@article {pmid42680271,
year = {2026},
author = {Zhu, D and Xie, J and Li, P and Mei, J},
title = {Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {119937},
doi = {10.1016/j.foodres.2026.119937},
pmid = {42680271},
issn = {1873-7145},
mesh = {*Multiomics ; *Food Microbiology/methods ; *Artificial Intelligence ; *Food Preservation/methods ; *Microbiota ; Metabolomics ; Metagenomics ; },
abstract = {In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.},
}

*Multiomics
*Food Microbiology/methods
*Artificial Intelligence
*Food Preservation/methods
*Microbiota
Metabolomics
Metagenomics

@article {pmid42680349,
year = {2026},
author = {Li, S and Zhang, H and Yang, Y and Xia, Y and Ni, B and Ai, L},
title = {Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {120059},
doi = {10.1016/j.foodres.2026.120059},
pmid = {42680349},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; *Food Microbiology ; Bacteria/metabolism/genetics/classification ; Metabolomics ; *Fermented Foods/microbiology/analysis ; Metagenomics ; Ethanol/analysis ; },
abstract = {Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.},
}

*Volatile Organic Compounds/analysis/metabolism
Fermentation
*Alcoholic Beverages/microbiology/analysis
*Microbiota
Gas Chromatography-Mass Spectrometry
*Food Microbiology
Bacteria/metabolism/genetics/classification
Metabolomics
*Fermented Foods/microbiology/analysis
Metagenomics
Ethanol/analysis

@article {pmid42680378,
year = {2026},
author = {Zhou, Y and Zhao, Z and Ke, T and Wang, Z and Wang, J},
title = {The global potential of freshwater microbes for plastic degradation.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {215-224},
doi = {10.1016/j.jes.2026.03.008},
pmid = {42680378},
issn = {1001-0742},
mesh = {*Plastics/metabolism ; *Biodegradation, Environmental ; *Fresh Water/microbiology ; *Water Pollutants, Chemical/metabolism ; *Water Microbiology ; Bacteria/metabolism ; Metagenome ; },
abstract = {Plastic pollution is becoming increasingly severe on a global scale, and the potential for biodegradation as a treatment method that is environmentally friendly merits greater attention. A significant number of genes that associated the degradation of plastic (PDAGs) have been identified, however, the distribution of these genes among microorganisms in global inland waters remains to be elucidated. A global-scale meta-analysis was conducted, incorporating approximately 1000 metagenome datasets of inland waters across seven continents. A total of 13,109 metagenome-assembled genomes (MAGs) were obtained by means of metagenomics binning, and 22,621 PDAGs were identified from these. Among these recognized PDAGs, phenylacetaldehyde dehydrogenase (PAD) was the most dominant (n = 16,664), followed by catalase (n = 5931). The predominant hosts for PAD and catalase were identified as Gamma-proteobacteria and Bacteroidia, respectively. The largest number of both PAD and catalase was found in MAGs from North America, while the average gene number in single MAG was highest in MAGs from Oceania. In accordance with the prediction of traits, PDAG-carrying MAGs from Europe demonstrated the fastest growth rate and the lowest optimal growth rate. Furthermore, 25 styrene monooxygenase (StyA) enzymes were identified, which were found to cluster into two distinct groups hosted by Alpha-proteobacteria and Gamma-proteobacteria, respectively. Moreover, 11 MAGs were observed to possess the complete pathway of polystyrene degradation. These results explored the potential of inland water microorganisms as a biological resource for plastic degradation and provided valuable microbial reference information that can be used to develop biological treatment technologies for mitigating plastics.},
}

*Plastics/metabolism
*Biodegradation, Environmental
*Fresh Water/microbiology
*Water Pollutants, Chemical/metabolism
*Water Microbiology
Bacteria/metabolism
Metagenome

@article {pmid42680395,
year = {2026},
author = {Zhang, Q and Nie, B and Yang, C and Wei, F and Deng, L and Chen, Z and Hua, S},
title = {Boosting domestic wastewater treatment with quorum signal-augmented heterotrophic nitrification-aerobic denitrification bacterial-algal aerobic granular sludge.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {381-391},
doi = {10.1016/j.jes.2026.03.078},
pmid = {42680395},
issn = {1001-0742},
mesh = {Denitrification ; Sewage/microbiology ; Nitrification ; *Waste Disposal, Fluid/methods ; *Wastewater/microbiology/chemistry ; Quorum Sensing ; Bacteria/metabolism ; Aerobiosis ; },
abstract = {The aerobic bacterial-algal granular sludge (ABGS) enhanced with heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria, as a novel symbiotic technology, exhibits fluctuating treatment efficiency and unstable performance primarily due to the unstable symbiotic relationship. This study proposes an innovative approach to strengthening the bacteria-algae symbiosis by introducing exogenous signaling molecules. Concurrently, high-throughput, correlation analysis of environmental factors and metagenomic sequencing techniques are employed to elucidate the enhancement mechanisms of the signaling molecules. The results demonstrate that signaling molecule enhancement boosted total nitrogen (TN) removal efficiency by 24.51 % in the bacteria-algae symbiotic system (X1). Scanning electron microscopy (SEM) characterization revealed that the addition of signaling molecules resulted in more compact aerobic granular sludge (AGS) and markedly improved stability. High-throughput sequencing showed signaling molecules enriched denitrifying bacteria (Hydrogenophaga, Pseudoxanthomonas, Thauera, Zoogloea) and organic-degrading Desulfomicrobium, optimizing microbial diversity and enhancing nitrogen/organic removal. Correlation analysis of environmental factors indicate that the addition of C8-HSL facilitates the enrichment and functional activation of specific genera. Metagenomic analysis revealed that signaling molecules enhanced the system's denitrification performance by modulating gene expression and associated metabolic pathways. Quantitative polymerase chain reaction (qPCR) analysis further confirmed that the signaling molecules upregulated the expression of the napA, nirK, and nirS genes. An increased abundance of the napA gene facilitated aerobic denitrification (NO3[-]-N→NO2[-]-N), while upregulated abundance of the nirK and nirS genes accelerated nitrite reduction (NO2[-]-N→N2). This study aims to provide theoretical and practical foundations for implementing advanced bacteria-algae symbiotic technologies.},
}

Denitrification
Sewage/microbiology
Nitrification
*Waste Disposal, Fluid/methods
*Wastewater/microbiology/chemistry
Quorum Sensing
Bacteria/metabolism
Aerobiosis

@article {pmid42680398,
year = {2026},
author = {Mao, Y and Wang, C and Zhang, L and Zou, B and Han, M and Wang, Z},
title = {Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {400-412},
doi = {10.1016/j.jes.2025.12.004},
pmid = {42680398},
issn = {1001-0742},
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; China ; Bacteria ; Eutrophication ; *Microbial Interactions ; *Environmental Monitoring ; Nitrogen Cycle ; },
abstract = {Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.},
}

*Lakes/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
China
Bacteria
Eutrophication
*Microbial Interactions
*Environmental Monitoring
Nitrogen Cycle

@article {pmid42680679,
year = {2026},
author = {Yang, X and Peng, AD and Cheng, JH and Huang, YH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG and Wen, G},
title = {A legacy pollutant deciphered by multiomics toxicology and targeted remediation by a synthetic microbial consortium: a case study of 2-chloroacetophenone from abandoned chemical weapons.},
journal = {Water research},
volume = {},
number = {},
pages = {126776},
doi = {10.1016/j.watres.2026.126776},
pmid = {42680679},
issn = {1879-2448},
abstract = {2-Chloroacetophenone (2-CA) is a typical organic poison found in abandoned Japanese chemical weapons, yet systematic research on its ecological risks and bioremediation strategies in aquatic environments remains scarce. Through a 120-day exposure experiment across three concentration gradients (10, 50, and 100 mg·L[-1]) coupled with multiomics analysis (physicochemical profiling, ionomics, 16S rRNA sequencing, metagenomics, and metabolomics), we systematically characterized the toxic effects of 2-CA on aquatic microbial communities and their molecular response mechanisms. The glutathione (GSH) metabolic pathway was identified as the core defense hub against 2-CA-induced oxidative stress, with multiomics data revealing its transition from compensatory activation to irreversible collapse. Guided by these mechanistic insights, we directionally isolated three cascade-degrading bacteria (Pseudomonas abietaniphila, Bacillus sp., and Arthrobacter agilis) harboring the key genes hapA, yjfP, and catA, which encode the three consecutive steps of Baeyer-Villiger oxidation, ester bond hydrolysis, and aromatic ring cleavage. The synthetic microbiome assembled from these three wild-type strains achieved 100% removal of 100 mg·L[-1] 2-CA within 24 h in vitro and within 10 days in simulated contaminated water, with the sequential detection of predicted intermediates (phenyl 2-chloroacetate, phenol, and pyruvic acid) confirming the operation of the cascade pathway. This study establishes a "toxicology diagnosis-functional deconstruction-synthetic reconstruction" paradigm, providing mechanistic understanding and a potential bioremediation strategy for organic toxicants at sites contaminated by relic Japanese chemical weapons, although direct ecotoxicological validation of detoxification remains to be confirmed.},
}

@article {pmid42680729,
year = {2026},
author = {Della Sala, S and Papadimitriou, V and Polymenakou, P and Kutterolf, S and Frieling, J and Pyle, DM and Mather, TA and Kilias, S and Jones, CK and Druitt, T and Preine, J and Hübscher, C and Nomikou, P and Koukousioura, O and Ronge, TA and Beethe, S and Pank, K and Berthod, C and Chen, H and Chiyonobu, S and Clark, A and DeBari, S and Gertisser, R and Johnston, R and Manga, M and McCanta, M and McIntosh, I and Peccia, A and Tominaga, M and Yamamoto, Y and Woodhouse, A and Bernard, A and Fernandez Perez, T and Joshi, KB and Kletetschka, G and Morris, A and Li, X and Papanikolaou, D},
title = {A prolonged hydrothermal past at Santorini Caldera revealed by sedimentary trace metal and microbial signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42680729},
issn = {2041-1723},
support = {NE/L002612/1//RCUK | Natural Environment Research Council (NERC)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 527924707//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 527924707//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC-2018-COG-8187 17-V-ECHO//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
mesh = {*Geologic Sediments/chemistry/microbiology ; *Hydrothermal Vents/microbiology/chemistry ; Volcanic Eruptions ; *Trace Elements/analysis ; *Metals/analysis ; Bacteria/genetics ; Metagenomics ; },
abstract = {Hydrothermal systems in volcanic calderas are critical in signalling volcanic unrest, forming ore deposits, and sustaining chemosynthetic microorganisms. Analysis of a ~3500-year sequence of sediments collected from the Santorini caldera, Greece, during International Ocean Discovery Program (IODP) Expedition 398 reveals the behaviour of a prolonged paleo-hydrothermal system. Sediment geochemical and metagenomic data record vigorous hydrothermal activity and metal fluxes for ~1100 years, within a 2270-year window between two major eruptions. Sediment hydrothermally-derived trace metals are significantly enriched over background (~200-fold for As and Hg, and 10-50-fold for Mn, Sb, Mo, and V), with long-term metal fluxes (9 t yr[-1] As, 2.5 t yr[-1] Cu, 7 kg yr[-1] Ag) comparable to fluxes from present-day geothermal fields in the Taupo Volcanic Zone. Metagenomic analysis identifies elevated metal resistance genes-signals of microbial adaptation to heightened hydrothermal stressors. Here we integrate geological and genomic evidence to decipher the paleoenvironmental and biogeochemical history of the past hydrothermal system at Santorini caldera.},
}

*Geologic Sediments/chemistry/microbiology
*Hydrothermal Vents/microbiology/chemistry
Volcanic Eruptions
*Trace Elements/analysis
*Metals/analysis
Bacteria/genetics
Metagenomics

@article {pmid42680742,
year = {2026},
author = {Low, A and Yang, Z and Anantaya, KT and Zhao, S and Tan, WC and Perez, RL and Chung The, H and Lim, SZY and Liu, L and Gounot, JS and Kwah, JS and Ong, RT and Nagarajan, N and Lee, JWJ and Mo, Y},
title = {Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42680742},
issn = {2041-1723},
mesh = {Humans ; *Escherichia coli/genetics/isolation & purification/classification ; *Escherichia coli Infections/microbiology/epidemiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metagenomics ; *Carrier State/microbiology ; Asia, Southeastern/epidemiology ; Intestines/microbiology ; },
abstract = {Escherichia coli sequence-type 131 (ST131) is the dominant global extraintestinal pathogen capable of asymptomatic intestinal carriage and sustained household transmission, challenging infection control. Despite its clinical significance, the ecological determinants of gut persistence remain poorly understood. We performed shotgun metagenomics on fecal samples to investigate gut microbiome features associated with ST131-positive samples, distinct host carrier statuses (persistent, intermittent and non-carriers) and household risks in a study of a Southeast Asian cohort. Here, we show that ST131 carriage was associated with compositional shifts without reducing species alpha-diversity. Regression analyses identified depletion of commensal taxa and the 1,5-anhydrofructose degradation pathway in ST131-positive samples. Persistent carriers exhibited highly perturbed microbiome enriched with pathobionts, aerobactin- and lipopolysaccharide (LPS)-biosynthesis pathways. Comparing household risk groups to control, revealed that biotin biosynthesis and 1,5-anhydrofructose degradation may influence ST131 co-colonization through both direct and indirect mechanisms. Machine learning analyses identified metabolic pathways as stronger discriminators of persistent carriage than taxonomic features. Genomic-resolved analysis of clinical ST131 isolates revealed conserved genes for iron-acquisition, LPS and antibiotic resistance determinants. Overall, while commensals and metabolism may influence initial ST131 colonization, persistent carriage is associated with specific microbial and metabolic adaptations, providing potential targets to limit intestinal ST131 persistence.},
}

Humans
*Escherichia coli/genetics/isolation & purification/classification
*Escherichia coli Infections/microbiology/epidemiology
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Cohort Studies
Metagenomics
*Carrier State/microbiology
Asia, Southeastern/epidemiology
Intestines/microbiology

@article {pmid42680886,
year = {2026},
author = {Liu, CC and Dong, SS and Guo, J and Xu, Z and Wang, C and Li, YX and Meng, LL and Yang, XC and Li, M and Fu, K and Guo, Y and Yang, TL},
title = {MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42680886},
issn = {2058-5276},
support = {2023M732810//China Postdoctoral Science Foundation/ ; 2024M762573//China Postdoctoral Science Foundation/ ; 82372458//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401762//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370653//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Recovering high-quality microbial genomes from metagenomic sequencing data is essential for accurate profiling and understanding microbial variation. However, existing clustering methods often suffer from limited accuracy and scalability. Here we present MetaCAT (Metagenome Clustering and Association Tool), a framework that combines recovery of microbial genomes from metagenomic data and analysis of their associations with host traits. MetaCAT incorporates a Sparse Weighted Dirichlet Process Gaussian Mixture Model (SWDPGMM) to accurately and efficiently decompose complex datasets and combines k-mer frequency with read coverage to improve genome reconstruction. It also provides a dedicated workflow for microbial single-nucleotide polymorphism identification and metagenome-wide association studies with the host. MetaCAT outperforms existing methods in both clustering accuracy and computational efficiency across diverse datasets. Using metagenomic data from colorectal cancer cohorts, it revealed previously unrecognized marker species and microbial single-nucleotide polymorphisms associated with colorectal cancer. MetaCAT provides a scalable framework for microbial community profiling and advances our understanding of host-microbe interactions.},
}

@article {pmid42681283,
year = {2026},
author = {Grasso, G and Marmeisse, R and Bianciotto, V},
title = {Metagenomics Approach for Identification of Arbuscular Mycorrhizal Fungal Sequences in Historical Herbarium Specimens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3045},
number = {},
pages = {209-215},
pmid = {42681283},
issn = {1940-6029},
mesh = {*Mycorrhizae/genetics/classification ; *Metagenomics/methods ; Soil Microbiology ; DNA, Fungal/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomics offers a powerful alternative to amplicon-based approaches for investigating arbuscular mycorrhizal fungi (AMF) in samples characterized by highly degraded DNA, such as historical herbarium specimens. Here, we present a dedicated bioinformatic pipeline for the retrieval and authentication of AMF sequences from shotgun metagenomic datasets generated from herbarium-associated soils. The workflow integrates quality control and reads preprocessing, taxonomic classification using Kraken2, targeted extrafction of AMF reads, and mapping to reference genomes using short-read-optimized alignment strategies. Authentication of historical DNA is achieved through the analysis of post-mortem damage patterns, including fragment length distributions and cytosine deamination profiles, using MapDamage2. This pipeline enables the detection of ancient AMF DNA, and it could provide a framework for studying long-term dynamics of plant-mycorrhizal associations from historical soil archives.},
}

*Mycorrhizae/genetics/classification
*Metagenomics/methods
Soil Microbiology
DNA, Fungal/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid42681569,
year = {2026},
author = {Zhang, Z and Ran, X and Lu, S and Chen, X and Ran, Y},
title = {Refractory Cutaneous Cunninghamella bertholletiae Infection Post-Polypectomy: Reversal With Amphotericin B Therapy Adjustment.},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.70672},
pmid = {42681569},
issn = {1365-4632},
}

@article {pmid42681574,
year = {2026},
author = {Campani, S and Stocco, S and Moriondo, M and Chiappini, E and Trapani, S},
title = {Oropharyngeal Kingella kingae Detection and Spondylodiscitis in Early Childhood-A Causal or Casual Association?: A Case Report and a Systematic Literature Review.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000005385},
pmid = {42681574},
issn = {1532-0987},
abstract = {BACKGROUND: Pediatric spondylodiscitis is a rare condition, primarily affecting children aged 6-48 months. Kingella kingae is the leading pathogen in this age group, often presenting with mild or atypical features, which delay diagnosis.

METHODS: We retrospectively reviewed pediatric spondylodiscitis cases discharged from our hospital between January 2010 and May 2026, identifying those attributable to K. kingae. In parallel, we conducted a systematic literature review using PubMed/MEDLINE and Embase (2000-2025) to identify pediatric cases confirmed by culture, nucleic acid amplification or metagenomic sequencing of plasma microbial cell-free DNA.

RESULTS: One case of K. kingae spondylodiscitis was identified at our center. The literature review yielded 59 cases (mean age 24 months). Clinical presentation was indolent: refusal to sit, limping, hip/back pain and minimal systemic symptoms. Laboratory findings were nonspecific, with erythrocyte sedimentation rate being the most elevated marker. All blood cultures were negative. Definitive diagnosis was achieved through molecular detection on blood or biopsy/drainage material; oropharyngeal swab-positive cases were considered presumptive. The lumbar spine (L4-L5) was the most involved site. Most patients responded well to antibiotic treatment; surgical intervention was rarely required.

CONCLUSIONS: Kingella kingae should be considered in young children with persistent gait disturbance or hip/back pain, even without fever or marked laboratory abnormalities. Early magnetic resonance imaging and molecular diagnostics on blood or infectious tissue enable timely, definitive diagnosis and targeted therapy. When isolation from a sterile site is not possible, K. kingae spondylodiscitis remains likely if age, clinical presentation, laboratory findings and polymerase chain reaction detection on a pharyngeal swab are consistent.},
}

@article {pmid42681733,
year = {2026},
author = {Ellis, EK and Ióca, LP and Liu, J and Chen, M and Bruner, SD and Ding, Y and Paul, VJ and Donia, MS and Luesch, H},
title = {Characterization of Dapalides D and E and Genomic Comparison of the Two Co-Occurring Dapalide-Producing Dapis spp.},
journal = {Journal of natural products},
volume = {89},
number = {8},
pages = {2373-2383},
doi = {10.1021/acs.jnatprod.6c00607},
pmid = {42681733},
issn = {1520-6025},
support = {R35GM128742/GM/NIGMS NIH HHS/United States ; RM1GM145426/GM/NIGMS NIH HHS/United States ; NA//University of Florida/ ; NA//Debbie and Sylvia DeSantis Chair professorship/ ; },
mesh = {*Cyanobacteria/genetics/chemistry ; *Depsipeptides/chemistry/pharmacology/isolation & purification ; Molecular Structure ; Phylogeny ; Guam ; Humans ; },
abstract = {Marine cyanobacteria are a rich source of diverse bioactive natural products, targeting proteins involved in many diseases. Here, we combined metagenomic analysis to enhance the structure elucidation process of two new cyclodepsipeptides named dapalides D (1) and E (2) from a collection of a cyanobacterial mat containing multiple Dapis species from Guam. Dapalides D/E are composed of 11 amino acids, including multiple identical units with different configurations. Enantioselective amino acid identification of the acid hydrolyzate established the identity of amino acids, including the configuration of α/β-stereogenic centers. Identification and analysis of the dapalides D/E biosynthetic gene cluster from a metagenome-assembled genome aided the elucidation of α-configuration and establishment of the order of individual building blocks, collectively revealing the total structure. Phylogenomic analysis indicates that the dapalides D/E producer belongs to Dapis sp. (Dapis sp. VPG23-80 MAG-2), which shares a 95.2% average nucleotide identity with Dapis sp. VPG23-80 MAG-1, the producer of dapalides A-C that cooccurs in the same assemblage. Dapalide D (1) showed moderate growth inhibitory activity against various cancer cell lines. This work expands the dapalide structure class and further highlights the use of combined chemical and metagenomic analyses for natural product structure elucidation.},
}

*Cyanobacteria/genetics/chemistry
*Depsipeptides/chemistry/pharmacology/isolation & purification
Molecular Structure
Phylogeny
Guam
Humans

@article {pmid42682513,
year = {2026},
author = {Zhang, W and Chen, M and Guo, T and Kuang, G and Ma, N},
title = {Gut microbiota dysbiosis and aromatic amino acid metabolism alterations: a multi-omics analysis of cognitive impairment following aneurysmal subarachnoid hemorrhage.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1870309},
pmid = {42682513},
issn = {1664-302X},
abstract = {BACKGROUND: Aneurysmal subarachnoid hemorrhage (aSAH) is frequently followed by persistent cognitive impairment, characterized by a complex and multifactorial pathological mechanism. While the role of the "microbiota-gut-brain axis" in neurocognition has garnered increasing attention, the specific ways in which gut microbiota and their derived metabolites might be associated with the development and progression of post-aSAH cognitive impairment remain largely undefined. Consequently, there remains a lack of systematic multi-omics evidence to elucidate these potential underlying associations.

METHODS: In this prospective observational study, we enrolled 48 patients with intracranial aneurysms. Among them, patients with aSAH (n = 33) were divided into a cognitive impairment group (aSAH-CI, n = 18) and a group without cognitive impairment (aSAH-WCI, n = 15) based on a 6-month longitudinal neurocognitive assessment. Patients with unruptured intracranial aneurysms (UIA, n = 15) served as the control group. We integrated a multi-omics approach encompassing fecal metagenomics, untargeted metabolomics, and serological profiles of inflammation, oxidative stress, and apoptosis to explore the potential correlations between the host and the microbiome, as well as to identify early diagnostic biomarkers.

RESULTS: Fecal metagenomics revealed distinct gut dysbiosis in aSAH-CI patients, characterized by reduced alpha diversity, depletion of beneficial commensals (e.g., Agathobacter), and expansion of opportunistic pathogens (e.g., Enterococcus). Functional and metabolomic analyses identified a significant alteration in aromatic amino acid biosynthesis. Specifically, tyrosine metabolism was altered, marked by reduced levels of neurotransmitter precursors and elevated neurotoxic trace amines (tyramine and phenylethylamine). Serologically, aSAH-CI patients exhibited heightened systemic inflammation, oxidative stress, and apoptosis. Integrated multi-omics network analysis underscored a strong correlation between elevated trace amines, depleted Agathobacter, and systemic pathological indices. Notably, Agathobacter rectalis and tyramine demonstrated robust potential as early diagnostic biomarkers for cognitive impairment following aSAH.

CONCLUSION: Our findings suggest a potential dual-hit correlative signature via the microbiota-gut-brain axis in cognitive impairment following aSAH. We hypothesize that the depletion of aromatic amino acid-producing microbiota correlates with reduced neurotransmitter precursors, theoretically impairing synaptic repair. Concurrently, observed associations among opportunistic pathogens, trace amines, and systemic inflammatory and oxidative stress markers suggest a synergistic effect potentially linked to further neuronal damage.},
}

@article {pmid42682792,
year = {2026},
author = {Lao, C and Li, Z and Lin, G and Li, C and Wang, Y},
title = {Employing Metagenomics Capture targeted next-generation sequencing for the etiological diagnosis of bloodstream infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905007},
pmid = {42682792},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; *Bacteremia/diagnosis/microbiology ; *Sepsis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; Bacteria/genetics/classification/isolation & purification ; Female ; Male ; },
abstract = {BACKGROUND: Bloodstream infections (BSIs) represent a significant public health concern. Metagenomic Capture targeted next-generation sequencing technology, as a newly emerging method for pathogen detection, has been applied in the etiological diagnosis of various infectious diseases and demonstrates good diagnostic efficacy. However, there is relatively limited research on the diagnostic value of this technology for the etiological diagnosis of BSIs.

METHODS: A comprehensive retrospective analysis was performed on patients suspected of having BSIs who were admitted to the Affiliated Guangdong Second Provincial General Hospital of Jinan University in 2024. These patients underwent both blood culture analysis and Metagenomic Capture targeted next-generation sequencing technology for diagnostic testing, and a detailed comparison of the results was conducted.

RESULTS: It was found that the Metagenomic Capture-targeted next-generation sequencing method has a shorter time to result [1.33 (1.18 - 1.69) vs 2.73 (1.89 - 3.84) days, p < 0.001], more pathogenic microbial species detected, higher positive detection rate and higher sensitivity than blood culture.

CONCLUSIONS: Metagenomic Capture targeted next-generation sequencing technology is a promising tool for pathogen identification in BSIs, offering substantial methodological advantages in terms of turnaround time, detection breadth, and sensitivity. These diagnostic performance characteristics support its potential utility in clinical microbiology practice.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Sensitivity and Specificity
*Bacteremia/diagnosis/microbiology
*Sepsis/diagnosis/microbiology
*Molecular Diagnostic Techniques/methods
Bacteria/genetics/classification/isolation & purification
Female
Male

@article {pmid42682809,
year = {2026},
author = {Gao, S and Song, L and Feng, Q and Li, Y and Liang, H and Lei, K and Li, Z and Kisembo, P},
title = {First case of neonatal bloodstream infection caused by Malassezia furfur in mainland China diagnosed via metagenomic next-generation sequencing: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {32},
number = {4},
pages = {267},
pmid = {42682809},
issn = {1792-1015},
abstract = {The present study reports, to the best of our knowledge, the first case of neonatal bloodstream infection caused by Malassezia furfur in mainland China identified using metagenomic next-generation sequencing (mNGS). Traditional microbiological methods have failed to identify causative organisms, highlighting the diagnostic limitations of neonatal sepsis with atypical presentations. Using this case as a clinical entry point, a systematic review was conducted to consolidate the epidemiological, clinical and prognostic characteristics of previously reported neonatal Malassezia infections and critically evaluate current diagnostic challenges. This case suggests the need to expand the pathogen spectrum of neonatal sepsis, particularly among extremely preterm and extremely low-birth-weight infants. Furthermore, it demonstrates the transformative potential of mNGS as an adjunctive diagnostic modality capable of identifying rare, fastidious organisms that evade conventional detection. Integrating mNGS into routine clinical workflows may not only facilitate early and precise pathogen identification but also redefine clinical decision-making paradigms in neonatal infectious disease management.},
}

@article {pmid42682910,
year = {2026},
author = {Jin, Y and Zhou, M and Gao, Y and Zhou, X and Tao, X},
title = {Lawsonella clevelandensis: a normal flora that bites deep.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1914466},
pmid = {42682910},
issn = {2235-2988},
mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; *Abscess/microbiology/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial ; },
abstract = {Since its formal description in 2016, Lawsonella clevelandensis-a strictly anaerobic, partially acid-fast bacterium-has been increasingly recognized as a cause of deep-seated abscesses, yet its fastidious nature and absence from routine diagnostic databases contribute to significant underdiagnosis. This narrative review synthesizes current knowledge on its microbiology, expanding clinical spectrum, diagnostic strategies, and treatment, based on a literature search of PubMed and Web of Science up to April 2026. Analysis of 27 documented publications, comprising 18 clinical cases, reveals a potential association with host risk factors including diabetes, immunosuppression, and prior surgical procedures, alongside a notable predilection for fat-rich tissues such as the breast and abdomen. While metagenomic next-generation sequencing and 16S rRNA gene amplification have become indispensable for definitive identification, antimicrobial susceptibility data-derived primarily from a single strain-demonstrate uniformly low minimum inhibitory concentrations for penicillins, carbapenems, clindamycin, and metronidazole, with no acquired resistance genes identified by whole-genome sequencing. However, the absence of established clinical breakpoints and limited tested isolates precludes definitive conclusions about universal susceptibility. Clinicians should maintain a high index of suspicion for L. clevelandensis in culture-negative deep abscesses, particularly those with acid-fast rods, as prompt diagnosis and empirical therapy with β-lactam/β-lactamase inhibitors or carbapenems appear reasonable based on current in vitro and clinical evidence, though further susceptibility surveillance is essential.},
}

Humans
Anti-Bacterial Agents/pharmacology/therapeutic use
RNA, Ribosomal, 16S/genetics
Microbial Sensitivity Tests
*Abscess/microbiology/diagnosis/drug therapy
High-Throughput Nucleotide Sequencing
Drug Resistance, Bacterial

@article {pmid42682993,
year = {2026},
author = {Wang, Y and Zhang, Y and Li, C and Liu, R and Zhang, S},
title = {Severity-stratified gut microbiome dysbiosis and systemic neuroinflammation in acute traumatic brain injury: a metagenomic and cytokine profiling study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1845360},
pmid = {42682993},
issn = {1664-302X},
abstract = {BACKGROUND: The gut-brain axis has increasingly been implicated in the pathophysiology of traumatic brain injury (TBI). However, few human studies have simultaneously examined gut functional metagenomics and peripheral cytokine profiles across mild to moderate-to-severe TBI, which limits our understanding of how gut health may influence recovery outcomes in TBI patients.

METHODS: This cross-sectional case-control investigation involved the collection of fecal and matched serum samples within 7 days post-injury from 60 mild TBI patients (MT; GCS 13-15), 45 moderate-to-severe TBI patients (MST; GCS ≤ 12), and 113 healthy controls (HC). Shotgun metagenomic sequencing examined gut microbiota. Serum IL-1β, IL-6, IL-8, and TNF-α were measured using a 4-plex Luminex test. Spearman correlation was utilized to construct a hypothesis relating cytokine levels to microbial severity-stratified abundance patterns.

RESULTS: TBI was associated with severity-dependent remodeling of the gut microbiota. Alpha diversity decreased from HC to MST (p < 10[-6]), and community structure varied significantly among all three groups (PERMANOVA, p = 0.001). Serum TNF-α increased in a severity-associated manner (MST vs. HC and MT, p adj < 0.015). Among 332 differentially abundant species, butyrate-producing commensals fell abruptly at MT with no additional decline in MST, suggesting an apparent floor-like pattern rather than confirming a true biological floor effect. For example, Faecalibacterium prausnitzii dropped from 9.02% in HC to 4.29% in MT. In terms of function, metagenomic inference indicated that pathways for fermentative metabolism and short-chain fatty acid (SCFA) biosynthesis were largely suppressed, suggesting a predicted reduction in microbial SCFA production capacity. On the other hand, secondary bile acid synthesis was specifically increased in MST-dominant KOs (85%). Systemically, reduced commensals showed weak, directionally consistent correlations with pro-inflammatory cytokines (|ρ| = 0.16-0.25), although none of the species-cytokine associations survived FDR correction.

CONCLUSION: Acute TBI is associated with severity-specific gut dysbiosis, which is accompanied by systemic neuroinflammation. The early reduction of butyrate-producing taxa in mild TBI suggests that the early post-injury period may represent a potential window for future gut-targeted intervention studies.},
}

@article {pmid42683082,
year = {2026},
author = {Khan, M and Patil, P and Rathored, J},
title = {Carbapenem-resistant Gram-negative pathogens: molecular epidemiology, diagnostic advances, and emerging therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1913726},
pmid = {42683082},
issn = {1664-302X},
abstract = {Carbapenem-resistant Gram-negative pathogens (CR-GNPs) have become an important global health problem, contributing significantly to healthcare-associated infections, extended hospital stays, high mortality rates, and higher healthcare costs. The dissemination of carbapenem resistance is mainly attributed to the spread of carbapenemase-encoding genes, such as the Klebsiella pneumoniae carbapenemase (KPC), the New Delhi metallo-β-lactamase (NDM), the Verona integron-encoded metallo-β-lactamase (VIM), the imipenemase (IMP), and the oxacillinase-48 (OXA-48)-like enzymes associated with clinically important Gram-negative pathogens, including Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. As well as carbapenemase production, resistance can also develop via alteration of porins, upregulation of efflux pumps, and the buildup of several resistance factors, generating highly adaptable and hard-to-treat microbes. Phenotypic resistance patterns may not predict the underlying mechanism and accurate laboratory detection remains challenging. The identification and monitoring of carbapenem-resistant organisms have undergone improvement in recent years thanks to molecular diagnostics, rapid phenotypic tests, whole-genome sequencing and metagenomics. At the same time, new drugs have been developed, such as ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol and combinations of aztreonam, offering increased treatment options, but with emerging resistance an issue. This mini review covers the molecular epidemiology of CR-GNPs, the latest developments and challenges in diagnosing these infections, new therapeutic options, and future perspectives on genomic surveillance, antimicrobial stewardship, and precision medicine strategies to address the increasing threat of carbapenem resistance.},
}

@article {pmid42683437,
year = {2026},
author = {Audemard, J and Creusot, N and Leloup, J and Duval, C and Halary, S and Mary, L and Eon, M and Forjonel, T and Mouffok, M and Puppo, R and Belmonte, E and Gautier, V and Got, J and Lefebvre, M and Markov, GV and Muller, C and Marie, B and Diémé, B and Frioux, C},
title = {Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivated Microcystis phycospheres.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag226},
pmid = {42683437},
issn = {2730-6151},
abstract = {Favored by global changes, freshwater cyanobacterial harmful blooms generate major ecological, economic, and public health challenges. Microcystis, one of the most widespread cyanobacterial genera, grows within a phycosphere where specialized interactions with its microbiome occur, that are suspected to influence bloom appearance and its potential toxicity. Using a combination of metagenomics, metabolomics, and metabolic modeling, we characterized the culture-associated phycospheres of 12 Microcystis strains isolated from a French pond. The distribution of metabolic reactions within Microcystis was consistent with their genospecies, whereas the metabolic landscape at the community level diverged from cyanobacterial phylogeny, indicating partial functional decoupling between cyanobacteria and their associated microbiomes. Bacteria associated with the simplified phycospheres substantially expanded the metabolic repertoire of the system, while maintaining functional redundancy within and across communities. On the other hand, endometabolomic profiles were largely driven by cyanobacterial metabolic outputs, whereas exometabolomic analysis did not reveal metabolites involved in exchange processes. Metabolic modeling, together with the identification of toxic specialized metabolites produced by specific biosynthetic gene clusters, further highlighted differences in metabolic potential among phycospheres. Together, these findings deepen the understanding of Microcystis' phycosphere functioning and demonstrate the value of multi-omics systems biology approaches, while suggesting that metabolic complementarity between species and across phycospheres could play a role in bloom-associated microbiome structure.},
}

@article {pmid42683603,
year = {2026},
author = {Fu, MX and Perdomo, MF and Lumley, SF and Ringlander, J and Kean, K and Reid, K and Mayne, R and Montaguth, OET and Forrest, L and Buddle, S and Botha, JC and Stenbäck, JB and Dickson, Z and Kent, C and Chai, H and Byott, M and Hannolainen, L and Secret, S and Airey, G and Hedman, K and Andersson, MI and Ansari, MA and Nastouli, E and Breuer, J and Matthews, PC and Golubchik, T and Irving, WL and Simmonds, P and Harvala, H},
title = {Next-Generation Sequencing Methods for Sensitive Hepatitis B Viral Genome Analysis: A European Study.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71130},
doi = {10.1002/jmv.71130},
pmid = {42683603},
issn = {1096-9071},
support = {NIHR203338//National Institute for Health and Care Research/ ; PG-23-0435//Svenska Sällskapet för Medicinsk Forskning/ ; GLS-1001038//Gothenburg Society for Medicine/ ; 220549/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; 220171/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; GNT2025445//National Health and Medical Research Council/ ; CC2223//Francis Crick Institute/ ; },
mesh = {*Hepatitis B virus/genetics/isolation & purification ; Humans ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Europe ; DNA, Viral/genetics/blood ; Viral Load ; *Hepatitis B/virology/diagnosis ; Metagenomics/methods ; Sensitivity and Specificity ; Polymerase Chain Reaction ; Genotype ; },
abstract = {This multicentre study investigated the utility of next-generation sequencing (NGS) to detect and generate hepatitis B virus (HBV) genomes in samples of low viral load (from 0.2 to 6207 IU/mL). 23 HBV DNA-positive plasma samples of genotypes A-E and one HBV-negative control sample were assayed blindly via 9 established NGS methods from 6 European laboratories. Methods included untargeted metagenomics, pre-enrichment by probe-capture followed by Illumina sequencing, and HBV-specific PCR pre-amplification followed by sequencing with Nanopore or Illumina. Full HBV genomes were obtained only from samples with viral loads > 1000 IU/mL using probe-capture methods, > 200 IU/mL using PCR-Illumina methods, > 10 IU/mL using PCR-Nanopore methods, and in no samples using metagenomic methods. Contamination was observed in the negative control and samples with very low viral loads in PCR-based methods. Probe-capture and metagenomic methods detected additional viruses not routinely screened in blood donations, including polyomaviruses and herpesviruses; positive results were confirmed by PCR. In conclusion, NGS may delineate whole-genome sequences at low viral loads if supported by a PCR pre-amplification step. Probe-capture methods also reliably detect HBV without pre-amplification but show limited genome coverage for samples with low viral loads; they may additionally detect a wide range of blood-borne viruses.},
}

*Hepatitis B virus/genetics/isolation & purification
Humans
*Genome, Viral
*High-Throughput Nucleotide Sequencing/methods
Europe
DNA, Viral/genetics/blood
Viral Load
*Hepatitis B/virology/diagnosis
Metagenomics/methods
Sensitivity and Specificity
Polymerase Chain Reaction
Genotype

@article {pmid42683728,
year = {2026},
author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G},
title = {Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725403},
doi = {10.1080/19490976.2026.2725403},
pmid = {42683728},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; Animals ; *Metagenome ; Mice ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Feces/microbiology ; Irritable Bowel Syndrome/therapy/microbiology ; Computer Simulation ; },
abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable and donor-selection strategies remain limited, in part because the role of donor‒recipient metabolic interactions in shaping the post-FMT community remains poorly understood. Here, we leverage metagenome-scale metabolic modeling to quantify metabolic niche complementarity between donor and recipient microbiomes and predict post-FMT community composition. Using MICOM-derived metabolic models, we show that donor genomes whose metabolic flux profiles are more dissimilar from the recipient community colonize at significantly higher rates in a murine FMT model. In a human IBS trial, the same metric predicted post-FMT community composition via leave-one-out cross-validation and captured known disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to evaluate personalized donor screening, identifying super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition. Together, these results support metabolic niche complementarity as a potential determinant of post-FMT community composition and provide a mechanistic basis for evaluating donor-recipient metabolic compatibility. This framework offers a scalable approach for generating testable hypotheses for personalized donor selection.},
}

*Fecal Microbiota Transplantation
Humans
Animals
*Metagenome
Mice
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Feces/microbiology
Irritable Bowel Syndrome/therapy/microbiology
Computer Simulation

@article {pmid42684052,
year = {2026},
author = {Chen, M and Grégoire, DS and Bain, JG and Blowes, DW and Hug, LA},
title = {Diverse microbial metal resistance and novel metal cycling organisms in copper/nickel mine tailings.},
journal = {Metallomics : integrated biometal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/mtomcs/mfag028},
pmid = {42684052},
issn = {1756-591X},
abstract = {Mine tailings contribute to environmental heavy metal contamination through the formation of acid mine drainage (AMD). Microbially-mediated processes such as iron and sulfur redox cycling influence metal mobility. Here, we applied an integrated metagenomic and metaproteomic approach to profile microbial communities across vertical geochemical gradients in legacy copper/nickel tailings in Sudbury, Ontario, Canada. From 43 samples, we recovered 454 non-redundant metagenome-assembled genomes (MAGs), revealing diverse populations within the Actinobacteriota, Desulfobacterota, and uncultured lineages such as Candidatus Eremiobacterota and SZUA-79. Functional profiling identified 301 putative iron- and sulfur-cycling MAGs, including those within the Ca. Eremiobacterota and SZUA-79 phyla. A custom set of Hidden Markov Models (HMMs) was used to annotate metal resistance genes, which were widespread and diverse, but whose abundances did not correlate with measured Cu, Ni, or Fe concentrations. This observation suggests that resistance traits are broadly encoded in these microbial communities regardless of environmental metal concentrations. Proteomic data confirmed in situ expression of selected metal resistance genes and iron/sulfur metabolism genes, although protein recovery was limited due to the difficult nature of mine tailings as an extraction matrix. Our findings highlight both the depth of microbial diversity in metal resistance and metal biogeochemical cycling in mining waste, as well as the technical challenges that currently limit genomic and proteomic sequencing coverage in low-biomass, metal-rich matrices.},
}

@article {pmid42684853,
year = {2026},
author = {Hassan, J and Matsuda, S and Ishii, E and Uda, T and Motooka, D and Iida, T},
title = {A plasmid-encoded T3SS underlies the virulence of enteropathogenic Providencia alcalifaciens strains isolated from a large foodborne outbreak in Japan.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0015126},
doi = {10.1128/iai.00151-26},
pmid = {42684853},
issn = {1098-5522},
abstract = {Providencia alcalifaciens is a gut commensal bacterium and also an emerging enteric pathogen associated with sporadic infections and outbreak cases in humans. The most notable outbreak caused by this bacterium occurred in 1996 in Fukui Prefecture, Japan, affecting 270 individuals. However, the pathogenic mechanisms responsible for this outbreak remain unknown. In this study, we identified the key virulence determinants of the Fukui outbreak strains through genomic and functional analyses. These strains uniquely carry a ~162 kb large plasmid encoding a type III secretion system (T3SS) closely homologous to the Salmonella SPI-1 T3SS. We also show that the plasmid-encoded T3SS (T3SSp) constitutes a functional secretion system and is essential for the pathogenicity of the Fukui outbreak strain, including the invasion of cultured epithelial cells and the induction of diarrhea in a rabbit model. Secretome analysis identified effectors secreted in a T3SSp-dependent manner, among which PipA-sharing limited sequence similarity with SipA, a SPI-1 T3SS effector-plays a crucial role in inducing diarrhea. Ectopic expression of PipA in HeLa cells caused focal accumulation of F-actin, indicating its cytoskeleton-modulating activity. Comparative genomics with other Providencia species revealed the dissemination of the large plasmid, with structural variations among enteropathogenic strains of P. alcalifaciens and Providencia rustigianii associated with clinical cases in humans and animals. Thus, our findings underscore the molecular basis of P. alcalifaciens pathogenicity in the Fukui outbreak and highlight the significance of the large plasmids encoding T3SS in driving pathogenic evolution among Providencia species.},
}

@article {pmid42684889,
year = {2026},
author = {Mueller, NT and Xiao, S and Liu, T and Debelius, J and Kress, AM and Zhao, N and Moore, B and McKee, KS and Jacobson, LP and Comstock, SS and , },
title = {Mother-infant sharing of gut and vaginal microbes at the species and strain level.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117920},
doi = {10.1016/j.celrep.2026.117920},
pmid = {42684889},
issn = {2211-1247},
abstract = {Mother-to-offspring microbial transmission is a foundational process for seeding the infant gut microbiome, yet the relative contributions of maternal body sites and the influence of birth delivery mode remain incompletely understood. We use shotgun metagenomic sequencing in 68 mother-infant dyads to investigate species- and strain-level sharing of the maternal gut and vaginal microbiomes with the infant gut during the first year of life. At 2-4 months of age, infants share an average of 35% of species with their mother's microbiomes, with markedly greater sharing from the maternal gut than the vagina. Vaginally delivered infants exhibit higher levels of sharing than those born by cesarean section (C-section). Strain-level analyses reveal persistent mother-infant transmission across multiple Bacteroides and Bifidobacterium species genome bins, with strain-sharing frequencies varying by species and birth mode. C-section reduces the extent of mother-infant species- and strain-level sharing.},
}

@article {pmid42685246,
year = {2026},
author = {Lei, S and Qiu, X and Wang, Z and Zhang, Z and Zha, A and Zhou, Y and Chen, H and Huang, J and Yu, Z},
title = {Gut microbial H2S promotes metabolic dysfunction in mice via hepatic PPARα suppression.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag226},
pmid = {42685246},
issn = {1751-7370},
abstract = {This study investigates the role of gut microbiota-derived hydrogen sulfide (H2S) in obesity and glucose metabolism disorders. By integrating human gut metagenomic data, intervention experiments in mouse models, and in vitro cellular assays, we identified a signature of microbial sulfur metabolism in human cohorts and provided experimental evidence for its causal role and underlying metabolic mechanisms in mice. In clinical cohorts with obesity and glucose metabolism disorders, we observed a notable enrichment of genes involved in sulfur transport and H2S production. In mouse models, administration of H2S-producing Desulfovibrio desulfuricans, engineered Escherichia coli expressing phsABC, and the H2S donor NaHS consistently induced body weight gain and impaired glucose tolerance. Transcriptome analysis and cellular experiments indicated that H2S was associated with downregulation of the PPAR signaling pathway and lipid metabolism pathways in the liver, which may contribute to the abnormal accumulation of lipids and glycogen. Furthermore, rescue experiments using a PPAR agonist and an H2S adsorbent partially reversed these metabolic abnormalities. Collectively, our work provides experimental evidence in mouse models demonstrating that gut microbial H2S promotes metabolic dysfunction through hepatic PPARα suppression, providing potential targets for microbiome-based therapeutic interventions.},
}

@article {pmid42341325,
year = {2026},
author = {Young, G and Angchaisuksiri, P and Apte, S and Frandsen, RB and Chan, AKC and Chowdary, P and Eichler, H and Lyu, CJ and Martinez Garcia, MF and Matsushita, T and Trakymienė, SŠ and Tran, H and Trinchero, A and Windyga, J and Astermark, J},
title = {Concizumab in patients with hemophilia A or B without inhibitors: 56-week cutoff results of the phase 3 explorer8 study.},
journal = {Blood advances},
volume = {10},
number = {17},
pages = {6032-6042},
doi = {10.1182/bloodadvances.2026019931},
pmid = {42341325},
issn = {2473-9537},
mesh = {Humans ; Male ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacokinetics/adverse effects/administration & dosage/pharmacology ; *Hemophilia A/drug therapy/blood ; Adult ; *Hemophilia B/drug therapy/blood ; Adolescent ; Treatment Outcome ; Young Adult ; },
abstract = {Concizumab is a novel nonfactor replacement therapy for once-daily subcutaneous prophylactic treatment of hemophilia A/B (HA/HB) with and without inhibitors. Concizumab was superior to on-demand treatment in patients with HA/HB without inhibitors in the prospective, multicenter, open-label phase 3 explorer8 study. Here, longer-term efficacy and safety results from the start of the study up to the 56-week cutoff are presented. Males aged ≥12 years with HA/HB were randomized 1:2 to no prophylaxis (group 1) or concizumab (group 2) or allocated to concizumab (groups 3 and 4). Assessments at the 56-week cutoff included efficacy, pharmacokinetics/pharmacodynamics, and safety. The 56-week cutoff was defined as when all patients in groups 2 to 4 had completed the visit at 56 weeks or permanently discontinued treatment. Of 148 patients in the full analysis set, 21 were randomized to no prophylaxis (group 1: HA, n = 9; HB, n = 12), 42 to concizumab (group 2: HA, n = 18; HB, n = 24), and 85 to the nonrandomized concizumab groups (groups 3 and 4: HA, n = 55; HB, n = 30). After ≥24 weeks of treatment, 17 patients in group 1 switched to concizumab. Low median annualized bleeding rates for treated spontaneous and traumatic bleeding episodes were maintained at the 56-week cutoff in patients receiving concizumab (HA, 1.7 [interquartile range (IQR), 0.0-4.5]; HB, 2.8 [IQR, 0.0-6.4]), consistent with 32-week cutoff results. Concizumab plasma concentration remained stable, with no new safety concerns. Concizumab showed longer-term efficacy in patients with HA/HB at the 56-week cutoff and was considered safe and well tolerated. This trial was registered at www.clinicaltrials.gov as #NCT04082429.},
}

Humans
Male
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacokinetics/adverse effects/administration & dosage/pharmacology
*Hemophilia A/drug therapy/blood
Adult
*Hemophilia B/drug therapy/blood
Adolescent
Treatment Outcome
Young Adult

@article {pmid42673797,
year = {2026},
author = {Li, L and Zhang, Z and Pang, H and Yang, J and Liu, Y and Lu, J},
title = {Antipyretic pharmaceuticals intensify sewer H2S accumulation linked to biofilm matrix remodeling and altered sulfur metabolic potential.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143343},
doi = {10.1016/j.jhazmat.2026.143343},
pmid = {42673797},
issn = {1873-3336},
abstract = {Pharmaceuticals enter sewer systems before wastewater treatment, but their role in hazardous gas accumulation remains poorly understood. This study used long-term gravity sewer reactors to examine how acetaminophen (APAP) and ibuprofen (IBU) affect headspace hydrogen sulfide (H2S) accumulation, the properties of extracellular polymeric substances (EPS), and microbial functional potential in sewer biofilms. Both pharmaceuticals changed H2S from a stable baseline to a staged pattern with early suppression followed by accumulation above the control level. IBU showed earlier and higher H2S peaks than APAP, with the peak under 500 μg/L IBU exceeding that under 5000 μg/L APAP. Pharmaceutical exposure depleted extracellular proteins, enriched polysaccharides and humic acid, and promoted the retention of matrix-forming components in tightly bound EPS. QCM-D analysis showed marked decreases in |ΔD/ΔF| from 0.35 in the control to 0.03 and 0.09 under 5000 μg/L APAP and IBU exposure, respectively, indicating EPS interfacial rigidification. Metagenomic profiling further indicated reduced flagellar assembly, enhanced attachment-related potential, increased dsrA/B-associated terminal sulfite reduction potential, and reduced sulfide oxidation potential. These findings suggest that enhanced sewer H2S accumulation under antipyretic pharmaceutical exposure is associated with EPS interfacial rigidification and shifts in sulfur metabolic potential. These results identify antipyretic pharmaceuticals as underrecognized biofilm-structuring stressors associated with intensified sewer H2S accumulation and altered sulfur metabolic potential.},
}

@article {pmid42673827,
year = {2026},
author = {Du, Q and Xu, R and Qin, Y and Cai, X and Zhan, C and Song, Z and Yu, L and Wang, Z and Li, C and Tang, Z and Li, Y and Wang, S and Zhu, G},
title = {Elevated water levels drive greenhouse gas mitigation in the riparian zone profile.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130803},
doi = {10.1016/j.jenvman.2026.130803},
pmid = {42673827},
issn = {1095-8630},
abstract = {Wetlands are critical for climate regulation, with their hyporheic zone serving as sensitive interfaces for groundwater-soil-atmosphere exchange. These zones are active hotspots for carbon-nitrogen cycling and greenhouse gas (GHG) emissions (CO2, CH4, N2O), yet the impact of water level fluctuations on these emissions and their microbial drivers in freshwater wetlands remains poorly understood. This study investigated the spatiotemporal dynamics of GHG emissions and carbon-nitrogen coupling processes along riparian soil profiles of Baiyangdian Lake during water level fluctuations. Employing static chamber measurements, microcosms, quantitative PCR, Metagenome-Assembled genome (MAG) analyses, and Structural Equation Modeling (SEM), we observed that GHG emissions were significantly affected by water level fluctuations. Specifically, CO2 and N2O fluxes, as well as CO2 production potential were significantly lower at high-water-level conditions. Water level also emerged as a key driver of microbial community structure, with Methylococcaceae and Methanosarcinaceae as key regulators of CH4 emission, and Anaeromyxobacteraceae as central to N2O dynamics. A high-quality Methylomirabilales-like MAG, possessing the complete pathway for coupled nitrate reduction and methane oxidation, was identified. Its abundance negatively correlated with water level, suggesting that these C-N coupling bacteria contribute to reducing GHG emissions. This study provides crucial theoretical insights and identifies microbial targets for mitigating wetland GHG emission through hydrological management.},
}

@article {pmid42673922,
year = {2026},
author = {Ning, J and Du, Y and Deng, B and Li, M and Wu, T and Lin, L and Yu, T and Gan, Y and Si, D and Zhang, W and Wang, Y},
title = {Seasonal dynamics of geogenic phosphorus in alluvial-lacustrine aquifers: Coupling of phosphorus-containing dissolved organic matter and microbes as a key driver.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126797},
doi = {10.1016/j.watres.2026.126797},
pmid = {42673922},
issn = {1879-2448},
abstract = {Geogenic phosphorus (P) enrichment in groundwater driven by dissolved organic matter (DOM) degradation has been well documented worldwide but remains underexplored regarding temporal dynamics. As microbial metabolism regulates P-containing DOM mineralization, resolving seasonal shifts in microbial strategies is essential for clarifying geogenic P mobilization. In this study, seasonal field monitoring was integrated with molecular DOM characterization and metagenomic analyses to elucidate the coupling among geogenic P, P-containing DOM, and microbial functional pathways. Dissolved inorganic phosphorus (DIP) fluctuations were controlled by a degradation gradient of P-containing DOM and concurrent adjustments in microbial metabolism. The seasonal oxidant influx from dry to wet seasons modified redox conditions and promoted the transformation of high-molecular-weight humic substances into low-molecular-weight polar compounds, thereby weakening the microbial degradation of P-containing DOM and reducing DIP enrichment. Meanwhile, microbial P metabolism shifted from multi-pathway degradation involving dephosphorylation and C-P bond cleavage to a single dominant dephosphorylation pathway. These findings indicate that seasonal redox dynamics restructure microbial metabolic strategies and ultimately regulate temporal DIP enrichment in groundwater system.},
}

@article {pmid42674139,
year = {2026},
author = {Jiang, K and Pan, X and Zhu, S and Dang, Z and Yang, Z and Huang, L and Pan, X and Zou, X and Zhang, J and Guo, Y and Zhang, W and Li, Z and Cong, X and Wang, Z},
title = {Cellulose/polyester-blended microplastics amplify plastisphere pathogen and antibiotic resistome risks.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135752},
doi = {10.1016/j.biortech.2026.135752},
pmid = {42674139},
issn = {1873-2976},
abstract = {Microplastics (MPs) are important vectors for antibiotic resistance genes (ARGs) in anaerobic digestion systems, yet the risks posed by cellulose/polyester-blended materials remain poorly understood. In this study, commercial airlaid paper (AP; 45 % cellulose and 55 % polyester), polyethylene (PE), polypropylene (PP), and polystyrene (PS) were incubated in anaerobic reactors for 60 days. Biofilm characterization, extracellular polymeric substances (EPS) analysis, 16 S rRNA sequencing, and metagenomics were used to compare plastisphere formation, microbial assembly, ARG/mobile genetic element (MGE) profiles, and potential pathogen composition. Owing to its fibrous structure and bioavailable cellulose fraction, AP exhibited the highest biofilm biomass and EPS content. In contrast, PE, PP, and PS induced stronger interfacial stress, especially PS, as indicated by increased reactive oxygen species, lactate dehydrogenase release, and enrichment of oxidative stress, SOS response, and multidrug efflux pump related genes. Metagenomic analysis showed that fully synthetic MPs mainly enriched multidrug resistance genes, whereas AP selectively enriched polymyxin resistance genes, particularly Mcr-5.1 and Mcr-5.2. AP also exhibited the highest ARG-MGE co-localization rate (12.7 %) and antibiotic resistance risk. Overall, these findings identify polymer composition as a key factor shaping plastisphere resistome assembly and indicate that cellulose/polyester-blended materials require specific consideration in sludge-associated antimicrobial resistance risk assessments.},
}

@article {pmid42674950,
year = {2026},
author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H},
title = {Retraction notice to "A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic" [Sci. Total Environ. 930 (2024) 172601].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {182281},
doi = {10.1016/j.scitotenv.2026.182281},
pmid = {42674950},
issn = {1879-1026},
}

@article {pmid42674953,
year = {2026},
author = {Bilal, M and Wang, Z and Cui, J and Ferreira, LFR and Bharagava, RN and Iqbal, HMN},
title = {Retraction notice to "Environmental impact of lignocellulosic wastes and their effective exploitation as smart carriers - A drive towards greener and eco-friendlier biocatalytic systems" [Sci. Total Environ. 722 (2020) 137903].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {182284},
doi = {10.1016/j.scitotenv.2026.182284},
pmid = {42674953},
issn = {1879-1026},
}

@article {pmid42675165,
year = {2026},
author = {Villada, JC and Vasquez, YM and Szabó, G and Whittaker-Walker, E and Romero, MF and Qin, S and Varghese, N and Eloe-Fadrosh, EA and Kyrpides, NC and , and Visel, A and Woyke, T and Schulz, F},
title = {A genomic catalog of Earth's bacterial and archaeal symbionts.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42675165},
issn = {1546-1696},
support = {https://ror.org/04xm1d337//DOE | Office of Science (SC)/ ; https://ror.org/04xm1d337//DOE | Office of Science (SC)/ ; },
abstract = {Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges. This study used machine learning (ML) to predict symbiotic lifestyles in more than a hundred thousand microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, an ML framework developed to identify genomic signatures of symbionts. Predictions were deposited in a catalog we established called Symbiont Genomes (SymGs). The results indicate that 15-23% of uncultivated microorganisms likely engage in symbiotic relationships with other organisms, categorized as host-associated or obligate intracellular lifestyles, and are present in half of all known bacterial and archaeal phyla. We also identify genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of metabolic modules that may enable host-dependent living. The symclatron software and the SymGs catalog represent valuable resources for studying symbioses, potentially facilitating future mechanistic investigations and engineering of host-microorganism associations.},
}

@article {pmid42675216,
year = {2026},
author = {Gong, J and Muranaka, H and Choi, SY and Tighiouart, M and Bhute, S and Aja, ER and Jacobs, JP and Stotland, A and Van Eyk, J and Elmadbouh, OHM and Edderkaoui, M and Tanaka, S and Furuya, H and Osipov, A and Lorber, J and Billet, S and Morris, A and Ten Hoeve-Scott, J and Graeber, T and Pandol, SJ and Hendifar, A and Bhowmick, NA},
title = {L-Glutamine in combination with first-line gemcitabine and nab-paclitaxel in advanced pancreatic ductal adenocarcinoma: an open-label, single-arm, phase 1 GlutaPanc trial.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {42675216},
issn = {2662-1347},
support = {UL1 TR001881-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P01CA233452//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; CA232859-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P01CA233452//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P01CA233452//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Exogenous L-glutamine has preclinical antitumor activity although formal clinical translation has not been attempted. We conducted a single-arm phase 1 trial to assess the safety and preliminary efficacy of clinical-grade, US Food and Drug Administration-approved L-glutamine therapy with gemcitabine and nab-paclitaxel (GA) in participants with treatment-naive, advanced pancreatic cancer (n = 16). The primary endpoint was to determine the recommended phase 2 dose (RP2D) by adaptive Bayesian design across standard doses of GA and a dose range of 0.1-0.3 g kg[-1] twice-daily oral L-glutamine. Secondary endpoints included safety and preliminary efficacy of the study combination. The primary endpoint was met with the RP2D reached at maximum doses of L-glutamine and GA. The grade ≥3 treatment-related adverse event rate was 66.7%, primarily from GA. Addition of L-glutamine to GA induced tumor shrinkage in 94% of subjects with a best overall response rate (ORR) of 44% (12.5% complete response). Median progression-free survival and overall survival (OS) were 8.5 months (95% confidence interval (CI) 6-not reached (NR)) and 22 months (95% CI 11-NR), respectively. L-Glutamine induced distinct metagenomic and metabolomic signatures on exploratory analyses in glutamine-treated subjects as a single agent, while the combination of L-glutamine and GA nearly doubled the ORR and tripled the OS compared to historical GA alone (ClinicalTrials.gov registration: NCT04634539).},
}

@article {pmid42675508,
year = {2026},
author = {Guo, W and Yu, Y and Wang, W and Yu, J and Zhou, M and Long, R},
title = {Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42675508},
issn = {1674-9782},
support = {32402705//National Natural Science Foundation of China/ ; XZ202502ZY0058//Science and Technology Projects of Xizang Autonomous Region, China/ ; },
abstract = {BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons.

RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes.

CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.},
}

@article {pmid42675564,
year = {2026},
author = {Akyol, CK and Bilaç, Ö and Çam, FS},
title = {Does the Gut Microbiota Play a Role in Attention-Deficit/Hyperactivity Disorder in Childhood? A Pilot Study From Turkey.},
journal = {Developmental neurobiology},
volume = {86},
number = {4},
pages = {e70057},
doi = {10.1002/dneu.70057},
pmid = {42675564},
issn = {1932-846X},
support = {2022-146//Manisa Celal Bayar University Scientific Research Projects Coordination Unit/ ; },
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology ; Male ; Pilot Projects ; *Gastrointestinal Microbiome/physiology ; Turkey ; Female ; Child ; Feeding Behavior/physiology ; Sleep/physiology ; },
abstract = {The pathophysiology of attention-deficit/hyperactivity disorder (ADHD) is not fully understood, but increasing evidence suggests that gut microbiota may play a role. This study compared the gut microbiota of children with ADHD with that of a control group of healthy children, and examined their dietary and sleep habits. Ten medication-naïve children aged 612 years who had recently been diagnosed with ADHD and ten healthy controls were included. ADHD diagnoses were confirmed using the Schedule for Affective Disorders and Schizophrenia for School-Age ChildrenPresent and Lifetime Version (K-SADS-PL). Sleep and eating habits were assessed using the 2nd Level Sleep Disorder Short Form, the Children's Eating Behaviour Inventory, and a form to collect sociodemographic and clinical information. The gut microbiota were analysed using 16S NGS metagenome analysis. A significant decrease in the Shannon and Simpson diversity index values was observed in the ADHD group compared to the control group. Despite the presence of a percentage difference, no statistically significant differences were observed between the groups with respect to species, genus, family, order, class or phylum. Following evaluation of the sleep and eating habit scale scores, no statistically significant difference between the groups was determined.These findings suggests that children with ADHD may alter gut microbiota diversity.However, the absence of significant taxonomic differences and the small sample size mean that these results should be interpreted with caution. Further, larger, adequately powered studies are needed to validate these findings and clarify the potential role of gut microbiota in the pathophysiology of ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology
Male
Pilot Projects
*Gastrointestinal Microbiome/physiology
Turkey
Female
Child
Feeding Behavior/physiology
Sleep/physiology

@article {pmid42675742,
year = {2026},
author = {Shaikh, SS and Malek, F},
title = {Healthy subjects gut microbiome modulation by Bacillus coagulans BCP92: A randomized, double-blind, placebo-controlled clinical trial.},
journal = {Medicine},
volume = {105},
number = {35},
pages = {e50435},
doi = {10.1097/MD.0000000000050435},
pmid = {42675742},
issn = {1536-5964},
mesh = {Humans ; *Probiotics/administration & dosage ; *Bacillus coagulans/physiology ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Male ; Adult ; Fatty Acids, Volatile/analysis/metabolism ; Female ; Healthy Volunteers ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: Probiotics are recognized for their ability to restore balance in the gut microbiome during dysbiosis. However, their effects on the gut microbiota of healthy individuals have rarely been investigated. This study aimed to evaluate the safety and efficacy of Bacillus coagulans (Heyndrickxia coagulans) BCP92 and its influence on microbiota composition in healthy subjects.

METHODS: In the present investigation, healthy participants (n = 48) were allocated into 2 groups and administered either Bacillus coagulans BCP92 capsules (1 billion CFU/capsule) or a placebo containing maltodextrin for 42 days. Microbiome composition and short-chain fatty acid analyses were subsequently conducted.

RESULTS: Analysis of metagenomes showed no major alterations in gut microbiome composition among participants who received B. coagulans BCP92 supplementation. However, subtle beneficial changes were observed in the treatment group, suggesting that probiotic administration may increase advantageous phyla, classes, orders, families, and some genera, while decreasing potentially harmful groups. A slight increase in short-chain fatty acids (SCFA) was also observed in the fecal samples.

CONCLUSIONS: This study implies that extended supplementation with the probiotic B. coagulans BCP92 may lead to substantial improvements in gut microbiome composition and SCFA levels.},
}

Humans
*Probiotics/administration & dosage
*Bacillus coagulans/physiology
Double-Blind Method
*Gastrointestinal Microbiome/drug effects
Feces/microbiology/chemistry
Male
Adult
Fatty Acids, Volatile/analysis/metabolism
Female
Healthy Volunteers
Young Adult
Metagenome

@article {pmid42675750,
year = {2026},
author = {Chang, K and Xie, H and Wang, Y and Zhao, X and Na, W and Xian, N and Liu, Y and Jiang, Z and Liu, C},
title = {An Aspergillus luchuensis isolated from a patient with hemoptysis insights from a comprehensive genome-based analysis: Case report.},
journal = {Medicine},
volume = {105},
number = {35},
pages = {e50486},
doi = {10.1097/MD.0000000000050486},
pmid = {42675750},
issn = {1536-5964},
support = {2026434//Chengdu Medical Research Project/ ; 2022346//Chengdu Medical Research Project/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Hemoptysis/microbiology/etiology ; Antifungal Agents/therapeutic use ; *Aspergillus/genetics/isolation & purification/pathogenicity ; *Invasive Pulmonary Aspergillosis/microbiology/drug therapy/diagnosis ; Voriconazole/therapeutic use ; Tomography, X-Ray Computed ; Amphotericin B/therapeutic use ; },
abstract = {RATIONALE: Asp luchuensis, a member of the A niger group, is widely used in food fermentation and rarely causes invasive pulmonary aspergillosis (IPA) in humans. Clinical cases of IPA induced by this strain are extremely scarce, and its genomic characteristics, virulence profiles, and pathogenic mechanisms remain poorly understood, resulting in insufficient clinical recognition of its invasive infection potential.

PATIENT CONCERNS: A 57-year-old immunocompetent non-neutropenic male patient with a long-term smoking and drinking history presented with unexplained severe cough and massive hemoptysis (approximately100 mL) without other typical infectious symptoms.

DIAGNOSES: Combined with chest computed tomography (CT) inflammatory lesions, positive galactomannan test, fungal PCR and metagenomic next-generation sequencing results, the patient was definitively diagnosed with probable A luchuensis-induced IPA. Genomic and transcriptomic analyses confirmed the pathogen as a variant A luchuensis strain with 3 key hypervirulence genes, highly active mitochondrial energy metabolism, and no specific antifungal resistance genes.

INTERVENTIONS: The patient received standardized intravenous antifungal combination therapy with voriconazole and amphotericin B after confirmed diagnosis.

OUTCOMES: The patient's cough and hemoptysis were significantly relieved after 10 days of treatment, with stable vital signs and no adverse drug reactions or disease progression.

LESSONS: A luchuensis possesses strong invasive pathogenicity and can trigger IPA even in non-neutropenic immunocompetent individuals. Negative conventional microbial tests cannot exclude its infection, and mNGS is a reliable diagnostic tool. This strain is susceptible to routine antifungal drugs, and clinicians should raise awareness of atypical Asp species-induced invasive pulmonary infections.},
}

Humans
Male
Middle Aged
*Hemoptysis/microbiology/etiology
Antifungal Agents/therapeutic use
*Aspergillus/genetics/isolation & purification/pathogenicity
*Invasive Pulmonary Aspergillosis/microbiology/drug therapy/diagnosis
Voriconazole/therapeutic use
Tomography, X-Ray Computed
Amphotericin B/therapeutic use

@article {pmid42676636,
year = {2026},
author = {Sabti, O and Lialin-Tzadikov, K and Ivanova, V and Dori-Bachash, M and Uzi-Gavrilov, S and Tik, Z and Mashiach, R and Zorea, A and Mizrahi, I and Segal, A and Moyal-Attias, K and Elinav, E and Meijler, MM},
title = {Disrupted terminal bilirubin catabolism links Lachnospiraceae depletion to inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1871609},
pmid = {42676636},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome mediates the reductive catabolism of bilirubin into urobilinoids, yet the bacteria and enzymes responsible for the later steps of this pathway remain largely unknown.

METHODS: Here, we combine untargeted UPLC/HRMS metabolomics with shotgun metagenomic sequencing of fecal samples from 119 participants, including patients with Crohn's disease, ulcerative colitis, and healthy controls, to map disruptions in the bilirubin catabolic pathway in inflammatory bowel disease (IBD).

RESULTS: We show that stercobilinogen and stercobilin, the terminal metabolites of this pathway, are depleted (p < 0.01) in IBD patients irrespective of disease subtype, while upstream intermediates, D-urobilinogen, remain unchanged. This metabolic bottleneck coincides with a marked reduction in members of the Lachnospiraceae family, specifically Blautia sp. SG-772 and three uncharacterized species, which show strong positive correlations with stercobilinogen and stercobilin levels.

DISCUSSION: These findings implicate Lachnospiraceae as key mediators of the yet unknown enzymatic conversion of I-urobilinogen to stercobilinogen, extending the family's known metabolic repertoire beyond short-chain fatty acid production. Given that bilirubin and its reduced metabolite stercobilinogen possess antioxidant properties, their depletion may contribute to the oxidative burden in the IBD gut. Conversely, the concurrent elevation of D-urobilin, which lacks these protective properties and has been linked to metabolic dysfunction in other contexts, may further exacerbate inflammation. Our results identify fecal bilirubin metabolites as candidate biomarkers of microbial dysbiosis in IBD and nominate specific Lachnospiraceae taxa for functional characterization of the missing stercobilinogen reductase.},
}

@article {pmid42676837,
year = {2026},
author = {Xia, Y and Peng, S and Yu, J and Wang, Y and Ye, Y and Liu, M and Shang, L and Cui, X and Wang, P and Ding, Z},
title = {Severity-dependent alterations in oral microbiota and antibiotic resistance in children with dental fluorosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2714622},
pmid = {42676837},
issn = {2000-2297},
abstract = {BACKGROUD: Dental fluorosis is a prevalent endemic condition, yet its impact on the oral microbiota structure and resistance in children remains understudied.

OBJECTIVE: To assess the microbial composition, diversity, functional pathways and co-occurrence patterns among urinary fluoride (UF), bacterial taxa and antibiotic resistance genes in relation to fluorosis severity. Design: Metagenomic analysis of dental plaque was conducted on 96 school-aged children, who were grouped into normal, dubious, very mild, mild, moderate and severe base on fluorosis severity.

RESULTS: Microbial diversity increased with fluorosis severity. Actinomyces sp. HMT 175, Actinomyces oris and Corynebacterium matruchotii, Fusobacterium nucleatum and Rothia dentocariosa were significantly enriched in the moderate and severe groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed a reduced relative abundance of genes involved in carbohydrate metabolism and genetic information processing in moderate and severe groups. Network analysis revealed positive correlations among Actinomyces sp. HMT 175, UF levels and GRD33_1 (a carbapenem resistance gene).

CONCLUSIONS: These findings highlight severity-dependent shifts in the oral microbiota and resistance, warranting further investigation into fluoride's public health implications.},
}

@article {pmid42677031,
year = {2026},
author = {Ceja-Navarro, JA and Patel, D and Genco, G and Byer, A and Ning, D and Wan, KH and Celniker, SE and Zhou, J and Dijkstra, P and Hungate, BA and Pett-Ridge, J and Brodie, EL},
title = {Ecosystem retrogression enhances cross-domain microbial stability and increases the genetic potential for nutrient cycling.},
journal = {mLife},
volume = {5},
number = {4},
pages = {486-506},
pmid = {42677031},
issn = {2770-100X},
abstract = {Ecosystem retrogression drives nutrient depletion, reduced productivity, and profound reorganization of soil microbial communities. Using amplicon sequencing and genome-resolved metagenomics, we examined how cross-domain microbial networks and functional gene potential respond to long-term phosphorus and nitrogen limitation along the well-characterized Ecological Staircase chronosequence in Mendocino, California, USA. Microbial diversity and abundance declined sharply with terrace age for prokaryotes, predatory protists, and bacteriophages, whereas fungi and phototrophic protists increased in nutrient-depleted, acidic soils. These compositional shifts were accompanied by major changes in reconstructed microbial networks: relative modularity increased alongside robustness, indicating adaptive reorganization that may sustain ecosystem function under resource scarcity. Fungi emerged as central stabilizers in these restructured networks, carrying enriched genetic potential to degrade plant polymers and mobilize phosphorus and nitrogen. Despite a decline in overall phage diversity, the relative abundance of phages encoding phosphorus-mobilizing auxiliary metabolic genes increased, suggesting that viral contributions to host phosphorus metabolism may be enhanced under nutrient limitation. Together, these results demonstrate that ecosystem retrogression drives cross-domain microbial reorganization toward fewer but more interconnected lineages, characterized by greater integration of functional genetic potential. This reorganization enhances the potential for functional resilience under extreme nutrient limitation, revealing how microbial networks adapt to maintain the capacity for nutrient cycling and stability as soils age and fertility declines.},
}

@article {pmid42677317,
year = {2026},
author = {Daniel, SG and Matute, JD and Dhudasia, MB and Rosewood, H and Wilson, NG and Patterson, A and Hao, F and Underwood, M and Bittinger, K and Mukhopadhyay, S},
title = {Gut microbiome in preterm infants with different weight gain outcomes.},
journal = {Gut microbiology},
volume = {2},
number = {},
pages = {},
pmid = {42677317},
issn = {3051-1720},
abstract = {BACKGROUND: Inadequate in-hospital weight gain among very low birth weight (VLBW; <1500g) infants is associated with adverse outcomes. Although microbiome alterations are linked to malnutrition in older children, their association with VLBW weight gain outcomes remains unclear.

OBJECTIVE: To evaluate associations between fecal microbiome composition, functional gene pathways, and metabolomic profile, and abnormal weight gain in VLBW infants.

METHODS: Prospective cohort study of VLBW infants from birth to hospital discharge with weekly fecal sampling. Inadequate weight gain was defined at 36 weeks post-menstrual age, as growth faltering (decline in weight-for-age z-scores from birth) and growth failure (<3[rd] percentile weight-for-age). Growth faltering was categorized as mild (0.8-1.2 decline) and moderate-severe (>1.2 decline). Fecal samples underwent shotgun metagenomic sequencing with KEGG-based functional annotation; [1]H NMR-based metabolomics was performed in a subset.

RESULTS: Among 101 enrolled infants, 54% had growth faltering (28 mild; 26 moderate-severe), and 18% had growth failure. The two outcomes rarely co-occurred (n=7). Microbiome diversity and taxonomic composition changed with age but did not differ by growth outcomes. Infants with moderate-to-severe faltering had reduced abundance of the glycolysis/gluconeogenesis pathway. Infants with growth failure showed a significant lag in microbiome maturity. Metabolite concentrations measured in a subset (n=46) were not significantly different in the study groups.

CONCLUSION: Abnormal weight gain in VLBW infants was not associated with major differences in microbial compositional or fecal metabolite levels. Differences identified in pathway analysis and in microbiome maturation may help focus future efforts to investigate the gut microbiome's role in VLBW weight gain.},
}

@article {pmid42677482,
year = {2026},
author = {Wu, Q and Xu, X and Guo, Y and Li, H and Hao, Y and Zhang, Z and Cai, Z and White, JC and Ma, C},
title = {Nano-boron nitride enhances soybean growth and symbiotic nitrogen fixation by modulating the rhizosphere microbiome and biogeochemical cycling.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6nr02400a},
pmid = {42677482},
issn = {2040-3372},
abstract = {Nanotechnology offers promising strategies for sustainable agriculture, yet the systemic mechanisms by which nanomaterials enhance legume nitrogen fixation remain insufficiently understood. The multi-scale impacts of nano-boron nitride (nano-BN) on soybean growth, biological nitrogen fixation, and rhizosphere microbial communities were investigated. Soil addition of 50 mg kg[-1] nano-BN significantly promoted plant biomass, nodule biomass, and leghemoglobin content by 10.0%, 27.4%, and 39.4%, respectively, compared to the untreated control. Nano-BN also enhanced the NH4[+]-N and NO3[-]-N content by 24.3% and 19.9% in root tissues, while reducing these levels in rhizosphere soil. Additionally, nano-BN enriched rhizosphere-dissolved organic matter, particularly humic-like components. Metagenomic analysis revealed that nano-BN reshaped carbon and nitrogen cycling functional genes, enhancing CO2 fixation and aerobic respiration; the nitrogen fixation functional gene nifH was upregulated by 27.7%. Microbial community analysis demonstrated increased bacterial diversity and abundance of beneficial taxa, particularly Bradyrhizobium, which increased by 24.9%. Co-occurrence network analysis revealed enhanced positive interactions and greater topological complexity upon the addition of nano-BN compared to the untreated control, indicating improved community stability. Collectively, these findings demonstrate that nano-BN promotes soybean growth through integrated regulation of nutrient cycling, symbiotic nitrogen fixation, and rhizosphere microbiome assembly. Nano-BN represents an innovative nano-fertilization strategy for enhancing biological nitrogen fixation, improving nutrient use efficiency, and advancing sustainable agricultural systems.},
}

@article {pmid42677827,
year = {2026},
author = {Chen, K and Yang, Z and Peng, J and Liu, C and Yu, Y and Cai, X and Liu, B and Li, S and Chen, T and Jung, S and Tian, Y and Xu, Q and Rao, X and Wu, Z and Wang, H and Di, Y and Wang, L and Wang, J and Lee, MS and Zou, Y and He, N and Li, S},
title = {Bacteroides cellulosilyticus-derived 2-hydroxyphenylacetic acid rectifies hepatic lipid homeostasis in MASLD by targeting the PPARγ-CD36 axis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725392},
doi = {10.1080/19490976.2026.2725392},
pmid = {42677827},
issn = {1949-0984},
mesh = {*PPAR gamma/metabolism/genetics ; *CD36 Antigens/metabolism/genetics ; Humans ; *Phenylacetates/metabolism ; *Lipid Metabolism/drug effects ; Homeostasis ; *Fatty Liver/metabolism/microbiology ; *Bacteroides/metabolism ; *Liver/metabolism ; Hepatocytes/metabolism ; Signal Transduction/drug effects ; Gastrointestinal Microbiome ; },
abstract = {The gut microbiota plays an important role in the occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD), but the specific molecular mechanisms involved have not been fully elucidated. In this study, human cohort studies were performed to identify that the relative abundance of Bacteroides cellulosilyticus (B. cellulosilyticus) was significantly decreased in patients with MASLD. Through the integration of metagenomic and metabolomic analyses, it was confirmed that B. cellulosilyticus and its metabolite 2-hydroxyphenylacetic acid (2HPAA) are key factors regulating the occurrence and development of MASLD. Single-cell sequencing and lipidomic analyses revealed that 2HPAA can enter the liver through the enterohepatic circulation to exert regulatory effects. Specifically, 2HPAA inhibits the peroxisome proliferator-activated receptor γ (PPARγ) signaling pathway, thereby suppressing the expression of the fatty acid transporter CD36. Meanwhile, 2HPAA regulates lipid metabolism in hepatocytes by significantly enhancing palmitate conversion efficiency and inhibiting CD36 palmitoylation. This dual regulatory effect on CD36 expression and palmitoylation can reduce lipid accumulation in hepatocytes and ultimately alleviate MASLD progression. These findings reveal the mechanism by which B. cellulosilyticus and 2HPAA alleviate MASLD by targeting the PPARγ-CD36 pathway. This work provides a new perspective for the study of gut microbiota-host interactions in regulating liver diseases.},
}

*PPAR gamma/metabolism/genetics
*CD36 Antigens/metabolism/genetics
Humans
*Phenylacetates/metabolism
*Lipid Metabolism/drug effects
Homeostasis
*Fatty Liver/metabolism/microbiology
*Bacteroides/metabolism
*Liver/metabolism
Hepatocytes/metabolism
Signal Transduction/drug effects
Gastrointestinal Microbiome

@article {pmid42677877,
year = {2026},
author = {Fukuda, Y and Horiba, K and Hashino, M and Kawabe, S and Miura, H and Kawamura, Y and Tanaka, M and Suzuki, T and Torii, Y and Muramatsu, H and Takahashi, Y and Yoshikawa, T and Kawada, JI},
title = {Comprehensive Viral Detection and Profiling of Plasma Cell-Free RNA in Patients With Suspected Hemophagocytic Lymphohistiocytosis.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71122},
doi = {10.1002/jmv.71122},
pmid = {42677877},
issn = {1096-9071},
support = {24K10975//Japan Society for the Promotion of Science/ ; 24FC1001//Health Labour Sciences Research Grant/ ; },
mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/virology/diagnosis ; Female ; Child ; Child, Preschool ; Male ; High-Throughput Nucleotide Sequencing ; *RNA, Viral/blood/genetics ; Infant ; *Cell-Free Nucleic Acids/blood/genetics ; Metagenomics ; Herpesvirus 4, Human/genetics ; Herpesvirus 6, Human/genetics/isolation & purification ; },
abstract = {Hemophagocytic lymphohistiocytosis (HLH) is a severe, rapidly progressive disease. While viral infection is considered a common etiology of pediatric HLH, specific causative viruses other than the Epstein-Barr virus (EBV) have been rarely identified. This study utilized metagenomic next-generation sequencing (NGS) to identify potential causative pathogens in plasma samples from 17 pediatric patients with suspected HLH. Additionally, one case each of confirmed EBV- and cytomegalovirus (CMV)-associated HLH was analyzed for methodological validation. Plasma cell-free RNA (cfRNA) profiling was performed using NGS data to assess the host transcriptome response. Significant viral reads of human herpesvirus-6B, human herpesvirus-7, and Hubei reo-like virus (HRLV) 14 were detected using metagenomic NGS in one patient each. Plasma cfRNA profiles from five patients with viral infection (including EBV and CMV) were compared to those of 14 patients without viral infection. By comparing the two patient groups, 1053 differentially expressed genes were identified. The gene ontology (GO) term of "adaptive immune response" (GO: 0002250) was significantly enriched among upregulated genes in the virus-positive group. Furthermore, an isolated cluster consisting specifically of mitochondrial RNAs, was identified in the upregulated genes of the virus-positive group. Using metagenomic NGS, several candidate viral pathogens were identified in patients with suspected infection-related HLH. The viral genome of HRLV 14, previously undetected in human clinical samples, was identified in one patient. The results from plasma cfRNA profiling suggest that mitochondrial RNAs may reflect the underlying pathogenesis of virus-associated HLH and have potential utility as disease biomarkers.},
}

Humans
*Lymphohistiocytosis, Hemophagocytic/virology/diagnosis
Female
Child
Child, Preschool
Male
High-Throughput Nucleotide Sequencing
*RNA, Viral/blood/genetics
Infant
*Cell-Free Nucleic Acids/blood/genetics
Metagenomics
Herpesvirus 4, Human/genetics
Herpesvirus 6, Human/genetics/isolation & purification

@article {pmid42678156,
year = {2026},
author = {Wu, Q-Q and Li, C-Y and Chen, S-S and Xu, J and Yan, W-H and Lu, L-N and Feng, H-X and Zhou, J-A and Wang, L and Liu, N-N and Jiang, L and Wang, Y},
title = {Multi-kingdom gut microbiota analyses identify biomarkers of different types of pediatric short bowel syndrome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0031626},
doi = {10.1128/msystems.00316-26},
pmid = {42678156},
issn = {2379-5077},
abstract = {Despite recent advances in bacterial profiling across the three anatomical types of pediatric short bowel syndrome (SBS), the gut multi-kingdom remains unexplored. We characterized the four-kingdom gut microbiota using modified DNA extraction and deep shotgun metagenomic sequencing of fecal samples from 26 healthy controls and 34 pediatric SBS patients comprising three types (8 SBS I, 15 SBS II, and 11 SBS III). Overall, children with SBS exhibited a significant reduction in α-diversity compared with controls, with no difference observed among SBS types. Compared with controls, the proportion of archaea was significantly decreased in all SBS types, while bacteria, fungi, and viruses remained similar across types. Different types of SBS exhibited distinct microbial signatures: SBS I was enriched with pathogens (such as species from the Streptococcus and Klebsiella genera); SBS II was marked by a depletion of beneficial short-chain fatty acid-producing species (such as Faecalibacterium prausnitzii); and SBS III displayed loss of bile acid-metabolizing species, alongside a significant expansion of Lactobacillus species. Ecological networks were rewired in SBS, with disruption pronounced in SBS I. Functional analysis revealed that core metabolic pathways were markedly suppressed in SBS I compared with controls. Integrated correlation analyses revealed ileocecal valve loss as the primary determinant of SBS I microbial profiles, linking it to impaired secretory functions and hepatic injury. Our findings deciphered type-specific alterations in the multi-kingdom microbiota and their functional profiles, providing the basis for designing precision microbial therapies aimed at improving long-term outcomes for children with SBS.IMPORTANCEPediatric short bowel syndrome (SBS) is a primary cause of intestinal failure, yet prior research characterizing the gut microbiota has focused almost exclusively on bacteria. In this study, we characterized the multi-kingdom microbiome (including bacteria, fungi, archaea, and viruses) across the three anatomical types of pediatric SBS. We found that different SBS subtypes showed distinct microbial patterns: SBS I was enriched in pathogens, SBS II exhibited a depletion of beneficial short-chain fatty acid-producing species, and SBS III was characterized by a loss of bile acid-metabolizing microbes with an expansion of Lactobacillus. Functional analysis showed that SBS I had markedly suppressed core metabolic pathways, and integrated analyses identified the ileocecal valve as a key determinant of microbial gene profiles, with its loss linked to impaired secretion and liver injury. These findings provide a comprehensive multi-kingdom view of the pediatric SBS microbiome and highlight anatomical determinants shaping host-microbiome dysfunction.},
}

@article {pmid42678158,
year = {2026},
author = {Kaur, S and Anand, A},
title = {xoxF-linked methanol oxidation signals recur across wetland metagenomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0088926},
doi = {10.1128/spectrum.00889-26},
pmid = {42678158},
issn = {2165-0497},
abstract = {UNLABELLED: Wetlands are globally important methane-cycling ecosystems, but methanol oxidation remains less frequently emphasized than methane oxidation in community-level metagenomic analyses. Recent studies have highlighted the ecological importance of the lanthanide-dependent methanol dehydrogenase XoxF, yet wetland-focused xoxF literature remains comparatively limited relative to marine, freshwater, and other environmental systems. Here, we screened wetland-associated records in IMG/M using methane-metabolism and enzyme-centered queries focused on EC 1.1.2.10/xoxF and related methanol-oxidation annotations. Wetland-associated data sets repeatedly returned xoxF-linked annotations. We then examined a representative data set, a Wetland Surface Sediment combined assembly, to assess the relative representation of methanol-oxidation-associated annotations. In this co-assembly, xoxF/EC 1.1.2.10 was the most frequently recovered methanol-oxidation-associated annotation in the queried annotation space, with 1,996 genes, compared with 428 genes assigned to mxa-like EC 1.1.2.7 functions and 235 genes assigned to mdo/EC 1.1.99.37. KEGG-linked organism context included canonical methanotrophic and methylotrophic genera, including Methylococcus, Methylomonas, Methylotuvimicrobium, Methylovulum, and Methylophaga, while also extending into broader environmental Proteobacteria. Together, these data indicate that xoxF-linked methanol oxidation annotations recur across wetland metagenomes and are strongly represented in a representative wetland surface sediment co-assembly. Because this study relies on database annotations rather than organism-resolved pathway reconstruction or activity measurements, the results are best interpreted as community-level functional potential rather than evidence of xoxF-mediated activity, flux, or ecological dominance. These findings support wetlands as an underexamined but relevant setting for future clade-resolved, genome-resolved, and activity-resolved studies of xoxF-associated methanol oxidation.

IMPORTANCE: Wetlands play a major role in Earth's methane cycle, but studies of wetland microbes often focus more on methane itself than on the downstream step of methanol oxidation. Our study shows that wetland metagenomes repeatedly contain strong signals for xoxF, a gene linked to lanthanide-dependent methanol oxidation. In a representative wetland surface sediment co-assembly, xoxF-associated annotations were much more abundant than classical methanol dehydrogenase annotations, suggesting that this pathway may be especially important in wetland microbial communities. Because most previous xoxF studies have focused on marine, freshwater, or other non-wetland systems, these findings highlight wetlands as an underexplored setting for methanol-processing metabolism. This work provides a foundation for future studies connecting these signals to specific microbes, environmental conditions, and methane-cycling processes in wetlands.},
}

@article {pmid42678565,
year = {2026},
author = {Xu, W and Wang, Y and Yuan, C and Yue, Z},
title = {Microbial signal profiles and organism-level concordance between plasma metagenomic sequencing and blood culture in suspected bloodstream infection.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42678565},
issn = {1573-0972},
mesh = {Humans ; *Blood Culture/methods ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Sepsis/diagnosis/microbiology/blood ; *Bacteria/genetics/isolation & purification/classification ; *Bacteremia/diagnosis/microbiology ; },
abstract = {Plasma metagenomic next-generation sequencing (mNGS) and blood culture detect different components of the microbial signal and frequently produce discordant organism reports. We characterized microbial signal class, report-derived burden, organism-level concordance, and independent clinical attribution in a retrospective, single-center, episode-level cohort. Among 329 episodes with evaluable plasma mNGS reports, 315 had blood culture performed; 232 were mNGS positive/culture negative and 53 were positive by both methods. In the 232 discordant episodes, the recorded routine-care diagnosis classified 124 as bloodstream infection (BSI) and 108 as non-BSI. Nonviral signals were present in 78.2% and 42.6%, respectively (P < 0.001), and median maximum report-derived sequence counts were 98.5 and 11.5 (P < 0.001). Two laboratory physicians then independently reviewed source records using structured criteria while masked to the recorded BSI label and mNGS organism and sequence-count information. Initial agreement for the five-category BSI assessment was 97.6% (Cohen's kappa, 0.960). Within the mNGS-positive/culture-negative subgroup, adjudicated BSI likelihood showed a modest ordinal association with report burden (Spearman rho = 0.190; P = 0.004), while mNGS organisms were considered supported in 1 episode, plausible in 158, unlikely or contaminant in 72, and unresolved in 1. Among 53 dual-positive episodes, 33 (62.3%) shared at least one species, but only 5 (9.4%) had complete species-set concordance. Plasma mNGS and blood culture therefore frequently generated non-equivalent organism sets. Signal class and report burden contributed graded contextual evidence, but organism-level attribution required clinical review and orthogonal microbiology rather than binary positivity alone.},
}

Humans
*Blood Culture/methods
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Sepsis/diagnosis/microbiology/blood
*Bacteria/genetics/isolation & purification/classification
*Bacteremia/diagnosis/microbiology

@article {pmid42679008,
year = {2026},
author = {Egholm Bruun Jensen, E and Nzoyikorera, N and Ivanova, M and Leekitcharoenphon, P and Noelle Uwineza, M and Diawara, I and Nyandwi, J and M Aarestrup, F and Otani, S},
title = {Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014175},
doi = {10.1371/journal.pntd.0014175},
pmid = {42679008},
issn = {1935-2735},
abstract = {BACKGROUND: Cholera outbreaks remain a major public-health challenge in sub-Saharan Africa, where diagnostic capacity is limited and clinical case definitions are non-specific and re ly heavily on syndromic diagnosis. Rapid identification of Vibrio cholerae is critical, yet cholera-suspected diarrhoea can have multiple infectious causes not captured by targeted diagnostics.

METHODS: We evaluated a mobile, culture-independent metagenomic sequencing workflow for on-site detection of gastrointestinal pathogens directly from faecal samples in Burundi. The offline workflow combined long-read Oxford Nanopore Technologies (ONT) sequencing with rapid, laptop-based taxonomic and antimicrobial resistance (AMR) screening and was deployed across a health centre, a district hospital, and a refugee transit camp. The frontline and real-time results were verified using both conventional culturing and in-depth bioinformatic analyses.

RESULTS: V. cholerae signals were only detected in a subset of suspected cholera cases, while many samples were dominated by alternative bacterial taxa, most frequently Escherichia coli. V. cholerae abundance correlated strongly with detection of the C holera T oxin P hage CTXφ, supporting differentiation between toxigenic signal and background exposure. AMR genes were detected across samples, providing early situational insight into resistance determinants among gastrointestinal bacteria.

CONCLUSIONS: Mobile, offline metagenomic sequencing enables rapid frontline characterization of gastrointestinal disease, especially cholera-suspected, in resource-limited settings and complements existing diagnostics by improving etiological resolution and outbreak response.},
}

@article {pmid42679417,
year = {2026},
author = {Li, H and Gao, H and Fu, J and Yang, S and Chen, L and Zhou, J},
title = {Comparative analysis of microbial communities, assembly processes, and life-history strategies in a mariculture-impacted eutrophic bay and adjacent coastal sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120750},
doi = {10.1016/j.ecoenv.2026.120750},
pmid = {42679417},
issn = {1090-2414},
abstract = {Coastal embayments are increasingly subjected to intensive mariculture, which delivers sustained nutrient, organic matter, and antibiotics to sediments, yet microbiome responses remain poorly understood. Here we compared sediment microbiomes of the eutrophic Xiangshan Bay (XSB) and oligotrophic East China Sea (ECS), integrating cell counts, 16S rRNA amplicon, metagenomics, and cultivation-based resistance assays. Cell counts and amplicon data showed that XSB harbored higher microbial abundance (1.28 ×10[8]-1.34 ×10[9] vs. 2.07 ×10[7]-4.43 ×10[8] cells g[-1]), Chao1 richness (10,374-16,674 vs. 8311-12,281), and Shannon diversity (6.31-7.43 vs. 5.95-6.68). Amplicon-based null and neutral models indicated that community assembly in XSB was less stochastic and more deterministically selected than in the ECS. Life-history traits inferred directly from metagenomic data were consistently elevated in XSB relative to ECS, including 16S rRNA gene copy number (3.35 vs. 2.37), codon usage bias (0.0219 vs. 0.0188), maximum growth potential (0.1208 vs. 0.0844 h[-1]), genome size (5.63 vs. 5.38 Mb), GC content (56.26% vs. 54.48%), and transposase abundance (3.91% vs. 2.55%), collectively indicating a transition from K- to r-selected life-history strategies. Moreover, metagenomic annotation revealed a similarly expanded resistome in XSB, with 4.5-fold higher antibiotic resistance gene abundance (17.40-45.37 vs. 7.96-25.96 RPM) dominated by efflux-pump mechanisms, while plate assays showed roughly two-fold higher phenotypic resistance to macrolides, tetracyclines, and sulfonamides. These findings demonstrate that microbial community, life-history strategies, and antibiotic resistance respond as a coupled system to mariculture-driven eutrophication, providing a trait-based framework for predicting microbiome trajectories under anthropogenic nutrient enrichment.},
}

@article {pmid42679669,
year = {2026},
author = {Yao, D and Xie, H and Hu, Z and Wu, H and Liang, S and Zhang, J},
title = {Root exudates stabilize denitrification yet amplify CO2 emissions by priming effect in constructed wetlands.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126787},
doi = {10.1016/j.watres.2026.126787},
pmid = {42679669},
issn = {1879-2448},
abstract = {Root‑exudated carbon is a key microbial substrate in constructed wetlands (CWs), yet its net impact remains unclear due to its relatively low flux and quantification challenges. Here, we traced its allocation and metabolic pathways using [13]C-DNA-stable isotope probing coupled with metagenomics, thereby decoupling its role under gradient exogenous carbon inputs. The denitrification potential derived from root‑exudated carbon remained stable regardless of exogenous carbon fluctuations, reducing 1.2-1.44 mg·L[-1] N per mg·L[-1] C. Root‑exudated carbon significantly enhanced the priming effect by 0.9-1.54 times with exogenous carbon inputs (p < 0.05), resulting in an amplification of CO2 emissions. The denitrification and carbon emissions derived by root exudates was non-linear effects mediated by microbial regulation. DNA-SIP coupled with metagenomics indicated that differences in denitrification and CO2 emissions response to root‑exudated carbon from substrate quality, microbial community dynamics, and metabolic strategies. The microbial community of the [13]C-labeled heavy fractions was characterized by active denitrifiers, including Pseudomonas, Aeromonas, and Pseudoxanthomonas, which contributed the highest direct positive effect (20.23 %) to denitrification. Root‑exudated carbon influenced CO2 emissions by directly altering the DOM composition (contributing 37.01 %) and upregulating C-degrading genes (contributing 13.04 %). These findings revealed root exudated-carbon differentially regulate carbon and nitrogen metabolisms, challenging our understanding of the synergistic enhancement of water purification and climate mitigation functions in CWs.},
}

@article {pmid42679805,
year = {2026},
author = {Samarra, A and Alcañiz, AJ and Quijada, NM and Renwick, S and George, S and Sinha, T and Martínez-Costa, C and Segata, N and Zhernakova, A and Bode, L and Collado, MC},
title = {Maternal secretor status and human milk oligosaccharides influence the infant gut resistome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103007},
doi = {10.1016/j.xcrm.2026.103007},
pmid = {42679805},
issn = {2666-3791},
abstract = {The infant gut resistome is established early in life and is shaped by perinatal exposures, yet the mechanisms underlying its modulation remain unclear. We combined shotgun metagenomics of fecal samples from 57 one-month-old infants and paired milk samples from 50 mothers in the MAMI cohort to investigate the influence of maternal secretor status on early-life resistome development. Longitudinal follow-up at 6 and 12 months, and also further validation in the independent Lifelines NEXT (LLNEXT) cohort, support our findings. Cesarean section (C-section) was associated with increased antibiotic resistance gene (ARG) diversity, whereas exclusive breastfeeding reduced ARG abundance and diversity. Maternal secretor status further modified resistome composition among exclusively breastfed infants. Human milk oligosaccharide profiling identified specific glycans underlying these associations, with 2'-fucosyllactose and 6'-sialyllactose showing negative correlations with distinct ARG classes. These findings identify human milk composition as a key determinant of early-life resistome assembly and a potential target for modulating antimicrobial resistance.},
}

@article {pmid42679877,
year = {2026},
author = {Chen, Y and Li, W and Ma, X and Chen, F and Zhang, Y and Rittmann, BE},
title = {Bioaugmentation enabled simultaneous biodegradation of sulfadiazine and nitrification.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125595},
doi = {10.1016/j.envres.2026.125595},
pmid = {42679877},
issn = {1096-0953},
abstract = {Antibiotics are detected in surface waters in part because classical wastewater-treatment processes are ineffective for biodegrading them. Furthermore, the presence of antibiotics can inhibit the performance of biological treatment, particularly for nitrification, but an effective strategy for simultaneous antibiotics and nitrogen removals was not reported so far. This work targeted biodegradation of the common sulfanilamide antibiotic sulfadiazine (SDZ) and its inhibition of nitrification. The experimental results showed that nitrification rate decreased to 3.4 mg/(L·h) and 1.9 mg/(L·h) (from 19 mg/(L·h)) when normal nitrifying biomass (NNB) was exposed to SDZ at 10 mg/L and 20 mg/L due to inhibition by SDZ. Bioaugmentation of NNB with a SDZ-acclimated biomass (SDAB) enabled biodegradation of SDZ, which relieved its inhibition of nitrification. In the presence of 20 mg/L of SDZ, the NH4[+]-N removal rate reached at 7.8 mg/(L·h), which was more than 4-fold faster with SDAB bioaugmentation. Metagenomic analysis supported that NNB was responsible for nitrification, while bioaugmented SDAB was responsible for SDZ biodegradation that allowed simultaneous removal of NH4[+]-N and SDZ. For example, metagenomic analysis further showed that SDAB contained 4 genes for monooxygenations critical to initiating SDZ biodegradation, but NNB was enriched in genes for oxidations of NH4[+] and NO2[-].},
}

@article {pmid42680085,
year = {2026},
author = {Liang, J and Zou, W and Du, Z and Tao, X and Wang, X and Zhang, Y and Zhang, G and Lv, L},
title = {Enhanced volatile fatty acid production from co-fermentation of spent mushroom waste and food waste with rumen microbes: Performance and mechanism.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103079},
doi = {10.1016/j.anaerobe.2026.103079},
pmid = {42680085},
issn = {1095-8274},
abstract = {OBJECTIVE: Co-fermentation of lignocellulosic biomass and food waste (FW) can enhance the production of volatile fatty acids (VFAs) during anaerobic fermentation. However, the effect and mechanism of co-fermentation of Auricularia auricula waste (AW) with FW remains unclear. This study aimed to investigate the effect and mechanism of co-fermentation of Auricularia auricula waste (AW) with food waste (FW) on volatile fatty acid (VFA) production.

METHODS: Anaerobic fermentation experiments were conducted at different AW/FW ratios (1:0, 1:1, 2:1, 3:1, 4:1, 0:1) based on volatile solids (VS). VS removal and VFA concentration were measured, and metagenomic sequencing was performed to elucidate the underlying enhancement mechanism.

RESULTS: Co-fermentation significantly improved VS removal and VFA production, with both parameters increasing as the proportion of FW increased. The highest VS removal (48.9%) and VFA concentration (7929 mg/L) were achieved at an AW/FW ratio of 1:1, which were approximately double those of AW alone (22.4% and 3659 mg/L, respectively). Metagenomic analysis revealed that co-fermentation enriched bacterial genera such as Rummeliibacillus (25.4%) and Leuconostoc (9.2%), while Fungal genera Piromyces and Neocallimastix became dominant. Moreover, co-fermentation increased the relative abundance of carbohydrate-active enzymes and activated key functional genes in the VFA production pathway (e.g., ackA, PTA, MDH, HBD).

CONCLUSION: Co-fermentation of AW and FW significantly enhanced the hydrolysis and VFA production. The enhancement mechanism of VFA production during co-fermentation primarily involved the synergistic interaction between substrate nutrient complementation and efficient microbial community. This study provides a feasible strategy for efficient VFA production from spent mushroom waste.},
}

@article {pmid42667585,
year = {2026},
author = {Zhang, D and Chen, C and Xie, Y and Zhou, S and Li, D and Zeng, F and Huang, S and Lv, Y and Huang, X and Mao, F and Chen, R and Mo, Y and Huang, Y and Chen, R and Zhang, X and Yao, Q and Du, Y and Bai, F},
title = {Gut Microbiota from Patients with Long COVID Persisting for 2 Years Result in Alterations in Mice that Resemble Post-COVID Symptoms.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42667585},
issn = {1867-1314},
support = {XSTS2025001//Hainan Medical University Academic Enhancement Support Program/ ; WSJK2024MS150//Joint Project on Health Science and Technology Innovation in Hainan Province/ ; YSPTZX202313//the specific research fund of The Innovation Platform for Academicians of Hainan Province/ ; hnjg2024-67//Hainan Province Education Reform Project/ ; 202330//National Clinical Key Speciality Capacity Building Project/ ; 2021818//Hainan Province Clinical Medical Center/ ; },
abstract = {Human gut microbiota (GM) has been identified as a potentially important factor influencing the development of long COVID (LCOVID). The aim of this study was to understand the GM of LCOVID, which lasted for two years, in order to improve public awareness. Human gut microbiota and its metabolites were assessed in a healthy control group (n = 11) (HC) unexposed to SARS-CoV-2 and an LCOVID group (n = 11) in Hainan, China, using Shotgun metagenomics and liquid chromatography-mass spectrometry (LC-MS) of feces. The causal role of the microbiota in LCOVID was further validated by transplanting feces from the subjects into ABx mice using Histopathology and 16 S rRNA sequencing. Fecal microbial diversity was lower in patients with LCOVID compared with that in HC. Pro-inflammatory bacteria such as Streptococcus_salivarius and Streptococcus_parasanguinis increased, whereas anti-inflammatory bacteria such as Faecalibacterium_SGB15346 and Alistipes_onderdonkii decreased. Fecal metabolites from LCOVID were impaired in carbohydrate degradation, indole production, SCFA production, and fatty acid degradation. Transplantation of feces from patients with LCOVID into mice results in lung inflammation, intestinal inflammation, and anxiety. In addition, transplanted mice showed worse outcomes during Klebsiella_pneumoniae infections. Transplanted mice and the key bacteria Streptococcus_salivarius had the same worse outcomes in the D-IBS model by limb binding. GM from patients with LCOVID was altered significantly and sufficiently to promote LCOVID symptoms in mice, suggesting that it may be a potential therapeutic target.},
}

@article {pmid42668212,
year = {2027},
author = {Huang, X and Luo, R and Wang, Y and Zheng, W and Lu, X and Liu, G and Abdulla, P and Niu, R and Tu, Y and Xing, J and Hong, J and Zheng, W and Liu, J},
title = {Correlation between microbial communities, metabolites, and bioactivities in fermented mare's milk revealed by metagenomics and metabolomics.},
journal = {Food microbiology},
volume = {141},
number = {},
pages = {105278},
doi = {10.1016/j.fm.2026.105278},
pmid = {42668212},
issn = {1095-9998},
mesh = {Animals ; Metagenomics ; Fermentation ; Metabolomics ; *Microbiota ; Horses ; *Milk/microbiology/chemistry/metabolism ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Cultured Milk Products/microbiology/analysis ; Lactobacillales/metabolism/genetics/isolation & purification/classification ; Female ; Antioxidants/metabolism/analysis ; },
abstract = {Koumiss exhibits various functional properties, including antioxidant, hypoglycemic, and antihypertensive effects; however, natural fermentation is characterized by an uncontrollable microbial community structure, significant fluctuations in product quality, and a lack of specialized fermentation agents. The mechanisms underlying the links between microbial communities, functional metabolites, and bioactivity in natural and inoculated fermentation systems remain unclear. Therefore, this study employed bioactivity assays, metagenomics, and non-targeted metabolomics to systematically analyze differences in microbial communities, metabolite composition, and functional activities of mare's milk under different fermentation regimes. The results indicated that, compared with natural fermentation, inoculated fermentation with a mixed lactic acid bacteria (LAB) culture significantly enhanced the antioxidant, α-glucosidase, α-amylase inhibitory activities, and ACE inhibitory activity of mare's milk; microbial diversity in fermented samples was significantly reduced, with a more pronounced decrease in the inoculated group. Metabolomic analysis revealed that inoculated fermentation significantly enriched functional metabolites, including lipids and organic acids. Correlation analysis indicated that the abundance of Lactiplantibacillus and Limosilactobacillus was significantly positively correlated with beneficial metabolites (e.g., linoleic acid, α-linolenic acid) and functional activities. The lipid and amino acid metabolic pathways are closely associated with the differences in in vitro biological activity of inoculated fermented mare's milk. This study provides a fermentation starter that can improve the in vitro functional activity of mare's milk and reveals the potential metabolic links between LAB fermentation and the altered functional traits of mare's milk, thereby providing a theoretical basis and technical support for the development of high-value-added fermented mare's milk products.},
}

Animals
Metagenomics
Fermentation
Metabolomics
*Microbiota
Horses
*Milk/microbiology/chemistry/metabolism
*Bacteria/genetics/classification/isolation & purification/metabolism
*Cultured Milk Products/microbiology/analysis
Lactobacillales/metabolism/genetics/isolation & purification/classification
Female
Antioxidants/metabolism/analysis

@article {pmid42668680,
year = {2026},
author = {Sommer, AJ and Auch, B and Khoruts, A and Bajaj, JS},
title = {Proximity-ligation metagenomics reveals differential plasmid and chromosomal antimicrobial resistance gene carriage in disrupted gut ecosystems.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117312},
pmid = {42668680},
issn = {2589-0042},
abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance genes (ARGs) and virulence genes in the gut microbiome. In this study, we used proximity ligation shotgun metagenomics to characterize bacterial host-mobilome relationships associated with antimicrobial resistance and virulence genes in two disease cohorts with microbiome dysbiosis: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. Microbiome dysbiosis in patients with rCDI is primarily driven by prolonged antibiotic exposure, whereas dysbiosis in patients with cirrhosis results from altered gut physiology. We found an increased relative abundance of chromosomally linked antibiotic resistance determinants in both disease cohorts compared with healthy controls. The rCDI cohorts additionally exhibited increased relative abundance of plasmid-mediated ARGs.},
}

@article {pmid42668932,
year = {2026},
author = {Yan, F and Lin, M and Fu, Q and Gao, Y and Hu, Y and Zhou, M},
title = {Ureaplasma parvum meningitis in neonates: A retrospective case study and literature review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {8},
pages = {2178-2184},
pmid = {42668932},
issn = {1682-024X},
abstract = {OBJECTIVE: To investigate the clinical characteristics and advances in diagnosis and treatment of neonatal Ureaplasma parvum (U. parvum) meningitis.

METHODOLOGY: Clinical manifestations, diagnosis, treatment, and follow-up data of a neonate with persistent fever, normal blood routine, but persistently abnormal cerebrospinal fluid (CSF) results due to U. parvum meningitis were retrospectively analyzed. A literature review was conducted to identify relevant studies reporting on neonatal U. parvum meningitis published until May 2025.

RESULTS: A male infant born at 35+2 weeks of gestation with eight hours of premature rupture of membranes (PROM) was admitted at 17 days of age with persistent fever. The routine blood test was normal, while the CSF suggested purulent meningitis. Empirical treatment was ineffective, and metagenomic next-generation sequencing (mNGS) of CSF confirmed U. parvum meningitis. The infant recovered after three weeks of azithromycin treatment, but a language delay was found at two-year follow-up. The literature review identified 16 previously reported cases of U. parvum meningitis, which were combined with the current case, totaling 17 cases. Main manifestations included fever and convulsions, or initial circulatory and respiratory symptoms. CSF in the included studies showed leukocytosis, decreased glucose, and elevated protein. Diagnosis was mainly based on mNGS, and the predominant treatment consisted of macrolides, sometimes combined with quinolones, for 3-10 weeks. Two patients relapsed after drug withdrawal, and one had elevated liver enzymes. Major neurological complications included lateral ventricular dilatation and hydrocephalus, cerebral hemorrhage, infarction, malacia, and herniation. Most cases had a favorable prognosis, with rare developmental delay.

CONCLUSION: Clinical manifestations of neonatal U. parvum meningitis are nonspecific. Some patients present with normal blood routine but purulent CSF. U. parvum meningitis should be suspected in patients with poor response to empirical antibiotics and confirmed by CSF mNGS. Macrolides are biologically rational and commonly used for neonatal U. parvum meningitis; however, the optimal regimen and duration remain unclear due to limited and heterogeneous case-based evidence.},
}

@article {pmid42669226,
year = {2026},
author = {Gongpan, P and Yang, J and Fu, H and Wu, S and Zhu, X and Chen, R and Liu, L and Geng, CA},
title = {Preparation and chemical characterization of polyphenol-rich extract from Tsaoko Fructus: alleviation of ulcerative colitis in mice by modulating gut microbiota and suppressing the JNK1-cJun signaling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {161},
number = {},
pages = {158752},
doi = {10.1016/j.phymed.2026.158752},
pmid = {42669226},
issn = {1618-095X},
abstract = {BACKGROUND: Tsaoko Fructus, a traditional Chinese medicinal herb, has long been used to alleviate gastritis and enteritis. Nevertheless, the active constituents and underlying anti-inflammatory mechanisms remain insufficiently characterized.

PURPOSE: This study aims to optimize a polyphenol-rich fraction (3CB) from Tsaoko Fructus, evaluate its effects against ulcerative colitis (UC), and reveal the underlying mechanisms of action.

METHODS: The preparation of 3CB was optimized using response surface methodology (RSM), and its major constituents were identified by LC-PDA-MS analysis. A murine UC model was established by administering dextran sulfate sodium (DSS). To evaluate the effects of 3CB on UC mice, metagenomic sequencing of the intestinal microbiome and RNA sequencing of colon tissues were conducted. The anti-inflammatory activity of 3CB and its principal constituents was further verified by quantitative real-time PCR (qPCR), Enzyme linked immunosorbent assay (ELISA), Western blotting, immunohistochemical staining, and histopathological analysis. Network pharmacology, molecular docking, and surface plasmon resonance (SPR) assays were employed to elucidate the molecular mechanisms underlying the anti-inflammatory effects of 3CB.

RESULTS: 3CB significantly alleviated UC symptoms in DSS-induced mice, reshaped the gut microbiota with reducing pathogenic Pseudomonadota and Deferribacterota while enriching beneficial Bacteroidota, and restored microbial amino sugar and nucleotide sugar metabolism pathways of intestinal flora. Additionally, 3CB preserved colonic oxidative phosphorylation, protected the mucus barrier, and suppressed inflammatory cell infiltration and the expression of cytokines. Seven major polyphenols were identified in 3CB, with epicatechin (3) and epiafzelechin (6) being the most abundant. Mechanistic investigation revealed that the anti-inflammatory effect of 3CB was partially dependent on the JNK1-modulated MAPK signaling pathway. JNK1 was identified as a direct target of 3CB, with epiafzelechin (6) exhibiting a high binding affinity (Kd = 10.4 μM).

CONCLUSION: 3CB ameliorates UC potentially through modulation of gut microbiota, protection of the mucus barrier, and JNK1-targeted anti-inflammatory effects, highlighting its potential as a protective intervention for inflammatory bowel disease (IBD).},
}

@article {pmid42669365,
year = {2026},
author = {Meng, Q and Xia, Y and Liu, F and Yan, B and Yang, J and Shi, L and Zhang, M and Wu, J},
title = {In situ fermentation-coupled symbiosis of polyphosphate-accumulating organisms and microalgae for efficient nutrient removal and sludge reduction in low carbon-to-nitrogen ratios wastewater.},
journal = {Bioresource technology},
volume = {463},
number = {},
pages = {135748},
doi = {10.1016/j.biortech.2026.135748},
pmid = {42669365},
issn = {1873-2976},
abstract = {Microalgae-bacteria consortia (MBC) integrated with polyphosphate-accumulating organisms (PAOs) treat wastewater sustainably, but face excess sludge and light-dark mismatch issues. This study developed in situ fermentation-coupled photo simultaneous nitrification-denitrification phosphorus removal (F/P-SNDPR) systems by incorporating fermentative PAOs into MBC for low carbon-to-nitrogen ratios (C/N) wastewater. The effects of light-dark cycles on nutrient removal, sludge fermentation, and microbial dynamics were investigated. Under an optimal 16 h dark/8h light cycle, the F/P-SNDPR system achieved > 83% nitrogen and > 95% phosphorus removal, with low sludge production (312.21 mgVSS/d) and low net CO2 emissions. Prolonged light and dark phases promoted early microbial apoptosis and subsequent cell lysis, respectively, thereby facilitating fermentation. Combined dark duration and photoinhibition suppress nitrite-oxidizing bacteria, enabling stable partial nitrification. Flow cytometry and metagenomic results identified Candidatus Phosphoribacter as the primary fermentative microorganism. Its fermentation-associated genes, including LivFGHMK and Pta, facilitated volatile fatty acid (VFA) production during the dark phase. The generated VFA supported Candidatus Accumulibacter/Candidatus Competibacter to enhance nutrient removal, driven by key functional genes for polyphosphate metabolism (Ppk and Ppx) and denitrification (NirS, NirK, and NosZ). Overall, The F/P-SNDPR system offers a low-carbon strategy for efficient low C/N wastewater treatment without mechanical aeration or external carbon addition, while reducing sludge production.},
}

@article {pmid42669658,
year = {2026},
author = {Huey, SL and Cole, NL and Pagani, I and González, A and Finkelstein, JL and Haas, JD and Udipi, SA and Ghugre, P and Potdar, RD and Knight, R and Mehta, S},
title = {Effect of a complementary feeding intervention based on iron- and zinc-biofortified pearl millet on the gut microbiota in 12-18-month-old children: a randomized trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42669658},
issn = {2041-1723},
support = {2021-67017-34008//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 5T32HD087137//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
mesh = {Humans ; *Zinc/administration & dosage ; *Pennisetum/chemistry ; Infant ; *Iron ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; *Food, Fortified ; *Infant Nutritional Physiological Phenomena ; Dietary Supplements ; Feces/microbiology ; },
abstract = {Iron supplementation studies in children under five suggest potentially adverse gut microbiota shifts. Given iron's importance during early childhood, food-based approaches may offer a more viable supplementation strategy. Using shotgun metagenomics, we examined the effects of 9 months' daily consumption of iron/zinc-biofortified pearl millet (FeZnPM; 8.70 mg/100 g iron) versus control pearl millet (CPM; 3 mg/100 g iron) on the gut microbiome in 12-18-month-old children without severe anemia (hemoglobin ≥9.0 g/dL) from Mumbai urban slums through a randomized controlled trial, the primary outcomes of which were iron status biomarkers and infant growth (ClinicalTrials.gov ID: NCT02233764). In paired (n = 81) and endpoint (n = 108) analyses, FeZnPM consumption was not associated with detectable adverse effects on developing microbiomes and exploratory analyses suggest that it may support beneficial metabolic adaptations via direct modulation of antibiotic, antioxidant, and pollutant degradation pathways. This suggests biofortified crops could provide a sustainable approach to addressing iron deficiency while maintaining healthy microbiome development in early life.},
}

Humans
*Zinc/administration & dosage
*Pennisetum/chemistry
Infant
*Iron
*Gastrointestinal Microbiome/drug effects
Female
Male
*Food, Fortified
*Infant Nutritional Physiological Phenomena
Dietary Supplements
Feces/microbiology

@article {pmid42669679,
year = {2026},
author = {Zheng, R and Wang, C and Sun, C},
title = {Multi-omics and cultivation reveal laminarin-degrading PVC bacteria in the deep sea.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42669679},
issn = {2041-1723},
mesh = {*Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Glucans/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Multiomics ; Microbiota/genetics ; Phylogeny ; Glycoside Hydrolases/metabolism/genetics ; },
abstract = {The deep sea is home to a vast and largely unexplored microbial biosphere, along with large amounts of complex organic matter (COM). However, the functional capacity of the deep-sea microbiome to metabolize organic matter across diverse regions remains poorly understood. Here, we combine 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics to comprehensively characterize prokaryotic communities across different years (2018 and 2022) and habitats (cold seeps, hydrothermal vents, and seamounts). Our results reveal spatio-temporal community heterogeneity driven by geochemical gradients, alongside a widespread genetic potential for organic matter metabolism. Notably, the PVC (Planctomycetota-Verrucomicrobiota-Chlamydiota) superphylum exhibits extensive polysaccharide degradation capabilities, exemplified by the isolation of Planctomycetota strain WC338 and Lentisphaerota strain WC36 via laminarin enrichment. Growth experiments and transcriptomics confirm their strict laminarin dependence and characterize the underlying catabolic machinery-specifically, the deployment of different glycoside hydrolase (GH) families, which are broadly distributed and prevalent across the PVC superphylum. Furthermore, we demonstrate that laminarin acts as an effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria. Collectively, these findings reveal that PVC bacteria-an overlooked group in laminarin degradation-possess specialized adaptations for polysaccharide breakdown and actively participate in laminarin turnover in deep-sea environments.},
}

*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Glucans/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Multiomics
Microbiota/genetics
Phylogeny
Glycoside Hydrolases/metabolism/genetics

@article {pmid42669940,
year = {2026},
author = {Jesús, IDY and Zárate-Nicolás, B and Aragón-Magadan, MA and Pérez-Pacheco, R and Pacheco-Esteva, MC and Martínez-Tomás, SH and Vásquez-López, A and Ambrosio-Martínez, CN and Quiroz-González, B},
title = {Chemical, biological, and metagenomic profile of biofertilizers containing native forest and whey microbiota and enriched with macronutrients and micronutrients.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.71026},
pmid = {42669940},
issn = {1097-0010},
support = {//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI) and the Instituto Politécnico Nacional for supporting the SIP 20260212 and SIP INNOVACIÓN 2025-A101 projects./ ; //Secretaría de Ciencia/ ; //Humanidades, Tecnología e Innovación (SECIHTI), Mexico/ ; 20260212//Instituto Politécnico Nacional/ ; },
abstract = {BACKGROUND: Biofertilizers are gaining interest as sustainable nutrient sources that enhance nutrient and soil biological quality. The chemical, biological, and metagenomic profiles of biofertilizers produced from native forest microbiota and acidic whey, and enriched with macronutrients and micronutrients through anaerobic fermentation, were evaluated.

RESULTS: Fermentation of the biofertilizer base over 4 days increased pH (3.0-3.8) and decreased oxidation-reduction potential (ORP, 178 to -173 mV), while electrical conductivity (EC) remained stable (3.7-4.1 mS cm[-1]). After enrichment with macronutrients and micronutrients, 35 days of fermentation, and formulation of the model nutrient solution (MNS), pH stabilized around 4.8, and EC decreased to 1.72 mS cm[-1]. Most biofertilizers, when enriched individually, maintained negative ORP values; however, the increase in ORP observed in the MNS (140 mV) suggests that incorporating the copper-enriched biofertilizer may have contributed to more oxidizing conditions. Biological analysis suggested enhanced nutrient transformation, as revealed by chromatographic complexity in most enriched treatments. The 16S rRNA gene amplicon-based metagenomic profiling showed higher amplicon sequence variant (ASV)-level richness and taxonomic diversity in MNS (592 ASV records and 57 resolved genera) than in the unenriched biofertilizer (342 ASV records and 41 resolved genera). At the genus level, both profiles shared a dominant taxonomic backbone but showed measurable differences in relative abundance patterns (Bray-Curtis = 0.266). Fermentative taxa, including lactic-acid-bacteria-associated genera and Clostridium, dominated both biofertilizers.

CONCLUSIONS: Mineral-source fermentation by native forest microbiota modified the chemical environment, increased microbial diversity and complexity, and enhanced biological indicators of nutrient transformation; these changes suggest potential for increased nutrient bioavailability. © 2026 Society of Chemical Industry.},
}

@article {pmid42670142,
year = {2026},
author = {Su, HB and Li, MJ and Qian, X and Fan, YF},
title = {[Impact of Microplastics in Sediments on Microbial Carbon Cycling Functions in Qinhuai River].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {8},
pages = {5723-5733},
doi = {10.13227/j.hjkx.202506279},
pmid = {42670142},
issn = {0250-3301},
mesh = {*Geologic Sediments/chemistry/microbiology ; Rivers/chemistry ; *Microplastics/analysis ; China ; *Water Pollutants, Chemical/analysis ; *Carbon Cycle ; Environmental Monitoring ; Bacteria/metabolism ; },
abstract = {Microplastics （MPs）， as emerging contaminants， have attracted widespread attention in recent years. Microorganisms， as key regulators of the cycling of elements such as carbon， are sensitive to MPs pollution. Urban river sediments are sinks for environmental MPs and also important habitats for microbial communities. MPs pollution may bring ecological risks to urban rivers by affecting the structure and function of microbial communities. To examine the impact of MPs on microbial carbon cycle functions， this study investigated the sediments from the Qinhuai River， a typical urban river. Sediment samples were collected in October 2024， and MPs analysis combined with metagenomic sequencing was performed to characterize MPs pollution and its effects on microbial community structure and carbon cycling functional genes in both sediments and the plastisphere. The results showed a 100% detection rate of MPs in sediments， with an average abundance （based on dry weight） of （520.56±202.01） n·kg[-1]. MPs were predominantly between 200-300 μm and 1 000-2 000 μm， transparent in color， and exhibited fibrous or fragmental morphologies. Metagenomic analysis revealed significant differences in microbial community structure between the plastisphere and sediments， with higher abundance of Methanomicrobia in the plastisphere， potentially driving the significant enrichment of methane metabolism genes （Wilcoxon rank-sum test， P<0.05）. The Mantel test further indicated that the abundance of carbon cycling genes in the plastisphere was significantly correlated with total nitrogen and a specific MP polymer type （epoxy resin） （P<0.05）. This study uncovered the mechanism by which MPs shape distinct ecological niches and modulate microbial carbon cycling in urban river sediments， providing a scientific basis for evaluating the ecological impacts of MPs.},
}

*Geologic Sediments/chemistry/microbiology
Rivers/chemistry
*Microplastics/analysis
China
*Water Pollutants, Chemical/analysis
*Carbon Cycle
Environmental Monitoring
Bacteria/metabolism

@article {pmid42670399,
year = {2026},
author = {Alemneh, T and Molla, W and Abdela, S and Medjekal, S and Guetouache, M},
title = {Avian malaria: an in-depth overview on its biology, epidemiology, pathogenesis, clinical features, economic impacts, diagnostic, treatment and control strategies.},
journal = {Journal of parasitic diseases : official organ of the Indian Society for Parasitology},
volume = {50},
number = {3},
pages = {538-577},
doi = {10.1007/s12639-025-01887-z},
pmid = {42670399},
issn = {0971-7196},
abstract = {UNLABELLED: Avian malaria is a serious disease affecting diverse bird species worldwide, caused by protozoan parasites of the genus Plasmodium and transmitted exclusively by infected mosquitoes. The parasite completes its life cycle in both the avian host and the mosquito vector, undergoing multiple developmental stages. Clinical signs range from mild to severe and may include lethargy, anemia, respiratory distress, altered feeding behavior, and reduced activity, with young or immunocompromised birds particularly vulnerable to mortality. Diagnosis relies on a combination of clinical observations and laboratory methods, including traditional blood smears and serology alongside molecular tools such as Polymerase Chain Reaction (PCR), Next-Generation Sequencing (NGS), metagenomics, and transcriptomics. Treatment options are limited, typically involving antimalarial drugs such as chloroquine phosphate, primaquine phosphate, mefloquine, sulfachloropyrazine, sulfaquinoxaline, Trimethoprim, and Pyrimethamine-sulfadoxine combination along with supportive care and environmental management. Control strategies target both vectors and hosts, including habitat modification, chemical application, chemo-sterilization, the use of endosymbionts like Wolbachia, housing management, drainage of water bodies, biosecurity measures, vaccination, and the rearing of genetically resistant avian breeds. Ongoing research into the ecology of avian malaria and its vectors is essential for developing effective prevention strategies and mitigating its impact on vulnerable bird populations. This review synthesizes current knowledge on the epidemiology, transmission dynamics, and ecological consequences of avian malaria, with the goal of informing conservation and management strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s12639-025-01887-z.},
}

@article {pmid42671175,
year = {2026},
author = {Schärer, MR and Yu, Y and Grawe, A and Christenson, JK and Robinson, SL and Bokulich, NA},
title = {Laccase-mediated biotransformation potential for fluorinated compounds by geographically diverse human gut microbiota.},
journal = {mBio},
volume = {},
number = {},
pages = {e0102626},
doi = {10.1128/mbio.01026-26},
pmid = {42671175},
issn = {2150-7511},
abstract = {The growing prevalence of synthetic organofluorine substances in agrochemicals, food packaging, and consumer products has led to increasing gastrointestinal exposure, with potential consequences for human health. Despite the extreme stability of fluorinated compounds, several microbial pathways for their transformation are known, including those involving laccases, a type of multicopper oxidase. However, the functionality of laccases in the gut microbiome, a natural contact point between food-associated chemicals and microbial biotransformation pathways, is poorly defined. Through a multi-study analysis of 1,578 human gut metagenomes spanning a global gradient from hunter-gatherer societies to industrialized urban populations, we found that laccase-coding gene homologs are widely distributed in the human gut microbiome. We identified a significant association between both the abundance and phylogenetic diversity of laccase homologs and the degree of urbanization. As human gut microbial laccase activity has not been experimentally demonstrated, eight gut metagenome-derived laccases were heterologously expressed and screened for activity with a redox mediator system. Six of the eight laccases demonstrated activity. One of these gut microbial laccases, derived from Veillonella, and three previously characterized laccases were then tested for their capacity to deplete 11 different food-associated chemicals. The Veillonella laccase depleted the agrochemicals cyflumetofen and fluazinam, as well as the industrial chemical bisphenol AF, to a lesser extent. By linking global gut metagenomes with activity assays, this work demonstrates the untapped potential of mining human gut metagenomes for laccases and other microbial enzymes that can actively modify various agricultural and industrial chemicals.IMPORTANCEAs adverse effects of fluorinated compounds on human health are emerging, the responsible enzymes from the human gut microbiome of geographically diverse human cohorts mediating interactions with fluorinated compounds in the gastrointestinal tract remain poorly characterized. In a multi-study analysis of publicly available microbiome sequencing data, we linked the abundance, diversity, and phylogeny of laccases within the gut microbiome to the degree of urbanization of human cohorts and experimentally demonstrated the ability of these laccases to deplete a range of food-associated fluorochemicals. Another significant contribution of our study is in the integration of rural catchment areas as a quantitative metric of urbanization in gut microbiome metagenomics and enzyme activity surveys.},
}

@article {pmid42671179,
year = {2026},
author = {Feng, Q and Liao, L and Gong, Y and Xu, J and Wei, X and Xiao, Z and Chen, P and Chen, B and Zhang, K and Wang, Q},
title = {Novel insights into Radix Pseudostellariae saponins assist Mycoplasma gallisepticum attenuated vaccine to enhance the immunoprotection of chicken.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0078126},
doi = {10.1128/msystems.00781-26},
pmid = {42671179},
issn = {2379-5077},
abstract = {Mycoplasma gallisepticum (MG) is a major pathogen causing chronic respiratory disease in chickens, and the MG-attenuated vaccine (MGAV) often fails to induce effective mucosal immunity. Radix Pseudostellariae saponins (RPS), important bioactive components of the traditional Chinese herb, have been utilized for immunomodulation, although the underlying mechanisms remain to be elucidated. In this study, chickens were randomly assigned to groups receiving intranasal MGAV alone, MGAV plus RPS at different doses, or appropriate controls. Serum, tracheal mucosa, and respiratory lavage samples were collected for antibody measurement, cytokine profiling, histological assessment, and metagenomic/metabolomic analyses. RPS significantly increased MG-specific antibody levels and enhanced expression of the immunomodulatory cytokines, while suppressing that of pro-inflammatory factors. It also promoted tracheal mucosal integrity by elevating goblet cell numbers and mucosal epithelial height. Through metagenomic and metabolomic analysis, RPS was found to enrich the respiratory bacterium Lactobacillus sp. UMNPBX13, which was positively correlated with the metabolite phosphatidylcholine (PC). Intranasal administration of Lactobacillus increased mucin 2 (MUC2) and PC levels in tracheal mucosa. Similarly, PC combined with MGAV enhanced mucosal immunity by modulating cytokines and increasing MG-specific antibodies. These findings demonstrate that RPS enhances MGAV-induced respiratory mucosal immunity and provides a novel adjuvant strategy for improving poultry respiratory disease vaccines by modulating the respiratory microbiota, specifically through enrichment of Lactobacillus sp. UMNPBX13, which promotes PC production.IMPORTANCEMycoplasma gallisepticum (MG) constitutes a notable challenge to poultry health. Although the MG-attenuated vaccine (MGAV) is widely used for disease control, it often fails to induce robust mucosal immunity. Here, we demonstrate that intranasal co-administration of Radix Pseudostellariae saponins (RPS) with MGAV augments mucosal immunoprotection. Integrated metagenomic and metabolomic analyses revealed that RPS enriches respiratory Lactobacillus, which in turn promotes the production of its key metabolite phosphatidylcholine (PC), thereby supporting mucosal immune enhancement. These findings offer a promising strategy for improving poultry vaccine efficacy and may provide a basis for future exploration of mucosal vaccination approaches in other animal species.},
}

@article {pmid42671180,
year = {2026},
author = {Li, T and Lu, X and Alomeir, N and Gaca, A and Sohn, M and Gill, S and Smith, B and Munger, J and Xiao, J},
title = {Longitudinal development of infant oral ecosystem: salivary metabolomic, bacteriome, and virome dynamics in early infancy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0094626},
doi = {10.1128/msystems.00946-26},
pmid = {42671180},
issn = {2379-5077},
abstract = {This prospective cohort study investigated the longitudinal development of the salivary bacteriome, virome, and metabolome during early infancy. We assessed the associations between oral bacteria, viruses, and metabolites from 10 mother-infant dyads, with oral samples collected at 1 and 2 years of age. Forty saliva and plaque samples underwent untargeted metabolomic analysis, and infant saliva samples underwent metagenomic sequencing. Maternal salivary and plaque metabolomic profiles remained largely stable, whereas infant profiles were clearly separated from maternal profiles and changed with age. Notably, infant dental plaque metabolism underwent more substantial changes from year 1 to year 2 than saliva, with age-dependent metabolite shifts mainly involving energy, amino acid, nucleotide, and lipid metabolic pathways. Our findings also revealed significant developmental shifts in salivary bacteriome, virome, and functional pathway profiles during early childhood. The most abundant oral bacteria in early life, comprising over 75% of total abundance, included Veillonella, Streptococcus, Rothia, Prevotella, Neisseria, and Actinomyces species. While human viruses like Roseolovirus were detected, bacteriophages constituted the majority of the virome. Comparing infants at year 1 and year 2, we identified differentially abundant bacteria, viruses, metabolic functional pathways, and specific metabolites. We observed associations between bacteria and viruses, noting that these cross-kingdom relationships attenuated as infants grew. The study results underscore the complex and dynamic development of the oral microbiome, virome, and metabolome during early childhood.IMPORTANCEThe human oral cavity undergoes substantial microbial and metabolic development during early childhood, yet the temporal changes in the infant oral ecosystem remain incompletely understood. In this study, we longitudinally profiled the salivary metabolome, bacteriome, and virome of infants at 1 and 2 years of age. We demonstrated that the infant oral metabolome undergoes substantial developmental shifts, particularly in pathways related to energy, amino acid, and lipid metabolism; whereas maternal metabolic profiles remained stable over the same period. Furthermore, our results revealed the dynamic assembly of infant salivary virome and bacteriome and their associations with the functional pathways and metabolites. These findings provide new insights into the complex and dynamic development of the oral microbiome, virome, and metabolome in early infancy.},
}

@article {pmid42671210,
year = {2026},
author = {Stephen, AS and Nagala, V and Fattah, B and Dhadwal, N and Gonzales-Marin, C and Gillam, DG and Bradshaw, DJ and Burnett, GR and Allaker, RP},
title = {Sulfur metabolism and immune-microbial networks across oral niches in periodontal disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0300825},
doi = {10.1128/spectrum.03008-25},
pmid = {42671210},
issn = {2165-0497},
abstract = {Volatile sulfur compounds (VSCs) integrate microbial metabolism with local inflammation in periodontal disease. We profiled five oral niches (saliva, tongue, subgingival, supragingival, and interdental plaque) across clinical health, gingivitis, and periodontitis by combining direct VSC measurements (subgingival and oral headspace H2S/CH3SH), functional cysteine/methionine degradation assays, 16S rRNA profiling, gingival crevicular fluid cytokines, and targeted qPCR. Subgingival H2S concentrations were significantly elevated in periodontitis after adjusting for age, sex, plaque index, and subgingival bacterial load (β = 1.24, P = 0.03), and tracked shifts in community composition and the cytokine milieu. Oral headspace CH3SH increased with disease, whereas headspace H2S showed a bimodal pattern (health and periodontitis). In cysteine assays, subgingival and tongue biofilms were the most efficient H2S producers per mg protein; this ranking was preserved after normalization to total bacteria by qPCR. Metagenome predictions indicated enhanced sulfur metabolism in disease, particularly in subgingival plaque, with relative enrichment of SAM-cycle/methionine biosynthesis pathways in health. Methionine degradation to CH3SH increased with disease severity, shifting from subgingival sites in health to interdental/supragingival plaque in disease, and occurring most frequently in saliva. Correlation networks revealed niche- and diagnosis-specific coupling among VSCs, cytokines, and taxa, including associations of Capnocytophaga, Fusobacterium, Prevotella, and Corynebacterium, with IL-1β, IL-4, IL-8, and MCP-1. Together, these data identify the subgingival crevice as a disproportionate source of sulfide and show that sulfur metabolism is spatially organized and disease-responsive. We show that subgingival H2S as a functional marker that integrates microbial dysbiosis and inflammation.IMPORTANCEWe asked how metabolism, microbes, and immunity fit together during gum disease. Using a systems approach across five oral sites, we combined sulfur metabolite measurements, functional assays, microbiome profiling, and cytokine data, and analyzed them as one network. The result is a comprehensive map showing that sulfur metabolism is spatially organized, disease-responsive, and tightly coupled to local immune signals, with the subgingival niche playing an outsized role. Further, this integrated readout turns sulfur metabolism into a useful window on dysbiosis and inflammation and offers a path toward simple monitoring of periodontal disease, such as point-of-care sensors detecting subgingival hydrogen sulfide or methanethiol, or functional assays in which a methionine rinse is followed by measurement of oral headspace gases to assess microbial sulfur metabolism.},
}

@article {pmid42671637,
year = {2026},
author = {Sample, JW and Johnson, S and Hoskin, TL and Redaelli, M and Walther-Antonio, MR and Chen, J and Degnim, AC and Hieken, TJ},
title = {Body mass index-associated gut microbial taxa and functional pathways in women with benign and malignant breast disease.},
journal = {Breast cancer research and treatment},
volume = {219},
number = {2},
pages = {},
pmid = {42671637},
issn = {1573-7217},
support = {UL1TR002377/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Female ; *Breast Neoplasms/pathology/microbiology/etiology ; *Body Mass Index ; Middle Aged ; *Gastrointestinal Microbiome ; *Obesity/complications/microbiology ; Aged ; Adult ; Metagenomics/methods ; Metagenome ; },
abstract = {PURPOSE: Obesity is an established risk factor for breast cancer and is associated with alterations in gut microbial composition. We evaluated associations among body mass index (BMI), breast density, gut microbial diversity and composition and microbial functional pathways in women undergoing surgery for benign, high-risk/non-invasive, and invasive breast disease.

METHODS: Preoperative stool samples were collected from 131 women (median age 59) with benign (n = 23), high-risk/non-invasive (n = 47), or malignant (n = 61) disease. Shallow shotgun metagenomic sequencing was performed. Taxonomic profiling used Sourmash 4.2.4 (GTDBv207 reference database); functional profiling employed HUMAnN 3.6 with gene families mapped to MetaCyc pathways.

RESULTS: α-diversity differed across diagnosis groups and inversely correlated with increasing BMI (Inverse Simpson p = 0.025). β-diversity differed by diagnosis group and BMI. No significant differences in diversity were observed based on age, menopausal status or mammographic breast density. BMI was also associated with enrichment of Dorea, Blautia, and Streptococcus species. Functional pathway profiling showed greater relative abundance of genes involved in NAD biosynthesis, folate metabolism, and aromatic amino acid metabolism pathways with higher BMI. Cross-referencing the most significant taxonomic and functional pathway findings suggested enrichment of Blautia species, via tryptophan metabolism, might link to NAD biosynthesis.

CONCLUSION: In this study of women with benign, high-risk/non-invasive, and invasive breast disease, BMI was associated with distinct differences in gut microbial taxonomy and functional pathway profiles. These hypothesis-generating findings provide a rationale for future study to determine how the obesity-associated microbiome contributes to breast cancer development.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Female
*Breast Neoplasms/pathology/microbiology/etiology
*Body Mass Index
Middle Aged
*Gastrointestinal Microbiome
*Obesity/complications/microbiology
Aged
Adult
Metagenomics/methods
Metagenome

@article {pmid42671657,
year = {2026},
author = {Nazrin, MRR and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Subramanian, S},
title = {Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {9},
pages = {},
pmid = {42671657},
issn = {1572-9699},
mesh = {Animals ; Bees/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Species Specificity ; Metagenomics ; Phylogeny ; Biodiversity ; *Mycobiome ; },
abstract = {Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon = 5.90; Simpson = 0.98) than in A. cerana (Shannon = 4.01; Simpson = 0.94; p > 0.05), while fungal diversity remained comparable between species (p > 0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R[2] = 0.7989, p > 0.05) and fungal communities (R[2] = 0.7218, p > 0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.},
}

Animals
Bees/microbiology
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
Species Specificity
Metagenomics
Phylogeny
Biodiversity
*Mycobiome

@article {pmid42671761,
year = {2026},
author = {do Socorro Foro Ramos, E and de Oliveira Guimaraes, L and de Oliveira Ribeiro, G and Santos, MA and Pandey, RP and Reginato, SL and Telles-de-Deus, J and Bergo, ES and Mucci, LF and de Camargo-Neves, VLF and da Costa, AC and Leal, E and Kirchgatter, K},
title = {Virome of neotropical Sabethes mosquitoes reveals two novel viruses in the Spiciviridae family.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {42671761},
issn = {1572-994X},
support = {2018/16232-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/50345-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 305566/2025-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303040/2025-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {The family Spiciviridae, belonging to the order Ghabrivirales, is currently composed of only one officially recognized genus, Spicivirus. However, metagenomic studies have revealed an increasing diversity of related viruses, suggesting that the current classification may underestimate their evolutionary complexity. In this context, the aim of the present study was to detect and characterize new viruses related to the Spiciviridae in the family Culicidae mosquitoes. A total of nineteen mosquito pools were sequenced and analyzed using metagenomic approaches and bioinformatics tools. Among these, two novel viruses were identified in four pools (S4, S11, S18, and S19), provisionally named Sabethes virus 1 (SV1) and Sabethes virus 2 (SV2). Phylogenetic inference revealed clades with strong statistical support and genetic divergences greater than 20% in the RNA-dependent RNA polymerase (RdRp) protein. These findings contribute to a detailed analysis of the genomic diversity associated with Spiciviridae. Although Spicivirus is currently the only genus officially recognized, our results suggest the presence of viruses that may represent new taxonomic groupings not yet described by the ICTV.},
}

@article {pmid42672116,
year = {2026},
author = {Andersen, SE and Kirsch, JM and Singh, N and Garrett, SR and Whitney, JC and Hesselberth, JR and Duerkop, BA},
title = {Small serine recombinases are markers for antiphage defense system discovery.},
journal = {PLoS biology},
volume = {24},
number = {8},
pages = {e3003991},
doi = {10.1371/journal.pbio.3003991},
pmid = {42672116},
issn = {1545-7885},
abstract = {Renewed interest in phage therapy has highlighted a need to understand how bacteria subvert phage infection through antiphage defense systems. Traditionally, strategies to identify antiphage defense systems lack throughput or have limitations for bacterial species where antiphage defense systems are understudied. Herein, we developed a bioinformatic pipeline that uses a small serine recombinase to identify known and unknown antiphage defense systems. Using this approach to query reference genomes and metagenomes, we show that small serine recombinase genes are genetically linked to antiphage defense systems and serve as bait for finding these systems across diverse bacterial phyla. Using co-transcription predictions and statistical analysis of protein domain abundances, we experimentally validated our bioinformatic approach by discovering that KAP P-loop NTPases are fused to putative antiphage domains and reinforce prokaryotic Schlafen proteins as a new class of antiphage defense. Our work shows that small serine recombinases are a reliable genetic marker for the discovery of antiphage defenses across diverse bacterial phyla.},
}

@article {pmid42673455,
year = {2026},
author = {Farrell, SP and D'Angelo, T and Yiu, DS and Kelminal Pakkir Shah, A and Stincone, P and Countway, PD and Petras, D and Brady, DC and Rasher, DB},
title = {Kelp forest collapse alters the reef microbiome and associated metabolome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {36},
pages = {e2525548123},
doi = {10.1073/pnas.2525548123},
pmid = {42673455},
issn = {1091-6490},
support = {OIA-1489227//NSF (NSF)/ ; NA//Louise H. & David S. Ingalls Foundation/ ; 2124-390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; NA//Essex Avenue Foundation/ ; NA//PADI Foundation (The PADI Foundation)/ ; },
mesh = {*Microbiota/physiology ; *Kelp/microbiology ; *Metabolome ; *Coral Reefs ; Ecosystem ; Climate Change ; },
abstract = {In many temperate regions experiencing rapid ocean warming, kelp forests are being replaced by low-lying turf algae. Yet, whether this change in biogenic habitat alters reef-level microbial structure and function, including carbon and nutrient cycling, remains largely unknown. Here, we integrated shotgun metagenomics and nontargeted metabolomics to reveal that kelp forest loss alters the composition of the reef microbial community and its associated biochemical machinery, resulting in distinct metabolomes and microbially driven elemental use/transformations on kelp- vs. turf-dominated reefs. Our results therefore suggest that microbes play a key role in shaping kelp forest ecosystem functioning. Further, they demonstrate that human-induced ocean warming has cascading effects on microbially mediated chemistry, with implications for coastal carbon storage and nutrient regeneration.},
}

*Microbiota/physiology
*Kelp/microbiology
*Metabolome
*Coral Reefs
Ecosystem
Climate Change

@article {pmid42673474,
year = {2026},
author = {Dragone, NB and Childress, MK and Mendez, N and Galletta, J and Vanderburgh, C and Bueno de Mesquita, CP and DeAngelis, KM and Quandt, CA and Leung, PM and Greening, C and Adams, BJ and Fierer, N},
title = {Evidence for endemism and local adaptation in Antarctic soil bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {37},
pages = {e2611373123},
doi = {10.1073/pnas.2611373123},
pmid = {42673474},
issn = {1091-6490},
support = {NSF 21-567//NSF (NSF)/ ; EAR 1950681//NSF (NSF)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Arthrobacter/genetics/physiology/classification ; *Adaptation, Physiological/genetics ; Phylogeny ; },
abstract = {Antarctic soils represent one of the most extreme environments for microbial life on Earth, yet they harbor heterogeneous and diverse microbial communities. Biologists have long hypothesized that Antarctic microorganisms are unique from those found on other continents due to the extreme geographic isolation and the cold, dry, and challenging conditions typical of Antarctica. To test this hypothesis, we focused on a cosmopolitan bacterial genus, Arthrobacter, that is widely distributed across global soils. We first profiled a global metagenomic dataset from both Antarctic and non-Antarctic surface soils to quantify the distributions of Arthrobacter strains. Despite high strain-level diversity, 90% of the strains found in the Antarctic soils were only found on the continent. We then used cultivation-based phenotypic analyses and strain-level genomic comparisons to assess how Antarctic strains and non-Antarctic strains differ in their traits and environmental preferences. Not only did we find evidence of endemism, but Antarctic Arthrobacter also have genomic characteristics and environmental tolerances that suggest they are uniquely adapted to Antarctic conditions.},
}

Antarctic Regions
*Soil Microbiology
*Arthrobacter/genetics/physiology/classification
*Adaptation, Physiological/genetics
Phylogeny

@article {pmid42666306,
year = {2026},
author = {Li, W and Yuan, Y and Li, X and Zhou, J},
title = {Ecological assembly of mucosal and fecal microbiomes in ulcerative colitis across genes, functions, and species.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851847},
pmid = {42666306},
issn = {1664-302X},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is associated with gut microbial dysbiosis, yet the ecological processes underlying community assembly remain unclear.

METHODS: Here, we applied Sloan's neutral community model to examine the relative contributions of stochastic and deterministic processes across multiple ecological layers, including metagenomic genes (MGs), molecular functions (MFs), and microbial species (archaea, bacteria, fungi, and viruses), in fecal and mucosal microbiota from healthy controls and ulcerative colitis (UC) patients.

RESULTS: Across all layers, most MGs, MFs, and species conformed to neutral expectations, indicating a dominant role of stochastic processes in community assembly. However, UC was consistently associated with an increased proportion of neutral MFs and species, accompanied by a reduction in non-neutral components, suggesting weakened selective constraints under disease conditions. Ecological niche further modulated these patterns. Fecal communities harbored significantly higher proportions of non-neutral MFs and species compared to mucosal communities, indicating stronger deterministic processes in feces. Analysis of selection-state transitions revealed extensive changes in selection status in UC, particularly in mucosal environments, where both functional and taxonomic profiles showed marked transition. These changes were primarily driven by the gain and loss of selection rather than directional switching, indicating that UC alters the strength and presence of selection rather than reversing its direction.

DISCUSSION: Together, these findings provide a multi-layered ecological framework for understanding UC-associated dysbiosis, highlighting increased neutrality and selection rewiring as key features of microbial community assembly under disease conditions.},
}

@article {pmid42666371,
year = {2026},
author = {Araneta, RP and Choi, Y and Lee, JH and Yoo, HJ and Lee, YY and Cho, A and Yoon, HY and Kim, JM and Park, NJ and Seo, I and Chong, GO and Park, CM},
title = {HPV vaccination associates with Lactobacillus crispatus-dominant vaginal microbiota in women with cervical lesions: a metagenomic study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1906211},
pmid = {42666371},
issn = {1664-302X},
abstract = {BACKGROUND: Human papillomavirus (HPV) vaccination provides high-level protection against cervical cancer through type-specific antibodies, although breakthrough and persistent high-risk HPV (hrHPV) infections may still occur in some vaccinated women. In addition to neutralizing antibodies, vaccination elicits other immune mechanisms that may influence viral persistence and disease progression. Because mucosal immunity is closely linked to the vaginal microbiota, microbial composition may also play an important role in HPV susceptibility, with Lactobacillus crispatus dominance associated with protection, and dysbiosis with impaired mucosal immunity. Whether HPV vaccination is associated with favorable microbiota signatures in women with confirmed cervical cancer-related conditions remains unknown.

METHOD: We analyzed vaginal samples via shotgun metagenomic sequencing from a cross-sectional study of 59 pre-menopausal women (<50 years) with confirmed cervical lesions (HPV-unvaccinated n = 26, vaccinated n = 33).

RESULTS: Alpha diversity (Shannon and Inverse Simpson indices) did not differ significantly by vaccination status, suggesting within-sample microbial diversity between the groups, but Bray-Curtis-based PERMANOVA indicated a statistically significant difference in overall community composition between groups (p = 0.042). Among women with CST I, 90.9% were vaccinated, whereas among women with CST IV, 60.0% were unvaccinated. At the species level, L. crispatus relative abundance was higher in vaccinated women in the unadjusted analysis; however, this association was attenuated and was not statistically significant after multivariable adjustment. HPV vaccination status was associated with a higher prevalence of L. crispatus-dominant, health-associated vaginal microbiota among women with cervical lesions.

CONCLUSION: These findings support the hypothesis that HPV vaccination status is associated with L. crispatus dominance in this population, but mechanistic pathways remain to be elucidated.},
}

@article {pmid42666411,
year = {2026},
author = {Liu, J and He, X and Zhao, W and Du, L and Qiao, L and Qing, L},
title = {Aztreonam-avibactam therapy following surgical source control for bla NDM -positive carbapenem-resistant Klebsiella pneumoniae intra-abdominal infection in an infant: a case report.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1897083},
pmid = {42666411},
issn = {1663-9812},
abstract = {Treating carbapenem-resistant Klebsiella pneumoniae (CRKP) is challenging, particularly when resistance is mediated by New Delhi metallo-β-lactamase (NDM). Clinical experience with fixed-combination aztreonam-avibactam (ATM-AVI) in young infants remains extremely limited. Here, we report a case of a 2-month-old boy who underwent emergency laparotomy for intestinal obstruction owing to small bowel volvulus with segmental necrosis, followed by bowel resection and reanastomosis. His postoperative course was complicated by respiratory failure, coagulopathy, septic shock, recurrent abdominal distension, and massive ascites. Blood cultures were negative, whereas metagenomic next-generation sequencing of blood detected K. pneumoniae and Enterococcus faecium. Owing to the worsening of his condition, diagnostic paracentesis and repeat laparotomy were performed, revealing an anastomotic leak. Intraoperative pus culture yielded bla NDM -positive CRKP. The isolate was resistant to carbapenems and ceftazidime-AVI but was susceptible to ATM-AVI, with a minimum inhibitory concentration of ≤4 mg/L. ATM-AVI was administered at 30 mg/kg every 8 h, based on the aztreonam component, for 14 days; linezolid and fluconazole were co-administered as part of the broader anti-infective regimen. The combination of definitive surgical source control, targeted antimicrobial therapy, and comprehensive intensive care successfully controlled the infection and stabilized his hemodynamics. The patient defervesced within 24 h of the first ATM-AVI dose. Inflammatory markers declined rapidly, allowing safe extubation. Follow-up abdominal cultures remained negative. No hepatic or renal toxicity was observed during treatment. This case suggests that, when combined with adequate surgical source control, ATM-AVI may represent a valuable mechanism- and susceptibility-guided pharmacological component in a multidisciplinary treatment paradigm for severe bla NDM -positive CRKP infections in selected infants.},
}

@article {pmid42667435,
year = {2026},
author = {De, P and Chakraborti, S and Bhabai, B and Nath, S and Ghosh, PK and Khatun, N and Asif, SM},
title = {From traditional retting to precision bioprocessing: microbial ecology, enzymatic selectivity, and systems biology of jute retting.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {9},
pages = {},
pmid = {42667435},
issn = {1572-9699},
mesh = {*Systems Biology/methods ; *Lignin/metabolism/chemistry ; Microbial Consortia ; Bacteria/metabolism ; },
abstract = {Jute is one of the world's most important lignocellulosic fibre crops, yet its commercial value remains highly dependent on retting, a biologically mediated fibre extraction process still largely governed by empirical practices and variable environmental conditions. Recent advances in microbial ecology, enzymology, molecular biology, and bioprocess engineering have transformed retting from a traditional post-harvest operation into a controllable lignocellulosic bioconversion process. This review synthesizes current understanding of the structural organization of jute bast fibres, selective degradation of plant cell-wall polymers, microbial succession, extracellular enzyme networks, and physicochemical factors regulating fibre liberation. It highlights the coordinated interactions among cell-wall architecture, microbial communities, enzyme specificity, and environmental conditions that collectively determine retting efficiency and fibre quality. Emerging precision retting strategies, including defined microbial consortia, enzyme-assisted retting, ribbon retting, controlled processing systems, and water-efficient technologies, are critically evaluated for their potential to improve process reproducibility, fibre quality, and environmental sustainability. The review also examines metagenomics, metatranscriptomics, metaproteomics, metabolomics, systems biology, and artificial intelligence as enabling technologies for microbiome-guided process monitoring, predictive modelling, and digital decision support. Furthermore, this review discusses the integration of precision retting within circular bioeconomy frameworks through resource recovery, pollution mitigation, climate-resilient processing, and lignocellulosic biorefineries. Key knowledge gaps, including limited understanding of microbial interactions, lack of standardized microbial consortia, insufficient process-monitoring tools, fragmented multi-omics datasets, and challenges in industrial scale-up, are identified. Overall, this review presents a systems-level framework for advancing jute retting toward standardized, predictive, and environmentally sustainable precision bioprocessing.},
}

*Systems Biology/methods
*Lignin/metabolism/chemistry
Microbial Consortia
Bacteria/metabolism

@article {pmid42664591,
year = {2026},
author = {Zhao, JY and Xu, L and Sun, RQ and Song, MQ and Zeng, JH and Wei, HM and Sun, JQ},
title = {Description of two novel Marinobacter species isolated from saline-alkali soil: Marinobacter alkalisoli sp. nov. and Marinobacter shunpengi sp. nov.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {5},
pages = {126757},
doi = {10.1016/j.syapm.2026.126757},
pmid = {42664591},
issn = {1618-0984},
abstract = {Four Gram-staining negative, non-motile, rod-shape bacteria, named strains GN3S48[T], HN1S83, LN3S78[T], and M1N3S26, were isolated from the bulk saline soils, in Baotou, China. Among them, strains GN3S48[T] and HN1S83 could degrade 100 mg l[-1]n-hexadecane as sole carbon and energy source for their growth. Phylogenetic analyses showed that the four strains always formed two distinct clades: Strain LN3S78[T] clustered with strain M1N3S26, and strain GN3S48[T] clustered with strain HN1S83. Nonetheless, all four strains tightly clustered and shared the highest 16S rRNA gene similarities with Marinobacter species. Specifically, clade of strains LN3S78[T] and M1N3S26 cluster with Marinobacter lipolyticus CGMCC 1.7282[T], while clade of strains GN3S48[T] and HN1S83 clustered with Marinobacter zhanjiangensis CCTCC AB 208029[T]. The ANIb and AAI values between strains GN3S48[T] and HN1S83 were 96.4% and 94.6%, respectively, while those between strains LN3S78[T] and M1N3S26 were 99.3% and 99.1%, respectively. All ANI and AAI values between the four strains and their closest relatives were below the 95.0% species delineation threshold. The predominant respiratory quinone of the four strains was Q-9. Based on this polyphasic result, the two clades should be identified as two novel species within the genus Marinobacter. Thus, Marinobacter alkalisoli sp. nov. (type strain GN3S48[T] = CGMCC 1.62232[T] = KCTC 8701[T] = JCM 37359 [T]) and Marinobacter shunpengi sp. nov. (type strain LN3S78[T] = CGMCC 1.62233[T] = KCTC 8702[T] = JCM 37360[T]) are proposed. The metagenomic analysis revealed that the two new species are globally distributed in high-salt habitats. In addition, comparative genomic analysis confirmed that alkane-degrading genes are ubiquitous in Marinobacter strains.},
}

@article {pmid42664608,
year = {2026},
author = {Hao, L and Zhang, D and Zhao, Z and Wang, J and Wang, R and Li, M},
title = {Application-dependent effects of tea waste biochar on PFAS mobility and N2O and CH4 emissions in agricultural soil.},
journal = {Waste management (New York, N.Y.)},
volume = {226},
number = {},
pages = {115839},
doi = {10.1016/j.wasman.2026.115839},
pmid = {42664608},
issn = {1879-2456},
abstract = {Per- and polyfluoroalkyl substances (PFAS) in agricultural soils can migrate into crops and may alter soil greenhouse gas emissions, yet remediation strategies rarely address these risks simultaneously. This study evaluated tea waste biochar (TWB) produced at 400, 500, and 600 °C and applied at 5-20 g per pot by whole-soil mixing or surface-layer placement in a simulated PFAS-contaminated soil-leachate-plant system. Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) distributions, nitrous oxide (N2O) and methane (CH4) fluxes, and microbial responses were examined. TWB produced at 500 °C showed the most favorable combination of pore accessibility, surface hydrophobicity, and interfacial charge, with material-associated PFOS and PFOA enrichments of 0.12 and 0.57 μg/g, respectively. Whole-soil mixing with TWB-500 lowered soil and leachate PFAS levels and reduced PFAS concentrations in plant shoots by approximately 36% relative to the contaminated control. TWB treatments also reduced cumulative N2O emissions and enhanced net CH4 uptake. Metagenomic analysis showed lower relative abundances of genes associated with nitrogen fixation, ammonia oxidation, and several N2O-producing pathways, whereas CH4-cycling genes responded differently to the two application methods. Organic fluorine transformation genes were not enriched, indicating that PFAS control mainly resulted from physicochemical retention rather than enhanced microbial defluorination. Overall, TWB-500 can integrate PFAS stabilization with greenhouse gas management, but the optimal placement depends on the remediation objective: whole-soil mixing favors PFAS immobilization, whereas surface-layer application provides greater greenhouse gas mitigation.},
}

@article {pmid42664817,
year = {2026},
author = {Sun, ZF and Chen, C and Xing, DF and Wang, AJ and Liu, DM and Ren, NQ and Zhao, L},
title = {Achieving mesophilic-level methane production in low-temperature anaerobic digestion by zero-valent iron-driven electron-transfer reconfiguration.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126766},
doi = {10.1016/j.watres.2026.126766},
pmid = {42664817},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) at low temperature is attractive for reducing the energy demand of sludge treatment, but methane production is strongly constrained by slow microbial kinetics and inefficient interspecies electron transfer. This study demonstrates that zero-valent iron (ZVI) exhibited a temperature-dependent shift in its dominant electron-transfer function. ZVI was applied to the AD of waste activated sludge across 20-35℃ at dosages of 0-20 g/L. Methane yield enhancement increased from 10.7% at 35℃ to 136.4% at 20℃, and the ZVI-amended reactor at 20℃ produced more methane than the unamended mesophilic control. The optimal ZVI dosage increased 60-fold as temperature decreased. A stoichiometric calculation based on endpoint dissolved Fe[2+] yielded a theoretical CH4 equivalent of 2.7 mL CH4/g VS at 20 °C, corresponding to <5% of the observed methane increment. Stage-specific kinetic rates changed little at 35℃, whereas acidogenesis and hydrogenotrophic methanogenesis increased at 20 °C. Paired metagenomic and metatranscriptomic analyses further supported a temperature-dependent electron-transfer reconfiguration. At 35℃, ZVI primarily promoted H2-associated hydrogenotrophic methanogenesis, whereas at 20℃ it promoted ZVI-assisted conductive electron exchange together with enhanced formate-associated electron transfer, as supported by increased activity of electroactive microorganisms, enrichment of formate-utilizing methanogens (Methanobacterium formicicum), and upregulation of formate-related genes including fdo and fdh. These findings establish a conceptual framework demonstrating that the electron-transfer function of ZVI is not a fixed property but dynamically regulated by environmental conditions, providing new insights into the adaptive roles of conductive materials for low-temperature anaerobic sludge digestion with reduced dependence on digester heating.},
}

@article {pmid42664954,
year = {2026},
author = {Zhang, B and Zhang, Y and Cai, Y and Cheng, S and Han, Z and Yin, X and Xie, T and Tan, Y and Feng, Y and Wang, Y and Guo, X and Shen, L and Peng, Z},
title = {Lactobacillus salivarius potentiates gastrointestinal cancer immunotherapy through its metabolite chenodeoxycholic acid.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103009},
doi = {10.1016/j.xcrm.2026.103009},
pmid = {42664954},
issn = {2666-3791},
abstract = {Immune checkpoint inhibitor therapy has improved gastrointestinal (GI) cancer management; however, many patients exhibit resistance. Although gut microbiota influences immunotherapeutic responses, the underlying mechanisms remain unclear. Metagenomic analysis of 278 GI cancer patients reveals that Lactobacillus salivarius (L. salivarius) is enriched in responders and enhances anti-PD-1 efficacy in syngeneic tumor models by increasing the infiltration of antitumor M1-like macrophages and CD8[+] T cells and enhancing CD8[+] T cell effector function. L. salivarius-associated chenodeoxycholic acid (CDCA) is identified as a functional metabolite. CDCA recapitulates the antitumor effects of L. salivarius and significantly improves anti-PD-1 efficacy in vivo, an effect attenuated by depleting macrophages or CD8[+] T cells. Mechanistically, CDCA-induced reactive oxygen species triggers immunogenic cell death in tumor cells and polarizes macrophages toward antitumor M1 phenotype, activating CD8[+] T cell antitumor immunity. These findings identify L. salivarius and its associated metabolite CDCA as a promising adjuvant for potentiating immunotherapy in GI cancers.},
}

@article {pmid42665077,
year = {2026},
author = {Fan, Q and Bai, J and Wang, X and Zhao, Z and Zhao, X},
title = {Metagenomic Characterization of Potential Exposure to Genetic Hazards at the Interface Between Grazing Livestock and Przewalski's Gazelle.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129059},
doi = {10.1016/j.envpol.2026.129059},
pmid = {42665077},
issn = {1873-6424},
abstract = {Livestock and endangered wildlife increasingly share grazing landscapes, yet the sources, mobility-associated contexts, and bacterial hosts of livestock-associated genetic hazards in wildlife microbiomes remain poorly resolved. We analyzed metagenomes from yak, Tibetan sheep, Przewalski's gazelle, and local topsoil within an Acquired Genetic Risk (AGR) conceptual framework integrating genetic hazard burden, compositional source attribution, mobility-associated evidence, and bacterial genomic context. MRGs and Rank I and Rank III ARGs were more abundant in livestock than in Przewalski's gazelle, whereas VF abundance was highest in yak. FEAST attributed approximately 64% of the Przewalski's gazelle resistome composition to the two livestock source profiles, less than 1% to sampled topsoil, and approximately 36% remained unassigned. MGE profiles were associated with ARGs, MRGs, and VFs, while tnpA ranked highest in random forest models and was associated with total ARG abundance (R[2] = 0.618). Short-read contigs containing hazard genes and MGE markers provided localized mobility-associated sequence context. Genome-resolved analysis identified distinct bacterial contexts: TS.Bin143, an Escherichia coli MAG from Tibetan sheep, contained ARGs, MRGs, VFs, tnpA, and IS91, whereas PG.Bin275, a Hylemonella sp. MAG from Przewalski's gazelle, contained tnpA. These findings extend wildlife resistome assessment beyond abundance profiling toward source attribution, mobility-associated sequence context, and bacterial host resolution, supporting multilevel surveillance of genetic hazard exposure at livestock-wildlife interfaces.},
}

@article {pmid42665338,
year = {2026},
author = {Orwa, S and Vlajic, M and Cavani, E and Devall, AE and Hugerth, LW and Brusselaers, N and De Vos, WM},
title = {PREVENT 1, a nationwide Swedish infant cohort for longitudinal gut microbiome profiling and early-life health outcomes: cohort profile.},
journal = {BMJ open},
volume = {16},
number = {8},
pages = {e118233},
doi = {10.1136/bmjopen-2026-118233},
pmid = {42665338},
issn = {2044-6055},
mesh = {Humans ; Infant ; Sweden/epidemiology ; Female ; *Gastrointestinal Microbiome ; Male ; Feces/microbiology ; Prospective Studies ; Infant, Newborn ; Surveys and Questionnaires ; Longitudinal Studies ; Breast Feeding/statistics & numerical data ; Metagenomics ; Child Development ; },
abstract = {PURPOSE: PREVENT 1 is a nationwide, prospective Swedish infant cohort established to characterise gut microbiome development during the first 2 years of life and to relate microbial trajectories to feeding, infections, growth and everyday well-being. The study integrates repeated infant stool sampling with shotgun metagenomics analysis with aligned parental questionnaires, stool photographs and infant cry recordings collected at three approximately 3-month intervals for each infant.

PARTICIPANTS: Families were recruited nationwide in Sweden from September 2023 through targeted digital channels. Eligible participants were term-born infants residing in Sweden and aged <1 year at enrolment. Baseline questionnaire data and stool samples were collected from 253 infants. Parents completed questionnaires covering socio-demographic characteristics and health, pregnancy and delivery, postnatal factors, infant environment, feeding and growth, infections and other health outcomes, gastrointestinal symptoms and everyday well-being.

FINDINGS TO DATE: Retention was high, with 248 families completing at least one follow-up questionnaire at Phase 2 and 243 at Phase 3. For stool samples, 250 infants provided at least two samples and 241 provided all three. At enrolment, 42.3% of infants were older than 7 months, 73.9% had weight-for-length z-scores in the normal range and exclusive breastfeeding at 4 months was reported for 58.9%.

FUTURE PLANS: Three-phase sample and questionnaire data collection was completed in December 2024. Future analyses will examine microbiome features, resistome profiles and functional pathways in relation to antibiotic exposure, feeding, growth and infant health outcomes. Subject to ethical approval and participant consent, follow-up may include further stool collection and Swedish register linkage.

TRIAL REGISTRATION NUMBER: NCT06285630.},
}

Humans
Infant
Sweden/epidemiology
Female
*Gastrointestinal Microbiome
Male
Feces/microbiology
Prospective Studies
Infant, Newborn
Surveys and Questionnaires
Longitudinal Studies
Breast Feeding/statistics & numerical data
Metagenomics
Child Development

@article {pmid42665791,
year = {2026},
author = {Lv, Y and Ye, C and Cao, H and Zhang, C and Wang, Y and Jiang, H},
title = {Presumably recurrent Ureaplasma parvum infection in a female peritoneal dialysis patient: a case report and literature review.},
journal = {BMC nephrology},
volume = {27},
number = {1},
pages = {},
pmid = {42665791},
issn = {1471-2369},
mesh = {Humans ; Female ; *Ureaplasma Infections/diagnosis/drug therapy/etiology ; Adult ; *Ureaplasma/isolation & purification ; *Peritonitis/etiology/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Recurrence ; *Peritoneal Dialysis, Continuous Ambulatory/adverse effects ; Azithromycin/therapeutic use ; Peritoneal Dialysis/adverse effects ; Levofloxacin/therapeutic use ; },
abstract = {BACKGROUND: Peritoneal dialysis-associated peritonitis (PDAP) caused by Ureaplasma parvum (U. parvum) is exceedingly rare, and its diagnosis is particularly challenging due to the organism's biological characteristics and the limitations of conventional detection methods. To date, only sporadic case reports are available, but the diagnostic processes and clinical characteristics of PDAP caused by U. parvum infection have not been comprehensively reported yet.

CASE PRESENTATION: We report a 35-year-old female patient undergoing continuous ambulatory peritoneal dialysis (CAPD) who experienced three episodes of peritonitis within a six-month period. Despite empirical antibiotic therapy leading to clinical improvement, routine microbiological cultures of the dialysate remained negative during each episode. During the third episode, metagenomic next-generation sequencing (mNGS) of the peritoneal dialysis (PD) effluent finally detected U. parvum as the causative pathogen. Following removing a potential risk factor, an intrauterine device (IUD), and adjusting the antimicrobial therapy to intraperitoneal (IP) levofloxacin and oral azithromycin, the patient achieved complete recovery and successfully resumed PD. Based on this experience, we documented the characteristic clinical profile of such infections and proposed an exploratory clinical diagnosis and treatment flowchart.

CONCLUSIONS: Patients with recurrent culture-negative PDAP, especially female with an IUD, should be evaluated for U. parvum infection as a potential pathogen. mNGS facilitates the rapid detection of pathogens that traditional methods may fail to identify. Effective management of such infections necessitates not only targeted antimicrobial therapy guided by precise pathogen identification, but also the removal of potential risk factors such as the IUD.},
}

Humans
Female
*Ureaplasma Infections/diagnosis/drug therapy/etiology
Adult
*Ureaplasma/isolation & purification
*Peritonitis/etiology/microbiology/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use
Recurrence
*Peritoneal Dialysis, Continuous Ambulatory/adverse effects
Azithromycin/therapeutic use
Peritoneal Dialysis/adverse effects
Levofloxacin/therapeutic use

@article {pmid42665998,
year = {2026},
author = {Lu, J and Sun, Y and Zeng, Y and Lau, EYT and Lan, Z and Ye, S and Zhang, R and Hu, R and Cui, C and Liang, JQ},
title = {Agathobacter rectalis suppresses colorectal tumorigenesis via an epigallocatechin-SREBF2 axis controlling cholesterol metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2724227},
doi = {10.1080/19490976.2026.2724227},
pmid = {42665998},
issn = {1949-0984},
mesh = {Animals ; *Cholesterol/metabolism ; *Sterol Regulatory Element Binding Protein 2/metabolism/genetics ; *Colorectal Neoplasms/metabolism/microbiology/prevention & control/pathology ; Mice ; *Catechin/metabolism/analogs & derivatives ; Humans ; *Eubacteriales/metabolism/physiology ; *Carcinogenesis/metabolism ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Feces/microbiology/chemistry ; },
abstract = {Beneficial effects of the gut commensal Agathobacter rectalis (Ar) are reported in diseases, yet its role in colorectal cancer (CRC) remains unclear. Here, metagenomic analysis revealed consistent fecal Ar depletion across CRC cohorts. In Apc [min/+] mice, Ar inhibited colon tumorigenesis, reducing tumor number and volume versus E. coli and PBS controls. LC-MS/MS metabolomics showed decreased fecal cholesterol and altered lipid/cholesterol pathways after Ar treatment. In vitro, Ar-conditioned medium suppressed CRC cell growth, clonogenicity, migration, and cell cycle progression. LC-MS/MS identified (-)-epigallocatechin (EGC) as an Ar-derived metabolite absent in control bacteria. EGC recapitulated Ar-mediated anti-CRC effects in vitro and in vivo, with metabolic changes linked to lipid/cholesterol pathways. Transcriptomics showed that EGC suppressed SREBP signaling, cholesterol metabolism, and MAPK pathways. Mechanistically, EGC reduced nuclear SREBF2 and its transcriptional activity, downregulated cholesterol synthesis/metabolism genes, including FDPS and PCSK9, and suppressed MAPK signaling. Molecular docking suggested that EGC may bind pSREBF2 or SCAP. Cellular thermal shift assay revealed that EGC interacts with and stabilizes pSREBF2, but not SCAP. Co-immunoprecipitation demonstrated that EGC reduces pSREBF2-SCAP interaction, thereby inhibiting SCAP-mediated SREBF2 cleavage activation. Together, these findings define an Ar-EGC microbe-metabolite axis and support Ar/EGC-based interventions targeting cholesterol metabolism in CRC.},
}

Animals
*Cholesterol/metabolism
*Sterol Regulatory Element Binding Protein 2/metabolism/genetics
*Colorectal Neoplasms/metabolism/microbiology/prevention & control/pathology
Mice
*Catechin/metabolism/analogs & derivatives
Humans
*Eubacteriales/metabolism/physiology
*Carcinogenesis/metabolism
Gastrointestinal Microbiome
Mice, Inbred C57BL
Feces/microbiology/chemistry

@article {pmid42666020,
year = {2026},
author = {Fan, Y and Tao, Y and Hua, B and Kardol, P and Kuzyakov, Y and Pang, S and Wu, Y and Li, T and Yang, W and Wu, H and Goncharov, AA and Korotkevich, AY and Mao, R and Zhang, Y and Zhang, X},
title = {Decadal Resampling Reveals Widespread Increases in Soil Microbial Diversity Associated With Nitrogen Deposition.},
journal = {Global change biology},
volume = {32},
number = {9},
pages = {e71083},
doi = {10.1111/gcb.71083},
pmid = {42666020},
issn = {1365-2486},
support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; //Top-Notch Young Talents Program (to Ximei Zhang) of China/ ; //RUDN University Strategic Academic Leadership Program/ ; },
mesh = {*Soil Microbiology ; *Nitrogen/analysis/metabolism ; China ; *Microbiota ; *Biodiversity ; Forests ; Grassland ; Metagenomics ; Nitrogen Cycle ; Soil/chemistry ; Bacteria ; },
abstract = {Simulated manipulation experiments, such as nitrogen addition to mimic atmospheric nitrogen deposition, are widely used in global change research. However, experimental manipulations may differ from real-world environmental change in their intensity, duration, and co-occurrence, leaving long-term changes in soil microbial communities and soil health insufficiently understood. To address this gap, we resampled soils from 38 forest and grassland ecosystems across eastern China in 2009 and 2019 and assessed microbial taxonomic and functional diversity using shotgun metagenomics. Microbial diversity increased by 17% over the decade, accompanied by clear shifts in community composition. Among the environmental variables considered, nitrogen deposition (~19 kg nitrogen ha[-1] year[-1] across ecosystems) was the strongest predictor of changes in seven of 12 microbial community metrics. Larger nitrogen deposition was also associated with increased relative abundances of nitrogen-cycling genes and reduced spatial turnover in microbial community composition. These effects were consistent with a potential alleviation of nitrogen limitation and weakening of deterministic community assembly, although these mechanisms could not be directly established. In addition, increases in genes associated with carbon degradation and phosphorus cycling, together with declines in the relative abundances of pathogens, antibiotic resistance genes, and DNA viruses, coincided with the raise of the composite soil health index. Our findings demonstrate widespread decadal increases in soil microbial diversity and soil health across eastern China, with nitrogen deposition emerging as their strongest environmental factor. These results highlight that microbial responses to long-term ambient environmental change can differ markedly from responses inferred from short-term or high-intensity manipulation experiments.},
}

*Soil Microbiology
*Nitrogen/analysis/metabolism
China
*Microbiota
*Biodiversity
Forests
Grassland
Metagenomics
Nitrogen Cycle
Soil/chemistry
Bacteria

@article {pmid42666033,
year = {2026},
author = {Zhou, Z and Yu, R and Zhou, X and Shi, F and Lin, Z and Gao, P and Wang, L and Feng, N and Wu, Z and Wang, D},
title = {Gut Microbiota-Isoallolithocholic Acid Crosstalk Promotes Calcium Oxalate Kidney Stone Formation via PARP1-Mediated Parthanatos.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77289},
doi = {10.1002/advs.77289},
pmid = {42666033},
issn = {2198-3844},
support = {82500928//National Natural Science Foundation of China/ ; },
abstract = {Bile acids have been implicated in calcium oxalate (CaOx) nephrolithiasis. Here, we employ multi-omics approaches to identify isoallolithocholic acid (isoalloLCA) as the key bile acid elevated in the feces, serum, kidney, and urine of CaOx rats, confirmed by spatial metabolomics. 16S sequencing and metagenomic analyses indicate that elevated isoalloLCA levels in CaOx rats or individuals are likely of microbial origin. Mechanistically, isoalloLCA binds to PARP1 via specific molecular interactions validated by surface plasmon resonance and cellular thermal shift assays. Knockdown of PARP1 by adeno-associated virus microinjection or pharmacological inhibition with PARP1 inhibitor AZD5305 significantly attenuates isoalloLCA-mediated crystal deposition, renal tubular injury, and mitochondrial functional impairment in both the CaOx rat and mouse models. Furthermore, the antibiotic-mediated depletion of the gut microbiota in mice markedly reduced isoalloLCA levels, whereas fecal microbiota transplantationut contributes to isoalloLCA-mediated CaOx stone formation, demonstrating a causal link between gut microbiota and isoalloLCA. In vitro, isoalloLCA promoted oxalate-induced renal tubular epithelial cell injury and parthanatos via targeting PARP1, including DNA damage, excessive PARP1 activation, PAR accumulation, mitochondrial damage, nuclear translocation of AIF and MIF. These findings establish the microbiota-isoalloLCA-PARP1-parthanatos axis in CaOx nephrolithiasis and identify PARP1 as a promising therapeutic target for kidney stone management.},
}

@article {pmid42666298,
year = {2026},
author = {Zhou, J and Du, P and Liu, L and Wang, L and Liu, S and Yan, G},
title = {Multi-layer gut microbiome variation in type 2 diabetes despite preserved higher-order community structure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1902019},
pmid = {42666298},
issn = {1664-302X},
abstract = {BACKGROUND: Type 2 diabetes (T2D) has been consistently associated with alterations in the gut microbiome, although disease, treatment, diet, and other host factors may contribute to the observed patterns. How these associations are organized across different biological levels of the microbial ecosystem remains incompletely understood.

METHODS: We performed shotgun metagenomic sequencing of fecal samples from 82 individuals, including 41 patients with T2D and 41 age-, sex-, and body mass index-matched healthy controls. Taxonomic profiling, functional pathway analysis, enterotype characterization, ecological network inference, and interpretable machine-learning approaches were integrated to characterize microbiome variation across multiple organizational levels.

RESULTS: Despite clear clinical differences between groups, particularly fasting blood glucose, the overall ecological architecture of the gut microbiome remained broadly preserved. Dominant phylum-level composition and enterotype structure were maintained, whereas variation became apparent at finer biological scales. Species-level analyses identified 42 differentially abundant taxa. Community diversity analysis showed reduced Chao1 richness (P = 0.024), increased Simpson diversity (P = 0.024), unchanged Shannon diversity (P = 0.126), and a modest shift in community composition (PERMANOVA, R [2] = 0.040, P = 0.006). Functional profiling showed no pathway-level significance after multiple-testing correction but directional trends across several metabolic modules. Exploratory Spearman-based networks differed in topology between groups; because relative-abundance data are compositional, these differences cannot be interpreted as direct ecological interactions or definitive network rewiring. Machine-learning models achieved a within-cohort cross-validated AUC of up to 0.91, but lacked independent external validation.

CONCLUSIONS: These findings provide a multi-layer description of T2D-associated gut microbiome variation within this cohort. The data are consistent with preserved higher-order community organization accompanied by finer-scale differences in species composition, functional potential, community-state occupancy, statistical co-occurrence, and within-cohort discriminative features. Medication confounding, compositional effects, technical artifacts, and the absence of external validation limit causal, ecological, and diagnostic interpretation. Larger longitudinal, multi-site, medication-resolved, and independently validated studies are required.},
}

@article {pmid42657522,
year = {2026},
author = {Zheng, Y and Zhuang, H and Dan, L and Zhou, Y and Yan, B and Zhang, Y and Zou, D and Wang, X and Sun, J},
title = {Resistant starch alleviates intestinal fibrosis involving an acetate-mediated HDAC2-H3K27ac axis in fibroblasts.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01179a},
pmid = {42657522},
issn = {2042-650X},
abstract = {Dietary fibre-based interventions are of growing interest for the prevention and treatment of digestive diseases. In this study, we investigated the effect of resistant starch (RS) on intestinal fibrosis, a stricturing condition driven by excessive extracellular matrix (ECM) accumulation. RS was found to alleviate intestinal fibrosis in a dextran sulfate sodium (DSS)-induced chronic colitis mouse model, as evidenced by restored colon length, reduced ECM deposition (fibronectin and collagen I), and decreased levels of α-smooth muscle actin. Given that RS is fermented by the gut microbiota in the colon, metagenomic sequencing revealed that RS reshaped the composition of the gut microbiota and increased the abundance of beneficial gut bacteria, including Bacteroides acidifaciens, Faecalibaculum rodentium, and Bifidobacterium pseudolongum, which are known to enhance the production of short-chain fatty acids. Targeted metabolomic analysis further showed a marked increase in acetate levels, which was associated with reduced intestinal fibrosis. However, direct in vivo evidence that acetate is required for the anti-fibrotic effect of RS remains lacking. Using human (CCD-18Co) and primary mouse intestinal fibroblasts, the major ECM-producing cells that drive fibrosis progression, we demonstrated that acetate inhibited TGF-β-induced fibroblast activation by inhibiting histone deacetylase 2, thereby enhancing the acetylation level of histone H3 at lysine 27. Collectively, these results suggest a potential microbial-metabolic-epigenetic axis linking RS and acetate to fibrosis attenuation, which awaits causal validation in vivo. This axis holds promise as a therapeutic target for fibrotic diseases.},
}

@article {pmid42657570,
year = {2026},
author = {Dong, HJ and Zhang, K and Wang, GJ and Pan, Z},
title = {Effects and mechanisms of exogenous acyl-homoserine lactones on nitrogen removal from aquaculture wastewater.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {37},
number = {7},
pages = {2402-2414},
doi = {10.13287/j.1001-9332.202607.031},
pmid = {42657570},
issn = {1001-9332},
mesh = {*Nitrogen/isolation & purification/metabolism ; *Wastewater/chemistry ; *Acyl-Butyrolactones/chemistry/pharmacology ; *Aquaculture ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; 4-Butyrolactone/analogs & derivatives/chemistry ; Nitrates/isolation & purification ; Quorum Sensing ; },
abstract = {To improve microbial nitrogen removal efficiency in aquaculture wastewater, we added different carbon-chain-length acyl-homoserine lactones (AHLs) to continuous-flow reactors, including N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL), N-dodecanoyl-L-homoserine lactone (C12-HSL). We investigated their effects on nitrogen removal performance, sludge characteristics, and microbial community functions, and further analyzed the underlying mechanisms with metagenomics. The results showed that, compared with the nitrate concentration of (5.09±2.79) mg·L[-1] in the control effluent, all AHLs improved nitrate removal, reducing the effluent nitrate concentrations during stable ope-ration to (2.60±2.20), (1.87±1.31), (2.55±1.92), and (2.51±2.12) mg·L[-1], respectively. Among them, C6-HSL showed the best performance, which increased the nitrate removal rate by 8.0%, while maintained nitrite and total ammonia nitrogen at relatively low levels of (0.62±0.61) mg·L[-1] and (0.13±0.13) mg·L[-1], respectively. AHLs altered sludge surface morphology and extracellular polymeric substance composition, and promoted the enrichment of nitrogen-removing functional bacteria such as Denitratisoma, with the relative abundance of which being increased by 1.4%-3.4%. Metagenomic analysis indicated that AHLs differentially regulated functional genes related to quorum sensing, two-component systems, and nitrogen metabolism. Specifically, C4-HSL mainly enhanced genes associated with complete denitrification and biofilm formation. C6-HSL increased the expression of genes related to denitrification and dissimilatory nitrate reduction to ammonium. C8-HSL strengthened genes involved in phosphorus stress response and nitrogen fixation. C12-HSL promoted the expression of iron-acquisition-related functional genes. In conclusion, exogenous AHLs could enhance nitrogen removal by regulating microbial quorum sensing and metabolic processes, with C6-HSL showing the best perforemence.},
}

*Nitrogen/isolation & purification/metabolism
*Wastewater/chemistry
*Acyl-Butyrolactones/chemistry/pharmacology
*Aquaculture
*Waste Disposal, Fluid/methods
Bioreactors/microbiology
4-Butyrolactone/analogs & derivatives/chemistry
Nitrates/isolation & purification
Quorum Sensing

@article {pmid42657575,
year = {2026},
author = {Yu, XQ and Gao, YZ},
title = {Research advances in the mechanisms of nitrogen-phosphorus synergy mediated by root exudates and mycorrhizal networks in cereal-legume intercropping systems.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {37},
number = {7},
pages = {2463-2472},
doi = {10.13287/j.1001-9332.202607.030},
pmid = {42657575},
issn = {1001-9332},
mesh = {*Mycorrhizae/physiology/metabolism ; *Phosphorus/metabolism ; *Nitrogen/metabolism ; *Edible Grain/growth & development/metabolism ; *Fabaceae/growth & development/metabolism ; *Plant Roots/metabolism ; *Agriculture/methods ; Rhizosphere ; Nitrogen Fixation ; *Plant Exudates/metabolism ; },
abstract = {The cereal-legume intercropping system achieves efficient utilization of nitrogen and phosphorus through interactions between roots and soil organisms, making it a key practice in sustainable agriculture. We systematically summarized the nitrogen and phosphorus mutual promotion mechanism mediated by root exudates and mycorrhizal networks in the cereal-legume intercropping system, and proposed future research directions. Cereal plants mobilize phosphorus in rhizosphere by secreting organic acids and phosphatases. The released phosphorus is then transferred to the rhizosphere of legumes via the common mycorrhizal network (CMN), alleviating phosphorus limitations, activating energy metabolism, initiating nodule formation, and promoting nitrogen fixation in legumes. Root exudates of cereal plants can directly enhance biological nitrogen fixation in legumes by stimulating the expression of key nodulation genes. The CMN transport nitrogen fixed by legumes to cereal plants in the form of amino acids and other compounds, thereby promoting root development and exudate release in cereal plants, and enhancing phosphorus mobilization capacity. Root exudates and CMN work together to form "nitrogen-phosphorus synergy" cycle, significantly enhancing nutrient use efficiency and productivity in cereal-legume intercropping systems. In the future, technologies such as metabolomics, metagenomics, rhizosphere in situ imaging, and artificial intelligence should be integrated to elucidate the multi-interface coupling mechanisms among roots, mycorrhizae, and microorganisms. This will enable the precise prediction and regulation of nitrogen-phosphorus synergy in intercropping systems, thereby providing a theoretical foundation for the development of green and smart agriculture.},
}

*Mycorrhizae/physiology/metabolism
*Phosphorus/metabolism
*Nitrogen/metabolism
*Edible Grain/growth & development/metabolism
*Fabaceae/growth & development/metabolism
*Plant Roots/metabolism
*Agriculture/methods
Rhizosphere
Nitrogen Fixation
*Plant Exudates/metabolism

@article {pmid42658844,
year = {2026},
author = {Chuang, HY and Wu, JH and Chen, SH and Chen, WY and Fong, LJ and Lin, YT},
title = {Enrichment and Characterization of a Haloalkaline-tolerant Anammox Bacterium.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag221},
pmid = {42658844},
issn = {1751-7370},
abstract = {Metagenomic surveys have substantially expanded the known diversity of anaerobic ammonium-oxidizing (anammox) bacteria. However, the physiological traits of newly proposed anammox genera remain largely hypothetical due to the lack of cultured representatives. Although niche differentiation driven by salinity, organic substrates, and oxygen is well documented in anammox bacteria, adaptations to alkaline environments remain uncharacterized. Moreover, no anammox lineage has been identified as an alkaline specialist. Herein, we report the enrichment (>80% relative abundance) of an anammox bacterium, provisionally named Candidatus Loosdrechtia alkalitolerans, which represents the cultured member of the genus Ca. Loosdrechtia. Ca. L. alkalitolerans exhibits marked haloalkaline tolerance, outcompeting other freshwater anammox genera under long-term saline-alkaline stress conditions (0.5% NaCl; pH~9.13). Comparative genomics revealed that among freshwater anammox lineages, only Ca. L. alkalitolerans encodes a complete multiple resistance and pH adaptation (Mrp) cation/proton antiporter operon. Batch assays with transcriptional profiling demonstrated that sodium addition upregulated mrp expression and recovered anammox activity under alkaline stress, suggesting that Mrp-mediated cation/proton exchange may contribute to pH homeostasis in Ca. L. alkalitolerans. Furthermore, database mining revealed that the habitat of Ca. L. alkalitolerans is not restricted to haloalkaline environments, but extends to diverse freshwater and wastewater ecosystems. These findings provide mechanistic insight into saline-alkaline tolerance in anammox bacteria, expanding understanding of their physiological plasticity and ecological roles.},
}

@article {pmid42658871,
year = {2026},
author = {Gonzales-Rodriguez, AO and Gonzales-Huerta, LE and Wong Chero, PA and Vera-Silva, LE and Uceda-Campos, G and Reale, FA},
title = {Breastmilk microbiota and its association with infant iron deficiency anaemia: A 16S rRNA metagenomic study in Peruvian mothers cohort.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0352428},
pmid = {42658871},
issn = {1932-6203},
mesh = {Humans ; Peru/epidemiology ; Female ; *RNA, Ribosomal, 16S/genetics ; *Anemia, Iron-Deficiency/microbiology/epidemiology ; Infant ; *Milk, Human/microbiology ; *Microbiota/genetics ; Mothers ; Adult ; Metagenomics ; Metagenome ; Bacteria/genetics/classification ; Male ; Cohort Studies ; },
abstract = {Anaemia is one of the most important public health challenges in developing countries. The global burden is estimated at 1.8 billion people, affecting approximately 30% of all children. Despite the implementation of multiple strategies over several decades, up to 42.5% of children under 3 years of age suffer anaemia in rural areas of Peru. We studied the microbiota of breastmilk (hBM) from mothers with children under the age of 1 and analysed its association with their iron deficiency anaemia. 46 mother-child pairs were recruited from Talara, a town on the northern coast of Peru and classified according to the clinical status of the children. Children with anaemia were also tested for ferritin level to classify them as iron deficiency anaemia (IDA) or non-iron deficiency anaemia (non-IDA). hBM samples were taken from the mothers after careful instruction to reduce the risk of sample contamination and the microbiome was analyzed using 16S rRNA sequencing. Streptococcus and Staphylococcus were the predominant genera, with 90% of bacterial abundance being explained by 14 genera. Alpha diversity analysis showed that hBM from mothers of children with non-IDA had higher levels of bacterial richness than hBM from healthy (p < 0.01) and IDA (p < 0.05) participants. Principal coordinates analysis did not yield differential clusters but showed a disparity in the spread of samples for non-IDA group when compared with the other groups. IDA group showed higher burden of Corynebacterium, Acinetobacter, Paludibacter and Nitrospira, while exhibiting a trend towards a lower burden of Streptococcus. No statistically significant differences were identified on demographic characteristics. This study suggests that hBM microbiota may differ in mothers of children with IDA and non-IDA, highlighting the necessity of further in-depth research to elucidate potential factors associated with its pathogenesis.},
}

Humans
Peru/epidemiology
Female
*RNA, Ribosomal, 16S/genetics
*Anemia, Iron-Deficiency/microbiology/epidemiology
Infant
*Milk, Human/microbiology
*Microbiota/genetics
Mothers
Adult
Metagenomics
Metagenome
Bacteria/genetics/classification
Male
Cohort Studies

@article {pmid42659434,
year = {2026},
author = {Estevam, LGTM and Kostygov, AY and Dutra-Rêgo, F and Martins, ALM and Freire, MA and Lima, ACVMDR and Avelar, DM and Almeida, GG and Andrade Filho, JD and Yurchenko, V and Paz, GF},
title = {Blechomonas campbelli from Ctenocephalides felis: in vitro development, thermotolerance, and phylogenetic insights.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {121},
number = {},
pages = {e250286},
pmid = {42659434},
issn = {1678-8060},
mesh = {Animals ; Phylogeny ; *Trypanosomatina/genetics/growth & development/isolation & purification/classification/physiology ; Dogs ; *Ctenocephalides/parasitology ; *Thermotolerance ; Brazil ; RNA, Ribosomal, 18S/genetics ; },
abstract = {BACKGROUND: Blechomonas spp. are flea-specific monoxenous trypanosomatids, whose biology, host range, and geographic distribution remain poorly understood, even for species inhabiting ubiquitous cat and dog fleas.

OBJECTIVES: To isolate and characterise blechomonads from fleas of domestic dogs in Brazil, focusing on culture growth, morphology, and phylogenetic relationships.

METHODS: Fleas collected from dogs in Sabará, Brazil, were morphologically identified and screened by cultivation. The isolate FL-1 was analysed for temperature-dependent growth, morphology, and phylogeny using 18S rRNA and gGAPDH sequences, including those mined from public metagenomic datasets.

FINDINGS: Of 340 fleas (four per pool), only one culture tested positive. Growth was optimal at 25ºC, reduced at 30ºC, and absent at 35ºC. Four cell types were revealed, including a predominant "uromonad" stage specialised for attachment and aggregation. Phylogenetic analyses placed the isolate within Blechomonas campbelli and indicated that this species and Blechomonas lauriereadi occur in Ctenocephalides spp. from multiple continents.

MAIN CONCLUSIONS: Blechomonas campbelli exhibits developmental adaptations to the flea gut and limited tolerance to elevated temperatures, constraining its potential to persist in warm-blooded hosts. These findings highlight the value of combining culture-based and in silico approaches to investigate flea-associated trypanosomatids.},
}

Animals
Phylogeny
*Trypanosomatina/genetics/growth & development/isolation & purification/classification/physiology
Dogs
*Ctenocephalides/parasitology
*Thermotolerance
Brazil
RNA, Ribosomal, 18S/genetics

@article {pmid42659882,
year = {2026},
author = {Gao, Q and Ai, S and Zhang, M and Li, Y and Li, Y and Ma, Y and Zhang, J and Yang, F and Cheng, K},
title = {Artificial humic acid reshapes microbial C-N metabolism and nitrogen partition in microplastic-contaminated soils.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143382},
doi = {10.1016/j.jhazmat.2026.143382},
pmid = {42659882},
issn = {1873-3336},
abstract = {Microplastics pose a serious threat to soil ecosystems, particularly nitrogen cycling. Among the diverse types of microplastics, polypropylene (PP) and polylactic acid (PLA) are frequently detected in agricultural soils. Artificial humic acid (A-HA), a humic-like substance derived from lignocellulosic waste, may regulate soil carbon and nitrogen dynamics, but its effects on nitrogen partitioning and microbial C-N metabolic potential under different microplastic stresses remain unclear. Here, a 90-day microcosm experiment integrating soil physicochemical analyses, dissolved organic matter characterization, bacterial community profiling, and metagenomics was conducted in PLA- and PP-contaminated soils. At day 15, 600 mg kg[-1] A-HA decreased nitrate (NO3[-]-N) by 11.36% and 6.46% in PLA- and PP-contaminated soils, respectively, while increasing soluble organic nitrogen (SON) by 17.32% and 23.89%. A-HA also enriched Nitrospira and Steroidobacter and altered the abundance of genes associated with nitrogen transformation, assimilation, and carbon metabolism, including nrfA, GLU, gltB, and icd. Increased abundance of nrfA suggested greater dissimilatory nitrate reduction to ammonium (DNRA) potential, while enrichment of NADP[+]-dependent icd indicated altered potential for 2-Oxoglutarate generation in the TCA cycle. Overall, A-HA modified nitrogen partitioning toward soluble and microbial organic pools and was associated with coordinated changes in microbial C-N metabolic potential under microplastic exposure.},
}

@article {pmid42660108,
year = {2026},
author = {Márquez, S and Salazar, L and Collins, J and Nipaz, V and Dávila Campos, V and Van der Ende, J and Wickiser, JK and Briese, T and Coloma, J},
title = {Group C Orthobunyavirus Infection in a Patient from the Amazon Putumayo Region of Colombia During an Oropouche Fever Epidemic.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.25-0652},
pmid = {42660108},
issn = {1476-1645},
abstract = {Orthobunyaviruses, one of the largest and most diverse genera of viruses, include numerous reassortant viruses and present diagnostic challenges due to similar clinical presentations with other arboviral infections. The detection and isolation of a group C orthobunyavirus from a patient with acute febrile illness from Puerto Ospina, Putumayo Department, Colombia during the 2023-2024 Latin American Oropouche fever regional outbreaks are reported in the present study. Using a vertebrate virus-focused metagenomics sequencing approach with VirCapSeq-VERT, a virus related to the Caraparu complex was identified, and a virus isolate was obtained. Although limited to a single case and without serological or longitudinal clinical confirmation, these findings underscore the value of unbiased molecular approaches for unresolved febrile illness diagnosis in endemic settings such as the Amazon basin.},
}

@article {pmid42660360,
year = {2026},
author = {Lu, X and Zhang, Q and Peng, Y and Liang, Z and Peng, Y and Zhang, X and Liu, G and Qin, G and Li, Q},
title = {Elucidating the aromatic formation of humus via quorum sensing and redox function of thermophilic microbiota in compost.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135739},
doi = {10.1016/j.biortech.2026.135739},
pmid = {42660360},
issn = {1873-2976},
abstract = {Quorum sensing (QS) modulates bacterial metabolism to regulate humus formation. However, the functional interaction modes of signal molecules, QS-related proteins, and microbial humification function during composting remain unclear. This study aimed to clarify the role of QS-related gene expression in regulating humification via applying metagenomics and metaproteomics. Combined addition of MnSO4 and Fe[0] (CMF) significantly raised humic acid (HA) content (33.53 mg g[-1]) and polymerization degree (2.60) compared with other treatments. Multi-dimensional results revealed that CMF-derived HA and its products exhibited greater thermal stability, high aromaticity, and practical applicability. CMF increased the relative abundances of most QS-related and humification-related oxidoreductase genes throughout composting, especially during the thermophilic stage. Metaproteomic profiles verified that both QS expression and humification metabolism were hyperactivated during the thermophilic stage of CMF. Correlation analysis showed that QS gene expression potentially and preferentially influenced lignin-protein and polyphenol pathways during humification. Overall, CMF enriched thermophiles (Bacillota, Chloroflexota, and Myxococcota), further up-regulated the expression of major QS-related genes [K02035 (ABC.PE.S), K13075 (ahlD), K14645, K15580 (oppA), and K02055 (ABC.SP.S)], elevated levels of signal molecules, and promoted QS effects. Network analysis, qPCR, and simulated in vitro validation experiments confirmed that the response of key QS modules [K13075 (ahlD) and 3-OXO-C8-HSL] potentially facilitated interspecies communication and cooperation among bacteria, which concurrently enhanced downstream microbial metabolic behaviors (microbial redox activities and the metabolism of carbohydrates and amino acids) that aid in driving HA aromatization. This work provides new insight into the ecological roles of QS-related microbes and their precise regulation of compost humification.},
}