Simmonds, P and Golubchik, T},
title = {A Snapshot of the UK Blood Donor Plasma Virome: A Retrospective Cross-Sectional Cohort Study.},
journal = {Journal of medical virology},
volume = {98},
number = {8},
pages = {e71081},
doi = {10.1002/jmv.71081},
pmid = {42515825},
issn = {1096-9071},
support = {NIHR203338//National Institute for Health and Care Research/ ; },
abstract = {Estimates of population prevalence and genetic diversity of bloodborne viruses in healthy humans are essential to support population-scale monitoring for transfusion transmission risk. In the UK and globally, blood donations are routinely screened for a limited number of high-consequence pathogens, but the full composition of the plasma virome remains to be characterized. Using a novel quantitative targeted metagenomics sequencing approach, we analyzed previously unscreened plasma donations collected by NHS Blood and Transplant in England for all major pathogenic and known commensal human bloodborne viruses, and quantified their viral burden. Here we show that in a representative sample of 5064 UK blood donors in pools of 24 collected over a 1-month period, the virome was dominated by a small number of largely persistent species, representing < 10% (10/106) of previously identified human bloodborne viruses. The principal genera of human anelloviruses (TTV, TTMV and TTMDV) were detected in 89% of pools, albeit at low read count, inconsistent with measured anellovirus viral loads. In contrast, human pegivirus type 1 (HPgV-1), had an estimated population prevalence of 3.7% (95% CI 3.0%-4.4%), with high read count and complete genome recovery in around one half of positive pools, consistent with high titer in plasma. Less common detections included one species of gemykibovirus in five separate plasma pools, one hepatitis C virus (genotype 1a), and polyomaviruses and herpesviruses with prevalences between 0.04% (parvovirus 4, BK polyomavirus) to 0.41% (human herpesvirus 6). Phylogenetic analyses revealed mixed TTV, TTMV, and TTMDV populations and almost exclusively genotype 2 HPgV-1, consistent with known genotype distributions in Europe. Our results provide a baseline for describing the healthy plasma virome in UK blood donors.},
}

@article {pmid42515960,
year = {2026},
author = {Kopp, AR and Uhlemann, AC},
title = {Gut dysbiosis and multidrug-resistant colonization in solid organ transplantation.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001303},
pmid = {42515960},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize recent advances in the understanding of the interplay between gut dysbiosis and MDRO colonization and infection in SOT patients.

RECENT FINDINGS: Recent studies have added complementary metagenomics, internal transcribed spacer sequencing, metabolomics, and pathway analysis to descriptive microbiome profiling. Enhanced ecologic frameworks have identified microbial, functional, and clinical signatures associated with MDRO colonization and infection. Microbiome-targeting interventions are emerging as strategies to reduce morbidity associated with MDRO infection.

SUMMARY: MDRO infection is a significant cause of post-transplant mortality. Persistent gut dysbiosis peri-transplant reduces colonization resistance and predisposes patients to adverse clinical outcomes. Understanding the dynamics of this process will aid in the care of these high-risk patients.},
}

@article {pmid42516269,
year = {2026},
author = {López-Martínez, KP and Hereira-Pacheco, S and Hernández-Oaxaca, D and López-Ruiz, F and Vázquez-Rosas-Landa, M},
title = {rbims: an R package for integrative functional profiling and pathway-level discrimination in metagenome-assembled genomes.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1831383},
pmid = {42516269},
issn = {2673-7647},
abstract = {Metagenomics enables the recovery of metagenome-assembled genomes (MAGs), providing access to the metabolic potential of uncultured microbial communities that drive ecosystem function and biogeochemical cycles. However, as MAGs datasets increase in size and complexity, comparing functional repertoires and identifying ecologically meaningful traits across experimental gradients becomes increasingly difficult. Here, we present rbims, a modular R package for integrative functional profiling of MAGs and metagenomic datasets. rbims supports annotations from KEGG, dbCAN, InterProScan, MEROPS, and PICRUSt2, and enables the calculation of gene presence/absence, raw abundance, and pathway coverage, as well as metadata-informed comparative analyses and publication-ready visualizations. Beyond descriptive profiling, rbims implements an exploratory discriminant framework that combines compositional differential analysis (ALDEx2) with random forest-based feature ranking to prioritize candidate metabolic traits associated with environmental factors. Importantly, it extends gene-level analysis to pathway-level directional bias testing, allowing users to evaluate whether the majority of genes within a metabolic route are consistently enriched toward a given condition. We applied rbims to 42 MAGs recovered from a hydrocarbon enrichment experiment in the North Atlantic Ocean. The workflow identified widespread hexadecane and phenanthrene degradation potential, detected enriched oxidoreductase-related protein families, and revealed a strong pathway-level directional bias toward deep-water MAGs for phenanthrene, naphthalene, and hexadecane degradation pathways. By integrating annotation parsing, quantitative trait analysis, statistical discrimination, and visualization in a reproducible framework, rbims provides a user-friendly platform for functional interpretation in genome-resolved metagenomics.},
}

@article {pmid42516368,
year = {2026},
author = {Zhang, Y and Wang, S and Chang, S and Li, Y and Dang, Y and Wang, Z},
title = {Navigating the gut-metabolite-immune axis: enhancing efficacy and mitigating toxicity of immune checkpoint inhibitors.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1803970},
pmid = {42516368},
issn = {1664-3224},
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the oncological landscape by disrupting inhibitory pathways, notably programmed cell death protein-1/programmed death-ligand 1 (PD-1/PD-L1) and cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) pathways, thereby reinvigorating host antitumor immunity. Although these agents have emerged as frontline standard therapies for malignancies, their clinical utility remains limited. Interpatient therapeutic variability is inextricably linked to the composition and functional capacity of the gut microbiome. The underlying mechanisms appear to involve a complex dialogue between the microbiota and host immune system, where microbial metabolites serve as critical mediators in remodeling the tumor microenvironment. Despite these insights, progression in the field remains constrained due to heterogeneity in study cohorts and sample-processing methodologies, hindering the establishment of reproducible individualized predictive models and clinical intervention strategies. Consequently, there is an urgent need to systematically delineate the microbiome-metabolite-immune axis to optimize the balance between ICI efficacy and systemic toxicity. By synthesizing the latest evidence, this review aimed to highlight the pivotal roles of specific taxa, including Bacteroides, Bifidobacterium, and Akkermansia muciniphila, in ICI efficacy. These microbes and their metabolic byproducts potentiate therapeutic responses by enhancing dendritic cell cross-presentation and promoting CD[8+] T-cell infiltration, often via activation of the cyclic GMP-AMP synthase-stimulator of interferon genes or nucleotide-binding oligomerization domain-containing protein 2 signaling pathways. Furthermore, these microbial components demonstrate the ability to protect the heart and colon against inflammation and barrier disruption, thereby mitigating immune-related adverse events. Although the feasibility and safety of interventions such as fecal microbiota transplantation and supplementation with next-generation encapsulated probiotics, postbiotics, or dietary fiber have been demonstrated in preclinical and Phase I trials, substantial hurdles remain. Future progress requires large-scale, multicenter, standardized, longitudinal studies integrating metagenomics and metabolomics to construct robust cross-cancer and cross-population predictive models. Such rigorous validation would enable the development of precise microbial interventions that maximize therapeutic gains while minimizing the incidence of adverse reactions.},
}

@article {pmid42516434,
year = {2026},
author = {Pan, M and Wei, Y and Luo, C and Lin, H and Lu, W and Lin, Y and Mai, Z and Deng, J and Huang, Y and Yu, H and Huang, J and Zhang, J},
title = {Tracheobronchial invasion by nontuberculous mycobacteria: a rare but overlooked clinical manifestation-a multicenter retrospective analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1872833},
pmid = {42516434},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis/epidemiology/pathology ; Female ; *Nontuberculous Mycobacteria/pathogenicity/isolation & purification ; Male ; Aged ; Bronchoscopy ; Middle Aged ; *Bronchi/microbiology/pathology ; Aged, 80 and over ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Nontuberculous mycobacteria (NTM) can disseminate and infect various organs throughout the body. However, whether NTM can infect tracheobronchial tissue is rarely reported. This study aimed to address the knowledge gap regarding the epidemiological, demographic, and clinical characteristics of patients with tracheobronchial NTM infection.

METHODS: In this multicenter retrospective cohort study, clinical, demographic, microbiological, and radiological data from hospitalized patients with tracheobronchial NTM infections from January 2015 to May 2025 were collected and analyzed descriptively.

RESULTS: Twenty-nine patients (2.3%) were included, and all the patients presented with disseminated NTM infection. Seventeen patients had comorbidities, including 5 with acquired immunodeficiency syndrome and 1 with anti-interferon-γ autoantibody syndrome. Median diagnostic delay was 130 days, and 89.7% of the patients were initially misdiagnosed with tuberculosis or malignancy. The most common symptoms were cough, expectoration, anemia, fever, weight loss, skin lesions, and bone pain. Chest CT revealed nodules, patchy opacities, mass-like shadows, and bronchial stenosis, with or without hilar/mediastinal lymphadenopathy, whereas osteolytic bone destruction was evident in 11 patients. The most common features of bronchoscopy were intraluminal masses/neoplasms/nodules. Metagenomic next-generation sequencing (mNGS) of BALF (n=12) demonstrated 100% positivity, outperforming BALF culture (46.2%, 12/26) and sputum culture (39.3%, 11/28). Mycobacterium colombiense accounted for 24.1% of cases. With respect to therapeutic management, 27 patients received systemic antimicrobial therapy, while 2 did not receive specific anti-N™ treatment. One patient underwent combined endoscopic resection. Overall, 23 patients (79.3%) achieved improvement or cure, 5 showed disease progression, 1 experienced relapse, and 1 died.

CONCLUSIONS: Tracheobronchial NTM infection is rare but clinically significant, often occurring in the context of disseminated disease with pulmonary involvement. Immunocompromised hosts, particularly those with AIDS or anti-IFN-γ autoantibody syndrome, are highly susceptible. Bronchoscopy typically reveals mass lesions causing luminal stenosis or occlusion. In this cohort, M. colombiense was the most frequently isolated NTM species. Early bronchoscopy, mNGS-based pathogen detection, and timely systemic or endoscopic intervention should be considered to prevent irreversible airway stenosis. Further studies are needed to validate optimal treatment strategies.

CLINICAL TRIAL REGISTRATION: https://www.ClinicalTrials.gov, identifier NCT07377864.},
}

Humans
Retrospective Studies
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis/epidemiology/pathology
Female
*Nontuberculous Mycobacteria/pathogenicity/isolation & purification
Male
Aged
Bronchoscopy
Middle Aged
*Bronchi/microbiology/pathology
Aged, 80 and over
Tomography, X-Ray Computed

@article {pmid42516567,
year = {2026},
author = {Figueroa-Pratts, PG and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimized Field Collection and Gut Dissection Workflows for Microbiome Studies of the Citrus Root Weevil, Diaprepes abbreviatus.},
journal = {Bio-protocol},
volume = {16},
number = {14},
pages = {e5761},
pmid = {42516567},
issn = {2331-8325},
abstract = {Careful dissection of insect gut tissues is essential for microbiome studies to ensure accurate characterization of internal microbial communities and preservation of DNA integrity. Because insect-associated microbiomes are highly sensitive to contamination, effective removal of external microbes prior to dissection is critical to minimize bias in downstream analyses. While ethanol- and bleach-based surface sterilization methods are commonly used, standardized workflows integrating field collection, sterilization, and dissection remain limited. Here, we present a step-by-step protocol for the field collection, surface sterilization, and dissection of gut tissues from the agricultural pest Diaprepes abbreviatus (Coleoptera: Curculionidae), optimized for genomic DNA extraction and microbiome analyses. Using wild-caught specimens, this workflow incorporates a rigorous surface sterilization and dissection strategy that minimizes external contamination while preserving biologically relevant microbial signatures and DNA integrity for downstream microbiome analyses. The protocol provides a standardized framework for insect gut microbiome studies and can be broadly adapted to other wild-caught insect species requiring careful collection, disinfection, and sterile dissection prior to molecular analysis. The protocol integrates field collection and laboratory processing steps into a streamlined workflow that minimizes contamination while preserving tissue integrity for downstream applications. Key features • Designed for wild-caught Diaprepes abbreviatus collected directly from agricultural host trees, this protocol can also be adapted for other insect species. • Integrates field collection, surface sterilization, and sterile gut dissection into a single workflow to minimize contamination. • Sequential ethanol and diluted bleach treatment effectively removes external microbes prior to dissection. • Enables isolation of intact gut tissues suitable for high-quality DNA extraction and downstream microbiome sequencing.},
}

@article {pmid42517159,
year = {2026},
author = {Xie, T and Xu, JY and Lin, D and Liu, Y and Wang, YF and Yang, ZG and Lee, PKH and Zhu, D},
title = {Cigarette Butts as an Emerging Urban Habitat Driving Microbial Niche Differentiation.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1380},
pmid = {42517159},
issn = {2639-5274},
abstract = {Cigarette butts are common yet overlooked pollutants in urban environments. How this anthropogenic niche shapes microbial life-history strategies and evolutionary mechanisms remains poorly understood, limiting assessments of microbial adaption and urban ecosystem health. However, systematic and multiscale evidence on the ecological effects of cigarette butts on microbial communities remains scarce. Here, we collected cigarette butts, litter, and soil samples from urban parks in 35 Chinese cities and integrated third-generation 16S ribosomal RNA sequencing, metagenomics, and transcriptomics to resolve microbial community composition, functional potential, and evolutionary patterns. The results revealed that microbial communities in cigarette butts were shaped by strong deterministic processes, showed low spatial heterogeneity, and were taxonomically distinct from those in natural niche (i.e., litter) and surrounding soil, with notable enrichment of Proteobacteria, particularly the family Pseudomonadaceae. Functional trait analysis showed that butt-associated communities favored environmental responsiveness and fast-growth strategies, contrasting with metabolism- and resource acquisition-oriented strategies in the litter. Population genomic analysis suggested stronger positive selection in cigarette butt-associated Pseudomonadaceae, while the pure culture experiment provided strain-level evidence that cigarette butt exposure induced the up-regulation of key functional genes in Pseudomonas aeruginosa PAO1. This study demonstrates that cigarette butts, as an emerging ecological niche, reshape microbial community assembly, life-history strategies, and adaptive evolution, offering new insights into microbe-driven evolution on artificial surfaces.},
}

@article {pmid42517538,
year = {2026},
author = {Fehr, D and Flack, N and Masenga, G and Mosha, N and Li, N and White, A and Semango, G and Distler, M and Lang, C and Grimm, F and Scharl, M and Mavura, D and Masenga, JE and Schmid-Grendelmeier, P and Brüggen, MC},
title = {Dietary Habits and Atopic Dermatitis Significantly Influence the Fecal Microbiome.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70459},
pmid = {42517538},
issn = {1398-9995},
support = {LF-OC-20-000418//LEO Fondet/ ; 0456/2024//Vontobel-Stiftung/ ; //Bruno Bloch Stiftung/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) has been associated with microbial gut dysbiosis in children. Data in adults is scarce.

OBJECTIVE: We sought to explore the fecal microbiome composition in AD patients versus healthy controls (HC) and investigate the impact of environmental aspects such as the geographical location and dietary habits.

METHODS: In this case control study, a total of 140 fecal samples from 69 AD patients and 71 HC from Tanzania (TZ) and Switzerland (CH) were analyzed. Illumina shotgun metagenomics sequencing was performed followed by taxonomic profiling, calculation of alpha/beta diversity, and permutational multivariate analysis of variance. Differentially abundant species and genera between AD and HC were evaluated.

RESULTS: Alpha diversity (Shannon Index) did not significantly differ between AD and HC. The presence of AD was identified as a significant source of fecal microbiome variation (Bray-Curtis beta diversity). On the species level, Faecalibacterium taiwanense was more abundant in AD, and Vescimonas sp000435555 in HC. On the genus level, CAG-302 (NCBI: Clostridium) was more abundant in HC. Geographical location was associated with distinct dietary habits. Prevotella was significantly more abundant in TZ, whereas Alistipes and Bacteroides were significantly more abundant in CH.

CONCLUSIONS: The presence of AD significantly impacted the fecal microbiome variation and was associated with a particular microbial composition. The impact of geographical location on the fecal microbiome may be related to nutritional differences. Our data support the rationale of a gut-skin axis and pave the way towards therapeutic approaches modulating the microbiome.},
}

@article {pmid42517626,
year = {2026},
author = {Price, DC and Bezhani, FL and Meng, Z and Porfirio-LaStrapes, M and Wagner, NE and Javanmard, M and Han, T and Barnes, MM},
title = {Metaviromic profiling of mosquito excreta using superhydrophobic collection devices expands the known RNA virome of North America.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093826},
doi = {10.1128/spectrum.00938-26},
pmid = {42517626},
issn = {2165-0497},
abstract = {Nearly 30% of emerging infectious disease events worldwide are transmitted by arthropod vectors, and this proportion continues to rise. Rapid and accurate detection is critical for directing vector control interventions, thereby reducing the likelihood of widespread transmission. Surveillance of infected mosquitoes can provide an early warning of impending human infection; however, conventional virus testing relies on processing large pools of mosquitoes and requires labor-intensive pre-processing. During rapidly developing epidemic or panzootic events, these delays may limit the effectiveness of public health responses. Mosquito excreta has recently emerged as a promising alternative substrate for pathogen detection. Sugar-fed mosquitoes regularly excrete gut contents, offering a rich source of nucleic acids. In this study, we developed and applied custom superhydrophobic excreta-collection funnels that efficiently aggregate excreta produced by field-collected Culex mosquitoes into attached microcentrifuge tubes. Shotgun metagenomic sequencing of this material revealed a diverse RNA virome, including both globally distributed viruses and those reported here for the first time from the Americas. Beyond virus detection, additional analyses enabled confirmation of host mosquito species and identification of trypanosomatid parasites, demonstrating the broader utility of mosquito excreta for integrated surveillance. We anticipate that methods and devices of this type will become valuable components of vector surveillance programs, particularly in remote or resource-limited settings where repeated collections are challenging. Overall, our findings highlight the potential of excreta-based monitoring to improve early detection of emerging or unknown pathogens of One Health importance, refine our understanding of mosquito virome biogeography, and facilitate the discovery of previously undescribed viruses.IMPORTANCEMany infectious diseases that affect people and animals are spread by mosquitoes and other biting insects, and the number of these outbreaks is increasing. Detecting pathogens in mosquito populations early can provide a critical warning before human cases begin, allowing health officials to act quickly. However, traditional surveillance requires collecting and processing large numbers of mosquitoes, which can be slow and labor-intensive during fast-moving outbreaks. Here we demonstrate a simpler approach: testing mosquito waste. When mosquitoes feed on sugar, they excrete material that contains genetic traces of viruses and other organisms. Using specially designed collection devices and modern genetic sequencing, we show that mosquito excreta can reveal a wide range of viruses and parasites while also identifying the mosquito species present. This method could make disease surveillance faster and more practical in remote or resource-limited settings, improving our ability to detect emerging pathogens that threaten human, animal, and environmental health.},
}

@article {pmid42518002,
year = {2026},
author = {Gao, Y and Dong, J and Peng, O and Yan, Z and Chen, M and Yin, Y and Sun, M and Zhang, J and Huang, Y and Xiang, Y and Qi, Z and Ge, J and Qin, L and Li, L and Zhang, Y},
title = {A novel Chaphamaparvovirus detected in breeding Muscovy Ducks with hepatitis.},
journal = {Veterinary research communications},
volume = {50},
number = {5},
pages = {},
pmid = {42518002},
issn = {1573-7446},
support = {202110TD, R2020PY-JX014, R2020QD-049, R2020PY-JC001//Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Scienc/ ; 2023B1212060040//Guangdong Province Key Laboratory of Livestock Disease Prevention/ ; },
abstract = {Since 2022, a decrease in egg production and hatchability, along with hepatitis-like symptoms, has been frequently reported in Muscovy duck farms in southern China. Using metagenomic sequencing, a novel Chaphamaparvovirus (ChPV), designated MuChPV-GD2022, was detected in the livers of the diseased ducks. Phylogenetic analysis revealed that the MuChPV-GD2022 strain shares 61.8-77.4% genome identity with duck-origin Chaphamaparvoviruses, and 44.3-77.4% with avian-origin Chaphamaparvoviruses. The NS1 protein amino acid sequence showed a 29.3-71.5% similarity to those of other known Chaphamaparvoviruses. These findings support the classification of MuChPV-GD2022 as a new species in the genus Chaphamaparvovirus, family Parvoviridae. Since virus isolation was not achieved due to technical constraints, the evidence suggests MuChPV may be associated with the hepatitis-like disease. Furthermore, a TaqMan qPCR assay targeting NS1 gene of the virus was developed and validated for specificity, sensitivity, and repeatability, which provides a sensitive tool not only for virus detection but also for epidemiological surveillance of MuChPV infections.},
}

@article {pmid42518032,
year = {2026},
author = {Li, F and Zhao, H and Lei, Y and Luo, J and Chen, B and Li, C and Zhao, X and Jiang, H},
title = {Fufangteng Yixin Formula alleviates myocardial ischemia-reperfusion injury by modulating gut microbiota and resultant metabolites in rats.},
journal = {Journal of natural medicines},
volume = {},
number = {},
pages = {},
pmid = {42518032},
issn = {1861-0293},
support = {2024GXNSFBA010207//Guangxi Natural Science Foundation Joint Special Project/ ; },
abstract = {This study aimed to explore whether Fufangteng Yixin Formula (FFTYXF) can ameliorate myocardial ischemia-reperfusion injury (MIRI) by regulating the gut microbiota and resultant metabolites. Wistar rats were given FFTYXF by gavage for 7 days, and MIRI rat model was established. Serum level of inflammatory markers was determined by ELISA, and heart function was evaluated by echocardiography. Myocardial histological changes and infarct size were examined by hematoxylin-eosin and triphenyltetrazolium chloride staining, respectively. 16S rRNA gene and metagenomics analyses were employed to explore gut microbiota, while untargeted metabolomics analysis was used to explore serum metabolites. FFTYXF pretreatment could significantly improve cardiac function, reduce infarct size, decrease level of inflammatory factors (TNF-α and IL-6) and inflammatory cells infiltration. At genus level, g__Oscillibacter and g__Rikenellaceae_RC9_gut_group were identified as key microbial bacteria in MIRI rat response to FFTYXF pretreatment. After FFTYXF pretreatment, the functional categories of gut microbiota were participated in fatty acid (FA) biosynthesis/metabolism, glycolysis _ gluconeogenesis and sphingolipid metabolism. Genes response to FFTYXF pretreatment in MIRI rats included K00023 (phbB), K00281 (GLDC, gcvP), K03879 (ND2), K07827 (KRAS) and K15192 (BTAF1), and they were mainly participated in carbon, butanoate, glyoxylate and dicarboxylate metabolism. Differential metabolites were also mainly participated in FA biosynthesis/metabolism, such as alpha-Linolenic acid, omega-3/omega-6 FA, and flavan-3-ol metabolic pathway. Abundance of g__Rikenellaceae_RC9_gut_group positively correlated with differential metabolites FAHFA 34:0, FAHFA 16:1/18:3, and FA 24:5. FFTYXF could alleviate MIRI by modulating gut microbial bacteria alteration and resultant metabolites, particularly short-chain FAs.},
}

@article {pmid42518220,
year = {2026},
author = {Di, D and Wang, S and Qiu, W and Gai, X and Xiao, J and Wang, S and Zhuo, R and Chen, G},
title = {Multi-omics analysis reveals the mechanisms on biochar-mediated cadmium transport in Salix: insight into rhizosphere phosphorus-iron coupling and transporter expression.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag104},
pmid = {42518220},
issn = {1758-4469},
abstract = {Biochar addition promoted cadmium (Cd) phytoremediation of woody plants, especially phosphors (P)-modified biochar. However, the underlying mechanism on the uptake and transport of Cd mediated by biochar remains unclear. Here, we integrated the physiological, metagenomics, transcriptomics, and in situ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging analysis to investigate how bamboo biochar (BBC) and phytic acid modified biochar (PABC) impact Cd accumulation and transport in Salix J1010 through root-soil interface. Our results showed that PABC significantly increased Cd translocation from roots to aboveground by 77.9% and total Cd accumulation in plan by 203%, respectively. Iron plaque emerged as a key factor, with PABC-mediated inhibition of iron plaque (-44.6%) accelerating Cd uptake. This iron plaque decrease is closely accompanied by the decreased soil redox potential (Eh), enriched resin-P and inorganic P fractions, and potential coupling of P mineralization and Fe(III)-reducing processes in the rhizosphere soil. Transcriptomics analysis further revealed that PABC influenced root metal transporter expression, downregulating vacuolar sequestration-related ABC, CAX, MTP gene families, while upregulating most ZIP, HMA, and YSL genes families involved in xylem loading. LA-ICP-MS imaging corroborated the enhanced Cd transport in xylem tissue. PABC enhanced leaf cell-wall Cd binding and antioxidant defenses, thereby promoting Cd detoxification and accumulation. Collectively, the enhanced phytoremediation capacity of willow was driven by coordinating trade-offs across multiple levels, including the rhizosphere, subcellular scales, and whole-plant. The results provide a mechanistic basis for biochar-assisted phytoremediation strategies in Cd-contaminated soils.},
}

@article {pmid42518254,
year = {2026},
author = {Van Etten, J and Johnson, MD},
title = {Beyond adaptive gene transfers: a primer on horizontal gene transfer across scales.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag125},
pmid = {42518254},
issn = {1557-7023},
abstract = {Horizontal gene transfer (HGT) is a fundamental ecological and evolutionary process involving the movement of genetic material across taxa within a single generation. While traditionally studied at the level of individual genes with encoded adaptive functions, recent advances in genomics and metagenomics highlight the need for a broader, integrative framework. Here, we expand the concept of the "ecology of DNA transfer," which conceptualizes HGT as a multi-layered process spanning the genome, cell, and ecological context. We further explore how the fate and expression of transferred DNA vary over evolutionary timescales, from recently acquired, transcriptionally silenced sequences to ancient, fully integrated genes. Together, this framework underscores HGT as a dynamic, context-dependent process shaped by interactions across biological scales.},
}

@article {pmid42518807,
year = {2026},
author = {Hamiyeh, R and Salhab, Z and Bahmad, HF and Abou Fayad, AG and Abou-Kheir, W},
title = {Anticancer natural products from the Middle East and North Africa: biodiversity, mechanisms, and translational challenges.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1846357},
doi = {10.3389/fonc.2026.1846357},
pmid = {42518807},
issn = {2234-943X},
abstract = {Cancer remains one of the leading causes of morbidity and mortality worldwide, imposing substantial clinical, societal, and economic burdens. Despite major advances in surgical oncology, systemic chemotherapy, radiation therapy, molecularly targeted therapeutics, and immune checkpoint inhibition, contemporary cancer treatment remains constrained by dose-limiting toxicities, intratumoral and intertumoral heterogeneity, and the inexorable emergence of multifaceted drug resistance mechanisms. These persistent therapeutic challenges have reinstated interest in natural products (NPs) as evolutionarily refined sources of anticancer agents characterized by structurally diverse molecular targets and pleiotropic mechanisms of action. Indeed, a substantial proportion of currently approved anticancer drugs are either directly derived from or structurally inspired by natural compounds. This comprehensive review examines the role of NPs as anticancer agents, with particular emphasis on bioactive compounds isolated from plants, fungi, marine organisms, and environmental bacteria indigenous to the Middle East and North Africa (MENA) region. We summarize exemplary MENA-derived NPs demonstrating cytotoxic, antiproliferative, pro-apoptotic, anti-angiogenic, anti-metastatic, and immunomodulatory activities across a wide range of preclinical cancer models. Mechanistically, these compounds converge on critical oncogenic signaling networks, including p53-caspase apoptotic cascades, NF-κB transcriptional inhibition, reactive oxygen species modulation, cell-cycle arrest, epigenetic reprogramming, and suppression of tumor invasion and chronic inflammation. In parallel, we highlight transformative technological innovations-including high-throughput phenotypic and biochemical screening platforms, metagenomics, genome mining algorithms, biosynthetic gene cluster activation, and synthetic biology approaches-that are fundamentally reshaping NP discovery and enabling access to previously cryptic or unculturable microbial biosynthetic pathways. These methodological advances, coupled with multi-omics integration, artificial intelligence-driven compound prediction, and heterologous expression systems, are accelerating the identification and characterization of structurally novel anticancer agents. Collectively, the evidence presented underscores the MENA region as a significantly underexplored yet exceptionally promising biodiverse reservoir of anticancer NPs with substantial therapeutic potential. Strategic harnessing of this biodiversity through interdisciplinary collaborative research, ethically governed bioprospecting frameworks, and translational development pipelines may yield structurally innovative, mechanistically distinct, and potentially safer therapeutic modalities to complement existing cancer treatments and address critical unmet clinical needs in precision oncology.},
}

@article {pmid42519007,
year = {2026},
author = {Zhao, Z and Zhao, F and Zhang, M and Sun, J and Wang, X and Lou, J and She, R and Kwok, LY and Sun, Z and Huangfu, W and Menghe, B},
title = {Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116622},
doi = {10.1016/j.isci.2026.116622},
pmid = {42519007},
issn = {2589-0042},
abstract = {Alzheimer's disease (AD) is increasingly being linked to gut microbial dysbiosis via the gut-brain axis. We applied integrated metagenomics and metabolomics to characterize gut microecology in 28 patients with AD and 33 controls. Metagenomic analysis revealed distinct microbial community structures, with increased abundance of Akkermansia massiliensis, Alistipes onderdonkii, and Barnesiella intestinihominis in AD. Phageome analysis revealed increased richness and altered composition, with more Podoviridae and fewer Microviridae. Functional profiling identified shifts in microbial metabolic pathways involving tryptophan and short-chain fatty acid metabolism. Untargeted metabolomics revealed elevated fecal spermidine, taurocholate, and glycerophosphocholine levels in patients with AD. A random forest model combining metabolites, gut metabolic modules, and bacteriophages achieved good within-cohort classification (AUC = 0.83) but lacked external validation due to unavailable matched fecal metabolomic data. Overall, these findings link AD to coordinated disruptions across bacterial, viral, and metabolic gut layers, highlighting the need for external validation and mechanistic studies.},
}

@article {pmid42519018,
year = {2026},
author = {Zhang, Z and Shu, Y and Liu, X and Xu, B and Chen, J and Zhang, Z and Wang, K and Hua, Y},
title = {Multi-omics reveals functional recovery of the gut microbiome in rescued Sunda pangolins (Manis javanica).},
journal = {iScience},
volume = {29},
number = {8},
pages = {116754},
doi = {10.1016/j.isci.2026.116754},
pmid = {42519018},
issn = {2589-0042},
abstract = {The Sunda pangolin (Manis javanica), a critically endangered myrmecophage, often develops severe gastrointestinal disturbance after trafficking, creating major challenges for post-rescue rehabilitation. We integrated 16S rRNA gene sequencing, shotgun metagenomics, untargeted metabolomics, and gas chromatography-mass spectrometry (GC-MS) quantification of short-chain fatty acids to investigate gut ecosystem recovery in rescued pangolins across the first abnormal fecal stage, 1 week post-rescue, and 1 month post-rescue. Fecal consistency improved during rehabilitation, accompanied by a shift from facultative taxa enriched in Streptococcus and Lactobacillus to a more anaerobic community containing Clostridium, Romboutsia, Bacteroides, and related taxa. Metagenomic and metabolomic profiles indicated recovery of functions associated with chitin degradation, short-chain fatty acid production, amino acid metabolism, and cofactor biosynthesis. Increased fecal butyrate and multi-omics associations supported recovery of microbial metabolic function. These findings provide insight into the microbial and metabolic dynamics of gut ecosystem recovery in rescued pangolins and may help assess rehabilitation progress in this critically endangered species.},
}

@article {pmid42519058,
year = {2026},
author = {Pi, N and He, X and Zhu, L and Hou, X and Wu, X and Zhang, J and Yang, L and Shen, D and Zou, Z and Xiang, R and Wu, X},
title = {City-scale resistome-mobilome architecture and mobility-associated ARG backbones across a megacity watershed.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116841},
doi = {10.1016/j.isci.2026.116841},
pmid = {42519058},
issn = {2589-0042},
abstract = {Antimicrobial resistance (AMR) in urban watersheds is shaped by diverse anthropogenic inputs, and linking reads-level resistome-mobilome associations to local antibiotic resistance gene (ARG) genetic contexts can strengthen environmental surveillance. Here, we analyzed 63 deeply sequenced shotgun metagenomes from a Chongqing megacity watershed spanning surface water, river sediments, wastewater treatment activated sludge, livestock wastewater, and hospital wastewater. Reads-based profiling revealed strong habitat structuring of ARG subtypes and MobileElementFinder-derived mobilome families, and total ARG loads co-varied with mobile genetic element (MGE), biocide resistance, and metal resistance axes. To add sequence-resolved context, we surveyed 8,043 ARG-carrying contigs and integrated element-level MGE calls with open reading frame (ORF)-level mobility functions to define putative mobility tiers. Wastewater-impacted habitats showed higher representation of contigs carrying conjugation-related mobility signals, whereas sediments exhibited high ARG and MGE loads but weaker ARG-MGE coupling. This megacity-scale framework prioritizes mobility-associated and co-selection genetic contexts for environmental AMR monitoring and mitigation.},
}

@article {pmid42519143,
year = {2026},
author = {Tan, X and Liao, J and Xu, Z},
title = {Misdiagnosed acute Q fever due to Coxiella burnetii in Guangxi China: A case report and literature review.},
journal = {IDCases},
volume = {45},
number = {},
pages = {e02661},
doi = {10.1016/j.idcr.2026.e02661},
pmid = {42519143},
issn = {2214-2509},
abstract = {Coxiella burnetii (C. burnetii), a Gram-negative obligate intracellular bacterium, is the etiological agent of Q fever. Timely diagnosis and initiation of appropriate therapy are critical for favorable clinical outcomes, particularly in cases of acute Q fever. This report describes a case of C. burnetii infection in a 35-year-old male electrical grid engineer who presented with a 4-day history of febrile illness, peaking at 40.0 °C. Associated symptoms included night sweats, chills, anorexia, nausea, non-productive cough, and chest tightness. During hospitalization, the patient also developed headache and vomiting. Metagenomic next-generation sequencing (mNGS) of peripheral blood identified C. burnetii as the causative pathogen. The patient was treated with oral doxycycline (100 mg twice daily) for 14 days and levofloxacin (500 mg once daily) for 5 days. Following antimicrobial therapy, the patient's symptoms resolved rapidly, with no clinical evidence of relapse or progression to chronic Q fever during follow-up. This report describes a case of Q fever diagnosed by mNGS. The case highlights the diagnostic value of mNGS in patients presenting with febrile illness of unknown origin. It also serves as a reminder to clinicians that, even in regions where Q fever is enzootic in animals but no human cases have been reported, the possibility of human infection should not be overlooked.},
}

@article {pmid42519144,
year = {2026},
author = {Asai, N and Igarashi, Y and Miyazaki, N and Shiota, A and Yamagishi, Y and Nakamura, A and Osugi, A and Matsumoto, Y and Nakamura, S and Murakami, S and Takami, A and Mitarai, S and Mikamo, H},
title = {First reported recovery and genomic characterization of a previously uncharacterized Mycobacterium species from human blood cultures in an immunocompromised patient: A case report.},
journal = {IDCases},
volume = {45},
number = {},
pages = {e02667},
doi = {10.1016/j.idcr.2026.e02667},
pmid = {42519144},
issn = {2214-2509},
abstract = {Mycobacteremia is an uncommon opportunistic infection in immunocompromised hosts. We report the recovery of a previously uncharacterized Mycobacterium species from two independent blood culture sets obtained from an immunocompromised patient with persistent fever. She presented with persistent fever, and two independent blood culture sets yielded a Mycobacterium species. No focal source of infection was identified. Initial identification by MALDI-TOF mass spectrometry suggested Mycobacterium diernhoferi; however, species-level identification could not be confirmed by molecular methods. Whole-genome sequencing demonstrated that the isolate could not be assigned to any currently recognized Mycobacterium species. Average nucleotide identity analysis showed 90.5% similarity to M. diernhoferi and 84.4% to Mycobacterium frederiksbergense, suggesting a previously uncharacterized species. Combination antimicrobial therapy was followed by resolution of fever and no recurrent positive blood cultures during treatment. Although the patient ultimately died because of progression of the underlying hematological malignancy, the patient showed sustained clinical improvement without recurrent positive blood cultures during therapy. To our knowledge, this is the first reported recovery of this genomically distinct Mycobacterium species from human blood cultures. This case highlights the value of whole-genome sequencing in recognizing previously uncharacterized Mycobacterium species recovered from human blood cultures. The pathogenic role of this organism requires further investigation.},
}

@article {pmid42519489,
year = {2026},
author = {Al Khafaji, A and Vallejo-España, D and Gómez-Llorente, C and Camacho, J},
title = {A realistic simulation-based benchmark of microbiome normalization in sample stratification and taxa-level analysis.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1863340},
doi = {10.3389/fbinf.2026.1863340},
pmid = {42519489},
issn = {2673-7647},
abstract = {MOTIVATION: Normalization is a critical step in microbiome studies because sequencing depth and sparsity can strongly affect downstream analyses. In real datasets, however, the underlying biological signal is unknown, making it difficult to determine whether a normalization method preserves true group differences or introduces distortions. To address this problem in a way that remains relevant to real applications, we developed a simulation-based evaluation framework informed by real microbiome data. The framework generates realistic datasets with known ground truth and enables quantitative comparison of normalization methods at both the sample and taxa levels.

RESULTS: Method performance depended on taxonomic resolution and on whether sequencing depth was confounded with group structure. In our case study, model-based normalization-factor methods, particularly edgeR-TMM and, in some settings, DESeq2, gave the closest match to the simulated biological contrast, indicating better recovery of taxa-level differences while preserving sample-level separation. TSS and rarefaction were often the next-best performers. Shannon diversity analyses further showed that sequencing-depth differences alone could create false-positive group differences for several methods, whereas rarefaction remained closest to nominal Type I error control. These results also showed that visual or statistical sample separation alone was not sufficient to judge normalization performance, because apparent group differences did not always correspond to correct taxa-level recovery. Rather than identifying a universally best method, the proposed framework provides a coherent strategy for evaluating existing and new normalization approaches under realistic, data-dependent scenarios.},
}

@article {pmid42519695,
year = {2026},
author = {Wang, X and Wang, J and Chen, W and Sun, J and Li, J and Hu, H},
title = {Metagenome analysis reveals multi-kingdom gut microbiota as diagnostic markers for colorectal cancer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805055},
doi = {10.3389/fmicb.2026.1805055},
pmid = {42519695},
issn = {1664-302X},
abstract = {BACKGROUND: Colorectal cancer (CRC) is a major contributor to cancer-related morbidity and mortality globally. Emerging evidence suggests that gut microbiota plays a pivotal role in CRC development. However, the precise link between CRC and gut microbial dysbiosis remains poorly understood.

METHODS: In this study, we analyzed metagenomic datasets from 578 samples, sourced from five geographically distinct cohorts, including CRC patients and healthy controls from China, Austria, and Spain. This diverse cohort enabled us to investigate changes in the gut microbiome-bacteria, viruses, fungi, and archaea-in CRC patients across varying genetic and environmental contexts.

RESULTS: Our analysis led to the identification of 12 bacterial, 18 viral, and 1 fungal marker using a diagnostic model based on the gut microbiome. Notably, the multi-kingdom model, incorporating these markers, outperformed single-domain models in diagnostic accuracy. Integrating 24 microbial markers-comprising 9 bacterial, 14 viral, and 1 fungal marker-yielded an impressive AUROC of 0.911 for CRC diagnosis.

CONCLUSION: This model demonstrated robust performance across four independent cohorts, confirming its potential as a highly accurate, non-invasive diagnostic tool for CRC.},
}

@article {pmid42519699,
year = {2026},
author = {Akbar, A and Rahmeh, R and Kishk, M and Almutairi, B and Al-Mutairi, S and Al-Waalan, T and Shajan, A},
title = {Microbial diversity and bioremediation potential in mangrove sediments-a metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1826301},
doi = {10.3389/fmicb.2026.1826301},
pmid = {42519699},
issn = {1664-302X},
abstract = {Mangroves in Kuwait are exposed to increasing levels of polycyclic aromatic hydrocarbons (PAHs) originating from industrial activities and urban runoff. However, the potential of native mangrove microbial communities for PAH bioremediation has not yet been explored. Sediment samples were collected from three locations (Shuwaikh, Al Khiran, and Sulaibikhat) at varying distances from Avicennia marina roots. The concentration of PAHs was determined using GC-MS. To assess microbial diversity, a metagenomic approach was used to evaluate diversity metrics. The statistical analysis included the non-parametric Kruskal-Wallis test (p < 0.05) to compare the median values of different groups and the non-parametric PERMANOVA test (p-values 0.001-0.009) to assess the differences among groups. The results of the study showed the presence of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and chrysene PAHs at varying concentrations across the studied sites. Naphthalene concentrations reached a maximum of 89.64 μg/kg at the Sulaibikhat site and a minimum of 12 μg/kg at the Shuwaikh site. Metagenomic analysis revealed significant differences in microbial diversity between root distances and sites. The rhizosphere samples had higher alpha diversity and richness than the other sediment samples. Beta diversity analysis clustered the samples into groups of sample types and sites. The pairwise comparison between rhizosphere and sediment samples revealed significant differences in microbial communities between rhizosphere and sediment samples in Shuwaikh (p = 0.012) and Al Khiran (p = 0.007) sites. The heatmap of gene presence/absence revealed the enrichment of genes involved in hydrocarbon degradation (alkB, nahA, nahB, phnABC) and plant growth promotion. Functional analysis using KEGG revealed the metabolic capabilities of the isolates, including the presence of peptide/nickel transporters. All bacterial strains were identified by 16S rRNA gene sequencing, and the major groups of bacteria identified were Pseudomonas, Burkholderia, and Rhodococcus, which are known to have the ability to degrade PAHs and promote plant growth. Microorganisms of different species at various sites of Kuwait mangroves showed higher diversity in rhizosphere areas. Microorganisms living in such zones possess the necessary genes to degrade oil as well as for plant growth and thus have the potential for bioremediation of polluted sites by oil. The high level of PAH contamination in the sediment close to the roots of mangroves indicates localized pollution.},
}

@article {pmid42519700,
year = {2026},
author = {Pellegrinetti, TA and Molligan, J and Mendes, LW and Pedrinho, A and Pérez-López, E},
title = {Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1884628},
doi = {10.3389/fmicb.2026.1884628},
pmid = {42519700},
issn = {1664-302X},
}

@article {pmid42519702,
year = {2026},
author = {Xiong, W and Yan, X and Guo, H and Yu, B and Qi, J and Li, H and Zeng, Z and Dai, Y and Yu, Z and Tang, D},
title = {Day-21 gut microbiota community state types are associated with bronchopulmonary dysplasia classification in preterm infants: a pilot shotgun metagenomic study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1835952},
doi = {10.3389/fmicb.2026.1835952},
pmid = {42519702},
issn = {1664-302X},
abstract = {INTRODUCTION: Bronchopulmonary dysplasia (BPD) is a major complication in preterm infants, and its clinical classification remains strongly influenced by gestational maturity and the evolving respiratory course. In this exploratory study, we investigated whether early-life gut microbiota configurations at postnatal day 21 are associated with subsequent formal BPD classification at 36 weeks postmenstrual age and whether they provide ecological information relevant to preterm infant microbiome development.

METHODS: In a prospective cohort of 23 preterm infants with gestational age <32 weeks or birth weight <1,500 g, shotgun metagenomic sequencing of day-21 fecal samples was performed. Community state types (CSTs) were identified using unsupervised clustering, and their taxonomic, functional, and exploratory discrimination patterns were assessed in relation to subsequent BPD classification.

RESULTS: Two CSTs were identified. CST1 was dominated by commensal taxa and exhibited functional enrichment in metabolic homeostasis pathways. CST2 was characterized by pathobionts, fragmented taxon-pathway association networks, and enrichment in virulence-related pathways. BPD was observed in 1 of 11 CST1 infants and 7 of 12 CST2 infants (9.1% vs. 58.3%; two-sided Fisher's exact test, p = 0.027), although this association was based on very small cell counts. In exploratory discrimination analysis, a model combining CST status with gestational age showed an apparent AUC of 0.892; however, leave-one-out cross-validation yielded a lower AUC of 0.800, indicating likely optimism in the apparent model performance.

DISCUSSION: These preliminary, observational findings suggest that day-21 gut microbiota profiles and CST classification may provide ecological information associated with formal BPD classification. However, this analysis should be interpreted as exploratory discrimination rather than validation of a clinically useful prediction model. Establishing causality or clinical utility requires validation in larger cohorts that systematically track longitudinal confounders such as gestational age, feeding mode, antibiotics, and probiotics.},
}

@article {pmid42519731,
year = {2026},
author = {Yi, M and Dai, Y and Liu, C and Lang, H and Jiang, X and Yuan, X},
title = {Case Report: Pediatric mediastinal actinomycosis mimicking lymphoma diagnosed by tissue metagenomic next-generation sequencing.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1882250},
doi = {10.3389/fped.2026.1882250},
pmid = {42519731},
issn = {2296-2360},
abstract = {Mediastinal actinomycosis is rare in children, and when it presents as a mass-like lesion, its clinical and imaging features overlap substantially with lymphoma, making differential diagnosis extremely challenging. We report a 2-year-1-month-old girl admitted with fever and cough. Contrast-enhanced chest computed tomography (CT) showed multiple enlarged mediastinal and bilateral hilar lymph nodes coalescing into a mass-like lesion with heterogeneous enhancement and small hypoenhancing foci, encasement of adjacent mediastinal vessels, and compression of the left main bronchus and the origin of the lingular bronchus. Magnetic resonance imaging (MRI) demonstrated heterogeneous signal intensity and enhancement; the radiologic differential included lymphoproliferative and granulomatous disease. Bone marrow biopsy, leukemia immunophenotyping, and tumor markers did not support malignancy. Ultrasound-guided biopsy of the mediastinal lesion revealed necrotizing granulomatous inflammation. Metagenomic next-generation sequencing (mNGS) of unstained tissue sections detected Actinomyces oris with mixed oropharyngeal flora, while Mycobacterium tuberculosis complex, fungi, viruses, and atypical pathogens were not detected. Pulmonary inflammation improved with antimicrobial therapy; however, repeat CT on January 28, 2026 showed little change in the mediastinal-hilar lesions. Because lymphoma could not be excluded, thoracoscopic partial resection was performed at another hospital, and postoperative pathology again showed granulomatous inflammation with caseous necrosis and negative acid-fast staining. Oral amoxicillin-clavulanate was continued postoperatively, in line with the principle of 2-6 weeks of intravenous therapy followed by 6-12 months of oral antibiotics for thoracic actinomycosis, with duration individualized to residual disease, imaging response, and drug tolerance. Follow-up ultrasonography on April 13, 2026 demonstrated reduction of the residual lesion, and the patient remained asymptomatic. This case highlights that pediatric mediastinal actinomycosis can mimic lymphoma and that integrated assessment of deep-tissue pathology, mNGS, serial imaging, and treatment response can guide diagnostic and therapeutic decision-making, preventing misdiagnosis and mistreatment.},
}

@article {pmid42519736,
year = {2026},
author = {Zhao, L and Ming, Y and Zeng, L and Yi, M and Tao, X and Yuan, W},
title = {Neonatal varicella complicated by Staphylococcus aureus lung abscess in a preterm infant: a case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1845229},
doi = {10.3389/fped.2026.1845229},
pmid = {42519736},
issn = {2296-2360},
abstract = {BACKGROUND: Neonatal varicella is a rare but potentially life-threatening condition, particularly in preterm infants. Although secondary bacterial infections are common complications, deep organ involvement such as lung abscess formation is exceedingly rare. Reports describing neonatal varicella complicated by Staphylococcus aureus lung abscess are scarce.

CASE PRESENTATION: We report a 26-day-old preterm infant (32 weeks' gestation, birth weight 1.94 kg) who developed a progressive vesiculopustular skin lesions and respiratory deterioration following exposure to maternal varicella. Despite initial topical treatment, the rash rapidly worsened and was accompanied by poor responsiveness, apnea, cyanosis, and hypothermia. On admission, the infant presented with extensive skin lesions, respiratory distress requiring non-invasive ventilation, coagulopathy, and thrombocytopenia. Intravenous acyclovir and immunoglobulin were initiated. Although the skin lesions gradually crusted and resolved, respiratory abnormalities persisted and oxygen supplementation remained necessary. Chest imaging subsequently revealed a right upper lobe abscess. Blood cultures remained negative; however, respiratory metagenomic next-generation sequencing (mNGS) identified Staphylococcus aureus, confirming secondary bacterial infection. Initial antibiotic therapy with vancomycin was selected because of severe pulmonary infection and the local prevalence of oxacillin-resistant Staphylococcus aureus. However, subtherapeutic trough concentrations and limited clinical response prompted a switch to linezolid. Following treatment adjustment, the infant showed gradual clinical and radiographic improvement and was discharged in stable condition. Follow-up imaging confirmed complete resolution of the lung abscess.

CONCLUSIONS: This case represents a rare presentation of neonatal varicella complicated by Staphylococcus aureus lung abscess in a preterm infant. It highlights that apparent resolution of cutaneous lesions does not exclude ongoing deep-seated bacterial infection and that persistent respiratory abnormalities should prompt early imaging evaluation, even in the absence of typical respiratory signs. In culture-negative cases, mNGS may facilitate pathogen identification and guide targeted antimicrobial therapy. Early recognition, individualized antimicrobial management, and therapeutic drug monitoring are important for optimizing outcomes in high-risk neonates. This case also underscores the importance of timely post-exposure prophylaxis and the limited availability of varicella-zoster immune globulin (VZIG) in some regions.},
}

@article {pmid42519816,
year = {2026},
author = {Wang, B and Xu, Z and Dong, B},
title = {Migration and biotransformation mechanisms of risk-priority antibiotics in wastewater biotreatment: An integrated multi-omics and molecular dynamics perspective.},
journal = {Eco-Environment & Health},
volume = {5},
number = {3},
pages = {100260},
doi = {10.1016/j.eehl.2026.100260},
pmid = {42519816},
issn = {2772-9850},
abstract = {Understanding the fate and transformation of antibiotics is essential for controlling antibiotic pollution in wastewater treatment plants (WWTPs). This study integrated metagenomics, metaproteomics, molecular dynamics (MD) simulations, and pathway analysis to elucidate the behavior of ciprofloxacin (CIP), sulfamethoxazole (SMX), and roxithromycin (ROX) under single- and mixed-antibiotic exposures in an activated sludge system. Fate analysis revealed divergent pathways: SMX was predominantly biodegraded (>70%), whereas CIP and ROX were mainly adsorbed onto sludge, showing poor removal and high effluent residuals (CIP > 50%, ROX > 60%). Under mixed-antibiotic stress, microorganisms favored lower-energy degradation pathways, leading to simplified (skip-step) transformations. MD simulations unveiled that within the extracellular polymeric substances (EPS) matrix, the protein fraction exhibited the strongest binding. Docking and MD simulations on a proteomics-derived interface-associated protein (OmpA) revealed a co-adsorption behavior under mixed-antibiotic exposure, where CIP strongly anchored through multipoint hydrogen bonding/electrostatic interactions and facilitated SMX stabilization in the same pocket via aromatic stacking. Multi-omics analyses revealed a microbial "survival-first" strategy dominated by resistance and repair. Notably, transporter-related stress responses were prominent under mixed stress, and several ABC transporter-associated components (e.g., K02003/K02004 and K02033) were negatively correlated with removal efficiency, coinciding with reduced degradation by key genera such as Micropruina and Ottowia. Under mixed-antibiotic stress, a confluence of reinforced resistance (e.g., Type IV secretion system K03205), altered EPS binding, and skewed energy allocation (e.g., downregulation of cofactor synthesis ko01240) led to incomplete degradation and widespread persistence. This study provides a multiscale theoretical framework for optimizing WWTPs to control antibiotic pollution.},
}

@article {pmid42519835,
year = {2026},
author = {Baertschi, I and Jordi, SBU and Gardaz, LJ and Bigi, FV and Sokollik, C and Juillerat, P and Yilmaz, B},
title = {Strain-level ecological filtering governs microbial colonization of the human gut.},
journal = {Cell reports},
volume = {45},
number = {8},
pages = {117775},
doi = {10.1016/j.celrep.2026.117775},
pmid = {42519835},
issn = {2211-1247},
abstract = {Microbial colonization of the human gut is typically inferred from species-level profiling, yet durable establishment operates at the strain level. Here, using longitudinal shotgun metagenomics across multiple donor-recipient pairs undergoing fecal microbiota transplantation, we show that colonization is governed by lineage-dependent strain-level ecological filtering. Strain-resolved analyses reveal that gut colonization imposes reproducible population-genetic bottlenecks, characterized by reduced nucleotide diversity and selective strain capture. Lineage identity is the primary determinant of strain fate: certain taxa exhibit high donor-strain fidelity, whereas dominant gut lineages, most notably Lachnospiraceae, display broad species-level engraftment but limited capture of donor-identical strains. Repeated transplantation progressively increases species-level retention, building ecological memory, yet fails to overcome intrinsic barriers to consensus-level donor-strain capture. Clinical remission aligned specifically with directional donor-strain replacement rather than taxonomic remodeling alone, identifying strain-level lineage compatibility as a candidate determinant of therapeutic success. Collectively, these findings establish that gut colonization is constrained by strain-level ecological filtering and reframe microbiota transplantation as a selective evolutionary process in which lineage identity, not inoculum diversity, gates therapeutic integration.},
}

@article {pmid42520232,
year = {2026},
author = {Bhuta, R and Kuntz, T and DeNardo, B and Morgan, X and Shapiro, J},
title = {Shotgun Metagenomics Identify Unique Changes of the Intestinal Microbiome in Pediatric Survivors of Acute Lymphoblastic Leukemia.},
journal = {Rhode Island medical journal (2013)},
volume = {109},
number = {8},
pages = {32-37},
pmid = {42520232},
issn = {2327-2228},
abstract = {BACKGROUND: Intestinal microbiota plays an important role in human health and metabolism. Microbial dysbiosis has been observed in various chronic conditions, many of which are late effects of leukemia treatment. We previously observed significant differences in the gut microbiome of pediatric ALL survivors compared to healthy sibling controls. Shotgun metagenomic analyses were completed to better characterize the durability and metabolic implication of these changes.

PROCEDURE: Shotgun metagenomic sequencing was completed on DNA extracted from stool samples obtained from nine survivors of childhood acute lymphoblastic leukemia (ALL) and 10 healthy sibling controls.

RESULTS: Beta diversity (dissimilarity between samples) was significant with survivors' microbiomes becoming more similar to siblings further from treatment. The functional potential of gluconate-5-dehydrogenase enzyme (Ga5DH) decreased significantly with time from treatment. Relative abundance of Faecalibacterium prausnitzii was identified as the major contributor to differential Ga5DH expression within subjects.

CONCLUSIONS: Time from treatment has a significant effect on functional microbial recovery in ALL. Increased time from chemotherapy corresponds to microbiomes becoming more similar to sibling controls in select dyads. More significant differences were noted in patients closer to treatment. Additional, prospective studies will focus on deeper characterization of these findings and further investigate the functional role of Ga5DH in ALL survivors.},
}

@article {pmid42520323,
year = {2026},
author = {Huang, Z and Li, Z and Wu, F and Zhou, D},
title = {Gut microbiota metabolites and microbiota-targeted interventions in bone metabolism: from SCFAs and TMAO to probiotics and FMT.},
journal = {Postgraduate medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/postmj/qgag099},
pmid = {42520323},
issn = {1469-0756},
abstract = {BACKGROUND: Accumulating evidence supports a microbiota-gut-bone axis in which intestinal microbes influence skeletal remodeling through barrier integrity, immune signaling, and metabolite production.

METHODS: This review emphasizes specific metabolites, strain-level intervention data, and translational limitations.

RESULTS: Preclinical studies consistently show that dysbiosis, barrier disruption, and altered microbial metabolites promote osteoclastogenesis and suppress osteoblast function. Among short-chain fatty acids, propionate and butyrate have the strongest direct anti-osteoclast evidence, whereas acetate a bone-relevant systemic substrate/signaling molecule with context-dependent skeletal effects. Trimethylamine N-oxide has been linked mechanistically to impaired osteogenic commitment of bone marrow stromal cells and inflammatory signaling, although human epidemiologic findings are not uniform. These mechanisms appear particularly relevant in postmenopausal osteoporosis and glucocorticoid-induced osteoporosis, where estrogen deficiency or glucocorticoid exposure amplifies intestinal permeability, inflammatory tone, and microbial dysbiosis. In humans, the clinical signal is promising but heterogeneous. Fecal microbiota transplantation remains largely preclinical in bone disease and faces major challenges in donor selection, protocol standardization, timing, and long-term safety.

CONCLUSIONS: Overall, the field is moving from associative observations toward causal and precision-oriented models, but large, well-phenotyped human studies integrating metagenomics, metabolomics, proteomics, and host clinical data are still needed before microbiota-targeted therapies can be routinely incorporated into osteoporosis care.},
}

@article {pmid42520350,
year = {2026},
author = {Chen, Q and Niu, X and Wu, W and Shi, H and Liu, G and Chen, L and Wang, H and Zhang, Y},
title = {Composted cattle manure enhances microbial nitrogen retention and increased seed watermelon yield in saline-alkali soil.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128647},
doi = {10.1016/j.micres.2026.128647},
pmid = {42520350},
issn = {1618-0623},
abstract = {Soil salinity and alkalinity represent a global environmental challenge that severely hampers agricultural productivity. While composted manure amendment represents a sustainable strategy relates to nutrient supplementation and soil health improvement. However, the influence of composted manure on microbial nitrogen cycles in a saline-alkali soil remains obscure. Saline-alkali soil amendment with cattle manure (CM) and composted CM (CCM) were conducted to systematically evaluate their efficacy in ameliorating soil physicochemical properties and enhancing crop productivity under saline-alkaline stress conditions. Physicochemical properties of saline-alkali soils under different amendments were investigated. The changes in microbial communities and nitrogen metabolism were analyzed using metagenomic sequencing and qPCR. Furthermore, the correlations between microbial nitrogen cycle and soil physicochemical factors were assessed. Compared to control (CK), soil salinity was significantly mitigated by 43.0%% and 51.9% in CM and CCM treatments. The organic matter, humus and nitrogen contents were also significantly increased in CM and CCM treatments. CCM significantly improved abundance of nrf in dissimilatory nitrate reduction to ammonium (DNRA), while reducing amoA abundance in nitrification. These findings suggest a potential redirection of microbial nitrogen fluxes toward retention rather than loss pathways, thereby enhances soil fertility. And the seed yield in CCM treatment was significantly higher than those of CM and CK. Our results provided mechanistic evidence for the use of composted manure as a sustainable strategy for enhancing soil fertility, mitigating salinization, and increasing crop yield of saline-alkali soils.},
}

@article {pmid42520695,
year = {2026},
author = {Zhou, HZ and He, T and Song, Z and Li, Z and Huang, JW and Min, J and Xu, ZM and Ma, K},
title = {Microplastics (PET and PVC) disrupt palygorskite-mediated cadmium stabilization in paddy soil: Polymer-specific rhizosphere mechanisms and ecological consequences.},
journal = {Journal of environmental management},
volume = {415},
number = {},
pages = {130590},
doi = {10.1016/j.jenvman.2026.130590},
pmid = {42520695},
issn = {1095-8630},
abstract = {Microplastics (MPs) are emerging disruptors to soil heavy metal remediation, yet how different polymer types undermine mineral-mediated in-situ immobilization remains unclear. Using a multi-omics approach (16S rRNA gene sequencing, metagenomics, transcriptomics and metabolomics), we aimed to elucidate the polymer-specific mechanisms by which polyethylene terephthalate (PET) and polyvinyl chloride (PVC) residues destabilize palygorskite-immobilized cadmium (Cd) in paddy soil, at both the soil and microbial levels. PET and PVC differentially induced the remobilization of palygorskite-immobilized Cd (F1: +132.43% and 85.52%) via distinct rhizosphere pathways. At the soil/plant level, PET enriched PETase-carrying Acidobacteriota and suppressed the ammonium transporter gene OsNRT2.3, lowering rhizosphere pH from 7.05 to 6.30. This acidification was associated with the remobilization of mineral-bound Cd and increased brown rice Cd from 0.03 to 0.06 mg/kg. PVC, in contrast, did not acidify the rhizosphere but instead induced severe root oxidative stress (MDA +78%, POD +60%), likely impairing root-barrier integrity and enhancing Cd uptake. At the microbial level, PET enriched keystone taxon Gaiella via homogeneous selection (HoS), supporting stress adaptation through branched-chain amino acid metabolism, whereas PVC redirected microbial carbon flux toward the pentose phosphate pathway and increased the genetic potential for acetate-dependent methanogenesis (acs +22.67%). These findings demonstrate that MPs compromise the durability of Cd immobilization through polymer-specific rhizosphere processes, with distinct ecological trade-offs, providing critical insights for heavy metal remediation in microplastic-polluted paddy soils.},
}

@article {pmid42520702,
year = {2026},
author = {Huang, J and Chen, F and Zhang, Z and Zu, Y and Cao, D and Huang, T and Li, Z and Wang, A},
title = {Electrode-Triggered niche differentiation and endogenous electron cycling boost bioremediation of mixed aromatic contaminants in oligotrophic groundwater.},
journal = {Water research},
volume = {306},
number = {},
pages = {126537},
doi = {10.1016/j.watres.2026.126537},
pmid = {42520702},
issn = {1879-2448},
abstract = {Chlorinated and non-chlorinated aromatic contaminants frequently co-occur in groundwater, but their synergistic bioremediation is often hindered by conflicting redox requirements, microbial niche competition, and the need for external organic carbon sources. Here, we present an electro-stimulated bio-circulation well (ES-BCW) that couples electrode-mediated redox regulation with internal hydraulic recirculation, enabling the simultaneous continuous reductive dechlorination and oxidative aromatic degradation without exogenous organic carbon supplementation. Under continuous operation (120 d), the ES-BCW system achieved average removal rates of 53.2 µmol L[-1] d[-1] for 1,2,4-trichlorobenzene (1,2,4-TCB) and 169.5 µmol L[-1] d[-1] for toluene, respectively, demonstrating competitive performance for anaerobic co-treatment of mixed aromatic contaminants. Optimal weak electrical stimulation (1.2 V) with a controlled reflux (50%) promoted spatial niche differentiation between cathodic reductive and anodic oxidative zones. Microbial analysis revealed selective enrichment of dechlorinating (Dechloromonas and Sphingobium), toluene-degrading (Azoarcus and Thauera), and electroactive (Geobacter and Sulfurospirillum) genera. Integrated metagenomic and metabolomic analyses revealed coordinated enrichment of dechlorination (pcpB, pcpC) and toluene oxidation (bssABC, bbsG) genes, coupled with increased abundances of energy carriers and key electron transfer components (i.e. cytochromes). These shifts collectively supported enhanced electron flux redistribution, metabolic synergy, and sustained acetate cycling, establishing a self-amplifying loop of endogenous carbon reuse that enabled redox partitioning between cathodic reductive and anodic oxidative niches. The ES-BCW system offers an endogenous carbon-driven strategy for synergistic bioremediation of mixed aromatic contaminated oligotrophic groundwater.},
}

@article {pmid42520798,
year = {2026},
author = {Zhang, WJ and Hu, A and Wu, Z and Liu, L and Li, C and Wang, Y and Wei, Z and Lu, R and Li, J and He, Y and Zhang, T and Liu, S and Wang, J and Meng, L and Xiao, X and Zhao, W},
title = {Unveiling active microbial processes in Earth's deepest seawater.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.07.001},
pmid = {42520798},
issn = {1934-6069},
abstract = {Microorganisms dominate life in the hadal zone, yet extreme sampling difficulty and low biomass have precluded characterization of their in situ activities. Here, we analyze microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives. DNA-protein co-extraction and metagenome-guided metaproteomic analysis identify 135,073 non-redundant active proteins, with over 95% being hadal-specific. Metaproteomic quantification distinguishes highly active and less active taxa that differ in biogeographic origins and genomic traits. Hadal microorganisms operate a metabolic regime fundamentally distinct from the upper ocean, preferentially utilizing refractory organic matter (aromatics, halogenated compounds, and D-amino acids) and expanded electron acceptors (thiosulfate and heavy metals), collectively shaping hadal element cycling. Active viruses extend beyond "Piggyback-the-Winner" dynamics, enhancing host adaptation through auxiliary metabolic genes. These findings provide proteome-level evidence of hadal microbial activities and reveal biogeochemical cycling distinct from that of the upper ocean, highlighting the underappreciated significance of hadal microbiomes within global ocean ecosystems.},
}

@article {pmid42520901,
year = {2026},
author = {Zhang, L and Zhao, B and Zhang, X and Li, Y and Li, H and Yuan, S and Ning, H and Lv, B and Li, L and Fan, X and Yue, X},
title = {Fe[2+] Alters Carbon and Nitrogen Metabolic Networks in a Composite Microbial Consortium: Metagenomic Insights into the Shift from Denitrification to DNRA.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125349},
doi = {10.1016/j.envres.2026.125349},
pmid = {42520901},
issn = {1096-0953},
abstract = {Conventional biological nitrogen removal processes are constrained by lengthy treatment trains and dependence on organic carbon sources, necessitating the development of novel enhanced nitrogen removal strategies that integrate multiple functions and ensure operational stability. In this study, a synthetic bacterial consortium was constructed, comprising the aerobic denitrifier Pseudomonas stutzeri, the facultative anaerobic denitrifier Klebsiella sp., and the heterotrophic nitrifying-aerobic denitrifying bacterium Alcaligenes sp. The effects of five iron species as well as their combined effects with polyacrylamide (PAM), on nitrogen removal performance and oxidative stress responses of the consortium were investigated, and metagenomic sequencing was employed to elucidate the regulatory mechanisms of Fe[2+] on metabolic processes. The results showed that, compared with the other iron species, the Fe[2+] group achieved a 20-30% increase in nitrate-N removal efficiency. The addition of PAM attenuated the specific regulatory effects of different iron species through physical mass-transfer limitation. Metagenomic analysis revealed that Fe[2+] modulated the carbon and nitrogen metabolic networks: in the carbon metabolic network, enrichment of the por gene in the glycolytic pathway generated substantial reducing power in the form of reduced ferredoxin; concomitantly, the transcript abundance of the dissimilatory nitrate reduction to ammonium pathway increased from 775 to 802, whereas that of the denitrification pathway decreased from 1259 to 1222. This study elucidates the intrinsic mechanism by which Fe[2+] promotes synergistic carbon and nitrogen removal, providing a theoretical foundation for the development of a multi-process coupled deep nitrogen removal system integrating bioaugmentation, chemical regulation, and physical sedimentation.},
}

@article {pmid42501817,
year = {2026},
author = {Gaye, A and Vaidya, V and Toure, M and Ndiaye, IM and Gallon, S and Yade, MS and Ngom, B and Sow, D and Diop, NC and Kebe, O and Ndiaye, YD and Diallo, MA and Sene, A and Tine, A and Deme, AB and Diedhiou, Y and Dia, AK and Badiane, AS and Sy, M and Ndiaye, D and Herrera, BB},
title = {A tiered molecular surveillance framework linking rapid dengue detection to genomic epidemiology in Senegal.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109009},
doi = {10.1016/j.ijid.2026.109009},
pmid = {42501817},
issn = {1878-3511},
abstract = {BACKGROUND: Arboviral surveillance in Africa is limited by fragmented diagnostic capacity and insufficient integration of molecular detection with genomic epidemiology, particularly in settings where dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV) viruses co-circulate and present with overlapping clinical syndromes.

METHODS: We conducted a molecular surveillance study across multiple regions in Senegal, including samples collected from 367 individuals with febrile or non-febrile illness. A tiered workflow was implemented using multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) screening for DENV, ZIKV, and CHIKV, performed on a combination of individually tested samples (n=43) and pooled samples (three individuals per pool). DENV RT-qPCR-positive samples were further characterized by reverse transcription recombinase polymerase amplification (RT-RPA) serotyping and genomic sequencing.

FINDINGS: Multiplex RT-qPCR revealed concurrent circulation of multiple arboviruses. Among individually tested samples, positivity rates were 20·9% (9/43) for DENV, 9·3% (4/43) for ZIKV, and 11·6% (5/43) for CHIKV. In pooled screening across all sites (108 pools), positivity rates were 18·5% for DENV (20/108), 5·6% for ZIKV (6/108), and 10·2% for CHIKV (11/108), indicating widespread arboviral transmission. DENV-1-4 serotyping by RT-RPA demonstrated complete concordance with RT-qPCR and identified exclusive circulation of DENV-2, enabling triage of samples for downstream genomic sequencing. Amplicon-based sequencing substantially improved genome recovery compared with metagenomic sequencing, yielding near-complete genomes in 77·8% (14/18) of RT-RPA-positive samples. Phylogenetic analyses demonstrated that all sequences clustered within the DENV-2 cosmopolitan genotype (genotype II), lineage II-F.1.1, closely related to recent strains from West Africa and Asia. Time-resolved reconstruction suggested recent emergence (∼2022-2023) and rapid expansion, consistent with ongoing transmission and regional dissemination.

INTERPRETATION: These findings demonstrate co-circulation of DENV, ZIKV, and CHIKV in Senegal and provide evidence of recent expansion of DENV-2 within a globally connected transmission network. A tiered strategy integrating pooled molecular screening with RT-RPA triage and genomic sequencing offers a scalable framework for arboviral surveillance in resource-limited settings.},
}

@article {pmid42501920,
year = {2026},
author = {Kim, JE and Cho, H and Lee, J and Park, JI and Koh, JH and Park, S and Kang, E and Kim, YC and Kim, DK and Kim, YS and Min, S and Song, EY and Moon, KC and Kim, BS and Lee, H},
title = {Pretransplant Gut Microbiome Signatures Predict Early Acute Rejection After Kidney Transplantation.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.07.023},
pmid = {42501920},
issn = {1600-6143},
abstract = {Early identification of rejection remains a critical unmet need in kidney transplantation, as conventional tools detect rejection only after irreversible allograft injury. The pre-transplant gut microbiome may provide novel predictive signals by modulating immune homeostasis. Pre-transplant stool samples underwent shotgun metagenomic sequencing. Composition, functional profiles, and networks were compared between rejection and non-rejection (protocol biopsy ≤ 2 weeks). A pre-specified SCFA biosynthetic KO panel was tested with FDR correction. Stepwise Random Forest models were developed with subgroup analyses and tested in a temporal validation cohort. Of 78 recipients, 26 (33.3%) developed biopsy-proven early acute rejection. Three taxa including Phascolarctobacterium faecium were FDR-significantly reduced. At the gene level, mcmB (a key propionate-biosynthetic enzyme) was the only KO reaching FDR significance in the pre-specified SCFA panel (q = 0.018). Network analysis revealed selective microstructural reorganization. AUC improved stepwise (0.565 → 0.681 → 0.765), was preserved across rejection subtypes (TCMR-spectrum 0.74; ABMR 0.85), and reached 0.721 in temporal validation with improved reclassification (NRI 0.11; IDI 0.055) and clinical net benefit at thresholds 0.2-0.5. Pre-transplant gut microbiome signatures were independently associated with early acute rejection. Microbiome-augmented models outperformed clinical-only models and remained robust in temporal validation, supporting microbiome-based pre-transplant risk stratification.},
}

@article {pmid42502253,
year = {2026},
author = {Niles, DT and Moulton, EA and Bocchini, CE},
title = {Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Pediatric Transplant Patients.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70272},
doi = {10.1111/tid.70272},
pmid = {42502253},
issn = {1399-3062},
abstract = {Metagenomic next-generation sequencing (mNGS) is a significant advancement in the diagnostic evaluation of infectious diseases, especially in immunocompromised patients at risk for complex, atypical, and opportunistic infections. In pediatric solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients, mNGS can augment a diagnostic evaluation when conventional microbiological testing (CMT) fails to identify the infectious etiology. Current evidence supports the use of mNGS for specific syndromes, including complicated pneumonia, central nervous system infections, and febrile neutropenia, due to greater sensitivity. While it is considered a second-line test, early application for high-risk infections, such as diagnosis of invasive fungal disease, has been shown to be impactful. Furthermore, mNGS can detect donor-derived infections (DDIs), where the breadth of the assay can identify unexpected pathogens transmitted via the graft that are often omitted from routine screening protocols. Despite the potential, interpretation remains challenging due to the detection of DNA from commensal organisms, latent viral reactivation, and low-level detection of pathogens that do not correlate with disease. Establishing diagnostic stewardship is key to directing testing to maximize diagnostic yield and improve clinical outcomes.},
}

@article {pmid42502975,
year = {2026},
author = {Taldaev, A and Smutin, D and Danilov, L and Kashchenko, G and Ryabova, A and Adonin, L},
title = {Brain Transcriptomic Reprogramming and Comb-Associated Microbiome Variation During the Larva-To-Pupa Transition in Apis Mellifera.},
journal = {Archives of insect biochemistry and physiology},
volume = {122},
number = {4},
pages = {e70196},
pmid = {42502975},
issn = {1520-6327},
support = {25-26-00381//Russian Science Foundation/ ; },
mesh = {Animals ; Bees/microbiology/growth & development/genetics/metabolism ; *Brain/metabolism/growth & development ; Larva/growth & development/microbiology/genetics/metabolism ; *Transcriptome ; *Microbiota ; Pupa/growth & development/microbiology/genetics/metabolism ; Metamorphosis, Biological ; },
abstract = {The larva-to-pupa transition in honey bees (Apis mellifera) involves extensive neural remodeling, yet the molecular dynamics of brain development and their relationship with the surrounding microbial environment remain poorly characterized. This study integrated brain transcriptomic profiling with comb-associated metagenomic analysis to characterize stage-specific molecular signatures during metamorphosis. RNA sequencing of larval and pupal brains was combined with honeycomb shotgun metagenomics from the same sample. Brain transcriptomes exhibited marked stage-specific divergence. Pupae displayed downregulation of transcriptional regulators, ecdysone and insulin signaling, and growth-related pathways, alongside upregulation of cuticular proteins, glutathione metabolism, and odorant-binding proteins. Notably, numerous poorly annotated, lineage-specific loci showed extreme stage-specific regulation. In contrast, comb-associated microbial communities remained globally stable across developmental stages, though supervised ordination identified stage-discriminatory taxa, including core symbionts and opportunistic pathogens. Integrative network analysis revealed significant correlations between comb potential bee pathogens' abundances and brain transcripts involved in translation, stress response, and metabolic regulation. Our data suggest that honey bee neural maturation is primarily driven by intrinsic transcriptional reprogramming, while structured variation in the external microbial milieu correlates with host neural gene expression. Honeycomb microbiome shift should be the consequence of the environmental conditions changes and host developmental shifts. Their roles in that process, as well as the brood immune system-comb microbiome interactions, may be part of future research.},
}

Animals
Bees/microbiology/growth & development/genetics/metabolism
*Brain/metabolism/growth & development
Larva/growth & development/microbiology/genetics/metabolism
*Transcriptome
*Microbiota
Pupa/growth & development/microbiology/genetics/metabolism
Metamorphosis, Biological

@article {pmid42503761,
year = {2026},
author = {Li, Z and Wang, L and Huang, F and Han, S and Zhang, Y},
title = {Root Metabolic Shifts Drive Genome-Resolved Cometabolism of Phthalates and Coupled Humification in Mollisols.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05506},
pmid = {42503761},
issn = {1520-5851},
abstract = {Extensive import of mixed phthalate esters (PAEs) threatens Mollisol ecosystems. Nevertheless, mechanisms through which plant roots orchestrate the cometabolic degradation of PAEs and couple this with soil humification remain unclear. This study integrated plant physiology, untargeted metabolomics, and genome-resolved metagenomics to decipher response trajectories of the Pak Choi-Mollisol root-microbe system across a mixed PAEs gradient. The findings indicated that under mild stress (5 mg/kg), plants sustained a "growth-driven" homeostasis alongside a stable rhizospheric microbiome. In contrast, acute toxicity (20 mg/kg) initiated pronounced metabolic shifts, characterized by a "survival-overgrowth" strategy. Specifically, carbon fluxes shifted from primary assimilation to secondary defense hubs. This physiological tradeoff reversed the root exudate profile, shifting from basic carbohydrates to massive efflux of specific organic acids and phenolics. Critically, these allelochemicals functioned as exogenous elicitors, selectively recruiting specific metagenome-assembled genomes (MAGs). Genomic evidence confirmed that single keystone MAGs (Pseudomonas and Burkholderia) coharbored pcaG/H and extracellular laccase genes, establishing a self-contained cometabolic module for concurrent PAEs degradation and carbon stabilization. Consequently, based on correlative multiomics evidence, extensive carbon efflux was associated with a putative coupling between PAEs detoxification and stable humic carbon accumulation, as indicated by a 48.7% increase in the humification index (HIX). Ultimately, this multiomics framework elucidates the plant-driven enhancement of carbon sinks within contaminated soils.},
}

@article {pmid42505077,
year = {2026},
author = {Zhang, Q and Li, D and Liu, B and Zhang, Y and Li, M and Guo, R and Ni, Y and Chen, S and Ni, B and Qiu, L and Xing, G and Dong, H and Yan, Q and Li, S and Zou, X and Cao, B},
title = {A Comprehensive Microbial Gene Catalog of the Human Airway Microbiome Across Anatomical Sites and Geographic Regions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76589},
doi = {10.1002/advs.76589},
pmid = {42505077},
issn = {2198-3844},
support = {BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; 82341113//National Natural Science Foundation of China/ ; 025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; 2022YFA1304303//National Key R&D Program of China/ ; },
abstract = {The respiratory microbiota is a critical determinant of airway health, yet functional characterization remains challenging due to the lack of a high-resolution reference catalog. To address this gap and enable systematic investigation at both species and gene levels, we constructed the integrated Human Airway Microbiome Gene Catalog (iHAMGC) through high-throughput metagenomic analysis of 12,273 airway samples. This catalog comprises 24,185,985 non-redundant microbial genes and provides extensive taxonomic and functional annotations, with a particular focus on clinically relevant elements, including antibiotic resistance genes, virulence factors, and antimicrobial peptides. We further resolved the bacterial hosts of resistance genes and virulence factor genes, as well as taxa contributing to antimicrobial peptide activity. The iHAMGC captures site-specific microbial and functional variations across distinct airway niches and reveals regional differences in functional potential. By offering a comprehensive, publicly accessible reference for airway microbial genes, the iHAMGC serves as a foundational resource for advancing our understanding of the airway microbiota in respiratory health and disease.},
}

@article {pmid42505127,
year = {2026},
author = {Díaz-Rúa, R and Drautz-Moses, DI and Zhao, X and Perumal, S and Esau, L and Angelov, A and Putra, A and Driguez, P and Cheung, MS and Palescandolo, E},
title = {Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0001326},
doi = {10.1128/spectrum.00013-26},
pmid = {42505127},
issn = {2165-0497},
abstract = {UNLABELLED: Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina-compatible short-read library preparation conditions in triplicate at 2 × 150 bp and 2 × 250 bp read lengths alongside PacBio HiFi long-read sequencing using a composite environmental sample of marine mangrove sediment and terrestrial palm tree soil. Longer short reads (2 × 250 bp) combined with optimal library preparation approaches improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results approaching those of long-read sequencing. TruSeq libraries at 2 × 250 bp recovered more than sevenfold more unique proteins than the same kit at 2 × 150 bp (811,701 vs 110,108) using the same number of sequencing reads, while recovering a comparable number of high-quality MAGs to PacBio HiFi long-read sequencing (11 vs 18) and surpassing it in protein discovery by almost 10-fold (811,701 vs 87,745) at less than half of the sequencing cost. Furthermore, biosynthetic gene cluster analysis identified 46 biosynthetic gene clusters in TruSeq-250PE assemblies compared to 38 in PacBio HiFi, with several showing no close match in the MIBiG database. Although long reads yield more contiguity and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating that strategic selection of library preparation chemistry and sequencing parameters can reveal more unknown microbial information in complex biomes without requiring additional sequencing depth.

IMPORTANCE: Metagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2 × 150 bp and 2 × 250 bp across multiple library preparation kits, alongside PacBio HiFi long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. These findings demonstrate that short-read sequencing at 2 × 250 bp, with appropriate library preparation, can match long-read technologies in MAG recovery while substantially surpassing them in protein discovery. With less than half of the sequencing price and a 3.5-fold reduction in cost per gigabase of usable data, this method facilitates more accessible large-scale metagenomic analysis within complex environmental systems.},
}

@article {pmid42505598,
year = {2026},
author = {Fortaleza, JAG and Cabuhat, KSP and Lagunzad, HC and Panizales, WB and Cruz, JTP and Matamis, JG and Mamaat, JER and Libres, AC and Dulay, RMR and Nuevo, JJM},
title = {Artificial Intelligence in Bacteriophage Science: A Comprehensive Narrative Review of Applications, Challenges, and Translational Opportunities.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/antibiotics15070635},
pmid = {42505598},
issn = {2079-6382},
abstract = {Antimicrobial resistance and persistent biofilm-associated infections have renewed interest in bacteriophages as alternatives or complements to conventional antibiotics. However, broader therapeutic adoption remains constrained by slow phage discovery, incomplete genome characterization, narrow host range, complex therapeutic matching, and manufacturing variability. Artificial intelligence (AI) offers computational approaches that may help address several of these limitations. This comprehensive narrative review discusses current AI applications across the bacteriophage pipeline, including metagenomic phage discovery, genome annotation, phage-host interaction prediction, personalized phage selection, cocktail optimization, and phage-antibiotic combination design. The review also examines AI-assisted synthetic biology approaches, including receptor-binding protein redesign, CRISPR-enabled engineering, generative genome design, and biosafety screening, as well as emerging applications in bioprocess optimization, yield prediction, purification analytics, quality assurance, and supply-chain management. Current evidence suggests that AI may accelerate phage identification, improve host-range prediction, support therapeutic optimization, and strengthen manufacturing consistency, potentially facilitating the transition of phage therapy from individualized rescue interventions toward more scalable antimicrobial platforms. Nevertheless, major limitations remain, including fragmented, taxonomically biased datasets; limited external validation; restricted interpretability; privacy concerns; biosafety oversight; and evolving regulatory frameworks. Future progress will depend on standardized datasets, multimodal validation, scalable manufacturing systems, experimental and clinical verification, and coordinated regulatory development.},
}

@article {pmid42505622,
year = {2026},
author = {Braunstein, R and Rimon, A and Teitelbaum, R and Coppenhagen-Glazer, S and Molho-Pessach, V and Hazan, R},
title = {Isolation and Characterization of ΦCA1NRNZ, a Lytic Bacteriophage Targeting the Emerging Device-Associated Pathogen Cutibacterium avidum.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/antibiotics15070659},
pmid = {42505622},
issn = {2079-6382},
support = {3015005777//Milgrom Family Support Program/ ; ISF1349/20//Israel Science Foundation/ ; A2232//Rosetrees Trust/ ; },
abstract = {Background: Cutibacterium avidum is an emerging opportunistic pathogen responsible for device-associated infections, including prosthetic joint and breast implant infections. Unlike its relative C. acnes, for which phage therapy has been explored, C. avidum infections are recalcitrant to antibiotics, and no infecting bacteriophages have been described to date. Here, we report the isolation and characterization of ΦCA1NRNZ, to the best of our knowledge, the first lytic phage described against C. avidum. Methods: ΦCA1NRNZ was obtained from wastewater sampling at the Sorek Treatment Facility in Jerusalem. Wastewater metagenomics, transmission electron microscopy, genome sequencing, host-range testing, efficiency of plating (EOP), aerobic and anaerobic lysis assays, and antibiofilm assays against mature C. avidum biofilms were performed. Results: Metagenomic analysis indicated low and transient detection of C. avidum-classified reads in wastewater. ΦCA1NRNZ was identified as a long-tailed Caudoviricetes with a ~320 nm virion. Its 33,712 bp dsDNA genome (GenBank PV441878.1) encodes 46 predicted proteins, shares 76.5% nucleotide identity with C. acnes phage ΦFD1, and contains divergent tail-fiber and host-recognition genes. No known bacterial virulence, toxin, human pathogenicity-associated, or antibiotic-resistance genes were identified. ΦCA1NRNZ lysed all 11 clinical C. avidum isolates tested under aerobic and anaerobic conditions, with EOP values of 0.11-5.55, mean 1.87, and showed no lytic activity against 25 C. acnes isolates. Against mature biofilms, ΦCA1NRNZ reduced total biomass by 28.4% (p = 0.014), reduced viable cell counts by approximately two logs, and increased extracellular ATP release (p < 0.001). Conclusions: The strict species specificity and significant in vitro antibiofilm activity of ΦCA1NRNZ support its potential for phage therapy of device-associated C. avidum infections.},
}

@article {pmid42505651,
year = {2026},
author = {Niculescu, AG and Iacob, CM and Brătilă, E and Tocariu, R and Coroleucă, CA and Corcionivoschi, N and Vrancianu, CO and Popescu, DL and Popa, GL and Popa, MI and Cristian, RE and Grigore, GA},
title = {Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/antibiotics15070688},
pmid = {42505651},
issn = {2079-6382},
support = {PN-IV-P2-2.1-TE-2023-1449//Executive Unit for Financing Higher Education, Research, Development and Innovation/ ; Component C9/Investment no. 8 (I8), PNRR-III-C9-2023-I8, contract no 760231, ID proiect - CF 53/28.12.2023//Ministry of Research and Innovation/ ; },
abstract = {The gut microbiome is a dynamic ecosystem that plays essential roles in host metabolism, immune regulation, colonization resistance, and maintenance of intestinal homeostasis. Antibiotic exposure profoundly disrupts this ecosystem by reducing microbial diversity, depleting beneficial commensals, reshaping microbial metabolic functions, and remodeling the gut resistome through the selection and dissemination of antibiotic resistance genes (ARGs). Increasing evidence from longitudinal metagenomic, multi-omics, and experimental studies indicates that these perturbations may persist long after antibiotic withdrawal due to incomplete ecological recovery, sustained mobile genetic element-mediated ARG dissemination, and altered microbiome resilience. Beyond antimicrobial resistance, antibiotic-induced dysbiosis has been associated with reduced short-chain fatty acid production, altered bile acid metabolism, impaired epithelial barrier function, and broader disturbances in host metabolic homeostasis, although many of these relationships remain associative rather than causal. This review provides an integrated overview of antibiotic-driven gut microbiome dysbiosis, emphasizing the ecological, functional, metabolic, and resistome-level consequences of antibiotic exposure together with the mechanisms governing microbiome recovery. Current microbiome-targeted restoration strategies, including probiotics, phage therapy, fecal microbiota transplantation, and next-generation microbiome therapeutics, are critically evaluated with particular attention to their evidence maturity, limitations, and translational potential. Finally, key knowledge gaps and future research priorities are discussed to support the development of more effective microbiome-preserving antimicrobial strategies and to limit the long-term dissemination of antimicrobial resistance.},
}

@article {pmid42505659,
year = {2026},
author = {Espinoza-Culupú, A and Vasquez, SR and Toribio, IV and Farfán-López, M and Ramos, BM and Távara, MC and Palacios-Rodriguez, AP and da Silva Junior, PI and Ramirez, P},
title = {Integrated Genome Mining, Bacterial Co-Culture Activation, and Peptidomic Analyses Identify Antimicrobial Peptide Candidates from South American Bacteria.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/antibiotics15070696},
pmid = {42505659},
issn = {2079-6382},
support = {PE501084176-2023-PROCIENCIA//PROCIENCIA/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a major global health threat that requires the discovery of new antimicrobial agents. Environmental microbiomes from understudied regions represent a valuable source of antimicrobial peptide (AMP) candidates. This study aimed to identify and prioritize AMP candidates from South American genomic and metagenomic datasets and to investigate the antimicrobial potential of bioactive secretomes obtained through bacterial co-culture. Methods: A total of 853 genomes and 360 metagenomes were analyzed using a reproducible genome- and metagenome-mining pipeline combined with machine learning-based AMP prediction. Predicted AMP candidates were further characterized using complementary bioinformatic tools to assess physicochemical, structural, hemolytic, toxicological, anti-inflammatory, and anticancer properties. Selected environmental isolates were subjected to bacterial co-culture, followed by SPE-C18 and HPLC fractionation. Antimicrobial activity, antioxidant activity, hemolysis, minimum inhibitory concentration (MIC), and LC-MS/MS peptidomic analyses were performed on bioactive secretome fractions. Results: Genome and metagenome mining identified diverse AMP candidate sequences associated with bacterial genera including Streptomyces, Bacillus, Burkholderia, and Shewanella. Structural predictions revealed a predominance of α-helical conformations among prioritized candidates. Several secretome fractions obtained from co-cultures displayed antimicrobial activity against Gram-positive and Gram-negative bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Active fractions showed no detectable hemolytic activity and exhibited antioxidant activity in DPPH assays. MIC analyses indicated broad-spectrum activity against Escherichia coli ATCC 11229, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae, carbapenem-resistant Acinetobacter baumannii, and MRSA, with an apparent MIC of 10,000 mg/L. LC-MS/MS analysis of bioactive fractions identified peptide sequences by de novo sequencing, including KTESHHK, KRVGPRR, GLFPRLGVSPR, and HHAEHLVHFR. Conclusions: Integrated genome mining, bacterial co-culture activation, and peptidomic analyses provide a useful framework for prioritizing antimicrobial peptide candidates from environmental microbiomes. The identification of peptide-containing bioactive fractions with antimicrobial and antioxidant activities highlights the potential of South American bacterial resources for the discovery of novel antimicrobial compounds. Further purification, peptide synthesis, and biological validation will be required to determine the contribution of individual peptides to the observed activities.},
}

@article {pmid42505669,
year = {2026},
author = {Kim, D and Lee, WS and Lee, KH and Choi, MH and Hong, JS and Park, YJ and Yoon, JG and Lee, K and Jeong, SH},
title = {Changes in the Gut Microbiome Following Perioperative Prophylactic Cefazolin Administration in Patients Undergoing Orthopedic Surgery: A Longitudinal Prospective Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/antibiotics15070706},
pmid = {42505669},
issn = {2079-6382},
support = {2022-ER2106-00//Korea Disease Control and Prevention Agency/ ; 2023-ER-2106-020//Korea Disease Control and Prevention Agency/ ; },
abstract = {INTRODUCTION: Cefazolin is a first-generation cephalosporin with a moderate antimicrobial spectrum and the ability to induce the production of beta-lactamases by bacterial hosts. We investigated the effect of prophylactic cefazolin administration on the gut microbiome in patients undergoing orthopedic surgery.

METHODS: A total of 42 patients were included in this study, and fecal samples were collected before cefazolin administration, within 3 days after administration, and 1 month after surgery. Shotgun whole-metagenome sequencing was performed with DNA extracted from fecal samples to assess the taxonomic composition and antimicrobial resistance genes (ARGs).

RESULTS: Within 3 days after perioperative prophylactic cefazolin administration, both the diversity indices and the Gut Microbiome Health Index were significantly decreased. Furthermore, a decrease in two beneficial anaerobic Gram-positive taxa, Ruminococcus and Fusicatenibacter, and an increase in Enterobacterales was observed. The relative abundances of ARGs related to fluoroquinolone and beta-lactam antimicrobials including penicillin, cephalosporin, carbapenem, and monobactam, were also significantly increased. The changes in the taxonomic composition and resistome related to perioperative cefazolin administration partially reverted after one month.

CONCLUSIONS: Our findings suggest that even perioperative administration of a single-class antimicrobial agent could be related to the decrease of the gut microbiome diversity with potentially unfavorable taxonomic changes and lead to an increase in ARGs.},
}

@article {pmid42505832,
year = {2026},
author = {Mancini, P and Brandtner, D and Cordeschi, G and Iaconelli, M and Mastrantonio, V and Porretta, D and La Rosa, G},
title = {Evaluating the Effect of Sampling Scale on Mosquito Virome Characterization Using PacBio HiFi Long-Read Metagenomics.},
journal = {Insects},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/insects17070721},
pmid = {42505832},
issn = {2075-4450},
abstract = {Characterizing the mosquito virome is essential for understanding host-microbiota interactions and vector competence, but it can be influenced by sample scale, sequencing strategy, and host depletion. This study evaluated the effect of sampling scale on mosquito virome characterization using a third-generation sequencing (TGS) metagenomics approach based on PacBio HiFi long reads, applied to L4 larvae and adults of Aedes mariae, analyzing single individuals and pools of increasing size before and after host genome removal. The results showed that sequencing yield did not increase with pool size, indicating that the total number of reads is not proportional to the number of individuals. Host genome removal reduced the overall number of reads but altered their composition, increasing the relative proportion of assigned viral reads and reducing unclassified sequences. Despite a similar total read output, virome diversity increased with pool size, with larger pools showing greater taxonomic richness driven by the contribution of each individual. However, the high proportion of unassigned reads suggests the presence of uncharacterized viruses. This methodological workflow was technically feasible for both single-individual and pooled samples. Single-individual analyses may provide complementary information on individual-level virome composition and on low-abundance viral taxa that could be less apparent in pooled samples, whereas pooled samples may facilitate the detection of a broader range of viral taxa and may better capture the shared component of viral diversity within the analyzed population.},
}

@article {pmid42505983,
year = {2026},
author = {Li, D and Wu, X and Yuan, F and Zhou, F and Cai, B and Wei, K and Huang, W},
title = {Microbial Community Differentiation and Predicted Chemical-Defense-Related Functional Potential Across Distinct Microhabitats of Cultured Hemicentrotus pulcherrimus.},
journal = {Marine drugs},
volume = {24},
number = {7},
pages = {},
doi = {10.3390/md24070243},
pmid = {42505983},
issn = {1660-3397},
support = {2025Y01//Ningde Normal University/ ; },
mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Sea Urchins/microbiology ; Aquaculture ; Quorum Sensing ; Ecosystem ; },
abstract = {Sea urchins harbor diverse microbial communities that may contribute to host-associated ecological interactions, microbial competition, and chemical defense. However, the compartment-specific organization of sea urchin-associated microbiota and their predicted chemical-defense-related functional potential remain poorly understood under aquaculture conditions. In this study, 16S rRNA gene amplicon sequencing was used to characterize microbial communities in rearing water, coelomic fluid, intestine, stomach contents, and surface mucus of Hemicentrotus pulcherrimus (H. pulcherrimus). KEGG Orthology (KO)-based functional prediction was further performed to evaluate predicted chemical-defense-related functional potential, including predicted chemical-defense-related pathways, siderophore-related functions, quorum sensing-related functions, and bacterial competition- and secretion system-related functions. Rarefaction curves and Coverage values indicated sufficient sequencing depth. Alpha diversity and Nonmetric multidimensional scaling (NMDS) analyses revealed clear microbial differentiation among the five sample types, with rearing water showing higher microbial richness. Taxonomic analysis identified Pseudomonadota, Bacteroidota, Campylobacterota, Bacillota, Planctomycetota, and Spirochaetota as dominant phyla, with several discriminative taxa across compartments. KO prediction showed that total predicted abundance of predicted chemical-defense-related KOs differed significantly among sample types. Among host-associated compartments, surface mucus showed relatively higher predicted siderophore-related KO potential, whereas stomach contents showed higher predicted quorum sensing-related KO potential among host-associated compartments. These findings suggest compartment-specific microbial communities and predicted chemical-defense-related functional potential in cultured H. pulcherrimus under aquaculture conditions. Because these functions were inferred from 16S-based KO prediction, they should be interpreted as preliminary hypotheses for future metagenomic, metabolomic, and culture-dependent validation.},
}

Animals
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Sea Urchins/microbiology
Aquaculture
Quorum Sensing
Ecosystem

@article {pmid42506218,
year = {2026},
author = {Abán, CL and Larama, G and Ducci, A and Fallard, A and Ortiz, J and Vargas-Gil, S and Pérez-Brandan, C},
title = {Legacy Effects of Urochloa brizantha Cover Cropping on Rhizosphere Fungal Communities and Soil Properties in a Degraded Common Bean System.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
doi = {10.3390/jof12070456},
pmid = {42506218},
issn = {2309-608X},
support = {2023-705 PD-I093-INTA, FONCyT-PICT 2019-00896, PIP 2022-2024 112202101 00162CO, ANID project, ATE220038.//National Institute of Agricultural Technology (INTA), The National Scientific and Technical Research Council (CONICET) and by the Concurso Anillos de Investigación en Áreas Temáticas,/ ; },
abstract = {Intensive agricultural practices based on continuous monocropping and prolonged bare-soil fallows have contributed to soil degradation and loss of biological functioning. Replacing fallows with cover crops (CCs) is a promising strategy to restore soil quality, yet their legacy effects on rhizosphere fungal communities remain poorly understood. This study evaluated the legacy effects of Urochloa (syn. Brachiaria) brizantha cover cropping on rhizosphere fungal communities, as well as soil physicochemical and biological properties, in a degraded common bean system. A field experiment with a randomized complete block design included: bare fallow (BM), one (B1) or two (B2) CC cycles before bean, a perennial pasture (PB), and a pristine soil reference (PS). High-throughput sequencing showed that Urochloa-based treatments significantly shifted fungal community composition compared to BM, increasing saprotrophic and beneficial taxa (e.g., Mortierella, Penicillium, Coprinellus) and reducing potential pathogens such as Fusarium. These changes were associated with higher soil organic carbon, aggregate stability, microbial biomass, and enzyme activities, especially in B2 and PB. Indicator taxa identified by LEfSe were linked to organic matter decomposition and nutrient cycling. Multivariate analyses revealed strong associations between fungal community structure and soil properties. Overall, U. brizantha cover cropping induced measurable legacy effects, promoting soil biological recovery even after short-term implementation.},
}

@article {pmid42506289,
year = {2026},
author = {Cruz, GMD and Fraga, AS and Garcia, MT and Junqueira, JC},
title = {Oral Mycobiome: Composition, Functionality and Clinical Implication.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
doi = {10.3390/jof12070528},
pmid = {42506289},
issn = {2309-608X},
support = {310265/2022-3//National Council for Scientific and Technological Development/ ; 88887.149515/2025-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
abstract = {Historically, the study of oral fungal species was limited by the inability to cultivate most of them. However, advances in metagenomic techniques have enabled the direct identification of microbial genomes from human samples, markedly broadening our understanding of the oral mycobiome. This narrative review aims to analyze the available scientific evidence on the composition and dynamics of the oral mycobiome, as well as its influence on the development of local pathological conditions. The oral mycobiome is highly diverse, with emphasis on genus Candida, followed by Cladosporium, Aureobasidium and Saccharomyces. Candida albicans remains the most frequently identified species in both health and diseases state. However, individuals with oral candidiasis present a higher detection of Candida dubliniensis, Candida parapsilosis, Pichia kudriavzevii, Antrodiella micra and Cladosporium sphaerospermum. In dental caries, C. albicans and C. dubliniensis are associated with advanced lesions, whereas Debaryomyces and Rhodotorula may exert protective effects against Streptococcus mutans, a cariogenic bacterium. In periodontitis, an increase in yeast-bacteria interactions is observed. Additionally, C. albicans has been implicated in oral carcinogenesis through multiple mechanisms. These findings highlight the need for a deeper understanding of the oral mycobiome to enable early detection of oral diseases and the development of therapeutic approaches.},
}