@article {pmid41658610,
year = {2026},
author = {Bautista, J and Bedón-Galarza, R and Martínez-Hidalgo, F and Masache-Cruz, M and Benítez-Núñez, M and Valencia-Arroyo, C and López-Cortés, A},
title = {Decoding the microbial blueprint of pancreatic cancer.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1737582},
pmid = {41658610},
issn = {2296-858X},
abstract = {Pancreatic cancer (PC) represents one of the most formidable challenges in oncology, characterized by its asymptomatic onset, delayed clinical detection, and dismal prognosis. Among pancreatic neoplasms, pancreatic ductal adenocarcinoma (PDAC) accounts for over 90% of cases and remains the most aggressive form, driven by late diagnosis, intrinsic chemoresistance, and a profoundly immunosuppressive tumor microenvironment. Recent advances have reframed the human microbiome not as a passive bystander but as an active architect of pancreatic tumor biology. This review delineates the mechanistic axes through which microbial ecosystems orchestrate PDAC progression across four key anatomical niches-gastrointestinal, oral, urogenital, and intrapancreatic. We elucidate how microbial dysbiosis fosters oncogenesis through immune evasion, metabolic reprogramming, and chronic inflammation, implicating specific taxa such as Fusobacterium nucleatum, Malassezia spp., and Porphyromonas gingivalis in immune suppression and chemoresistance. Microbial enzymatic inactivation of gemcitabine and modulation of cytokine networks further underscore the microbiome's pivotal role in therapeutic failure. Conversely, commensal and probiotic species may potentiate immunosurveillance and enhance treatment efficacy. This review also explores microbiota-derived biomarkers for early detection and the translational promise of microbiome-targeted interventions, including fecal microbiota transplantation, probiotics, and selective antibiotics. By decoding the microbial blueprint of PC, we propose a paradigm in which the microbiome emerges as both a biomarker and a therapeutic axis, offering novel avenues for precision oncology. Furthermore, this integrative synthesis emphasizes the multi-omic, immunometabolic, and therapeutic dimensions of the pancreatic cancer-microbiome interface, where metagenomic, transcriptomic, metabolomic, and immunomic layers converge to shape tumor evolution and therapeutic response, advancing the vision of microbiome-informed precision oncology.},
}

@article {pmid41658353,
year = {2026},
author = {Liu, X and Li, Y and Xiao, J and Zhang, X and Liu, Y and Li, Z and Wang, L and Zhang, L and Liu, Y and Liang, P and Xu, Z and Liu, Y and Song, C},
title = {Emergence of a Novel CRESS-DNA Virus Associated with Swine Reproductive Failure in China.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {},
pages = {4053892},
pmid = {41658353},
issn = {1865-1682},
mesh = {Animals ; Swine ; China/epidemiology ; *Swine Diseases/virology/epidemiology ; *Circoviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; *DNA Viruses/genetics/isolation & purification/classification ; *Circovirus/isolation & purification/genetics ; Genome, Viral ; },
abstract = {The continuous emergence of circular Rep-encoding single-stranded (CRESS) DNA viruses across diverse hosts has been closely associated with the occurrence of severe diseases. Four circoviruses within the genus Circovirus have been identified in pigs, including porcine circovirus Type 1 (PCV1), PCV2, PCV3, PCV4, and PCV5. In late 2021, a large pig farm experienced an outbreak of reproductive disorders that were undiagnosed by standard tests. Subsequent viral metagenomic analysis of stillborn piglets identified a novel single-stranded circular DNA virus, designated porcine megalocircovirus (PMCV). PMCV has a large genome of 9426 nt and encodes nine open reading frames. Biochemical analyses of Rep confirm PMCV as a CRESS DNA virus. However, PMCV Rep showed low amino acid sequence identities to the four PCV species and several human CRESS DNA viruses, with the highest identity of 23.6% to PCV4 Rep. The genetic evolutionary tree indicates that PMCV belongs to an unknown family of the CRESS DNA viruses. The positive detection rate for PMCV in tested samples was 24% (30/125), while the positive rate regarding pig farms was 41.18% (14/34) in China. The emergence of PMCV warrants further investigation.},
}

Animals
Swine
China/epidemiology
*Swine Diseases/virology/epidemiology
*Circoviridae Infections/veterinary/virology/epidemiology
Phylogeny
*DNA Viruses/genetics/isolation & purification/classification
*Circovirus/isolation & purification/genetics
Genome, Viral

@article {pmid41658007,
year = {2025},
author = {Alfonsi, S and Racciatti, F and Guzman, F and Fabbretti, A and Milon, P and Vitali, LA and Spurio, R and Petrelli, D},
title = {The plastisphere and river systems as reservoirs for antibiotic resistant bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721325},
pmid = {41658007},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a critical global health threat. This phenomenon involves the diffusion of bacteria and genes among humans, animals and the environment. In particular, the presence of third generation cephalosporin (3GC)-resistant Enterobacteriaceae in natural environments is of high concern as they are classified as critical-priority pathogens of public health importance. In this work we studied the relation among plastic pollution in freshwater ecosystems, the spread of multidrug-resistant (MDR) bacteria and diffusion of antibiotic resistance genes (ARGs). Caged plastic fragments were deliberately introduced in a river of central Italy. Plastic samples were collected and analyzed in parallel with river water samples. Out of 267 cefotaxime (CTX) resistant isolates obtained, 65 CTX-resistant Enterobacteriaceae were selected for further analysis. Most of the isolates (75% of plastic-derived and 84% of water-derived isolates) were MDR with seven being carbapenem-resistant enterobacteria (CRE). Five of them synthesize KPC (Klebsiella pneumoniae carbapenemases) enzymes, and two strains were positive for metallo-β-lactamases (NDM). Among the KPC producers, three isolates were identified as K. pneumoniae sequence type ST1519. Their isolation in a natural ecosystem is alarming because they can potentially re-enter human populations through environmental pathways. Shotgun metagenomic analysis provided a comprehensive snapshot of the microbial communities associated to the plastisphere, revealing dominance of families such as Comamonadaceae, Sphaerotilaceae, and Flavobacteriaceae, which play key roles in environmental biofilm formation and stability. The resistome analysis highlighted the presence of ARGs conferring resistance to clinically important antibiotics, such as beta-lactams, vancomycin, and tetracyclines, alongside mobile genetic elements (MGEs) such as integrons, which facilitate the horizontal transfer of resistance genes. This study provides crucial experimental evidence that riverine plastic debris acts as a genetic reservoir and could act as an efficient vehicle for the accumulation and transfer of clinically relevant resistance determinants.},
}

@article {pmid41658006,
year = {2025},
author = {Tada, Y and Nakajima, R and Kitamura, M and Marumoto, K},
title = {Distribution and function of prokaryotes involved in mercury methylation, demethylation, and reduction in the western North Pacific Subtropical Gyre.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1642479},
pmid = {41658006},
issn = {1664-302X},
abstract = {Methylmercury (MeHg), a bioaccumulative neurotoxic heavy metal, substantially threatens environmental and human health. In natural environments, MeHg formation and degradation are primarily mediated by microorganisms containing hgcAB, merA, or merB genes. However, these genes have not been simultaneously analyzed in open-ocean samples. This study aimed to investigate the distribution and phylogeny of functional genes associated with mercury (Hg) methylation (hgcA and hgcB), demethylation (merB), and reduction (merA), as well as dissolved total Hg (THg) and MeHg concentrations in the western North Pacific Subtropical Gyre (WNPSG) using metagenomic analysis. Although THg levels varied across sampling sites, MeHg concentrations consistently increased with depth. A strong correlation between dissolved MeHg and apparent oxygen utilization indicated a link between Hg methylation and microbial respiration. hgcA, merB, and merA were predominantly detected at depths of 500-1,500 m, where MeHg concentrations peaked, indicating active microbial Hg speciation within mesopelagic layers. A higher abundance of hgcA than merB suggests that microbial Hg methylation may surpass demethylation in this region. Phylogenetic analyses of hgcAB identified the Nitrospina lineage as dominant Hg methylators. Metabolic pathway analyses of metagenome-assembled genomes (MAGs) showed that Nitrospina harboring hgcAB possesses the nitrite reductase pathway, suggesting a linkage between Hg methylation and nitrogen cycling. MAGs with hgcA affiliated with Myxococcota (Deltaproteobacteria) exhibited a strong association with sulfur cycling. Diverse lineages harboring merB and merA genes were identified, suggesting that MeHg demethylation and Hg(II) reduction likely co-occur. Methanogenesis pathways in some Alphaproteobacteria with merB or merA suggest a potential connection between methane production and MeHg degradation and Hg(II) reduction. These findings provide novel insights into the intricate interactions between microbial communities, functional gene distributions, and Hg biogeochemical cycling in the WNPSG.},
}

@article {pmid41657996,
year = {2025},
author = {Kong, M and Pan, Z and Wang, X and Huang, J and Tulafu, H and Xu, Y and Sulaiman, Y and Wu, W},
title = {Integrated multi-omics analysis reveals rumen and rectal microbiota-metabolite interaction features in polytocous fine-wool sheep with divergent residual feed intake.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1712307},
pmid = {41657996},
issn = {1664-302X},
abstract = {Residual feed intake (RFI) is a key indicator of feed efficiency in ruminants. To elucidate the potential regulatory roles of microorganisms and metabolites under different RFI levels, we investigated 24 polytocous fine-wool sheep (12 high-RFI and 12 low-RFI) using metagenomic sequencing and non-targeted metabolomics of rumen and rectal contents. Significant differences in average daily feed intake, residual feed intake, and feed conversion ratio were observed between groups (p < 0.001). LEfSe analysis identified four and seventeen RFI-associated microbial biomarkers in the rumen and rectum, respectively, with s_Ruminococcus_albus and s_Ruminococcus_bicirculans as common core taxa. Functional annotation revealed that high-RFI sheep were enriched in amino acid metabolism and xenobiotic degradation pathways in the rumen, whereas low-RFI sheep were enriched in pathways related to development and regeneration. In the rectum, high-RFI sheep showed enrichment in protein folding and degradation, carbohydrate metabolism, and energy metabolism, while low-RFI sheep were enriched in transcriptional regulation and signal transduction pathways. Metabolomic analysis detected 297 and 1,130 differential metabolites in the rumen and rectum, respectively, mainly lipids, organic acids, and derivatives. KEGG enrichment indicated that rumen metabolites were primarily involved in bile acid biosynthesis and riboflavin metabolism, while rectal metabolites were enriched in energy metabolism and multiple amino acid pathways, including arachidonic acid, tryptophan, tyrosine, lysine, and methionine metabolism. Integrated analysis revealed significant associations between key bacterial taxa and metabolites, and network construction identified core nodes potentially engaged in synergistic regulation, providing insights into their roles in RFI phenotype formation. Collectively, these findings highlight the distinct contributions of the rumen and rectum to feed efficiency in sheep and offer theoretical support for nutritional regulation strategies to improve ruminant production performance.},
}

@article {pmid41657984,
year = {2025},
author = {Li, JL and Hu, W and Chen, XQ and Li, LH and Phurbu, D and Zheng, YY and Zhang, YW and Sun, J and Yang, ZF and Xie, KQ and Yang, LQ and Yin, YR},
title = {Characterization of thermophilic xylanases from Tengchong Qiaoquan hot spring for lignocellulose bioprocessing and prebiotic production.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1731615},
pmid = {41657984},
issn = {1664-302X},
abstract = {INTRODUCTION: Xylanases are key catalysts for valorizing lignocellulosic biomass, yet many available enzymes lack sufficient thermal stability and exhibit suboptimal activity on complex substrates. To address these limitations, we combined enrichment culturing with metagenomic analysis to discover and characterize two novel GH10 family xylanases, Tc15-Xyn6 and Tc15-Xyn10, from the Qiaoquan geothermal area in Tengchong, Yunnan Province.

METHODS: Following molecular cloning, heterologous expression, and purification by Ni[2+]-chelating affinity chromatography, both enzymes were comprehensively profiled.

RESULTS: Tc15-Xyn6 displayed optimal activity at 65 °C and pH 6.6 with a half-life of 2 h at 65 °C, while Tc15-Xyn10 exhibited optimal activity at 60 °C and pH 6.0 with a half-life of 1 h at 60 °C. Both enzymes showed broad pH stability at low temperature: after incubation at 4 °C for 12-24 h across pH 4.0-10.0, Tc15-Xyn6 and Tc15-Xyn10 retained more than 60 and 40% of their initial activity, respectively. Both efficiently hydrolyzed xylan in alkali-treated wheat straw, rice straw, and corn stover, as well as xylan from hot water-treated wheat bran, but yielded distinct product profiles: Tc15-Xyn6 primarily produced xylobiose and xylotetraose, whereas Tc15-Xyn10 generated xylotriose as the main product. The resulting xylooligosaccharides significantly promoted the growth of Lactococcus lactis. Kinetic analyses showed K m and V max values of 4.675 mg/mL and 125 μmol/min/mg for Tc15-Xyn6, and 9.36 mg/mL and 59.52 μmol/min/mg for Tc15-Xyn10.

DISCUSSION: Collectively, Tc15-Xyn6 and Tc15-Xyn10 combine thermophilicity, thermostability, near-neutral pH preference, and strong performance on complex lignocellulosic substrates, supporting their application in feed processing and targeted production of prebiotic xylooligosaccharides from biomass.},
}

@article {pmid41657910,
year = {2026},
author = {Pilgrim, J and Widlake, E and Wilson, R and Vaux, AGC and Medlock, JM and Darby, AC and Baylis, M and Blagrove, MSC},
title = {Mosquito viromes across England and Wales reveal hidden arbovirus signals and limited ecological structuring.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1749228},
pmid = {41657910},
issn = {1664-302X},
abstract = {Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of Culex mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (Peribunyaviridae), Umatilla virus (Sedoreoviridae), and Atherstone virus (Peribunyaviridae), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of Culex mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.},
}

@article {pmid41657906,
year = {2026},
author = {Wu, H and Qin, J and Li, B and Huang, Z and Liao, G and Tang, X and Li, Z and Xiong, J and Gao, Z and Jiang, J and Zhong, R and Han, Z and He, L and Tang, R},
title = {The combined application of chemical and microbial fertilizers enhanced microbial diversity and improved soil fertility in the peanut rhizosphere within a sugarcane-peanut intercropping system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1751211},
pmid = {41657906},
issn = {1664-302X},
abstract = {The decline in soil microecological balance and fertility caused by continuous cropping obstacles and excessive application of chemical fertilizers has become a critical bottleneck restricting the sustainable development of the peanut industry. However, intercropping can enhance resource utilization efficiency, and microbial fertilizers can improve soil properties and increase nutrient usability. Therefore, we evaluated the effects of six fertilization treatments [no fertilization (CK), 100% chemical fertilizer (T1), microbial fertilizer (T2), 100%chemical fertilizer+microbial fertilizer (T3), 80% chemical fertilizer+microbial fertilizer (T4) and 60% chemical fertilizer+microbial fertilizer (T5)] on chemical properties and microbial communities of the rhizosphere soil of intercropped peanuts. The results showed that compared with T1, the combined application of chemical and microbial fertilizers significantly increased soil organic matter content and alleviated soil acidification. Microbial analysis indicated that the T4 treatment had the highest Shannon diversity, which was significantly higher than T1, demonstrating its effectiveness in reversing the suppressive effect of chemical fertilizer alone on microbial diversity. Principal coordinate analysis and redundancy analysis further confirmed that fertilization significantly altered microbial community structure, with a clear separation between the combined application and chemical-fertilizer-alone treatments, forming a distinct microbial community. Specifically, the T4 treatment significantly increased the abundance of rhizobia. Under T4 treatment, the abundance of assimilatory nitrate reductase genes (such as nasB and NR) decreased, while that of narB, and nirA increased; simultaneously, the abundance of dissimilatory nitrate reductase and denitrification-specific genes significantly increased. Mantel test analysis revealed significant positive correlations between soil total nitrogen, available nitrogen content, microbial communities, and crop yield. In summary, the combined application of chemical and microbial fertilizers optimizes the soil microenvironment by synergistically enhancing soil fertility (increasing organic matter, regulating pH) and reshaping microbial community structure (increasing diversity, enriching beneficial bacteria). These findings can provide theoretical basis for the optimization of fertilization strategy in peanut intercropping system.},
}

@article {pmid41657901,
year = {2026},
author = {Farinas, LMF and Dela Peña, LBRO and Rivera, WL},
title = {Shotgun metagenomics reveals the prevalence and mobility of antibiotic resistance genes in the West Bay of the human-impacted Laguna Lake.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1742578},
pmid = {41657901},
issn = {1664-302X},
abstract = {Laguna Lake, the largest freshwater lake in the Philippines, has been reported to harbor antibiotic-resistant bacteria, posing health risks to the millions who depend on it. However, limited knowledge of antibiotic resistance genes (ARGs) in the lake highlights the need for a comprehensive assessment of its resistome. In line with this, we characterized ARGs in the West Bay of Laguna Lake using shotgun metagenomic sequencing based on six metagenomes collected from three stations across two sampling months at a single depth. ARGs were quantified from short reads, and assembled contigs containing these genes-antibiotic-resistant contigs (ARCs)-were analyzed to assess mobility through associations with plasmids and mobile genetic elements (MGEs). β-lactam resistance genes (0.023-0.048 copies per cell) were the most prevalent, corroborating previous reports. Meanwhile, the detection of bacitracin (0.013-0.028 cpc) and polymyxin (0.009-0.011 cpc) resistance genes raises new concerns, as resistance to these antibiotic classes has not been previously reported in the lake. Furthermore, 44.8 and 30.4% of ARCs were associated with plasmids and MGEs, respectively. ARCs carrying genes for resistance to β-lactams, chloramphenicol, and tetracyclines were frequently identified as mobile, indicating a high potential for horizontal gene transfer and suggesting possible antibiotic contamination in the lake. Overall, this study provides the first metagenomic insight into the resistome of Laguna Lake using short-read sequencing and highlights its role as an environmental reservoir of mobile ARGs. The findings underscore the need for expanded ARG surveillance to improve antimicrobial resistance risk prediction.},
}

@article {pmid41657896,
year = {2026},
author = {Wicaksono, WA and Thorsen, J and Stokholm, J and Berg, G},
title = {Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1729707},
pmid = {41657896},
issn = {1664-302X},
abstract = {INTRODUCTION: The nasopharyngeal microbiome presents an important environmental human interface and a window in the fight against chronic diseases like asthma, respiratory infections, and antimicrobial resistance. To identify the microbial structure and function, we designed a pilot study with individuals with asthma, COVID-19 infection, and healthy controls.

METHODS: We compare the microbial and resistome profiles of healthy individuals, patients with asthma, and patients with PCR-confirmed COVID-19 using shotgun metagenome sequencing. Additionally, metagenome-assembled genomes were generated to assess the virulence potential of the bacteria identified in the nasopharynx.

RESULTS: We found different patterns in microbial diversity, richness, and structure between individuals with asthma and those who are healthy, but not for those with COVID-19. Our results revealed unexpected insights into the quite diverse nasopharynx resistome encompassing 23 distinct drug classes, mainly based on antibiotic efflux (63.9%) and antibiotic inactivation (24.6%), regardless of the disease state. The majority of the antimicrobial resistance genes (ARGs) confer resistance to multidrug (45%), followed by those genes that confer resistance to aminoglycosides, tetracyclines, polymyxin, beta-lactam, and macrolide-lincosamide-streptogramin. A high proportion of ARGs was associated with various Pseudomonas species, which was confirmed by analysing metagenome-assembled genomes. Pseudomonas brenneri exhibited the highest number of ARGs and virulence factors, indicating notable pathogenic potential.

CONCLUSION: The study reveals distinct bacterial community compositions in healthy individuals and individuals with asthma. Pseudomonadales, particularly Pseudomonas species, contribute to the nasopharyngeal resistome. No association was found between nasopharyngeal resistome profiles and asthma development. Future research may explore airway microbial functions' influence on asthma development.},
}

@article {pmid41657444,
year = {2026},
author = {Zhong, S and Shan, W and Xiang, L and Wang, Y and Zhang, L},
title = {Human bocavirus 1 viremia-associated pediatric sepsis with a triphasic urinary course: a case report.},
journal = {Translational pediatrics},
volume = {15},
number = {1},
pages = {22},
pmid = {41657444},
issn = {2224-4344},
abstract = {BACKGROUND: Human bocavirus 1 (HBoV1) is a common pediatric respiratory virus, yet, its potential to cause severe systemic illness as a sole pathogen and its specific effects on the urinary system are not fully recognized. This report describes the first case of pediatric sepsis, meeting the 2024 Phoenix sepsis criteria, caused by high-load HBoV1 viremia, which was characterized by a novel triphasic urinary course.

CASE DESCRIPTION: A previously healthy 4-year-old girl presented with fever and cough and developed asymptomatic sterile pyuria on illness day 4. On day 7, her condition deteriorated to sepsis (Phoenix Sepsis Score of 2), with acute respiratory distress and a depressed level of consciousness. Blood metagenomic next-generation sequencing (mNGS) identified high-load HBoV1 viremia (7,513 reads) as the sole pathogen, with negative blood and urine cultures. During the septic peak, urinary tract ultrasonography was normal; however, follow-up imaging on day 13 revealed delayed-onset, non-obstructive pyelectasis and increased post-void residual (PVR) volume. These functional abnormalities were resolved completely within 2.5 months.

CONCLUSIONS: HBoV1 can act as a sole pathogen to cause pediatric sepsis. The observed triphasic urinary course-early sterile pyuria, imaging quiescence at the sepsis peak, and delayed functional impairment-supports an inflammation-mediated pathogenesis rather than direct viral invasion. This case highlights the critical role of advanced molecular diagnostics in identifying viral etiologies in culture-negative sepsis and underscores the necessity of longitudinal functional surveillance, as clinically significant organ dysfunction may manifest after the acute inflammatory phase has resolved.},
}

@article {pmid41656820,
year = {2025},
author = {Zhang, W and Han, K and Zhao, K and Yang, C and Jin, M and Wang, Y and Jiang, Z},
title = {[Application of flavonoid in disease treatment based on multi-omics technologies].},
journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences},
volume = {50},
number = {10},
pages = {1915-1929},
doi = {10.11817/j.issn.1672-7347.2025.250227},
pmid = {41656820},
issn = {1672-7347},
support = {XZ202201ZR0061G//the Natural Science Foundation of Xizang Autonomous Region/ ; 24MDQ05//Nationalities Youth Fund Project of Xizang Minzu University/ ; },
mesh = {*Flavonoids/therapeutic use/pharmacology ; Humans ; Metabolomics/methods ; Proteomics/methods ; Genomics/methods ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Multiomics ; },
abstract = {Flavonoids are naturally occurring polyphenolic compounds widely distributed in nature, exhibiting pharmacological activities including anti-inflammatory effects and inhibition of cell proliferation. Their broader application has been constrained by unclear therapeutic targets. Recent advances in high-throughput sequencing and high-resolution mass spectrometry have elevated the importance of multi-omics analysis for elucidating flavonoid pharmacological effects, therapeutic targets, and regulatory networks. Integration of genomics, transcriptomics, proteomics, metabolomics, and metagenomics enables systematic characterization of flavonoid targets and modulation networks. Clarifying the application of multi-omics technologies in this field may support the clinical translation of flavonoids and provide new strategies for precision research in traditional Chinese medicine.},
}

*Flavonoids/therapeutic use/pharmacology
Humans
Metabolomics/methods
Proteomics/methods
Genomics/methods
Medicine, Chinese Traditional
*Drugs, Chinese Herbal/therapeutic use/pharmacology
Multiomics

@article {pmid41656480,
year = {2026},
author = {da Silva, EC and Beserra, MMN and Leitão, MGS and Vieira Camelo Maia, IF and de Souza Alves, BE and Gonçalves, PG and de Assis Leite, DC and Neves, BG and Pereira, KMA and Rodrigues, LKA and Gondim, DV},
title = {Fermentation time Determines Anti-inflammatory and Osteoprotective Activity of Green Tea Kombucha in a Rat Model of Experimental Periodontitis.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41656480},
issn = {1867-1314},
abstract = {This study aimed to characterize the microbial composition of green tea-fermented kombucha at different fermentation times and to evaluate its effects on inflammation and alveolar bone loss in rats with periodontitis. Microbial diversity was first assessed by metagenomic sequencing targeting bacterial 16 S rRNA and fungal 18 S rRNA regions. Sixty male rats were divided into six groups: control, periodontitis without treatment, green tea treatment, and kombucha fermented for 4, 8, or 12 days. Kombucha or green tea was administered daily by oral gavage for 39 days. Periodontitis was induced by ligation of the maxillary second molar on day 28. After euthanasia, hemimaxillae, liver, kidney, and blood samples were collected for analysis. Kombucha fermented for 4 days showed the highest abundance of bacteria from the Acetobacteraceae family and yeasts from the Saccharomycetaceae family. This fermentation time also produced the most pronounced reduction in periodontal inflammation and alveolar bone loss, with lower expression of tumor necrosis factor-alpha (42,9%) and receptor activator of nuclear factor kappa-B (43,6%), as well as higher expression of osteoprotegerin (approximately 55,4%) in periodontal tissues compared to animals with periodontitis without treatment. Notably, kombucha did not induce renal or hepatic toxicity regardless of fermentation time. These findings suggest that kombucha, particularly after 4 days of fermentation, reduces inflammation and alveolar bone loss without systemic toxicity, supporting its potential as an adjunctive therapy for periodontitis.},
}

@article {pmid41656341,
year = {2026},
author = {Cai, J and Wu, W and Wang, L and Meng, D and Yang, H and Liu, S and Hou, S and Cao, Y},
title = {Dietary β-hydroxy-β-methyl butyrate supplementation improves intestinal health and growth performance in Tibetan sheep lambs via modulating small intestinal microbiota.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {25},
pmid = {41656341},
issn = {1674-9782},
support = {2022-NK-169//Construction of Standardized Production System for Improving quality and efficiency of Tibetan sheep industry/ ; 2025-YYKF-03//Key Laboratory of Qinghai-Tibet Plateau Grazing Yak and Tibetan Sheep Animal Nutrition and Feed-Forage, Ministry of Agriculture and Rural Affairs, P. R. China/ ; },
abstract = {BACKGROUND: Tibetan sheep grazing on the Qinghai-Tibet Plateau require dietary protein supplementation; however, they face economic constraints due to the high cost of feed transportation in this region. Given that the leucine metabolite β-hydroxy-β-methyl butyrate (HMB) enhances both protein synthesis and intestinal nutrient absorption, this study employed metagenomics and untargeted metabolomics to systematically evaluate HMB's effects on antioxidant capacity, immune response, microbiota, metabolites, and the health of the small intestine in Tibetan sheep. A total of 120 healthy weaned 60-day-old male Tibetan lambs were assigned to diets containing 0 mg/kg (control group, CON), 430 mg/kg (low HMB, L-HMB), 715 mg/kg (medium HMB, M-HMB), or 1,000 mg/kg (high HMB, H-HMB) for 90 d. At the end of the experiment, 6 lambs from each group were slaughtered for intestinal tissue and content sampling.

RESULTS: The M-HMB treatment significantly increased average daily gain of the lambs without affecting feed intake, thereby improving feed utilization efficiency. M-HMB promoted the development of small intestinal morphological and elevated villus height, while also enhancing the activities of digestive enzyme and disaccharidase activities. Furthermore, M-HMB enhanced the antioxidant capacity, immune response, and barrier function of the small intestine. Metagenomic analysis revealed that M-HMB supplementation improved the composition of the small intestinal microbiota in Tibetan sheep, specifically increasing the relative abundance of Ruminococcus bacterium P7 and R. bromii, and enhanced microbial carbohydrate degradation capacity. Metabolomic analysis demonstrated that M-HMB supplementation significantly altered the small intestinal metabolite profile, enhancing carbohydrate metabolic pathways and increased the production of short-chain fatty acids (SCFAs). M-HMB upregulated PLCβ1 and ERK1/2 protein expression levels in small intestinal tissue and elevated the proportion of Ki67-positive cells at the basal crypt region of small intestinal crypts, suggesting enhanced proliferative activity of intestinal epithelial cells.

CONCLUSIONS: In summary, dietary supplementation with M-HMB (715 mg/kg) promoted small intestinal growth and development, enhanced digestive and absorptive functions, optimized the microbial composition, improved carbohydrate degradation, and increased the production of SCFAs, ultimately improving the growth performance of Tibetan sheep lambs.},
}

@article {pmid41656299,
year = {2026},
author = {Fang, T and Bogensperger, L and Feer, L and Allam, A and Bezshapkin, V and Balázs, Z and von Mering, C and Sunagawa, S and Krauthammer, M and Schwank, G},
title = {Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69098-5},
pmid = {41656299},
issn = {2041-1723},
abstract = {Recognition of protospacer adjacent motifs (PAMs) is crucial for target site recognition by CRISPR-Cas systems. In genome editing applications, the requirement for specific PAM sequences at the target locus imposes substantial constraints, driving efforts to search for novel Cas9 orthologs with extended or alternative PAM compatibilities. Here, we present CRISPR-PAMdb, a comprehensive and publicly accessible database compiling Cas9 protein sequences from 3.8 million bacterial and archaeal genomes and PAM profiles from 7.4 million phage and plasmid sequences. Through spacer-protospacer alignment, we infer consensus PAM preferences for 8003 unique Cas9 clusters. To extend PAM discovery beyond traditional alignment-based approaches, we develop CICERO, a machine learning model predicting PAM preferences directly from Cas9 protein sequences. Built on the ESM2 protein language model and trained on the CRISPR-PAMdb database, CICERO achieves an average cosine similarity of 0.69 on test data and 0.75 on experimentally validated Cas9 orthologs. For Cas9 clusters where alignment-based predictions are infeasible, CICERO generates PAM profiles for an additional 50,308 Cas9 proteins, including 17,453 high-confidence predictions with CICERO confidence scores above 0.8. Together, CRISPR-PAMdb and CICERO enable large-scale exploration of PAM diversity across Cas9 proteins, accelerating design of next-generation CRISPR-Cas9 tools for precise genome engineering.},
}

@article {pmid41655932,
year = {2026},
author = {Kannan, EP and Venkatachalam, P and Gopal, J and Sarkaraisamy, P and Muthu, M},
title = {Antimicrobial resistance status of small marine fishes off the coastal cities of east and west coast of India: an adaptive nanopore sequencing based metagenomics raises concerns.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150754},
doi = {10.1016/j.ijbiomac.2026.150754},
pmid = {41655932},
issn = {1879-0003},
abstract = {Transmission of AMR through edible fishes has recently upsurged as a global health hazard owing to its potential impact on human and one health. India, as the second largest consumer of edible fish faces a high risk of AMR transmission, given the nutritional value, accessibility and affordability of fishes to people from all economic classes. The present study investigated the presence of ARGs in edible muscle, gills and intestines of five commercially important fishes, Nemipterus japonicus, Sardinella longiceps, Selaroides leptolepis, Stolephorus indicus, and Sardinella gibbosa sourced from two major densely populated cities of the East coast (Chennai) and the West coast (Mangalore) using adaptive nanopore sequencing technique. A total of 54 distinct ARGs associated with 12 classes of AMR were detected across both coasts with enhanced resistance observed towards aminoglycosides, macrolides, beta lactam, tetracycline and chloramphenicol. Cumulatively, the most abundant ARGs across both coasts includes cxpE, aac(3')-IIa, aac(6)-IB-cr, oqxA and oqxB. However, significant variation in the distribution of ARGs among the two coasts were studied with varying abundance patterns. Furthermore, this study predicted human pathogens such as Klebsiella sp., Escherichia sp., Staphylococcus sp. and Pseudomonas sp. as putative reservoirs of ARGs indicating potential zoonotic and foodborne transmission to humans. This study offers a novel, and in-depth characterization of edible fish associated AMR contamination in east and West coast of India, providing essential data for assessing the public health hazards posed by ARGs and the pathogenic taxa.},
}

@article {pmid41655773,
year = {2026},
author = {Bouali, ML and Kezai, AM and Beaulieu, MJ and Roy, J and Badiane, PY and Lévesque, V and Filion, L and Vallières, L and Blanchet, MR and Hébert, SS},
title = {Indoor rewilding of laboratory mice recalibrates pulmonary mucosal immunity and mechanics.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2026.02.003},
pmid = {41655773},
issn = {1935-3456},
abstract = {Laboratory mice raised under specific-pathogen-free (SPF) conditions experience restricted microbial and antigenic exposure, which favours an immature immune system and limits their translational value for respiratory research. While microbial enrichment in "dirty" mouse models restores immune maturation, its impact on integrated respiratory function and model transferability to human disease remains understudied. Here, we tested whether ecological exposure through indoor rewilding of SPF-reared mice could reshape immune complexity and recalibrate pulmonary physiology. Two-month-old female C57BL/6J mice were housed for three months under SPF or indoor-rewilding conditions and assessed for immune, mechanical, and systemic parameters. Rewilded mice exhibited expanded pulmonary immune subsets, increased dendritic-cell immune checkpoint, with TNF/IFN-γ activation coupled to regulatory IL-10 signaling. Despite sustained exposure, the alveolar-capillary barrier integrity was preserved. Functionally, respiratory oscillometry revealed improved pulmonary mechanics, including lower airway resistance, higher compliance, and reduced airway responsiveness to methacholine. Systemic cytokine analyses indicated compartmentalized pulmonary immune activation, maintaining an overall anti-inflammatory balance. Importantly, PRIA screening detected no reportable pathogens introduced during rewilding, while cecal shotgun metagenomics confirmed microbial enrichment. Together, these findings demonstrate that indoor rewilding reestablishes coordinated lung immune and mechanical homeostasis in SPF-reared mice, providing a safe and scalable model for studying human-like mucosal immunity and respiratory physiology with broad implications for preclinical respiratory research and therapeutic testing.},
}

@article {pmid41655688,
year = {2026},
author = {Jin, M and Xu, F and Liu, Y and Jiang, Z},
title = {Limosilactobacillus fermentum LF61: A Multidimensional Study on Safety and Functionality from Genomics to Clinical Application.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {116002},
doi = {10.1016/j.fct.2026.116002},
pmid = {41655688},
issn = {1873-6351},
abstract = {This study presents a comprehensive multidimensional assessment of the safety and functional efficacy of Limosilactobacillus fermentum LF61, a strain isolated from human milk. Genomic analysis revealed no virulence factors (VFDB), drug resistance genes (CARD), or toxin synthesis gene cluster (antiSMASH) within its chromosome (2.04 Mb) and plasmid (15.5 kb), meeting EFSA's QPS safety criteria. In vitro studies demonstrated that LF61 exhibited a 2-hour survival rate of > 98% in gastric acid (pH 2.0) and a survival rate of 99.66% in intestinal fluid (pH 8.0). LF61 was also nontoxic to Caco-2 cells (metabolic activity at 20% concentration: 100.3 ± 2.1%). An acute oral toxicity test (in ICR mice) demonstrated an LD50 >2 × 10[10] CFU/kg. In a randomized, double-blind clinical trial (n = 49), daily intake of 3×10[10] CFU of LF61 for 8 weeks increased serum levels of the antimicrobial peptide LL-37 by 12.3% (p < 0.05), and IgA, IgG, and IgM by 18.7%, 15.2%, and 9.8%, respectively (p < 0.05). Metagenomic analysis revealed that LF61 promoted colonization by short-chain fatty acid-producing bacteria, such as Mitsuokella and Turicibacter (LDA > 3), activated the carbohydrate metabolism pathway (p = 0.002), and maintained stable α-diversity in the microbiome (Shannon index p > 0.05).Collectively, our findings indicate that LF61 exerts beneficial effects via a gut-immune axis bidirectional regulatory mechanism, offering a theoretical basis and clinical evidence for the development of novel immunomodulatory probiotics targeting the gut-immune axis.},
}

@article {pmid41655600,
year = {2026},
author = {Susiyanti, M and Febrina, F and Putera, I and Jelita, A and Rokim, FS and Edwar, L and Aziza, Y and Sitompul, R and Distia Nora, R},
title = {METAGENOMIC SEQUENCING IN VARIOUS OCULAR INFECTIONS: A SYSTEMATIC REVIEW OF DIAGNOSTIC UTILITY.},
journal = {Survey of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.survophthal.2026.01.006},
pmid = {41655600},
issn = {1879-3304},
abstract = {Ocular infections are a common cause of visual morbidity worldwide and continue to pose significant diagnostic and therapeutic challenges. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of wide range of pathogens; however, its diagnostic utility in ocular infections warrant further evaluation. We evaluate the diagnostic performance of mNGS, highlighting its advantages, limitations, and future directions for the clinical application. Twenty-one studies involving 1219 eyes were included. mNGS positivity rates ranged from 10% to 94%. Sensitivity ranged from 15% to 100% and specificity from 12% to 100%. Viral pathogens were the most frequently detected (15 out of 21 studies), followed by bacteria (14 out of 21), fungi (10 out of 21), and parasites (6 out of 21). A broad spectrum of pathogens at both the genus and species levels was identified. mNGS also helps in assessing AMR-associated genes and mutations linked to therapy susceptibility. mNGS appears to be a valuable tool for pathogen indentification in ocular infections, particularly for organisms undetectable by conventional diagnostic methods, although careful interpretation is required. Overall, mNGS demonstrated promising diagnostic performance across different types of ocular infections. Larger, well-designed studies employing standardized protocols are needed to address current limitations and to enhance the clinical applicability of mNGS in routine clinical practice.},
}

@article {pmid41655422,
year = {2026},
author = {Wang, L and Liang, Z and Lu, D and Lv, S and Li, Z and Tan, R and Guo, Z and Wu, H and Wang, Y and Xu, X and Yu, J and Li, Z and Zhang, W and Zheng, W and Jiang, F and Yao, M and Zhou, P and Jiang, Z},
title = {Artificial reefs promote coastal carbon stabilization potential through hydrological condition and microbial pathways.},
journal = {Water research},
volume = {294},
number = {},
pages = {125502},
doi = {10.1016/j.watres.2026.125502},
pmid = {41655422},
issn = {1879-2448},
abstract = {Artificial reefs (ARs) reshape near-bed hydrodynamics and benthic microbial functions, yet links to coastal carbon stabilization remain insufficiently resolved. Here, we combined hydrodynamic modeling with sediment geochemistry, fluorescence spectroscopy, and metagenomics across contrasting AR habitats in the northern Yellow Sea. Structurally complex ARs enhanced upwelling and wake turbulence and were associated with finer sediments and higher sediment total organic carbon (TOC). Path modeling showed that hydrodynamic indices, hydrographic state variables, and microbial functional gene profiles jointly explained spatial variations in sediment TOC and humic-like fluorescent. During a 42-day dark incubation, protein-like fluorescent dissolved organic matter (FDOM) fractions declined while the humic-like component (C2) increased, indicating net enrichment of humic-like byproducts during microbial reworking of labile DOC. Microbial succession included increased relative abundance of ammonia oxidizing archaea (e.g., Crenarchaeota, Nitrososphaeria), and the SAR202 clade, accompanied by higher functional potentials related to aromatic-compound transformation and nitrogen redox pathways. Collectively, these results support a framework in which AR-induced hydrodynamic modulation couples with nitrogen-redox linked microbial functions, promoting carbon stabilization potential reflected by humic-like DOM enrichment and benthic carbon storage proxies.},
}

@article {pmid41655417,
year = {2026},
author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P},
title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.},
journal = {Water research},
volume = {294},
number = {},
pages = {125493},
doi = {10.1016/j.watres.2026.125493},
pmid = {41655417},
issn = {1879-2448},
abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.},
}

@article {pmid41655382,
year = {2026},
author = {Gupta, N and Biswas, R and Koley, A and Mukherjee, R and Das, N and Balachandran, S and Hoque, RR},
title = {Degradation of chrysene by Rhodococcus pyridinivorans C7 isolated from earthworm gut - Deciphering microbial community dynamics of the earthworm gut.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141328},
doi = {10.1016/j.jhazmat.2026.141328},
pmid = {41655382},
issn = {1873-3336},
abstract = {This study investigates the degradation of chrysene (a priority polycyclic aromatic hydrocarbon) by Rhodococcus pyridinivorans C7, isolated from the gut of Perionyx excavatus after 60 days acclimatization in petroleum-contaminated soil. After six days of incubation, strain C7 exhibited notable enzymatic activities, with catechol 1,2-dioxygenase (1.72 ± 0.14 U/mL) and catechol 2,3-dioxygenase (2.26 ± 0.19 U/mL). The strain achieved up to 75 % degradation of chrysene (40 mg/L) within this period. Gas chromatography-mass spectrometry analysis identified dibutyl phthalate as an intermediate product on day 2 and phenol 2,6-di-tert-butyl on days 4 and 6. Cytotoxicity assays revealed that the initial byproduct was highly toxic (IC50 = 0.19 µg/mL), whereas the final metabolite exhibited markedly reduced toxicity (IC50 = 19 µg/mL), indicating detoxification. Comparative genomics using Mauve software revealed strong genomic synteny between strain C7 and other PAH-degrading Rhodococcus species. Metagenomic analysis of earthworm gut microbiomes under different treatment - control (EG-C), petroleum contaminated (EG-P) and fly ash (EG-F) identified Proteobacteria as the predominant phylum with relative abundance of 21.17 %, 33.3 %, and 34.53 % respectively. Notably, the Rhodococcus genus exhibited a 1.46-fold and 1.42-fold increase in EG-P and EG-F, respectively compared to EG-C. R. pyridinivorans was detected in both EG-P and EG-F gut samples confirming its isolation through the earthworm gut. These results demonstrate that environmental perturbations can drive distinct shifts in gut microbial composition, enriching for hydrocarbon-degrading taxa. Understanding such adaptive microbial communities provides valuable insights for developing sustainable bioremediation strategies and identifying novel microbes for environmental cleanup.},
}

@article {pmid41655310,
year = {2026},
author = {Cheng, L and Li, H and Luo, C and Zhang, Y and Cheng, K and Wang, S and Hu, Z},
title = {In situ reactivation of aerobic granular sludge after extended idle conditions: Effect of different N-acyl-homoserine lactones (AHLs).},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128866},
doi = {10.1016/j.jenvman.2026.128866},
pmid = {41655310},
issn = {1095-8630},
abstract = {Prolonged idle conditions pose a major challenge to aerobic granular sludge (AGS) systems by compromising granule integrity and pollutant removal performance. This study investigates the in situ reactivation of AGS after three months of static storage using two quorum sensing molecules, N-hexanoyl-L-homoserine lactone (C6-HSL) and N-octanoyl-homoserine lactone (C8-HSL). All reactors rapidly restored COD and NH4[+]-N removal efficiencies to >92% and >98%, respectively. C6-HSL significantly accelerated phosphorus recovery, reaching removal efficiencies above 90% by day 26, compared to day 34 in the control and C8-HSL groups. C8-HSL enhanced EPS secretion and granule growth, yielding the largest granule size (1210 μm), which was 1.26-fold and 1.71-fold larger than those in the control and C6-HSL groups, respectively. Metagenomic analysis revealed comparable microbial structures at the phylum level, but distinct functional responses. C6-HSL increased the abundances of phosphorus metabolism genes (ppk, ppx, ppa), while C8-HSL notably upregulated genes related to the biosynthesis of tyrosine, tryptophan, and structural polysaccharides (e.g., alginate and Psl), supporting enhanced EPS production and granule stability. These results demonstrate molecule-specific regulatory roles of individual N-acyl-homoserine lactones during AGS reactivation, linking functional recovery and structural regeneration to distinct quorum sensing pathways. This study provides mechanistic and engineering insights into an energy-efficient strategy for restoring AGS performance after prolonged ambient idle conditions, with direct relevance to the stable operation and management of full-scale wastewater treatment systems.},
}

@article {pmid41655253,
year = {2026},
author = {Shi, Y and He, S and Li, C and Chan, H and Liu, Z and Yang, B and Li, Q},
title = {Bifidobacterium Breve Yang08 Alleviates Atopic Dermatitis By Enriching Akkermansia Muciniphila and Inhibiting Neutrophil Extracellular Traps Formation In Mice.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18588},
doi = {10.1002/advs.202518588},
pmid = {41655253},
issn = {2198-3844},
support = {32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 82574001//National Natural Science Foundation of China/ ; 2025A04J4030//Guangdong Provincial Science and Technology Plan Project/ ; },
abstract = {Atopic dermatitis (AD) is linked to gut microbiota dysbiosis, yet the mechanisms connecting specific commensals to cutaneous immunoregulation remain elusive. We observed reduced Bifidobacterium breve (B. breve) abundance in AD patients. A new B. breve strain was isolated from human stools and nomenclated as Yang08. In MC903-induced AD-like mouse models, Yang08 outperformed a standard strain, ameliorating disease severity, including reduced ear thickening, epidermal hyperplasia, and mast cell infiltration in a manner dependent on viable bacteria and an intact gut microbiota. Antibiotic-mediated microbiota depletion abrogated its efficacy, while fecal microbiota transfer from Yang08-treated mice conferred protection, confirming microbial remodeling as essential. Metagenomics revealed Yang08 specifically enriched Akkermansia muciniphila, which was required for therapeutic effects in germ-free mice. Mechanistically, Yang08 abolished both neutrophil influx and NET deposition in lesions, with ex vivo experiments showing blunted NETosis capacity. Its therapeutic benefits were reversed by neutrophil depletion, NET degradation, or PAD4 inhibition. Overall, Yang08 alleviates AD by enriching A. muciniphila and inhibiting skin NETosis, emerging as a promising prophylactic candidate prevention for AD prevention.},
}

@article {pmid41655211,
year = {2026},
author = {Su, XJ and Ma, L and Xiong, X and Meng, JH and Wu, Q and Zhang, Y and Dong, SG and Wang, YF and Wu, JH and Zeng, QY and Zhang, HF and Li, LL and Meng, L and Peng, M and Huang, XD and Wu, LQ and Wang, X},
title = {DRD2 Deficiency Underlies Pituitary Adenoma Dependent on Escherichia coli Translocation from the Gut.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04247},
doi = {10.1002/advs.202504247},
pmid = {41655211},
issn = {2198-3844},
support = {2020]74//Hubei Provincial Engineering Research Center for Inflammation Repair/ ; 2020ZYYD026//Special Funds for Local Science and Technology Development guided by the Central Government/ ; 2023AFA079//Hubei Science Foundation for Distinguished Young Scholars/ ; WX23Z27//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ22A01//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ24B86//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; },
abstract = {Pituitary adenoma (PA) are common intracranial tumor types that have harmful effects on human health. However, the pathogenesis of PA remains unclear yet. The intratumoral microbiome has been reported playing an important impact on the occurrence, metastasis, immune monitoring, and drug resistance of various tumors. While normal dopamine receptor D2 (DRD2) expression is enriched in the apical junction of pituitary epithelium and colonic enterocytes, various factors-induced drd2 loss dampened its expression at both sites. DRD2 deficiencies are characterized by chronic hyperprolactinemia, pituitary lactotroph hyperplasia, and prolactinomas in mice, but the role of intratumoral microbiome in prolactinomas is not known. We employed specific pathogen-free (SPF) and germ-free (GF) mice models and patient samples of pituitary adenoma. In the mice pituitary tumor model, we used mice that developed prolactinomas following estradiol treatment or DRD2 deficiencies. Pituitary tumor samples from patients with nonfunctional pituitary adenoma or prolactinomas were obtained after surgical excision. Various molecular, cellular, and sequencing techniques were used to determine the role of intratumoral microbiome in pituitary adenoma. We demonstrate that human patients or murine bearing estradiol-induction or DRD2 loss are all characterized by the presence of live intratumor bacteria in the pituitary adenoma. Using metagenomic next-generation sequencing and mass spectrometry techniques, we confirm that the bacterial species of pituitary tumor tissues is Escherichia coli. In vitro tracing and immunofluorescence assay results showed that the pathobiont Escherichia coli translocates from the gut into the pituitary gland along with DRD2 loss while the blood pituitary barrier were both destroyed in mice. The Escherichia coli are phagocytosed by the microglial cells in the pituitary gland, then activate GSDMD protein releasing HMGB1, and promote the tumorigenesis of pituitary adenoma by activating the MAPK pathway. The depletion of bacteria systemically, microglial depletion or HMGB1 inhibitor ethyl pyruvate rescued prolactinomas. Our findings suggest that DRD2 deficiency underlies pituitary adenoma dependent on Escherichia coli translocation from the gut and activating microglia GSDMD/ HMGB1/MAPK pathway, and provide a novel preclinical rationale for antimicrobial agents, microglial depletion, or HMGB1 inhibitor ethyl pyruvate for the treatment of pituitary adenoma.},
}

@article {pmid41654875,
year = {2026},
author = {Chen, Y and Ding, C and Ren, M and Li, Z and Liu, S and Sun, H and Yu, S and Niu, Q and Li, X and Li, B and Li, L and Yang, X and Sun, Q},
title = {Liver-muscle metabolic crosstalk: xanthosine as a key effector of broiler myogenesis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {24},
pmid = {41654875},
issn = {1674-9782},
support = {No.2022YFF1001000//National Key Research and Development Program of China/ ; NSFC, No.82370639//the National Natural Science Foundation of China/ ; 2023-YBSF-138//Shaanxi Provincial Key R&D Program General Project-Social Development Field/ ; No. 2022JC-11//Science Fund for Distinguished Young Scholars of Shaanxi Province/ ; },
abstract = {BACKGROUND: Nutritional strategies aimed at augmenting growth performance remain a central focus in poultry science. The liver, as a pivotal metabolic organ, exerts profound influence on skeletal muscle development. Nevertheless, the mechanistic interplay between hepatic metabolism and myogenesis has not been fully delineated. Here, by integrating multi-omics analyses with functional validation, we identified xanthosine, a metabolic derivative of hepatic caffeine catabolism, as a previously unrecognized regulator of broiler muscle growth. We further elucidated its mechanistic role in promoting myoblast proliferation.

RESULTS: Comparative phenotypic assessment of high- and low-body-weight broilers revealed substantial differences in breast muscle mass. Metagenomic profiling of cecal microbiota demonstrated only a limited association between microbial composition and body weight. In contrast, untargeted plasma metabolomics uncovered a systemic upregulation of amino acid metabolism in high-body-weight broilers, concomitant with a pronounced activation of caffeine metabolism. Consistently, hepatic transcriptomic profiling revealed marked induction of cytochrome P450 family 1 subfamily A member 2 (CYP1A2), encoding a key enzyme catalyzing caffeine catabolism. Integrated KEGG pathway enrichment across metabolomic and transcriptomic datasets highlighted caffeine metabolism as a significantly perturbed pathway. Among its downstream metabolites, plasma xanthosine was robustly elevated in high-body-weight broilers. Functional validation via in ovo injection demonstrated that xanthosine administration significantly augmented post-hatch growth performance by increasing skeletal muscle mass. Mechanistic investigations further established that xanthosine drives myoblast proliferation through activation of the ERK/GSK3β/β-catenin signaling cascade.

CONCLUSIONS: Together, these findings delineate a liver-muscle metabolic axis in which hepatic CYP1A2-driven caffeine metabolism elevates circulating xanthosine, which in turn acts as a pivotal molecular effector of myogenic growth. This study uncovers a previously unappreciated metabolic mechanism by which hepatic activity orchestrates skeletal muscle development. It also highlights targeted modulation of xanthosine metabolism as a promising strategy to enhance broiler growth performance and production efficiency.},
}

@article {pmid41654729,
year = {2026},
author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J},
title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04500-8},
pmid = {41654729},
issn = {1471-2180},
abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.

METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.

RESULTS: Our study confirmed a statistically significant difference in the β-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.

CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.},
}

@article {pmid41654659,
year = {2026},
author = {Damgaard, F and Jespersen, MG and Møller, JK and Coia, JE and Dessau, RB and Sydenham, TV and Strube, ML and Møller-Jensen, J and Justesen, US},
title = {Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01403-1},
pmid = {41654659},
issn = {2730-664X},
abstract = {BACKGROUND: Colorectal cancer (CRC) patients exhibit distinct gut microbiota disruption, known as dysbiosis, which is believed to play a causative role in CRC. One of the key bacterial species implicated in CRC dysbiosis is Bacteroides fragilis, which presents a paradox as it is also present in most healthy individuals. This discrepancy underscores the need for analysis beyond species-level associations and to investigate intraspecies variation within B. fragilis.

METHODS: From a highly specific collection of B. fragilis isolates from CRC patients and controls, a pangenome-wide association study was conducted, identifying intraspecies genetic variations associated with CRC. The CRC association of these genetic variations were then validated in a metagenome sequencing cohort of faecal samples from 877 individuals, with and without CRC. To test group differences a mixed effects logistic regression with cohort as a random effect was performed for each genetic variation.

RESULTS: Here we show that CRC-associated B. fragilis isolates are infected with specific Caudoviricetes prophages, significantly more often than negative controls. The initial discovery was made in our highly specific isolate collection and then validated in an independent metagenome sequencing cohort, finding that CRC patients were twice as likely to have detectable levels of these phages (OR = 2.05, p = 2.522E-7, SE = 0.139).

CONCLUSIONS: To our knowledge, these findings mark the first link between one of the most implicated driver bacteria and phages in CRC and suggest a more complex role of phages in CRC dysbiosis than current models suggest and highlights the potential of phages as CRC biomarkers.},
}

@article {pmid41654251,
year = {2026},
author = {Sun, L and Wang, Y and Fang, J and Li, Z and Yin, Y and Guo, Y and Wang, Q and Chen, H and Cao, B and Wang, H},
title = {Clinical Experience with Metagenomic Next-Generation Sequencing (mNGS) for the Detection of Tropheryma Whipplei in Respiratory Specimens: A Multicenter Retrospective Observational Study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108457},
doi = {10.1016/j.ijid.2026.108457},
pmid = {41654251},
issn = {1878-3511},
abstract = {BACKGROUND: Tropheryma whipplei (T. whipplei) is the causative bacterium of Whipple's disease (WD), a chronic and systemic infectious condition that predominantly affects the gastrointestinal tract. Sporadic cases of T. whipplei pneumonia have been documented recently.

METHODS: This multicenter retrospective observational study was conducted on patients with T.whipplei positive respiratory specimens admitted to Peking University People's Hospital and China-Japan Friendship Hospital, from Apr 2021 to Jul 2024. Metagenomic next-Generation sequencing (mNGS) was performed using the patient'sbronchoalveolar lavage fluid (BALF), and the quantitative polymerase chain reaction (qPCR) of T. whipplei was also adopted. The clinical data of patients were systematically evaluated.

RESULTS: Among 91 patients (aged 25-82, mean 57; 48% male), common symptoms included cough (60%), expectoration (48%), dyspnea (42%), and fever (30%). Notably, 22% were asymptomatic. Besides,20 patients (22%) had a pre-existing condition of interstitial lung disease. Among all 91 patients, 14 were diagnosed with pneumonia, while the remaining 77had bacterial colonization.Pneumonia cases showed higher T. whipplei mNGS reads than colonization (P=0.0298). Samples testing positive for T. whipplei by qPCR exhibited significantly higher mNGS sequence reads compared to qPCR-negative samples (P<0.0001). All pneumonia patients received antibioticstherapy tailored to their condition. One died from respiratory failure, while the remaining 13 recovered.

CONCLUSION: The application of mNGS on respiratory specimens stands as an exceptional diagnostic modality, proficient in identifying rare microbial infections, exemplified by those induced by T. whipplei. Future research should launch prospective trials to optimize regimens, assess outcomes, and track long - term survival precisely.},
}

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household Environmental Characteristics Influence House Dust Metagenome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5,821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

@article {pmid41653605,
year = {2026},
author = {Cho, DY and Haque, MA and Lee, HY and Jang, MY and Jeong, JB and Lee, GY and Son, KH and Lee, JH and Cho, KM},
title = {Amending metagenomic bacterial community in soybean-cultivated soils to enhance phytoestrogen in soybean roots by communicating with mixture of culturable rhizospheric bacteria.},
journal = {Plant physiology and biochemistry : PPB},
volume = {232},
number = {},
pages = {111093},
doi = {10.1016/j.plaphy.2026.111093},
pmid = {41653605},
issn = {1873-2690},
abstract = {The amendment of metagenomic bacterial community in soybean-cultivated soils to enhance phytoestrogen levels in soybean roots through communicating with mixture of culturable rhizospheric bacteria (RB) were rarely studied. RB from soybean roots and soybean-cultivated soils were isolated and applied to soybean plants. Treated soybean plants were divided into three groups: control (CTL), soybean root RB (SRR), and soybean-cultivated soil RB (SSR). Each group had a distinct influence on the metagenomic bacterial community of the soybean rhizosphere. The α-proteobacteria were the dominant class in all three groups, although SRR was enriched with Actinomycetes, Fimbriimonadia, and γ-proteobacteria, while SSR was enriched with Bacilli, Chitinophagia, and Gemmatimonadia classes. Additionally, at the significantly species level, SRR was enriched with Arthrobacter sp. and Azospirillum lipoferum, while SSR was enriched with Bradyrhizobium sp. and Rhizobium sp. Moreover, the RB treatment significantly affected the root metabolite composition. In the SSR-treated group, phenylalanine (18.80-47.81 mg/100 g) and tyrosine (8.03-21.98 mg/100 g) tended to be significantly enhanced. Additionally, secondary metabolites, such as isoflavones, total phenolics, and total flavonoids, were also significantly affected by the RB treatment; secondary metabolites were the highest in the SSR-treated group. These changes in metabolites also affected radical scavenging activities, with the SSR-treated group displaying significantly increased activities compared to the other groups. As a result, DPPH increased from 32.44 % to 47.21 % and ABTS from 53.41 % to 74.23 %. Therefore, RB treatment can influence the bacteria and root metabolite compositions within the soybean rhizosphere, revealing its potential applications in soybean productivity.},
}

@article {pmid41653157,
year = {2026},
author = {Qian, J and Fang, J},
title = {Letter to the editor regarding: 'Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios - a retrospective study from a single center'.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2624190},
doi = {10.1080/07853890.2026.2624190},
pmid = {41653157},
issn = {1365-2060},
}

@article {pmid41653012,
year = {2026},
author = {Asis, A and Rodríguez, A and Reyes, LF and Díaz, E and Nseir, S and Martín-Loeches, I},
title = {The double threat: bacterial and fungal co-/superinfection in viral pneumonia.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2026.2629003},
pmid = {41653012},
issn = {1747-6356},
abstract = {INTRODUCTION: Respiratory viral pneumonias are a leading cause of severe respiratory failure and intensive care unit (ICU) admission worldwide. Although viral infection itself drives significant morbidity and mortality, secondary bacterial and fungal superinfections represent a critical 'double threat' in critically ill adults, exacerbating lung injury, prolonging organ dysfunction, and complicating antimicrobial management. Experience from the Influenza A (H1N1) pdm09 and SARS-CoV-2 pandemics highlights a persistent mismatch between low documented bacterial co-infection rates and widespread empiric antibiotic exposure, underscoring diagnostic uncertainty and antimicrobial stewardship challenges in the ICU.

AREAS COVERED: This review examines the epidemiology, immunopathogenesis, and diagnostic approaches to bacterial and fungal superinfection in adult ICU patients with severe viral pneumonia. Evidence is synthesized from large ICU cohorts, pandemic data, and established consensus definitions for influenza- and COVID-19-associated pulmonary aspergillosis (IAPA, CAPA). The review discusses advances in molecular diagnostics, lower respiratory tract sampling, bronchoalveolar lavage - based mycology, and biomarker-guided strategies, with a focused literature search of ICU-specific studies.

EXPERT OPINION: Bacterial and fungal superinfections, while infrequent, carry substantial clinical impact in severe viral pneumonia. A multimodal, ICU-adapted diagnostic strategy integrating pathogen detection with host-response assessment is essential to support timely therapy, enable antimicrobial de-escalation, and align superinfection management with stewardship principles.},
}

@article {pmid41652998,
year = {2026},
author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I},
title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {10998004261423546},
doi = {10.1177/10998004261423546},
pmid = {41652998},
issn = {1552-4175},
abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.},
}

@article {pmid41652580,
year = {2026},
author = {He, L and Cheng, Y and Huang, L and Zhang, Z and Zhang, Q and Gong, L and Li, T and Lu, X and Cai, X and Yan, G},
title = {Metagenomic next-generation sequencing to detect Pneumocystis jirovecii pneumonia in critically ill, HIV-negative children: a retrospective multicenter study.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04163-9},
pmid = {41652580},
issn = {1471-2466},
support = {2021YFC2701800//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) plays a critical role in the rapid detection of infectious pathogens. We aimed to analyze the clinical characteristics of Pneumocystis jirovecii infection in children without HIV infection and to evaluate the performance of mNGS in distinguishing P. jirovecii colonization from true infection.

METHODS: A multicenter, retrospective analysis was conducted on critically ill, non-HIV-infected pediatric patients who tested positive for P. jirovecii via mNGS analysis of bronchoalveolar lavage fluid (BALF). Group differences were assessed using Mann-Whitney U-tests (for continuous data) and chi-square tests (for categorical data). Discriminatory performance was evaluated by calculating the area under the receiver operating characteristic curve.

RESULTS: A total of 59 HIV-negative children (age range: 2 months to 14 years) from four children's hospitals were included and classified into two groups based on P. jirovecii status: P. jirovecii pneumonia (PCP; n = 51) and P. jirovecii colonization (PCC; n = 8). Compared with the PCC group, the PCP group had significantly higher serum C-reactive protein levels and median P. jirovecii read counts in mNGS (both P < 0.05). The optimal threshold value for discriminating P. jirovecii infection from colonization appeared to be 556 reads (sensitivity, 77.6%; specificity, 100.0%). Eighteen patients (35.3%) in the PCP group died. Compared with survivors, these patients were significantly younger, had lower T-cell subset counts (CD3[+], CD4[+], and CD8[+]), and a higher prevalence of primary immunodeficiency (all P < 0.05).

CONCLUSIONS: BALF mNGS analysis may have utility for differentiating between colonization and infection by P. jirovecii, warranting further investigation.},
}

@article {pmid41651909,
year = {2026},
author = {Kanyerezi, S and Ayitewala, A and Kabahita, JM and Oundo, HR and Sseruyange, J and Tenywa, W and Tusabe, G and Were, S and Murungi, M and Nabukyu, M and Nakintu, V and Makoha, C and Sserwadda, I and Onywera, H and Tanui, C and Mugerwa, I and Kagirita, A and Lubwama, B and Michael, ER and Kateete, DP and Otita, M and Giduddu, S and Jjingo, D and Nsawotebba, A and Mboowa, G and Ssemaganda, A and Nabadda, S and Tessema, SK and Ssewanyana, I},
title = {Targeted metagenomics reveals hidden chickenpox epidemic amid Mpox surveillance in Uganda.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38778-z},
pmid = {41651909},
issn = {2045-2322},
}

@article {pmid41651883,
year = {2026},
author = {Pantiukh, K and Org, E},
title = {Human gut archaea collection from Estonian population.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06742-1},
pmid = {41651883},
issn = {2052-4463},
support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; },
abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.},
}

@article {pmid41651877,
year = {2026},
author = {Zhang, E and Claesson, MJ and Cotter, PD},
title = {Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00740-8},
pmid = {41651877},
issn = {2396-8370},
support = {23/FFP-A/11857//Research Ireland/ ; 23/FFP-A/11857//Research Ireland/ ; 101060218//European Commission/ ; },
abstract = {The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.},
}

@article {pmid41651389,
year = {2026},
author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M},
title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.},
journal = {Developmental and comparative immunology},
volume = {176},
number = {},
pages = {105565},
doi = {10.1016/j.dci.2026.105565},
pmid = {41651389},
issn = {1879-0089},
abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.},
}

@article {pmid41651377,
year = {2026},
author = {Scholand, KK and Schaefer, L and Shao, J and Yu, Z and Pflugfelder, SC and Britton, RA and de Paiva, CS},
title = {Investigating conjunctival immune pathways in Sjögren and non-Sjögren disease associated dry eye.},
journal = {The ocular surface},
volume = {40},
number = {},
pages = {52-62},
doi = {10.1016/j.jtos.2026.02.001},
pmid = {41651377},
issn = {1937-5913},
abstract = {PURPOSE: Dry eye disease (DED) is classified based on its predominant etiology into aqueous tear-deficient (ATD), evaporative, or mixed. Sjӧgren disease keratoconjunctivitis sicca (SjD-KCS) is a very severe autoimmune form of ATD DED. The purpose of this work was to compare transcriptomic changes in the conjunctiva sampled from patients with ATD, SjD-KCS, and healthy controls (HC) to evaluate distinctions in the immune response on the ocular surface based on diagnosis.

METHODS: Impression cytology of the temporal bulbar conjunctiva was collected using the EyePrim device. RNA was extracted and submitted with the Nanostring nCounter Human Immunology V2 panel for gene expression analysis. Results were uploaded to ROSALIND and Metascape to identify DEGs by comparison (all DED vs HC; SjD vs HC; ATD vs HC) and associated predicted pathways. A subset of samples (n = 4 per group) were used for immunofluorescent staining of LAMP3 and HLA-DR.

RESULTS: 49 patients were enrolled in the study (25 HC; 12 SjD; 12 ATD). 100 DEGs were found in the comparison of all DED vs HC. 69 DEGs were found in the SjD vs HC. 11 DEGs were found in the ATD vs HC. There were no DEGs identified in the SjD vs ATD comparison. DEGs were involved in immune pathways related to viral response, adaptive immunity, and cell to cell communication. DED conjunctiva had increased expression of LAMP3 and HLA-DR compared to HC.

CONCLUSIONS: Our findings demonstrate that DED, regardless of the diagnosis, have similar immune-related DEGs and associated pathways on the ocular surface.},
}

@article {pmid41651145,
year = {2026},
author = {Wang, Y and Sun, T and Li, L and Wang, M and Hu, B and Chen, Z and Hu, S},
title = {Synergistic effects of carbon dots and arbuscular mycorrhizal fungi on mitigating PFAS stress and reinforcing the purification performance of constructed wetlands.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123952},
doi = {10.1016/j.envres.2026.123952},
pmid = {41651145},
issn = {1096-0953},
abstract = {Per- and polyfluoroalkyl substances (PFASs) are highly persistent pollutants that disrupt plant-microbe interactions and compromise the performance of constructed wetlands (CWs). Here, we demonstrate a synergistic strategy combining carbon dots (CDs) and arbuscular mycorrhizal fungi (AMF) to alleviate PFAS-induced stress and enhance CW remediation efficiency. CD amendment markedly improved plant physiological performance under PFAS exposure, increasing photosynthetic efficiency and antioxidant enzyme activities, while simultaneously facilitating AMF colonization. Under high PFAS concentrations, the AMF-CDs treatment increased AMF colonization density by 33.3-100% relative to AMF alone, indicating substantial protection of symbiotic functionality. Metagenomic and community analyses revealed that the AMF- CDs combination reshaped the rhizosphere microbiome, enriching taxa such as Chloroflexi, Planctomycetes, and Campylobacterota that are functionally linked to nitrogen cycling, PFAS transformation, and metabolic resilience. These microbial shifts enhanced nutrient turnover and strengthened redox coupling processes critical for pollutant degradation. Consequently, the AMF-CDs system achieved pronounced improvements in water quality, with total phosphorus (TP), chemical oxygen demand (COD), total nitrogen (TN), and NH4[+]-N removal efficiencies elevated by 34.3-158.3% compared with untreated controls. This study provides the first evidence that CDs function as nano-bridging agents that stabilize the root-microbe interface, reinforce AMF-plant symbiosis, and drive microbial community specialization toward pollutant degradation. The AMF-CDs synergistic mechanism offers a sustainable and scalable nano-bio strategy for restoring PFAS-contaminated ecosystems and advancing next generation constructed wetland technologies.},
}

@article {pmid41651131,
year = {2026},
author = {Hantsoo, L and Ford, E and Friedman, ES and Hao, F and Patterson, AD and Bittinger, K and Wu, GD and Zemel, BS and Tanes, C},
title = {The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression.},
journal = {Brain, behavior, and immunity},
volume = {134},
number = {},
pages = {106479},
doi = {10.1016/j.bbi.2026.106479},
pmid = {41651131},
issn = {1090-2139},
abstract = {BACKGROUND: Adverse childhood experiences (ACEs) are associated with poor health outcomes in adulthood including obesity, psychiatric symptoms, and elevated levels of inflammatory markers. Our previous work found ACEs are associated with altered gut microbiota composition. In the present work, we examined ACE associations with gut microbiota and peripheral measures of inflammation in pregnant women with or without obesity, and explored potential modifying factors including diet and depressive symptoms.

METHODS: Female participants were recruited in the third trimester of pregnancy as part of a larger growth study of African-American infants. Participants were categorized as healthy weight (BMI < 25) or obese (BMI ≥ 30) based on their early pregnancy BMI. They completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and Center for Epidemiologic Studies Depression Scale (CES-D). Stool samples, blood, and dietary data were collected in the third trimester. Shotgun metagenomic sequencing was performed on DNA isolated from stool. Statistical models assessed relationships between gut microbiota and ACE. A false discovery rate (fdr) adjusted p-value q < 0.1 was considered statistically significant.

RESULTS: 107 women completed questionnaires and provided stool in the third trimester. ACEs were positively associated with BMI and depressive symptom severity but not with gut microbiota composition. Depressive symptoms were significantly negatively associated with abundance of gut Bifidobacterium longum (q = 0.02) and positively associated with Bacteroides thetaiotaomicron (q = 0.02). Path analysis revealed that ACEs predicted pre-pregnancy BMI which predicted elevated inflammatory markers. ACEs also predicted more severe depressive symptoms in pregnancy, which was associated with gut microbiome composition. Finally, ACEs interacted with dietary intake of sugar and whole grains to impact markers of inflammation, the gut microbiome, and enzymes produced by gut microbiota.

DISCUSSION: ACEs led to two risk pathways in pregnancy: one in which high pre-pregnancy BMI was linked with high levels of serum inflammatory markers during pregnancy, and the other in which greater depressive symptom severity was associated with alterations to the gut microbiome. Further, data suggested ACEs may influence the metabolic potential of the gut microbiome.},
}

@article {pmid41651079,
year = {2026},
author = {Xin, Y and Ma, H and Li, X and Sun, R and Fang, L and Pan, L},
title = {Multi-omics reveal the key role of gut microbiota metabolism in adenine-induced chronic kidney disease.},
journal = {Toxicology and applied pharmacology},
volume = {509},
number = {},
pages = {117754},
doi = {10.1016/j.taap.2026.117754},
pmid = {41651079},
issn = {1096-0333},
abstract = {The gut microbiota plays a crucial role in the progression of chronic kidney disease (CKD). The adenine-induced CKD mouse model is widely employed in preclinical research, yet the effects of adenine on the composition and metabolic function of the gut microbiota remain to be elucidated. This study aimed to test the hypothesis that adenine-induced alterations in the structure and function of the gut microbiota are significantly associated with the onset and progression of CKD. To this end, a mouse CKD model was established by alternating feeding with 0.15% and 0.20% adenine for 7 weeks. Multi-omics analysis (untargeted metabolomics, metagenomics, and spatial metabolomics) was performed to compare the adenine-induced CKD group with a standard diet-fed normal control group. Integrated analysis of plasma metabolomics and intestinal content metabolomics identified 94 differentially co-regulated metabolites: among these, indolelactic acid was significantly upregulated, while indole-3-propionic acid was significantly downregulated. The bile acid metabolic pathway also underwent marked perturbations: taurochenodeoxycholic acid and tauro-β-muricholic acid (two taurine-conjugated bile acids) were significantly elevated, whereas nordeoxycholic acid and norcholic acid were notably reduced. Integrated metabolomics-metagenomics analysis further demonstrated that Lactobacillus exhibited a significant positive correlation with a subset of upregulated metabolites (including indolelactic acid), while Taurinivorans muris showed a strong negative correlation with the taurine-conjugated bile acids. Additionally, renal spatial metabolomics revealed that phospholipid metabolic disorders in the adenine-induced CKD group directly contributed to the aggravation of renal inflammatory responses. Collectively, these findings reveal a gut microbiota-metabolite-kidney axis perturbed by adenine, providing novel insights into the pathogenesis of CKD and potential targets for metabolic intervention.},
}

@article {pmid41650863,
year = {2026},
author = {Wang, X and Zhao, HP and Lai, CY},
title = {Anaerobic biodegradation of ceftriaxone: Transformation pathways, toxicity assessment, and microbial mechanisms.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128859},
doi = {10.1016/j.jenvman.2026.128859},
pmid = {41650863},
issn = {1095-8630},
abstract = {The overuse of ceftriaxone has resulted in its widespread occurrence in aquatic environments, posing ecological and health risks. An anaerobic membrane bioreactor (AnMBR) was operated for 128 days to systematically investigate the anaerobic microbial transformation of CTX. The AnMBR exhibited stable and efficient performance, maintaining chemical oxygen demand removal above 90% and achieving an average CTX removal efficiency of 65.0 ± 15.2%. Several potential degradation pathways are proposed, involving β-lactam ring hydrolysis, C-S bond cleavage, and decarboxylation reactions. Toxicity assessments using ADMETlab 3.0 platform reveal that although most TPs showed reduced ecotoxicity and dermal toxicity compared to the parent compound, several intermediates exhibited elevated risks of nephrotoxicity and genotoxicity. Metagenomic analysis indicates that long-term CTX exposure reshaped the microbial community, enriching methanogens such as Methanothrix soehngenii and Methanosarcina mazei, though these taxa might not directly participate in CTX degradation. Several archaeal and bacterial MAGs carrying functional genes, including lactam hydrolase, thioesterase, and decarboxylase, were identified, suggesting a collaborative and functionally diverse microbial network involved in CTX transformation. This study offers mechanistic insights and technical foundations for advancing anaerobic biotechnologies in the treatment of antibiotic-contaminated wastewater, while highlighting the need for ongoing monitoring of potential long-term risks associated with TPs.},
}

@article {pmid41650859,
year = {2026},
author = {Wei, W and Zhang, Z and Li, J and Du, H and Wu, Q and Cui, R and Wang, X and Ren, L and Zhang, M and Wang, Y},
title = {Effects of microbial inoculation on mitigating odor release, curtailing nitrogen and sulfur losses, and accelerating the maturation during food-waste composting.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128800},
doi = {10.1016/j.jenvman.2026.128800},
pmid = {41650859},
issn = {1095-8630},
abstract = {A thermotolerant, odor-suppressing microbial agent was inoculated into food-waste (FW) composting to systematically evaluate its influence on odorants, volatile organic compounds (VOCs), microbial community structure, extracellular enzyme activities, and the transcriptional profile of nitrogen- and sulfur-cycle genes. Compared with the uninoculated control, cumulative emissions of NH3, H2S, ethanol, and acetaldehyde declined by 73.45%, 65.30%, 40.22%, and 37.20%, respectively, in the bio-augmented reactor. NH3 High-throughput 16S rRNA sequencing revealed that the inoculation enhanced the microbial richness and diversity, while increasing the abundance of thermophilic strains that promote compost maturation and reduce nitrogen loss. Concomitantly, the relative abundances of acid-producing and skatole-generating populations were suppressed. Quantitative PCR showed that the expression of narG, norB, nif, nrfA, nirB, aprA, and sat genes was down-regulated. This consequently reduced the production of NH4[+]-N and inhibited the sulfate reduction process, thereby coordinating nitrogen and sulfur metabolic transformations and significantly lowering NH3 and H2S emissions. Overall, this study demonstrates the feasibility of microbial inoculation for mitigating odor emissions, retaining nutrients, and accelerating compost maturation, while providing mechanistic insights into how microbial formulations regulate enzyme activities and the expression of functional genes during composting.},
}

@article {pmid41650846,
year = {2026},
author = {Hosen, ME and Dunsdon, S and Sarker, S},
title = {Mosquito-borne viruses in Australia: An emerging trend of increasing prevalence in Northern Queensland.},
journal = {Virology},
volume = {617},
number = {},
pages = {110825},
doi = {10.1016/j.virol.2026.110825},
pmid = {41650846},
issn = {1096-0341},
abstract = {Mosquito-borne viruses (MBVs) remain a significant public health concern in Northern Queensland, Australia, with dengue virus (DENV), Ross River virus (RRV), and Barmah Forest virus (BFV) representing the most common pathogens. Wolbachia-based biological control programs have made notable contributions to reducing dengue transmission by suppressing Aedes aegypti vector competence. Recent surveillance data indicates increased MBV activity, with national case numbers nearly doubling between 2023 and 2024 and early 2025 data suggesting sustained transmission during seasonal peak. Traditional surveillance approaches, while highly valuable for disease monitoring, have limitations in detecting novel or divergent viral strains in real time. Over the past decades, more than 919 unclassified flaviviruses have been reported nationwide, including 117 in Queensland. The advent of metagenomic and metatranscriptomic approaches now enable enhanced, field-based detection of both known and emerging arboviruses. Strengthening mosquito control programs through continued Wolbachia releases, alongside integrated genomic surveillance, predictive modelling, and community engagement will enhance early detection, guide targeted interventions, and reduce the MBV burden in Northern Queensland. This integrated framework provides a strategic pathway to sustains and expand vector control effectiveness while safeguarding public health in high-risk regions.},
}

@article {pmid41650276,
year = {2026},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb6265},
pmid = {41650276},
issn = {2375-2548},
mesh = {*Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology ; Animals ; Humans ; Metagenome ; Phylogeny ; Genome, Viral ; Bacteroides/virology ; },
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

*Gastrointestinal Microbiome
*Bacteriophages/genetics/physiology
Animals
Humans
Metagenome
Phylogeny
Genome, Viral
Bacteroides/virology

@article {pmid41650192,
year = {2026},
author = {Wang, H and Shan, X and Xing, D and Wang, Y and Jin, C and Zhao, Y and Guo, L},
title = {Rhamnolipid Modulates Microbial Interspecies Electron Transfer for Synchronous Sulfidogenesis and Acidogenesis from Mariculture Solid Wastes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16493},
pmid = {41650192},
issn = {1520-5851},
abstract = {Synchronous sulfidogenesis and acidogenesis (SSA) are critical for pollutant removal and resource recovery. However, inefficient electron transfer and metabolic imbalance between acidogenic bacteria and sulfidogens limit SSA performance, especially from mariculture solid wastes (MSW) containing high-strength sulfate. This work unveiled the neglected role and mechanism of rhamnolipid (RL) in modulating microbial interspecies electron transfer for SSA during MSW anaerobic fermentation. RL, at environmentally relevant levels of 20-200 mg/g suspended solids, simultaneously improved sulfide (40.1-87.9%) and short-chain fatty acids (8.0-19.3-fold) yield. Extracellular polymeric substances (EPSs) exhibited higher capacitance and electroactivity to store or transfer electrons in the presence of RL. Proper RL facilitated pili-like filament formation and redox mediator secretion. The flavins and cytochrome c combination was promoted by RL to mediate one-electron transfer with a higher transfer rate via the flavin semiquinone intermediate. RL increased the dipole moment of the α-helix peptide and spontaneously interacted with the C═O of amide groups, enabling efficient electron hopping in EPSs. RL also activated key components in the intracellular electron transfer system, delivering more electron flow to sulfate reductase. Metagenomic and metatranscriptomic analyses verified the differential enrichment of microorganisms and key gene upregulation related to SSA, EPS secretion, quorum sensing, ATP, type IV pili, and electron shuttle synthesis. These findings provide new insight into the roles and interactive mechanisms of biosurfactants in modulating microbial electron transfer.},
}

@article {pmid41649661,
year = {2025},
author = {Romão, IR and do Carmo Gomes, J and Silva, D and Vilchez, JI},
title = {The seed microbiota from an application perspective: an underexplored frontier in plant-microbe interactions.},
journal = {Crop health},
volume = {3},
number = {1},
pages = {12},
pmid = {41649661},
issn = {2948-1945},
support = {UIDB/04551/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04551/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0087/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Seed-associated microbiota represent a critical yet underexplored frontier in plant-microbe interactions, offering unique insights into plant health, resilience, and development. Unlike the soil or rhizosphere microbiome, the seed microbiota is closely tied to plant reproduction, facilitating both vertical and horizontal transmission of microbes. These microbial communities influence key plant processes, including germination, stress tolerance, nutrient acquisition, and pathogen resistance, providing plants with a pre-assembled microbial consortium tailored to their needs. Despite recent advances, significant gaps remain in understanding how seed-associated microbes are acquired, their ecological dynamics, and their functional roles. High-throughput sequencing, metagenomics, and spatial imaging techniques have revealed the diversity and complexity of the seed microbiota, emphasizing their potential for agricultural innovation. This research highlights the importance of these communities in shaping plant resilience and productivity, yet questions about their ecological and evolutionary significance persist. The present review synthesizes current knowledge on the composition, inheritance mechanisms, and functional roles of the seed microbiota. It also explores strategies to harness these microbes for sustainable agriculture, including microbiome engineering and breeding for microbial compatibility. By addressing these gaps, seed microbiota research could revolutionize sustainable agriculture, enhancing crop resilience and reducing reliance on chemical inputs.},
}

@article {pmid41649278,
year = {2026},
author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA},
title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117325},
doi = {10.1128/msystems.01173-25},
pmid = {41649278},
issn = {2379-5077},
abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.

IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.},
}

@article {pmid41649276,
year = {2026},
author = {Castillo-Ramírez, S and López-Sánchez, R and Peralta, H},
title = {Acinetobacter-the bad, the ugly, but also the good!.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0001026},
doi = {10.1128/msphere.00010-26},
pmid = {41649276},
issn = {2379-5042},
abstract = {The genus Acinetobacter is vast and diverse regarding its hosts. However, it is best known as an opportunistic pathogen that causes hard-to-treat nosocomial infections. Yet, some species of the genus can be beneficial for some hosts. Such is the case of Acinetobacter calcoaceticus, which can have a significant impact on tomato plants, as was recently shown in a paper by Robertson et al. (S. Robertson, A. Mosca, S. Ashraf, A. Corral, et al., mSphere 11:e00842-25, 2026, https://doi.org/10.1128/msphere.00842-25). Importantly, that study also exemplifies how metagenomics in general, but metagenome-assembled genomes in particular, can be employed to understand the functional specialization and identity of the bacterial species dwelling in particular environments.},
}

@article {pmid41648756,
year = {2025},
author = {Grønbæk, IMB and Halkjær, SI and Hansen, EH and Mollerup, S and Paulsen, SJ and Konrad, CV and Engel, S and Bulinska-Balas, M and Wellejus, A and Haaber, AB and Christensen, AH and Engsbro, AL and Petersen, AM},
title = {Eight weeks of treatment with probiotic Bifidobacterium breve, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome: results from a randomised, clinical trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1701341},
pmid = {41648756},
issn = {2296-861X},
abstract = {UNLABELLED: Patients with irritable bowel syndrome experience abdominal pain and stool habit disturbances, and often also extraintestinal symptoms, such as fatigue. The disorder is linked to gut dysbiosis, and manipulation of the microbiota is considered a possible treatment strategy. This randomised, double-blinded, placebo-controlled study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (DSM 33360) (Bif195), on symptoms and gut microbiome composition in patients with diarrhoea-predominant irritable bowel syndrome. Sixty-one patients with moderate-severe disease activity were allocated to 8 weeks of treatment with either Bif195 or placebo (1:1), followed by 8 weeks of follow-up. The primary outcome was a change in symptom scores measured by the validated questionnaire, IBS-symptom severity scale. Secondary and explorative outcomes were the effects of Bif195 on intestinal symptoms, quality of life, fatigue, and the gut microbiota. Modulation of the transepithelial electrical resistance (TEER) of Caco-2 cells by Bif195 was investigated in vitro as a model of barrier integrity. The results showed no effect of Bif195 on primary or secondary outcomes; however, Bif195 lowered fatigue scores compared to placebo. Significantly increased TEER readings in vitro indicated enhanced barrier integrity, suggesting GI permeability as a mechanism for further clinical exploration.

CLINICAL TRIAL REGISTRATION: clinicaltrials.gov, identifier NCT04808271.},
}

@article {pmid41648417,
year = {2026},
author = {Arasti, S and Şapcı, AOB and Rachtman, E and El-Kebir, M and Mirarab, S},
title = {Deconvolving Phylogenetic Distance Mixtures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.18.700179},
pmid = {41648417},
issn = {2692-8205},
abstract = {Mixtures of multiple constituent organisms are sequenced in several widely used applications, including metagenomics and metabarcoding. Characterizing the elements of the sequence mixture and their abundance with respect to a reference set of known organisms has been the subject of intense research across several domains, including microbiome analyses, and methods must overcome two key challenges. First, the mixture constituents are related to each other through an evolutionary history, and hence, should not be considered independent entities. Second, sequence data is noisy, with each short read providing a limited signal. While existing approaches attempt to address these challenges, addressing both challenges simultaneously has proved challenging. For evolutionary dependencies, methods either define hierarchical clusters (e.g., taxonomies or operational taxonomic/genomic units) or use phylogenetic trees. For the second challenge, they either assemble reads into contigs, use statistical priors to summarize read placements, or attempt to analyze all reads jointly using k-mers. Despite this rich literature, a natural approach to simultaneously address both challenges has been underexplored: compute a distance from the mixture to all references, deconvolve those distances, and place the sample on multiple branches of a reference phylogeny with associated abundances. This multi-placement approach is a natural extension of the single-read phylogenetic placement used in practice. We argue that by placing the entire sample on multiple branches instead of placing reads individually, we can obtain a less noisy profile of the mixture. We formalize this approach as the phylogenetic distance deconvolution (PDD) problem, show some limits on the identifiability of PDDs, propose a slow exact algorithm, and an efficient heuristic greedy algorithm with local refinements. Benchmarking shows that these heuristics are effective and that our implementation of the PDD approach (called DecoDiPhy) can accurately deconvolve phylogenetic mixture distances while scaling quadratically. Applied to metagenomics, DecoDiPhy consolidates reads mapped to a large number of branches on a reference tree to a much smaller number of placements. The consolidated placements improve the accuracy of downstream tasks, such as sample differentiation and detection of differentially abundant taxa.},
}

@article {pmid41648334,
year = {2026},
author = {Romo Bechara, N and Bardeskar, N and Hopkins, HA and Raymann, K},
title = {Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.13.699197},
pmid = {41648334},
issn = {2692-8205},
abstract = {UNLABELLED: Opportunistic bacterial pathogens often encounter strong selective pressures outside their hosts, yet the evolutionary consequences of long-term predator exposure remain poorly understood. Here, we used experimental evolution to examine how sustained interaction with a eukaryotic predator shapes genomic adaptation, phenotypic diversification, and virulence-associated traits in Pseudomonas aeruginosa . Replicate populations of P. aeruginosa were evolved for 60 days in the presence or absence of the ciliate predator Tetrahymena thermophila , followed by whole-population metagenomic sequencing, isolate-level genome sequencing, and quantitative phenotypic assays. We observed extensive genetic diversification across all populations, with strong signatures of both positive and purifying selection and pervasive parallel evolution at gene and nucleotide levels. Predator-exposed populations accumulated mutations enriched in regulatory, metabolic, and virulence-associated pathways, revealing predictable genomic targets of selection. However, many parallel mutations were shared between predator-exposed and predator-free populations, indicating that adaptation to the abiotic environment represented a dominant selective force. Genotype-phenotype analyses revealed pleiotropic effects and trade-offs linking motility, growth, and virulence-associated traits. Despite pronounced genomic adaptation and coordinated phenotypic shifts, changes in virulence in an in vivo host model were modest and context dependent. Taken together, our results indicate that predator exposure can influence evolutionary trajectories in P. aeruginosa and highlight the value of extending such approaches across multiple ecological and host contexts.

SIGNIFICANCE: Many bacterial pathogens spend much of their evolutionary history outside hosts, where they face intense ecological pressures such as predation. How these pressures shape pathogen evolution and disease potential remains unclear. Using experimental evolution, genomics, and phenotypic analyses, we show that prolonged exposure to a eukaryotic predator drives predictable genetic and phenotypic changes in the opportunistic pathogen Pseudomonas aeruginosa . Predator exposure altered regulatory, metabolic, and virulence-associated pathways, yet much adaptation was shared with predator-free populations, highlighting the dominant role of abiotic environments. Although predator-driven evolution reshaped traits linked to motility and growth, its effects on virulence were modest and context dependent. These findings clarify how environmental interactions influence pathogen evolution and underscore the importance of studying pathogens across diverse ecological settings.},
}

@article {pmid41648310,
year = {2026},
author = {Szenei, J and Burke, A and Liong, A and Korenskaia, A and Lukowski, AL and Ziemert, N and Nikel, PI and Leão, PN and Moore, BS and Weber, T and Blin, K},
title = {Computational pipeline reveals nature's untapped reservoir of halogenating enzymes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.20.700248},
pmid = {41648310},
issn = {2692-8205},
abstract = {Microbial halogenated natural products (hNPs) hold ecological, agricultural, and biomedical relevance. The hNP-producing potential of the organism can be assessed by the precise prediction of biosynthetic enzymes, yet the detailed annotations of halogenases are often missing from genomic and metagenomic data. We created a manually curated database (https://halogenases.secondarymetabolites.org/) containing information on the halide-specificity, role, and position of verified catalytic residues and results of the mutagenesis studies of more than 120 experimentally validated or in silico inferred halogenases. The collection of experimental data supports a computational pipeline that allows the family-, substrate-, and halide-scope-level annotation of halogenating enzymes by relying on catalytic residues, conserved motifs, and profile Hidden Markov Models (pHMMs). Our analysis with sequence similarity networks (SSNs) highlighted several underexplored clusters in the UniRef50 database. Such finding was a halogenase from Rhodopirellula baltica (Rhoba VHPO) previously labelled as a hypothetical chloroperoxidase, which clustered apart from the known chloroperoxidases and bromoperoxidases, but accepted chloride and preferred bromide. Our database and workflow provide extensive and scalable solutions for the systematic and precise annotation of halogenating enzymes in genomic and metagenomic data. The in-depth categorization of halogenases will improve the chemical structure prediction of microbial hNPs, supporting ecological assessments and natural product discovery.},
}

@article {pmid41648142,
year = {2026},
author = {Mastrorilli, E and Herd, P and Rey, FE and Goodman, AL and Zimmermann, M},
title = {Linking interpersonal differences in gut microbiota composition and drug biotransformation activity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.21.700809},
pmid = {41648142},
issn = {2692-8205},
abstract = {Individuals vary widely in their responses to drugs, and growing evidence implicates the gut microbiome as a contributor to this variability. While prior studies show that gut bacteria can metabolize drugs, how differences in microbial community composition influence drug metabolism remains poorly understood. Here, we characterize the biotransformation of 271 drugs by 89 gut microbial communities derived from human donors and preclinical animal models. Over 90% of tested drugs were metabolized by at least one microbiome. We identified 66 drugs exhibiting highly variable metabolism across human-derived microbiomes and several drugs whose biotransformation differed markedly between human and animal microbiomes. To enable prediction of microbiota-mediated drug metabolism, we developed and compared multiple modeling approaches based on metagenomic data. These results, together with the provided data and analytical resources contribute to a better understanding of microbiome-drug interactions and support their future integration into drug discovery, personalized prescription, and therapeutic drug monitoring.},
}

@article {pmid41648008,
year = {2025},
author = {Pasquali, F and Crippa, C and Lucchi, A and Manfreda, G},
title = {Artisanal food of animal origin as reservoir of putative pathogenic Escherichia coli: a combined genomic and in vivo approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718380},
pmid = {41648008},
issn = {1664-302X},
abstract = {The lack of a full automation and control of environmental parameters might result in potential risk of microbial contamination in small-scale production plants such as artisanal cheese and salami Italian productions. In a previous study, genomes of 33 E. coli isolates were sequenced. In the present study, the pathogenicity potential of E. coli strains was investigated by: (1) phylogenomic comparison with 202 public genomes of human, animal and environmental Italian origin; (2) pathogenicity assessment of strains with virulence patterns predicting specific E. coli pathotypes by using larvae of Galleria mellonella as in vivo infection model. Phylogenetic reconstruction revealed raw material and not the processing environment as source of salami contamination. Moreover, close proximity of some strains isolated from salami production with wild boar and extraintestinal human public strains was observed suggesting pigs and wild boar as potential reservoirs of pathogenic E. coli. The virulome of salami strains revealed the presence of genes already described as gene markers of atypical enteropathogenic E. coli (aEPEC; bfp-, eae+). Interestingly the analysis of virulence genes pointed toward additional genomes which showed genetic markers previously described as strongly associated to and/or extraintestinal pathogenic E. coli (ExPEC). In vivo experiments, confirmed the higher pathogenicity of strain 5STM5 with genetic pattern corresponding to hybrid aEPEC/ExPEC and two strains 3CP1522 and 6MB5 of cheese and salami production, respectively, with virulence genes previously associated to ExPEC pathotype. The combined approach pointed toward two genes espC for aEPEC, as well as malX for ExPEC which were significantly enriched in clinical genomes in comparison to genomes of other origins. These genes are worth of future investigations which could help to assess the risk for consumers after the consumption of contaminated artisanal food.},
}

@article {pmid41648007,
year = {2025},
author = {Schnabel, E and Vuillemin, A and Esser, S and Griesdorn, L and Soares, AR and Mørkved, PT and Jørgensen, SL and Probst, AJ and Kallmeyer, J and , },
title = {Geochemical variability and microbial metabolic functions in oligotrophic sediments exposed to minor seepage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720187},
pmid = {41648007},
issn = {1664-302X},
abstract = {Low primary productivity in Barents Sea surface waters and limited nutrient flux to the seafloor favor nitrification and nitrogen fixation in deep waters, resulting in a dearth of organic substrates in local sediments. The addition of labile hydrocarbons naturally occurring through seepage from subsurface reservoirs could promote microbial activity in organic-lean sediments, notably by denitrifying and sulfate-reducing microbes. Using gravity cores from an area with numerous hydrocarbon reservoirs, we document pore water geochemistry, dissolved gas concentrations, and total cell counts supplemented with taxonomic and functional marker gene analyses from metagenomes and metagenome-assembled genomes. We assess the contribution of the subsurface biosphere in producing geochemical gradients in oligotrophic sediments facing different exposure to minor seepage. In pristine seabed, i.e., not affected by hydrocarbon seepage, nitrate and ammonium profiles were consistent with denitrification down to 1 m below seafloor. By contrast, minor hydrocarbon seepage caused very different pore water profiles, which were indicative of more reducing geochemical conditions in the sediment and more advanced consumption of electron acceptors in pore water. Delivery of favorable organic substrates to anaerobic microbes through seepage was reflected in slightly higher cell densities, CH4 and CO2 concentrations, but appeared to have little impact on community diversity. This could be explained by metabolic versatility across functional guilds, with limited differentiation of sedimentary niches, favoring polyvalent fermenters at the expense of canonical denitrifiers and sulfate reducers. These versatile fermenters exhibited diverse predicted capabilities for nitrate and sulfate reduction combined with hydrocarbon degradation, (homo)acetogenesis, and nitrogen fixation. Our results further indicate that specific clades of homoacetogens (Lokiarchaeia, Bathyarchaeia, and Dehalococcoidia) could support cross-feeding interactions when fueled by simple hydrocarbons through seepage, particularly those associated with dissimilatory sulfur metabolism and fermentation of intermediate metabolites. In the absence of hydrocarbon-derived electron donors, the same clades appear capable of energy-conserving (homo)acetogenic fermentation on organic residues. Thus, we conclude that slow-growing (homo)acetogens that are ubiquitous in the marine subseafloor actively contribute to balancing biogeochemical cycles in oligotrophic sediments impacted by minor hydrocarbon seepage.},
}

@article {pmid41648005,
year = {2025},
author = {Liu, JJ and Yang, H and Xiao, ZY and Xie, JH and Su, L and Li, YT and Zheng, XY and Hu, WH and Fu, SJ and Li, CL and Huang, L and Yu, SY and Yu, Z and Yang, S and Yang, J},
title = {Gut microbiota and metabolic dysregulation in polycystic ovary syndrome: effects of acupuncture as an adjunct to in vitro fertilization on gut dysbiosis, metabolism, and oocyte quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1730714},
pmid = {41648005},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is marked by disruptions in metabolic and reproductive endocrine functions. This study synthesizes systemic metabolic profiles, alterations in gut microbiota, and follicular fluid metabolism to elucidate the reproductive and endocrine metabolic changes associated with PCOS. Furthermore, it aims to elucidate the potential mechanisms through which acupuncture may exert therapeutic effects.

METHODS: In this open-label randomized controlled trial conducted in China (November 2021-January 2023), 60 women with PCOS scheduled for In Vitro Fertilization (IVF) were randomized to receive acupuncture combined with IVF treatment or IVF treatment alone, with 30 healthy women serving as controls. Gut microbiota was sequenced and analyzed by 16S rRNA and metagenomics; follicular fluid metabolites were determined by untargeted metabolomics.

RESULTS: Compared with healthy controls, PCOS exhibited gut microbiota dysbiosis and metabolic disorders. The specific gut microbiota in PCOS dominated by s_Lachnospiraceae, s_Blautia_sp. and g_Escherichia-Shigella, which correlated with body mass index (BMI), waist circumference, waist-to-hip ratio, and hormone levels. Acupuncture combined with IVF significantly regulated glucose and lipid metabolism, reduced g_Escherichia-Shigell abundance, and showed potential advantages in enhancing oocyte quality and embryonic developmental potential (p = 0.011). Analysis of the correlation between differential metabolites and oocyte and embryo quality demonstrated that methionine sulfoxide and boldione may be key metabolites to affect follicle quality.

CONCLUSION: PCOS is associated with systemic multi-pathway metabolic dysregulation and gut microbiota dysbiosis. It described the potential therapeutic benefits of acupuncture combined with IVF for PCOS, laying a foundation for further understanding the disease and the mechanisms of acupuncture for PCOS metabolic disorders, and providing directions for future research.},
}

@article {pmid41648004,
year = {2025},
author = {Goncalves, AR and Ranganathan, H and Valdes, C and Zhu, H and Zhang, B and Kok, CR and Martí, JM and Mulakken, NJ and Thissen, JB and Jaing, C and Be, NA},
title = {Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1695501},
pmid = {41648004},
issn = {1664-302X},
abstract = {Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.},
}

@article {pmid41648002,
year = {2025},
author = {Zhang, H and Chen, K and Chen, R and Jia, E},
title = {Feeding patterns reprogram a gut microbial virulence-iron-quorum sensing functional axis linked to atherosclerotic risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1751844},
pmid = {41648002},
issn = {1664-302X},
abstract = {The feeding rhythm is a major temporal regulator of metabolic physiology, yet its impact on microbiome-derived functional traits relevant to cardiometabolic disease remains insufficiently understood. Our previous work demonstrated that ad libitum, daytime-restricted, and nighttime-restricted feeding produce markedly different atherosclerotic outcomes in Apoe[-]/[-] mice, indicating that the feeding rhythm acts as a modifiable determinant of atherogenic susceptibility. Here, we used shotgun metagenomics to profile risk-associated microbial functional modules-including Type III and Type VI secretion systems (T3SS/T6SS), siderophore-based iron acquisition pathways, quorum-sensing (QS) regulators, and antimicrobial resistance determinants-across feeding regimens. The feeding rhythm induced pronounced functional segregation independent of α-diversity, which was consistent with selective functional reprogramming rather than taxonomic restructuring. Daytime feeding, which is misaligned with the murine active phase, is associated with coordinated enrichment of the T3SS/T6SS, iron uptake, and QS pathways, forming a tightly interconnected "virulence-iron-QS-ARG" functional consortium. In contrast, circadian-aligned nighttime feeding resulted in attenuated virulence orientation and enhanced metabolic-cooperative signatures. Network inference further revealed strong coactivation of virulence secretion, iron mobilization, and QS modules under circadian misalignment. These findings show that the feeding rhythm modulates atherogenic susceptibility not only through host metabolism but also by remodeling gut microbial functional capacities, highlighting microbial functional ecology as an integral component of diet-host interactions.},
}

@article {pmid41647993,
year = {2025},
author = {Jayakrishnan, T and Sangwan, N and Nair, KG and Kamath, SD and Patel, MH and Joyce, D and Walsh, M and Simon, R and Vadehra, D and Iyer, RV and Fountzilas, C and Khorana, AA},
title = {Tumor microbiome differences in early-onset versus average-onset pancreatic adenocarcinoma.},
journal = {ESMO gastrointestinal oncology},
volume = {9},
number = {},
pages = {100194},
pmid = {41647993},
issn = {2949-8198},
abstract = {BACKGROUND: Compelling evidence supports the biomarker potential of microbiome in pancreatic adenocarcinoma. Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age <50 years), we aimed to evaluate microbiome profiles in resected specimens from individuals with eoPDAC and average-onset PDAC (aoPDAC, age >50 years).

MATERIALS AND METHODS: We carried out shotgun metagenomic sequencing in resected specimens from individuals with eoPDAC (n = 24) and aoPDAC (n = 20). Statistical tests included Wilcoxon test, permutational analysis of variance, multiomic classifier modeling, differential abundance analysis, and linear regression. All P values were adjusted for multiple testing and P < 0.05 was considered statistically significant.

RESULTS: We successfully sequenced several bacteria and fungi in the tumor specimens from 44 individuals with resected PDAC (24 eoPDAC and 20 aoPDAC). The alpha diversity of the bacterial microbiome was higher in eoPDAC tumor tissue compared with aoPDAC (P = 0.04). In contrast, the fungal mycobiome's alpha diversity was higher for aoPDAC tumor tissue (P = 0.02). Key organisms with differential abundance between tumor tissue from individuals with eoPDAC and aoPDAC included Bacillus, Candida, Collimonas, Cupriavidus, Enterobacter, Escherichia, Klebsiella, Malasseiza, Mucilaginibacter, Neisseria, and Sphingomonas. Higher bacterial diversity in tumor tissue was associated with better overall survival for individuals with eoPDAC (R = 0.26, P = 0.02).

CONCLUSIONS: Shotgun metagenomic sequencing identified bacterial microbiome and fungal mycobiome in tumors from individuals with eoPDAC and aoPDAC. We observed significant differences in alpha and beta diversity and relative abundances of organisms suggesting distinct microbiome signatures. Microbiome associations with survival were observed in eoPDAC indicating unique potential as prognostic biomarker.},
}

@article {pmid41647522,
year = {2026},
author = {Liu, J and Chen, Y and Sheng, X and Gao, Y},
title = {Case Report: Nocardia farcinica infectious arthritis and myositis in an immunocompromised host: diagnostic and management challenges.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1762442},
pmid = {41647522},
issn = {2296-858X},
abstract = {BACKGROUND: Nocardia farcinica is a rare opportunistic pathogen predominantly affecting immunocompromised hosts. Infectious arthritis, cutaneous and deep soft tissue infections caused by this organism often present with nonspecific clinical manifestations. Additionally, due to its slow-growing and oligotrophic nature, both cultivation and identification pose considerable challenges, thereby complicating clinical diagnosis and management.

CASE PRESENTATION: This case report described an elderly female patient presenting with right shoulder redness, swelling, and pain. Her history included diabetes, local corticosteroid injections, and newly identified humoral immunodeficiency (hypogammaglobulinemia with low B-cell count). Imaging revealed infectious arthritis of the right shoulder, accompanied by infectious myositis and an intermuscular abscess in the right upper arm. Nocardia farcinica was confirmed by metagenomic next-generation sequencing (mNGS) and culture of aspirated fluid. Initial therapy with trimethoprim-sulfamethoxazole (TMP-SMX) and ceftriaxone was limited by renal impairment and gastrointestinal intolerance, and susceptibility testing indicated TMP-SMX resistance. Treatment was switched to linezolid. Due to inadequate clinical response, multiple surgical debridements were performed. Subsequently, therapy was changed to oral minocycline because of linezolid-induced bone marrow suppression and intolerance. At discharge, the maintenance regimen consisted of moxifloxacin combined with minocycline.

CONCLUSION: This case highlights the importance of considering low-virulence pathogens such as Nocardia in immunocompromised patients with atypical infections that respond poorly to initial empiric therapy. Pathogen identification, aided by tools like mNGS for rapid detection, is essential. When classic regimens are limited by adverse effects, susceptibility-guided alternative therapies can be effective. For localized infections refractory to medical management, multidisciplinary surgical intervention remains a critical component of care.},
}

@article {pmid41646408,
year = {2026},
author = {Bosquet, JG and Osazuwa-Peters, O and Wagner, VM and Polio, A and Hoyd, R and Tarhini, AA and Cosgrove, CM and Huang, MS and Corr, BR and Leiser, AL and Salhia, B and Darcy, K and Dood, RL and Dockery, LE and Cavnar, MJ and Landrum, L and Chambers, L and Tan, AC and Jin, N and Rounbehler, RJ and Churchman, ML and Spakowicz, D},
title = {Intrinsic tumor factors and extrinsic environmental and social exposures contribute to endometrial cancer recurrence patterns.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8682460/v1},
pmid = {41646408},
issn = {2693-5015},
abstract = {Purpose In a previous study, we trained, validated and tested models of endometrial cancer (EC) recurrence integrating clinical, genomic and pathological data from the Oncology Research Information Exchange Network (ORIEN). Preliminary studies also have demonstrated that bacterial communities may influence the risk of EC recurrence by altering the local environment within the upper female genital tract. The objective of this study was to evaluate whether extrinsic and environmental factors, including tumor-associated bacterial communities, tumor immune contexture and air pollution alongside clinical, pathologic and genomic features are associated with EC recurrence across clinically relevant risk groups. Patients and Methods: We performed a retrospective, multi-institution, case-control study with data from the ORIEN network EC dataset. Data was stratified into low-risk, FIGO grade 1 and 2, stage I (N = 329), high-risk, or FIGO grade 3 or stages II-IV (N = 324), and non-endometrioid histology (N = 239) groups. RNA and DNA were extracted from tumor specimens and processed to obtain the necessary genomic/metagenomic data. Genus level microbiome data were extracted and curated) from RNA sequencing using Kraken2 , Bracken and exotic software packages. Risk of EC recurrence was evaluated by integrating microbiome and environmental data alongside existing clinical, pathological and genomic data using topic modelling with latent dirichlet allocation (LDA). Prediction models of EC recurrence were created using machine and deep learning analytics (ML and DL) with MATLAB apps and TensorFlow . Finally, performance of both topic and prediction models were externally validated in an independent EC dataset from TCGA. Results The resulting models, analyzed with topic modelling, demonstrated the complexity of factors involved in recurrence of disease for EC. The components of the resulting topic models, and specifically the microbiome, changed when environmental factors, like air pollutants, were introduced in the model. In the low-risk EC group, microbes that were quite abundant in models before introducing environmental factors, were scarcely seen afterwards, like genera Thermothielavioides , Theileria , Rhizoctonia . Bacillus was the genus with higher per-topic probability within all risk groups, especially for low-risk EC (28%). Ozone (O 3) was a resulting component of all risk groups' models. BMI was the sole informative clinical variable after data integration, and only present in the low-risk group. Resulting models from the high-risk and non-endometrioid groups included differential gene expressions: MMP13, S100A7, SMOC1, ACACA and ADD2, DLX5, SLCO2B1, NWD1 respectively. CNVs also were present in both low-risk and non-endometrioid groups, but their per-topic probabilities were low. The same was true for the immune contexture data. The components of the resulting topic models were used to train, validate and test prediction models of EC recurrence by risk groups. Performances of these models were excellent (@ 0.9). Despite some missing microbiome data in TCGA from resulting topic models, prediction models trained in the ORIEN set, had similar performances in TCGA testing set, with overlapping AUC 95% CIs. Conclusion Both extrinsic factors (tumor-associated bacterial communities, tumor immune contexture and air pollution) and intrinsic factors predict EC recurrence. The complexity of tumor and host factors influencing cancer relapses underscore the need for more individualized prediction models of disease outcomes.},
}

@article {pmid41645540,
year = {2026},
author = {Cuong, TM and Dan, NH and Hang, TTT and Le Luu, T and Scheynen, J and Dries, J},
title = {Enhanced the Treatment of Seafood Processing Wastewater Using the Anaerobic-Anoxic-Oxic (AAO) Process With Granular Sludge.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {2},
pages = {e70293},
doi = {10.1002/wer.70293},
pmid = {41645540},
issn = {1554-7531},
support = {FWO.105-2022.03//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; },
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Wastewater ; Bioreactors/microbiology ; *Seafood ; Phosphorus ; Bacteria/classification/genetics ; Nitrogen ; Aerobiosis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Seafood processing wastewater contains high concentrations of organics and nutrients that need to have an effective solution. This study aims to explore the use of granular sludge in seafood wastewater treatment using anaerobic-anoxic-aerobic (AAO) process. The results showed that the granular sludges were successfully cultivated from the traditional activated sludge sources. The bioreactor demonstrated robust treatment performance, achieving a high chemical oxygen demand (COD) removal efficiency exceeding 93%, total nitrogen (TN) removal ranging from 56.6% to 68.6%, and ammonium removal (NH4 [+]-N) of 80% to 88.57%. However, total phosphorus (TP) removal efficiency was relatively moderate at 47.36% ± 10.33%. Metagenomic analysis (16S rRNA) revealed a diverse and evenly distributed microbial community within the granular sludge. In anaerobic granular sludge, the dominant phylum was Bacillota (45.3%), followed by Thermodesulfobacteriota (18.2%) and Synergistota (11.24%), with minor contributions from Campylobacterota (7.58%), Chloroflexota (3.98%), and Bacteroidota (3.6%), alongside other less abundant phyla (10.1%). Anoxic granular sludge exhibited a shift, with Pseudomonadota (32.87%) and Thermodesulfobacteriota (25.08%) dominating, while Bacillota (11.95%), Bacteroidota (7.9%), and Chloroflexota (4.1%) contributed less, and other phyla comprised 18.21%. For aerobic granular sludge, Pseudomonadota represented the most prevalent phylum (42.21%), followed by Thermodesulfobacteriota (14.94%) and Bacillota (14.87%), with lower abundances of Bacteroidota (7.74%) and Chloroflexota (4.91%), while other phyla accounted for 15.42%.},
}

*Sewage/microbiology
Anaerobiosis
*Waste Disposal, Fluid/methods
*Wastewater
Bioreactors/microbiology
*Seafood
Phosphorus
Bacteria/classification/genetics
Nitrogen
Aerobiosis
RNA, Ribosomal, 16S/genetics

@article {pmid41645099,
year = {2026},
author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z},
title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04800-7},
pmid = {41645099},
issn = {1471-2180},
support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.

RESULTS: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.

CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.},
}

@article {pmid41645073,
year = {2026},
author = {Xu, C and Zhang, L and Liu, T and Zhu, G and Wei, H and Zheng, Y and Shi, J and Qiu, L and Xiao, Z and Zhu, X and Wang, J and Guo, J and Fan, Y and Song, Y and Jiang, E and Feng, S},
title = {Respiratory and blood samples metagenomic sequencing in diagnosing pulmonary infections in hematologic patients.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12734-8},
pmid = {41645073},
issn = {1471-2334},
support = {2021-I2M-1-039//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2021-I2M-1-017//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2023ZD0510400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 3332024210//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; 82470208//National Natural Sciences Foundation of China/ ; },
}

@article {pmid41645054,
year = {2026},
author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H},
title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12575-4},
pmid = {41645054},
issn = {1471-2164},
support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; },
abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.},
}

@article {pmid41644796,
year = {2026},
author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J},
title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41644796},
issn = {2058-5276},
support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.},
}

@article {pmid41644585,
year = {2026},
author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E},
title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37092-y},
pmid = {41644585},
issn = {2045-2322},
abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.},
}

@article {pmid41644553,
year = {2026},
author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J},
title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00929-5},
pmid = {41644553},
issn = {2055-5008},
support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; },
abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.},
}

@article {pmid41644450,
year = {2026},
author = {Yan, D and Huang, W and Li, KS},
title = {[Advances in clinical diagnosis and treatment of pythium keratitis].},
journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology},
volume = {62},
number = {2},
pages = {156-160},
doi = {10.3760/cma.j.cn112142-20250820-00351},
pmid = {41644450},
issn = {0412-4081},
support = {2025JJ90271//Enterprise Joint Fund Project/ ; },
mesh = {Humans ; *Pythium ; *Keratitis/diagnosis/therapy/microbiology ; *Pythiosis/diagnosis/therapy ; },
abstract = {Pythium insidiosum is an aquatic algal oomycete that can induce Pythium insidiosum keratitis (PIK). PIK typically presents as acute, highly invasive corneal ulcers, rapidly progressing to corneal dissolution and perforation, and in severe cases, may lead to blindness. Due to its clinical presentation resembling fungal infections, it is often misdiagnosed as fungal keratitis. Epidemiological studies indicate that PIK is predominantly found in tropical and subtropical regions, with a higher incidence during the monsoon season. It is often associated with exposure to contaminated water sources or minor trauma caused by plants. Diagnostic methods include staining of corneal scrapings, PCR, metagenomic next-generation sequencing, and confocal microscopy. Since PIK shows a poor response to conventional antifungal treatments, antibiotics are the preferred treatments, with a combination of linezolid and azithromycin often used as the first-line therapy. Severe cases may require penetrating keratoplasty. In China, reports of PIK cases are relatively rare. This review summarizes the epidemiology, etiology, clinical manifestations, diagnosis, and treatment of PIK, aiming to provide a reference for its clinical management.},
}

Humans
*Pythium
*Keratitis/diagnosis/therapy/microbiology
*Pythiosis/diagnosis/therapy

@article {pmid41644290,
year = {2026},
author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y},
title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {2},
pages = {e70714},
doi = {10.1111/jocd.70714},
pmid = {41644290},
issn = {1473-2165},
support = {//Proya Cosmetics Co. Ltd/ ; },
mesh = {Humans ; Female ; *Sebum/metabolism ; *Lipidomics/methods ; *Scalp/microbiology/metabolism ; Young Adult ; Adult ; *Dermatitis, Seborrheic/microbiology ; Metagenomics ; Microbiota ; *Scalp Dermatoses/microbiology ; China ; Dandruff/microbiology ; Lipids/analysis ; Paper ; East Asian People ; },
abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.

AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.

METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.

RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).

CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.},
}

Humans
Female
*Sebum/metabolism
*Lipidomics/methods
*Scalp/microbiology/metabolism
Young Adult
Adult
*Dermatitis, Seborrheic/microbiology
Metagenomics
Microbiota
*Scalp Dermatoses/microbiology
China
Dandruff/microbiology
Lipids/analysis
Paper
East Asian People

@article {pmid41644119,
year = {2026},
author = {Hung, JY and Cooke, I and Sato, Y and Miller, DJ and Bourne, DG},
title = {Microbial Metabolism and Disease Virulence Changes Across Day and Night in Coral Black Band Disease Lesions.},
journal = {Environmental microbiology},
volume = {28},
number = {2},
pages = {e70219},
doi = {10.1111/1462-2920.70219},
pmid = {41644119},
issn = {1462-2920},
support = {//Earthwatch Institute/ ; //James Cook University/ ; //Mitsubishi Corporation/ ; //JCU CTBMB grant/ ; //JCU OIRS Morris Family Trust grant/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; Virulence ; *Bacteria/metabolism/genetics/pathogenicity ; *Cyanobacteria/metabolism/genetics ; Photosynthesis ; Metagenome ; Microbiota ; Light ; },
abstract = {Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.},
}

*Anthozoa/microbiology
Animals
Virulence
*Bacteria/metabolism/genetics/pathogenicity
*Cyanobacteria/metabolism/genetics
Photosynthesis
Metagenome
Microbiota
Light

@article {pmid41642221,
year = {2026},
author = {Pavan, RR and Sullivan, MB and Tisza, MJ},
title = {CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
doi = {10.1099/mgen.0.001632},
pmid = {41642221},
issn = {2057-5858},
mesh = {*Computational Biology/methods ; Genome, Viral ; *DNA Viruses/genetics/classification ; *DNA, Single-Stranded/genetics ; Phylogeny ; Metagenomics/methods ; *Molecular Sequence Annotation/methods ; *Software ; },
abstract = {ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.},
}

*Computational Biology/methods
Genome, Viral
*DNA Viruses/genetics/classification
*DNA, Single-Stranded/genetics
Phylogeny
Metagenomics/methods
*Molecular Sequence Annotation/methods
*Software

@article {pmid41642002,
year = {2026},
author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB},
title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0364525},
doi = {10.1128/mbio.03645-25},
pmid = {41642002},
issn = {2150-7511},
abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.},
}

@article {pmid41641352,
year = {2025},
author = {Cao, XG and Zhu, XF and Ni, JX and Meng, HD and Huang, CJ},
title = {Optimizing metagenomic next-generation sequencing in CNS infections: a diagnostic model based on CSF parameters.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1681643},
pmid = {41641352},
issn = {2235-2988},
mesh = {Humans ; Female ; Male ; Retrospective Studies ; Middle Aged ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Aged ; ROC Curve ; *Cerebrospinal Fluid/cytology/chemistry ; Logistic Models ; Young Adult ; },
abstract = {OBJECTIVE: This study aimed to assess the association between routine cerebrospinal fluid (CSF) biochemical parameters and metagenomic next-generation sequencing (mNGS) results, and to develop a predictive model to optimize mNGS testing strategies in patients with suspected central nervous system (CNS) infections.

METHODS: We retrospectively enrolled 110 patients with suspected CNS infections between December 2019 and January 2024. All underwent both CSF analysis and mNGS testing. Patients were divided into mNGS-positive (n = 62) and negative (n = 48) groups. Logistic regression identified independent predictors, and a nomogram was constructed based on CSF cell count and protein concentration. Model performance was assessed via receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA). Internal validation included 10-fold cross-validation and 1000-sample bootstrap. An external validation was performed using a cohort of 40 patients enrolled from another hospital campus (May-October 2024). The derivation cohort was retrospectively collected, whereas the external validation cohort was prospectively enrolled.

RESULTS: mNGS positivity rate was 56.36%, significantly higher than CSF culture (6.36%), with an overall diagnostic concordance of 79.09%. Compared to the mNGS-negative group, positive patients had significantly higher CSF cell counts, protein levels, turbidity, ICU admission (ICUA), antimicrobial regimen adjustment (AAR), and mortality, while glucose was significantly lower (P < 0.05). Logistic regression confirmed CSF cell count binary variables (BV) and protein-BV as independent predictors (P < 0.05). The areas under curve (AUCs) for the cell-count, protein-only, and combined models were 0.827, 0.813, and 0.782, respectively. Internal validation showed stable results: 10-fold CV AUC = 0.773 ± 0.184 (95% CI: 0.641-0.904), bootstrap AUC = 0.770 ± 0.064 (95% CI: 0.766-0.774). External validation yielded an AUC of 0.763 (95% CI: 0.554-0.918), with sensitivity and specificity of 77.8% and 67.7%. Calibration and DCA demonstrated good agreement and clinical utility.

CONCLUSION: CSF cell count and protein are reliable predictors of mNGS positivity. The model for practice showed consistent diagnostic performance and may aid in guiding precision mNGS testing, particularly in resource-constrained settings.},
}

Humans
Female
Male
Retrospective Studies
Middle Aged
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Adult
Aged
ROC Curve
*Cerebrospinal Fluid/cytology/chemistry
Logistic Models
Young Adult

@article {pmid41641055,
year = {2025},
author = {Lai, SY and Chang, L and Duan, JX and Che, GL and Yang, QX and Teng, J and Jian, H and Liu, XJ and Liu, F},
title = {Clinical and epidemiological characteristics of cat scratch disease in children from southwestern China: a retrospective analysis of mNGS-confirmed cases.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1743423},
pmid = {41641055},
issn = {2296-2565},
mesh = {Humans ; *Cat-Scratch Disease/epidemiology/diagnosis/drug therapy ; Child ; Male ; Retrospective Studies ; Female ; China/epidemiology ; Adolescent ; *Bartonella henselae/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; Cats ; Animals ; },
abstract = {BACKGROUND AND AIM: Cat scratch disease (CSD) is a zoonotic infection predominantly caused by Bartonella henselae, typically featured by regional lymphadenopathy and febrile illness. Although these classic features characterize most cases, the clinical spectrum extends to severe systemic manifestations including meningitis and neuroretinitis, leading to poor prognosis. Given this potential for diverse clinical presentations, prompt microbiological confirmation becomes essential for accurate diagnosis and appropriate management of CSD. The present study aimed to provide a comprehensive analysis of epidemiological patterns, clinical characteristics, diagnostic findings, and therapeutic outcomes in pediatric CSD cases, with the ultimate goal of optimizing early detection and enhancing the clinical understanding of this disease.

METHODS: This single-center retrospective study analyzed 20 pediatric cases diagnosed with CSD at West China Second University Hospital in southwestern China between September 2021 and July 2025. All diagnoses were established based on comprehensive clinical evaluation including medical history, characteristic symptoms, and imaging findings. Definitive B. henselae identification was achieved through metagenomic next-generation sequencing (mNGS). These diagnostic characteristics were systematically evaluated and discussed in detail.

RESULTS: Among the 20 patients with CSD included in the study, 18 (90.00%) reported a history of cat contact. Ten patients were male (50.00%). School-aged children (6-14 years) accounted for the majority of patients. Eleven cases (55.00%) occurred in autumn. Fever and lymphadenopathy were the primary reasons for hospitalization. B. henselae was detected in all cases using mNGS. Nine patients were diagnosed with atypical CSD, seven of whom were female. Atypical CSD was associated with higher body temperature and longer hospitalization stay. Antimicrobial agents, including azithromycin, doxycycline, and rifampin, achieved satisfactory therapeutic outcomes.

CONCLUSION: This study elucidates the epidemiological, clinical, and laboratory characteristics of CSD in children. mNGS may serve as a powerful tool to facilitate the diagnosis of CSD, including its atypical manifestations.},
}

Humans
*Cat-Scratch Disease/epidemiology/diagnosis/drug therapy
Child
Male
Retrospective Studies
Female
China/epidemiology
Adolescent
*Bartonella henselae/isolation & purification/genetics
Anti-Bacterial Agents/therapeutic use
Cats
Animals

@article {pmid41640977,
year = {2026},
author = {Xia, L and Xu, J and Chen, Z and Shen, Y and Zou, Y},
title = {Disseminated tuberculosis secondary to polymicrobial co-infection following long-term immunotherapy for sarcomatoid mesothelioma: A case report.},
journal = {Respiratory medicine case reports},
volume = {59},
number = {},
pages = {102367},
pmid = {41640977},
issn = {2213-0071},
abstract = {Malignant pleural mesothelioma (MPM), particularly its sarcomatoid subtype, is a highly aggressive sarcoma of the pleural lining with a dismal prognosis. Prolonged use of immune checkpoint inhibitors (ICIs), while improving survival in selected patients, can induce profound immunosuppression, increasing susceptibility to life-threatening opportunistic infections. This report describes a 77-year-old male with sarcomatoid MPM who developed fatal disseminated tuberculosis (TB), accompanied by concurrent Aspergillus and herpesvirus infections during extended immunotherapy. The case underscores the critical role of metagenomic next-generation sequencing (mNGS) in enabling rapid diagnosis of atypical TB reactivation in an immunocompromised host, even when conventional cultures are negative. mNGS identified co-infections with Aspergillus flavus and herpesviruses (HHV-5, HHV-4, HHV-1), demonstrating its superiority in polymicrobial infection detection.},
}

@article {pmid41640872,
year = {2026},
author = {Chen, YX and Sun, NQ and Mo, SJ},
title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.},
journal = {World journal of gastroenterology},
volume = {32},
number = {4},
pages = {114468},
pmid = {41640872},
issn = {2219-2840},
mesh = {*NF-E2-Related Factor 2/metabolism ; Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Parkinson Disease/complications ; *Gastrointestinal Diseases/etiology/therapy/microbiology ; Mice ; Disease Models, Animal ; Kelch-Like ECH-Associated Protein 1/metabolism ; Signal Transduction/drug effects ; Fecal Microbiota Transplantation ; Brain-Gut Axis/drug effects ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; },
abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.},
}

*NF-E2-Related Factor 2/metabolism
Gastrointestinal Microbiome/drug effects
Animals
Humans
*Parkinson Disease/complications
*Gastrointestinal Diseases/etiology/therapy/microbiology
Mice
Disease Models, Animal
Kelch-Like ECH-Associated Protein 1/metabolism
Signal Transduction/drug effects
Fecal Microbiota Transplantation
Brain-Gut Axis/drug effects
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine

@article {pmid41640705,
year = {2026},
author = {Wang, HJ and Zhang, YN and An, L},
title = {Clinical and radiographic feature of pulmonary nocardiosis: A study of 102 cases.},
journal = {World journal of radiology},
volume = {18},
number = {1},
pages = {114552},
pmid = {41640705},
issn = {1949-8470},
abstract = {BACKGROUND: Nocardia pneumonia is an infection that occurs in patients with underlying diseases. Previously, due to limited detection methods, its detection rate and typing posed significant challenges. However, with advancements in detection techniques, the detection rate has significantly increased, and different Nocardia species exhibit distinct imaging characteristics.

AIM: To retrospectively analyze the etiological and imaging features of pulmonary Nocardia pneumonia and to examine the differences in chest imaging manifestations among different Nocardia species.

METHODS: The medical records of 102 patients with pulmonary nocardiosis who were admitted to Beijing Chaoyang Hospital from January 2017 to December 2024 were collected. Data including name, gender, underlying comorbidities, etiological characteristics, diagnostic methods, chest computed tomography features, and therapeutic agents were recorded.

RESULTS: Among the 102 patients, 55 were male and 47 were female, with a median age of 61 years. Bronchiectasis was the most common comorbidity, observed in 54 patients (52.9%). Sixty percent were diagnosed using metagenomic next-generation sequencing. Nocardia gelsenkin was the most prevalent Nocardia specie, while Aspergillus and Pseudomonas aeruginosa were identified as the predominant co-pathogens in these pulmonary nocardiosis cases. Pneumonia caused by Nocardia wallacei primarily presented with bronchopneumonia as the main imaging feature, while other Nocardia species more commonly manifested as consolidation, often accompanied by nodules, cavities, and pleural effusion. The imaging features in immunosuppressed patients were more diverse, with frequent coexistence of multiple patterns.

CONCLUSION: Nocardia pneumonia commonly coexists with bronchiectasis. While metagenomic next-generation sequencing has greatly enhanced its detection rate, Nocardia wallacei pneumonia is distinguished on chest computed tomography by its primary presentation of bronchopneumonia, unlike other types.},
}

@article {pmid41640408,
year = {2025},
author = {Sun, G and Zou, Q and Wang, B},
title = {The interplay of carbon and nitrogen cycling driven by watershed microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1696238},
pmid = {41640408},
issn = {1664-302X},
abstract = {Microorganisms play central roles in regulating carbon and nitrogen cycling across watersheds, driving processes such as organic matter decomposition, primary production, nitrification, and denitrification. Rapid advances in high-throughput sequencing and environmental monitoring have enabled unprecedented insights into the taxonomic diversity and functional capacities of microbial communities under global change. In this review, we synthesize findings from studies published in recent years to evaluate how hydrological connectivity, redox gradients, temperature shifts, and nutrient loading shape microbial metabolism across rivers, lakes, wetlands, and coastal interfaces. We further summarize emerging evidence on how antibiotic resistance genes (ARGs) propagate through these ecosystems and influence microbial functions. The integration of multi-omics technologies including metagenomics, metatranscriptomics, combined with ecological and biogeochemical modeling provides new opportunities to quantify microbe-mediated carbon sequestration and nitrogen transformation. Finally, we discuss current knowledge gaps, including the limited understanding of ARG-driven community restructuring and the insufficient mechanistic resolution of microbe-environment interactions under future climate scenarios. This review highlights the need for cross-scale, data-integrated frameworks to better predict how microbial processes regulate watershed-level biogeochemical cycles in a rapidly changing world.},
}

@article {pmid41640402,
year = {2025},
author = {Williams, AD and Hooton, SPT and King, E and Avery, LM and Hough, RL and Hobman, JL and Stekel, DJ and Neal, AL and West, HM},
title = {Temporal signals in dairy cattle slurry and fertilized field soil resistomes and bacterial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666851},
pmid = {41640402},
issn = {1664-302X},
abstract = {INTRODUCTION: Dairy cattle waste is a globally significant source of organic fertilizer which contains a cocktail of microbes and antibiotic resistance genes (ARGs). These ARGs may present a risk to human and animal health, yet there is still limited farm-system-level understanding of how long-term and multiple slurry applications alter field soil resistomes and total microbial communities.

METHODS: Using metagenomics, we assessed both immediate and longer-term changes in grassland field soil resistomes and bacterial communities over a year of routine cattle slurry application.

RESULTS: Our findings suggest that soil microbial communities are resilient to bacteria and ARGs introduced via slurry, even after repeated applications. Most slurry-borne ARGs were not enriched in field soil, however, those common in soil, such as rifamycin resistance genes, were consistently elevated relative to field soil with no history of slurry application. We observed transient increases in slurry-associated macrolide-lincosamide-streptogramin ARGs, however, their persistence appeared to be influenced by timing of slurry application. Similar transient effects were shown by the recovery of a high quality, slurry-associated Proteiniphilum spp. metagenome assembled genome (MAG).

DISCUSSION: We show that MAGs represent a powerful tool for examining the transfer of slurry-borne microorganisms, as they can be more characteristic of these environments than typical sentinel organisms which are easily cultivated. Our findings indicate that while the soil bacterial community shows considerable resilience to slurry-borne bacteria and ARGs, this may be diminished by temporal factors that remain largely unexplored and poorly understood. This is important because resilience inferred from short-term observations may not fully capture delayed or transient responses, potentially leading to underestimation of the persistence of slurry-borne bacteria and ARGs.},
}

@article {pmid41640388,
year = {2026},
author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J},
title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e72952},
pmid = {41640388},
issn = {2045-7758},
abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.},
}

@article {pmid41639832,
year = {2026},
author = {Ma, R and Sun, J and Zhu, J and Wu, Y and Shi, Y and Yang, Y and Wang, S and Han, X and Li, S and Gao, L and Zhao, X and Hua, R and Wang, Y},
title = {Metagenomic next-generation sequencing for efficient detection of human parvovirus B19 in amniotic fluid: a case study of diagnosis and prenatal management of fetal infection.},
journal = {BMC pregnancy and childbirth},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12884-026-08743-9},
pmid = {41639832},
issn = {1471-2393},
support = {HHJH2412//Medical Science and Technology Talent Promotion Project of The International Peace Maternity and Child Health Hospital/ ; 2023YFC2705901//National Science and Technology Major Project/ ; 22Y11902300//Science and Technology Commission of Shanghai Municipality/ ; 202440131//Shanghai Municipal Health Commission/ ; YG2023ZD26//Shanghai Jiao Tong University/ ; },
}

@article {pmid41639568,
year = {2026},
author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X},
title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38440-8},
pmid = {41639568},
issn = {2045-2322},
support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity & Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; },
abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.},
}

@article {pmid41639269,
year = {2026},
author = {Piera Líndez, P and Danielsen, LS and Kovačić, I and Pielies Avellí, M and Nesme, J and Jensen, LJ and Andersen, JN and Sørensen, SJ and Rasmussen, S},
title = {Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41639269},
issn = {1546-1696},
support = {NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistance. Despite their importance, plasmids are underrepresented in genomic databases because of challenges in assembling them, caused by mosaicism and microdiversity. Current plasmid assemblers rely on detecting circular paths in single-sample assembly graphs but face limitations because of graph fragmentation, entanglement and low coverage. We introduce PlasMAAG (plasmid and organism metagenomic binning using assembly-alignment graphs), a method to recover plasmids and cellular genomes from metagenomic samples. PlasMAAG complements assembly graph signals across samples by generating an 'assembly-alignment graph', which is used alongside common binning features for improved plasmid reconstruction. On synthetic benchmark datasets, PlasMAAG reconstructed 50-121% more near-complete plasmids than competing methods and improved the Matthews correlation coefficient of geNomad contig classification by 28-106%. On hospital sewage samples, PlasMAAG outperformed competing methods, reconstructing 33% more plasmid sequences. PlasMAAG enables the study of organism-plasmid associations and intraplasmid diversity across samples.},
}

@article {pmid41639055,
year = {2026},
author = {Lai, D and Mosier, D and Palmer, M and Mayali, X and Johnston, J and Saldivar, W and Covington, JK and Jiao, JY and Murali, R and Seymour, CO and Liu, L and Hua, ZS and Li, WJ and Weber, PK and Pett-Ridge, J and Colman, DR and Boyd, ES and Nunoura, T and Dodsworth, JA and Hedlund, BP},
title = {Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68859-6},
pmid = {41639055},
issn = {2041-1723},
support = {1557042//National Science Foundation (NSF)/ ; 2038420//National Science Foundation (NSF)/ ; 80NNSC17KO548//National Aeronautics and Space Administration (NASA)/ ; 80NSSC25M0046//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370011//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10[6] cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.},
}

@article {pmid41638592,
year = {2026},
author = {Xiao, Y and Cheng, Z and Cai, J and Guo, Z and Chen, J and Su, Y and Cao, F and Chen, D},
title = {Metagenomic and metatranscriptomic analysis of sulfur-driven autotrophic denitrification coupled with carbon assimilation: roles of sulfur-to-nitrogen ratio and hydraulic retention time.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134153},
doi = {10.1016/j.biortech.2026.134153},
pmid = {41638592},
issn = {1873-2976},
abstract = {The sulfur autotrophic denitrification (SAD) process is a promising technology for nitrogen-containing wastewater treatment, with research predominantly focused on nitrate and sulfide transformations, while the potential for inorganic carbon assimilation remains underexplored. In this study, a long-term stable SAD system was maintained in an airlift bioreactor by adding an inorganic carbon source to evaluate the effects of sulfur-to-nitrogen (S/N) ratio and hydraulic retention time (HRT) on operational performance. Under optimal operating conditions (S/N = 3:2; HRT = 8h), the system sustained high performance, achieving 99.56 ± 1.47% nitrate removal, 60.28 ± 4.19% elemental sulfur yield, and 46.48 ± 4.07% inorganic carbon assimilation efficiency. Biomass sulfur acted as a sink for extracellular free organic carbon (EFOC), thereby alleviating its accumulation-induced negative feedback on carbon assimilation. Microbial community analysis revealed a substantial enrichment of the autotrophic sulfur-oxidizing bacterium Sulfurovum, showing a marked 9.46-fold increase in relative abundance compared with the original sludge. At S/N = 3:2, metagenomic and metatranscriptomic analyses detected a 6.39-fold increase in the transcription of CBB cycle genes (rbcL/rbcS), driving a clear shift in metabolic flux toward carbon assimilation. Shortening the HRT (4 h) preferentially activated the denitrification pathway, which was evidenced by an 84.65% rise in nosZ expression (from 2,623.29 to 4,844.01 TPM), thereby bolstering N2O reduction. Our findings offered critical insights for designing engineering solutions that enable concurrent efficient denitrification, sulfur recovery, and reduced carbon emissions.},
}

@article {pmid41638346,
year = {2026},
author = {Behrens, LMP and Fernandes, GDS and Gonçalves, GF and Nunes, FVM and Weimer, RD and Moreira, JCF and Dorn, M},
title = {Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.019},
pmid = {41638346},
issn = {1873-7544},
abstract = {Recent advances in high-throughput technologies have led to an increased generation of biological data across genomics, transcriptomics, proteomics, epigenomics, and metabolomics. However, a major challenge remains: effectively integrating these multi-omics datasets to allow a more holistic understanding of the complex, interconnected mechanisms underlying human diseases. Neurodevelopmental, neurodegenerative, and psychiatric disorders are particularly multifactorial and heterogeneous, making them candidates for multi-omics approaches. In this context, this systematic review assesses the current state of multi-omics integration in neurological research. Records retrieved from five major databases were processed, and 156 studies were included for further analysis. The most frequently studied conditions were Alzheimer's Disease, Depressive Disorder and Parkinson's Disease, with epigenomics-transcriptomics and metagenomics-metabolomics emerging as the most common omics pairings. The field remains dominated by studies integrating pairs of omics layers. Only a limited number of computational tools are currently being applied to the integration of more than two omics layers, highlighting a gap in comprehensive multi-omics modeling. Despite progress, key challenges persist, including data accessibility and the need for standardized frameworks to allow cross-study comparisons. Moreover, most computational findings lack experimental validation in wet-laboratory settings. Future research should address these challenges, develop scalable algorithms for integrating multi-omics data, and leverage large, open-access datasets. Integrating computational predictions with experimental validation could help researchers prioritize high-confidence biomarkers relevant to clinical applications. Collaborative efforts among bioinformaticians, clinicians, and experimentalists will be essential to translating these advances into clinically actionable solutions.},
}

@article {pmid41638332,
year = {2026},
author = {Wu, B and Zhang, N and Yang, G and Yu, N and Xie, Z and Xia, J and Luo, W and Liu, X and Wang, D and Zhang, Y and Tang, L},
title = {Unraveling the microbial and functional mechanisms driving rapid algal-bacterial granular sludge formation in mariculture wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123941},
doi = {10.1016/j.envres.2026.123941},
pmid = {41638332},
issn = {1096-0953},
abstract = {Algal-bacterial granular sludge (ABGS) has unique advantages and broad application prospects in the treatment of mariculture wastewater. However, the rapid granulation process and performance evolution of ABGS under high salt stress have not been clearly defined. Compared with AGS, the influence of algal intervention on the structural integrity and metabolic activity of particles under the same salinity gradient is also unknown. Therefore, in this study, a parallel ABGS and AGS system was established. The results showed that intertwined algal filaments provided a structural skeleton for particle formation and led to complete granulation of ABGS within 20 days. Compared with conventional AGS, ABGS formed under high-salinity conditions exhibited a larger average particle size (1.07 mm), higher biomass (7.59 g/L) and higher extracellular polymeric substance (EPS) secretion (258.56 mg/g VSS). Additionally, chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal efficiencies exceeded 99% and 66%, respectively. Metagenomic analysis revealed that Thauera, Fragilaria and Nitzschia were dominant taxa associated with granule formation and stabilization. ABGS also showed an elevated abundance of functional genes associated with nitrogen metabolism (nxrA, nasA, and nasD) and polysaccharide metabolism (glmM, glmU, and pmm-pgm), which were in accordance with the enhanced nitrogen removal and granulation capability. Increased abundance of tricarboxylic acid cycle genes further indicated the superior granulation performance of ABGS. Overall, this study clarifies the morphological evolution and microbial functional mechanisms underlying rapid ABGS formation in mariculture wastewater, offering valuable insights for engineering optimisation and application of this technology in saline wastewater treatment.},
}

@article {pmid41638014,
year = {2026},
author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L},
title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {292},
number = {},
pages = {107742},
doi = {10.1016/j.aquatox.2026.107742},
pmid = {41638014},
issn = {1879-1514},
abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.},
}

@article {pmid41637515,
year = {2026},
author = {Liu, X and Cheng, X and Zhang, Y and Zhao, R and Wang, W and Li, Y and Chen, ZQ and Qiu, X and Tuovinen, OH and Bull, ID and Evershed, RP and Wang, H},
title = {High-efficiency methane consumption by atmospheric methanotrophs in subsurface karst caves: The irrefutable methane sink.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eady5942},
pmid = {41637515},
issn = {2375-2548},
mesh = {*Methane/metabolism ; *Caves/microbiology ; Oxidation-Reduction ; *Atmosphere/chemistry ; Soil Microbiology ; Phylogeny ; },
abstract = {Subsurface karst systems represent substantial but underexplored methane sinks, yet the identities and activities of cave-dwelling methanotrophs remain poorly characterized. We detected increased methane oxidation rates from 2.9 ± 0.1 to 90.7 ± 4.5 ng·g[-1]·hour[-1] while supplied with 2 to 500 parts per million (ppm) CH4 to cave sediments. Atmospheric methanotroph Upland Soil Clusters γ (USCγ), responsible for this oxidation, was further assigned to three genera within the family Candidatus (Ca.) Methyloligotrophaceae, including two previously unrecognized genera. Nano-scale secondary ion mass spectrometry (NanoSIMS) imaging and the produced [13]C-PLFAs (phospholipid fatty acids) and [13]CO2 in [13]CH4-fed microcosm confirmed methane as both carbon and energy sources. These methanotrophs exhibited low half-saturation constant (Km; 138.8 ± 15.8 ppm), high carbon assimilation efficiency (>50%), and metabolic versatility, as revealed by metagenomics and metatranscriptomics analyses. By extrapolating global distribution of Ca. Methyloligotrophaceae and comparing methane oxidation rates between caves and soil ecosystems, we conservatively estimate that subsurface karst in southwest China sequester ~0.56 Tg CH4 annually. These findings highlight the ecological importance of karst ecosystems as a previously overlooked methane sink.},
}

*Methane/metabolism
*Caves/microbiology
Oxidation-Reduction
*Atmosphere/chemistry
Soil Microbiology
Phylogeny

@article {pmid41637508,
year = {2026},
author = {Kaur, G and Crawford, SE and Javornik Cregeen, S and Surathu, A and Ayyar, BV and Apostol, CV and Phuc, HN and Ettayebi, K and Boussattach, A and Zeng, XL and Blutt, SE and Doddapaneni, H and Muzny, DM and Coarfa, C and Anish, R and Prasad, BVV and Atmar, RL and Ramani, S and Estes, MK},
title = {Overcoming host restrictions to enable continuous passaging of GII.3 human norovirus in human intestinal enteroids.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb0455},
pmid = {41637508},
issn = {2375-2548},
mesh = {Humans ; *Norovirus/physiology/genetics ; Virus Replication/drug effects ; *Caliciviridae Infections/virology ; *Intestines/virology ; *Host-Pathogen Interactions ; *Organoids/virology ; Chemokines/metabolism/genetics ; Gastroenteritis/virology ; },
abstract = {The establishment of human intestinal enteroids (HIEs) as a model for human norovirus (HuNoV) replication has been transformative for studying this leading cause of gastroenteritis. However, indefinite passaging of HuNoVs in HIEs remained a challenge, necessitating the use of patient stool samples as viral inocula. Using RNA-seq, we identified CXCL10, CXCL11, and CCL5 as up-regulated chemokines, suggesting their potential as host restriction factors. TAK-779, a CXCR3/CCR5/CCR2 antagonist, enhanced GII.3 HuNoV replication and viral spread in a dose- and time-dependent manner, enabling successful passaging of GII.3 HuNoV in two different HIE lines and generation of viral stocks. Sequencing passaged virus revealed one consensus change in the major capsid protein and several dynamic adaptations, suggesting emergence of variants. TAK-779 also enhanced replication of GI.1 and GII.17 strains, but not GII.4, suggesting strain-specific host interactions. This breakthrough in passaging provides insight into HuNoV-host interactions, establishes a scalable in vitro system for virus propagation, and opens avenues for structural, biochemical, and therapeutic studies.},
}

Humans
*Norovirus/physiology/genetics
Virus Replication/drug effects
*Caliciviridae Infections/virology
*Intestines/virology
*Host-Pathogen Interactions
*Organoids/virology
Chemokines/metabolism/genetics
Gastroenteritis/virology

@article {pmid41637142,
year = {2026},
author = {Dos Santos, SJ and Gloor, GB},
title = {Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.},
journal = {Current protocols},
volume = {6},
number = {2},
pages = {e70307},
pmid = {41637142},
issn = {2691-1299},
mesh = {Uncertainty ; *Gene Expression Profiling/methods ; *Software ; *Transcriptome ; Humans ; Principal Component Analysis ; *Metagenomics/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods ; },
abstract = {Differential abundance or expression analyses are routinely performed on metagenomic, metatranscriptomic, and amplicon sequencing data. In such datasets, analysts usually have no information regarding the true scale (i.e., size) of the microbial community or sample under study, with inter-sample differences in sequencing depth instead being driven by technical variation rather than biological factors. Recent work has demonstrated that normalizations used in all analysis tools make incorrect assumptions about the biological scale of the system in question, leading to unacceptably high false-discovery rates in the output. To mitigate this, analysts can acknowledge and account for the uncertainty of the overall system scale during normalization by building scale models of the data-a feature that has been integrated into the ALDEx2 R package. Here, we provide reproducible examples that demonstrate how to incorporate scale models into differential expression analyses of RNA-seq data using bulk transcriptome and metatranscriptomic datasets, as well as the consequences of not doing so. We also show how to use the output of ALDEx2 to create high-level exploratory visualizations of their data through principal component analysis. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using a simple scale model for differential expression analysis to avoid dual-cutoff P value/significance thresholds Basic Protocol 2: Implementing a full informed scale model to correct scale-related data asymmetry in differential expression analyses Basic Protocol 3: Visualizing ALDEx2 outputs using a compositional approach: Principal component analysis.},
}

Uncertainty
*Gene Expression Profiling/methods
*Software
*Transcriptome
Humans
Principal Component Analysis
*Metagenomics/methods
Sequence Analysis, RNA/methods
RNA-Seq/methods

@article {pmid41636536,
year = {2026},
author = {Della-Negra, O and Servien, R and Milferstedt, K and Hamelin, J and Klopp, C and Hoede, C},
title = {Metagenome-assembled genomes from oxygenic photogranules obtained from photobioreactors treating synthetic wastewater.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0131025},
doi = {10.1128/mra.01310-25},
pmid = {41636536},
issn = {2576-098X},
abstract = {Twenty-five high-quality metagenome-assembled genomes (MAGs) were recovered from photogranules to treat synthetic wastewater. They were dominated by Leptolyngbya boryana. Cyanobacterial MAGs encoded photosynthesis and nitrogen fixation pathways, supporting internal oxygen and nitrogen cycling. Most heterotrophic MAGs contributed to nitrogen removal, highlighting the metabolic complementarity within photogranules studied for wastewater treatment.},
}

@article {pmid41636510,
year = {2026},
author = {Anne Hallowell, H and Malogan, J and Suez, J},
title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100225},
doi = {10.1128/msystems.01002-25},
pmid = {41636510},
issn = {2379-5077},
abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.},
}

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0226425},
doi = {10.1128/spectrum.02264-25},
pmid = {41636495},
issn = {2165-0497},
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

@article {pmid41636304,
year = {2026},
author = {Brown, LP and Marizzi, A and Borrego, CM and Gionchetta, G and Zhengzheng, Z and Carneiro, RB and Gago-Ferrero, P and Matamoros, V and Subirats, J},
title = {Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13541},
pmid = {41636304},
issn = {1520-5851},
abstract = {The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse-oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel antibiotic resistance families for monitoring. Reclaimed effluents exhibited lower AMR exposure levels than those typically reported for secondary effluents (<0.5 ARGs/cell), while mobile genetic element (MGE) abundances were comparable to secondary effluents (1-2 MGEs/cell). Effluent communities differed by WWTP configuration: membrane bioreactor combined with ultrafiltration favored nutrient-removal/oxidative-stress taxa and reduced transferable MGEs, whereas plants relying on physical separation (sand filtration or reverse osmosis) retained fecal-associated taxa and MGEs. Specific clinically relevant ARGs persisted after treatments, including aadA and aph(3'')-Ibs (resistance to aminoglycosides), ermB and mphA (resistance to macrolides), and blaOXA-129 (resistance to beta-lactams), which we identify as sentinel markers for monitoring reclaimed water and sludge. We advance a generalizable two-step framework, metagenomic discovery to identify sentinel markers, followed by targeted assays for streamlined surveillance, that provides the first operational blueprint for integrating AMR into water reuse management under the EU regulation.},
}

@article {pmid41635749,
year = {2025},
author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É},
title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100333},
pmid = {41635749},
issn = {2667-114X},
abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.},
}