@article {pmid43024015,
year = {2026},
author = {Gowtham, S and Sugumaran, MP and Parameswari, E and Pragadeesh, ARU and Kalaiselvi, T and Saravanan, NA and Elayarajan, M and Selva Kumar, M and Surya, K},
title = {Chromium pollution and its effects on soil health, microbial diversity, and sugarcane production in the Vellore sugarcane belt: a metagenomic and geochemical assessment.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {12},
pages = {},
pmid = {43024015},
issn = {1573-0972},
mesh = {*Saccharum/growth & development/microbiology ; *Chromium/analysis/toxicity ; *Soil Microbiology ; India ; *Soil/chemistry ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *Soil Pollutants/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Metals, Heavy/analysis ; Hydrogen-Ion Concentration ; Biodiversity ; Tanning ; },
abstract = {Disposal of tannery effluent has elevated soil chromium (Cr) across the Vellore sugarcane belt of southern India, yet its integrated consequences for soil health, bacterial communities and sugarcane productivity remain poorly characterised. Nine composite soil samples from a recognised tannery-affected belt were pre-stratified into High, Low and Near-threshold Cr sites. Soils and irrigation water were geochemically characterised for total and speciated heavy metals and profiled by full length (V1-V9) 16 S rRNA gene amplicon sequencing on an Oxford Nanopore GridION. Soil total Cr increased from 29.10 ± 0.14 to 180.51 ± 2.95 mg kg[- 1], the alkaline-extractable Cr (VI) fraction rising from 2.92 ± 0.09 to 52.07 ± 0.11 mg kg[-1] and co-occurring Cd and Ni increasing across strata. Soil pH shifted alkaline (7.74 to 8.48), organic carbon declined by up to 31.7% and exchangeable Ca and Mg by up to 40.4%. Tissue Cr followed root > shoot > leaf but peaked at Near-threshold rather than High Cr sites, indicating bioavailability-driven uptake. Cane and stalk fresh weight declined 25.8-31.3% at High Cr sites, whereas sucrose, Brix, purity and fibre remained largely unchanged. Alpha diversity followed a threshold structured rather than linear dose response, with observed richness in High Cr levels reduced to 74-76% that in Low Cr levels alongside parallel declines in Shannon diversity and Pielou's evenness. NMDS resolved three non-overlapping community clusters. A Cr-resilient core (Sphingomonas panacis, Nitrospira lenta) persisted alongside elevated prediction of azoR/acpD and chrA abundance, defining a chromium-tolerance signature in tannery-impacted sugarcane soils.},
}

*Saccharum/growth & development/microbiology
*Chromium/analysis/toxicity
*Soil Microbiology
India
*Soil/chemistry
*Bacteria/classification/genetics/drug effects/isolation & purification
*Soil Pollutants/analysis
RNA, Ribosomal, 16S/genetics
Metagenomics
Metals, Heavy/analysis
Hydrogen-Ion Concentration
Biodiversity
Tanning

@article {pmid43024025,
year = {2026},
author = {Chigozie, VU and Oghonyon, EI and Enyi, EO},
title = {Environmental Microbiomes as Sources of Postbiotic Therapeutics: A One Health Perspective on Translational Applications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {43024025},
issn = {1867-1314},
abstract = {Environmental microbiomes are reservoirs of specialized microorganisms with implications for ecosystem functionality, host health, and therapeutic discovery. Soil, marine, plant-associated, wastewater, freshwater, and extreme-environment microbiomes contain communities capable of producing bioactive metabolites and functional biomolecules. Postbiotics-non-viable microorganisms and their functional components that confer health benefits-offer potential advantages in stability, safety, scalability, and pharmaceutical development. This review examines environmental microbiomes as sources of postbiotic therapeutics within a One Health framework. A critical integrative translational review synthesized literature on environmental microbiomes, postbiotic diversity, molecular mechanisms, therapeutic applications, technological advances, and barriers to clinical translation. Evidence was organized across ecological sources, postbiotic classes, human-health applications, discovery platforms, pharmaceutical development, and translational challenges. Environmental microbiomes represent chemically and functionally diverse reservoirs of postbiotic candidates shaped by ecological adaptation, microbial competition, and environmental selection. Major classes-including short-chain fatty acids, bacteriocins, extracellular vesicles, indole and tryptophan metabolites, exopolysaccharides, and microbial/lytic enzymes-act through receptor signaling, immune modulation, barrier protection, antimicrobial activity, metabolic regulation, intercellular communication, and enzymatic target modification. Metagenomics, metabolomics, artificial intelligence, synthetic biology, organoid and microfluidic models, advanced delivery systems, and biomanufacturing increasingly enable discovery and development. However, reproducibility, microbiome variability, manufacturing scalability, regulatory standardization, cost, and equitable translation remain barriers. Environmental microbiomes provide important reservoirs for postbiotic discovery. Integrating ecological microbiology with multi-omics, computational innovation, pharmaceutical engineering, and human-relevant validation could accelerate development of defined, reproducible, and scalable postbiotic therapeutics. Preserving microbial ecosystem diversity is relevant to environmental sustainability and future microbiome-derived therapeutic innovation within One Health medicine.},
}

@article {pmid43024663,
year = {2026},
author = {Qin, Z and Yang, Z and Zhang, Y and Qi, L and Peng, Y and Deng, S and Wang, Y},
title = {Biotin Limitation Attenuates Streptococcus mutans Cariogenicity by Disrupting Metabolic Flux and Virulence Pathways.},
journal = {Caries research},
volume = {60},
number = {4},
pages = {344-358},
doi = {10.1159/000548822},
pmid = {43024663},
issn = {1421-976X},
support = {82201035//National Natural Science Foundation of China/ ; 2022C03060//Key R&D Program of Zhejiang/ ; },
mesh = {*Streptococcus mutans/pathogenicity/metabolism/genetics/drug effects/growth & development ; *Biotin/metabolism/pharmacology ; Virulence/genetics ; Biofilms/growth & development/drug effects ; *Dental Caries/microbiology ; Microscopy, Confocal ; Polysaccharides, Bacterial/metabolism ; Phenotype ; Gene Expression Regulation, Bacterial ; Microscopy, Electron, Scanning ; Real-Time Polymerase Chain Reaction ; Metabolomics ; },
abstract = {INTRODUCTION: Our previous metagenomic analysis revealed higher frequencies of biotin-related genes (i.e., bioY, bioM, bccP) in caries-active children, indicating a potential role of biotin in caries pathogenesis. This study investigated a biotin limitation strategy against the primary cariogenic bacterium Streptococcus mutans (S. mutans), including its effects on cariogenic phenotypes, gene expression, and metabolomics.

METHODS: S. mutans UA159 was cultured in biotin-free medium supplemented with different biotin concentrations. The cariogenic phenotypes of the strain, including growth kinetics, biofilm formation, exopolysaccharide production, lactate synthesis, acid/oxidative tolerance, and membrane fluidity, were measured and compared across biotin concentrations. Biofilm architecture was visualized via confocal laser-scanning microscopy and scanning electron microscopy. Quantitative real-time polymerase chain reaction was employed to analyze the expression of genes associated with virulence and biotin metabolism. Metabolomic analysis was performed to characterize metabolic perturbations induced by biotin limitation in S. mutans.

RESULTS: Under biotin limitation, S. mutans exhibited significantly reduced cariogenic phenotypes, accompanied by cell elongation and reduced membrane fluidity. At the molecular level, biotin limitation suppressed the expression of key virulence-associated genes and induced a compensatory upregulation of genes involved in biotin uptake and biotin-dependent carboxylases. Metabolomic analysis under biotin-limited conditions in S. mutans revealed perturbed pathways in central carbon metabolism and nucleotide metabolism.

CONCLUSION: Biotin limitation significantly reduced the cariogenic potential of S. mutans by disrupting metabolic flux and virulence gene expression, highlighting biotin uptake and metabolism as potential targets for anticaries therapies.},
}

*Streptococcus mutans/pathogenicity/metabolism/genetics/drug effects/growth & development
*Biotin/metabolism/pharmacology
Virulence/genetics
Biofilms/growth & development/drug effects
*Dental Caries/microbiology
Microscopy, Confocal
Polysaccharides, Bacterial/metabolism
Phenotype
Gene Expression Regulation, Bacterial
Microscopy, Electron, Scanning
Real-Time Polymerase Chain Reaction
Metabolomics

@article {pmid43025069,
year = {2026},
author = {Dong, J and Liu, P and Kang, Y and Lu, J and Zhuang, L and Xie, H and Wu, H and Hu, Z and Guo, Z and Zhang, J},
title = {Mechanistic insights into static magnetic field-enhanced removal of polycyclic aromatic hydrocarbons from wastewater by constructed wetlands: Computational simulation and microbial community dynamics.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127275},
doi = {10.1016/j.watres.2026.127275},
pmid = {43025069},
issn = {1879-2448},
abstract = {Microbial degradation is the dominant pathway for pollutant removal in constructed wetlands (CWs). Static magnetic fields (SMFs) were employed as a promising strategy to enhance pollutant removal, as they can effectively promote microbial activity and metabolic capacity without additional chemical amendments. Here, COMSOL-based magnetic-field simulation, plant physiological assays, extracellular polymeric substance (EPS) characterization, and metagenomics were integrated to examine the regulatory effects of SMF intensity and spatial heterogeneity on microbial community structure, functional potential, and benzo[k]fluoranthene (B[k]F) biodegradation. B[k]F removal showed an intensity-dependent threshold response, with 150 mT increasing mean removal efficiency by 14.31% relative to the control. COMSOL simulations showed that 150 mT produced the largest effective SMF zone, covering 39.53% of the reactor volume. This treatment enhanced plant photosynthetic performance, potentially supporting rhizosphere microbial metabolism through plant-derived carbon and oxygen supply and increased EPS concentrations to 30.01 ± 3.19 and 23.59 ± 4.68 mg L[-1] in the upper and lower layers, respectively. Metagenomic analysis revealed enrichment of key polycyclic aromatic hydrocarbon (PAH) degrading bacteria affiliated with Actinomycetota (45.20%). At 150 mT, enhanced tricarboxylic acid cycling and oxidative phosphorylation accelerated microbial energy metabolism and promoted conversion of high-molecular-weight B[k]F into low-molecular-weight aromatic acids. These findings suggest that optimized SMFs enhance PAH removal through coordinated plant-microbe responses, thereby providing a basis for designing magnetically intensified CWs as a chemical-free wastewater treatment strategy.},
}

@article {pmid43025070,
year = {2026},
author = {Yu, X and Wu, Z and Liu, G and Wang, L and Wang, L and Liu, J and Bian, Z and Wu, X and Jiang, J and Qiao, W},
title = {Isolation of Dehalococcoides mccartyi JC20 and genome-centric metatranscriptomic identification of Aminivibrio sp. as a candidate vitamin B12 producer.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127267},
doi = {10.1016/j.watres.2026.127267},
pmid = {43025070},
issn = {1879-2448},
abstract = {Vitamin B12 is an essential cofactor for reductive dehalogenases, yet many organohalide-respiring bacteria, including Dehalococcoides mccartyi, are B12-auxotrophic and rely on syntrophic partners for B12 supply. Here, we used genome-centric metatranscriptomics to investigate the B12-cross-feeding network sustaining 1,2-dichloroethane dechlorination in a defined enrichment consortium. Sustained dechlorination proceeded in both B12-free (with other vitamins retained) and completely vitamin‑free treatments at rates of 10.03 ± 0.73 and 9.66 ± 0.05 μM Cl[-] released·day[-1], respectively, with B12 detected at 1.7-3.3 µg∙L[-1] after successive transfers. Metagenomic and metatranscriptomic analyses revealed that Aminivibrio possesses a complete de novo B12 biosynthesis pathway, which was significantly upregulated 123.38-fold under B12-limited conditions, substantially higher than the 7.98-fold upregulation observed in the established B12 producer Acetobacterium. In response to B12 deprivation, D. mccartyi significantly upregulated its B12 transporter operon (btuFCD) and sustained dechlorination via the reductive dehalogenase TceA. Most recovered MAGs were fermentative bacteria that supplied acetate and hydrogen to D. mccartyi. A pure strain of D. mccartyi, designated JC20, was further isolated by dilution-to-extinction and achieved cell densities of 10[9] cells∙mL[-1]. Collectively, these findings identify the fermentative Aminivibrio as a previously unrecognized candidate for B12 production and highlight its potential role in supporting Dehalococcoides-mediated dechlorination. This work expands our understanding of the diversity of B12-producing partners in organohalide‑respiring communities and provides insights into the microbial interactions underpinning bioremediation in oligotrophic contaminated environments.},
}

@article {pmid43025101,
year = {2026},
author = {Qiao, Y and Pan, H and Yue, C and Tian, W and Shi, J and Sun, Y and Tao, Z and Gao, Y and Li, Y and Zang, B and Xue, CX and Liu, Y},
title = {Resolving the mechanisms on immobilized microspheres enhancing oil cleanup under typical deep-sea conditions via tracing the ecological and evolutionary dynamics of microbial generalists and specialists.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120561},
doi = {10.1016/j.marpolbul.2026.120561},
pmid = {43025101},
issn = {1879-3363},
abstract = {Deep-sea oil pollution has garnered global concern yet. Immobilization-assisted bioremediation depending on microbial interactions represents a critical strategy for mitigating petroleum contamination. However, the behaviors of bacteria occupying distinct ecological niches during such remediation at deep-sea conditions remain inadequately understood. Herein, via multiple sequencing techniques and biochemical detection, the ecological and evolutionary characteristics of generalists and specialists were tracked under the microsphere-driven bioremediation of oily sediment at deep-sea microcosm. Ecologically, the microspheres increased the diversity of active niche bacteria (RNA-based consortium) in sediment and introduced more stochastic processes into community assembly. Meanwhile, they reinforced the community stability of the two niche taxa by increasing the number of nodes and edges, as well as the robustness of molecular networks in sediment. Genomic analyses revealed the division of labor between generalist and specialist communities. Notably, the microspheres increased the abundance of generalists and specialists that possessed higher gene number associated with petroleum decomposition. Evolutionarily, ecological equilibrium was maintained via a reduced transition rate from specialists to generalists and an elevated diversification rate within specialists. Furthermore, global dataset analysis showed the important niche bacteria activated by the microsphere were widely distributed in the deep sea, indicating the broad applicability of microsphere-based remediation in diverse deepwater habitats. Collectively, the findings highlight that the microspheres likely govern the ecological and evolutionary traits of niche bacteria to improve system stability and function, thereby enhancing oil cleanup. This work provides a novel mechanistic perspective to guide the application and design of microsphere-mediated remediation plan against in-situ pollution.},
}

@article {pmid43025213,
year = {2026},
author = {Dey, P},
title = {Dietary shifts across human evolution reveal a progressive loss of gut microbial diversity and functions.},
journal = {Nutrition research (New York, N.Y.)},
volume = {155},
number = {},
pages = {214-232},
doi = {10.1016/j.nutres.2026.10.009},
pmid = {43025213},
issn = {1879-0739},
abstract = {This narrative review summarizes the evolutionary, archaeological, and metagenomic evidence to illustrate how significant dietary shifts, from Paleolithic hunter-gatherer lifestyles to Neolithic agricultural practices and ultimately to modern industrial diets, have gradually transformed the human gut microbiome. The objective is to position diet as a dominant influence on gut microbial evolution, and to demonstrate that the contemporary Western diet signifies a profound divergence from the nutritional context to which our microbiota has coevolved over thousands of years. The available data uncovers three main conclusions. First, hunter-gatherer communities exhibit remarkably elevated α-diversity, a predominance of Prevotella and Treponema, and an abundance of cellulose-degrading Ruminococcus, which together facilitate substantial short-chain fatty acid synthesis. Second, comparative studies reveal a notable shift from Prevotella to Bacteroides in industrialized societies, along with a substantial decline in microbial diversity and a deterioration of carbohydrate-metabolizing pathways. Third, preindustrial gut microbiota were fundamentally different from Westernized ones, emphasizing that both dietary processing and food type influenced the evolution of human gut microbiota. Collectively, the modern industrial diet has created an evolutionary discord, leading to the gradual decline of ancient microbial lineages and their metabolic capabilities. This functional deterioration, especially in fiber fermentation and short-chain fatty acid production, is mechanistically associated with the increase of chronic inflammatory and metabolic disorders. These observations establish a historical reference point for gut microbiota composition, highlighting that dietary rewilding and targeted microbial restoration are empirically supported methods for mitigating contemporary dysbiosis.},
}

@article {pmid43025422,
year = {2026},
author = {Jiang, S and Lin, X and Ni, L and Zhang, Y and Chen, H and Liu, C and Yuan, H and Kang, Z and Jiao, J and Han, T and Zhuo, M and Wu, X and Zhou, J and Sun, R and Hu, M and Deng, Z and Jiang, Y and Zhang, C and Xu, P and Li, P and Li, Q and Chen, YX and Xiao, XY and Fang, JY},
title = {Targeting F.nucleatum with metronidazole plus tislelizumab and fruquintinib in MSS colorectal cancer: A multicenter phase 2 study.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2026.10.012},
pmid = {43025422},
issn = {1878-3686},
abstract = {Fusobacterium nucleatum has been linked to chemoresistance and immune evasion in colorectal cancer (CRC), but therapeutic strategies targeting this bacterium remain limited. In this multicenter, single-arm, phase 2 trial (NCT06356597), 33 patients with Fusobacterium nucleatum-positive, microsatellite-stable metastatic CRC received the combination treatment of tislelizumab, fruquintinib, and the antimicrobial metronidazole. The primary endpoint was met, with a median progression-free survival of 6.0 months. The objective response rate and disease control rate were 19.4% and 83.9%, respectively. Grade 3 treatment-related adverse events occurred in 30.3% of patients, with no grade 4 or 5 events. Metagenomic analysis showed that metronidazole reduced Fusobacterium nucleatum abundance. Exploratory analyses associated clinical benefit with enrichment of Lactobacillus species and nonresponse with Enterococcus. Fecal microbiota transplantation from responders sensitized germ-free mice to the treatment, which enhanced cytotoxic CD8[+] T cell differentiation and reduced terminal exhaustion. These findings support further evaluation of this combination in Fusobacterium nucleatum-positive metastatic CRC.},
}

@article {pmid43025576,
year = {2026},
author = {Shan, C and Geng, T and Wang, P and Wang, L and Huang, R and Zhu, X and Zhang, Q},
title = {Descriptive genomic characterization of selected Klebsiella pneumoniae-positive clinical samples from two tertiary hospitals in China by mNGS.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {106064},
doi = {10.1016/j.meegid.2026.106064},
pmid = {43025576},
issn = {1567-7257},
abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) is an attractive method for identifying diverse pathogens and has been used for diagnosing infectious diseases. This study aimed to perform a descriptive genomic characterization of AMR-associated and virulence factor genes in a selected analytic subset of Klebsiella pneumoniae-positive clinical samples detected by mNGS, rather than to estimate the prevalence of these genes among all mNGS-positive specimens.

METHODS: Clinical samples were collected from patients at two tertiary hospitals between July 1, 2021, and July 17, 2023. Sequence types, AMR-associated genes, and virulence factors of K. pneumoniae were identified using mNGS in the selected analytic subset of samples with detectable AMR/VF gene signals and sufficient sequencing coverage.

RESULTS: Thirty-three samples were collected from 31 patients as a pre-selected analytic subset enriched for AMR/VF gene signals and sufficient sequencing coverage, rather than a representative cohort of all K. pneumoniae-positive mNGS specimensAmong these, 25/31 (80.6%) of the patients underwent invasive procedures. Multilocus Sequence Typing (MLST) analysis identified eight STs, and a phylogenetic tree further categorized the samples into three major clusters. Within this selected subset, β-lactam resistance-associated genes were detected in 30/33 samples, indicating the presence of β-lactam resistance-associated genetic determinants identified from metagenomic sequences in the analyzed specimens. These values represent detection frequencies within the selected analytic subset and should not be interpreted as prevalence estimates among all K. pneumoniae-positive mNGS specimens. Notably, 48.5%(16/33) of the samples carried five or more types of virulence genes. These samples were observed more frequently among fatal cases; however, this exploratory observation should not be interpreted as evidence of a causal relationship or prognostic association.Based on mNGS findings, empirical antimicrobial therapy was modified in 64.5% of patients. The in-hospital survival rate was 74.2%.

CONCLUSION: mNGS provides descriptive genomic information on K. pneumoniae in clinical specimens and may help identify sequence types, AMR-associated genes, and virulence factors in selected samples.},
}

@article {pmid43025638,
year = {2026},
author = {Copes, J and Godeaux, E and Yan, S},
title = {Chronic ethanol feeding drives gut microbiome remodeling and influences cholestatic liver injury in mice.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2026.10.012},
pmid = {43025638},
issn = {1525-2191},
abstract = {Alcohol-associated liver disease (ALD) is a major cause of liver-related mortality worldwide and encompasses steatosis, cirrhosis, and alcohol-associated hepatitis (AH). AH is frequently accompanied by cholestasis, characterized by impaired bile flow and disrupted bile acid homeostasis. Although gut microbiome (GM) dysbiosis has been linked to ALD progression and cholestatic injury, its functional role in alcohol-associated cholestasis remains unclear. Mice were subjected to chronic ethanol-feeding (EF) or pair-feeding (PF) for 4 weeks. Fecal samples collected at 10 days and 4 weeks underwent shotgun metagenomic sequencing. To assess the functional impact of microbiome alterations, cecal contents from male mice after 4 weeks of EF or PF were used for fecal microbiota transplantation (FMT). Recipient mice received antibiotics during acclimatization, followed by 10 days of EF and FMT every other day. Forty-eight hours before sacrifice, mice were challenged with α-naphthylisothiocyanate (ANIT; 25 mg/kg) to induce cholestatic liver injury. Liver injury, cholestasis, and inflammation were evaluated biochemically and histologically. EF induced progressive GM remodeling, whereas PF did not. Unexpectedly, FMT from PF donors aggravated ANIT-promoted liver injury, cholestasis, and hepatic inflammation in EF recipients of both sexes. In contrast, FMT from EF donors did not significantly alter injury compared with non-FMT controls. These findings suggest that GM derived from PF and chronic EF mice differentially influence susceptibility to cholestatic liver injury in EF recipients.},
}

@article {pmid43025784,
year = {2026},
author = {Xue, W and Zhu, Y and Al-Dhabi, NA and He, Q and Xu, R and Huang, L and Li, J and Xu, Y and Tang, W},
title = {Ecological trade-offs of S-nZVI-assisted phytoremediation in sulfamethoxazole-copper co-contaminated soil: Plant stress, contaminant attenuation and contrasting resistome responses.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126187},
doi = {10.1016/j.envres.2026.126187},
pmid = {43025784},
issn = {1096-0953},
abstract = {Antibiotic-metal co-contamination can select for environmental resistomes, but how nanomaterial-assisted phytoremediation alters resistance profiles remains uncertain. We conducted a pot experiment with Tradescantia pallida (T. pallida) to evaluate an integrated S-nZVI-plant remediation system in soil co-contaminated with sulfamethoxazole (SMX) and copper (Cu) and to identify environmental and microbial factors associated with resistome responses. S-nZVI showed context-dependent effects on plant performance: biomass increased in uncontaminated soil but decreased under pollutant exposure, mainly through root biomass loss. Nevertheless, S-nZVI decreased Cu bioavailability, partially restored root cell-wall integrity, and reduced SMX and Cu concentrations in plant tissues by 6.84-28.52% and 1.27-3.30%, respectively. Lipid peroxidation generally declined and antioxidant enzyme activities partially recovered, whereas H2O2 accumulation under co-contamination indicated a treatment-dependent redox response. Metagenomic profiling showed that Cu-containing treatments increased ARG subtype richness by 52.61-93.62%, with β-lactams predominating. The integrated S-nZVI-plant treatment reduced ARG subtype richness by 45.91% under Cu contamination and by 13.82% under co-contamination. However, ARG relative abundance decreased by 23.58% under Cu contamination but increased by 18.05% under co-contamination, indicating resistome restructuring rather than uniform attenuation. Network analysis suggested that S-nZVI application was associated with increased ARG-MRG-MGE co-occurrence connectivity, whereas planting substantially weakened MGE-associated statistical connections. Partial least squares path modeling explained 84.5% of the variation in ARG abundance and identified microbial α-diversity and MRG abundance as the major positive predictors, while β-diversity exerted the largest negative total effect. These findings reveal a trade-off among contaminant attenuation, plant stress, and compartment-specific resistome responses.},
}

@article {pmid43025791,
year = {2026},
author = {Zeng, H and Wang, L and Muhammad, I and Zhao, D and Li, R and Lei, Y and Sun, G},
title = {Polylactic acid microplastics alter dissolved organic matter transformation in karst and non-karst lake microcosms of the Tibetan Plateau.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129554},
doi = {10.1016/j.envpol.2026.129554},
pmid = {43025791},
issn = {1873-6424},
abstract = {Biodegradable plastics are widely promoted as eco-friendly alternatives, but their degradation generates biodegradable microplastics (BMPs) that threaten aquatic systems. This study compared the impacts of polylactic acid (PLA) microplastics and conventional polyethylene (PE) microplastics on dissolved organic matter (DOM) dynamics and microbial ecology in microcosms established with water from a karst and a non-karst lake on the Tibetan Plateau, using FT-ICR MS, metagenomics, machine learning and dPMD network analysis. Under extreme exposure, PLA microplastics suppressed DOM photodegradation by 28% in the karst-lake microcosms, compared with 20% for PE microplastics. PLA microplastics reshaped DOM composition by reducing recalcitrant lignin-like formulae while increasing bioavailable lipid- and protein-like formulae by 4.8- and 2.0-fold, and shifted DOM assembly toward stochastic processes. Machine learning identified PLA microplastic treatment as the dominant predictor of DOM reactivity in the karst-lake microcosms. PLA microplastics were associated with a selective decline in Dormibacteraeota and with a restructuring of key microbial guilds and putative enzymatic pathways toward carbon and nitrogen lyase reactions, whereas microbial co-occurrence networks in the non-karst-lake microcosms remained stable. These microcosm results challenge the eco-friendly narrative of biodegradable plastics by showing that, under extreme exposure, PLA can alter DOM molecular composition and potential DOM-transforming microbial groups in Karst lake water, underscoring the need for further validation under environmentally relevant field conditions.},
}

@article {pmid43025862,
year = {2026},
author = {Qiao, J and Chen, M and Ye, M and Chen, Y and Gao, R and Fang, L and Li, F},
title = {Humic Fractions Are Linked to Distinct Arsenic-Mobilizing Host-Virome Assemblages and Enrichment of Large Temperate Phages Carrying Receiver-Only AioR-Like Loci.},
journal = {Environmental microbiology},
volume = {28},
number = {11},
pages = {},
doi = {10.1111/1462-2920.70496},
pmid = {43025862},
issn = {1462-2920},
support = {42321005//National Natural Science Foundation of China/ ; 42277119//National Natural Science Foundation of China/ ; 42377243//National Natural Science Foundation of China/ ; 2025TQ09A637//Guangdong Special Support Program for High-Level Talents/ ; 2024A1515012654//Natural Science Foundation of Guangdong Province/ ; 2023B0303000006//Guangdong Major Project of Basic and Applied Basic Research/ ; },
mesh = {*Arsenic/metabolism ; *Humic Substances/analysis ; *Bacteriophages/genetics/metabolism ; Soil Microbiology ; Genome, Viral ; Soil/chemistry ; },
abstract = {Arsenic mobilization in flooded rice paddies is driven by microbial redox reactions, but how redox-active organic matter coordinates arsenic-gene-bearing hosts and soil viromes remains unresolved. We examined the effects of fulvic acid (FA), humic acid (HA) and humin (HM) on arsenic-mobilizing host-virome assemblages using sequential anoxic slurry-transfer enrichments, genome-resolved metagenomics and curated virome analysis. FA and HA produced greater late-transfer arsenite accumulation than HM or unamended soil, while treatment-associated host genomes carried contrasting arsenic redox and detoxification repertoires. We identified two large temperate phages (> 100 kb) carrying receiver-only AioR-like loci in the FA and HA enrichments, with host-prediction signals converging on Bacillaceae. These loci were supported by hallmark-rich viral scaffold context and intact-locus read coverage and remained invariant despite genome-wide polymorphism. Reanalysis of 49,649 soil-derived viral genomes showed that arsenic-associated viral genes were rare among the 9518 quality-filtered genomes (0.29%) and occurred mainly as truncated regulatory architectures, particularly AioR-like receiver and AioS-like kinase-core fragments, on putatively lytic 30-70 kb genomes. By contrast, arsenic-associated viral-gene carriers were more frequent in our enrichment viromes (3.7%). These findings link distinct humic fractions to arsenic-mobilizing host-virome assemblages and reveal a candidate regulatory layer involving rare large temperate phages carrying receiver-only AioR-like loci.},
}

*Arsenic/metabolism
*Humic Substances/analysis
*Bacteriophages/genetics/metabolism
Soil Microbiology
Genome, Viral
Soil/chemistry

@article {pmid43026532,
year = {2026},
author = {Liu, Y and Lin, M and Luo, J and Yang, J and Yao, Z and Lin, D and Qiu, H and Zhang, Z and Huang, S and Zheng, E and Cai, G and Wu, Z and Liu, L and Wu, JJ},
title = {Integrating whole-genome sequencing and metagenomics improves phenotype prediction of fat deposition traits in pigs.},
journal = {Genetics, selection, evolution : GSE},
volume = {58},
number = {1},
pages = {},
pmid = {43026532},
issn = {1297-9686},
support = {2025B0202080002//Natural Science Foundation of Guangdong Province project/ ; 2025-XPY-01-002//Guangdong Provincial Special Finance Project for Seed Industry Revitalization Action/ ; NYQN2025004//Guangdong Special Support Program/ ; 2019BT02N630//Local Innovative and Research Teams Project of Guangdong Province/ ; 32502844//National Natural Science Foundation of China/ ; GZB20230230//the Postdoctoral Fellowship Program of CPSF/ ; GZB20250817//the Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Animals ; *Metagenomics/methods ; Phenotype ; *Whole Genome Sequencing/methods ; Swine/genetics ; *Gastrointestinal Microbiome/genetics ; Polymorphism, Single Nucleotide ; *Adipose Tissue ; Genotype ; },
abstract = {BACKGROUND: Fat deposition is a key economic trait affecting production efficiency and carcass quality in pigs and is influenced by both genetic and environmental factors. Although increasing evidence indicates that the gut microbiome contributes to host phenotypic variation, current genomic evaluation and prediction models largely rely on host genotype information and rarely account for microbiome effects. This study aimed to quantify the contribution of the gut microbiome to fat deposition traits and to evaluate whether incorporating microbiome information could improve phenotypic prediction in pigs.

RESULTS: We collected phenotypic characteristics of six fat deposition traits including the shoulder backfat thickness, the 6th-7th rib backfat thickness, the last rib backfat thickness, waist backfat thickness, the 3rd-4th last rib backfat thickness, and the average backfat thickness from 478 Duroc × Landrace × Yorkshire pigs. Using whole-genome resequencing and metagenomic sequencing, we identified 21 million single nucleotide variants and quantified the abundances of 20,336 gut microbial species across 478 pigs. Distinct fecal microbial community structures were observed between pigs with high- and low-fat deposition, and 27 bacterial species were identified as potential biomarkers associated with fat deposition. Microbiability estimates for the six backfat thickness traits ranged from 0.17 to 0.44, indicating that the gut microbiome accounted for a considerable proportion of phenotypic variance beyond host genetic contributions. In contrast, the interaction effects between the host genome and gut microbiome accounted for only a negligible proportion of phenotypic variance across the six traits. Incorporating overall microbiome information into genomic prediction models resulted in mean phenotypic predictive abilities ranging from 0.082 to 0.292, representing increases in predictive ability of 0.023 to 0.084 across traits and reductions in the mean squared error of prediction of 0.001 to 0.009 compared with the additive genetic model.

CONCLUSIONS: Our findings demonstrate that the gut microbiome makes a substantial contribution to variation in fat deposition traits in pigs. Integrating host whole-genome resequencing and gut metagenomic information yielded modest absolute gains in phenotypic predictive ability, suggesting that the gut microbiome may provide complementary information for prediction models of complex traits in pigs.},
}

Animals
*Metagenomics/methods
Phenotype
*Whole Genome Sequencing/methods
Swine/genetics
*Gastrointestinal Microbiome/genetics
Polymorphism, Single Nucleotide
*Adipose Tissue
Genotype

@article {pmid43026571,
year = {2026},
author = {Zhang, Y and Guo, S and Lu, L and Li, Y and Wu, Y},
title = {Correction: Metagenomic next-generation sequencing for pathogen detection of pulmonary infections in persons living with HIV.},
journal = {AIDS research and therapy},
volume = {23},
number = {1},
pages = {},
pmid = {43026571},
issn = {1742-6405},
}

@article {pmid43026629,
year = {2026},
author = {Boer, MD and Peets, P and van Eijnatten, AL and Nelson, CE and do Canto Brum de Menezes Pena, MM and Karancz, S and Humphreys, MP and van Duyl, FC and Meesters, EH and Snoek, BL and Melkonian, C and Haas, AF and Dutilh, BE},
title = {A specialized microbiome enriched in nitrification and halogen cycling potential resolved from multi-omics investigation of a Caribbean suboxic and acidic marine sinkhole.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {43026629},
issn = {2049-2618},
mesh = {*Nitrification ; *Microbiota ; Multiomics ; Metagenomics/methods ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Halogens/metabolism ; *Lakes/microbiology/chemistry ; Metabolomics ; Hydrogen-Ion Concentration ; },
abstract = {BACKGROUND: The Luymes Sinkholes, located on the Luymes Bank northwest of Saba, represent a unique marine environment characterized by distinct biogeochemical gradients. Most noticeable is an acidic (pH ≈ 6.25) and suboxic (O2 < 60 µmol/kg) submerged 'lake' at ~ 220 m depth exhibiting extreme deviations from standard oceanographic patterns, including elevated inorganic carbon, nitrate, and phosphate, and a lower temperature (20.3 ºC vs 26.4 ºC). To determine how the microbiome within the submerged acid lake adapted to these unique conditions, we collected 59 coupled samples of size-filtered (0.22 µm) planktonic microbes for shotgun metagenomics and solid-phase extracted dissolved organic matter for untargeted metabolomics from 21 stations at depths ranging from 2 to 600 m during a 10-day research cruise in December 2019.

RESULTS: We identified a distinct microbial community within the submerged acid lake different from the non-acidic sinkholes, with increased abundances of Nitrospinota, Thermoproteota, Planctomycetota, and Actinobacteriota. We also found three enriched classes of dissolved compounds within the submerged acid lake: (1) large, (2) low-polarity, and (3) halogenated metabolites, including iodides and halobenzoic acids. Correlations between microbial taxa and metabolite classes show potential links between nitrifying archaea and halogenated compound cycling. We further supported these findings using the functional annotation of metagenome-assembled genomes (MAGs) and protein clusters showing enrichment of nitrification and halogen cycling genes, suggesting the presence of specialized degradation and biosynthetic pathways, directly connecting microbial metabolism to the observed geochemical conditions.

CONCLUSION: These findings demonstrate that the submerged acid lake contains specific microbially driven biogeochemical processes under acidified and low-oxygen conditions, providing a natural model for future extreme ocean acidification scenarios. With this multi‑omics approach, we were able to connect the microbial metabolism with this unique environment, thereby expanding our understanding of how both are interconnected. Video Abstract.},
}

*Nitrification
*Microbiota
Multiomics
Metagenomics/methods
*Bacteria/classification/metabolism/genetics/isolation & purification
*Halogens/metabolism
*Lakes/microbiology/chemistry
Metabolomics
Hydrogen-Ion Concentration

@article {pmid43026631,
year = {2026},
author = {Tian, J and Dong, J and Guan, W},
title = {A fatal case of concurrent EBV-induced meningitis, ARDS, and HLH in an immunocompetent adult: a case report.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {43026631},
issn = {1743-422X},
mesh = {Humans ; Female ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/complications/pathology/virology ; *Epstein-Barr Virus Infections/complications/diagnosis/pathology/virology ; Adult ; *Respiratory Distress Syndrome/diagnosis/pathology/complications/virology ; Fatal Outcome ; *Herpesvirus 4, Human/isolation & purification/genetics ; Immunocompetence ; },
abstract = {RATIONALE: Epstein-Barr virus (EBV) typically causes self-limited infections in immunocompetent adults. Life-threatening complications such as hemophagocytic lymphohistiocytosis (HLH), meningitis, and acute respiratory distress syndrome (ARDS) are exceptionally rare and have not been previously reported to occur concurrently in a single patient. This case highlights the catastrophic potential of EBV and underscores a critical therapeutic dilemma: balancing the need for aggressive immunosuppressive therapy to control life‑threatening HLH against the risk of exacerbating uncontrolled EBV viremia and severe infections in a critically ill patient.

PATIENT CONCERNS: A 34-year-old immunocompetent woman presented with a 10-day history of high-grade fever (39.9 °C) and persistent headache.

DIAGNOSES: The diagnosis of Epstein-Barr virus (EBV)-associated hemophagocytic lymphohistiocytosis (HLH) was confirmed by meeting 5 of 8 HLH-2004 criteria in the setting of extreme EBV viremia (1.48 × 10⁸copies/mL), with high EBV DNA load additionally detected by metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid (239 EBV reads) and lower respiratory tract samples (145,386 EBV reads). Concurrently, EBV meningitis was confirmed by CSF findings (lymphocytic pleocytosis, elevated protein, and hypoglycorrhachia) alongside positive mNGS. She also met the Berlin criteria for ARDS, with bilateral pulmonary infiltrates on imaging and a PaO₂/FiO₂ ratio of 200 prior to ICU admission (on low-flow oxygen, consistent with moderate ARDS). Shortly after ICU admission, her oxygenation deteriorated to a PaO₂/FiO₂ ratio of 81 on mechanical ventilation with PEEP of 10 cmH₂O, meeting criteria for severe ARDS.

INTERVENTIONS: Management was restricted to organ support (mechanical ventilation, continuous renal replacement therapy), ganciclovir antiviral therapy, and broad-spectrum antibiotics. Crucially, guideline-directed immunomodulatory therapy for HLH (e.g., corticosteroids/etoposide per HLH-2004) was not administered due to delayed diagnosis, lack of institutional expertise, and socioeconomic constraints.

OUTCOMES: The patient's condition deteriorated rapidly, with progression to fatal multi-organ failure and death on hospital day 5 (illness day 15).

LESSONS: This case demonstrates that EBV can trigger a fulminant, lethal triad of HLH, meningitis, and ARDS even in immunocompetent hosts, which has not been previously reported in a single patient. It underscores that high-risk EBV-HLH mandates immediate immunomodulation, as antiviral and supportive care alone are catastrophically insufficient. Early recognition and overcoming barriers to administering complex, urgent therapies are essential to improving outcomes.},
}

Humans
Female
*Lymphohistiocytosis, Hemophagocytic/diagnosis/complications/pathology/virology
*Epstein-Barr Virus Infections/complications/diagnosis/pathology/virology
Adult
*Respiratory Distress Syndrome/diagnosis/pathology/complications/virology
Fatal Outcome
*Herpesvirus 4, Human/isolation & purification/genetics
Immunocompetence

@article {pmid43027094,
year = {2026},
author = {Dong, H and Zeng, X and Hu, Y and Zheng, X and Zhang, J},
title = {Modulatory Effects of Water Extract from Eleutherine americana on Intestinal Health: Insights from Growth, Morphology, Microbiota and Metabolomics in Plectropomus leopardus.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {21},
pages = {},
pmid = {43027094},
issn = {2076-2615},
abstract = {This study evaluated dietary Eleutherine americana water extract (EAW, 0 [NC], 1 [LD], 5 [MD], and 10 [HD] mL/kg) in 480 juvenile leopard coral grouper (Plectropomus leopardus; initial body weight, 11.72 ± 0.34 g) over 8 weeks, with four replicate tanks of 30 fish per treatment. EAW did not significantly improve growth performance, but survival was higher in MD and HD than in NC (p < 0.05). Histological observations indicated more intact mucosal folds, greater crypt depth, and higher goblet-cell counts. Metabolomic analysis showed lower carnitine levels and higher phospholipid and prostaglandin metabolites, with annotated differences in bile acid biosynthesis, amino acid metabolism, and carbon metabolism pathways. Intestinal microbiota profiles showed lower relative abundances of Pseudomonadota and Basidiomycota in EAW groups, lower Actinomycetota in LD and MD, and higher Bacteroidota and Bacillota in MD. At the genus level, Bradyrhizobium, Microbacterium, and Sphingobium abundances were lower, and Afipia abundance was higher, in EAW groups. Functional profiles varied in carbohydrate, amino acid, and lipid metabolism categories. Microbiota-metabolite correlation networks identified Pseudomonadota, Actinomycetota, hexosylceramides, and carnitines as highly connected features. Network pharmacology identified pdgfra, pdgfrb, and sirt1 as candidate targets of the major EAW components eleutherol, eleutherin, and isoeleutherin. The survival and intestinal findings support further evaluation of EAW as a feed additive for intestinal health in leopard coral grouper.},
}

@article {pmid43027216,
year = {2026},
author = {Li, N and Li, F and Zhang, M and Zhang, F and Wu, C and Hu, L and Xu, J},
title = {Testicular and Rumen Microbial Responses to Selenium-Enriched Malt in Heat-Exposed Simmental Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {21},
pages = {},
pmid = {43027216},
issn = {2076-2615},
support = {JXSNKYJCRC202442//Jiangxi Academy of Agricultural Sciences/ ; },
abstract = {This study evaluated testicular and rumen microbial responses to selenium-enriched malt in heat-exposed Simmental bulls. Eighteen bulls received a basal diet alone or supplemented to provide target supplemental Se levels of 0.3 or 0.5 mg/kg dietary DM. Metagenomics included six bulls per group, host assays four per group, and RNA sequencing three per group. Compared with controls, the high-dose group had higher serum antioxidant indices and reproductive hormone concentrations, lower inflammatory markers, higher Johnsen scores, and lower TUNEL positivity. Gene-level FDR control identified 23, 1, and 4 differentially expressed genes in the low-dose versus control, high-dose versus control, and high-dose versus low-dose contrasts, respectively. Provider-reported GSEA showed negative normalized enrichment scores for steroid biosynthesis in the control-versus-low-dose and control-versus-high-dose contrasts, indicating enrichment toward the supplemented side under the provider's contrast convention. qPCR showed lower CYP11A1, CYP17A1, SCARB1, and LDLR expression at the low dose, whereas Bax, Bcl-2, and CYP17A1 protein abundance did not differ. Rumen microbial diversity and community composition differed among groups, and two post hoc selected cofactor-related pathways had lower abundance at the low dose. None of the 160 microbiome-testis or 720 microbiome-serum associations survived FDR correction. Supplementation was associated with favorable systemic and testicular histological responses and dose-specific molecular and microbial changes under heat exposure.},
}

@article {pmid43027271,
year = {2026},
author = {Sun, S and Zhang, Z and Yang, P and Ye, S and Hu, J and Zheng, J and Zhao, Y and Li, X and Zhi, R and Dou, X and Zhang, H and Song, Y and Dou, X and An, X and Bati, H and Yao, S and Tao, Y and Tan, R and Liu, S},
title = {Microbial Functional Carriers and Metabolic Background Associated with Natural Musk Quality in Forest Musk Deer.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {21},
pages = {},
pmid = {43027271},
issn = {2076-2615},
support = {2025HXFWBH-LSQ-01//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; },
abstract = {Whether differences in natural musk quality are associated with identifiable microbial ecological and metabolic configurations remains unclear, as studies integrating phenotype, community composition, functional sources, and non-muscone metabolic background are lacking. In this study, integrated metagenomic and GC-MS/LC-MS analyses were conducted on six natural musk samples from forest musk deer on a single farm, categorized into low-quality-associated (S1, S2, and S6) and high-quality-associated (S3, S4, and S5) groups. The two groups exhibited phenotypic differentiation in muscone, moisture, and sensory characteristics. Genus-level composition revealed quality-associated consortia with individual heterogeneity. KEGG Level 3 pathway decomposition into taxonomic carriers showed that similar functional potential could be achieved across genera, particularly lipid, ketone-body, and terpenoid pathways. After excluding muscone, candidate features related to lipid/membrane components, sterols, macrocyclic ketones, and volatiles changed coordinately along the quality axis. These results outline a multi-omics evidence chain of "phenotypic differentiation-consortium reorganization-functional carrier redistribution-background metabolic remodeling", in which the identity of the organisms carrying each function provides an additional explanatory layer beyond total pathway abundance. This exploratory cross-sectional study provides testable hypotheses on the quality-associated ecological-metabolic organization of natural musk and targets for subsequent mechanistic validation.},
}

@article {pmid43027480,
year = {2026},
author = {Abou-Emera, OK and Aladhadh, M},
title = {Hen Egg-Derived Bioactive Proteins and Peptides at the Gut Interface: From Molecular Characterization and Digestion to Microbiome Interactions and Prospective Precision Nutrition.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {21},
pages = {},
pmid = {43027480},
issn = {2304-8158},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {Hen eggs (Gallus gallus domesticus) contain bioactive proteins, peptides and lipids, but compound characterization, mechanistic cell and animal studies, and human consumption trials have developed largely in isolation. This narrative review, supported by a documented literature search, follows one pathway: egg composition, molecular characterization, processing and digestion, bioaccessibility, intestinal and microbial interaction, host signaling, and a prospective precision-nutrition outlook. Findings are classified into translational evidence categories (a heuristic classification of experimental systems, not a ranking of study quality) and summarized in a multidimensional evidence matrix. Egg white and yolk proteins, including ovotransferrin, ovomucin and lysozyme, yield characterized peptides, notably the ovotransferrin tripeptides IRW (Ile-Arg-Trp), IQW (Ile-Gln-Trp) and LKP (Leu-Lys-Pro), and ovomucin hydrolysates, whose activities in cell and animal models are compound-specific: LKP, for example, did not reproduce the effect of IRW on insulin resistance in muscle cells. In humans, one small ileostomy study (n = 5) reports higher ileal protein digestibility for cooked than raw egg, short-term trials show that whole-egg intake raises plasma choline, and an antibiotic-suppression study shows that trimethylamine-N-oxide formation after eggs plus phosphatidylcholine depends on gut microbiota. No study identified shows that IRW, IQW or LKP are generated, survive digestion or reach the circulation after ordinary egg consumption, and only six human studies address egg intake and the gut microbiome. Dose-response, delivery-system and safety data are largely missing, and precision nutrition for egg bioactives remains a research framework. Priorities are human pharmacokinetic confirmation, longer trials with shotgun metagenomics and functional readouts, and independent safety testing.},
}

@article {pmid43027566,
year = {2026},
author = {Lynett, ML and Dickson, CA and Memory, T},
title = {Exploratory Amplicon-Based Metagenomic Profiling and Chemical Fingerprinting of Three Spontaneously Fermented Southern African Traditional Products.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {21},
pages = {},
pmid = {43027566},
issn = {2304-8158},
abstract = {Traditional fermented foods are integral to African culinary heritage and nutrition, yet their microbial ecology remains underexplored in many regions. This study employed amplicon sequencing (16S rRNA and ITS) and Fourier Transform Infrared (FTIR) spectroscopy to characterize the microbial communities and biochemical profiles of spontaneously fermented cow's milk (amasi), sorghum-maize slurry (ting-type gruel), and sour maize gruel (mahewu). Amasi displayed the highest diversity, dominated by Lactococcus and Malassezia restricta. Mahewu was dominated by Clostridium sensu stricto and Malassezia restricta. The ting-variant showed low diversity with Weissella dominance and Symbiotaphrina species. FTIR spectra corroborated these patterns, highlighting lipid/protein bands in amasi and carbohydrate/organic acid signatures in the fermented cereal products. Beta-diversity analyses confirmed strong substrate-driven separation, with limited shared taxa underscoring ecological specialization. These findings reveal how raw material composition and processing shape spontaneous fermentation outcomes, while highlighting potential safety risks from opportunistic taxa and opportunities for probiotic strain isolation from beneficial taxa. Future studies are required to determine the viability and characteristics of the microbial flora in these fermented beverages to determine if their occurrence is significant. The results in this study show that metagenomic and FT-IR spectroscopy can be used to profile traditional fermented products, but this must be coupled with in-depth metabolite analyses using quantitative instruments and machine learning technologies for predictive fingerprinting to determine the identity, safety, and functionality of these culturally significant foods.},
}

@article {pmid43027762,
year = {2026},
author = {Escobar-Niño, A and Calcis-Marzán, MV and Forján-Miguéns, A and Punta-Sánchez, I and Coste, O and Pérez-Hurtado, A and Fernández-Acero, FJ},
title = {Unlocking the Power of Metaproteomics: A Novel Tool for Enhancing Shorebird Conservation and Blue-Economy Management.},
journal = {International journal of molecular sciences},
volume = {27},
number = {21},
pages = {},
pmid = {43027762},
issn = {1422-0067},
support = {RESBIOMAR LiA 4, SP18//Plan Complementario de I+D+i en el área de Biodiversidad (PCBIO)/ ; FEDER-UCA-2024-A2-14 (2024-095 / PVA / R&D+I FEDER Junta Andalucía / PR)(BIOPAB)//Universidad de Cádiz/ ; },
mesh = {Animals ; *Proteomics/methods ; *Conservation of Natural Resources/methods ; *Birds/metabolism/microbiology ; Feces/microbiology/chemistry ; Metagenomics/methods ; Proteome ; Microbiota ; },
abstract = {Metaproteomics, the large-scale analysis of proteins from environmental or host-associated samples, has emerged as a transformative tool for characterizing microbial communities and their functional roles. Unlike metagenomics or metatranscriptomics, metaproteomics directly captures phenotypic expression, linking molecular function to ecological and physiological outcomes. Beyond its established applications in human microbiome and dietary research, metaproteomics enables the precise identification of food-derived protein biomarkers, including the discrimination of tissue-specific origins. This level of resolution is not attainable through DNA-based approaches. Here, we applied metaproteomics for the first time to analyze the feces of shorebirds in the salt flats and salt marshes of Cadiz Bay, aiming to determine their diet with unprecedented resolution. Conventional methods, based on direct observation or fecal inspection, are labor-intensive and risk losing critical dietary information. By contrast, metaproteomics provides rapid, high-resolution insights, offering a robust alternative for ecological monitoring. Our results demonstrate the potential of this technique to transform natural area management, optimize conservation strategies for avian species, and support the sustainable development of the blue economy. This study highlights metaproteomics as an innovative, cross-sectoral approach capable of advancing both fundamental ecological research and practical conservation outcomes.},
}

Animals
*Proteomics/methods
*Conservation of Natural Resources/methods
*Birds/metabolism/microbiology
Feces/microbiology/chemistry
Metagenomics/methods
Proteome
Microbiota

@article {pmid43027795,
year = {2026},
author = {Issilbayeva, A and Kozhakhmetov, S and Kushugulova, A and Askarova, S and Kaiyrlykyzy, A and Tuigunov, D and Dolmatova, O and Zholdassova, Z and Omarov, Y and Nurgozhin, T},
title = {Gut Microbiome Alterations in Alzheimer's Disease: A Shotgun Metagenomic Case-Control Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {21},
pages = {},
pmid = {43027795},
issn = {1422-0067},
support = {AP23489983//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Male ; Aged ; Metagenome ; Shotgun Sequencing ; Cross-Sectional Studies ; Bacteria/classification/genetics ; Kazakhstan ; },
abstract = {The gut microbiome has been proposed as a contributor to Alzheimer's disease (AD) pathogenesis via the microbiota-gut-brain axis, but findings across cohorts are inconsistent and scarce data exist from Central Asian populations. We used shotgun metagenomic sequencing to compare the gut microbiome of AD patients and cognitively healthy controls from Kazakhstan. In a cross-sectional case-control study (35 AD, 39 Control), we profiled taxonomic and functional (HUMAnN pathway) composition, and compared alpha/beta diversity, individual taxa and pathways, and their association with clinical and demographic variables (Mann-Whitney U test, PERMANOVA/PERMDISP, OLS regression, all BH-FDR corrected, sensitivity analysis using ANCOM-BC2), with sensitivity analyses adjusting for age and BMI and applying Bonferroni correction. Within the AD group, circulating adiponectin-measured only in this group-was examined for associations with microbiome features in an exploratory analysis. Alpha diversity was lower in AD (q < 0.05). Community composition also separated by group on PERMANOVA (R[2] = 8.6%, p = 0.001), and this separation held after adjusting for age and BMI. A total of 178 taxa differed significantly between groups (BH-FDR; 37 were also Bonferroni-significant), most prominently depletion of Faecalibacterium and enrichment of Eisenbergiella and Desulfovibrio in AD; 100 pathways differed significantly (20 Bonferroni-significant). Three clinical/demographic variables (total bilirubin, atherogenic index, BMI) were associated with specific taxa or pathways. Within the AD group, adiponectin correlated negatively with the pathway assimilatory sulfate reduction IV (rho = -0.60, q = 0.015). AD in this Central Asian cohort was associated with a less diverse, compositionally distinct gut microbiome, with depletion of butyrate-producing Firmicutes and enrichment of sulfate-reducing taxa, alongside other taxa whose direction of association differed from prior reports.},
}

Humans
*Alzheimer Disease/microbiology
Case-Control Studies
Female
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Male
Aged
Metagenome
Shotgun Sequencing
Cross-Sectional Studies
Bacteria/classification/genetics
Kazakhstan

@article {pmid43027887,
year = {2026},
author = {Giza, A and Iwan, E and Bomba, A and Orłowska, A and Smreczak, M and Pietruk, M and Chudzik, A and Olejnik, M and Domańska-Blicharz, K},
title = {A Tailored Sequencing Approach for Identifying SARS-CoV-2 Variants in Challenging Samples from Mink.},
journal = {International journal of molecular sciences},
volume = {27},
number = {21},
pages = {},
pmid = {43027887},
issn = {1422-0067},
support = {S/445//National Veterinary Research Institute/ ; No.773830//European Union/ ; },
mesh = {Animals ; *Mink/virology ; *SARS-CoV-2/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *COVID-19/virology/veterinary ; Metagenomics/methods ; Genome, Viral ; },
abstract = {High-throughput sequencing (HTS) is an essential tool for genomic surveillance of infectious agents, including SARS-CoV-2 in farmed mink. However, sample quality varies, hindering high-quality sequencing results. In this study, six mink-origin SARS-CoV-2-positive samples were sequenced using two hybrid-capture methods (commercial and custom) and a shotgun metagenomic approach. All methods consistently identified SARS-CoV-2 variants. The metagenomic approach yielded the lowest mapping rate (up to 0.35%), breadth of coverage (97-100%), depth of coverage (9-932×), and mean mapq (30-59), and one sequence did not meet the quality criteria. In contrast, both hybrid-capture methods achieved higher mapping rates (47-99%), breadth of coverage (99.9-100%), and depth of coverage (508-115,846×). The custom hybrid-capture approach was selected because of its superior coverage uniformity, the lowest number of ambiguous bases (N), adjustability to low RNA levels and degraded material, and streamlined laboratory workflow. To further evaluate its applicability, it was applied to 35 clinical samples collected as part of routine genomic surveillance. This method generated sequencing data with high mapping rates (median 95%), depth of coverage (median 13,238×), breadth of coverage (median 100%), and mean mapq (median 60). These findings demonstrate that the custom hybrid-capture approach is a useful tool for genomic surveillance of SARS-CoV-2 in mink-origin samples.},
}

Animals
*Mink/virology
*SARS-CoV-2/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
*COVID-19/virology/veterinary
Metagenomics/methods
Genome, Viral

@article {pmid43028045,
year = {2026},
author = {Sadurski, J and Staniszewski, A and Muyanlı, EB and Yılmaz, R and Waśko, A},
title = {Global Analysis of Public Cheese Microbiomes Reveals Widespread Bacterial Taxa and Geographic Community Structure.},
journal = {International journal of molecular sciences},
volume = {27},
number = {21},
pages = {},
pmid = {43028045},
issn = {1422-0067},
support = {SD/81/TŻ/2023//Doctoral School of the University of Life Sciences in Lublin/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Geography ; Biodiversity ; },
abstract = {Cheese microbiomes remain difficult to compare globally because public sequencing datasets are fragmented and methodologically heterogeneous. Here, we curated 14,203 sequencing records from 233 BioProjects and retained 8910 records from 112 BioProjects for standardized reanalysis, establishing a global comparative framework for cheese microbiome research. Three taxonomic profiling pipelines (QIIME2, Kraken2 and mOTUs) recovered broadly consistent genus-level patterns dominated by lactic acid bacteria, although quantitative concordance varied between methods and study collections. Whole-genome shotgun analysis identified 12 widespread bacterial species independently detected in at least 50% of BioProjects by both Kraken2 and mOTUs, with Lactococcus lactis, Streptococcus thermophilus and Lactococcus cremoris detected in at least 84% of BioProjects in both analyses. Geographic structure remained evident after accounting for dominant community composition: sample-origin country explained 36.6% of community variation in the primary analysis and remained associated with community composition in balanced subsampling and analyses removing or continuously adjusting for five dominant lactic acid bacterial genera. However, public datasets were strongly geographically imbalanced, with European BioProjects dominating the available collection. Together, these results establish a reproducible framework and comparative baseline for investigating cheese microbiome diversity, geographic structure and cross-study patterns across globally distributed public sequencing datasets.},
}

*Cheese/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics
Metagenomics/methods
Phylogeny
RNA, Ribosomal, 16S/genetics
Geography
Biodiversity

@article {pmid43028125,
year = {2026},
author = {Sahin, B and Eken, Y and Sahin, F and Karaman, T and Sezerman, OU and Ozer, S and Kaya, ZZ and Karagözlü, MZ and Serdar, MA and Serteser, M and Baykal, AT},
title = {Genotype-Associated Molecular Phenotypes Across Brain and Gut Compartments in Male 5xFAD Mice: Shared Latent Structure and the Limits of Individual-Level Inference.},
journal = {International journal of molecular sciences},
volume = {27},
number = {21},
pages = {},
pmid = {43028125},
issn = {1422-0067},
support = {TSA-2024-2169//Acıbadem Mehmet Ali Aydınlar University Scientific Research Projects Commission (ABAPKO)/ ; },
mesh = {Animals ; Male ; Mice ; *Alzheimer Disease/genetics/metabolism ; *Brain/metabolism ; Phenotype ; Genotype ; Proteomics/methods ; Disease Models, Animal ; Proteome ; *Gastrointestinal Microbiome ; Mice, Transgenic ; Feces/microbiology ; Hippocampus/metabolism ; Metagenomics ; Multiomics ; },
abstract = {Whether gut and brain molecular states covary within individual animals, rather than merely co-occurring at the group level, has rarely been tested in Alzheimer's disease models. We profiled the hippocampus, cortex, cerebellum, intestine and feces of 18 male 5xFAD (5 familial AD mutations) (B6SJL background) mice and wild-type littermates at 3, 6 and 9 months by label-free proteomics, and feces additionally by shotgun metagenomics. The hippocampal proteome reproduced the amyloid-associated signature (App, Apoe, Hexb, Clu, Gfap), and protein-set analysis showed elevated microglial, lysosomal, astrocytic and endoplasmic reticulum chaperone proteins in the hippocampus and cortex, with no detectable difference in synaptic or mitochondrial sets. Fecal Shannon diversity was reduced, and the bile-acid-modifying genera Romboutsia and Turicibacter were nearly absent in all 5xFAD animals from 3 months (cage nested within genotype). Multi-omics factor analysis recovered a genotype-associated factor shared across brain and gut views (exact permutation p = 0.00125) that explained at most 6.3% of variance in any view and was preprocessing-dependent. After removal of group structure, correlation burden did not exceed a within-cell permutation null, and neither did same-animal positive controls. The 5xFAD genotype thus alters every compartment examined, and a modest latent structure links them; because the design excludes only strong or dense individual-level coupling, the null result bounds design resolution rather than showing that gut and brain are uncoupled.},
}

Animals
Male
Mice
*Alzheimer Disease/genetics/metabolism
*Brain/metabolism
Phenotype
Genotype
Proteomics/methods
Disease Models, Animal
Proteome
*Gastrointestinal Microbiome
Mice, Transgenic
Feces/microbiology
Hippocampus/metabolism
Metagenomics
Multiomics

@article {pmid43028184,
year = {2026},
author = {Yang, S and Tang, W and Wang, Y and Yang, H and Wang, W and Cao, Z and Wang, W and Li, S and Bai, Y and Hao, Y},
title = {Paper-Mulberry-Silage-Enhanced Lipid Metabolism and Milk Polyunsaturated Fatty Acid Concentration in Dairy Cows: A Multi-Omics Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {21},
pages = {},
pmid = {43028184},
issn = {1422-0067},
support = {BX2025003//China Postdoctoral Science Foundation/ ; 2022YFD1301001//National Natural Science Foundation of China/ ; 241111110100//Henan Science and Technology Department/ ; 242102111039//Henan Science and Technology Department/ ; },
mesh = {Animals ; *Milk/chemistry/metabolism ; Cattle ; *Fatty Acids, Unsaturated/metabolism/analysis ; Female ; *Lipid Metabolism ; *Silage/analysis ; *Morus/chemistry ; Rumen/microbiology/metabolism ; Multiomics ; Lactation ; Animal Feed ; },
abstract = {Developing alternative forages that modify milk fatty acid composition is important for improving milk nutritional quality and diversifying feed resources in dairy production. Previous studies have demonstrated the potential of paper mulberry (PM, Broussonetia papyrifera) silage to partially replace conventional roughages and influence antioxidant status and milk fatty acid composition. However, its effects on milk polyunsaturated fatty acids (PUFAs) and the associated ruminal microbial and metabolic mechanisms remain insufficiently characterized. This study aimed to evaluate the effects of feeding PM silage on the concentration of polyunsaturated fatty acids in milk, the structure of the rumen microbial community, and lipid metabolic functions, as well as to analyze the associations between rumen microbial and metabolic profiles and the fatty acid composition of milk. Thirty lactating Holstein cows were randomly assigned to control and PM groups, with 15 cows per group. The PM group received diets containing 9% PM silage for the first 28 days and 18% for the subsequent 28 days on a dry matter basis. Rumen fluid, plasma, and milk were collected on day 56 for integrated analyses combining fatty acid profiling, ruminal fermentation measurements, 16S rRNA gene sequencing, metagenomics, and metabolomics. Milk PUFA concentration was significantly higher in the PM group than in controls, with no significant differences in dry matter intake or milk yield. PM feeding also altered ruminal microbial community composition and lipid-metabolism-related functional gene abundances, accompanied by increased glycerophosphocholine and glycerophosphoethanolamine levels. Integrated analyses linked these changes to fatty acid profiles in rumen fluid, plasma, and milk, supporting ruminal lipid remodeling as a candidate mechanism underlying the increase in milk PUFA concentrations. These findings provide evidence for the microbial and metabolic basis of the effects of PM silage on milk fatty acid composition and inform its development as a functional forage and the optimization of dairy cow feeding strategies.},
}

Animals
*Milk/chemistry/metabolism
Cattle
*Fatty Acids, Unsaturated/metabolism/analysis
Female
*Lipid Metabolism
*Silage/analysis
*Morus/chemistry
Rumen/microbiology/metabolism
Multiomics
Lactation
Animal Feed

@article {pmid43028548,
year = {2026},
author = {Liu, L and Zhang, B and Sang, K and Lin, J and Li, M and Zhong, P and Huang, N and Lai, J and Xu, L and Chen, L and Liu, Y and Chen, S},
title = {Legionella Pneumonia in the Molecular Diagnostics Era: From Intracellular Pathogenesis to Precision Management.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {21},
pages = {},
pmid = {43028548},
issn = {2075-4418},
abstract = {Legionella pneumophila is a major cause of severe community-acquired pneumonia and one of the most lethal respiratory pathogens. Nevertheless, it remains substantially underdiagnosed because conventional diagnostic assays are slow, insensitive, or limited to specific serogroups. In this narrative review, we integrate fragmented literature regarding Legionella pneumonia, covering its intracellular pathogenesis, clinical spectrum and patient management. Evidence was identified through a structured search of PubMed/MEDLINE and Europe PMC (23 September 2026) and prioritized by design, with primary clinical and mechanistic studies and systematic reviews taking precedence over narrative summaries and with society guidelines used to anchor management recommendations. We argue that this field is undergoing a diagnostic paradigm shift fueled by culture-independent molecular assays. We first review the Dot/Icm type IV secretion system and intracellular lifecycle that allow Legionella to replicate within macrophages while evading host innate immunity. We then summarize the full clinical spectrum, ranging from self-limited Pontiac fever to fatal Legionnaires' disease complicated by acute respiratory distress syndrome, as well as epidemiological characteristics including waterborne transmission and outbreak risks. The core of this review examines how metagenomic next-generation sequencing, targeted NGS, plasma microbial cell-free DNA and syndromic multiplex PCR are reshaping diagnostic workflows, and compares the strengths and limitations of these novel tools with urinary antigen testing and bacterial culture. Pooled estimates place the sensitivity of urinary antigen testing at 0.79 overall and 0.86 for serogroup 1, and that of respiratory PCR at 97.4%, with specificities of 1.00 and 0.99, respectively. We further evaluate contemporary therapeutic evidence, including fluoroquinolone versus macrolide monotherapy, combination regimens, and adjunctive corticosteroid therapy. Throughout this review, we highlight that Legionella is a pathogen whose clinical presentation, diagnostic yield and prognosis are highly dependent on host immune status, exposure setting and appropriate diagnostic stewardship. We conclude by identifying critical knowledge gaps and outlining a framework for diagnosis-driven precision antimicrobial management of this underrecognized pathogen. That framework is an evidence-informed synthesis rather than a validated pathway: no prospective study has yet shown that it improves patient outcomes, and its cost-effectiveness has not been measured.},
}

@article {pmid43028980,
year = {2026},
author = {Lei, J and Lv, N and Liu, P and Liu, C and Peng, G},
title = {Taxonomic Guilds, Action Mechanisms, and Agronomic Deployment of Maize Rhizosphere Microbiota for Yield Enhancement: Unraveling G×M×E Interactions and Translational Barriers via Multi Omics.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {21},
pages = {},
pmid = {43028980},
issn = {2223-7747},
support = {CSTB2025TIAD-LYKJXZLHGGXO004//Chongqing Key Special Project of Technological Innovation and Application Development/ ; NW-CSTB2025NYKJGGXMLSGXZYLXMX0001//the Agricultural Science and Technology R&D Program of Chongqing/ ; WSWZZ 2020004//Chongqing Entomopathogenic Fungi Strain Resource Bank/ ; },
abstract = {Maize (Zea mays L.) productivity is increasingly constrained by edaphic stressors-including soil salinization, drought, and acidification-posing mounting threats to global food security. Plant growth-promoting microorganisms (PGPM) offer a sustainable alternative to synthetic fertilizers, yet despite their pronounced performance under controlled laboratory settings, their beneficial effects often prove inconsistent in open-field environments, largely due to spatial heterogeneity and genotype-specific responses. Herein, we present a comprehensive synthesis of the core microbial guilds that have been robustly associated with maize yield enhancement. The mechanisms underlying these effects are examined across several dimensions, including biological nitrogen fixation, phosphate and potassium solubilization, phytohormone production, ethylene regulation, stress tolerance, and rhizosphere colonization. Genomic, transcriptomic, metagenomic, and metabolomic data are integrated to construct an interaction network between maize and rhizosphere microbes. We identify the genotype-by-microbiome-by-environment (G×M×E) interplay as the principal bottleneck hampering field-scale translational success. To address this issue, three priorities are proposed: (i) designing synthetic microbial consortia, (ii) using multi-omics to examine mechanisms, and (iii) developing tools for site-specific deployment. In conclusion, these sections provide a framework for developing more reliable microbial inoculants for maize.},
}

@article {pmid43029048,
year = {2026},
author = {Wu, Y and Wang, F and Liu, S and Dai, T and Deng, J and Jiang, L and Yimingniyazi, A and Wang, S},
title = {Density-Dependent Changes in Root Exudates, Rhizosphere Microbes, and Soil Metabolites of Solanum rostratum.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {21},
pages = {},
pmid = {43029048},
issn = {2223-7747},
support = {32460684//National Natural Science Foundation of China/ ; 2023D01B37//Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; XKLEAEEEO-09//Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms/ ; //Forage Germplasm Resources Survey in Xinjiang/ ; },
abstract = {Intraspecific competition shapes high-density monodominant communities of invasive plants, but how density is associated with rhizosphere microbial reassembly and soil metabolite accumulation via root exudates remains unclear. We established four planting densities (1, 3, 5, and 10 plants per pot) and integrated growth and photosynthetic physiology, root exudate metabolomics, rhizosphere metagenomics, and soil metabolomics using Mantel tests and variable-level correlation analysis. Increasing density reduced all traits except plant height, which showed a slight, non-significant increase followed by a significant decrease. Root exudates shifted from phenolic acid/terpenoid dominance at low density to sugar/peptide dominance at high density. Low-density-enriched bacterial genera were positively correlated with biomass, whereas high-density-enriched genera (e.g., Ilumatobacter, Allosphingosinicella) were negatively correlated. Soil metabolites such as Glutarate Semialdehyde and Sutherlandin D were negatively correlated with biomass, root traits, and photosynthesis. Mantel tests showed strong correlations between plant phenotypes and root exudates (r = 0.80) and between exudates and soil metabolites (r = 0.83). Variable-level analysis linked phenolic acid exudates to putatively growth-associated bacteria (e.g., Flavitalea, Blastococcus) and sugar/peptide exudates to putatively stress-adapted bacteria (e.g., Allosphingosinicella, Ilumatobacter), which were positively correlated with Glutarate Semialdehyde and Sutherlandin D accumulation. These results indicate that density-associated exudate changes synchronized with rhizosphere microbial reassembly and soil metabolite accumulation, forming an "exudate-microbe-metabolite" cascade. This cascade may buffer against high-density intraspecific competition and help explain monodominant community formation in invaded ranges.},
}

@article {pmid43030384,
year = {2026},
author = {You, Y and Li, H and Pei, X and Wu, D and Lv, X and Wu, Y},
title = {Tuberculosis-Associated Hemophagocytic Lymphohistiocytosis with Bone Marrow Involvement: Case Report and Literature Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {21},
pages = {},
pmid = {43030384},
issn = {2077-0383},
abstract = {Tuberculosis is a rare but fatal trigger of secondary hemophagocytic lymphohistiocytosis (HLH). Its diagnosis is challenging because clinical manifestations overlap with HLH, and immunological tests may be falsely negative in HLH-related immune dysfunction. We report a case of a 34-year-old male with fever and pancytopenia. The patient's diagnostic course was protracted and misleading: all conventional tuberculosis immunological tests were negative, and he initially did not meet HLH-2004 criteria. The diagnosis of TB-HLH was eventually established by a second bone marrow biopsy and metagenomic next-generation sequencing. We also reviewed 66 TB-HLH cases, revealing frequent negative immunological test results and showing that timely anti-tuberculosis therapy was associated with reduced mortality (78.3% vs. 15.0%, p < 0.001). This case and our review underscore the importance of early bone marrow biopsy and molecular testing in unexplained HLH, particularly when tuberculosis tests are negative. Given the high mortality and frequent diagnostic delay, clinicians should maintain a high index of suspicion and pursue aggressive diagnostic workup for tuberculosis in HLH patients without a clear trigger. Furthermore, we emphasize the need to raise awareness of TB-HLH and to interpret immunological test results with caution in HLH patients, as negative findings should not be used to exclude tuberculosis.},
}

@article {pmid43031543,
year = {2026},
author = {Grekova, A and Schudoma, C and Letunic, I and Kim, CY and Podlesny, D and Fullam, A and Schmidt, TSB and Orakov, A and Mende, D and Schiller, J and Erbstein, KOE and Bartmanski, B and Zimmermann-Kogadeeva, M and Zimmermann, M and Kuhn, M and Bork, P and Khedkar, S},
title = {proMGE2-a planetary-scale resource of mobile genetic elements in microbial (meta)genomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1163},
pmid = {43031543},
issn = {1362-4962},
support = {//Ministry of Science, Research and the Arts Baden-Württemberg (MWK)/ ; W-de.NBI-014//Federal Ministry of Research, Technology and Space in the frame of de.NBI & ELIXIR-DE/ ; //European Molecular Biology Laboratory/ ; 555128266//Deutsche Forschungsgemeinschaft/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; //EMBL Planetary Biology Transversal Theme/ ; },
abstract = {proMGE is a resource of prokaryotic mobile genetic elements (MGEs) that systematically catalogues MGEs from prokaryotes, their intercellular spread, antimicrobial resistance gene carriage, and MGE nesting interactions. We present proMGE2 featuring a 6X expansion, a total of >16.4 million MGEs from 670k high-quality isolate genomes, and 180k metagenome-assembled genomes (MAGs), spanning diverse MGE categories: transposons and insertion sequences, phages, phage-like elements, conjugative elements, mobility islands, and integrons. proMGE2 includes MGEs from MAGs derived from environmental microbiomes, encompassing ~50k samples across several major habitat types. proMGE2 provides a standardized MGE reference collection of >5 million non-redundant MGE sequences drawn from our curated database, and enables identification of MGEs in user-provided genomes. proMGE2 captures MGE diversity and their functional potential at unprecedented scale to support future research of mobile genetic elements and transfer of genetic material in microbes. The database is available at http://promge.embl.de/.},
}

@article {pmid43031719,
year = {2026},
author = {Geng, S and Yang, J and Shi, X and Zhang, Q and Yang, C},
title = {Variation in rhizosphere microbial communities and nitrogen- and phosphorus-cycling functional genes among rubber plantations in Yunnan, China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1977925},
pmid = {43031719},
issn = {1664-302X},
abstract = {INTRODUCTION: Rhizosphere microorganisms are important participants in soil nutrient transformation. However, variation in rhizosphere microbial community composition and nitrogen (N)- and phosphorus (P)-cycling functional gene profiles among rubber plantations in Yunnan Province remains unclear.

METHODS: Metagenomic sequencing was used to compare rhizosphere microbial community composition and N- and P-cycling functional gene profiles among the rubber plantations located in five major natural rubber-producing areas in Yunnan Province, China: Gengma (MD), Ximeng (XM), Mengla (ML), Jinghong (JH), and Jiangcheng (JC).

RESULTS: Bacterial and fungal community composition and N- and P-cycling functional gene profiles differed significantly among the five rubber plantations. JC exhibited higher fungal diversity and richness, but its bacterial diversity was significantly lower than that in MD. The bacterial communities were dominated by Pseudomonadota, Acidobacteriota, and Actinomycetota, and the relative abundance of Acidobacteria was significantly enriched in JC compared to JH. Furthermore, Mucoromycota, Ascomycota, and Basidiomycota were the dominant phyla in the fungal community. At the functional level, compared to JC, key genes associated with N cycling were significantly enriched in ML, including N assimilation (glnA, gltB, gltD), dissimilatory nitrate reduction to ammonium (narG, narH, nirB), nitrification (nxrA, nxrB), and denitrification (napA, napB). Furthermore, the nosZ gene was also significantly enriched in MD compared to JC. Regarding the P cycle, compared to JC, genes associated with high-affinity phosphate transporters (pstA, pstB, pstC) and polyphosphate degradation (ndk) were significantly enriched in MD, whereas the organic phosphorus mineralization-related gene phnX exhibited the opposite trend. Meanwhile, compared to MD, the polyphosphate degradation-related gene ppk2 was significantly enriched in ML, whereas the inorganic phosphorus solubilization-related gene pqqC exhibited the opposite pattern. Hierarchical partitioning identified soil pH, total phosphorus (TP), and total potassium (TK) as the primary factors significantly associated with variations in bacterial community composition and P-cycling functional gene profiles.

CONCLUSION: In summary, the composition of rhizosphere bacterial and fungal communities, as well as the functional gene profiles related to N and P cycling, differed significantly among the investigated rubber plantations. These variations were closely associated with soil physicochemical factors. These findings may provide a microbiological basis for further developing site-specific nutrient management strategies in rubber plantations.},
}

@article {pmid43031837,
year = {2026},
author = {Xu, J and Tong, D and Shi, J and Xie, J and Zhang, N and Dai, Z and Zhang, S and Dahlgren, RA and Ma, B},
title = {The Temperature Sensitivity of Soil CO2 Release Is Modified by Virus-Bacteria Interactions.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1479},
pmid = {43031837},
issn = {2639-5274},
abstract = {The temperature sensitivity (Q 10) of soil carbon (C) release is key to predicting C-climate feedback, yet omitting microbial interactions, especially with soil viruses, introduces substantial uncertainty. To address this, we performed 30- and 365-d incubations with metagenomics and metatranscriptomics profiling. We found that soil viruses markedly decreased Q 10 during 30-d incubation. Over 365-d incubation, however, their effects on microbial metabolism and Q 10 were temperature-dependent. The relative abundance of pathways related to viral replication, including those for lytic cycle initiation (e.g., propanoate metabolism decreased by 15.24%) and the energy supply (e.g., lipoic acid metabolism decreased by 20.95%), became less abundant as temperature rose from 15 to 35 °C. Metatranscriptomics data confirmed this trend, with up-regulation of metabolic functions related to viral infection and replication at 15 °C. Thus, temperature-driven variations in viral activity underlie the contrasting roles of soil viruses in regulating Q 10. This study provides the first evidence of temperature-dependent viral regulation of microbial metabolism and Q 10, highlighting the need to incorporate soil viruses into C-climate models.},
}

@article {pmid43031840,
year = {2026},
author = {Li, X and Xu, S and Feng, Y and Wang, R and Wang, X},
title = {A fatal threat: Pneumocystis jirovecii pneumonia with rapidly progressive interstitial lung disease in anti-MDA5-positive dermatomyositis-a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1977161},
pmid = {43031840},
issn = {2296-858X},
abstract = {Pneumocystis jirovecii pneumonia (PJP) is a respiratory infection caused by Pneumocystis organisms, representing an opportunistic fungal infection. The clinical occurrence of PJP combined with rapidly progressive interstitial lung disease (RP-ILD) in dermatomyositis (DM) have also been reported occasionally, but patients with this combination of conditions experience rapid disease progression and high mortality rates. We reported a 70-year-old female patient with dyspnea and fever, detailing her laboratory tests, computed tomography (CT) findings and bronchoalveolar lavage fluid findings. The patient's main clinical manifestations were dyspnea and fever. CT scans revealed scattered reticular opacities and ground-glass opacities in both lungs and metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid detected Pneumocystis jirovecii. Laboratory tests revealed positive anti-MDA5 antibodies during hospitalization. The patient was treated with high-flow oxygen therapy and methylprednisolone upon admission. Subsequently, the patient received mechanical ventilator support and was administered trimethoprim-sulfamethoxazole (TMP-SMX), plasma exchanges and immunoglobulin treatment. The patient's fever subsided, but respiratory failure and interstitial lung disease continued to progressively worsen. Ground-glass opacities, mixed ground-glass opacities, consolidations and reticular opacities were significantly more pronounced than on admission, indicating RP-ILD changes post-treatment. The patient succumbed after 13 days of treatment. PJP complicated by rapidly progressive interstitial lung disease can be fatal in patients, emphasizing the critical importance of early identification of PJP and prompt initiation of anti-PJP treatment. It is crucial to recognize that some MDA5+ DM patients may not present with the typical rash, and in certain cases, RP-ILD may be the primary manifestation. Therefore, early screening for anti-MDA5 antibodies is essential for patients presenting with unexplained early-stage RP-ILD.},
}

@article {pmid41509546,
year = {2026},
author = {Steriade, C},
title = {The Gut Feeling Behind Autoimmune Encephalitis.},
journal = {Epilepsy currents},
volume = {26},
number = {3},
pages = {231-233},
pmid = {41509546},
issn = {1535-7597},
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.

METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.

RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.

SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}

@article {pmid43017131,
year = {2026},
author = {Tayeb, HT and Abouelhoda, M and Alqasabi, A and Magrashi, A and Nafe, G and Alzahrani, T and Alzeer, S and Bakheet, R},
title = {Metagenomic next-generation sequencing improves pathogen detection in culture-negative infections: a diagnostic performance study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1971380},
pmid = {43017131},
issn = {1664-302X},
abstract = {The conventional microbiological diagnosis is frequently insensitive, time consuming and targeted. Patients with underlying immune suppression and those who have recently been on antibiotics often have culture-negative infections. In recent years, metagenomic next-generation sequencing (mNGS) has emerged as a novel, pathogen-agnostic diagnostic approach. A total of 136 clinical specimens were submitted for metagenomic next-generation sequencing (mNGS) between August 2022 and January 2024. Of these samples, 86 from 73 patients were included in this retrospective study. Thirteen patients had more than one specimen included in the study. All specimens were processed using conventional microbiological methods and analyzed using mNGS technology, either by using Illumina next-generation sequencing technology or Oxford Nanopore long-read technology. The diagnostic performance characteristics, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were calculated for both methods. The agreement between the two methods was evaluated using Cohen's kappa coefficient. The paired comparisons were made using the McNemar test. The areas under the ROC curves for both methods were calculated, and the multivariable logistic regression analysis was used to identify the variables that were independently associated with mNGS positivity. Here, conventional microbiology identified pathogens in 16.3% of samples, whereas mNGS identified pathogens in 45.3% of samples. The sensitivity and specificity of mNGS were 57.1 and 84.2%, respectively. By McNemar testing, there was significant detection of pathogens by mNGS (p = 0.0015). The agreement between two methods was poor (kappa = 0.20). The ROC curve for mNGS results showed moderate diagnostic accuracy with an AUC of 0.71. By multivariable logistic regression, immunocompromised status (OR 2.8, 95% CI 1.3-6.0, p = 0.018) and positive imaging findings (OR 3.1, 95% CI 1.4-6.9, p = 0.010) were independently associated with mNGS positivity. mNGS is able to identify more pathogens in culture-negative cases than conventional methods. There is scope for mNGS to be used in a complementary fashion, whilst relying on conventional methods as the primary tool for diagnosis of infections. Notably, the greatest additional information will come from the use of mNGS in immunocompromised patients.},
}

@article {pmid43017153,
year = {2026},
author = {Feng, Y and Sha, Y and Xu, L and Tian, J and Gao, Y and Zhou, R and Liu, G},
title = {Integrated gut microbiome and fecal metabolome profiling identifies taurine-associated microbial dysbiosis across the Alzheimer's disease clinical spectrum.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1981076},
pmid = {43017153},
issn = {1663-4365},
abstract = {BACKGROUND: Gut microbiome alterations have been associated with Alzheimer's disease (AD), but how microbial composition, fecal metabolites, and cognitive function relate across the cognitive impairment spectrum-from subjective cognitive decline (SCD) through mild cognitive impairment (MCI) to AD-remains unclear. We integrated microbiome and metabolome profiles across this clinical spectrum.

METHODS: Fecal samples from 84 participants [10 healthy controls (HC), 22 SCD, 23 MCI, 29 AD] underwent 16S rRNA V3-V4 sequencing and untargeted LC-MS metabolomics. Profiles were integrated via Procrustes analysis, sparse canonical correlation, MIMOSA2 community-metabolism modeling, and mediation analysis. Differential abundance was assessed by Kruskal-Wallis, ANCOM-BC2, and LinDA.

RESULTS: Microbial composition differed across groups (ANOSIM R = 0.111, p = 0.001; Adonis R [2] = 0.070, p = 0.002). Cross-method validation confirmed 8 differentially abundant genera in AD vs. HC with 100% directional concordance between ANCOM-BC2 and LinDA, including depletion of butyrate-producing Lachnospiraceae (Blautia, Dorea, Fusicatenibacter) and enrichment of opportunistic pathobionts (Klebsiella, Escherichia-Shigella). Taurine showed the highest MIMOSA2 community-prediction R [2] (0.129; n = 62) and was positively associated with MMSE scores (r = 0.45, BH-FDR Q = 0.0005). A multi-omic random forest model (5 genera + 5 metabolites + age + sex) discriminated AD-clinical spectrum participants from HC with AUC = 0.86 (95% CI 0.82-0.90), although pairwise differences from the age + sex baseline (AUC = 0.75) did not reach statistical significance. Statistical mediation analysis was consistent with a Blautia → taurine → MMSE statistical mediation [ACME = 0.21, p = 0.008; 54% proportion mediated, bootstrap 95% CI (9%, 58%)].

CONCLUSION: Integrated multi-omic profiling reveals coordinated microbiome-metabolome dysregulation across the AD clinical spectrum, with taurine as a candidate microbial-metabolic node linking gut dysbiosis to cognitive performance. Microbial and metabolic alterations are detectable at the SCD stage, before objective cognitive impairment. These findings warrant validation in larger, age-matched cohorts and higher-resolution metagenomic studies.},
}

@article {pmid43017160,
year = {2026},
author = {Zhang, L and He, X and Xu, L and Xiao, J and Lin, J and Song, B and Chen, L and Chen, G and Liu, K},
title = {Improving Talaromycosis Infection Diagnosis and Prognosis with Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {606899},
pmid = {43017160},
issn = {1178-6973},
abstract = {BACKGROUND: Early diagnosis and timely initiation of appropriate antifungal treatment are critical for improving the prognosis of talaromycosis infection. We aimed to test whether metagenomic next-generation sequencing (mNGS), versus conventional microbiological testing (CMT), improves talaromycosis diagnosis and management in HIV-negative patients via higher sensitivity and faster detection.

METHODS: We retrospectively investigated the clinical data of patients with Talaromyces marneffei (T. marneffei) infection in six hospitals in Fujian, China, between July 2015 and June 2024. The diagnostic performance and clinical impact of mNGS were compared with those of CMT.

RESULTS: Seventy-four patients were included, with 38 cases in the mNGS group and 36 cases for CMT group, based on the method that established the definitive diagnosis. The median duration from hospitalization to confirmed diagnosis was significantly shorter in the mNGS group than in the CMT group (5.0 vs 12.0 days, p < 0.0001). The turnround time for mNGS was shorter than that of CMT (1.0 days vs 6.5 days, p < 0.0001). The mNGS detected more mycobacteria and other fungal infection co-infections than CMT (36.8% vs 13.9%, p = 0.033; 26.3% vs 5.56%, p = 0.025). The mNGS group has a trend of lower mortality compared with the CMT group (18.4% vs 38.9%, p = 0.072). In addition, the length of stay was significantly shorter in the mNGS group than in the CMT group (14.5 days vs 21.0 days, p = 0.007).

CONCLUSION: mNGS facilitates rapid diagnosis and improves administration of targeted antimicrobial therapy, thus improving the prognosis of T. marneffei infection. The clinical utility of mNGS for talaromycosis in at-risk populations should be investigated in prospective and large studies.},
}

@article {pmid43017163,
year = {2026},
author = {Liu, M and Yan, L and Lai, J and Xu, X and Cheng, S},
title = {Effects of different concentrations of exogenous methyl jasmonate on tuber metabolism and rhizosphere bacterial community dynamics in Polygonatum cyrtonema Hua.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1950448},
pmid = {43017163},
issn = {1664-462X},
abstract = {Polygonatum cyrtonema Hua is a traditional medicinal and edible plant valued for its tubers, which are rich in bioactive components such as polysaccharides, flavonoids, and saponins. The phytohormone methyl jasmonate (MeJA) regulates plant secondary metabolism and stress responses, promoting the accumulation of medicinal compounds in P. cyrtonema. However, the temporal dynamics of the rhizosphere microbiome and its association with the tuber metabolism under different MeJA concentrations remain poorly understood. In this study, three-year-old P. cyrtonema plants were treated with rhizosphere sprays of 200 μmol L[-1] and 400 μmol L[-1] MeJA. Plants were sampled at 7, 14, 21, and 28 days post-treatment to evaluate tuber physiology and metabolite profiles, and metagenomic sequencing was used to characterize the structure and function of the rhizosphere bacterial community. Application of 200 μmol L[-1] MeJA significantly enhanced tuber peroxidase (POD) activity, which peaked at 2.29 times that of the control on day 14 (P < 0.05), and increased total flavonoid and saponin contents by 22.58% and 13.85%, respectively (P < 0.05). In contrast, 400 μmol L[-1] MeJA mainly inhibited antioxidant enzyme activities and delayed the induction of secondary metabolism. Metagenomic analysis revealed that the two MeJA concentrations shared the same dominant bacterial phyla but showed concentration-dependent differences in relative abundance dynamics, alpha diversity trajectories, and temporal patterns of community structure. The 200 μmol L[-1] MeJA group exhibited a directional temporal shift (PERMANOVA R[2] = 0.79, P = 0.003) and continuously rising alpha diversity, whereas the 400 μmol L[-1] treatment showed nonspecific stress fluctuations, with reduced alpha diversity, a weaker temporal gradient in community structure, and increased community homogenization. At the functional level, the 200 μmol L[-1] MeJA group had higher relative abundances of microbial genes associated with nitrogen, carbon, and secondary metabolic pathways. In contrast, the 400 μmol L[-1] MeJA group showed disrupted coordination among functional genes and persistently higher abundances of genes involved in antioxidant pathways. Correlation analysis identified associations between specific phyla and host traits: Nitrospirota was positively correlated with POD activity (r = 0.48, P < 0.05); Methylomirabilota was positively correlated with total flavonoid and saponin contents (r ≥ 0.41, P < 0.05); and Verrucomicrobiota was negatively correlated with these components (r < -0.55, P < 0.01). These findings suggest that 200 μmol L[-1] MeJA promotes the accumulation of bioactive metabolites in P. cyrtonema through two proposed ways: the direct activation of host metabolism and the indirect association with shifts in potentially beneficial rhizosphere microbial taxa. This study provides a practical foundation for selective MeJA concentrations in medicinal plant cultivation.},
}

@article {pmid43017556,
year = {2026},
author = {Huang, X and Zhang, X and Zhu, Q},
title = {Microbiome-targeted strategies for Alzheimer's disease: multi-omics signatures, mechanistic links, and intervention evidence.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1828118},
pmid = {43017556},
issn = {1664-302X},
abstract = {Alzheimer's disease (AD) is increasingly studied in relation to gut microbial mechanisms because microbial metabolism, mucosal barrier function, and peripheral immune activation may influence neuroinflammation and host metabolic stress. This review evaluates microbiome-linked evidence in AD with emphasis on studies that combine metagenomics, metabolomics, inflammatory markers, neuroimaging, cerebrospinal fluid or blood biomarkers, and cognitive phenotyping. Current data support several recurring but not yet causal axes, including bile acid transformation, short-chain fatty acid (SCFA) production, trimethylamine N-oxide (TMAO), bacterial product-related inflammatory signaling, and barrier dysfunction. We also review microbiome-targeted interventions, including diet and prebiotics, strain-specified probiotics and synbiotics, oligosaccharide-based agents, gut-restricted antimicrobials, and fecal microbiota transplantation (FMT). The strength of evidence differs substantially across these strategies: sodium oligomannate has been tested in a phase 3 trial, whereas many probiotic, antimicrobial, and FMT approaches remain early clinical, preclinical, or mechanism-generating. Future trials should define a priori microbial, metabolite, immune, and brain biomarker endpoints; control diet, medication, and comorbidity confounding; and validate candidate signatures across independent cohorts before using microbiome profiles for screening or treatment selection.},
}

@article {pmid43018149,
year = {2026},
author = {Cluett, H and Chandler, JC and Bisha, B},
title = {Near-complete genome of Tetraparvovirus sp. specimen WTD-TP1-22 identified in white-tailed deer (Odocoileus virginianus).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0078226},
doi = {10.1128/mra.00782-26},
pmid = {43018149},
issn = {2576-098X},
abstract = {Tetraparvovirus sp. specimen WTD-TP1-22 was recovered from a wild white-tailed deer (Odocoileus virginianus) nasal swab in Pennsylvania. The near-complete genome is 4,980 bp with a guanine-cytosine content of 47.9%, and this virus shares 95.91% nucleotide identity with isolate tetra-CA1 (GenBank NC_031670.1) from mule deer.},
}

@article {pmid43018641,
year = {2026},
author = {Bespiatykh, D and Leão, P},
title = {ArchaeaHQ: a curated reference database of archaeal genomes.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
pmid = {43018641},
issn = {2057-5858},
mesh = {*Genome, Archaeal ; *Archaea/genetics/classification ; *Databases, Genetic ; Metagenome ; Metagenomics ; Biocuration ; Computational Biology/methods ; Phylogeny ; },
abstract = {Archaea have proven to be major players in biogeochemical cycles across diverse ecosystems, yet we still see an underrepresentation of archaeal genomes in the datasets used by popular computational biology tools. Here, we present ArchaeaHQ, a quality-controlled, systematically curated reference database of 25,584 archaeal genomes compiled initially from 43,045 assemblies from all four archaeal kingdoms retrieved from NCBI: Methanobacteriati (Euryarchaeota), Thermoproteati (TACK), Nanobdellati (DPANN) and Promethearchaeati (Asgard). All genomes in the database passed standardized quality control, requiring ≥70% completeness and ≤10% contamination. A total of 44.0% of genomes in ArchaeaHQ achieved ≥90% completeness, while 92.7% exhibited ≤5% contamination. ArchaeaHQ comprises 18,701 metagenome-assembled genomes (MAGs; 73.1%) and 6,883 isolate genomes (26.9%). Approximately 76% of MAGs are assigned to 17 ecologically meaningful categories based on sampling origin, and around 65% of genomes include geographic metadata. ArchaeaHQ is available at https://doi.org/10.6084/m9.figshare.32266599 for download and at https://vee-lab.eu/archaeahq for online browsing. This resource was designed to provide an analysis-ready reference set for metagenomic, biogeochemical and ecological studies, comparative genomics analyses and the development of archaeal-specific bioinformatic tools.},
}

*Genome, Archaeal
*Archaea/genetics/classification
*Databases, Genetic
Metagenome
Metagenomics
Biocuration
Computational Biology/methods
Phylogeny

@article {pmid43018675,
year = {2026},
author = {Zade, OS and Yandrapally, S and Choudari, K and Gaikwad, AV and Panda, R and Neela, VSK and Prudhula, DK and Eedara, VVR and Ansari, MS and Chandrashekhar, C and Sriram, D and Mohareer, K and Valluri, VL and Somvanshi, PR and Banerjee, S},
title = {Immunologically optimized Zmp1 peptides reveal a translational serological biomarker platform for tuberculosis diagnosis across disease manifestations.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {43018675},
issn = {1435-4373},
support = {(5/8/5/21/ITRC/Diag/2021/ECD-1).//Indian Council of Medical Research/ ; (5/8/5/21/ITRC/Diag/2021/ECD-1).//Indian Council of Medical Research/ ; },
abstract = {Tuberculosis (TB) diagnosis remains challenging, particularly for extrapulmonary TB (EPTB), where invasive sampling, low bacillary burden, and limited sensitivity of nucleic acid-based tests in peripheral specimens hinder timely detection. Here, we report an immunology-driven strategy for biomarker discovery and development of a peptide-based serological assay targeting Mycobacterium tuberculosis zinc metalloprotease-1 (Zmp1). Based on the principle that antigenic regions containing overlapping B-cell and CD4[+]T-cell epitopes can promote strong antibody responses through linked recognition and cognate T-cell help, we used an immunoinformatics pipeline to identify two nested immunodominant Zmp1 peptide regions, Mtb-Zp-NT and Mtb-Zp-CT, enriched for overlapping B- and T-cell epitopes.Their diagnostic potential was evaluated using ELISA-based serological assays. A blinded pilot study (N = 137) demonstrated clear discrimination between active TB and TB-recovered individuals. An expanded validation cohort (N = 875), identified from screening approximately 6,086 individuals, included pulmonary TB (PTB), EPTB, TB-recovered individuals, household contacts, non-specific infection/inflammation, and healthy controls. Receiver operating characteristic analyses, supported by DeLong and bootstrap comparisons, demonstrated superior diagnostic performance of the peptide assays compared with Mtb-FL-Zmp1. Mtb-Zp-CT showed the highest accuracy (AUC = 0.93), with > 93% specificity and ~ 76% sensitivity.These findings establish immunologically optimized Zmp1 peptides as promising serological biomarkers for TB, including EPTB. Although further optimization may be required to meet WHO target product profiles, their high specificity supports potential use as an adjunctive diagnostic, particularly for EPTB, and as components of future multi-antigen panels. More broadly, this study demonstrates how mechanistically informed epitope selection can facilitate translation of pathogen-specific immune signatures into minimally invasive diagnostic platforms.},
}

@article {pmid43019118,
year = {2026},
author = {Quiñones-Sanchez, CL and Bilbao-Del Valle, JL and Urdaneta-Colon, MA and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimizing tissue lysis and DNA extraction protocols to enhance bacterial diversity profiling in the Drosophila melanogaster gut microbiome.},
journal = {Scientific reports},
volume = {16},
number = {},
pages = {34962},
pmid = {43019118},
issn = {2045-2322},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; R25 HG012702/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *Drosophila melanogaster/microbiology ; RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {UNLABELLED: The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two lysis methods (manual pestle homogenization and bead-beating) and two commercial DNA extraction kits (Qiagen and Zymo) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and Drosophila melanogaster gut samples, a tractable model for host-microbe interactions. Full-length 16S rRNA sequencing was performed using Oxford Nanopore Technologies (ONT), followed by taxonomic classification with EPI2ME and downstream diversity analyses using standard pipelines implemented through a custom script. Our data revealed that extraction and lysis methods influence microbial composition, with some protocols resulting in additional species-level assignments in MCS samples, likely reflecting limitations of sequencing technology and taxonomic misidentifications. Pestle homogenization, combined with the Qiagen kit, recovered the highest number of detected taxa and showed a more balanced representation of both Gram-positive and Gram-negative bacteria across the Drosophila gut samples. These findings highlight that extraction methodology influences microbial diversity estimates in Drosophila gut samples, although sequencing approach and taxonomic classification accuracy may also contribute to the observed differences. Our results emphasize that the choice of DNA extraction protocol should be guided by the biological question being addressed and highlight the need for standardized protocols to ensure reproducibility across microbiome studies, particularly those using model systems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-63122-w.},
}

Animals
*Drosophila melanogaster/microbiology
RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/isolation & purification/genetics
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification
Biodiversity
Sequence Analysis, DNA

@article {pmid43020003,
year = {2026},
author = {Luo, S and Song, Y and Zhao, Y and Zhang, H and Ren, J and Zhang, J and Song, C},
title = {Nitrogen availability modulates soil microbial carbon fixation in wetland through community and metabolic remodelling.},
journal = {Water research},
volume = {309},
number = {Pt C},
pages = {127239},
doi = {10.1016/j.watres.2026.127239},
pmid = {43020003},
issn = {1879-2448},
abstract = {Excess agricultural nitrogen (N) from farm drainage and runoff causes wetland water N pollution and destabilizes soil carbon (C) sinks, however, how this N enrichment regulates wetland soil microbial autotrophic C fixation remains unclear. Here, we combined field experiments, [13]CO2 continuous pulse labeling, DNA-stable isotope probing and metagenomics to investigate the dose-dependent effects of N input on soil microbial community assembly, co-occurrence networks, C-fixation pathways, and soil physicochemical properties in Songnen Plain saline-alkali wetlands of China. The results indicate that N input exerts a threshold regulation on microbial C fixation, with distinct depth-dependent responses. Intermediate N input (N2, 10 g N m[-2] yr[-1]) alleviates soil microbial N limitation, elevates RubisCO and hydrolase activities, optimizes soil CN-phosphorus stoichiometry, and promotes the accumulation of mineral-associated organic C. Such intermediate N input remodels microbial community structure, increases microbial diversity and network stability, and enriches key C-fixing taxa including Cyanobacteriota and Alphaproteobacteria, thereby upregulating six core autotrophic C-fixation pathways. In contrast, excessive N (N4, 24 g N m[-2] yr[-1]) input induces soil acidification and nutrient imbalance, disrupts microbial network stability, declines functional C-fixing microbiota and suppresses C-fixation gene expression, ultimately reducing soil CO2 assimilation and organic C accumulation. Structural equation modelling and random forest analyses further reveal soil microbial biomass N and RubisCO activity are the primary drivers of microbial C fixation, mediated by soil microbial C metabolic pathways and community diversity. This work reveals mechanisms of wetland soil C fixation under agricultural N pollution and informs wetland nutrient management and C-sink conservation.},
}

@article {pmid43020410,
year = {2026},
author = {Zou, J and Zhang, C and Fang, Z},
title = {Microbial-driven cryptic sulfur recycling in volcanic barrier lakes: seasonal dynamics of biogenic sulfide.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126159},
doi = {10.1016/j.envres.2026.126159},
pmid = {43020410},
issn = {1096-0953},
abstract = {Seasonal hydrological fluctuations shape biogeochemical cycling of carbon-nitrogen-sulfur (C-N-S) and sustain aquatic ecosystem functioning, wherein biogenic sulfide (BioS) acts as a critical cryptic regulator. Microbial sulfur cycling is well-recognized, yet the functional importance of BioS - re-oxidized intermediates of dissimilatory sulfate reduction fueling internal sulfur recycling - remains poorly constrained. Using Wudalianchi as a model system, we examined seasonal sulfate dynamics across summer, autumn and late winter. We integrated isotopic tracing, functional-gene profiling and metagenomics alongside statistical screening, machine-learning driver identification, and isotopic quantitative modelling. Microbial community dynamics were primarily governed by seasonal changes in temperature (63 %), sulfate concentration (37 %), and sulfur and oxygen isotopes (δ[18]OSO4, 49%; δ[34]SSO4, 45%). Sulfate sources shifted from precipitation-dominated inputs in summer (∼73 %) toward sediment-derived sulfide oxidation in autumn and winter (∼74-83 %), concurrent with elevated BioS fractions (up to ∼20 %). This seasonal transition was controlled by turnover of key bacterial taxa (Microcystis, Limnohabitans, Polynucleobacter) and topological rewiring of microbial co-occurrence networks. Summer-dominant Microcystis may modulate BioS via oxygenic Fe(II) oxidation, whereas autumn-enriched Limnohabitans has genomic potential for sulfide re-oxidation via the SOX system. In winter, sulfur-metabolizing and disproportionating consortia sustained low-magnitude but persistent cryptic sulfur recycling. BioS forms an essential cryptic cycling loop that stabilizes sulfur availability, modulates isotopic signatures, and sustains seasonal C-N-S cycling under limited external inputs. This work elucidates the underrecognized BioS-mediated mechanism connecting seasonal hydrological variability to internal nutrient cycling. It advances mechanistic insights into freshwater sulfur biogeochemistry with broader implications for aquatic management under global environmental change.},
}

@article {pmid43020474,
year = {2026},
author = {Gruzdev, EV and Dorofeev, AG and Pelevina, AV and Beletsky, AV and Pimenov, NV and Ravin, NV and Mardanov, AV},
title = {Metagenome-assembled genomes from lab-scale phosphorus-removal bioreactor.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0107126},
doi = {10.1128/mra.01071-26},
pmid = {43020474},
issn = {2576-098X},
abstract = {We report the metagenome of a microbial community enriched in phosphate-accumulating organisms (PAOs) from a laboratory batch reactor. A total of 23 metagenome-assembled genomes of the community members were obtained, including putative PAOs, glycogen-accumulating microorganisms, and nitrifiers. These data will contribute to the study of the metabolic capabilities of phosphate-removing communities.},
}

@article {pmid43020834,
year = {2026},
author = {Pan, Z and Glover, L and Reidy, F and McAuliffe, FM and Wingfield, M and van Sinderen, D and Saldova, R and MacSharry, J},
title = {Vaginal resistome redundancy is associated with microbial metabolic potential and host glycomic features in endometriosis.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {43020834},
issn = {2055-5008},
mesh = {Female ; Humans ; *Endometriosis/microbiology/metabolism ; *Vagina/microbiology ; *Microbiota ; *Glycomics ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Shotgun Sequencing ; Metagenome ; Metabolic Networks and Pathways ; },
abstract = {The vaginal microbiome plays a critical role in reproductive health, yet most studies remain descriptive and functional features connecting microbial communities to host physiology remain poorly understood. In endometriosis, alterations in the vaginal microbiome and host glycosylation have been reported, yet ecological properties connecting these systems remain unclear. We investigated whether vaginal resistome functional redundancy (FR) represents a functional link between microbial community structure, microbial metabolic capacity, and host glycomic variation across endometriosis severity. Shotgun metagenomic sequencing was performed on high vaginal swabs from women with healthy controls, minimal/mild, and moderate/severe endometriosis (n = 40). While total antibiotic resistance genes (ARG) abundance remained relatively stable across disease groups, resistome FR increased significantly in moderate/severe endometriosis, reflecting a transition from low-diversity, Lactobacillus-dominated communities toward more taxonomically diverse, ARG-harbouring taxa. Increased redundancy was associated with higher microbial alpha diversity and enrichment of glycan-related metabolic pathways, particularly UDP-N-acetyl-D-glucosamine biosynthesis, a precursor pathway for glycan assembly. These microbial functional features correlated with host glycomic signatures in serum and urine. Mediation and path modelling analyses supported associations among resistome FR, predicted UDP-sugar pathway potential, host glycomic variation, and endocrine-related traits. Our findings identify resistome FR as a quantifiable ecological property of the vaginal microbiome that is associated with microbial metabolic capacity and host glycomic variation in endometriosis. Rather than acting as a direct driver, FR may serve as a marker of microbiome organisation that relates to host-associated phenotypes, providing a framework for understanding microbiome-glycome interactions in reproductive tract disease.},
}

Female
Humans
*Endometriosis/microbiology/metabolism
*Vagina/microbiology
*Microbiota
*Glycomics
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
Shotgun Sequencing
Metagenome
Metabolic Networks and Pathways

@article {pmid43020865,
year = {2026},
author = {Rahman, B and Saroyia, AP and Blackburn, D and Parish, AJ and Szewczyk, N and Driscoll, M and Samuel, BS and Vanapalli, SA},
title = {NemaCapsules: microfluidics-integrated biocells for investigating C. elegans host-microbiome interactions in spaceflight.},
journal = {NPJ microgravity},
volume = {12},
number = {1},
pages = {},
pmid = {43020865},
issn = {2373-8065},
support = {project# 80NSSC22K0250//NASA/ ; },
abstract = {Spaceflight studies in humans show that microgravity alters the gut microbiome, posing a risk to health. Understanding how microbiomes and host genetics influence physiology is critical for long-duration missions. The low-cost spaceflight model C. elegans provides a suitable means to study host-microbiome interactions. However, whole-organism measurements are limited by lacking suitable flight-ready hardware that enables long-term nematode culture compatible with on-orbit imaging. These limitations were addressed through development of NemaCapsules- microfluidics-integrated biocells, for spaceflight assessment of C. elegans locomotion under defined microbiome conditions, with minimal astronaut workload. This provided a fully sealed, gas-permeable system with media reservoir, enabling passive, long-term nematode culturing. NemaCapsules were evaluated across four host strains and three model microbiomes. Multi-day worm viability studies demonstrated high resilience across diverse host strains and microbiomes except for daf-16 mutants. Crawling and swimming studies of worms with model microbiomes of C. elegans natural microbiota exhibited distinct locomotory activity from those exposed to E. coli OP50. Wild-type N2 generally exhibited the highest activity, followed by wild isolate strains; daf-16 mutants demonstrated lowest activity. Compared to crawling, swimming better revealed differences arising from host-microbiome interactions. NemaCapsules provide a modular solution for on-orbit, multi-functional readouts in C. elegans with minimal crew intervention.},
}

@article {pmid43021054,
year = {2026},
author = {Saraiva, JP and Borim Corrêa, F and Bernt, M and Ghanem, N and Nieto, E and Brizola Toscan, R and Wick, LY and Chatzinotas, A},
title = {PHI: a Galaxy-based workflow for reproducible prophage-host interaction analysis and standardized viral-genomics reporting.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {43021054},
issn = {1471-2105},
mesh = {*Prophages/genetics/physiology ; *Genomics/methods ; *Genome, Viral ; *Software ; Workflow ; Genome, Bacterial ; *Host-Pathogen Interactions ; Computational Biology/methods ; Bacteria/virology/genetics ; },
abstract = {BACKGROUND: Viruses that infect bacteria, known as bacteriophages or phages, are widespread in nature and play important roles in shaping microbial communities and ecosystem functions. Some phages can integrate into bacterial genomes as "prophages", where they may influence the biology of their host by carrying genes that affect metabolism, virulence, or environmental adaptation. Despite their importance, studying prophages and their interactions with bacterial hosts remains challenging because it typically requires combining many complex computational tools and can be resource-intensive.

RESULTS: In this study, we introduce the Prophage-Host Interaction Toolkit (PHI), a user-friendly and automated workflow available through the Galaxy platform. PHI brings together multiple established tools into a single, reproducible pipeline that identifies candidate prophages, evaluates their quality, predicts host relationships, and characterizes key functional genes. Importantly, all results are summarized in an interactive report that simplifies interpretation. Applied to the MBARC22 mock community of 22 bacterial reference genomes as a workflow demonstration, PHI identified 41 candidate prophages across 14 hosts, including high- and medium-quality viral genomes. Most host genomes exhibited > 99% completeness and < 1% contamination, while DefenseFinder identified between 3 and 24 antiviral defense systems per genome. To further evaluate applicability to metagenome-derived assemblies, PHI was also applied to three MAGs and their matched reference genomes. Differences in candidate prophage counts and sequence-level correspondence between MAGs and references demonstrated that prophage recovery can be strongly influenced by genome fragmentation and assembly continuity, even in otherwise high-quality MAGs.

CONCLUSIONS: By removing installation barriers and consolidating the outputs of multiple established tools, PHI lowers the barrier to advanced phage analysis, enabling both specialists and non-experts to explore phage-host interactions and their implications in areas such as microbiome research, biotechnology, and environmental science.},
}

*Prophages/genetics/physiology
*Genomics/methods
*Genome, Viral
*Software
Workflow
Genome, Bacterial
*Host-Pathogen Interactions
Computational Biology/methods
Bacteria/virology/genetics

@article {pmid43021070,
year = {2026},
author = {Carpallo-Porcar, B and García-Martínez, L and Jiménez-Sánchez, C and Calvo, S and Roig, FJ},
title = {Gut microbiota dysbiosis in Post-COVID condition symptoms: relation with chronic fatigue and functional limitation.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43021070},
issn = {1471-2180},
support = {B61_23D//Departamento de Ciencia, Universidad y Sociedad del Conocimiento, from the Gobierno de Aragón (Spain)/ ; T71_23D//Departamento de Ciencia, Universidad y Sociedad del Conocimiento, from the Gobierno de Aragón (Spain)/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Cross-Sectional Studies ; *Fatigue Syndrome, Chronic/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Male ; *COVID-19/complications/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Pilot Projects ; Post-Acute COVID-19 Syndrome ; Adult ; Spain ; SARS-CoV-2 ; Feces/microbiology ; },
abstract = {BACKGROUND: Post-COVID Condition (PCC) is a heterogeneous clinical syndrome in which chronic fatigue and functional limitation are among the most disabling manifestations. Alterations in the gut microbiota have been proposed as contributors to PCC pathophysiology; however, it remains unclear whether distinct clinical PCC phenotypes are associated with specific microbiota signatures.

RESULTS: This cross-sectional pilot study analysed gut microbiota composition and predicted functional capacity in 50 participants from Aragón (Spain), including 30 patients with PCC and 20 healthy controls. PCC patients were stratified according to the presence of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)-like symptoms and functional limitation assessed using the 6-Minute Walking Test. Alpha and beta diversity did not differ significantly between groups (Figs. 2 and 3). Differential abundance analysis identified taxon-level differences between groups. Escherichia/Shigella was enriched in PCC-CFS relative to controls, both overall and in the subgroup without functional limitation, representing the most consistent signal. Additional differences included higher Streptococcus and Veillonella in controls, and higher Flavonifractor and Hungatella in PCC-NCFS. After adjustment for digestive symptoms and vaccine dose, these associations attenuated and none remained significant, indicating that they may be partly driven by confounding.PICRUSt2 functional predictions suggested differences in pathways related to nucleotide and amino acid metabolism; however, none remained significant after correction for multiple testing and should therefore be considered exploratory.

CONCLUSIONS: These findings suggest the presence of phenotype-associated taxonomic differences within PCC despite the absence of global diversity alterations. The results should be considered exploratory and hypothesis-generating due to the limited subgroup sample sizes. Larger studies incorporating metagenomic and metabolomic approaches are needed to validate these observations and clarify their potential clinical relevance.},
}

Humans
*Dysbiosis/microbiology
Cross-Sectional Studies
*Fatigue Syndrome, Chronic/microbiology
Female
*Gastrointestinal Microbiome
Middle Aged
Male
*COVID-19/complications/microbiology
*Bacteria/classification/genetics/isolation & purification
Pilot Projects
Post-Acute COVID-19 Syndrome
Adult
Spain
SARS-CoV-2
Feces/microbiology

@article {pmid43021133,
year = {2026},
author = {Huang, S and Bei, Y and Yuan, L and Su, T and Gao, W and Zhou, S and Nan, H},
title = {Nocardia farcinica brain abscess in an immunocompromised patient receiving tofacitinib: a case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {43021133},
issn = {1471-2334},
support = {D202319019427//The Scientific Research Project of Hunan Provincial Health Commission/ ; kq2208144//The Natural Science Foundation Project of Changsha/ ; Grant No. HZ2026ZCYX002//Xuanwu Hospital Talent Convergence Program/ ; },
mesh = {Humans ; Female ; *Brain Abscess/microbiology/drug therapy/diagnostic imaging/diagnosis ; Middle Aged ; *Immunocompromised Host ; *Nocardia Infections/drug therapy/microbiology/diagnosis/diagnostic imaging ; *Nocardia/isolation & purification/genetics/drug effects ; *Pyrimidines/therapeutic use/adverse effects ; *Piperidines/therapeutic use/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Magnetic Resonance Imaging ; Anti-Bacterial Agents/therapeutic use ; Cilastatin, Imipenem Drug Combination/therapeutic use ; Brain/diagnostic imaging/pathology/microbiology ; Opportunistic Infections/drug therapy/microbiology ; Cilastatin/therapeutic use ; Imipenem/therapeutic use ; },
abstract = {BACKGROUND: Nocardia farcinica (N. farcinica) brain abscess is a rare but potentially life-threatening opportunistic infection that predominantly occurs in immunocompromised individuals. Patients receiving immunosuppressive therapies may be at increased risk of opportunistic infections; however, the clinical recognition and diagnosis of N.farcinica brain abscess remain challenging.

CASE PRESENTATION: A 55-year-old woman presented with a one-month history of headache and right-sided limb numbness. Brain magnetic resonance imaging (MRI) revealed multiple intracranial space-occupying lesions. Brain biopsy excluded primary or metastatic malignancy and suggested an infectious etiology. The patient had been receiving long-term tofacitinib therapy for two years, with prednisolone and azathioprine discontinued approximately two years before the onset of infection. Next-generation sequencing (NGS) combined with circulating tumor DNA (ctDNA) analysis of brain tissue identified N. farcinica as the causative pathogen. Tofacitinib was discontinued, and the patient was treated with intravenous imipenem-cilastatin (0.5 g every 8 h) and amikacin (0.4 g once daily), combined with oral trimethoprim-sulfamethoxazole (0.48 g every 12 h). After 2.5 months of antimicrobial therapy, the patient showed marked clinical and radiological improvement. Treatment was continued for a total of six months, with no evidence of recurrence during follow-up.

CONCLUSION: This case highlights the importance of considering N. farcinica brain abscess in immunocompromised patients presenting with intracranial lesions. Tissue-based metagenomic sequencing combined with ctDNA analysis may facilitate rapid and accurate identification of N. farcinica, enabling the timely initiation of targeted antimicrobial therapy.

CLINICAL TRIAL NUMBER: Not applicable. This report retrospectively describes the clinical course and management of a patient and did not involve any experimental interventions on a live subject.},
}

Humans
Female
*Brain Abscess/microbiology/drug therapy/diagnostic imaging/diagnosis
Middle Aged
*Immunocompromised Host
*Nocardia Infections/drug therapy/microbiology/diagnosis/diagnostic imaging
*Nocardia/isolation & purification/genetics/drug effects
*Pyrimidines/therapeutic use/adverse effects
*Piperidines/therapeutic use/adverse effects
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
Magnetic Resonance Imaging
Anti-Bacterial Agents/therapeutic use
Cilastatin, Imipenem Drug Combination/therapeutic use
Brain/diagnostic imaging/pathology/microbiology
Opportunistic Infections/drug therapy/microbiology
Cilastatin/therapeutic use
Imipenem/therapeutic use

@article {pmid43021363,
year = {2026},
author = {Zhang, X and Qin, C and Zhao, Y and Li, Z and Xie, Y and Yan, Y and Li, T and Huang, L and Shi, H and Lin, C and Wang, W},
title = {Gut microbiota-driven hippuric acid hydrolysis promotes pancreatic tumorigenesis by suppressing NK cell activity.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {43021363},
issn = {1479-5876},
support = {No. 82573412//National Natural Science Foundation of China/ ; No. 82503800//National Natural Science Foundation of China/ ; 2025-PUMCH-C-018//National High Level Hospital Clinical Research Funding/ ; 2025-PUMCH-A-073//National High Level Hospital Clinical Research Funding/ ; 2025-PUMCH-A-075//National High Level Hospital Clinical Research Funding/ ; 2024-2-4017//Capital's Funds for Health Improvement and Research/ ; ZK12101//National Multidisciplinary Cooperative Diagnosis and Treatment Capacity Building Project for Major Diseases/ ; No.UGG04598//Peking Union Medical College Hospital Talent Cultivation Program (Category B)/ ; No. 2024-I2M-ZD-001//CAMS Innovation Fund for Medical Sciences/ ; No. 2024bkjg015，No.2025bkjg005//Peking Union Medical College Hospital Undergraduate Educational Reform Project/ ; No. 2024dcxm100, No.2026dcxm275//Student Research Training Project, Chinese Academy of Medical Sciences & Peking Union Medical College/ ; Number GZC20240146//Postdoctoral Fellowship Program of CPSF under Grant/ ; 3332025001//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; },
mesh = {*Killer Cells, Natural/immunology ; Animals ; Humans ; *Pancreatic Neoplasms/pathology/microbiology/immunology ; *Hippurates/metabolism ; *Carcinogenesis/pathology ; *Gastrointestinal Microbiome ; Hydrolysis ; Cell Line, Tumor ; Carcinoma, Pancreatic Ductal/pathology/microbiology ; Mice, Inbred C57BL ; Male ; Signal Transduction ; },
abstract = {BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, characterized by a lack of effective early detection, profoundly immunosuppressive microenvironment, and poor responsiveness to current therapies. Emerging evidence suggests that gut microbiota and their metabolites play important roles in pancreatic tumorigenesis. Glycoproteins shed from pancreatic precancerous lesions may influence the composition of the gut microbiota and their metabolites.

METHODS: We established a pancreatic precancerous lesion mouse model and performed integrated fecal metagenomic sequencing and non-targeted metabolomic profiling to characterize microbiota composition and metabolite alterations. Further we use plasma samples from patients, in vitro cytotoxicity assays and in vivo orthotopic pancreatic tumor models, fecal microbiota transplantation and pancreatic homogenate gavage to assess the effect of microbiota and metabolite alterations. And we conduct RNA sequencing, qPCR, ELISA, flow cytometry, molecular docking, and surface plasmon resonance to further explore its mechanisms.

RESULTS: We identified hippuric acid as a key microbiota-derived metabolite that was significantly reduced during pancreatic tumorigenesis, which was associated with suppressed anti-tumor immunity and enhanced PDAC progression. This reduction was associated with enrichment of microbiota harboring hippurate hydrolase and correlated with poor prognosis in PDAC patients. Mechanistically, hippuric acid activated IL-21R-STAT3-TBX21 signaling axis, promoting the expression of cytotoxic effector molecules, including granzyme B and perforin, thus enhancing NK cell cytotoxicity. Molecular docking and surface plasmon resonance analyses further suggested a direct interaction between hippuric acid and IL-21R.

CONCLUSIONS: Collectively, our study uncovers a previously unrecognized positive feedback regulatory loop involving the PDAC-gut microbiota-hippuric acid-NK cell-PDAC axis and highlights the critical role of gut microbiota and their metabolites in pancreatic tumorigenesis.},
}

*Killer Cells, Natural/immunology
Animals
Humans
*Pancreatic Neoplasms/pathology/microbiology/immunology
*Hippurates/metabolism
*Carcinogenesis/pathology
*Gastrointestinal Microbiome
Hydrolysis
Cell Line, Tumor
Carcinoma, Pancreatic Ductal/pathology/microbiology
Mice, Inbred C57BL
Male
Signal Transduction

@article {pmid43021616,
year = {2026},
author = {Clari, MÁ and Carbonell, N and Navarro, D},
title = {Syndromic diagnosis and precision medicine in severe infections.},
journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia},
volume = {},
number = {},
pages = {},
doi = {10.37201/req/v39.s01.03.2026},
pmid = {43021616},
issn = {1988-9518},
abstract = {The implementation of syndromic PCR panels has transformed the management of severe infections, including bloodstream, lower respiratory tract, and central nervous system infections, by enabling rapid pathogen identification and earlier optimization of antimicrobial therapy. As regulatory, technical, and interpretative challenges are overcome, unbiased shotgun metagenomic next-generation sequencing is expected to complement these platforms and become integrated into routine clinical practice, offering comprehensive, hypothesis-free detection of known and emerging pathogens in a single assay.},
}

@article {pmid43021617,
year = {2026},
author = {Rua, M and Pina-Sánchez, M and Candel, FJ and Del Pozo, JL},
title = {Molecular diagnostics in immunocompromised patients: promises, pitfalls, and practical strategies.},
journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia},
volume = {},
number = {},
pages = {},
doi = {10.37201/req/v39.s01.04.2026},
pmid = {43021617},
issn = {1988-9518},
abstract = {Infections remain a leading cause of morbidity and mortality in immunocompromised patients, frequently presenting with atypical clinical manifestations and a broad spectrum of potential pathogens. Advances in molecular diagnostics, particularly multiplex PCR panels and metagenomic next-generation sequencing, have substantially improved pathogen detection rates and reduced time to diagnosis. Nevertheless, their routine clinical implementation remains challenging. Key limitations include: the inability to reliably distinguish colonization from active infection, high costs, and the risk of over-interpretation in the absence of clinical correlation. This mini-review provides an etiological framework for infections in immunocompromised hosts, critically examines the indications and limitations of current molecular diagnostic platforms, and proposes integrated multimodal strategies to optimize clinical decision-making and antimicrobial stewardship.},
}

@article {pmid43021990,
year = {2026},
author = {Zhou, X and Peng, S and Tan, R and Wang, J and Hu, H and Zhang, K and Liu, A},
title = {Diagnostic performance of metagenomic next-generation sequencing in Mycobacterium and non-Mycobacterium infection patients: a retrospective study at a large comprehensive medical center.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1935536},
pmid = {43021990},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sensitivity and Specificity ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Tuberculosis/diagnosis/microbiology ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Diagnosis, Differential ; *Mycobacterium/genetics ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a potentially valuable complementary test, if not an essential one, in some challenging clinical cases. This study comprehensively compared mNGS with other methods, including TB-IgG, TB-IGRA, TB-DNA, Xpert, culture, and AFS for the diagnosis of and differentiation between TB infection from NTM infection using multiple sample types, including BALF, CSF, blood, pus, tissue, hydrothorax, and ascites.

METHODS: From 2021 to 2024, the clinical data, including imaging, laboratory results, and medical records, of 425 patients with suspected TB infection were retrospectively collected and classified as PTB [306 (72%)], EPTB [67 (15.76%)], and non-TB [52 (12.24%)], according to the final clinical diagnosis.

RESULTS: Among the three groups, significant differences were observed in age, sex, cough, smoking history, hsCRP, IFN-γ, and hypertension (P < 0.05). According to the final clinical diagnosis, the sensitivity and specificity of mNGS in all samples were 90.1% (95% CI: 0.866-0.927) and 75.0% (95% CI: 0.618-0.848), respectively. The sensitivity of mNGS was higher than that of TB-IGRA (79.1%), Xpert (72.4%), culture (52.3%), TB-DNA (45.6%), TB-IgG (36.4%), and AFS (10.7%). For distinguishing TB from non-TB, the sensitivity of mNGS was approximately 37.8% higher than that of standard test culture (90.1% vs 36.4%; P < 0.001). Further analysis also showed that MTB read counts from mNGS were highly correlated with MTB burden measured by other laboratory tests (P < 0.05). Analysis of the ROC curve of mNGS reads showed that the AUC for MTB diagnosis was 0.9073, with a sensitivity of 73.19% and specificity of 96.15% when the recommended cutoff value of 4 reads (Youden's index, 0.6934) was applied.

CONCLUSIONS: For patients with suspected TB or NTM infection, mNGS may serve as a helpful adjunctive tool, particularly when routine diagnostic tests are unrevealing or indeterminate. It has the potential to assist in distinguishing MTB from NTM and to provide additional evidence to guide appropriate treatment choices, though its results should always be interpreted alongside clinical findings and conventional microbiological testing.},
}

Humans
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Sensitivity and Specificity
Female
Male
Middle Aged
Adult
Aged
*Tuberculosis/diagnosis/microbiology
*Mycobacterium Infections, Nontuberculous/diagnosis/microbiology
Diagnosis, Differential
*Mycobacterium/genetics

@article {pmid43022205,
year = {2026},
author = {Hu, X and Ma, G and Han, J and Zhu, L and He, Y and Zhu, D},
title = {From maternal microbial transmission to neonatal gut microbiota restoration: the potential and challenges of maternal fecal microbiota transplantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1972665},
pmid = {43022205},
issn = {1664-302X},
abstract = {Early-life gut microbiota establishment is a critical developmental process shaped by maternal microbial transmission and ecological succession. Microorganisms from the maternal gut, vagina, breast milk, skin, and oral cavity contribute to neonatal microbial acquisition, while strain-resolved studies increasingly support the maternal gut as an important reservoir of strains capable of persistent colonization in the infant intestine. This transmission can be disrupted by cesarean delivery, prematurity, perinatal antibiotic exposure, and neonatal intensive care, resulting in delayed acquisition of maternal commensals, altered microbial succession, and increased colonization by opportunistic microorganisms. Current restoration strategies, including probiotics, synbiotics, and vaginal microbiota seeding, can modify early microbial communities but do not fully reproduce the diversity, maternal specificity, and persistence of naturally transmitted maternal gut strains. Maternal fecal microbiota transplantation (FMT) has therefore emerged as a potential strategy to restore disrupted maternal gut-to-infant microbial transmission. Initial proof-of-concept and strain-resolved studies suggest that carefully screened maternal FMT can increase mother-to-infant strain sharing, promote recovery from cesarean-associated microbiota perturbations, and reduce colonization by potential pathogens. However, evidence for durable engraftment, functional benefits, clinical efficacy, and long-term safety remains limited. Future studies should prioritize rigorous donor screening, standardized intervention protocols, appropriate recipient selection, and longitudinal integration of strain-resolved metagenomics, metabolomics, immune profiling, and clinical outcomes. Maternal FMT remains investigational but provides a promising framework for precision early-life microbiota restoration.},
}

@article {pmid43022214,
year = {2026},
author = {Shen, C and Li, Y and Xiang, Z and Zhao, M and Wang, J and Wang, X},
title = {Recurrent pulmonary infection, a vicious cycle of multifactorial interactions, and prevention/treatment strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1945273},
pmid = {43022214},
issn = {1664-3224},
mesh = {Humans ; *Respiratory Tract Infections/prevention & control/therapy/immunology/diagnosis ; Recurrence ; Host-Pathogen Interactions/immunology ; Animals ; *Reinfection/prevention & control ; Risk Factors ; Disease Susceptibility ; Vaccination ; },
abstract = {Recurrent pulmonary infection (RPI) refers to the frequent and repeated episodes of lower respiratory tract infections. At its core, it represents a vicious cycle arising from the disruption of the homeostatic balance among pathogens, host immunity, and pulmonary architecture. RPI accounts for a considerable proportion of pediatric pneumonia cases, and the cumulative incidence among elderly patients hospitalized for pneumonia is also markedly elevated, imposing a substantial disease burden. The etiologies are notably diverse, beyond common pathogens such as bacteria and viruses, the ubiquity of asymptomatic colonization, underlying comorbidities, immune deficiencies, medication-related factors, and aspiration all constitute critical predisposing factors. This review summarizes the pathogenic characteristics of RPI, host-related factors, and the mechanistic roles of structural lung damage in infection recurrence. It further focuses on the current advances and limitations of precision diagnostic approaches (metagenomic sequencing), immunomodulatory and microbiome-targeted interventions, and vaccination strategies. Existing evidence suggests that the clinical benefits of these interventions in RPI remain to be validated by more high-quality studies. The aim of this article is to provide a reference for the clinical management of RPI and to inform future research directions.},
}

Humans
*Respiratory Tract Infections/prevention & control/therapy/immunology/diagnosis
Recurrence
Host-Pathogen Interactions/immunology
Animals
*Reinfection/prevention & control
Risk Factors
Disease Susceptibility
Vaccination

@article {pmid43022273,
year = {2026},
author = {Almusallam, AA and Allemailem, KS},
title = {Decoding multispecies oral biofilms: molecular architecture, host modulation and systems-guided precision anti-biofilm strategies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {2002174},
pmid = {43022273},
issn = {2235-2988},
mesh = {*Biofilms/drug effects/growth & development ; Humans ; *Mouth/microbiology ; Bacteria/genetics/drug effects ; Microbiota ; },
abstract = {Oral biofilms are spatially ordered microbial communities whose pathogenic behavior is shaped by more than taxonomic composition. Their development reflects the combined effects of adhesin-receptor recognition, interspecies coaggregation, matrix formation, metabolite exchange, local physicochemical gradients and host-derived selection. Here, we synthesize molecular and ecological evidence on the bacterial cell surface-matrix interface and consider how these interactions contribute to cariogenic, periodontal and peri-implant biofilms. Particular attention is given to glucosyltransferase-dependent polysaccharides, extracellular DNA, amyloidogenic proteins, sortase-anchored surface factors and outer membrane vesicles, together with metabolic interactions involving lactate, arginine, hydrogen peroxide and heme. We further evaluate functional-genomic and systems-level approaches (including transposon sequencing, CRISPR interference, metagenomics, metatranscriptomics, metaproteomics, metabolomics, spatial imaging, genome-scale metabolic modeling and machine learning) while distinguishing association and prediction from experimentally demonstrated mechanism. Emerging interventions are assessed according to their biological target and evidence level, including adhesion blockade, specifically targeted antimicrobials, matrix synthesis inhibition and degradation, quorum interference, probiotics, catalytic nanoparticles, antimicrobial photodynamic therapy and antibiofilm dental materials. Across these approaches, reduction in biofilm biomass is not equivalent to ecological restoration or clinical benefit. Key translational barriers include model fidelity, donor-to-donor variation, spatial heterogeneity, treatment durability, endpoint selection and the limited external validation of many computational and preclinical findings. Future precision strategies should therefore integrate microbial identity, matrix architecture, spatial metabolism and host context, with experimental perturbation used to establish causal vulnerabilities before therapeutic translation.},
}

*Biofilms/drug effects/growth & development
Humans
*Mouth/microbiology
Bacteria/genetics/drug effects
Microbiota

@article {pmid43022326,
year = {2026},
author = {Kim, DW and Kim, JY and Lee, DW and Lee, YJ and Tseren-Ochir, EO and Kwon, JH},
title = {Detection and genomic characterization of an avian orthoavulavirus 1 from wild birds in Mongolia in 2022 using metagenomic analysis.},
journal = {Clinical and experimental vaccine research},
volume = {15},
number = {4},
pages = {346-352},
pmid = {43022326},
issn = {2287-3651},
abstract = {PURPOSE: Mongolia encompasses the breeding areas of various migratory wild birds along multiple flyways, making it important for the study of virus circulation in wild bird populations. While previous surveillance has primarily focused on avian influenza, metagenomic next-generation sequencing offers an opportunity to detect and characterize a broader range of viral pathogens. This study aimed to characterize viral communities and potential avian pathogens in wild bird samples from Mongolia and to investigate the genetic and phylogenetic characteristics of recovered viral genomes.

MATERIALS AND METHODS: Egg-propagated samples derived from wild bird feces, which showed hemagglutination-positive but influenza-negative results, were subjected to metagenomic next-generation sequencing. Sequence reads were taxonomically classified using Kraken2, and samples with substantial viral reads were further analyzed. The recovered viral genome was characterized by phylogenetic and phylogenetic incongruence analyses.

RESULTS: Metagenomic analysis identified abundant bacteriophage reads from seven genera, Asteriusvirus, Saphexavirus, Krischvirus, Mooglevirus, Tequatrovirus, Kagunavirus, and Felixounavirus, as well as Avian orthoavulavirus 1. The complete avian orthoavulavirus 1 genome was recovered and classified as class II genotype I.2. The isolate clustered with recent wild bird strains from Ukraine and Russia, and its fusion protein cleavage-site motif was consistent with a lentogenic pathotype. No clear evidence of phylogenetic incongruence was identified.

CONCLUSION: This study highlights the value of metagenomic surveillance of wild birds for early detection and genomic characterization of avian pathogens, with potential relevance to disease preparedness and subsequent vaccine-related evaluation.},
}

@article {pmid43022586,
year = {2026},
author = {Ben Brahim, S and Royer, G and Jacquier, H and Lepeule, R and Goehringer, F and Cheval, J and Rodriguez, C and Alauzet, C and Woerther, PL},
title = {Shotgun Metagenomics Versus 16S rDNA Sanger Sequencing for the Diagnosis of Blood Culture-Negative Endocarditis: A Draw?.},
journal = {Open forum infectious diseases},
volume = {13},
number = {11},
pages = {ofag720},
pmid = {43022586},
issn = {2328-8957},
abstract = {Although valuable for diagnosing blood culture-negative infective endocarditis, 16S rDNA sequencing and metagenomics on valve/vegetation have never been compared using identical DNA extracts. We compared methods on surgical samples from definite, possible, and rejected infective endocarditis involving culture-negative native valves. Positivity rates were similar, with taxonomic resolution being higher for metagenomics.},
}

@article {pmid43022730,
year = {2026},
author = {Li, Z and Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Tang, X},
title = {Oral-predominant microbial and functional dysbiosis in craniofacial microsomia: species-level profiling with compartment-matched statistical testing.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2754580},
pmid = {43022730},
issn = {2000-2297},
abstract = {BACKGROUND: Craniofacial microsomia (CFM) is the second most common congenital craniofacial anomaly. Oral dysbiosis has been described at genus level, but whether it extends beyond the mouth, or relates to the defining alveolar bone deficiency, is unknown.

Oral and gut microbiomes of 45 children with CFM and 18 matched controls were profiled at species level by 2bRAD-M, alongside shotgun metagenomes and blood, faecal and oral metabolomes. Alveolar bone loss was quantified on computed tomography against each patient's contralateral side. Centred-log-ratio methods with Benjamini-Hochberg false-discovery-rate (FDR) control were used throughout. Compartment specificity was tested formally by a group-by-compartment interaction model in the 58 participants with paired oral and gut profiles, by sample-size-matched subsampling, and by minimum-detectable-effect calculation.

RESULTS: Oral alpha diversity was higher in CFM than in controls (Shannon P = 0.014; all three alpha-diversity indices P < 0.05). Four species-level taxa were depleted after false-discovery-rate (FDR) correction (q < 0.05), and 21 interpretable metagenomic pathways differed between groups among 38 FDR-significant pathways. These annotations were enriched for carbohydrate transport, glycan processing and cell-surface or biofilm-related functions, but they are not specific markers of a cariogenic or pathogenic community. No FDR-robust gut or systemic signature was detected. At the species level, the oral and gut analyses were power-matched (minimum detectable |r| = 0.74 at the FDR-equivalent threshold), and the group-by-compartment interaction for Shannon diversity was significant (P = 0.026). This comparison supports an oral-predominant taxonomic pattern but does not establish biological absence of a gut effect. The functional comparison was not power-matched. In the patient-only post hoc analyses, the oral functional pattern was not associated with tooth-brushing frequency, sugary-drink intake or caries burden. Affected-side alveolar bone density was lower than contralateral density (paired P < 0.001) and was not associated with anatomical severity grade.

CONCLUSIONS: CFM was associated with an oral-predominant taxonomic and functional microbiome pattern. The matched-power comparison is informative for taxonomic analyses but does not exclude a biologically meaningful gut effect, and the functional comparison remains underpowered. These observations motivate prospective investigation of local, biofilm-directed interventions and of quantitative alveolar bone assessment as a follow-up endpoint.},
}

@article {pmid43023095,
year = {2026},
author = {Goren, LR and Lehman, AC and Drozdov, D and Thielen, BK},
title = {Plasma metagenomic cell-free DNA sequencing identifies clinically unsuspected cases of Toxoplasma gondii infection in immunocompromised patients: a single-centre experience.},
journal = {Access microbiology},
volume = {8},
number = {11},
pages = {},
pmid = {43023095},
issn = {2516-8290},
abstract = {Toxoplasmosis can be challenging to diagnose, particularly in immunocompromised patients with nonspecific clinical presentations. We present a retrospective, single-centre case series of eight Toxoplasma gondii infections identified by plasma metagenomic cell-free DNA (cfDNA) sequencing in allogeneic haematopoietic stem cell transplant recipients. Nested within a larger cohort evaluating cfDNA utilization, this case series highlights a positive clinical impact of cfDNA testing in 5 out of 8 (62.5%) patients, including earlier diagnosis and changes in clinical management. These findings illustrate the potential utility of plasma cfDNA sequencing as a complement to conventional diagnostics across diverse clinical presentations of toxoplasmosis.},
}

@article {pmid43023715,
year = {2026},
author = {Merges, D},
title = {Predominance of viral core functions over auxiliary metabolism among carbohydrate-active enzymes annotated in the global soil virosphere.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0181326},
doi = {10.1128/aem.01813-26},
pmid = {43023715},
issn = {1098-5336},
abstract = {UNLABELLED: Soil viruses are increasingly recognized as components of microbial communities with the potential to alter ecosystem functioning, yet the frequency and functional distribution of virus-encoded metabolic genes in soils remain poorly understood. Here, the Global Soil Virus Atlas gene catalog, comprising 1,432,147 viral genes from 1,223 samples across 12 ecosystem types, was searched against KEGG, Pfam, and CAZy for functions related to carbon cycling, nitrogen cycling, and antimicrobial resistance. Annotations associated with host entry or cell-wall lysis were separated from putative auxiliary metabolic functions. Of 5,020 initial gene-level functional annotations across the three categories, 3,322 (66.2%) were classified as peptidoglycanases. Their exclusion left 1,698 genes (0.14% of the gene catalog restricted to contigs ≥10 kb), and carbon-cycling functions represented 96.7% of the enzyme-resolved annotations. Chitinase-associated genes formed the largest carbon category, but 78.0% belonged to GH19, a family containing both chitinases and phage endolysins. Among GH19 genes on contigs encoding detectable holins or spanins, 84.2% occurred within three genes of these lysis components, a distribution comparable to that of canonical phage lysozymes. Across six matched metagenomic studies, estimated viral contributions to the targeted functions ranged from 0.00% to 8.45% (mean: 2.27%). Two of the three estimates exceeding 2% were GH19-associated chitinase estimates from rhizosphere soils and were therefore treated as upper estimates. Thus, the putative soil viral metabolic inventory was sparse and concentrated in carbon-degradation functions, whereas much of the initial carbohydrate-active enzyme signal reflected core viral lysis functions rather than auxiliary metabolism.

IMPORTANCE: Soil microorganisms drive decomposition and nutrient cycling, and the viruses that infect them may alter these processes by carrying genes that affect host metabolism. However, genes annotated as carbohydrate-degradation enzymes may instead help viruses enter cells or break host cell walls when new virus particles are released. In a worldwide catalog of soil viruses, approximately two-thirds of the initial functional assignments represented these infection or release activities. After their removal, putative viral auxiliary metabolic genes were uncommon and concentrated mainly in carbon degradation. Genes potentially involved in chitin degradation were most frequent, but many occurred near viral genes used to break host cells; their estimated contribution should therefore be viewed as an upper limit. Distinguishing core viral functions from host metabolic modification is essential to avoid overestimating viral contributions to soil processes and to identify the strongest candidates for experimental testing.},
}

@article {pmid43023736,
year = {2026},
author = {Cui, Y and Qiu, Q and Chen, Y and Ding, T},
title = {Characterizing gut microbial structural variation reveals strain heterogeneity and metabolic dysfunction in colorectal cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0110926},
doi = {10.1128/msystems.01109-26},
pmid = {43023736},
issn = {2379-5077},
abstract = {Previous studies investigating gastrointestinal (GI) diseases have primarily focused on the composition, gene expression, and specific strains of gut microbiota. However, the impact of genetic variations, especially structural variations (SVs) in microbial genomes, on the development of GI tumors has been largely overlooked. In this study, we analyzed 1,027 fecal metagenomes from seven data sets and identified 8,278 coverage-defined SVs across 51 bacterial species in the gut microbiomes. We found that SVs were prevalent in the gut microbiota of studied cohorts. Surprisingly, the genetic makeup of SV-based clusters differed significantly between healthy individuals and those with colorectal cancer (CRC), indicating substantial intra-specific diversity within these populations. By integrating taxonomic-SV markers, we achieved optimal accuracy in early CRC detection, and the SVs also displayed regional heterogeneity. Microbial genetic variation provides additional insights into taxonomy and functionality, allowing us to have a more precise understanding of the microbiota associated with CRC. Notably, our study uncovered potential links between microbial SVs and metabolic disorders of CRC, including SV regions that encode glycoside hydrolases associated with disordered carbohydrate metabolism in CRC. We integrated a framework called MicroSVsProfiler to identify and classify SVs in individuals diagnosed with CRC, as well as in healthy controls. Our findings underscore the importance of considering SVs in microbiome studies, especially in the absence of strain-specific differences in abundance. Future research should explore the deeper layer of the microbiota's structural variantome for a better understanding of the occurrence and characteristics of CRC across different stages.IMPORTANCEMost microbiome studies of colorectal cancer focus on which bacterial species are more or less abundant, potentially overlooking genetic differences among strains of the same species. By analyzing 1,027 fecal metagenomes from seven independent cohorts, we show that large-scale changes in bacterial genomes, known as structural variations, provide disease-related information that is not captured by species abundance alone. These strain-level SV signatures distinguished healthy individuals from patients with colorectal cancer, improved early-cancer classification when combined with taxonomic markers, and varied across geographic populations. We also found that cancer-associated structural variations were linked to altered microbial metabolic functions, particularly carbohydrate metabolism and glycoside hydrolases. Together, these findings establish microbial structural variation as a complementary dimension of the gut microbiome and provide a framework for developing more precise, population-aware biomarkers and for investigating how strain-level genetic changes may contribute to metabolic disturbances associated with colorectal cancer.},
}

@article {pmid43013265,
year = {2026},
author = {Valk, LC and Ruigrok, RAAA and Timmerman, H and Björk, JR and Li, Q and Zhang, S and Meneses, R and Vázquez Castellanos, JF and de Wit, N and Raes, J and Weersma, RK and Kleerebezem, M and Vich-Vila, A and Boekhorst, J},
title = {Mapping the genetic landscape of microbial lipid transformation in the intestinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2756735},
doi = {10.1080/19490976.2026.2756735},
pmid = {43013265},
issn = {1949-0984},
mesh = {*Lipid Metabolism/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Colon/microbiology ; Metagenome ; Intestine, Small/microbiology ; Bile Acids and Salts/blood ; },
abstract = {Dietary lipids are a key component in our diet, and fats and their derivatives have been associated with both beneficial as well as adverse effects on host health. However, the contribution of the gut microbiome to lipid metabolism remains understudied. Recognizing the importance of this interplay, we conducted extensive literature reviews to identify key bacterial genes involved in lipid metabolism, and created 88 Hidden Markov Models to allow rapid and accurate identification of these genes in genome and metagenome data. We applied these models to over 1000 metagenomes representative of the small intestine and colon, from both population-based and disease cohorts (LLDeep, MetaCardis and 1000IBD) to determine their lipolytic capacity. We observed that microbiome community types (enterotypes) carry different lipolytic potential. Serum levels of conjugated and sulfonated secondary bile acids were significantly associated with increased abundance of sterol-sulfonation genes (cysC, cysD and BtSULT). Small-intestinal communities were enriched in lipid genes compared to the colonic microbiota, underscoring the importance of microbial lipid metabolism in the small intestine compared to the colon. Overall, we demonstrate the value of our lipid metabolism models for functional microbiome profiling. Additionally, our study suggests that microbial activity in the upper gut might play a direct role in shaping host lipid metabolism, with potential implications for cardiometabolic health.},
}

*Lipid Metabolism/genetics
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/genetics/metabolism/classification/isolation & purification
Colon/microbiology
Metagenome
Intestine, Small/microbiology
Bile Acids and Salts/blood

@article {pmid43014061,
year = {2026},
author = {Li, H and Zhang, X and Liu, J and Chen, X and Liao, B and Zhang, Y and Li, W and Sun, B and Li, X},
title = {Microbiome evidence-guided construction of a defined microbial consortium for light-aroma Baijiu fermentation and flavor development.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112147},
doi = {10.1016/j.ijfoodmicro.2026.112147},
pmid = {43014061},
issn = {1879-3460},
abstract = {Natural fermentation systems harbor microbial resources, but translating microbiome information into cultivable and controllable defined communities remains challenging. We integrated 74 metagenomic datasets from light-aroma Baijiu-associated Daqu and fermented grains with metagenome-assembled genome (MAG) functional profiles and independent 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) amplicon time series to propose four candidate functional roles: substrate conversion, acid/acyl-precursor formation, alcoholic fermentation, and aroma formation. Metagenomic profiling revealed community heterogeneity, whereas MAG analysis showed widespread genetic potential for starch conversion and lactic- and acetic-acid-related metabolism. Amplicon data revealed genus-level temporal distributions of Bacillus, Weissella, Wickerhamomyces, and Saccharomyces. Bacillus amyloliquefaciens, Weissella confusa, Saccharomyces cerevisiae, and Wickerhamomyces anomalus were selected from the available laboratory culture collection as candidate representatives of these roles. A three-factor Box-Behnken design optimized the two bacterial inoculum volumes and the combined yeast volume, with the yeast ratio fixed at 1:1 (v/v). For 500 g of substrate, inoculation volumes were 7 mL for B. amyloliquefaciens, 20 mL for W. confusa, 41 mL for S. cerevisiae, and 41 mL for W. anomalus, yielding 2.28 ± 0.12 g/L ethyl acetate (HPLC). During 28 d of solid-state fermentation, starch, reducing sugars, acidity, and volatile profiles changed, with 51 volatile compounds detected. The final base Baijiu contained 33 volatile compounds, including 13 with odor activity values (OAVs) >1, of which 11 were also detected by gas chromatography-olfactometry (GC-O). These findings support a role-guided route from natural fermentation microbiome evidence to a defined consortium with measurable fermentation and flavor phenotypes.},
}

@article {pmid43014163,
year = {2026},
author = {Liu, S and Timmers, PHA and Mohammad-Pajooh, E and Leão, P and Seelen, AM and Cremers, G and van Niftrik, L and van Kessel, MAHJ and Lücker, S},
title = {Identification and genomic characterization of the nitrifiers in a full-scale municipal wastewater treatment plant with efficient, year-round nitrogen removal.},
journal = {Water research},
volume = {309},
number = {Pt C},
pages = {127237},
doi = {10.1016/j.watres.2026.127237},
pmid = {43014163},
issn = {1879-2448},
abstract = {Effective nitrogen removal from wastewater is crucial for environmental preservation. However, wastewater treatment plants (WWTPs) often experience decreased nitrogen removal rates during winter months when water temperatures decrease. This study investigated the microbial community of a full-scale WWTP that maintains efficient nitrogen removal even at temperatures as low as 7 °C. The nitrifying community was primarily composed of Nitrosomonas and Nitrospira, as demonstrated by 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization. Metagenomic analysis revealed a nitrifying community affiliated with Nitrosomonas cluster 6a and cluster DK-WWTP, comammox Nitrospira clade A, as well as canonical Nitrospira lineage I. A large-scale metagenomic screening showed that these nitrifiers are widespread in WWTPs worldwide across a broad temperature range. Furthermore, a pangenome analysis identified putative genetic traits which are potentially involved in adaptations to lower temperatures. These findings not only demonstrate the potential for maintaining high nitrification rates at lower temperatures, but also provide genomic evidence for adaptive traits that support stable nitrogen removal at lower temperatures. The presence of these nitrifiers can serve as an indicator of temperature-independent efficient nitrogen removal. Engineering strategies aimed at obtaining or maintaining these nitrifying microorganisms might lead toward year-round efficient wastewater treatment.},
}

@article {pmid43014167,
year = {2026},
author = {Zhang, M and Liu, J and Shen, Y and Chen, J and Li, J and Fang, Q and Huang, J and Zhang, S and Shao, Z and Yang, J and Luo, Y and Zhang, D and Imanmadi, D and Pan, X},
title = {Potential of foaming events in reshaping vertical distribution of waterborne antibiotic-resistant human pathogens and signaling public health risks in surface waters.},
journal = {Water research},
volume = {309},
number = {Pt C},
pages = {127268},
doi = {10.1016/j.watres.2026.127268},
pmid = {43014167},
issn = {1879-2448},
abstract = {While pathogens in surface waters frequently cause epidemic outbreaks and millions of annual deaths worldwide, their association with natural aqueous foaming, a common yet overlooked phenomenon, remains unexplored. This study investigated whether foaming is associated with changes in the distribution and potential risk of antibiotic-resistant human pathogens (ARHPB) in surface waters, challenging the traditional view that sediments are the primary sink for waterborne pathogens. The surface foam layer was found to coincide with selective transport of bacteria (particularly, the potential priority multidrug-resistant genera like Acinetobacter and Enterobacter) from benthic sediments into the water column via bubble adhesion, a mechanism linked to the bacterial virulence trait of motility. Meanwhile, bacteriophages were predominantly distributed in the water column, where genes associated with immune modulation were more abundant. Metagenomic analysis reveals that the relative abundance of potential human-pathogenic bacteria harboring co-localized antibiotic resistance genes and mobile genetic elements was greater in the water column during foaming (from near-zero to markedly higher levels) than under unfoamed conditions, suggesting enhanced potential for horizontal gene transfer. However, foamed and unfoamed samples were collected in July and October, respectively, and the temporal confound prevented causal attribution to foaming alone. Nevertheless, consistent patterns across four independent water bodies indicate that foaming events are among the covarying factors for the elevated potential ARHPB relative abundance and deserve further exploration as potential sentinels for public health risks. Inclusion of foam monitoring in aquatic risk assessment frameworks warrants consideration, pending prospective validation.},
}

@article {pmid43014168,
year = {2026},
author = {Li, J and Zhong, Y and Yang, S and Wu, J and Zhang, Y and Zeng, Y and Song, J and Zhu, X and Li, D and Ling, J and Yu, Z and Häggblom, MM and Peng, P},
title = {Dehalobacter-mediated reductive dechlorination of the organophosphorus insecticide chlorpyrifos in mangrove sediments.},
journal = {Water research},
volume = {309},
number = {Pt C},
pages = {127280},
doi = {10.1016/j.watres.2026.127280},
pmid = {43014168},
issn = {1879-2448},
abstract = {Mangrove sediments are important sinks for organic contaminants, including the widely used chlorinated organophosphorus insecticide chlorpyrifos (CPF). Although CPF degradation under oxic conditions has been extensively studied, its anaerobic transformation in reducing coastal environments remains poorly understood. Here, a mangrove sediment-derived anaerobic enrichment culture achieved nearly complete transformation of 10 mg L[-1] CPF within 10 days. Ultraperformance liquid chromatography-Orbitrap high-resolution mass spectrometry (UPLCOrbitrap-HRMS) revealed the formation of a mono-dechlorinated CPF product, which was tentatively assigned as O,Odiethyl O-(3,5-dichloro-2-pyridinyl) phosphorothioate based on tandem mass spectrometry (MS/MS) evidence and density functional theory (DFT) calculations of C-Cl bond dissociation energies. The enrichment culture also reductively dechlorinated 3,5,6-trichloro-2-pyridinol (TCP), a common CPF transformation product, primarily to 5,6-dichloro-2-pyridinol, with Ecological Structure-Activity Relationships (ECOSAR) modeling predicting lower aquatic toxicity for the dechlorinated products than for their parent compounds. 16S rRNA gene amplicon sequencing and metagenomic analyses revealed marked enrichment of Dehalobacter during active CPF transformation, strongly implicating this organohalide-respiring lineage in CPF dechlorination. A high-quality Dehalobacter metagenome-assembled genome harboring 39 rdhA homologs was recovered. Integrated metatranscriptomic and metaproteomic analyses further prioritized four candidate reductive dehalogenases (CPF-RDH1/2/3/9), with CPF-RDH2 showing the strongest proteomic support. Together, these findings uncover an overlooked anaerobic transformation route of CPF through direct reductive dechlorination and highlight the potential role of Dehalobacter-associated organohalide respiration in the environmental fate of chlorinated organophosphorus contaminants in mangrove sediments.},
}

@article {pmid43014178,
year = {2026},
author = {Sabar, MA and Than, VH and Sugie, Y and Wada, H and Zhao, B and Matsuura, N and Ihara, M and Watanabe, T and Tanaka, H and Honda, R},
title = {Environmental media-based microbial source tracking enables source identification of antimicrobial resistance in urban rivers.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144103},
doi = {10.1016/j.jhazmat.2026.144103},
pmid = {43014178},
issn = {1873-3336},
abstract = {Urban rivers receiving treated wastewater remain hotspots for antimicrobial resistance genes (ARGs), yet quantitative source attribution remains challenging. Conventional microbial source tracking (MST) cannot distinguish ARG contributions from treated effluent, untreated sewage, and environmental reservoirs such as sediments. Here, we developed an environmental media-based MST (EM-MST) framework integrating source-enriched microbial markers to quantify ARG sources in an urban river impacted by two wastewater treatment plants (WWTPs) and combined sewer overflow (CSO). From fifteen screened markers, NOB-16S (effluent-enriched nitrite-oxidizing bacteria), dsrA (sediment-enriched sulfate-reducing bacteria), and crAssphage (sewage-associated) were selected using qPCR validation and multivariate analysis. Combined with shotgun metagenomic profiling of 676 ARGs and a non-negative least squares mixing model, these markers enabled source attribution. During dry weather, WWTP effluent accounted for the largest source proportion (81.5-93.1%), with efflux pump, sulfonamide, macrolide, and aminoglycoside ARGs. During the sampled CSO event, untreated sewage accounted for 91%-100% of the estimated source contribution, delivering β-lactam, macrolide-lincosamide-streptogramin, and tetracycline ARGs associated with gut microbiota. River sediments showed greater resistome similarity to WWTP effluent, consistent with an effluent-associated ARG reservoir, while the estimated sediment contribution remained minor (3.0 ± 5.3%). The EM-MST enables quantitative differentiation of ARG sources in wastewater-impacted urban rivers.},
}

@article {pmid43014428,
year = {2026},
author = {Jia, M and Hong, L and Xia, J and Zhang, J and Xu, J and Chen, D and Wang, F and Feng, J and Chen, M and Wu, D and Xie, B},
title = {A rapid, low-cost, and validated TaqMan qPCR assay for blaKPC surveillance in community wastewater.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107769},
doi = {10.1016/j.mimet.2026.107769},
pmid = {43014428},
issn = {1872-8359},
abstract = {The rapid global dissemination of carbapenem-resistant Enterobacteriaceae, particularly those harboring Klebsiella pneumoniae carbapenemase (blaKPC) genes, poses a critical threat to public health. Effective containment requires robust diagnostic tools applicable to both clinical and complex environmental matrices. We developed and validated a TaqMan-based qPCR method targeting a hyper-conserved region of blaKPC identified through alignment of 271 full-length sequences. Optimized at an annealing temperature of 62 °C, the assay achieved a nominal limit of detection (LOD) of 0.98 copies per reaction (estimated from genomic DNA mass), a linear quantification across nearly seven orders of magnitude (1.53 to 1 × 10[7] copies/reaction, R[2] > 0.99) with an amplification efficiency of 98.61%, and good repeatability (CV < 3% based on Ct values). Validation with three wastewater metagenomic samples and 33 bacterial isolates (including 5 blaKPC-positive isolates recovered from wastewater, and 28 blaKPC-negative bacteria), using WGS as the reference, showed perfect agreement (Kappa = 1.00). Among 50 community wastewater samples, 22.00% (11/50) were blaKPC-positive, and culture yielded five blaKPC-positive K. pneumoniae strains, all confirmed by whole-genome sequencing as high-risk ST15 harboring the yersiniabactin-associated virulence locus ybt14/ICEKp12, blaKPC-2 and blaSHV-28, and porin- and quinolone-resistance-associated mutations. With a 40-min amplification time, simple operation, and a reagent cost of USD 0.13 per reaction, this method is well-suited for large-scale environmental surveillance and early warning of antimicrobial resistance dissemination.},
}

@article {pmid43014929,
year = {2026},
author = {Guo, Z and Jiang, T and Wang, X and Liu, F and Guan, X},
title = {The transfer event of antibiotic resistance genes in groundwater of the reclaimed water infiltration areas.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {469-477},
doi = {10.1016/j.jes.2026.03.097},
pmid = {43014929},
issn = {1001-0742},
mesh = {*Groundwater/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; *Environmental Monitoring ; Water Microbiology ; Genes, Bacterial ; Waste Disposal, Fluid ; },
abstract = {The migration of pollutants from reclaimed water infiltrating into groundwater has become a worldwide environmental problem, especially in terms of the ecological risks associated with the spread of antibiotic resistance genes (ARGs). Based on metagenomic, SameStr and MetaCHIP analysis, the microbial communities of reclaimed water and groundwater samples collected during the wet and normal water seasons were studied. It was found that reclaimed water infiltration significantly affected the microbial community composition in groundwater. The genera Novosphingobium, Sphingorhabdus, and Panacacagrimonas were transferred into the groundwater and became keystone genera in microbial community of groundwater. The horizontal gene transfer (HGT) rates of ARGs were 7.04 % and 4.71 % in normal water season and wet season, respectively. Gallionella and Sideroxydans, Panacagrimonas and Nevskia were the main contributors and recipients of ARGs in the normal water and wet season, respectively. Antibiotics with nutrients such as total organic carbon and total nitrogen together drove the occurrence of HGT, which could encourage the bacteria to acquire ARGs and occupy an ecological niche. This study tried to reveal the microbial community dynamics and ARGs transfer mechanism in reclaimed water infiltration areas and provide help for the risk assessment of reclaimed water and groundwater protection.},
}

*Groundwater/microbiology/chemistry
*Drug Resistance, Microbial/genetics
*Gene Transfer, Horizontal
*Environmental Monitoring
Water Microbiology
Genes, Bacterial
Waste Disposal, Fluid

@article {pmid43014933,
year = {2026},
author = {Duan, L and Chen, F and Chen, H and Shang, S and Song, M and Qin, S and Tang, J and Zhou, Q and Zhao, Z and Chen, J},
title = {Horizontal gene transfer and bacterial host composition govern contrasting antibiotic resistomes in coastal ecosystems across different niches and geographic regions.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {517-527},
doi = {10.1016/j.jes.2026.04.036},
pmid = {43014933},
issn = {1001-0742},
mesh = {*Gene Transfer, Horizontal ; China ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; },
abstract = {Understanding the mechanisms underlying the development and dissemination of antibiotic resistance is crucial for mitigating global public health threats. Nevertheless, the ecological dynamics of antibiotic resistance gene (ARG) evolution across diverse environmental niches remain insufficiently understood. In this study, we employed metagenomic analyses to characterize the distribution of ARGs and mobile genetic elements (MGEs) in water and sediments from two Chinese coastal ecosystems: a hydrologically dynamic estuary (Wenzhou, China, WZ) and a port area with intense anthropogenic influence (Xiangshan, China, XS). In total, 111 ARG and 31 MGE subtypes were identified, with multidrug resistance genes and transposase being the most abundant and diverse gene types, respectively. Across ecological niches, water samples exhibited greater diversity of ARGs and MGEs, while sediments harbored higher overall abundances. Gamma-proteobacteria were the predominant hosts of ARGs across all samples. Four ARGs (rsmA, PNGM-1, tetA, and rpoB) were consistently detected and strongly correlated with total ARG loads, indicating their potential as indicators. Multidimensional correlation and variance partitioning analyses indicated that horizontal gene transfer predominantly shaped antibiotic resistome assembly in water, whereas vertically inherited ARGs governed their distribution in sediments by shifts in the composition of ARG-bearing bacterial hosts. In contrast, at the coastal scale, horizontal gene transfer showed a stronger contribution in the WZ area, while vertical gene transfer played a more prominent role in XS. The findings provide new insights into the ecological drivers of antibiotic resistance and offer a scientific foundation for environmental surveillance and risk assessment.},
}

*Gene Transfer, Horizontal
China
*Ecosystem
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Bacteria/genetics
Genes, Bacterial
Anti-Bacterial Agents

@article {pmid43014934,
year = {2026},
author = {Chen, Z and Li, Q and Jin, L and Fang, X and Ren, H and Huang, H},
title = {Microbial community steady state driven by metabolic integration under combined stress: A case study of moving bed biofilm reactor.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {528-538},
doi = {10.1016/j.jes.2026.03.019},
pmid = {43014934},
issn = {1001-0742},
mesh = {*Bioreactors/microbiology ; *Biofilms ; *Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; *Microbiota ; Stress, Physiological ; },
abstract = {This study investigates microbial community responses in moving bed biofilm reactors under combined stress from dynamic temperature (10-35 °C) and emerging contaminants (ECs). The three-stage adaptation process of microbial community "stress perception-metabolic integration-steady state establishment" is revealed. At low temperature (10 °C), microorganisms concentrate metabolic resources on core functions including energy metabolism and nitrogen transformation, while suitable temperature (25-35 °C) activates contaminant degradation pathways, enabling synergistic metabolism of carbon, nitrogen and ECs. ECs serve as environmental selection pressures that drive directional succession of microbial communities toward specialized taxa with degradation capabilities such as Azospira, which demonstrates dual functionality in simultaneous denitrification and ECs degradation. Molecular mechanism studies demonstrate that ECs exert bidirectional regulation on nitrogen metabolism: while promoting the expression of nitrogen assimilation genes, they also competitively inhibit the activity of key denitrification enzymes, ultimately leading to nitrite accumulation. Metagenomic binning confirms that microorganisms achieve functional steady state through ecological structure classification and metabolic function optimization. From a multi-scale perspective, this study elucidates the adaptation patterns of microbial systems under complex environmental stress, providing an important theoretical foundation for enhancing microbial resilience and process efficiency in wastewater treatment systems.},
}

*Bioreactors/microbiology
*Biofilms
*Waste Disposal, Fluid/methods
Nitrogen/metabolism
*Microbiota
Stress, Physiological

@article {pmid43014937,
year = {2026},
author = {Qiu, P and Li, C and Liu, C and Mi, W and Song, G and Rao, B and Wu, H and Bi, Y},
title = {Filamentous cyanobacterial blooms (Pseudanabaena and Cylindrospermopsis) result in the simplification of functional genes involved in nitrogen and phosphorus cycles.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {55-66},
doi = {10.1016/j.jes.2026.01.057},
pmid = {43014937},
issn = {1001-0742},
mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Cyanobacteria/physiology/genetics ; *Harmful Algal Bloom ; China ; *Nitrogen Cycle ; },
abstract = {Harmful algal blooms (HABs) threaten freshwater ecosystems and are linked to nutrient cycling. We conducted a metagenomic investigation in China's Yuqiao Reservoir, which experiences filamentous cyanobacterial blooms (Pseudanabaena and Cylindrospermopsis), to elucidate microbial mechanisms driving nitrogen and phosphorus cycling during HABs. 28 genes for both nitrogen-cycling and phosphorus-cycling showed significantly different abundances between bloom and non-bloom periods. Bloom periods exhibited unified, energy-efficient metabolic strategies, featuring upregulated genes for nitrogen uptake via ammonia assimilation (gltB/D) and enhanced inorganic phosphorus uptake, including high-affinity phosphate transporters (pstA/B/C) and polyphosphate storage genes (ppk1, phoU), supporting rapid microbial proliferation. Conversely, non-bloom periods showed a metabolic transition to diversified nitrogen acquisition, including upregulation of nitrate assimilation, nitrification, denitrification, coupled nitrification-denitrification, and nitrogen fixation. Organic phosphorus mineralization genes became predominant. Concurrently, significant restructuring occurred in both nitrogen- and phosphorus-cycling communities. Although composed predominantly of Actinobacteria, Cyanobacteria, and Proteobacteria in both periods, keystone taxon analysis revealed a critical functional shift from an "autotrophic cyanobacteria-driven" pattern during blooms to a "heterotrophic bacteria-mediated metabolism" in non-bloom phases. Microbial co-occurrence network analysis indicated that the algal bloom triggered a fundamental community reorganization, from a broadly cooperative and stable structure to a more partitioned and potentially specialized state, reflecting strong niche partitioning due to altered environmental conditions. Partial least squares path modeling confirmed that algal blooms govern functional gene abundance by driving microbial community restructuring. Our findings demonstrate that microbial metabolic pattern mediated by algal blooms determined the unification of nitrogen and phosphorus cycling genes, revealing the mechanisms of HABs' ecological impacts.},
}

*Phosphorus/metabolism
*Nitrogen/metabolism
*Cyanobacteria/physiology/genetics
*Harmful Algal Bloom
China
*Nitrogen Cycle

@article {pmid43014947,
year = {2026},
author = {Sun, X and Tang, J and Ma, Z and Yang, E and Lu, Y and Zou, D and Guan, Q},
title = {Important roles of environmental filter in shaping the taxonomic and functional traits of bioaerosol in semi-arid environments.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {67-78},
doi = {10.1016/j.jes.2026.03.081},
pmid = {43014947},
issn = {1001-0742},
mesh = {Aerosols/analysis ; *Air Microbiology ; *Environmental Monitoring ; Seasons ; Bacteria/classification ; },
abstract = {Specific taxonomic and functional traits of bioarosols in certain habitats are likely filtered from the regional species pool. To explore which specific factors act as primary selective filters in semi-arid urban environments, shaping microbial taxa and functions to drive community assembly, this study conducted a one-year metagenomic study in a typical semi-arid city. As a result, seasonal divergence was observed in community structure, community diversity, and metabolic pathways. Specifically, among the predominant taxa and abundant functions, several drought-adapted taxa (e.g., Deinococcota, Stenotrophomonas) and drought-adapted functions (Ligninolysis, Chitinolysis, Aromatic compound degradation, Saprotrophs, Endophyte, and Epiphyte) were identified, along with multiple pathogens (125 pathogenic species and 57 pathogenic genera) and pathogen-related functions (human pathogens all, human pathogens nosocomia, human pathogens pneumonia, human pathogens septicemia). Deterministic processes dominated the annual assembly of the bioaerosol community. Abundant taxa (17.0 % taxonomic profiles, 94.3 % sequences) of bioaerosols drove > 90.0 % of core functional profiles through deterministic assembly and broad niche breadth. In contrast, rare taxa (78.2 % of taxonomic profiles, 0.5 % of sequences) exhibited high functional diversity and higher stochastic processes. The influence of meteorological factors (12.7 % explained variance) outweighed that of pollutants (8.0 %), resulting in seasonal dynamics of bioaerosols. Among meteorological factors, the explanatory power of temperature is the largest (6.2 %), followed by wind speed (2.4 %) and relative humidity (0.4 %).},
}

Aerosols/analysis
*Air Microbiology
*Environmental Monitoring
Seasons
Bacteria/classification

@article {pmid43015262,
year = {2026},
author = {Long, J and Tao, X and Wang, J and Yang, S and Tie, D and Jiang, L and Zhang, J},
title = {Development and clinical validation of a multiplex PCR-based targeted next-generation sequencing panel for simultaneous DNA/RNA pathogen detection in respiratory tract infections: a comprehensive performance evaluation.},
journal = {Clinical chemistry and laboratory medicine},
volume = {},
number = {},
pages = {},
pmid = {43015262},
issn = {1437-4331},
abstract = {OBJECTIVES: Lower respiratory tract infections (LRTI) remain a leading cause of global morbidity and mortality, with approximately 62 % of cases lacking definitive etiological diagnoses via conventional methods. This study aimed to develop and validate a multiplex PCR-based targeted next-generation sequencing (mp-tNGS) panel for comprehensive pathogen detection in respiratory samples.

METHODS: We conducted a combined retrospective (n=209) and prospective (n=256) study involving 465 bronchoalveolar lavage fluid (BALF) samples from patients with suspected LRTI. The mp-tNGS panel was designed to detect 277 clinically relevant pathogens, integrating simultaneous DNA/RNA co-detection and single-nucleotide polymorphism (SNP)-based contamination control. Diagnostic performance was evaluated against conventional microbiological tests (CMTs) and metagenomic next-generation sequencing (mNGS).

RESULTS: The mp-tNGS assay revealed a limit of detection (LoD) of 25 copies/mL for bacteria/fungi and 50 copies/mL for viruses, with acceptable precision (intrabatch CV=9.42 %; interbatch CV=26.03 %). A novel SNP-based bioinformatics pipeline achieved exceptional discriminative performance (AUC=0.992) for distinguishing true infections from contamination. Compared with CMTs and mNGS, mp-tNGS showed superior sensitivity (93.59 %, 95 % CI: 90.81-95.73 %), particularly for viruses (AUC=0.92 vs. 0.845). The assay reliably identified fastidious pathogens (e.g., Pneumocystis jirovecii and Legionella pneumophila) and predicted antimicrobial resistance (97.08 % concordance with phenotypic testing).

CONCLUSIONS: We developed an mp-tNGS panel with diagnostic performance comparable to that of mNGS. The panel integrates broad pathogen coverage, rapid turnaround time, machine learning-based false-positive reduction, and concordance with phenotypic susceptibility testing, positioning it as a promising molecular diagnostic tool for LRTI.},
}

@article {pmid43015352,
year = {2026},
author = {Harada, K and Nakamura, T and Honda, K and Takaki, T and Osuga-Yoshiike, Y and Kubota-Sakashita, M and Haraguchi, S and Kato, T and Takata, A and Tsuboi, T},
title = {Dysfunction of hepatic lipid metabolism in mice haploinsufficient for the histone methyltransferase Kmt2c.},
journal = {Communications medicine},
volume = {6},
number = {1},
pages = {},
pmid = {43015352},
issn = {2730-664X},
support = {20H04121, 23H03303, 23K27993, 23K14499//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {BACKGROUND: Metabolic dysfunction is influenced by various factors including environmental effects and genetic variants, and recent evidence reveals close associations between metabolic dysfunction and neurodevelopmental or neuropsychiatric disorders. However, the mechanistic link between them remains unclear. To clarify these relationships, we utilized mice with haploinsufficiency in the autism spectrum disorder-related gene lysine methyltransferase 2c (Kmt2c) (Kmt2c[+/fs] mice), in which we previously confirmed significantly less body weight.

METHODS: We characterized body composition, small intestinal transcriptome, fecal metagenome, plasma metabolome, and hepatic mitochondrial morphology and biochemical activity in male Kmt2c[+/fs] mice and wild-type controls. Hepatic transcriptomic changes and lipid accumulation were also assessed. Group comparisons were performed using two-sided Mann-Whitney U-tests, two-way repeated measures ANOVA, and enrichment analyses with appropriate multiple-testing correction.

RESULTS: Here we show that Kmt2c[+/fs] mice have decreased body mass index and body fat mass. The small intestine and fecal metagenome show minimal alterations, while plasma metabolomic analysis reveals an increase of metabolites related to glucose and amino acid metabolism. Hepatic mitochondria display altered morphology and biochemical activity. The liver of Kmt2c[+/fs] mice exhibits decreased lipid accumulation and the downregulation of genes related to lipid metabolism, particularly fatty acid synthesis.

CONCLUSIONS: These findings indicate that KMT2C deficiency triggers functional defects in lipid metabolism in the liver, accompanied by upregulation of glucose and amino acid metabolism and consequently less body weight.},
}

@article {pmid43015413,
year = {2026},
author = {Anjaria, P and Soni, M and Bhedi, K and Kabariya, D and Parasana, D and Saiyad, S},
title = {The wild avian resistome: metagenomic insights into antimicrobial resistance ecology.},
journal = {Veterinary research communications},
volume = {51},
number = {1},
pages = {},
pmid = {43015413},
issn = {1573-7446},
mesh = {Animals ; *Birds/microbiology/genetics ; Animals, Wild/microbiology ; Metagenomics ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Metagenome ; },
abstract = {Antimicrobial resistance (AMR) in wild birds is increasingly studied as an ecological component of the wider One Health resistome, yet the evidentiary meaning of a resistance gene detected in avian material varies markedly with study design. This review synthesizes culture-based, whole-genome and metagenomic evidence with emphasis on what modern sequencing can and cannot establish about acquisition, persistence, mobility and transmission. Wild birds encounter antimicrobial-resistant bacteria and antibiotic resistance genes (ARGs) through wastewater, landfills, livestock-associated environments, surface waters, sediments and food webs; resident synanthropic species can be as informative as long-distance migrants. Shotgun and genome-resolved metagenomics have expanded the known avian resistome, enabled host assignment and revealed links with mobile genetic elements and viromes, but DNA detection alone does not demonstrate viable carriage or directional dissemination. We therefore organize the evidence through an evidence-to-inference framework of five complementary domains: ARG detection, microbial-host assignment, genomic mobility, viable carriage and persistence, and transmission, the last separated into sharing between compartments and direction of movement. Applying the framework to published sequencing studies shows that most reach only detection or host assignment, rely on relative abundance, rarely report negative controls and come predominantly from China. The framework clarifies why wild birds are often best regarded as ecological sentinels unless persistence, viable hosts and directionality are shown. Combining metagenomics with long-read sequencing, targeted culture, isolate genomics, environmental sampling and movement ecology offers the strongest route toward biologically meaningful One Health surveillance.},
}

Animals
*Birds/microbiology/genetics
Animals, Wild/microbiology
Metagenomics
*Bacteria/drug effects/genetics
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Metagenome

@article {pmid43015616,
year = {2026},
author = {Jia, Y and Yuan, P and Zhang, Y and Meng, S and Li, M and Liu, W and Nanaei, HA and Liu, X and Jiang, L},
title = {Metagenomics analysis reveals horse feces as a reservoir of putative ARG-like sequences.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015616},
issn = {1471-2180},
support = {20190102//the International Postdoctoral Program/ ; 101027750//EU H2020 MSCA/ ; 31560620, 32002144, 31972530, 31772553//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2019D01B14//the Xinjiang Natural Science Foundation/ ; ASTIP-IAS01//the Agricultural Science and Technology Innovation Program of China/ ; Y2025YC50//the CAAS Fundamental Research Fund/ ; },
mesh = {Animals ; Horses/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; China ; Metagenome ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics ; Genes, Bacterial ; },
abstract = {BACKGROUND: Despite the widespread distribution of horses and their close interface with human environments, the equine antibiotic resistance gene (ARG) reservoir remains insufficiently characterized. This study aimed to comprehensively elucidate the equine resistome by analyzing 104 equine fecal metagenomes sampled across China, thereby establishing a critical baseline for antimicrobial stewardship in equine husbandry.

RESULTS: Through a non-redundant gene catalog approach, we identified 3,264 unique ARG-related coding sequences (CDSs). To detect distant homologs, hidden Markov model (HMM) profiling was applied, revealing 2,420 putatively novel ARG-like sequences. Functional classification indicated that over 90% of these sequences mediate resistance through antibiotic inactivation or target protection, whereas efflux and impaired penetration accounted for less than 10%. Taxonomic profiling attributed these predicted sequences to 23 phyla and 146 genera, with Firmicutes, Bacteroidetes, and Proteobacteria identified as the detected taxa. Furthermore, we identified 731 plasmid-associated ARG-like candidates, of which 446 is novel variants, predominantly conferring resistance to macrolides, streptogramins, aminoglycosides, and β-lactams. Experimental validation confirmed that the novel gene abc-f(9) significantly reduced macrolide susceptibility in vitro, elevating the tilmicosin minimum inhibitory concentration (MIC) of Escherichia coli from 64 to 256 μg/mL.

CONCLUSIONS: These findings provide the first systematic characterization of the equine ARG repertoire, significantly expanding the known global resistome. Our results offer a foundational resource for assessing the risks of antimicrobial resistance (AMR) transmission and implementing informed surveillance strategies in horse farming.},
}

Animals
Horses/microbiology
*Feces/microbiology
*Metagenomics/methods
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
China
Metagenome
Microbial Sensitivity Tests
Phylogeny
Plasmids/genetics
Genes, Bacterial

@article {pmid43015656,
year = {2026},
author = {Wang, X and Lu, J and Zhang, Y and Wang, D and Lu, H and Su, N and Yuan, L and Xu, H and Li, W},
title = {Delayed diagnosis of intrauterine tuberculosis during mid-pregnancy leading to fetal loss and maternal disseminated tuberculosis: a case report and literature review.},
journal = {BMC pregnancy and childbirth},
volume = {26},
number = {1},
pages = {},
pmid = {43015656},
issn = {1471-2393},
support = {Grant No. MQ2024016//General Program of Jiangsu Commission of Health/ ; Grant No.82502817//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; Pregnancy ; *Pregnancy Complications, Infectious/diagnosis/microbiology ; Adult ; *Delayed Diagnosis/adverse effects ; Mycobacterium tuberculosis/isolation & purification ; *Fetal Death/etiology ; *Tuberculosis, Pulmonary/diagnosis/complications ; Tuberculosis, Meningeal/diagnosis ; },
abstract = {Atypical pregnancy symptoms lead to delayed diagnosis of tuberculosis (TB), resulting in serious harm to both the fetus and mother. We reported a patient with recurrent vaginal bleeding in mid-pregnancy accompanied by persistent low fever. Labor was induced after failed preservation treatment. The patient developed unexplained high fever postoperatively, while pathogens could not be identified by traditional detection methods. Finally, Mycobacterium tuberculosis (MTB) was detected when metagenomic next-generation sequencing (mNGS) was performed on the contents of the uterus. The patient was confirmed to have acute hematogenous disseminated pulmonary TB, tuberculous toxemia, accompanied by liver injury, and later developed into tuberculous meningitis. This case reminds the clinicians that pre-pregnancy TB screening is of great significance, and TB should be considered for pregnant patient with unexplained symptoms during pregnancy.},
}

Humans
Female
Pregnancy
*Pregnancy Complications, Infectious/diagnosis/microbiology
Adult
*Delayed Diagnosis/adverse effects
Mycobacterium tuberculosis/isolation & purification
*Fetal Death/etiology
*Tuberculosis, Pulmonary/diagnosis/complications
Tuberculosis, Meningeal/diagnosis

@article {pmid43015880,
year = {2026},
author = {Schrieke, H and Trouche, B and Kerrigan, D and Pondeville, E and Reveillaud, J},
title = {Optimizing bacterial enrichment procedures to improve mosquito midgut microbiome research.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {43015880},
issn = {2524-4671},
support = {MC_UU_00034/8/MRC_/Medical Research Council/United Kingdom ; 948135/ERC_/European Research Council/International ; },
abstract = {Mosquitoes are major vectors of infectious diseases, with their midgut microbiota playing a crucial role in host development, reproduction, and pathogen interactions. However, characterizing midgut microbial communities remains challenging because host DNA often dominates metagenomic libraries, reducing the resolution of bacterial community profiling and hindering the recovery of microbial genomes. To evaluate strategies for bacterial DNA enrichment in this context, we compared three DNA extraction protocols applied to pooled Aedes aegypti midguts: (i) the QIAGEN DNeasy Blood and Tissue kit without filtration (DNeasy NF), (ii) the same kit preceded by a 5 μm filtration step to reduce eukaryotic material (DNeasy F), and (iii) the QIAGEN QIAamp Microbiome kit, which combines differential host cell lysis and enzymatic DNA depletion. Each method was assessed using qPCR-based quantification of bacterial and host DNA, SSU rRNA-based taxonomic profiling of metagenomic reads, and Metagenome-Assembled Genomes (MAGs) reconstruction using advanced binning approaches. Our results show that while the Microbiome kit provided the highest bacterial enrichment and captured a large fraction (> 85%) of the bacterial taxa detected with the other kits, it yielded a higher relative abundance of Gammaproteobacteria. This occurred without a loss of overall diversity, suggesting improved recovery of microbial taxa rather than a compositional bias. The filtration step associated with the DNeasy kit significantly reduced host DNA but also lowered bacterial material, allowing MAG reconstruction, though less efficiently than the Microbiome kit. Despite this, the DNeasy methods allowed recovering a broader range of bacterial phyla with a more even distribution across taxa, while each extraction method also detected a unique set of NTUs. Overall, a combination of DNA extraction methods may be necessary to optimize microbiome analysis in mosquito midguts, facilitating a more comprehensive understanding of microbial diversity and its potential applications in vector control strategies.},
}

@article {pmid43016099,
year = {2026},
author = {Chen, KH and Liu, HW and Hao, YY and Sun, R and Yang, M and Liu, Q and Jia, H and Liu, YR},
title = {Aerobic methane oxidation by microorganisms exacerbates neurotoxic methylmercury accumulation in rice paddy fields.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag282},
pmid = {43016099},
issn = {1751-7370},
abstract = {Aerobic methane (CH4) oxidation is the dominant biological sink for CH4 in wetland soils and is increasingly linked to diverse biogeochemical processes; however, whether and how aerobic CH4 oxidation influences the production of the neurotoxin methylmercury (MeHg) through microbial mercury (Hg) methylation remains poorly understood. Here, we combined a ~3300 km field survey across the main rice-producing areas of China with 13CH4-DNA-stable isotope probing (SIP) to investigate the microbial linkage between aerobic CH4 oxidation and Hg methylation in paddy fields. Field observations showed positive relationships between CH4 oxidation activity and the ratio of MeHg at a continental scale, as well as between gene abundances of CH4 oxidation (pmoA) and Hg methylation (hgcA). Microcosm experiments further demonstrated that CH4 addition significantly increased MeHg production by 40.7-177.7% and enhanced hgcA gene expression by 49.5-416.0% across three typical paddy soils. Moreover, 13CH4-DNA-SIP analyses identified 112 hgcA-containing operational taxonomic units (OTUs) that incorporated 13CH4-derived 13C, of which 75.0-85.5% were affiliated with the families Geobacteraceae, Anaerolineaceae, and unclassified Desulfobacterales. Integrated analyses of 13C-metagenome-assembled genomes and metabolomics indicated that this carbon transfer was likely mediated by metabolic handoffs from methanotrophs to Hg-methylating microorganisms through intermediates (e.g., malate and fumarate) released during aerobic CH4 oxidation. Soil incubation and pure-culture experiments further confirmed the functional significance of methanotroph-derived metabolites, as their addition significantly enhanced MeHg production. These findings highlight microbial metabolic handoffs as an important mechanism linking aerobic CH4 oxidation and Hg methylation, with implications for developing synergistic strategies for MeHg pollution mitigation and carbon reduction.},
}

@article {pmid43016569,
year = {2026},
author = {Mei, Y and Shi, L and He, S and Liu, C and Liu, M and Hou, Y},
title = {Reduced classical probiotic-associated butyrate biosynthetic potential predicts early primary resistance to anti-PD-1 therapy in advanced non-small cell lung cancer: a shotgun metagenomic study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1975315},
pmid = {43016569},
issn = {2235-2988},
mesh = {Humans ; *Probiotics ; *Butyrates/metabolism ; Metagenomics ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology ; *Lung Neoplasms/drug therapy/microbiology ; Female ; *Drug Resistance, Neoplasm ; Feces/microbiology ; Microbiota ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Male ; Coenzyme A-Transferases/genetics ; Metagenome ; },
abstract = {BACKGROUND: Early primary resistance to anti-PD-1 therapy is common in advanced non-small cell lung cancer (NSCLC). Existing microbiome biomarkers largely rely on individual species and lack stability across populations.

OBJECTIVE: The aim of this study was to construct the classical probiotic-butyrate axis score (PBAS), perform external validation, and evaluate its value for risk stratification of 90-day early primary resistance and PFS.

METHODS: This study adopted a dual-cohort, patient-level secondary analysis design and reanalyzed pretreatment fecal shotgun metagenomic data from two public cohorts, including 70 and 40 patients in the discovery and external validation cohorts, respectively. An equally weighted PBAS was constructed based on predefined classical probiotic-associated taxa and the butyryl-CoA:acetate CoA-transferase (but) and the butyrate kinase (buk) genes. ANCOM-BC2 was used for differential analysis, Firth logistic regression for association analysis of early primary resistance, 2,000 patient-level bootstrap resampling for internal validation, and Cox proportional hazards models for PFS analysis.

RESULTS: Early primary resistance occurred in 41/70 and 23/40 patients in the two cohorts, respectively. Classical probiotic-associated taxa, the butyrate functional subscore, and PBAS were lower in the resistant group than in the nonresistant group, whereas buk and Akkermansia muciniphila showed no significant differences. After adjustment for age, sex, and BMI, acetyl-CoA pathway potential was also reduced. For each 1-SD increase in PBAS, the OR for early primary resistance was 0.39 and 0.37 after adjustment for clinical variables. The bootstrap-corrected area under the receiver operating characteristic curve (AUC) was 0.733, and the external validation AUC was 0.726 (95% CI: 0.559-0.894). Increased PBAS was associated with a lower risk of progression or death, with HRs of 0.54 and 0.61 in the two cohorts, respectively (both p < 0.001).

CONCLUSION: Combined reductions in pretreatment classical probiotic-associated ecology and butyrate biosynthetic potential indicate a high risk of early primary resistance to anti-PD-1 therapy in advanced NSCLC and support PBAS as an exploratory outcome risk marker for cross-cohort risk stratification among patients receiving anti-PD-1 therapy, without establishing treatment-specific predictive value.},
}

Humans
*Probiotics
*Butyrates/metabolism
Metagenomics
*Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology
*Lung Neoplasms/drug therapy/microbiology
Female
*Drug Resistance, Neoplasm
Feces/microbiology
Microbiota
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Male
Coenzyme A-Transferases/genetics
Metagenome

@article {pmid43016811,
year = {2026},
author = {Liu, X and Song, L},
title = {Case Report: Hemorrhagic fever with renal syndrome caused by Seoul orthohantavirus mimicking severe acute pancreatitis: dynamic imaging evolution and pathogen confirmation by mNGS.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1995402},
pmid = {43016811},
issn = {2296-858X},
abstract = {BACKGROUND: Hemorrhagic fever with renal syndrome (HFRS) is a zoonotic disease caused by orthohantaviruses, characterized by fever, thrombocytopenia, renal impairment, and capillary leak syndrome. Its atypical presentations can closely mimic acute pancreatitis (AP), posing substantial diagnostic challenges.

CASE PRESENTATION: A 33-year-old man presented with fever, vomiting, and watery diarrhea. Initial computed tomography (CT) revealed peripancreatic and perirenal exudation suggestive of severe acute pancreatitis. He already had profound thrombocytopenia on admission (nadir 29  ×  10⁹/L), progressive renal impairment, hematuria, and proteinuria, without typical pancreatitis risk factors or elevated pancreatic enzymes. Contrast-enhanced CT demonstrated progressive retroperitoneal exudation with relatively mild pancreatic parenchymal changes and newly developed bilateral pleural effusion. Whole-blood metagenomic next-generation sequencing (mNGS) detected high-copy Seoul orthohantavirus, with concurrent hepatitis B virus. The patient recovered fully with supportive care, intravenous immunoglobulin, and symptomatic treatment; pre-discharge ultrasound showed normal pancreatic morphology.

CONCLUSION: Seoul orthohantavirus infection can closely mimic severe acute pancreatitis clinically and radiologically. Disproportionate thrombocytopenia, renal involvement, and progressive retroperitoneal exudation with preserved pancreatic parenchyma are key diagnostic clues, and mNGS enables early definitive pathogen confirmation, facilitating appropriate management.},
}

@article {pmid42962555,
year = {2026},
author = {Cordova, B and Milletich, PL and Jones, MP and McKinley, KL and Mearig, AJ and Triplett, EW and Ludvigsson, J},
title = {Gut microbial functional associations with subsequent irritable bowel syndrome in a prospective, paediatric case-control study.},
journal = {EBioMedicine},
volume = {133},
number = {},
pages = {106521},
pmid = {42962555},
issn = {2352-3964},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/etiology/epidemiology/diagnosis ; Case-Control Studies ; Female ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Male ; Infant ; Child ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis ; },
abstract = {BACKGROUND: The infant gut microbiome undergoes rapid maturation that shapes lifelong gastrointestinal health. Although adults with irritable bowel syndrome (IBS) show characteristic microbial and metabolic alterations, it remains unclear whether these differences precede disease onset. Here, microbiome composition and function in infancy were prospectively associated with future IBS development.

METHODS: Stool samples collected from the All Babies in Southeast Sweden (ABIS) cohort at a mean age of 12.4 (±1.5) months, were analysed using a nested case-control design. Cases included future IBS and/or pelvic and abdominal pain, with the average time between age at stool collection and diagnosis being 11.8 (±5.2) years and a mean age at diagnosis of 12.8 (±5.2) years. Microbial composition was profiled with 16S rRNA gene sequencing (n = 396). Data were processed with DADA2, taxonomically assigned using SILVA database, and predicted functionally with PICRUSt2. Descriptive statistics were analysed using χ[2] or Fisher's exact test, global differences with PERMANOVA, differential abundance with ANCOM-BC2, and pathway enrichment with GSEA.

FINDINGS: Infants with future IBS risk demonstrated microbial divergence, marked by depletion of short-chain fatty acid producers and expansion of facultative and mucosa-disruptive taxa. Inferred functional profiles exhibited reduced fermentative capacity, greater respiratory potential, accelerated degradation of neuroactive aromatic amines, and case-enrichment of cytochrome bc1 complex respiratory unit.

INTERPRETATION: Gut microbiome dysbiosis in infants with IBS risk is present many years prior to diagnosis and includes early disruptions in fermentation, redox balance, and amine metabolism that potentially compromise epithelial resilience and promote visceral hypersensitivity. Early detection of microbiome dysbiosis suggests probiotic-based interventions.

FUNDING: Barndiabetesfonden; Swedish Council for Working Life and Social Research; Swedish Research Council; Östgöta Brandstodsbolag; Medical Research Council of Southeast Sweden; JDRF-Wallenberg Foundation; Linköping University; Horizon Europe INITIALISE grant.},
}

Humans
*Irritable Bowel Syndrome/microbiology/etiology/epidemiology/diagnosis
Case-Control Studies
Female
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Male
Infant
Child
Prospective Studies
Feces/microbiology
Metagenomics/methods
Dysbiosis

@article {pmid43007868,
year = {2026},
author = {Chen, XX and Xie, QJ and Qu, YN and Tang, Q and Cai, C and Chen, LX and Hua, ZS},
title = {Lineage-specific metabolic transcription across environmental gradients in geothermal microbial communities.},
journal = {Cell reports},
volume = {45},
number = {11},
pages = {118279},
doi = {10.1016/j.celrep.2026.118279},
pmid = {43007868},
issn = {2211-1247},
abstract = {Understanding how environmental heterogeneity shapes microbial metabolism remains a central challenge. While metagenomics has revealed extensive metabolic potential, how these functions are transcriptionally represented across environmental gradients and microbial lineages remains unclear. Here, we integrated genome-resolved metagenomics and metatranscriptomics with co-expression network analysis to examine metabolic transcription across geothermal environments. Across Tengchong hot springs, metabolic transcription varies with pH, temperature, and organic matter. Acidic, organic-rich springs show prominent heterotrophic and sulfur-metabolism-related transcription, with Mesoaciditogales primarily associated with coenzyme and purine biosynthesis and Thermoplasmatales with sulfur reduction and central carbon metabolism. In contrast, non-acidic thermal springs show carbon fixation transcripts from Aquificales and Cyanobacteriales and sulfur oxidation transcripts from Aquificales and Deinococcales. Under more extreme conditions, carbon-fixation pathways become less diverse and increasingly biased toward energetically efficient strategies, while nitrogen-cycling transcription remains restricted. These findings reveal how microbial functional programs and their lineage associations reflect environmental heterogeneity across geothermal habitats.},
}

@article {pmid43008439,
year = {2026},
author = {Liu, Y and Tong, B and Lu, H and Han, X and Wang, J and Song, L and Zuo, R and Zhai, Y},
title = {Dissolved organic nitrogen and ammonium trigger distinct pathways of geogenic Mn mobilization in groundwater.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144167},
doi = {10.1016/j.jhazmat.2026.144167},
pmid = {43008439},
issn = {1873-3336},
abstract = {Nitrogen (N) is a key groundwater quality indicator and an important component of biogeochemical cycleing. Existing evidence indicates that elevated manganese (Mn) concentrations in groundwater are closely associated with increases in dissolved organic nitrogen (DON) and ammonium nitrogen (NH4[+]-N). However, the mechanisms by which N influences Mn mobilization in aquifer sediment remain poorly understood. In this study, through microcosm experiments, 16S rRNA analysis, and metagenomic techniques, we elucidated the effects of exogenous DON and NH4[+]-N inputs on dissolved Mn release from aquifer sediments and the underlying microbial mechanisms. At the same N loading, proteinaceous DON induced greater dissolved Mn release than amino acid DON; relative to day 0, dissolved Mn concentrations in the G and B groups increased by 278.5% and 994.7% at day 30, respectively, and this process was mainly associated with microbial processes. In the NH4[+]-N system, dissolved Mn release was likely driven by both biotic and abiotic processes. Relative to day 0, dissolved Mn increased by 70.3% in the N group at day 30, and by 111.9% with AQDS addition at day 30. These findings demonstrate that distinct N-driven Mn mobilization pathways in aquifer sediments, providing mechanistic insights into geogenic Mn release under high-N-loading conditions.},
}

@article {pmid43008440,
year = {2026},
author = {Huang, L and Chen, B and Liu, X and Guo, Z and Zhang, G and Li, J and Fu, Q},
title = {Seasonal variation in the spatial distribution, community assembly, and associated factors of antibiotic resistance genes in tropical drinking water reservoirs of Hainan, China.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144123},
doi = {10.1016/j.jhazmat.2026.144123},
pmid = {43008440},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) have been widely investigated in temperate and subtropical reservoirs but remain poorly understood in tropical drinking-water reservoirs. We sampled four drinking-water reservoirs in Hainan during both winter and summer, integrating physicochemical, heavy-metal, and metagenomic data to investigate the diversity, spatiotemporal patterns, and assembly of ARGs, mobile genetic elements (MGEs), and microbial communities. ARG composition and community structure differed significantly by season and reservoir. Contig-based analysis identified ARG-MGE arrangements in diverse putative hosts; sul1 and qacEdelta1 co-occurred with integrases and transposases, demonstrating MGE co-localization. Null-model analysis indicated reservoir-specific ARG assembly in winter but predominantly stochastic assembly in summer, whereas microbial community assembly was deterministic in both seasons. Mantel and Spearman analyses showed seasonal variation in ARG relationships: stronger correlations with environmental factors in winter and more positive correlations with MGEs in summer. Summer co-occurrence networks were larger and more connected, with more positive ARG-MGE-microbial genus associations. Partial least squares path modeling (PLS-PM) showed positive MGE-ARG associations in both seasons, whereas microbial community composition was negatively associated with ARGs only in winter. These results characterize seasonal ARG variation and its associations with MGEs and microbial communities in tropical reservoirs, providing a baseline for monitoring regional drinking-water sources.},
}

@article {pmid43008445,
year = {2026},
author = {Xu, Y and Chen, Z and Capo, E and Kang, S and Guo, J and Wang, S and Zhang, W and Liu, G and Chen, T and Zhang, B},
title = {Microbial lineages and metabolic capacities associated with mercury methylation in supraglacial cryoconite.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144159},
doi = {10.1016/j.jhazmat.2026.144159},
pmid = {43008445},
issn = {1873-3336},
abstract = {Supraglacial cryoconite concentrates mercury (Hg), but the transcriptionally active putative Hg-methylating lineages and their metabolic organization remain poorly resolved. We combined an 8 h in situ HgCl2 perturbation with metagenomics, metatranscriptomics, expression-based functional prioritization, and genome-resolved analyses. Initial post-dose total Hg (THg) was positively associated with endpoint methylmercury (MeHg) after controlling for sampling site (within-site ρ = 0.749, permutation P = 0.0002). hgcA transcripts were detected in 29 of 30 treatment units across all six treatment levels, with prominent contributions from Bacteroidota and Desulfobacterota. We recovered 512 HgcA-like sequences, including 258 with conserved cap-helix motifs. Among 34 candidate metagenome-assembled genomes (MAGs), 26 had same-contig HgcAB support and 32 reached ≥ 90% genome breadth in at least one 2023 DNA sample. Functional prioritization highlighted corrinoid, heme/siroheme, and amino-acid/C1 metabolism. Their recurrence in candidate MAGs, together with model-predicted cobalt, iron, and amino-acid uptake, defines cofactor, methyl-donor, and cellular redox capacities relevant to established HgcAB biochemistry. These findings resolve transcriptionally active putative Hg-methylating lineages and their metabolic organization in glacier-surface ecosystems.},
}

@article {pmid43008459,
year = {2026},
author = {Sun, J and Zhao, X and Yan, WJ and Li, WT and Sun, WL and Zhang, PD},
title = {Roots through time: dynamics of the rhizosphere microbiome and its nutrient-cycling potential in Zostera marina meadows with implications for microbiome-based restoration.},
journal = {Marine environmental research},
volume = {223},
number = {},
pages = {108529},
doi = {10.1016/j.marenvres.2026.108529},
pmid = {43008459},
issn = {1879-0291},
abstract = {The seagrass rhizosphere microbiome is critical for sedimentary nutrient turnover, yet the spatiotemporal dynamics of carbon, nitrogen, phosphorus, and sulfur cycling across Zostera marina developmental stages remain poorly understood. Leveraging metagenomic sequencing and 147 metagenome-assembled genomes (MAGs), we resolved functional gene profiles in rhizosphere and bulk sediments across three discrete developmental stage (vegetative, reproductive and dormant). Temporal variation (i.e., sampling period) explained 48.1-57.4% of the variance in nutrient-cycling-associated microbial community composition, whereas spatial partitioning between rhizosphere and bulk compartments accounted for 11.6-20.0%. Carbon fixation genes were significantly enriched in the rhizosphere during reproduction but reached peak abundance in bulk sediments during dormancy. Nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA) genes were enriched in the rhizosphere during both vegetative and dormant stages. Phosphorus mobilization-associated genes displayed parallel enrichment patterns, with the regulatory two-component system gene phoR broadly conserved across MAGs. Sulfur oxidation genes were enriched in the rhizosphere during vegetative and dormant stages, yet exhibited higher relative abundance in bulk sediments during reproduction. Critically, multiple Desulfobacterota MAGs co-occurred with nitrogen fixation and sulfate reduction genes, and the alkaline phosphatase gene phoD was identified in several of these genomes. Together, these findings reveal developmentally orchestrated shifts in microbial nutrient-cycling potential, underscoring the importance of protecting the native rhizosphere microbiome in eelgrass restoration, while considering site-specific biogeochemical constraints, particularly nutrient availability and sulfide conditions.},
}

@article {pmid43008853,
year = {2026},
author = {Luo, Y and Chen, J and Ye, F and Zhang, M and Zhang, Y and Zhan, Z and He, Y and Zhu, Z},
title = {Tumor-mimicking brain parenchymal granuloma with molecular detection of Mycobacterium xenopi by metagenomic sequencing and targeted PCR: a case report.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {32},
number = {12},
pages = {103121},
doi = {10.1016/j.jiac.2026.103121},
pmid = {43008853},
issn = {1437-7780},
abstract = {Central nervous system infection caused by Mycobacterium xenopi is exceptionally rare and may mimic intracranial neoplasia. A 60-year-old woman with poorly controlled diabetes presented with progressive headache and left homonymous hemianopia. Magnetic resonance imaging showed an irregularly enhancing right occipital mass-like lesion with marked edema and tumor-like magnetic resonance spectroscopy. Stereotactic biopsy demonstrated chronic granulomatous inflammation without neoplasia; periodic acid-Schiff, Gomori methenamine silver, and acid-fast stains were negative. Metagenomic next-generation sequencing of sterile, unfixed lesional brain tissue detected 2347 species-specific reads assigned to M. xenopi, with a negative laboratory control. Targeted mycobacterial PCR performed during the diagnostic work-up on remaining biopsy-derived brain tissue was also reported positive for M. xenopi, providing concordant molecular support. Because tissue was limited, no separate specimen was submitted for culture or susceptibility testing. The patient received oral rifampicin, ethambutol, clarithromycin, and moxifloxacin. Headache resolved within 2 weeks, bedside visual-field assessment suggested partial improvement, and available records documented treatment for more than 6 months without clinically apparent adverse events. One-year non-contrast computed tomography showed right occipital encephalomalacic evolution without an obvious persistent mass-like lesion or mass effect. This case highlights the value of tissue-based molecular testing in tumor-mimicking central nervous system granulomas when conventional staining is nondiagnostic, while underscoring the continuing importance of culture, susceptibility testing, and prolonged objective follow-up.},
}

@article {pmid43008859,
year = {2026},
author = {Zheng, Y and Zhi, L and Wang, T and Gao, X and Yu, H and Teng, Y},
title = {Highly effective removal of trichloroethylene in groundwater by modified nano zero-valent iron coupled with microbial degradation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136223},
doi = {10.1016/j.biortech.2026.136223},
pmid = {43008859},
issn = {1873-2976},
abstract = {Trichloroethylene (TCE) contamination in groundwater poses a serious environmental concern due to its persistence, toxicity, and potential risks to human health. Although nano-zero-valent iron (nZVI) coupled with microbial degradation has shown promise for TCE remediation, the limited stability, aggregation, and potential microbial toxicity of nZVI remain major challenges. In this study, a carboxymethyl cellulose-stabilized nZVI (CMC-nZVI) coupled with an aerobic microbial consortium was developed to enhance TCE removal and improve the compatibility between nZVI and microorganisms. The effects of CMC modification on nZVI stability, microbial activity, and TCE degradation performance were systematically investigated. Results demonstrated that CMC modification improved the dispersion stability and environmental compatibility of nZVI, thereby promoting synergistic interactions between nZVI and microorganisms. The optimized CMC-nZVI coupled system containing 4% microbial inoculum and 1.0 g/L CMC-nZVI achieved 83.21% removal of 100 mg/L TCE within 5 days and maintained sustainable degradation performance during the subsequent degradation cycle. CMC-nZVI reduced the accumulation of toxic intermediates and facilitated a more favorable TCE transformation pathway. Furthermore, metagenomic analysis indicated that the coupled system caused limited disturbance to microbial community richness while enriching potential TCE-degrading genera and enhancing the abundance of functional genes associated with pollutant transformation. These findings provide direction for further elucidating the mechanisms of coupled dehalogenation processes, optimizing coupled systems, and advancing in-situ remediation.},
}

@article {pmid43008860,
year = {2026},
author = {Kuang, Y and Chen, S and Ma, D and Zhao, J and Wang, H and Sun, Y and Wang, J},
title = {Perfluorooctane sulfonate impairs propionate-to-methane carbon transfer by disrupting syntrophic electron and thermodynamic coupling during sludge anaerobic digestion.},
journal = {Bioresource technology},
volume = {465},
number = {},
pages = {136219},
doi = {10.1016/j.biortech.2026.136219},
pmid = {43008860},
issn = {1873-2976},
abstract = {Perfluorooctane sulfonate (PFOS) accumulates in sewage sludge, yet the metabolic step most sensitive to PFOS during anaerobic digestion remains unclear. Here, substrate-specific activity tests, [13]C3-propionate tracing, redox and thermodynamic measurements, metagenomics, and microbial network analysis were combined to investigate how PFOS disrupts propionate-to-methane conversion. At 5.0 mg/L PFOS, cumulative methane production decreased by 12.2%, whereas the maximum propionate degradation rate declined by 47.8%. Under the same exposure, acetoclastic and H2/CO2-dependent methanogenic activities decreased by 18.0% and 21.0%, respectively. The propionate fraction in residual volatile fatty acid‌ (VFA) increased from 22.6% to 51.8%. [13]C tracing showed that [13]CH4 recovery fell from 41.6% to 13.9% and carbon-transfer efficiency from 45.7% to 26.1%. PFOS also caused H2 accumulation to 4.9 × 10[-4] atm, reduced ATP and ETSA by 42.8% and 39.9%, and shifted the ΔG of propionate oxidation to - 1.9 kJ/mol. Metagenomic and network analyses further showed losses of propionate oxidizers, hydrogenotrophic methanogens, related functions, and syntrophic connectivity. PFOS therefore primarily destabilized anaerobic digestion by decoupling syntrophic propionate oxidation.},
}

@article {pmid43008925,
year = {2026},
author = {Tan, L and Mei, J and Song, X and Bai, X and Chen, B and Wang, Y and Shi, J and Xu, X and Jiang, Z and Liu, Z and Liu, W and Yue, X and Zhou, A},
title = {Coordinating substrate accessibility with indigenous microorganisms functionality to enhance medium-chain fatty acid production from waste activated sludge.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126132},
doi = {10.1016/j.envres.2026.126132},
pmid = {43008925},
issn = {1096-0953},
abstract = {Efficient medium-chain fatty acid (MCFA) production from waste activated sludge (WAS) depends on both substrate accessibility and microbial conversion. To clarify their roles in chain elongation (CE), three pretreatments were evaluated in a two-stage fermentation system with indigenous microorganisms retained or inactivated. Thermal-alkaline pretreatment achieved the highest MCFA production (4973.9 ± 274.2 mg COD/L) by improving substrate accessibility, although its relatively low selectivity indicated that greater precursor availability did not necessarily favor carbon allocation to MCFA. Retaining indigenous microorganisms increased MCFA production by 35.8-76.9% compared with corresponding autoclaved reactors and altered ethanol consumption and short-chain fatty acid dynamics, suggesting their involvement in intermediate utilization. Community analysis associated effective CE with complementary hydrolytic, acidogenic, and chain-elongating populations, including Macellibacteroides, Romboutsia, Clostridium, and Caproiciproducens, rather than the enrichment of chain-elongating bacteria alone. Metagenomic analysis of the thermal-alkaline system indicated differences in genetic potential for substrate degradation, glycolysis, electron transfer, acetyl-CoA formation, and reverse β-oxidation. These results suggest that coordinating pretreatment-driven substrate supply with indigenous microbial conversion capacity is essential for improving sludge-derived MCFA production.},
}

@article {pmid43009102,
year = {2026},
author = {Bouzid, YY and Oliver, A and Blecksmith, SE and Wilson, SMG and Alkan, Z and Huang, L and Bennett, BJ and Kable, ME and Stephensen, CB and Lemay, DG},
title = {Cross-Sectional Association between Fiber Intake and Gastrointestinal Inflammation is Dependent on FUT2 Secretor Status in Healthy Adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101938},
doi = {10.1016/j.tjnut.2026.101938},
pmid = {43009102},
issn = {1541-6100},
abstract = {BACKGROUND: Gut microbes consume mucins in the absence of dietary fermentable fiber. People with non-secretor alpha-1-2-L-fucosyltransferase 2 (FUT2) genotypes produce gastrointestinal (GI) mucins that lack terminal fucose and have increased risk for inflammatory bowel disease.

OBJECTIVES: This study aimed to determine whether associations between fiber intake and subclinical GI inflammation and/or microbiome function are modified by FUT2 genotype in healthy adults.

METHODS: We assessed interactions between fiber intake, FUT2 genotype, and GI inflammation markers in a cross-sectional observational study of healthy adults. Participants with 24-h dietary recalls and food frequency questionnaires to characterize recent and habitual diet, respectively, and fecal samples, plasma samples and/or shotgun metagenomes (n=297) were included in this analysis. Differences in microbiome composition between secretors and non-secretors were analyzed using PERMANOVA and machine learning. A custom-designed TaqMan[TM] probe was used to genotype a single nucleotide polymorphism (rs601338) to determine secretor status. ELISA was used to measure fecal calprotectin, myeloperoxidase, and neopterin, as well as plasma lipopolysaccharide binding protein. Short-chain fatty acids (SCFAs) were measured in fecal samples. Relationships between fiber intake, FUT2 genotype and outcomes were analyzed using linear mixed effect models.

RESULTS: Higher energy-adjusted total recent fiber, total habitual fiber, and soluble fiber intake was associated with lower calprotectin levels in secretors, but not in non-secretors. Overall microbiome composition did not differ by secretor status. However, the ratio of mucin-degrading to plant-degrading enzymes, Muc2Plant, in the gut microbiome was positively associated with increased fecal calprotectin in secretors, but not in non-secretors. There was no interaction between dietary fiber intake, the FUT2 genotype, and fecal SCFAs.

CONCLUSION: The association of higher dietary fiber intake with lower subclinical GI inflammation and lower mucin-degrading enzymes was observed in secretors, but not in non-secretors. Clinical trials in nutrition are needed to determine if non-secretors are less responsive to dietary fiber.},
}

@article {pmid43009116,
year = {2026},
author = {Zhao, X and Sun, Y and Ding, J and Fei, F and Gu, W and Qu, X and Wang, B and Jiang, X},
title = {Herbicide-based control of Spartina alterniflora disrupts microbial functional potential in a coastal wetland.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129508},
doi = {10.1016/j.envpol.2026.129508},
pmid = {43009116},
issn = {1873-6424},
abstract = {Herbicide-based control of invasive plants is increasingly implemented in coastal wetlands, yet the ecological consequences of herbicide residues for sediment microbiome-mediated biogeochemical functioning remain poorly understood. Here, we investigated how herbicide exposure associated with Spartina alterniflora management reshapes sediment microbial communities and biogeochemical potentials in Hangzhou Bay, China. Using metagenomic sequencing and a microbe-based Index of Functional Integrity (M-IFI), we quantified alterations in microbial potentials involved in methane, nitrogen, phosphorus, and sulfur cycling. Higher concentrations of haloxyfop and imazapyr were detected in areas subjected to herbicide-based management. Treated sediments exhibited lower α-diversity of methane-cycling genes, and more than 65% of reconstructed biogeochemical pathways had lower relative abundances, with reductions in methanogenesis-associated genes. Nitrogen and sulfur cycling pathways underwent extensive restructuring, whereas phosphorus acquisition, transport, and utilization potentials were broadly impaired. Genome-resolved analyses recovered 300 metagenome-assembled genomes and revealed distinct patterns of functional specialization and metabolic complementarity among microbial populations. Complete methane, nitrogen, and sulfur cycling potentials were sustained through community-level metabolic cooperation, whereas phosphorus cycling was disproportionately supported by a limited number of metabolically versatile populations. Herbicide exposure markedly decreased M-IFI values, with over 70% of treated sediments classified as moderately or severely disturbed. Collectively, our findings reveal that chemical control of invasive plants can impose hidden belowground ecological costs by disrupting microbiome-supported biogeochemical networks and reducing microbial functional integrity, highlighting the need to incorporate microbiome-based indicators into sustainable coastal wetland management.},
}